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Abiotic Factors Influencing Aquatic Biomes
Like terrestrial biomes, aquatic biomes are influenced by a series of abiotic factors. The aquatic medium—water— has different physical and chemical properties than air, however. Even if the water in a pond or other body of water is perfectly clear (there are no suspended particles), water, on its own, absorbs light. As one descends into a deep body of water, there will eventually be a depth which the sunlight cannot reach. While there are some abiotic and biotic factors in a terrestrial ecosystem that might obscure light (like fog, dust, or insect swarms), usually these are not permanent features of the environment. The importance of light in aquatic biomes is central to the communities of organisms found in both freshwater and marine ecosystems. In freshwater systems, stratification due to differences in density is perhaps the most critical abiotic factor and is related to the energy aspects of light. The thermal properties of water (rates of heating and cooling) are significant to the function of marine systems and have major impacts on global climate and weather patterns. Marine systems are also influenced by large-scale physical water movements, such as currents; these are less important in most freshwater lakes.
The ocean is categorized into several areas or zones (Figure \(1\)). All of the ocean’s open water is referred to as the pelagic realm (or zone). The benthic realm (or zone) extends along the ocean bottom from the shoreline to the deepest parts of the ocean floor. Within the pelagic realm is the photic zone, which is the portion of the ocean that light can penetrate (approximately 200 m or 650 ft). At depths greater than 200 m, light cannot penetrate; thus, this is referred to as the aphotic zone. The majority of the ocean is aphotic and lacks sufficient light for photosynthesis. The deepest part of the ocean, the Challenger Deep (in the Mariana Trench, located in the western Pacific Ocean), is about 11,000 m (about 6.8 mi) deep. To give some perspective on the depth of this trench, the ocean is, on average, 4267 m or 14,000 ft deep. These realms and zones are relevant to freshwater lakes as well.
Marine Biomes
The ocean is the largest marine biome. It is a continuous body of saltwater that is relatively uniform in chemical composition; it is a weak solution of mineral salts and decayed biological matter. Within the ocean, coral reefs are the second kind of marine biome. Estuaries, coastal areas where salt water and fresh water mix, form a third unique marine biome.
Ocean
The physical diversity of the ocean is a significant influence on plants, animals, and other organisms. The ocean is categorized into different zones based on how far light reaches into the water. Each zone has a distinct group of species adapted to the biotic and abiotic conditions particular to that zone.
The intertidal zone, which is the zone between high and low tide, is the oceanic region that is closest to land (Figure \(1\)). Generally, most people think of this portion of the ocean as a sandy beach. In some cases, the intertidal zone is indeed a sandy beach, but it can also be rocky or muddy. The intertidal zone is an extremely variable environment because of tides. Organisms are exposed to air and sunlight at low tide and are underwater most of the time, especially during high tide. Therefore, living things that thrive in the intertidal zone are adapted to being dry for long periods of time. The shore of the intertidal zone is also repeatedly struck by waves, and the organisms found there are adapted to withstand damage from the pounding action of the waves (Figure \(2\)). The exoskeletons of shoreline crustaceans (such as the shore crab, Carcinus maenas) are tough and protect them from desiccation (drying out) and wave damage. Another consequence of the pounding waves is that few algae and plants establish themselves in the constantly moving rocks, sand, or mud.
The neritic zone (Figure \(1\)) extends from the intertidal zone to depths of about 200 m (or 650 ft) at the edge of the continental shelf. Since light can penetrate this depth, photosynthesis can occur in the neritic zone. The water here contains silt and is well-oxygenated, low in pressure, and stable in temperature. Phytoplankton and floating Sargassum (a type of free-floating marine seaweed) provide a habitat for some sea life found in the neritic zone. Zooplankton, protists, small fishes, and shrimp are found in the neritic zone and are the base of the food chain for most of the world’s fisheries.
Beyond the neritic zone is the open ocean area known as the oceanic zone (Figure \(1\)). Within the oceanic zone, there is thermal stratification where warm and cold waters mix because of ocean currents. Abundant plankton serves as the base of the food chain for larger animals such as whales and dolphins. Nutrients are scarce and this is a relatively less productive part of the marine biome. When photosynthetic organisms and the protists and animals that feed on them die, their bodies fall to the bottom of the ocean where they remain; unlike freshwater lakes, the open ocean lacks a process for bringing the organic nutrients back up to the surface. The majority of organisms in the aphotic zone include sea cucumbers (phylum Echinodermata) and other organisms that survive on the nutrients contained in the dead bodies of organisms in the photic zone.
Beneath the pelagic zone is the benthic realm, the deepwater region beyond the continental shelf (Figure \(1\)). The bottom of the benthic realm is comprised of sand, silt, and dead organisms. Temperature decreases, remaining above freezing, as water depth increases. This is a nutrient-rich portion of the ocean because of the dead organisms that fall from the upper layers of the ocean. Because of this high level of nutrients, a diversity of fungi, sponges, sea anemones, marine worms, sea stars, fishes, and bacteria exist.
The deepest part of the ocean is the abyssal zone, which is at depths of 4000 m or greater. The abyssal zone (Figure \(1\)) is very cold and has very high pressure, high oxygen content, and low nutrient content. There are a variety of invertebrates and fishes found in this zone, but the abyssal zone does not have plants because of the lack of light. Hydrothermal vents are found primarily in the abyssal zone; chemosynthetic bacteria utilize the hydrogen sulfide and other minerals emitted from the vents. These chemosynthetic bacteria use hydrogen sulfide as an energy source and serve as the base of the food chain found in the abyssal zone.
Coral Reefs
Coral reefs are ocean ridges formed by marine invertebrates living in warm shallow waters within the photic zone of the ocean. They are found within 30˚ north and south of the equator. The Great Barrier Reef is a well-known reef system located several miles off the northeastern coast of Australia. Other coral reef systems are fringing islands, which are directly adjacent to land, or atolls, which are circular reef systems surrounding a former landmass that is now underwater. The coral organisms (members of phylum Cnidaria) are colonies of saltwater polyps that secrete a calcium carbonate skeleton. These calcium-rich skeletons slowly accumulate, forming the underwater reef (Figure \(3\)). Corals found in shallower waters (at a depth of approximately 60 m or about 200 ft) have a mutualistic relationship with photosynthetic unicellular algae. The relationship provides corals with the majority of the nutrition and the energy they require. The waters in which these corals live are nutritionally poor and, without this mutualism, it would not be possible for large corals to grow. Some corals living in deeper and colder water do not have a mutualistic relationship with algae; these corals attain energy and nutrients using stinging cells on their tentacles to capture prey.
It is estimated that more than 4,000 fish species inhabit coral reefs. These fishes can feed on coral, the cryptofauna (invertebrates found within the calcium carbonate substrate of the coral reefs), or the seaweed and algae that are associated with the coral. In addition, some fish species inhabit the boundaries of a coral reef; these species include predators, herbivores, or planktivores. Predators are animal species that hunt and are carnivores or “flesh-eaters.” Herbivores eat plant material, and planktivores eat plankton.
Evolution Connection – Global Decline of Coral Reefs
It takes a long time to build a coral reef. The animals that create coral reefs have evolved over millions of years, continuing to slowly deposit the calcium carbonate that forms their characteristic ocean homes. Bathed in warm tropical waters, the coral animals and their symbiotic algal partners evolved to survive at the upper limit of ocean water temperature.
Together, climate change and human activity pose dual threats to the long-term survival of the world’s coral reefs. As global warming due to fossil fuel emissions raises ocean temperatures, coral reefs are suffering. The excessive warmth causes the reefs to expel their symbiotic, food-producing algae, resulting in a phenomenon known as bleaching. When bleaching occurs, the reefs lose much of their characteristic color as the algae and the coral animals die if the loss of the symbiotic zooxanthellae is prolonged.
Rising levels of atmospheric carbon dioxide further threaten the corals in other ways; as CO2 dissolves in ocean waters, it lowers the pH and increases ocean acidity. As acidity increases, it interferes with the calcification that normally occurs as coral animals build their calcium carbonate homes.
When a coral reef begins to die, species diversity plummets as animals lose food and shelter. Coral reefs are also economically important tourist destinations, so the decline of coral reefs poses a serious threat to coastal economies.
Human population growth has damaged corals in other ways, too. As human coastal populations increase, the runoff of sediment and agricultural chemicals has increased, too, causing some of the once-clear tropical waters to become cloudy. At the same time, overfishing of popular fish species has allowed the predator species that eat corals to go unchecked.
Although a rise in global temperatures of 1–2˚C (a conservative scientific projection) in the coming decades may not seem large, it is very significant to this biome. When change occurs rapidly, species can become extinct before evolution leads to new adaptations. Many scientists believe that global warming, with its rapid (in terms of evolutionary time) and inexorable increases in temperature, is tipping the balance beyond the point at which many of the world’s coral reefs can recover.
Estuaries: Where the Ocean Meets Fresh Water
Estuaries are biomes that occur where a source of fresh water, such as a river, meets the ocean. Therefore, both fresh water and salt water are found in the same vicinity; mixing results in a diluted (brackish) saltwater. Estuaries form protected areas where many of the young offspring of crustaceans, mollusks, and fish begin their lives. Salinity is a very important factor that influences the organisms and the adaptations of the organisms found in estuaries. The salinity of estuaries varies and is based on the rate of flow of its freshwater sources. Once or twice a day, high tides bring salt water into the estuary. Low tides occurring at the same frequency reverse the current of salt water.
The short-term and rapid variation in salinity due to the mixing of fresh water and salt water is a difficult physiological challenge for the plants and animals that inhabit estuaries. Many estuarine plant species are halophytes: plants that can tolerate salty conditions. Halophytic plants are adapted to deal with the salinity resulting from saltwater on their roots or from sea spray. In some halophytes, filters in the roots remove the salt from the water that the plant absorbs. Other plants are able to pump oxygen into their roots. Animals, such as mussels and clams (phylum Mollusca), have developed behavioral adaptations that expend a lot of energy to function in this rapidly changing environment. When these animals are exposed to low salinity, they stop feeding, close their shells, and switch from aerobic respiration (in which they use gills) to anaerobic respiration (a process that does not require oxygen). When high tide returns to the estuary, the salinity and oxygen content of the water increases and these animals open their shells, begin feeding, and return to aerobic respiration.
Freshwater Biomes
Freshwater biomes include lakes and ponds (standing water) as well as rivers and streams (flowing water). They also include wetlands, which will be discussed later. Humans rely on freshwater biomes to provide aquatic resources for drinking water, crop irrigation, sanitation, and industry. These various roles and human benefits are referred to as ecosystem services. Lakes and ponds are found in terrestrial landscapes and are, therefore, connected with abiotic and biotic factors influencing these terrestrial biomes.
Lakes and Ponds
Lakes and ponds can range in area from a few square meters to thousands of square kilometers. Temperature is an important abiotic factor affecting living things found in lakes and ponds. In the summer, thermal stratification of lakes and ponds occurs when the upper layer of water is warmed by the sun and does not mix with deeper, cooler water. Light can penetrate within the photic zone of the lake or pond. Phytoplankton (algae and cyanobacteria) are found here and carry out photosynthesis, providing the base of the food web of lakes and ponds. Zooplankton, such as rotifers and small crustaceans, consume these phytoplankton. At the bottom of lakes and ponds, bacteria in the aphotic zone break down dead organisms that sink to the bottom.
Nitrogen and phosphorus are important limiting nutrients in lakes and ponds. Because of this, they are determining factors in the amount of phytoplankton growth in lakes and ponds. When there is a large input of nitrogen and phosphorus (from sewage and runoff from fertilized lawns and farms, for example), the growth of algae skyrockets, resulting in a large accumulation of algae called an algal bloom. Algal blooms (Figure \(4\)) can become so extensive that they reduce light penetration in water. As a result, the lake or pond becomes aphotic and photosynthetic plants cannot survive. When the algae die and decompose, severe oxygen depletion of the water occurs. Fishes and other organisms that require oxygen are then more likely to die, and resulting dead zones are found across the globe. Lake Erie and the Gulf of Mexico represent freshwater and marine habitats where phosphorus control and storm water runoff pose significant environmental challenges.
Rivers and Streams
Rivers and streams are continuously moving bodies of water that carry large amounts of water from the source, or headwater, to a lake or ocean. The largest rivers include the Nile River in Africa, the Amazon River in South America, and the Mississippi River in North America.
Abiotic features of rivers and streams vary along the length of the river or stream. Streams begin at a point of origin referred to as source water. The source water is usually cold, low in nutrients, and clear. The channel (the width of the river or stream) is narrower than at any other place along the length of the river or stream. Because of this, the current is often faster here than at any other point of the river or stream.
The fast-moving water results in minimal silt accumulation at the bottom of the river or stream; therefore, the water is clear. Photosynthesis here is mostly attributed to algae that are growing on rocks; the swift current inhibits the growth of phytoplankton. An additional input of energy can come from leaves or other organic material that falls into the river or stream from trees and other plants that border the water. When the leaves decompose, the organic material and nutrients in the leaves are returned to the water. Plants and animals have adapted to this fast-moving water. For instance, leeches (phylum Annelida) have elongated bodies and suckers on both ends. These suckers attach to the substrate, keeping the leech anchored in place. Freshwater trout species (phylum Chordata) are important predators in these fast-moving rivers and streams.
As the river or stream flows away from the source, the width of the channel gradually widens and the current slows. This slow-moving water, caused by the gradient decrease and the volume increase as tributaries unite, has more sedimentation. Phytoplankton can also be suspended in slow-moving water. Therefore, the water will not be as clear as it is near the source. The water is also warmer. Worms (phylum Annelida) and insects (phylum Arthropoda) can be found burrowing into the mud. The higher-order predator vertebrates (phylum Chordata) include waterfowl, frogs, and fishes. These predators must find food in these slow-moving, sometimes murky, waters, and, unlike the trout in the waters at the source, these vertebrates may not be able to use vision as their primary sense to find food. Instead, they are more likely to use taste or chemical cues to find prey.
Wetlands
Wetlands are environments in which the soil is either permanently or periodically saturated with water. Wetlands are different from lakes because wetlands are shallow bodies of water whereas lakes vary in depth. Emergent vegetation consists of wetland plants that are rooted in the soil but have portions of leaves, stems, and flowers extending above the water’s surface. There are several types of wetlands including marshes, swamps, bogs, mudflats, and salt marshes (Figure \(5\)). The three shared characteristics among these types—what makes them wetlands—are their hydrology, hydrophytic vegetation, and hydric soils.
Freshwater marshes and swamps are characterized by slow and steady water flow. Bogs develop in depressions where water flow is low or nonexistent. Bogs usually occur in areas where there is a clay bottom with poor percolation. Percolation is the movement of water through the pores in the soil or rocks. The water found in a bog is stagnant and oxygen-depleted because the oxygen that is used during the decomposition of organic matter is not replaced. As the oxygen in the water is depleted, decomposition slows. This leads to organic acids and other acids building up and lowering the pH of the water. At a lower pH, nitrogen becomes unavailable to plants. This creates a challenge for plants because nitrogen is an important limiting resource. Some types of bog plants (such as sundews, pitcher plants, and Venus flytraps) capture insects and extract nitrogen from their bodies. Bogs have low net primary productivity because the water found in bogs has low levels of nitrogen and oxygen.
Summary
Aquatic ecosystems include both saltwater and freshwater biomes. The abiotic factors important for the structuring of aquatic ecosystems can be different than those seen in terrestrial systems. Sunlight is a driving force behind the structure of forests and also is an important factor in bodies of water, especially those that are very deep, because of the role of photosynthesis in sustaining certain organisms. Density and temperature shape the structure of aquatic systems. Oceans may be thought of as consisting of different zones based on water depth and distance from the shoreline and light penetrance. Different kinds of organisms are adapted to the conditions found in each zone. Coral reefs are unique marine ecosystems that are home to a wide variety of species. Estuaries are found where rivers meet the ocean; their shallow waters provide nourishment and shelter for young crustaceans, mollusks, fishes, and many other species. Freshwater biomes include lakes, ponds, rivers, streams, and wetlands. Bogs are an interesting type of wetland characterized by standing water, lower pH, and a lack of nitrogen. | textbooks/bio/Introductory_and_General_Biology/Principles_of_Biology/03%3A_Chapter_3/24%3A_Ecology_and_the_Biosphere/24.04%3A_Aquatic_Biomes.txt |
All biomes are universally affected by global conditions, such as climate, that ultimately shape each biome’s environment. Scientists who study climate have noted a series of marked changes that have gradually become increasingly evident during the last sixty years. Global climate change is the term used to describe altered global weather patterns, including a worldwide increase in temperature, due largely to rising levels of atmospheric carbon dioxide.
Climate and Weather
A common misconception about global climate change is that a specific weather event occurring in a particular region (for example, a very cool week in June in central Indiana) is evidence of global climate change. However, a cold week in June is a weather-related event and not a climate-related one. These misconceptions often arise because of confusion over the terms climate and weather.
Climate refers to the long-term, predictable atmospheric conditions of a specific area. The climate of a biome is characterized by having consistent temperature and annual rainfall ranges. Climate does not address the amount of rain that fell on one particular day in a biome or the colder-than-average temperatures that occurred on one day. In contrast, weather refers to the conditions of the atmosphere during a short period of time. Weather forecasts are usually made for 48-hour cycles. Long-range weather forecasts are available but can be unreliable.
To better understand the difference between climate and weather, imagine that you are planning an outdoor event in northern Wisconsin. You would be thinking about climate when you plan the event in the summer rather than the winter because you have long-term knowledge that any given Saturday in the months of May to August would be a better choice for an outdoor event in Wisconsin than any given Saturday in January. However, you cannot determine the specific day that the event should be held on because it is difficult to accurately predict the weather on a specific day. Climate can be considered “average” weather.
Global Climate Change
Climate change can be understood by approaching three areas of study:
• current and past global climate change
• causes of past and present-day global climate change
• ancient and current results of climate change
It is helpful to keep these three different aspects of climate change clearly separated when consuming media reports about global climate change. It is common for reports and discussions about global climate change to confuse the data showing that Earth’s climate is changing with the factors that drive this climate change.
Evidence for Global Climate Change
Since scientists cannot go back in time to directly measure climatic variables, such as average temperature and precipitation, they must instead indirectly measure temperature. To do this, scientists rely on historical evidence of Earth’s past climate.
Antarctic ice cores are a key example of such evidence. These ice cores are samples of polar ice obtained by means of drills that reach thousands of meters into ice sheets or high mountain glaciers. Viewing the ice cores is like traveling backward through time; the deeper the sample, the earlier the time period. Trapped within the ice are bubbles of air and other biological evidence that can reveal temperature and carbon dioxide data. Antarctic ice cores have been collected and analyzed to indirectly estimate the temperature of the Earth over the past 400,000 years (Figure \(1\)). The 0 °C on this graph refers to the long-term average. Temperatures that are greater than 0 °C exceed Earth’s long-term average temperature. Conversely, temperatures that are less than 0 °C are less than Earth’s average temperature. This figure shows that there have been periodic cycles of increasing and decreasing temperature.
Before the late 1800s, the Earth has been as much as 9 °C cooler and about 3 °C warmer. Note that the graph in Figure \(1\) shows that the atmospheric concentration of carbon dioxide has also risen and fallen in periodic cycles; note the relationship between carbon dioxide concentration and temperature. Figure \(1\) shows that carbon dioxide levels in the atmosphere have historically cycled between 180 and 300 parts per million (ppm) by volume.
Figure \(1\) does not show the last 2,000 years with enough detail to compare the changes of Earth’s temperature during the last 400,000 years with the temperature change that has occurred in the more recent past. Two significant temperature anomalies, or irregularities, have occurred in the last 2000 years. These are the Medieval Climate Anomaly (or the Medieval Warm Period) and the Little Ice Age. A third temperature anomaly aligns with the Industrial Era. The Medieval Climate Anomaly occurred between 900 and 1300 AD. During this time period, many climate scientists think that slightly warmer weather conditions prevailed in many parts of the world; the higher-than-average temperature changes varied between 0.10 °C and 0.20 °C above the norm. Although 0.10 °C does not seem large enough to produce any noticeable change, it did free seas of ice. Because of this warming, the Vikings were able to colonize Greenland.
The Little Ice Age was a cold period that occurred between 1550 AD and 1850 AD. During this time, a slight cooling of a little less than 1 °C was observed in North America, Europe, and possibly other areas of the Earth. This 1 °C change in global temperature is a seemingly small deviation in temperature (as was observed during the Medieval Climate Anomaly); however, it also resulted in noticeable changes. Historical accounts reveal a time of exceptionally harsh winters with much snow and frost.
The Industrial Revolution, which began around 1750, was characterized by changes in much of human society. Advances in agriculture increased the food supply, which improved the standard of living for people in Europe and the United States. New technologies were invented and provided jobs and cheaper goods. These new technologies were powered using fossil fuels, especially coal. The Industrial Revolution starting in the early nineteenth century ushered in the beginning of the Industrial Era. When fossil fuel is burned, carbon dioxide is released. With the beginning of the Industrial Era, atmospheric carbon dioxide began to rise (Figure \(2\)).
Current and Past Drivers of Global Climate Change
Since it is not possible to go back in time to directly observe and measure climate, scientists use indirect evidence to determine the drivers, or factors, that may be responsible for climate change. The indirect evidence includes data collected using ice cores, boreholes (a narrow shaft bored into the ground), tree rings, glacier lengths, pollen remains, and ocean sediments. The data shows a correlation between the timing of temperature changes and drivers of climate change: before the Industrial Era (pre-1780), there were three drivers of climate change that were not related to human activity or atmospheric gases. The first of these is the Milankovitch cycles. The Milankovitch cycles describe the effects of slight changes in the Earth’s orbit on Earth’s climate. The length of the Milankovitch cycles ranges between 19,000 and 100,000 years. In other words, one could expect to see some predictable changes in the Earth’s climate associated with changes in the Earth’s orbit at a minimum of every 19,000 years.
The variation in the sun’s intensity is the second natural factor responsible for climate change. Solar intensity is the amount of solar power or energy the sun emits in a given amount of time. There is a direct relationship between solar intensity and temperature. As solar intensity increases (or decreases), the Earth’s temperature correspondingly increases (or decreases). Changes in solar intensity have been proposed as one of several possible explanations for the Little Ice Age.
Finally, volcanic eruptions are a third natural driver of climate change. Volcanic eruptions can last a few days, but the solids and gases released during an eruption can influence the climate over a period of a few years, causing short-term climate changes. The gases and solids released by volcanic eruptions can include carbon dioxide, water vapor, sulfur dioxide, hydrogen sulfide, hydrogen, and carbon monoxide. Generally, volcanic eruptions cool the climate. This occurred in 1783 when volcanos in Iceland erupted and caused the release of large volumes of sulfuric oxide. This led to haze-effect cooling, a global phenomenon that occurs when dust, ash, or other suspended particles block out sunlight and trigger lower global temperatures as a result; haze-effect cooling usually extends for one or more years. In Europe and North America, haze-effect cooling produced some of the lowest average winter temperatures on record in 1783 and 1784.
Greenhouse gases are probably the most significant drivers of the climate. When heat energy from the sun strikes the Earth, gases known as greenhouse gases trap the heat in the atmosphere, as do the glass panes of a greenhouse keep heat from escaping. The greenhouse gases that affect Earth include carbon dioxide, methane, water vapor, nitrous oxide, and ozone. Approximately half of the radiation from the sun passes through these gases in the atmosphere and strikes the Earth. This radiation is converted into thermal radiation on the Earth’s surface, and then a portion of that energy is re-radiated back into the atmosphere. Greenhouse gases, however, reflect much of the thermal energy back to the Earth’s surface. The more greenhouse gases there are in the atmosphere, the more thermal energy is reflected back to the Earth’s surface. Greenhouse gases absorb and emit radiation and are an important factor in the greenhouse effect: the warming of Earth due to carbon dioxide and other greenhouse gases in the atmosphere.
Evidence supports the relationship between atmospheric concentrations of carbon dioxide and temperature: as carbon dioxide rises, global temperature rises. Since 1950, the concentration of atmospheric carbon dioxide has increased from about 280 ppm to 382 ppm in 2006. In 2011, the atmospheric carbon dioxide concentration was 392 ppm. However, the planet would not be inhabitable by current life forms if water vapor did not produce its drastic greenhouse warming effect.
Scientists look at patterns in data and try to explain differences or deviations from these patterns. The atmospheric carbon dioxide data reveal a historical pattern of carbon dioxide increasing and decreasing, cycling between a low of 180 ppm and a high of 300 ppm. Scientists have concluded that it took around 50,000 years for the atmospheric carbon dioxide level to increase from its low minimum concentration to its higher maximum concentration. However, starting recently, atmospheric carbon dioxide concentrations have increased beyond the historical maximum of 300 ppm. The current increases in atmospheric carbon dioxide have happened very quickly—in a matter of hundreds of years rather than thousands of years. What is the reason for this difference in the rate of change and the amount of increase in carbon dioxide? A key factor that must be recognized when comparing the historical data and the current data is the presence of modern human society; no other driver of climate change has yielded changes in atmospheric carbon dioxide levels at this rate or to this magnitude.
Human activity releases carbon dioxide and methane, two of the most important greenhouse gases, into the atmosphere in several ways. The primary mechanism that releases carbon dioxide is the burning of fossil fuels, such as gasoline, coal, and natural gas (Figure \(3\)). Deforestation, cement manufacture, animal agriculture, the clearing of land, and the burning of forests are other human activities that release carbon dioxide. Methane (CH4) is produced when bacteria break down organic matter under anaerobic conditions. Anaerobic conditions can happen when organic matter is trapped underwater (such as in rice paddies) or in the intestines of herbivores. Methane can also be released from natural gas fields and the decomposition that occurs in landfills. Another source of methane is the melting of clathrates. Clathrates are frozen chunks of ice and methane found at the bottom of the ocean. When the water warms, these chunks of ice melt and methane is released. As the ocean’s water temperature increases, the rate at which clathrates melt is increasing, releasing even more methane. This leads to increased levels of methane in the atmosphere, which further accelerates the rate of global warming. This is an example of the positive feedback loop that is leading to the rapid rate of increase in global temperatures.
Documented Results of Climate Change: Past and Present
Scientists have geological evidence of the consequences of long-ago climate change. Modern-day phenomena such as retreating glaciers and melting polar ice cause a continual rise in sea level. Meanwhile, changes in climate can negatively affect organisms.
Geological Climate Change
Global warming has been associated with at least one planet-wide extinction event during the geological past. The Permian extinction event occurred about 251 million years ago toward the end of the roughly 50-million-year-long geological time span known as the Permian period. This geologic time period was one of the three warmest periods in Earth’s geologic history. Scientists estimate that approximately 70 percent of the terrestrial plant and animal species and 84 percent of marine species became extinct, vanishing forever near the end of the Permian period. Organisms that had adapted to wet and warm climatic conditions, such as annual rainfall of 300–400 cm (118–157 in) and 20 °C–30 °C (68 °F–86 °F) in the tropical wet forest, may not have been able to survive the Permian climate change.
Present Climate Change
A number of global events have occurred that may be attributed to climate change during our lifetimes. Glacier National Park in Montana is undergoing the retreat of many of its glaciers, a phenomenon known as glacier recession. In 1850, the area contained approximately 150 glaciers. By 2010, however, the park contained only about 24 glaciers greater than 25 acres in size. One of these glaciers is the Grinnell Glacier (Figure \(4\)) at Mount Gould. Between 1966 and 2005, the size of Grinnell Glacier shrank by 40 percent. Similarly, the mass of the ice sheets in Greenland and the Antarctic is decreasing: Greenland lost 150–250 km3 of ice per year between 2002 and 2006. In addition, the size and thickness of the Arctic sea ice is decreasing.
This loss of ice is leading to increases in the global sea level. On average, the sea is rising at a rate of 1.8 mm per year. However, between 1993 and 2010 the rate of sea level increase ranged between 2.9 and 3.4 mm per year. A variety of factors affect the volume of water in the ocean, including the temperature of the water (the density of water is related to its temperature) and the amount of water found in rivers, lakes, glaciers, polar ice caps, and sea ice. As glaciers and polar ice caps melt, there is a significant contribution of liquid water that was previously frozen.
In addition to some abiotic conditions changing in response to climate change, many organisms are also being affected by the changes in temperature. Temperature and precipitation play key roles in determining the geographic distribution and phenology of plants and animals. (Phenology is the study of the effects of climatic conditions on the timing of periodic lifecycle events, such as flowering in plants or migration in birds.) Researchers have shown that 385 plant species in Great Britain are flowering 4.5 days sooner than was recorded earlier during the previous 40 years. In addition, insect-pollinated species were more likely to flower earlier than wind-pollinated species. The impact of changes in flowering dates would be mitigated if the insect pollinators emerged earlier. This mismatched timing of plants and pollinators could result in injurious ecosystem effects because, for continued survival, insect-pollinated plants must flower when their pollinators are present.
Summary
The Earth has gone through periodic cycles of increases and decreases in temperature. During the past 2000 years, the Medieval Climate Anomaly was a warmer period, while the Little Ice Age was unusually cool. Both of these irregularities can be explained by natural causes of changes in climate, and, although the temperature changes were small, they had significant effects. Natural drivers of climate change include Milankovitch cycles, changes in solar activity, and volcanic eruptions. None of these factors, however, leads to rapid increases in global temperature or sustained increases in carbon dioxide. The burning of fossil fuels is an important source of greenhouse gases, which plays a major role in the greenhouse effect. Long ago, global warming resulted in the Permian extinction: a large-scale extinction event that is documented in the fossil record. Currently, modern-day climate change is associated with the increased melting of glaciers and polar ice sheets, resulting in a gradual increase in sea level. Plants and animals can also be affected by global climate change when the timing of seasonal events, such as flowering or pollination, is affected by global warming. | textbooks/bio/Introductory_and_General_Biology/Principles_of_Biology/03%3A_Chapter_3/24%3A_Ecology_and_the_Biosphere/24.05%3A_Climate_and_the_Effects_of_Global_Climate_Change.txt |
Imagine sailing down a river in a small motorboat on a weekend afternoon; the water is smooth and you are enjoying the warm sunshine and cool breeze when suddenly you are hit in the head by a 20-pound silver carp. This is a risk now on many rivers and canal systems in Illinois and Missouri because of the presence of Asian carp (Figure \(1\)).
This fish—actually a group of species including the silver, black, grass, and big head carp—has been farmed and eaten in China for over 1000 years. It is one of the most important aquaculture food resources worldwide. In the United States, however, Asian carp is considered a dangerous invasive species that disrupts community structure and composition to the point of threatening native species.
25: Population and Community Ecology
Populations are dynamic entities. Populations consist of all the species living within a specific area, and populations fluctuate based on a number of factors: seasonal and yearly changes in the environment, natural disasters such as forest fires and volcanic eruptions, and competition for resources between and within species. The statistical study of population dynamics, demography, uses a series of mathematical tools to investigate how populations respond to changes in their biotic and abiotic environments. Many of these tools were originally designed to study human populations. For example, life tables, which detail the life expectancy of individuals within a population, were initially developed by life insurance companies to set insurance rates. In fact, while the term “demographics” is commonly used when discussing humans, all living populations can be studied using this approach.
Population Size and Density
The study of any population usually begins by determining how many individuals of a particular species exist, and how closely associated they are with each other. Within a particular habitat, a population can be characterized by its population size (N), the total number of individuals, and its population density, the number of individuals within a specific area or volume. Population size and density are the two main characteristics used to describe and understand populations. For example, populations with more individuals may be more stable than smaller populations based on their genetic variability, and thus their potential to adapt to the environment. Alternatively, a member of a population with low population density (more spread out in the habitat), might have more difficulty finding a mate to reproduce compared to a population of higher density. As is shown in Figure $1$, smaller organisms tend to be more densely distributed than larger organisms.
Exercise $1$
As this graph shows, population density typically decreases with increasing body size. Why do you think this is the case?
Answer
Smaller animals require less food and other resources, so the environment can support more of them.
Population Research Methods
The most accurate way to determine population size is to simply count all of the individuals within the habitat. However, this method is often not logistically or economically feasible, especially when studying large habitats. Thus, scientists usually study populations by sampling a representative portion of each habitat and using this data to make inferences about the habitat as a whole. A variety of methods can be used to sample populations to determine their size and density. For immobile organisms such as plants, or for very small and slow-moving organisms, a quadrat may be used (Figure $2$). A quadrat is a way of marking off square areas within a habitat, either by staking out an area with sticks and string, or by the use of a wood, plastic, or metal square placed on the ground. After setting the quadrats, researchers then count the number of individuals that lie within their boundaries. Multiple quadrat samples are performed throughout the habitat at several random locations. All of this data can then be used to estimate the population size and population density within the entire habitat. The number and size of quadrat samples depend on the type of organisms under study and other factors, including the density of the organism. For example, if sampling daffodils, a 1 m2 quadrat might be used whereas with giant redwoods, which are larger and live much further apart from each other, a larger quadrat of 100 m2 might be employed. This ensures that enough individuals of the species are counted to get an accurate sample that correlates with the habitat, including areas not sampled.
For mobile organisms, such as mammals, birds, or fish, a technique called mark and recapture is often used. This method involves marking a sample of captured animals in some way (such as tags, bands, paint, or other body markings), and then releasing them back into the environment to allow them to mix with the rest of the population; later, a new sample is collected, including some individuals that are marked (recaptures) and some individuals that are unmarked (Figure $3$).
Using the ratio of marked and unmarked individuals, scientists determine how many individuals are in the sample. From this, calculations are used to estimate the total population size. This method assumes that the larger the population, the lower the percentage of tagged organisms that will be recaptured since they will have mixed with more untagged individuals. For example, if 80 deer are captured, tagged, and released into the forest, and later 100 deer are captured and 20 of them are already marked, we can determine the population size (N) using the following equation:
$\dfrac{(\text{number marked first catch} \times \text{total number of second catch})} {\text{number marked second catch}} = N \nonumber$
Using our example, the population size would be estimated at 400.
$\dfrac{(80 \times 100)} {20} = 400 \nonumber$
Therefore, there are an estimated 400 total individuals in the original population.
There are some limitations to the mark and recapture method. Some animals from the first catch may learn to avoid capture in the second round, thus inflating population estimates. Alternatively, animals may preferentially be retrapped (especially if a food reward is offered), resulting in an underestimate of population size. Also, some species may be harmed by the marking technique, reducing their survival. A variety of other techniques have been developed, including the electronic tracking of animals tagged with radio transmitters and the use of data from commercial fishing and trapping operations to estimate the size and health of populations and communities.
Species Distribution
In addition to measuring simple density, further information about a population can be obtained by looking at the distribution of the individuals. Species dispersion patterns (or distribution patterns) show the spatial relationship between members of a population within a habitat at a particular point in time. In other words, they show whether members of the species live close together or far apart, and what patterns are evident when they are spaced apart.
Individuals in a population can be more or less equally spaced apart, dispersed randomly with no predictable pattern, or clustered in groups. These are known as uniform, random, and clumped dispersion patterns, respectively (Figure $4$). Uniform dispersion is observed in plants that secrete substances inhibiting the growth of nearby individuals (such as the release of toxic chemicals by the sage plant Salvia leucophylla, a phenomenon called allelopathy) and in animals like the penguin that maintain a defined territory. An example of random dispersion occurs with dandelion and other plants that have wind-dispersed seeds that germinate wherever they happen to fall in a favorable environment. A clumped dispersion may be seen in plants that drop their seeds straight to the ground, such as oak trees, or animals that live in groups (schools of fish or herds of elephants). Clumped dispersions may also be a function of habitat heterogeneity. Thus, the dispersion of the individuals within a population provides more information about how they interact with each other than does a simple density measurement. Just as lower density species might have more difficulty finding a mate, solitary species with a random distribution might have a similar difficulty when compared to social species clumped together in groups.
Demography
While population size and density describe a population at one particular point in time, scientists must use demography to study the dynamics of a population. Demography is the statistical study of population changes over time: birth rates, death rates, and life expectancies. Each of these measures, especially birth rates, may be affected by the population characteristics described above. For example, a large population size results in a higher birth rate because more potentially reproductive individuals are present. In contrast, a large population size can also result in a higher death rate because of competition, disease, and the accumulation of waste. Similarly, a higher population density or a clumped dispersion pattern results in more potential reproductive encounters between individuals, which can increase birth rate. Lastly, a female-biased sex ratio (the ratio of males to females) or age structure (the proportion of population members at specific age ranges) composed of many individuals of reproductive age can increase birth rates.
In addition, the demographic characteristics of a population can influence how the population grows or declines over time. If birth and death rates are equal, the population remains stable. However, the population size will increase if birth rates exceed death rates; the population will decrease if birth rates are less than death rates. Life expectancy is another important factor; the length of time individuals remain in the population impacts local resources, reproduction, and the overall health of the population. These demographic characteristics are often displayed in the form of a life table.
Life Tables
Life tables provide important information about the life history of an organism. Life tables divide the population into age groups and often sexes, and show how long a member of that group is likely to live. They are modeled after actuarial tables used by the insurance industry for estimating human life expectancy. Life tables may include the probability of individuals dying before their next birthday (i.e., their mortality rate), the percentage of surviving individuals dying at a particular age interval, and their life expectancy at each interval. An example of a life table is shown in Table $1$ from a study of Dall mountain sheep, a species native to northwestern North America. Notice that the population is divided into age intervals (column A). The mortality rate (per 1000), shown in column D, is based on the number of individuals dying during the age interval (column B) divided by the number of individuals surviving at the beginning of the interval (Column C), multiplied by 1000.
$\text{mortality rate} = \frac{\text{number of individuals dying}} {\text{number of individuals surviving}} \times 1000 \nonumber$
For example, between ages three and four, 12 individuals die out of the 776 that were remaining from the original 1000 sheep. This number is then multiplied by 1000 to get the mortality rate per thousand.
$\text{mortality rate} = \dfrac{12} {776} \times 1000 \approx 15.5 \nonumber$
As can be seen from the mortality rate data (column D), a high death rate occurred when the sheep were between 6 and 12 months old, and then increased even more from 8 to 12 years old, after which there were few survivors. The data indicate that if a sheep in this population were to survive to age one, it could be expected to live another 7.7 years on average, as shown by the life expectancy numbers in column E.
This life table of Ovis dalli shows the number of deaths, number of survivors, mortality rate, and life expectancy at each age interval for the Dall mountain sheep.
Table $1$: Life Table of Dall Mountain Sheep (Data Adapted from Deevey, D. 1947)
Age interval (years) Number dying in age interval out of 1000 born Number surviving at beginning of age interval out of 1000 born Mortality rate per 1000 alive at beginning of age interval Life expectancy or mean lifetime remaining to those attaining age interval
0-0.5 54 1000 54.0 7.06
0.5-1 145 946 153.3
1-2 12 801 15.0 7.7
2-3 13 789 16.5 6.8
3-4 12 776 15.5 5.9
4-5 30 764 39.3 5.0
5-6 46 734 62.7 4.2
6-7 48 688 69.8 3.4
7-8 69 640 107.8 2.6
8-9 132 571 231.2 1.9
9-10 187 439 426.0 1.3
10-11 156 252 619.0 0.9
11-12 90 96 937.5 0.6
12-13 3 6 500.0 1.2
13-14 3 3 1000 0.7
Survivorship Curves
Another tool used by population ecologists is a survivorship curve, which is a graph of the number of individuals surviving at each age interval plotted versus time (usually with data compiled from a life table). These curves allow us to compare the life histories of different populations (Figure $5$). Humans and most primates exhibit a Type I survivorship curve because a high percentage of offspring survive their early and middle years—death occurs predominantly in older individuals. These types of species usually have small numbers of offspring at one time, and they give a high amount of parental care to them to ensure their survival. Birds are an example of an intermediate or Type II survivorship curve because birds die more or less equally at each age interval. These organisms also may have relatively few offspring and provide significant parental care. Trees, marine invertebrates, and most fishes exhibit a Type III survivorship curve because very few of these organisms survive their younger years; however, those that make it to an old age are more likely to survive for a relatively long period of time. Organisms in this category usually have a very large number of offspring, but once they are born, little parental care is provided. Thus these offspring are “on their own” and vulnerable to predation, but their sheer numbers assure the survival of enough individuals to perpetuate the species.
Summary
Populations are individuals of a species that live in a particular habitat. Ecologists measure characteristics of populations: size, density, dispersion pattern, age structure, and sex ratio. Life tables are useful to calculate life expectancies of individual population members. Survivorship curves show the number of individuals surviving at each age interval plotted versus time. | textbooks/bio/Introductory_and_General_Biology/Principles_of_Biology/03%3A_Chapter_3/25%3A_Population_and_Community_Ecology/25.01%3A_Population_Demography.txt |
The logistic model of population growth, while valid in many natural populations and a useful model, is a simplification of real-world population dynamics. Implicit in the model is that the carrying capacity of the environment does not change, which is not the case. The carrying capacity varies annually: for example, some summers are hot and dry whereas others are cold and wet. In many areas, the carrying capacity during the winter is much lower than it is during the summer. Also, natural events such as earthquakes, volcanoes, and fires can alter an environment and hence its carrying capacity. Additionally, populations do not usually exist in isolation. They engage in interspecific competition: that is, they share the environment with other species, competing with them for the same resources. These factors are also important to understanding how a specific population will grow.
Nature regulates population growth in a variety of ways. These are grouped into density-dependent factors, in which the density of the population at a given time affects growth rate and mortality, and density-independent factors, which influence mortality in a population regardless of population density. Note that in the former, the effect of the factor on the population depends on the density of the population at onset. Conservation biologists want to understand both types because this helps them manage populations and prevent extinction or overpopulation.
Density-dependent Regulation
Most density-dependent factors are biological in nature (biotic) and include predation, inter- and intraspecific competition, accumulation of waste, and diseases such as those caused by parasites. Usually, the denser a population is, the greater its mortality rate. For example, during intra- and interspecific competition, the reproductive rates of the individuals will usually be lower, reducing their population’s rate of growth. In addition, low prey density increases the mortality of its predator because it has more difficulty locating its food source.
An example of density-dependent regulation is shown in Figure \(1\) with results from a study focusing on the giant intestinal roundworm (Ascaris lumbricoides), a parasite of humans and other mammals (Croll et al. 1982). Denser populations of the parasite exhibited lower fecundity: they contained fewer eggs. One possible explanation for this is that females would be smaller in more dense populations (due to limited resources) and that smaller females would have fewer eggs. This hypothesis was tested and disproved in a 2009 study which showed that female weight had no influence (Walker et al, 2009). The actual cause of the density-dependence of fecundity in this organism is still unclear and awaiting further investigation.
Density-independent Regulation and Interaction with Density-dependent Factors
Most density-independent factors are physical or chemical in nature (abiotic) These factors influence the mortality of a population regardless of its density, including weather, natural disasters, and pollution. An individual deer may be killed in a forest fire regardless of how many deer happen to be in that area. Its chances of survival are the same whether the population density is high or low. The same holds true for cold winter weather.
In real-life situations, population regulation is very complicated and density-dependent and independent factors can interact. A dense population that is reduced in a density-independent manner by some environmental factor(s) will be able to recover differently than a sparse population. For example, a population of deer affected by a harsh winter will recover faster if there are more deer remaining to reproduce.
Evolution Connection – Why Did the Woolly Mammoth Go Extinct?
It’s easy to get lost in the discussion of dinosaurs and theories about why they went extinct 65 million years ago. Was it due to a meteor slamming into Earth near the coast of modern-day Mexico, or was it from some long-term weather cycle that is not yet understood? One hypothesis that will never be proposed is that humans had something to do with it. Mammals were small, insignificant creatures of the forest 65 million years ago, and no humans existed.
Woolly mammoths, however, began to go extinct about 10,000 years ago, when they shared the Earth with humans who were no different anatomically than humans today (Figure \(2\)). Mammoths survived in isolated island populations as recently as 1700 BC. We know a lot about these animals from carcasses found frozen in the ice of Siberia and other regions of the north. Scientists have sequenced at least 50 percent of its genome and believe mammoths are between 98 and 99 percent identical to modern elephants.
It is commonly thought that climate change and human hunting led to their extinction. A 2008 study estimated that climate change reduced the mammoth’s range from 3,000,000 square miles 42,000 years ago to 310,000 square miles 6,000 years ago (Nogués-Bravo et al. 2008). It is also well documented that humans hunted these animals. A 2012 study showed that no single factor was exclusively responsible for the extinction of these magnificent creatures (MacDonald et al. 2012). In addition to human hunting, climate change, and reduction of habitat, these scientists demonstrated another important factor in the mammoth’s extinction was the migration of humans across the Bering Strait to North America during the last ice age 20,000 years ago.
The maintenance of stable populations was and is very complex, with many interacting factors determining the outcome. It is important to remember that humans are also part of nature. Once we contributed to a species’ decline using primitive hunting technology only.
Life Histories of K-selected and r-selected Species
While reproductive strategies play a key role in life histories, they do not account for important factors like limited resources and competition. The regulation of population growth by these factors can be used to introduce a classical concept in population biology, that of K-selected versus r-selected species.
Early Theories about Life History: K-selected and r-selected Species
By the second half of the twentieth century, the concept of K- and r-selected species was used extensively and successfully to study populations. The concept relates not only to reproductive strategies but also to a species’ habitat and behavior, especially in the way that they obtain resources and care for their young. It includes length of life and survivorship factors as well. For this analysis, population biologists have grouped species into the two large categories—K-selected and r-selected—although they are really two ends of a continuum.
K-selected species are species selected by stable, predictable environments. Populations of K-selected species tend to exist close to their carrying capacity (hence the term K-selected) where intraspecific competition is high. These species have few, large offspring, a long gestation period, and often give long-term care to their offspring (Table \(1\)). While larger in size when born, the offspring are relatively helpless and immature at birth. By the time they reach adulthood, they must develop skills to compete for natural resources. In plants, scientists think of parental care more broadly: how long fruit takes to develop or how long it remains on the plant are determining factors in the time to the next reproductive event. Examples of K-selected species are primates (including humans), elephants, and plants such as oak trees (Figure \(3\)a).
Oak trees grow very slowly and take, on average, 20 years to produce their first seeds, known as acorns. As many as 50,000 acorns can be produced by an individual tree, but the germination rate is low as many of these rot or are eaten by animals such as squirrels. In some years, oaks may produce an exceptionally large number of acorns, and these years may be on a two- or three-year cycle depending on the species of oak (r-selection).
As oak trees grow to a large size and for many years before they begin to produce acorns, they devote a large percentage of their energy budget to growth and maintenance. The tree’s height and size allow it to dominate other plants in the competition for sunlight, the oak’s primary energy resource. Furthermore, when it does reproduce, the oak produces large, energy-rich seeds that use their energy reserve to become quickly established (K-selection).
In contrast, r-selected species have a large number of small offspring (hence their r designation (Table \(1\))). This strategy is often employed in unpredictable or changing environments. Animals that are r-selected do not give long-term parental care and the offspring are relatively mature and self-sufficient at birth. Examples of r-selected species are marine invertebrates, such as jellyfish, and plants, such as the dandelion (Figure \(3\)b). Dandelions have small seeds that are wind-dispersed long distances. Many seeds are produced simultaneously to ensure that at least some of them reach a hospitable environment. Seeds that land in inhospitable environments have little chance for survival since their seeds are low in energy content. Note that survival is not necessarily a function of energy stored in the seed itself.
Table \(1\): Characteristics of K-selected and r-selected species
Characteristics of K-selected species Characteristics of r-selected species
Mature late Mature early
Greater longevity Lower longevity
Increased parental care Decreased parental care
Increased competition Decreased competition
Fewer offspring More offspring
Larger offspring Smaller offspring
Modern Theories of Life History
The r– and K-selection theory, although accepted for decades and used for much groundbreaking research, has now been reconsidered, and many population biologists have abandoned or modified it. Over the years, several studies attempted to confirm the theory, but these attempts have largely failed. Many species were identified that did not follow the theory’s predictions. Furthermore, the theory ignored the age-specific mortality of the populations which scientists now know is very important. New demographic-based models of life history evolution have been developed which incorporate many ecological concepts included in r– and K-selection theory as well as population age structure and mortality factors.
Body Size correlates with Generation Time
Generation time is the average span of time between the birth of an individual and the birth of its offspring. The general trend is that the larger the species, the longer the generation time (Figure \(4\)).
Summary
Populations are regulated by a variety of density-dependent and density-independent factors. Species are divided into two categories based on a variety of features of their life history patterns: r-selected species, which have large numbers of offspring, and K-selected species, which have few offspring. The r– and K-selection theory has fallen out of use; however, many of its key features are still used in newer, demographically-based models of population dynamics. | textbooks/bio/Introductory_and_General_Biology/Principles_of_Biology/03%3A_Chapter_3/25%3A_Population_and_Community_Ecology/25.02%3A_Population_Dynamics_and_Regulation.txt |
A species’ life history describes the series of events over its lifetime, such as how resources are allocated for growth, maintenance, and reproduction. Life history traits affect the life table of an organism. A species’ life history is genetically determined and shaped by the environment and natural selection.
Life History Patterns and Energy Budgets
Energy is required by all living organisms for their growth, maintenance, and reproduction; at the same time, energy is often a major limiting factor in determining an organism’s survival. Plants, for example, acquire energy from the sun via photosynthesis but must expend this energy to grow, maintain health, and produce energy-rich seeds to produce the next generation. Animals have the additional burden of using some of their energy reserves to acquire food. Furthermore, some animals must expend energy caring for their offspring. Thus, all species have an energy budget: they must balance energy intake with their use of energy for metabolism, reproduction, parental care, and energy storage (such as bears building up body fat for winter hibernation).
Parental Care and Fecundity
Fecundity is the potential reproductive capacity of an individual within a population. Fecundity describes how many offspring could ideally be produced if an individual has as many offspring as possible, repeating the reproductive cycle as soon as possible after the birth of the offspring. In animals, fecundity is inversely related to the amount of parental care given to an individual offspring. Species, such as many marine invertebrates, that produce many offspring usually provide little if any care for the offspring (they would not have the energy or the ability to do so anyway). Most of their energy budget is used to produce many tiny offspring. Animals with this strategy are often self-sufficient at a very early age. This is because of the energy tradeoff these organisms have made to maximize their evolutionary fitness. Because their energy is used for producing offspring instead of parental care, it makes sense that these offspring have some ability to be able to move within their environment and find food and perhaps shelter. Even with these abilities, their small size makes them extremely vulnerable to predation, so the production of many offspring allows enough of them to survive to maintain the species.
Animal species that have few offspring during a reproductive event usually give extensive parental care, devoting much of their energy budget to these activities, sometimes at the expense of their own health. This is the case with many mammals, such as humans, kangaroos, and pandas. The offspring of these species are relatively helpless at birth and need to develop before they achieve self-sufficiency.
Plants with low fecundity produce few energy-rich seeds (such as coconuts and chestnuts) with each having a good chance to germinate into a new organism; plants with high fecundity usually have many small, energy-poor seeds (like orchids) that have a relatively poor chance of surviving. Although it may seem that coconuts and chestnuts have a better chance of surviving, the energy tradeoff of the orchid is also very effective. It is a matter of where the energy is used, for large numbers of seeds or for fewer seeds with more energy.
Early versus Late Reproduction
The timing of reproduction in a life history also affects species survival. Organisms that reproduce at an early age have a greater chance of producing offspring, but this is usually at the expense of their growth and the maintenance of their health. Conversely, organisms that start reproducing later in life often have greater fecundity or are better able to provide parental care, but they risk that they will not survive to reproductive age. Examples of this can be seen in fishes. Small fish like guppies use their energy to reproduce rapidly, but never attain the size that would give them defense against some predators. Larger fish, like the bluegill or shark, use their energy to attain a large size but do so with the risk that they will die before they can reproduce or at least reproduce to their maximum. These different energy strategies and tradeoffs are key to understanding the evolution of each species as it maximizes its fitness and fills its niche. In terms of energy budgeting, some species “blow it all” and use up most of their energy reserves to reproduce early before they die. Other species delay having reproduction to become stronger, more experienced individuals and to make sure that they are strong enough to provide parental care if necessary.
Single versus Multiple Reproductive Events
Some life history traits, such as fecundity, the timing of reproduction, and parental care, can be grouped together into general strategies that are used by multiple species. Semelparity occurs when a species reproduces only once during its lifetime and then dies. Such species use most of their resource budget during a single reproductive event, sacrificing their health to the point that they do not survive. Examples of semelparity are bamboo, which flowers once and then dies, and the Chinook salmon (Figure \(1\)), which uses most of its energy reserves to migrate from the ocean to its freshwater nesting area, where it reproduces and then dies. Scientists have posited alternate explanations for the evolutionary advantage of the Chinook’s post-reproduction death: a programmed suicide caused by a massive release of corticosteroid hormones, presumably so the parents can become food for the offspring, or simple exhaustion caused by the energy demands of reproduction; these are still being debated.
Iteroparity describes species that reproduce repeatedly during their lives. Some animals are able to mate only once per year but survive multiple mating seasons. The pronghorn antelope is an example of an animal that goes into a seasonal estrus cycle (“heat”): a hormonally induced physiological condition preparing the body for successful mating (Figure \(1\)). Females of these species mate only during the estrus phase of the cycle. A different pattern is observed in primates, including humans and chimpanzees, which may attempt reproduction at any time during their reproductive years, even though their menstrual cycles make pregnancy likely only a few days per month during ovulation (Figure \(1\)).
Evolution Connection – Energy Budgets, Reproductive Costs, and Sexual Selection in Drosophila
Research into how animals allocate their energy resources for growth, maintenance, and reproduction has used a variety of experimental animal models. Some of this work has been done using the common fruit fly, Drosophila melanogaster. Studies have shown that not only does reproduction have a cost as far as how long male fruit flies live, but also fruit flies that have already mated several times have limited sperm remaining for reproduction. Fruit flies maximize their last chances at reproduction by selecting optimal mates.
In a 1981 study, male fruit flies were placed in enclosures with either virgin or inseminated females. The males that mated with virgin females had shorter life spans than those in contact with the same number of inseminated females with which they were unable to mate. This effect occurred regardless of how large (indicative of their age) the males were. Thus, males that did not mate lived longer, allowing them more opportunities to find mates in the future.
More recent studies, performed in 2006, show how males select the female with which they will mate and how this is affected by previous matings (Figure \(2\)) (Byrne & Rice, 2006). Males were allowed to select between smaller and larger females. Findings showed that larger females had greater fecundity, producing twice as many offspring per mating as the smaller females did. Males that had previously mated, and thus had lower supplies of sperm, were termed “resource-depleted,” while males that had not mated were termed “non-resource-depleted.” The study showed that although non-resource-depleted males preferentially mated with larger females, this selection of partners was more pronounced in the resource-depleted males. Thus, males with depleted sperm supplies, which were limited in the number of times that they could mate before they replenished their sperm supply, selected larger, more fecund females, thus maximizing their chances for offspring. This study was one of the first to show that the physiological state of the male affected its mating behavior in a way that clearly maximizes its use of limited reproductive resources.
These studies demonstrate two ways in which the energy budget is a factor in reproduction. First, energy expended on mating may reduce an animal’s lifespan, but by this time they have already reproduced, so in the context of natural selection this early death is not of much evolutionary importance. Second, when resources such as sperm (and the energy needed to replenish it) are low, an organism’s behavior can change to give them the best chance of passing their genes on to the next generation. These changes in behavior, so important to evolution, are studied in a discipline known as behavioral biology, or ethology, at the interface between population biology and psychology.
Summary
All species have evolved a pattern of living, called a life history strategy, in which they partition energy for growth, maintenance, and reproduction. These patterns evolve through natural selection; they allow species to adapt to their environment to obtain the resources they need to successfully reproduce. There is an inverse relationship between fecundity and parental care. A species may reproduce early in life to ensure surviving to a reproductive age or reproduce later in life to become larger and healthier and better able to give parental care. A species may reproduce once (semelparity) or many times (iteroparity) in its life. | textbooks/bio/Introductory_and_General_Biology/Principles_of_Biology/03%3A_Chapter_3/25%3A_Population_and_Community_Ecology/25.03%3A_Life_Histories_and_Natural_Selection.txt |
Although life histories describe the way many characteristics of a population (such as their age structure) change over time in a general way, population ecologists make use of a variety of methods to model population dynamics mathematically. These more precise models can then be used to accurately describe changes occurring in a population and better predict future changes. Certain models that have been accepted for decades are now being modified or even abandoned due to their lack of predictive ability, and scholars strive to create effective new models.
Exponential Growth
Charles Darwin, in his theory of natural selection, was greatly influenced by the English clergyman Thomas Malthus. Malthus published a book in 1798 stating that populations with unlimited natural resources grow very rapidly, and then population growth decreases as resources become depleted. This accelerating pattern of increasing population size is called exponential growth.
The best example of exponential growth is seen in bacteria. Bacteria are prokaryotes that reproduce by prokaryotic fission. This division takes about an hour for many bacterial species. If 1000 bacteria are placed in a large flask with an unlimited supply of nutrients (so the nutrients will not become depleted), after an hour, there is one round of division and each organism divides, resulting in 2000 organisms—an increase of 1000. In another hour, each of the 2000 organisms will double, producing 4000, an increase of 2000 organisms. After the third hour, there should be 8000 bacteria in the flask, an increase of 4000 organisms. The important concept of exponential growth is that the population growth rate—the number of organisms added in each reproductive generation—is accelerating; that is, it is increasing at a greater and greater rate. After 1 day and 24 of these cycles, the population would have increased from 1000 to more than 16 billion. When the population size, N, is plotted over time, a J-shaped growth curve is produced (Figure $1$).
The bacteria example is not representative of the real world where resources are limited. Furthermore, some bacteria will die during the experiment and thus not reproduce, lowering the growth rate. Therefore, when calculating the growth rate of a population, the death rate (D) (number of organisms that die during a particular time interval) is subtracted from the birth rate (B) (number of organisms that are born during that interval). This is shown in the following formula:
$\dfrac{\boldsymbol{\Delta N} \text{ (change in number)}} {\boldsymbol{\Delta T} \text{ (change in time)}} = B \text{ (birth rate)} - D \text{ (death rate)} \nonumber$
The birth rate is usually expressed on a per capita (for each individual) basis. Thus, B (birth rate) = bN (the per capita birth rate “b” multiplied by the number of individuals “N”) and D (death rate) =dN (the per capita death rate “d” multiplied by the number of individuals “N”). Additionally, ecologists are interested in the population at a particular point in time, an infinitely small time interval. For this reason, the terminology of differential calculus is used to obtain the “instantaneous” growth rate, replacing the change in number and time with an instant-specific measurement of number and time.
$\dfrac{d N} {d T} = bN - dN = (b - d)N \nonumber$
Notice that the “d” associated with the first term refers to the derivative (as the term is used in calculus) and is different from the death rate, also called “d.” The difference between birth and death rates is further simplified by substituting the term “r” (intrinsic rate of increase) for the relationship between birth and death rates:
$\dfrac{d N} {d T} = rN \nonumber$
The value “r” can be positive, meaning the population is increasing in size; or negative, meaning the population is decreasing in size; or zero, where the population’s size is unchanging, a condition known as zero population growth. A further refinement of the formula recognizes that different species have inherent differences in their intrinsic rate of increase (often thought of as the potential for reproduction), even under ideal conditions. Obviously, a bacterium can reproduce more rapidly and have a higher intrinsic rate of growth than a human. The maximal growth rate for a species is its biotic potential, or rmax, thus changing the equation to:
$\dfrac{d N} {d T} = r_\text{max}N \nonumber$
Logistic Growth
Exponential growth is possible only when infinite natural resources are available; this is not the case in the real world. Charles Darwin recognized this fact in his description of the “struggle for existence,” which states that individuals will compete (with members of their own or other species) for limited resources. The successful ones will survive to pass on their own characteristics and traits (which we know now are transferred by genes) to the next generation at a greater rate (natural selection). To model the reality of limited resources, population ecologists developed the logistic growth model.
Carrying Capacity and the Logistic Model
In the real world, with its limited resources, exponential growth cannot continue indefinitely. Exponential growth may occur in environments where there are few individuals and plentiful resources, but when the number of individuals gets large enough, resources will be depleted, slowing the growth rate. Eventually, the growth rate will plateau or level off (Figure $1$). This population size, which represents the maximum population size that a particular environment can support, is called the carrying capacity, or K.
The formula we use to calculate logistic growth adds the carrying capacity as a moderating force in the growth rate. The expression “KN” is indicative of how many individuals may be added to a population at a given stage, and “KN” divided by “K” is the fraction of the carrying capacity available for further growth. Thus, the exponential growth model is restricted by this factor to generate the logistic growth equation:
$\dfrac{d N} {d T} = r_\text{max} \dfrac{d N} {d T} = r_\text{max}N \dfrac{(K-N)} {K} \nonumber$
Notice that when N is very small, (K-N)/K becomes close to K/K or 1, and the right side of the equation reduces to rmaxN, which means the population is growing exponentially and is not influenced by carrying capacity. On the other hand, when N is large, (K-N)/K come close to zero, which means that population growth will be slowed greatly or even stopped. Thus, population growth is greatly slowed in large populations by the carrying capacity K. This model also allows for the population of a negative population growth, or a population decline. This occurs when the number of individuals in the population exceeds the carrying capacity (because the value of (K-N)/K is negative).
A graph of this equation yields an S-shaped curve (Figure $1$), and it is a more realistic model of population growth than exponential growth. There are three different sections to an S-shaped curve. Initially, growth is exponential because there are few individuals and ample resources available. Then, as resources begin to become limited, the growth rate decreases. Finally, growth levels off at the carrying capacity of the environment, with little change in population size over time.
Role of Intraspecific Competition
The logistic model assumes that every individual within a population will have equal access to resources and, thus, an equal chance for survival. For plants, the amount of water, sunlight, nutrients, and the space to grow are the important resources, whereas in animals, important resources include food, water, shelter, nesting space, and mates.
In the real world, phenotypic variation among individuals within a population means that some individuals will be better adapted to their environment than others. The resulting competition between population members of the same species for resources is termed intraspecific competition (intra- = “within”; -specific = “species”). Intraspecific competition for resources may not affect populations that are well below their carrying capacity—resources are plentiful and all individuals can obtain what they need. However, as population size increases, this competition intensifies. In addition, the accumulation of waste products can reduce an environment’s carrying capacity.
Examples of Logistic Growth
Yeast, a microscopic fungus used to make bread and alcoholic beverages, exhibits the classical S-shaped curve when grown in a test tube (Figure $2$a). Its growth levels off as the population depletes the nutrients that are necessary for its growth. In the real world, however, there are variations to this idealized curve. Examples in wild populations include sheep and harbor seals (Figure $2$b). In both examples, the population size exceeds the carrying capacity for short periods of time and then falls below the carrying capacity afterward. This fluctuation in population size continues to occur as the population oscillates around its carrying capacity. Still, even with this oscillation, the logistic model is confirmed.
Summary
Populations with unlimited resources grow exponentially, with an accelerating growth rate. When resources become limiting, populations follow a logistic growth curve. The population of a species will level off at the carrying capacity of its environment. | textbooks/bio/Introductory_and_General_Biology/Principles_of_Biology/03%3A_Chapter_3/25%3A_Population_and_Community_Ecology/25.04%3A_Environmental_Limits_to_Population_Growth.txt |
Concepts of animal population dynamics can be applied to human population growth. Humans are not unique in their ability to alter their environment. For example, beaver dams alter the stream environment where they are built. Humans, however, have the ability to alter their environment to increase its carrying capacity sometimes to the detriment of other species (e.g., via artificial selection for crops that have a higher yield). Earth’s human population is growing rapidly, to the extent that some worry about the ability of the earth’s environment to sustain this population, as long-term exponential growth carries the potential risks of famine, disease, and large-scale death.
Although humans have increased the carrying capacity of their environment, the technologies used to achieve this transformation have caused unprecedented changes to Earth’s environment, altering ecosystems to the point where some may be in danger of collapse. The depletion of the ozone layer, erosion due to acid rain, and damage from global climate change are caused by human activities. The ultimate effect of these changes on our carrying capacity is unknown. As some point out, it is likely that the negative effects of increasing carrying capacity will outweigh the positive ones—the carrying capacity of the world for human beings might actually decrease.
The world’s human population is currently experiencing exponential growth even though human reproduction is far below its biotic potential (Figure \(1\)). To reach its biotic potential, all females would have to become pregnant every nine months or so during their reproductive years. Also, resources would have to be such that the environment would support such growth. Neither of these two conditions exists. In spite of this fact, the human population is still growing exponentially.
A consequence of exponential human population growth is the time that it takes to add a particular number of humans to the Earth is becoming shorter. Figure \(2\) shows that 123 years were necessary to add 1 billion humans in 1930, but it only took 24 years to add two billion people between 1975 and 1999. As already discussed, at some point it would appear that our ability to increase our carrying capacity indefinitely on a finite world is uncertain. Without new technological advances, the human growth rate has been predicted to slow in the coming decades. However, the population will still be increasing and the threat of overpopulation remains.
Overcoming Density-Dependent Regulation
Humans are unique in their ability to alter their environment with the conscious purpose of increasing its carrying capacity. This ability is a major factor responsible for human population growth and a way of overcoming density-dependent growth regulation. Much of this ability is related to human intelligence, society, and communication. Humans can construct shelter to protect themselves from the elements and have developed agriculture and domesticated animals to increase their food supplies. In addition, humans use language to communicate this technology to new generations, allowing them to improve upon previous accomplishments.
Other factors in human population growth are migration and public health. Humans originated in Africa, but have since migrated to nearly all inhabitable land on the Earth. Public health, sanitation, and the use of antibiotics and vaccines have decreased the ability of infectious disease to limit human population growth. In the past, diseases such as the bubonic plague of the fourteenth century killed between 30 and 60 percent of Europe’s population and reduced the overall world population by as many as 100 million people. Today, the threat of infectious disease, while not gone, is certainly less severe. According to the World Health Organization, global death from infectious disease declined from 16.4 million in 1993 to 14.7 million in 1992. To compare to some of the epidemics of the past, the percentage of the world’s population killed between 1993 and 2002 decreased from 0.30 percent of the world’s population to 0.24 percent. Thus, it appears that the influence of infectious disease on human population growth is becoming less significant.
Age Structure, Population Growth, and Economic Development
The age structure of a population is an important factor in population dynamics. Age structure is the proportion of a population at different age ranges. Age structure allows better prediction of population growth, plus the ability to associate this growth with the level of economic development in the region. Countries with rapid growth have a pyramidal shape in their age structure diagrams, showing a preponderance of younger individuals, many of whom are of reproductive age or will be soon (Figure \(3\)). This pattern is most often observed in underdeveloped countries where individuals do not live to old age because of less-than-optimal living conditions. Age structures of areas with slow growth, including developed countries such as the United States, still have a pyramidal structure, but with many fewer young and reproductive-aged individuals and a greater proportion of older individuals. Other developed countries, such as Italy, have zero population growth. The age structure of these populations is more conical, with an even greater percentage of middle-aged and older individuals. The actual growth rates in different countries are shown in Figure \(4\), with the highest rates tending to be in the less economically developed countries of Africa and Asia.
Long-Term Consequences of Exponential Human Population Growth
Many dire predictions have been made about the world’s population leading to a major crisis called the “population explosion.” In the 1968 book The Population Bomb, biologist Dr. Paul R. Ehrlich wrote, “The battle to feed all of humanity is over. In the 1970s hundreds of millions of people will starve to death in spite of any crash programs embarked upon now. At this late date, nothing can prevent a substantial increase in the world death rate” (Erlich, 1968). While many critics view this statement as an exaggeration, the laws of exponential population growth are still in effect, and unchecked human population growth cannot continue indefinitely.
In spite of population control policies such as the one-child policy in China, the human population continues to grow. At some point, the food supply may run out because of the subsequent need to produce more and more food to feed our population. The United Nations estimates that future world population growth may vary from 6 billion (a decrease) to 16 billion people by the year 2100. There is no way to know whether human population growth will moderate to the point where the crisis described by Dr. Ehrlich will be averted.
Another result of population growth is the endangerment of the natural environment. Many countries have attempted to reduce the human impact on climate change by reducing their emission of the greenhouse gas carbon dioxide. However, these treaties have not been ratified by every country, and many underdeveloped countries trying to improve their economic condition may be less likely to agree with such provisions if it means slower economic development. Furthermore, the role of human activity in causing climate change has become a hotly debated socio-political issue in some developed countries, including the United States. Thus, we enter the future with considerable uncertainty about our ability to curb human population growth and protect our environment.
Summary
The world’s human population is growing at an exponential rate. Humans have increased the world’s carrying capacity through migration, agriculture, medical advances, and communication. The age structure of a population allows us to predict population growth. Unchecked human population growth could have dire long-term effects on our environment. | textbooks/bio/Introductory_and_General_Biology/Principles_of_Biology/03%3A_Chapter_3/25%3A_Population_and_Community_Ecology/25.05%3A_Human_Population_Growth.txt |
Populations rarely, if ever, live in isolation from populations of other species. In most cases, numerous species share a habitat. The interactions between these populations play a major role in regulating population growth and abundance. All populations occupying the same habitat form a community: populations inhabiting a specific area at the same time. The number of species occupying the same habitat and their relative abundance is known as species diversity. Areas with low diversity, such as the glaciers of Antarctica, still contain a wide variety of living things, whereas the diversity of tropical rainforests is so great that it cannot be counted. Ecology is studied at the community level to understand how species interact with each other and compete for the same resources.
Predation and Herbivory
Perhaps the classical example of species interaction is predation: the hunting of prey by its predator. Nature shows on television highlight the drama of one living organism killing another. Populations of predators and prey in a community are not constant over time: in most cases, they vary in cycles that appear to be related. The most often cited example of predator-prey dynamics is seen in the cycling of the lynx (predator) and the snowshoe hare (prey), using nearly 200 year-old trapping data from North American forests (Figure \(1\)). This cycle of predator and prey last approximately 10 years, with the predator population lagging 1–2 years behind that of the prey population. As the hare numbers increase, there is more food available for the lynx, allowing the lynx population to increase as well. When the lynx population grows to a threshold level, however, they kill so many hares that hare population begins to decline, followed by a decline in the lynx population because of scarcity of food. When the lynx population is low, the hare population size begins to increase due, at least in part, to low predation pressure, starting the cycle anew.
The idea that the population cycling of the two species is entirely controlled by predation models has come under question. More recent studies have pointed to undefined density-dependent factors as being important in the cycling, in addition to predation. One possibility is that the cycling is inherent in the hare population due to density-dependent effects such as lower fecundity (maternal stress) caused by crowding when the hare population gets too dense. The hare cycling would then induce the cycling of the lynx because it is the lynxes’ major food source. The more we study communities, the more complexities we find, allowing ecologists to derive more accurate and sophisticated models of population dynamics.
Herbivory describes the consumption of plants by insects and other animals, and it is another interspecific relationship that affects populations. Unlike animals, most plants cannot outrun predators or use mimicry to hide from hungry animals. Some plants have developed mechanisms to defend against herbivory. Other species have developed mutualistic relationships; for example, herbivory provides a mechanism of seed distribution that aids in plant reproduction.
Defense Mechanisms against Predation and Herbivory
The study of communities must consider evolutionary forces that act on the members of the various populations contained within it. Species are not static, but slowly changing and adapting to their environment by natural selection and other evolutionary forces. Species have evolved numerous mechanisms to escape predation and herbivory. These defenses may be mechanical, chemical, physical, or behavioral.
Mechanical defenses, such as the presence of thorns on plants or the hard shell on turtles, discourage animal predation and herbivory by causing physical pain to the predator or by physically preventing the predator from being able to eat the prey. Chemical defenses are produced by many animals as well as plants, such as the foxglove which is extremely toxic when eaten. Figure \(2\) shows some organisms’ defenses against predation and herbivory.
Many species use their body shape and coloration to avoid being detected by predators. The tropical walking stick is an insect with the coloration and body shape of a twig which makes it very hard to see when stationary against a background of real twigs (Figure \(3\)). In another example, the chameleon can change its color to match its surroundings. Both of these are examples of camouflage or avoiding detection by blending in with the background.
Some species use coloration as a way of warning predators that they are not good to eat. For example, the cinnabar moth caterpillar, the fire-bellied toad, and many species of beetle have bright colors that warn of a foul taste, the presence of toxic chemicals, and/or the ability to sting or bite, respectively. Predators that ignore this coloration and eat the organisms will experience their unpleasant taste or presence of toxic chemicals and learn not to eat them in the future. This type of defensive mechanism is called aposematic coloration, or warning coloration (Figure \(4\)).
While some predators learn to avoid eating certain potential prey because of their coloration, other species have evolved mechanisms to mimic this coloration to avoid being eaten, even though they themselves may not be unpleasant to eat or contain toxic chemicals. In Batesian mimicry, a harmless species imitates the warning coloration of a harmful one. Assuming they share the same predators, this coloration then protects the harmless ones, even though they do not have the same level of physical or chemical defenses against predation as the organism they mimic. Many insect species mimic the coloration of wasps or bees, which are stinging, venomous insects, thereby discouraging predation (Figure \(5\)).
In Müllerian mimicry, multiple species share the same warning coloration, but all of them actually have defenses. Figure \(6\) shows a variety of foul-tasting butterflies with similar coloration. In Emsleyan/Mertensian mimicry, a deadly prey mimics a less dangerous one, such as the venomous coral snake mimicking the non-venomous milk snake. This type of mimicry is extremely rare and more difficult to understand than the previous two types. For this type of mimicry to work, it is essential that eating the milk snake has unpleasant but not fatal consequences. Then, these predators learn not to eat snakes with this coloration, protecting the coral snake as well. If the snake were fatal to the predator, there would be no opportunity for the predator to learn not to eat it, and the benefit for the less toxic species would disappear.
Competitive Exclusion Principle
Resources are often limited within a habitat and multiple species may compete to obtain them. All species have an ecological niche in the ecosystem, which describes how they acquire the resources they need and how they interact with other species in the community. The competitive exclusion principle states that two species cannot occupy the same niche in a habitat. In other words, different species cannot coexist in a community if they are competing for all the same resources. An example of this principle is shown in Figure \(7\), with two protozoan species, Paramecium aurelia and Paramecium caudatum. When grown individually in the laboratory, they both thrive. But when they are placed together in the same test tube (habitat), P. aurelia outcompetes P. caudatum for food, leading to the latter’s eventual extinction.
This exclusion may be avoided if a population evolves to make use of a different resource, a different area of the habitat, or feeds during a different time of day, called resource partitioning. The two organisms are then said to occupy different microniches. These organisms coexist by minimizing direct competition.
Symbiosis
Symbiotic relationships, or symbioses (plural), are close interactions between individuals of different species over an extended period of time which impact the abundance and distribution of the associating populations. Most scientists accept this definition, but some restrict the term to only those species that are mutualistic, where both individuals benefit from the interaction. In this discussion, the broader definition will be used.
Commensalism
A commensal relationship occurs when one species benefits from the close, prolonged interaction, while the other neither benefits nor is harmed. Birds nesting in trees provide an example of a commensal relationship (Figure \(8\)). The tree is not harmed by the presence of the nest among its branches. The nests are light and produce little strain on the structural integrity of the branch, and most of the leaves, which the tree uses to get energy by photosynthesis, are above the nest so they are unaffected. The bird, on the other hand, benefits greatly. If the bird had to nest in the open, its eggs and young would be vulnerable to predators. Another example of a commensal relationship is the clownfish and the sea anemone. The sea anemone is not harmed by the fish and the fish benefits with protection from predators who would be stung upon nearing the sea anemone.
Mutualism
A second type of symbiotic relationship is called mutualism, where two species benefit from their interaction. Some scientists believe that these are the only true examples of symbiosis. For example, termites have a mutualistic relationship with protozoa that live in the insect’s gut (Figure \(9\)). The termite benefits from the ability of bacterial symbionts within the protozoa to digest cellulose. The termite itself cannot do this, and without the protozoa, it would not be able to obtain energy from its food (cellulose from the wood it chews and eats). The protozoa and the bacterial symbionts benefit by having a protective environment and a constant supply of food from the wood chewing actions of the termite. Lichens have a mutualistic relationship between fungus and photosynthetic algae or bacteria (Figure \(9\)). As these symbionts grow together, the glucose produced by the algae provides nourishment for both organisms, whereas the physical structure of the lichen protects the algae from the elements and makes certain nutrients in the atmosphere more available to the algae.
Parasitism
A parasite is an organism that lives in or on another living organism and derives nutrients from it. In a parasitic relationship, the parasite benefits, but the organism being fed upon, the host, is harmed. The host is usually weakened by the parasite as it siphons resources the host would normally use to maintain itself. The parasite, however, is unlikely to kill the host, especially not quickly, because this would allow no time for the organism to complete its reproductive cycle by spreading to another host.
The reproductive cycles of parasites are often very complex, sometimes requiring more than one host species. A tapeworm is a parasite that causes disease in humans when contaminated, undercooked meat such as pork, fish, or beef is consumed (Figure \(10\)). The tapeworm can live inside the intestine of the host for several years, benefiting from the food the host is bringing into its gut by eating, and may grow to be over 50 ft long by adding segments. The parasite moves from species to species in a cycle, making two hosts necessary to complete its life cycle. Another common parasite is Plasmodium falciparum, the protozoan cause of malaria, a significant disease in many parts of the world. Living in human liver and red blood cells, the organism reproduces asexually in the gut of blood-feeding mosquitoes to complete its life cycle. Thus malaria is spread from human to human by mosquitoes, one of many arthropod-borne infectious diseases.
Characteristics of Communities
Communities are complex entities that can be characterized by their structure (the types and numbers of species present) and dynamics (how communities change over time). Understanding community structure and dynamics enable community ecologists to manage ecosystems more effectively.
Foundation Species
Foundation species are considered the “base” or “bedrock” of a community, having the greatest influence on its overall structure. They are usually the primary producers: organisms that bring most of the energy into the community. Kelp, brown algae, is a foundation species, forming the basis of the kelp forests off the coast of California.
Foundation species may physically modify the environment to produce and maintain habitats that benefit the other organisms that use them. An example is the photosynthetic corals of the coral reef (Figure \(11\)). Corals themselves are not photosynthetic, but harbor symbionts within their body tissues (dinoflagellates called zooxanthellae) that perform photosynthesis; this is another example of a mutualism. The exoskeletons of living and dead coral make up most of the reef structure, which protects many other species from waves and ocean currents.
Biodiversity, Species Richness, and Relative Species Abundance
Biodiversity describes a community’s biological complexity: it is measured by the number of different species (species richness) in a particular area and their relative abundance (species evenness). The area in question could be a habitat, a biome, or the entire biosphere. Species richness is the term that is used to describe the number of species living in a habitat or biome. Species richness varies across the globe (Figure \(12\)). One factor in determining species richness is latitude, with the greatest species richness occurring in ecosystems near the equator, which often have warmer temperatures, large amounts of rainfall, and low seasonality. The lowest species richness occurs near the poles, which are much colder, drier, and thus less conducive to life in Geologic time (time since glaciations). The predictability of climate or productivity is also an important factor. Other factors influence species richness as well. For example, the study of island biogeography attempts to explain the relatively high species richness found in certain isolated island chains, including the Galápagos Islands that inspired the young Darwin. Relative species abundance is the number of individuals in a species relative to the total number of individuals in all species within a habitat, ecosystem, or biome. Foundation species often have the highest relative abundance of species.
Keystone Species
A keystone species is one whose presence is key to maintaining biodiversity within an ecosystem and to upholding an ecological community’s structure. The intertidal sea star, Pisaster ochraceus, of the northwestern United States is a keystone species (Figure \(13\)). Studies have shown that when this organism is removed from communities, populations of their natural prey (mussels) increase, completely altering the species composition and reducing biodiversity. Another keystone species is the banded tetra, a fish in tropical streams, which supplies nearly all of the phosphorus, a necessary inorganic nutrient, to the rest of the community. If these fish were to become extinct, the community would be greatly affected.
Everyday Connection – Invasive Species
Invasive species are non-native organisms that, when introduced to an area out of their native range, threaten the ecosystem balance of that habitat. Many such species exist in the United States, as shown in Figure \(14\). Whether enjoying a forest hike, taking a summer boat trip, or simply walking down an urban street, you have likely encountered an invasive species.
One of the many recent proliferations of an invasive species concerns the growth of Asian carp populations. Asian carp were introduced to the United States in the 1970s by fisheries and sewage treatment facilities that used the fish’s excellent filter feeding capabilities to clean their ponds of excess plankton. Some of the fish escaped, however, and by the 1980s they had colonized many waterways of the Mississippi River basin, including the Illinois and Missouri Rivers.
Voracious eaters and rapid reproducers, Asian carp may outcompete native species for food, potentially leading to their extinction. For example, black carp are voracious eaters of native mussels and snails, limiting this food source for native fish species. Silver carp eat plankton that native mussels and snails feed on, reducing this food source by a different alteration of the food web. In some areas of the Mississippi River, Asian carp species have become the most predominant, effectively outcompeting native fishes for habitat. In some parts of the Illinois River, Asian carp constitute 95 percent of the community’s biomass. Although edible, the fish is bony and not a desired food in the United States. Moreover, their presence threatens the native fish and fisheries of the Great Lakes, which are important to local economies and recreational anglers. Asian carp have even injured humans. The fish, frightened by the sound of approaching motorboats, thrust themselves into the air, often landing in the boat or directly hitting the boaters.
The Great Lakes and their prized salmon and lake trout fisheries are also being threatened by these invasive fish. Asian carp have already colonized rivers and canals that lead into Lake Michigan. One infested waterway of particular importance is the Chicago Sanitary and Ship Channel, the major supply waterway linking the Great Lakes to the Mississippi River. To prevent the Asian carp from leaving the canal, a series of electric barriers have been successfully used to discourage their migration; however, the threat is significant enough that several states and Canada have sued to have the Chicago channel permanently cut off from Lake Michigan. Local and national politicians have weighed in on how to solve the problem, but no one knows whether the Asian carp will ultimately be considered a nuisance, like other invasive species such as the water hyacinth and zebra mussel, or whether it will be the destroyer of the largest freshwater fishery of the world.
The issues associated with Asian carp show how population and community ecology, fisheries management, and politics intersect on issues of vital importance to the human food supply and economy. Socio-political issues like this make extensive use of the sciences of population ecology (the study of members of a particular species occupying a particular area known as a habitat) and community ecology (the study of the interaction of all species within a habitat).
Community Dynamics
Community dynamics are the changes in community structure and composition over time. Sometimes these changes are induced by environmental disturbances such as volcanoes, earthquakes, storms, fires, and climate change. Communities with a stable structure are said to be at equilibrium. Following a disturbance, the community may or may not return to the equilibrium state.
Succession describes the sequential appearance and disappearance of species in a community over time. In primary succession, newly exposed or newly formed land is colonized by living things; in secondary succession, part of an ecosystem is disturbed and remnants of the previous community remain.
Primary Succession and Pioneer Species
Primary succession occurs when new land is formed or rock is exposed: for example, following the eruption of volcanoes, such as those on the Big Island of Hawaii. As lava flows into the ocean, new land is continually being formed. On the Big Island, approximately 32 acres of land is added each year. First, weathering and other natural forces break down the substrate enough for the establishment of certain hearty plants and lichens with few soil requirements, known as pioneer species. These species help to further break down the mineral rich lava into soil where other, less hardy species will grow and eventually replace the pioneer species. In addition, as these early species grow and die, they add to an ever-growing layer of decomposing organic material and contribute to soil formation. Over time the area will reach an equilibrium state, with a set of organisms quite different from the pioneer species.
Secondary succession
A classic example of secondary succession occurs in oak and hickory forests cleared by wildfire (Figure \(15\)). Wildfires will burn most vegetation and kill those animals unable to flee the area. Their nutrients, however, are returned to the ground in the form of ash. Thus, even when areas are devoid of life due to severe fires, the area will soon be ready for new life to take hold.
Before the fire, the vegetation was dominated by tall trees with access to the major plant energy resource: sunlight. Their height gave them access to sunlight while also shading the ground and other low-lying species. After the fire, though, these trees are no longer dominant. Thus, the first plants to grow back are usually annual plants followed within a few years by quickly growing and spreading grasses and other pioneer species. Due to, at least in part, changes in the environment brought on by the growth of the grasses and other species, over many years, shrubs will emerge along with small pine, oak, and hickory trees. These organisms are called intermediate species. Eventually, over 150 years, the forest will reach its equilibrium point where species composition is no longer changing and resembles the community before the fire. This equilibrium state is referred to as the climax community, which will remain stable until the next disturbance.
Summary
Communities include all the different species living in a given area. The variety of these species is called species richness. Many organisms have developed defenses against predation and herbivory, including mechanical defenses, warning coloration, and mimicry, as a result of evolution and the interaction with other members of the community. Two species cannot exist in the same habitat competing directly for the same resources. Species may form symbiotic relationships such as commensalism or mutualism. Community structure is described by its foundation and keystone species. Communities respond to environmental disturbances by succession (the predictable appearance of different types of plant species) until a stable community structure is established. | textbooks/bio/Introductory_and_General_Biology/Principles_of_Biology/03%3A_Chapter_3/25%3A_Population_and_Community_Ecology/25.06%3A_Community_Ecology.txt |
Behavior is the change in activity of an organism in response to a stimulus. Behavioral biology is the study of the biological and evolutionary bases for such changes. The idea that behaviors evolved as a result of the pressures of natural selection is not new. Animal behavior has been studied for decades, by biologists in the science of ethology, by psychologists in the science of comparative psychology, and by scientists of many disciplines in the study of neurobiology. Although there is overlap between these disciplines, scientists in these behavioral fields take different approaches. Comparative psychology is an extension of work done in human and behavioral psychology. Ethology is an extension of genetics, evolution, anatomy, physiology, and other biological disciplines. Still, one cannot study behavioral biology without touching on both comparative psychology and ethology.
One goal of behavioral biology is to dissect out the innate behaviors, which have a strong genetic component and are largely independent of environmental influences, from the learned behaviors, which result from environmental conditioning. Innate behavior, or instinct, is important because there is no risk of an incorrect behavior being learned. They are “hard wired” into the system. On the other hand, learned behaviors, although riskier, are flexible, dynamic, and can be altered according to changes in the environment.
Innate Behaviors: Movement and Migration
Innate or instinctual behaviors rely on response to stimuli. The simplest example of this is a reflex action, an involuntary and rapid response to stimulus. To test the “knee-jerk” reflex, a doctor taps the patellar tendon below the kneecap with a rubber hammer. The stimulation of the nerves there leads to the reflex of extending the leg at the knee. This is similar to the reaction of someone who touches a hot stove and instinctually pulls his or her hand away. Even humans, with our great capacity to learn, still exhibit a variety of innate behaviors.
Kinesis and Taxis
Another activity or movement of innate behavior is kinesis, or the undirected movement in response to a stimulus. Orthokinesis is the increased or decreased speed of movement of an organism in response to a stimulus. Woodlice, for example, increase their speed of movement when exposed to high or low temperatures. This movement, although random, increases the probability that the insect spends less time in the unfavorable environment. Another example is klinokinesis, an increase in turning behaviors. It is exhibited by bacteria such as E. coli which, in association with orthokinesis, helps the organisms randomly find a more hospitable environment.
A similar, but more directed version of kinesis is taxis: the directed movement towards or away from a stimulus. This movement can be in response to light (phototaxis), chemical signals (chemotaxis), or gravity (geotaxis) and can be directed toward (positive) or away (negative) from the source of the stimulus. An example of a positive chemotaxis is exhibited by the unicellular protozoan Tetrahymena thermophila. This organism swims using its cilia, at times moving in a straight line, and at other times making turns. The attracting chemotactic agent alters the frequency of turning as the organism moves directly toward the source, following the increasing concentration gradient.
Fixed Action Patterns
A fixed action pattern is a series of movements elicited by a stimulus such that even when the stimulus is removed, the pattern goes on to completion. An example of such a behavior occurs in the three-spined stickleback, a small freshwater fish (Figure \(1\)). Males of this species develop a red belly during breeding season and show instinctual aggressiveness to other males during this time. In laboratory experiments, researchers exposed such fish to objects that in no way resemble a fish in their shape, but which were painted red on their lower halves. The male sticklebacks responded aggressively to the objects just as if they were real male sticklebacks.
Migration
Migration is the long-range seasonal movement of animals. It is an evolved, adapted response to variation in resource availability, and it is a common phenomenon found in all major groups of animals. Birds fly south for the winter to get to warmer climates with sufficient food, and salmon migrate to their spawning grounds. The popular 2005 documentary March of the Penguins followed the 62-mile migration of emperor penguins through Antarctica to bring food back to their breeding site and to their young.
Although migration is thought of as innate behavior, only some migrating species always migrate (obligate migration). Animals that exhibit facultative migration can choose to migrate or not. Additionally, in some animals, only a portion of the population migrates, whereas the rest does not migrate (incomplete migration). For example, owls that live in the tundra may migrate in years when their food source, small rodents, is relatively scarce, but not migrate during the years when rodents are plentiful.
Foraging
Foraging is the act of searching for and exploiting food resources. Feeding behaviors that maximize energy gain and minimize energy expenditure are called optimal foraging behaviors, and these are favored by natural section.
Innate Behaviors: Living in Groups
Not all animals live in groups, but even those that live relatively solitary lives, with the exception of those that can reproduce asexually, must mate. Mating usually involves one animal signaling another so as to communicate the desire to mate. There are several types of energy-intensive behaviors or displays associated with mating, called mating rituals. Other behaviors found in populations that live in groups are described in terms of which animal benefits from the behavior. In selfish behavior, only the animal in question benefits; in altruistic behavior, one animal’s actions benefit another animal; cooperative behavior describes when both animals benefit. All of these behaviors involve some sort of communication between population members.
Communication within a Species
Animals communicate with each other using stimuli known as signals. An example of this is seen in the three-spined stickleback, where the visual signal of a red region in the lower half of a fish signals males to become aggressive and signals females to mate. Other signals are chemical (pheromones), aural (sound), visual (courtship and aggressive displays), or tactile (touch). These types of communication may be instinctual or learned or a combination of both. These are not the same as the communication we associate with language, which has been observed only in humans and perhaps in some species of primates and cetaceans.
A pheromone is a secreted chemical signal used to obtain a response from another individual of the same species. The purpose of pheromones is to elicit a specific behavior from the receiving individual. Pheromones are especially common among social insects, but they are used by many species to attract the opposite sex, to sound alarms, to mark food trails, and to elicit other, more complex behaviors. Even humans are thought to respond to certain pheromones called axillary steroids. These chemicals influence human perception of other people, and in one study were responsible for a group of women synchronizing their menstrual cycles. The role of pheromones in human-to-human communication is still somewhat controversial and continues to be researched.
Songs are an example of an aural signal, one that needs to be heard by the recipient. Perhaps the best known of these are songs of birds, which identify the species and are used to attract mates. Other well-known songs are those of whales, which are of such low frequency that they can travel long distances underwater. Dolphins communicate with each other using a wide variety of vocalizations. Male crickets make chirping sounds using a specialized organ to attract a mate, repel other males, and to announce a successful mating.
Courtship displays are a series of ritualized visual behaviors (signals) designed to attract and convince a member of the opposite sex to mate. These displays are ubiquitous in the animal kingdom. Often these displays involve a series of steps, including an initial display by one member followed by a response from the other. If at any point, the display is performed incorrectly or a proper response is not given, the mating ritual is abandoned and the mating attempt will be unsuccessful.
Aggressive displays are also common in the animal kingdom. An example is when a dog bares its teeth when it wants another dog to back down. Presumably, these displays communicate not only the willingness of the animal to fight but also its fighting ability. Although these displays do signal aggression on the part of the sender, it is thought that these displays are actually a mechanism to reduce the amount of actual fighting that occurs between members of the same species: they allow individuals to assess the fighting ability of their opponent and thus decide whether it is “worth the fight.” The testing of certain hypotheses using game theory has led to the conclusion that some of these displays may overstate an animal’s actual fighting ability and are used to “bluff” the opponent. This type of interaction, even if “dishonest,” would be favored by natural selection if it is successful more times than not.
Distraction displays are seen in birds and some fish. They are designed to attract a predator away from the nest that contains their young. This is an example of an altruistic behavior: it benefits the young more than the individual performing the display, which is putting itself at risk by doing so.
Many animals, especially primates, communicate with other members in the group through touch. Activities such as grooming, touching the shoulder or root of the tail, embracing, lip contact, and greeting ceremonies have all been observed in the Indian langur, an Old World monkey. Similar behaviors are found in other primates, especially in the great apes.
Altruistic Behaviors
Behaviors that lower the fitness of the individual but increase the fitness of another individual are termed altruistic. Examples of such behaviors are seen widely across the animal kingdom. Social insects such as worker bees have no ability to reproduce, yet they maintain the queen so she can populate the hive with her offspring. Meerkats keep a sentry standing guard to warn the rest of the colony about intruders, even though the sentry is putting itself at risk. Wolves and wild dogs bring meat to pack members not present during a hunt. Lemurs take care of infants unrelated to them. Although on the surface, these behaviors appear to be altruistic, it may not be so simple.
There has been much discussion over why altruistic behaviors exist. Do these behaviors lead to overall evolutionary advantages for their species? Do they help the altruistic individual pass on its own genes? And what about such activities between unrelated individuals? One explanation for altruistic-type behaviors is found in the genetics of natural selection. In the 1976 book, The Selfish Gene, scientist Richard Dawkins attempted to explain many seemingly altruistic behaviors from the viewpoint of the gene itself. Although a gene obviously cannot be selfish in the human sense, it may appear that way if the sacrifice of an individual benefits related individuals that share genes that are identical by descent (present in relatives because of common lineage). Mammal parents make this sacrifice to take care of their offspring. Emperor penguins migrate miles in harsh conditions to bring food back for their young. The selfish gene concept has been controversial over the years and is still discussed among scientists in related fields.
Even less-related individuals, those with less genetic identity than that shared by parent and offspring, benefit from seemingly altruistic behavior. The activities of social insects such as bees, wasps, ants, and termites are good examples. Sterile workers in these societies take care of the queen because they are closely related to it, and as the queen has offspring, she is passing on genes from the workers indirectly. Thus, it is of fitness benefit for the worker to maintain the queen without having any direct chance of passing on its genes due to its sterility. The lowering of individual fitness to enhance the reproductive fitness of a relative and thus one’s inclusive fitness evolves through kin selection. This phenomenon can explain many superficially altruistic behaviors seen in animals. However, these behaviors may not be truly defined as altruism in these cases because the actor is actually increasing its own fitness either directly (through its own offspring) or indirectly (through the inclusive fitness it gains through relatives that share genes with it).
Unrelated individuals may also act altruistically to each other, and this seems to defy the selfish gene explanation. An example of this observed in many monkey species where a monkey will present its back to an unrelated monkey to have that individual pick the parasites from its fur. After a certain amount of time, the roles are reversed and the first monkey now grooms the second monkey. Thus, there is reciprocity in the behavior. Both benefit from the interaction and their fitness is raised more than if neither cooperated nor if one cooperated and the other did not cooperate. This behavior is still not necessarily altruism, as the giving behavior of the actor is based on the expectation that it will be the receiver of the behavior in the future, termed reciprocal altruism. Reciprocal altruism requires that individuals repeatedly encounter each other, often the result of living in the same social group and that cheaters (those that never give back) are punished.
Evolutionary game theory, a modification of classical game theory in mathematics, has shown that many of these so-called altruistic behaviors are not altruistic at all. The definition of pure altruism, based on human behavior, is an action that benefits another without any direct benefit to oneself. Most of the behaviors previously described do not seem to satisfy this definition, and game theorists are good at finding selfish components in them. Others have argued that the terms “selfish” and “altruistic” should be dropped completely when discussing animal behavior, as they describe human behavior and may not be directly applicable to instinctual animal activity. What is clear, though, is that heritable behaviors that improve the chances of passing on one’s genes or a portion of one’s genes are favored by natural selection and will be retained in future generations as long as those behaviors convey a fitness advantage. These instinctual behaviors may then be applied, in special circumstances, to other species, as long as it doesn’t lower the animal’s fitness.
Finding Sex Partners
Not all animals reproduce sexually, but many that do have the same challenge: they need to find a suitable mate and often have to compete with other individuals to obtain one. Significant energy is spent in the process of locating, attracting, and mating with the sex partner. Two types of selection occur during this process and can lead to traits that are important to reproduction called secondary sexual characteristics: intersexual selection, the choosing of a mate where individuals of one sex choose mates of the other sex, and intrasexual selection, the competition for mates between species members of the same sex. Intersexual selection is often complex because choosing a mate may be based on a variety of visual, aural, tactile, and chemical cues. An example of intersexual selection is when female peacocks choose to mate with the male with the brightest plumage. This type of selection often leads to traits in the chosen sex that do not enhance survival but are those traits most attractive to the opposite sex (often at the expense of survival). Intrasexual selection involves mating displays and aggressive mating rituals such as rams butting heads—the winner of these battles is the one that is able to mate. Many of these rituals use up considerable energy but result in the selection of the healthiest, strongest, and/or most dominant individuals for mating. Three general mating systems, all involving innate as opposed to learned behaviors, are seen in animal populations: monogamous, polygynous, and polyandrous.
In monogamous systems, one male and one female are paired for at least one breeding season. In some animals, such as the gray wolf, these associations can last much longer, even a lifetime. Several explanations have been proposed for this type of mating system. The “mate-guarding hypothesis” states that males stay with the female to prevent other males from mating with her. This behavior is advantageous in such situations where mates are scarce and difficult to find. Another explanation is the “male-assistance hypothesis,” where males that remain with a female to help guard and rear their young will have more and healthier offspring. Monogamy is observed in many bird populations where, in addition to the parental care from the female, the male is also a major provider of parental care for the chicks. A third explanation for the evolutionary advantages of monogamy is the “female-enforcement hypothesis.” In this scenario, the female ensures that the male does not have other offspring that might compete with her own, so she actively interferes with the male’s signaling to attract other mates.
Polygynous mating refers to one male mating with multiple females. In these situations, the female must be responsible for most of the parental care as the single male is not capable of providing care to that many offspring. In resourced-based polygyny, males compete for territories with the best resources and then mate with females that enter the territory, drawn to its resource richness. The female benefits by mating with a dominant, genetically fit male; however, it is at the cost of having no male help in caring for the offspring. An example is seen in the yellow-rumped honeyguide, a bird whose males defend beehives because the females feed on their wax. As the females approach, the male defending the nest will mate with them. Harem mating structures are a type of polygynous system where certain males dominate mating while controlling a territory with resources. Elephant seals, where the alpha male dominates the mating within the group, are an example. A third type of polygyny is a lek system. Here there is a communal courting area where several males perform elaborate displays for females, and the females choose their mate from this group. This behavior is observed in several bird species including the sage grouse and the prairie chicken.
In polyandrous mating systems, one female mates with many males. These types of systems are much rarer than monogamous and polygynous mating systems. In pipefishes and seahorses, males receive the eggs from the female, fertilize them, protect them within a pouch, and give birth to the offspring (Figure \(2\)). Therefore, the female is able to provide eggs to several males without the burden of carrying the fertilized eggs.
Simple Learned Behaviors
The majority of the behaviors previously discussed were innate or at least have an innate component (variations on the innate behaviors may be learned). They are inherited and the behaviors do not change in response to signals from the environment. Conversely, learned behaviors, even though they may have instinctive components, allow an organism to adapt to changes in the environment and are modified by previous experiences. Simple learned behaviors include habituation and imprinting—both are important to the maturation process of young animals.
Habituation
Habituation is a simple form of learning in which an animal stops responding to a stimulus after a period of repeated exposure. This is a form of non-associative learning, as the stimulus is not associated with any punishment or reward. Prairie dogs typically sound an alarm call when threatened by a predator, but they become habituated to the sound of human footsteps when no harm is associated with this sound, therefore, they no longer respond to them with an alarm call. In this example, habituation is specific to the sound of human footsteps, as the animals still respond to the sounds of potential predators.
Imprinting
Imprinting is a type of learning that occurs at a particular age or a life stage that is rapid and independent of the species involved. Hatchling ducks recognize the first adult they see, their mother, and make a bond with her. A familiar sight is ducklings walking or swimming after their mothers (Figure \(3\)). This is another type of non-associative learning but is very important in the maturation process of these animals as it encourages them to stay near their mother so they will be protected, greatly increasing their chances of survival. However, if newborn ducks see a human before they see their mother, they will imprint on the human and follow it in just the same manner as they would follow their real mother. The International Crane Foundation has helped raise the world’s population of whooping cranes from 21 individuals to about 600. Imprinting hatchlings has been a key to success: biologists wear full crane costumes so the birds never “see” humans.
Conditioned Behavior
Conditioned behaviors are types of associative learning, where a stimulus becomes associated with a consequence. During operant conditioning, the behavioral response is modified by its consequences, with regards to its form, strength, or frequency.
Classical Conditioning
In classical conditioning, a response called the conditioned response is associated with a stimulus that it had previously not been associated with, the conditioned stimulus. The response to the original, unconditioned stimulus is called the unconditioned response. The most cited example of classical conditioning is Ivan Pavlov’s experiments with dogs (Figure \(4\)). In Pavlov’s experiments, the unconditioned response was the salivation of dogs in response to the unconditioned stimulus of seeing or smelling their food. The conditioning stimulus that researchers associated with the unconditioned response was the ringing of a bell. During conditioning, every time the animal was given food, the bell was rung. This was repeated during several trials. After some time, the dog learned to associate the ringing of the bell with food and to respond by salivating. After the conditioning period was finished, the dog would respond by salivating when the bell was rung, even when the unconditioned stimulus, the food, was absent. Thus, the ringing of the bell became the conditioned stimulus and the salivation became the conditioned response. Although it is thought by some scientists that the unconditioned and conditioned responses are identical, even Pavlov discovered that the saliva in the conditioned dogs had characteristic differences when compared to the unconditioned dog.
It had been thought by some scientists that this type of conditioning required multiple exposures to the paired stimulus and response, but it is now known that this is not necessary in all cases and that some conditioning can be learned in a single pairing experiment. Classical conditioning is a major tenet of behaviorism, a branch of psychological philosophy that proposes that all actions, thoughts, and emotions of living things are behaviors that can be treated by behavior modification and changes in the environment.
Operant Conditioning
In operant conditioning, the conditioned behavior is gradually modified by its consequences as the animal responds to the stimulus. A major proponent of such conditioning was psychologist B.F. Skinner, the inventor of the Skinner box. Skinner put rats in his boxes that contained a lever that would dispense food to the rat when depressed. While initially the rat would push the lever a few times by accident, it eventually associated pushing the lever with getting the food. This type of learning is an example of operant conditioning. Operant learning is the basis of most animal training. The conditioned behavior is continually modified by positive or negative reinforcement, often a reward such as food or some type of punishment, respectively. In this way, the animal is conditioned to associate a type of behavior with the punishment or reward, and, over time, can be induced to perform behaviors that they would not have done in the wild, such as the tricks dolphins perform at marine amusement park shows (Figure \(5\)).
Cognitive Learning
Classical and operant conditioning are inefficient ways for humans and other intelligent animals to learn. Some primates, including humans, are able to learn by imitating the behavior of others and by taking instructions. The development of complex language by humans has made cognitive learning, the manipulation of information using the mind, the most prominent method of human learning. In fact, that is how students are learning right now by reading this book. As students read, they can make mental images of objects or organisms and imagine changes to them, or behaviors by them, and anticipate the consequences. In addition to visual processing, cognitive learning is also enhanced by remembering past experiences, touching physical objects, hearing sounds, tasting food, and a variety of other sensory-based inputs. Cognitive learning is so powerful that it can be used to understand conditioning in detail. In the reverse scenario, conditioning cannot help someone learn about cognition.
Classic work on cognitive learning was done by Wolfgang Köhler with chimpanzees. He demonstrated that these animals were capable of abstract thought by showing that they could learn how to solve a puzzle. When a banana was hung in their cage too high for them to reach, and several boxes were placed randomly on the floor, some of the chimps were able to stack the boxes one on top of the other, climb on top of them, and get the banana. This implies that they could visualize the result of stacking the boxes even before they had performed the action. This type of learning is much more powerful and versatile than conditioning.
Cognitive learning is not limited to primates, although they are the most efficient in using it. Maze running experiments done with rats by H.C. Blodgett in the 1920s were the first to show cognitive skills in a simple mammal. The motivation for the animals to work their way through the maze was a piece of food at its end. In these studies, the animals in Group I were run in one trial per day and had food available to them each day on completion of the run (Figure \(6\)). Group II rats were not fed in the maze for the first six days and then subsequent runs were done with food for several days after. Group III rats had food available on the third day and every day thereafter. The results were that the control rats, Group I, learned quickly, and figured out how to run the maze in seven days. Group III did not learn much during the three days without food but rapidly caught up to the control group when given the food reward. Group II learned very slowly for the six days with no reward to motivate them, and they did not begin to catch up to the control group until the day food was given, and then it took two days longer to learn the maze.
It may not be immediately obvious that this type of learning is different than conditioning. Although one might be tempted to believe that the rats simply learned how to find their way through a conditioned series of right and left turns, E.C. Tolman proved a decade later that the rats were making a representation of the maze in their minds, which he called a “cognitive map.” This was an early demonstration of the power of cognitive learning and how these abilities were not just limited to humans.
Sociobiology
Sociobiology is an interdisciplinary science originally popularized by social insect researcher E.O. Wilson in the 1970s. Wilson defined the science as “the extension of population biology and evolutionary theory to social organization” (Wilson, 1978). The main thrust of sociobiology is that animal and human behavior, including aggressiveness and other social interactions, can be explained almost solely in terms of genetics and natural selection. This science is controversial; noted scientists such as the late Stephen Jay Gould criticized the approach for ignoring the environmental effects on behavior. This is another example of the nature versus nurture debate of the role of genetics versus the role of the environment in determining an organism’s characteristics.
Sociobiology also links genes with behaviors and has been associated with “biological determinism,” the belief that all behaviors are hardwired into our genes. No one disputes that certain behaviors can be inherited and that natural selection plays a role in retaining them. It is the application of such principles to human behavior that sparks this controversy, which remains active today.
Summary
Behaviors are responses to stimuli. They can either be instinctual/innate behaviors, which are not influenced by the environment, or learned behaviors, which are influenced by environmental changes. Instinctual behaviors include mating systems and methods of communication. Learned behaviors include imprinting and habituation, conditioning, and, most powerfully, cognitive learning. Although the connection between behavior, genetics, and evolution is well established, the explanation of human behavior as entirely genetic is controversial. | textbooks/bio/Introductory_and_General_Biology/Principles_of_Biology/03%3A_Chapter_3/25%3A_Population_and_Community_Ecology/25.07%3A_Behavioral_Biology_-_Proximate_and_Ultimate_Causes_of_Behavior.txt |
In 1993, an interesting example of ecosystem dynamics occurred when a rare lung disease struck inhabitants of the southwestern United States (Figure \(1\)). This disease had an alarming rate of fatalities, killing more than half of early patients, many of whom were Native Americans. These formerly healthy young adults died from complete respiratory failure. The disease was unknown, and the Centers for Disease Control (CDC), the United States government agency responsible for managing potential epidemics, was brought in to investigate. The scientists could have learned about the disease had they known to talk with the Navajo healers who lived in the area and who had observed the connection between rainfall and mice populations, thereby predicting the 1993 outbreak.
The cause of the disease, determined within a few weeks by the CDC investigators, was the hantavirus known as Sin Nombre, the virus with “no name.” With insights from traditional Navajo medicine, scientists were able to characterize the disease rapidly and institute effective health measures to prevent its spread. This example illustrates the importance of understanding the complexities of ecosystems and how they respond to changes in the environment.
26: Ecosystems
Life in an ecosystem is often about competition for limited resources, a characteristic of the theory of natural selection. Competition in communities (all living things within specific habitats) is observed both within species and among different species. The resources for which organisms compete include organic material from living or previously living organisms, sunlight, and mineral nutrients, which provide the energy for living processes and the matter to make up organisms’ physical structures. Other critical factors influencing community dynamics are the components of its physical and geographic environment: a habitat’s latitude, amount of rainfall, topography (elevation), and available species. These are all important environmental variables that determine which organisms can exist within a particular area.
An ecosystem is a community of living organisms and their interactions with their abiotic (non-living) environment. Ecosystems can be small, such as the tide pools found near the rocky shores of many oceans, or large, such as the Amazon Rainforest in Brazil (Figure \(1\)).
There are three broad categories of ecosystems based on their general environment: freshwater, ocean water, and terrestrial. Within these broad categories are individual ecosystem types based on the organisms present and the type of environmental habitat.
Ocean ecosystems are the most common, comprising 75 percent of the Earth’s surface and consisting of three basic types: shallow ocean, deep ocean water, and deep ocean surfaces (the low depth areas of the deep oceans). The shallow ocean ecosystems include extremely biodiverse coral reef ecosystems, and the deep ocean surface is known for its large numbers of plankton and krill (small crustaceans) that support it. These two environments are especially important to aerobic respirators worldwide as the phytoplankton perform 40 percent of all photosynthesis on Earth. Although not as diverse as the other two, deep ocean ecosystems contain a wide variety of marine organisms. Such ecosystems exist even at the bottom of the ocean where light is unable to penetrate through the water.
Freshwater ecosystems are the rarest, occurring on only 1.8 percent of the Earth’s surface. Lakes, rivers, streams, and springs comprise these systems; they are quite diverse, and they support a variety of fish, amphibians, reptiles, insects, phytoplankton, fungi, and bacteria.
Terrestrial ecosystems, also known for their diversity, are grouped into large categories called biomes, such as tropical rain forests, savannas, deserts, coniferous forests, deciduous forests, and tundra. Grouping these ecosystems into just a few biome categories obscures the great diversity of the individual ecosystems within them. For example, there is great variation in desert vegetation: the saguaro cacti and other plant life in the Sonoran Desert, in the United States, are relatively abundant compared to the desolate rocky desert of Boa Vista, an island off the coast of Western Africa (Figure \(2\)).
Ecosystems are complex with many interacting parts. They are routinely exposed to various disturbances or changes in the environment that affect their compositions: yearly variations in rainfall and temperature and the slower processes of plant growth, which may take several years. Many of these disturbances are a result of natural processes. For example, when lightning causes a forest fire and destroys part of a forest ecosystem, the ground is eventually populated by grasses, then by bushes and shrubs, and later by mature trees, restoring the forest to its former state. The impact of environmental disturbances caused by human activities is as important as the changes wrought by natural processes. Human agricultural practices, air pollution, acid rain, global deforestation, overfishing, eutrophication, oil spills, and illegal dumping on land and into the ocean are all issues of concern to conservationists.
Equilibrium is the steady-state of an ecosystem where all organisms are in balance with their environment and with each other. In ecology, two parameters are used to measure changes in ecosystems: resistance and resilience. The ability of an ecosystem to remain at equilibrium in spite of disturbances is called resistance. The speed at which an ecosystem recovers equilibrium after being disturbed is called its resilience. Ecosystem resistance and resilience are especially important when considering human impact. The nature of an ecosystem may change to such a degree that it can lose its resilience entirely. This process can lead to the complete destruction or irreversible altering of the ecosystem.
Food Chains and Food Webs
The term food chain is sometimes used metaphorically to describe human social situations. It is not surprising that in our competitive society, individuals who are considered successful are seen as being at the top of the food chain, consuming all others for their benefit, whereas the less successful are seen as being at the bottom.
The scientific understanding of a food chain is more precise than in its everyday usage. In ecology, a food chain is a linear sequence of organisms through which nutrients and energy pass: primary producers, primary consumers, and higher-level consumers are used to describe ecosystem structure and dynamics. There is a single path through the chain. Each organism in a food chain occupies what is called a trophic level. Depending on their role as producers or consumers, species or groups of species can be assigned to various trophic levels.
In many ecosystems, the bottom of the food chain consists of photosynthetic organisms (plants and/or phytoplankton), which are called primary producers. The organisms that consume the primary producers are herbivores: the primary consumers. Secondary consumers are usually carnivores that eat the primary consumers. Tertiary consumers are carnivores that eat other carnivores. Higher-level consumers feed on the next lower trophic levels, and so on, up to the organisms at the top of the food chain: the apex consumers. In the Lake Ontario food chain shown in Figure \(3\), the Chinook salmon is the apex consumer at the top of this food chain.
One major factor that limits the length of food chains is energy. Energy is lost as heat between each trophic level due to the second law of thermodynamics. Thus, after a limited number of trophic energy transfers, the amount of energy remaining in the food chain may not be great enough to support viable populations at yet a higher trophic level.
The loss of energy between trophic levels is illustrated in the 1940s by the pioneering studies of Howard T. Odum of the Silver Springs ecosystem located in Florida (Figure \(4\)). The primary producers generated 20,819 kcal/m2/yr (kilocalories per square meter per year), the primary consumers generated 3368 kcal/m2/yr, the secondary consumers generated 383 kcal/m2/yr, and the tertiary consumers only generated 21 kcal/m2/yr. Thus, there is little energy remaining for another level of consumers in this ecosystem.
There is one problem when using food chains to accurately describe most ecosystems. Even when all organisms are grouped into appropriate trophic levels, some of these organisms can feed on species from more than one trophic level; likewise, some of these organisms can be eaten by species from multiple trophic levels. In other words, the linear model of ecosystems, the food chain, is not completely descriptive of ecosystem structure. A holistic model—which accounts for all the interactions between different species and their complex interconnected relationships with each other and with the environment—is a more accurate and descriptive model for ecosystems. A food web is a graphic representation of a holistic, non-linear web of primary producers, primary consumers, and higher-level consumers used to describe ecosystem structure and dynamics (Figure \(5\)).
A comparison of the two types of structural ecosystem models shows strength in both. Food chains are more flexible for analytical modeling, are easier to follow, and are easier to experiment with, whereas food web models more accurately represent ecosystem structure and dynamics, and data can be directly used as input for simulation modeling.
Two general types of food webs are often shown interacting within a single ecosystem. A grazing food web has plants or other photosynthetic organisms at its base, followed by herbivores and various carnivores. A detrital food web consists of a base of organisms that feed on decaying organic matter (dead organisms), called decomposers or detritivores. These organisms are usually bacteria or fungi that recycle organic material back into the biotic part of the ecosystem as they themselves are consumed by other organisms. As all ecosystems require a method to recycle material from dead organisms, most grazing food webs have an associated detrital food web. For example, in a meadow ecosystem, plants may support a grazing food web of different organisms, primary and other levels of consumers, while at the same time supporting a detrital food web of bacteria, fungi, and detrivorous invertebrates feeding off dead plants and animals.
Evolution Connection – Three-spined Stickleback
It is well established by the theory of natural selection that changes in the environment play a major role in the evolution of species within an ecosystem. However, little is known about how the evolution of species within an ecosystem can alter the ecosystem environment. In 2009, Dr. Luke Harmon, from the University of Idaho in Moscow, published a paper that for the first time showed that the evolution of organisms into subspecies can have direct effects on their ecosystem environment (Harmon, 2009).
The three-spines stickleback (Gasterosteus aculeatus) is a freshwater fish that evolved from a saltwater fish to live in freshwater lakes about 10,000 years ago, which is considered a recent development in evolutionary time (Figure \(6\)). Over the last 10,000 years, these freshwater fish then became isolated from each other in different lakes. Depending on which lake population was studied, findings showed that these sticklebacks then either remained as one species or evolved into two species. The divergence of species was made possible by their use of different areas of the pond for feeding called micro niches.
Dr. Harmon and his team created artificial pond microcosms in 250-gallon tanks and added muck from freshwater ponds as a source of zooplankton and other invertebrates to sustain the fish. In different experimental tanks, they introduced one species of stickleback from either a single-species or double-species lake.
Over time, the team observed that some of the tanks bloomed with algae while others did not. This puzzled the scientists, and they decided to measure the water’s dissolved organic carbon (DOC), which consists of mostly large molecules of decaying organic matter that give pond-water its slightly brownish color. It turned out that the water from the tanks with two-species fish contained larger particles of DOC (and hence darker water) than water with single-species fish. This increase in DOC blocked the sunlight and prevented algal blooming. Conversely, the water from the single-species tank contained smaller DOC particles, allowing more sunlight penetration to fuel the algal blooms.
This change in the environment, which is due to the different feeding habits of the stickleback species in each lake type, probably has a great impact on the survival of other species in these ecosystems, especially other photosynthetic organisms. Thus, the study shows that, at least in these ecosystems, the environment and the evolution of populations have reciprocal effects that may now be factored into simulation models.
Research into Ecosystem Dynamics: Ecosystem Experimentation and Modeling
The study of the changes in ecosystem structure caused by changes in the environment (disturbances) or by internal forces is called ecosystem dynamics. Ecosystems are characterized using a variety of research methodologies. Some ecologists study ecosystems using controlled experimental systems, while some study entire ecosystems in their natural state, and others use both approaches.
A holistic ecosystem model attempts to quantify the composition, interaction, and dynamics of entire ecosystems; it is the most representative of the ecosystem in its natural state. A food web is an example of a holistic ecosystem model. However, this type of study is limited by time and expense, as well as the fact that it is neither feasible nor ethical to do experiments on large natural ecosystems. To quantify all different species in an ecosystem and the dynamics in their habitat is difficult, especially when studying large habitats such as the Amazon Rainforest, which covers 1.4 billion acres (5.5 million km2) of the Earth’s surface.
For these reasons, scientists study ecosystems under more controlled conditions. Experimental systems usually involve either partitioning a part of a natural ecosystem that can be used for experiments, termed a mesocosm, or by re-creating an ecosystem entirely in an indoor or outdoor laboratory environment, which is referred to as a microcosm. A major limitation to these approaches is that removing individual organisms from their natural ecosystem or altering a natural ecosystem through partitioning may change the dynamics of the ecosystem. These changes are often due to differences in species numbers and diversity and also to environmental alterations caused by partitioning (mesocosm) or re-creating (microcosm) the natural habitat. Thus, these types of experiments are not totally predictive of changes that would occur in the ecosystem from which they were gathered.
As both of these approaches have their limitations, some ecologists suggest that results from these experimental systems should be used only in conjunction with holistic ecosystem studies to obtain the most representative data about ecosystem structure, function, and dynamics.
Scientists use the data generated by these experimental studies to develop ecosystem models that demonstrate the structure and dynamics of ecosystems. Three basic types of ecosystem modeling are routinely used in research and ecosystem management: a conceptual model, an analytical model, and a simulation model. A conceptual model is an ecosystem model that consists of flow charts to show interactions of different compartments of the living and nonliving components of the ecosystem. A conceptual model describes ecosystem structure and dynamics and shows how environmental disturbances affect the ecosystem; however, its ability to predict the effects of these disturbances is limited. Analytical and simulation models, in contrast, are mathematical methods of describing ecosystems that are indeed capable of predicting the effects of potential environmental changes without direct experimentation, although with some limitations as to accuracy. An analytical model is an ecosystem model that is created using simple mathematical formulas to predict the effects of environmental disturbances on ecosystem structure and dynamics. A simulation model is an ecosystem model that is created using complex computer algorithms to holistically model ecosystems and to predict the effects of environmental disturbances on ecosystem structure and dynamics. Ideally, these models are accurate enough to determine which components of the ecosystem are particularly sensitive to disturbances, and they can serve as a guide to ecosystem managers (such as conservation ecologists or fisheries biologists) in the practical maintenance of ecosystem health.
Conceptual Models
Conceptual models are useful for describing ecosystem structure and dynamics and for demonstrating the relationships between different organisms in a community and their environment. Conceptual models are usually depicted graphically as flow charts. The organisms and their resources are grouped into specific compartments with arrows showing the relationship and transfer of energy or nutrients between them. Thus, these diagrams are sometimes called compartment models.
To model the cycling of mineral nutrients, organic and inorganic nutrients are subdivided into those that are bioavailable (ready to be incorporated into biological macromolecules) and those that are not. For example, in a terrestrial ecosystem near a deposit of coal, carbon will be available to the plants of this ecosystem as carbon dioxide gas in a short-term period, not from the carbon-rich coal itself. However, over a longer period, microorganisms capable of digesting coal will incorporate its carbon or release it as natural gas (methane, CH4), changing this unavailable organic source into an available one. This conversion is greatly accelerated by the combustion of fossil fuels by humans, which releases large amounts of carbon dioxide into the atmosphere. This is thought to be a major factor in the rise of atmospheric carbon dioxide levels in the industrial age. The carbon dioxide released from burning fossil fuels is produced faster than photosynthetic organisms can use it. This process is intensified by the reduction of photosynthetic trees because of worldwide deforestation. Most scientists agree that high atmospheric carbon dioxide is a major cause of global climate change.
Conceptual models are also used to show the flow of energy through particular ecosystems. Figure \(7\) is based on Howard T. Odum’s classical study of Silver Springs, Florida, in the mid-twentieth century (Odum. 1957). This study shows the energy content and transfer between various ecosystem compartments.
Analytical and Simulation Models
The major limitation of conceptual models is their inability to predict the consequences of changes in ecosystem species and/or environment. Ecosystems are dynamic entities and subject to a variety of abiotic and biotic disturbances caused by natural forces and/or human activity. Ecosystems altered from their initial equilibrium state can often recover from such disturbances and return to a state of equilibrium. As most ecosystems are subject to periodic disturbances and are often in a state of change, they are usually either moving toward or away from their equilibrium state. There are many of these equilibrium states among the various components of an ecosystem, which affects the ecosystem overall. Furthermore, as humans have the ability to greatly and rapidly alter the species content and habitat of an ecosystem, the need for predictive models that enable understanding of how ecosystems respond to these changes becomes more crucial.
Analytical models often use simple, linear components of ecosystems, such as food chains, and are known to be complex mathematically; therefore, they require a significant amount of mathematical knowledge and expertise. Although analytical models have great potential, their simplification of complex ecosystems is thought to limit their accuracy. Simulation models that use computer programs are better able to deal with the complexities of ecosystem structure.
A recent development in simulation modeling uses supercomputers to create and run individual-based simulations, which account for the behavior of individual organisms and their effects on the ecosystem as a whole. These simulations are considered to be the most accurate and predictive of the complex responses of ecosystems to disturbances.
Summary
Ecosystems exist on land, at sea, in the air, and underground. Different ways of modeling ecosystems are necessary to understand how environmental disturbances will affect ecosystem structure and dynamics. Conceptual models are useful to show the general relationships between organisms and the flow of materials or energy between them. Analytical models are used to describe linear food chains, and simulation models work best with holistic food webs. | textbooks/bio/Introductory_and_General_Biology/Principles_of_Biology/03%3A_Chapter_3/26%3A_Ecosystems/26.01%3A_Ecology_of_Ecosystems.txt |
All living things require energy in one form or another. Energy is required by most complex metabolic pathways (often in the form of adenosine triphosphate, ATP), especially those responsible for building large molecules from smaller compounds, and life itself is an energy-driven process. Living organisms would not be able to assemble macromolecules (proteins, lipids, nucleic acids, and complex carbohydrates) from their monomeric subunits without a constant energy input.
It is important to understand how organisms acquire energy and how that energy is passed from one organism to another through food webs and their constituent food chains. Food webs illustrate how energy flows directionally through ecosystems, including how efficiently organisms acquire it, use it, and how much remains for use by other organisms of the food web.
How Organisms Acquire Energy in a Food Web
Energy is acquired by living things in three ways: photosynthesis, chemosynthesis, and the consumption and digestion of other living or previously living organisms by heterotrophs.
Photosynthetic and chemosynthetic organisms are both grouped into a category known as autotrophs: organisms capable of synthesizing their own food (more specifically, capable of using inorganic carbon as a carbon source). Photosynthetic autotrophs (photoautotrophs) use sunlight as an energy source, whereas chemosynthetic autotrophs (chemoautotrophs) use inorganic molecules as an energy source. Autotrophs are critical for all ecosystems. Without these organisms, energy would not be available to other living organisms and life itself would not be possible.
Photoautotrophs, such as plants, algae, and photosynthetic bacteria, serve as the energy source for a majority of the world’s ecosystems. These ecosystems are often described by grazing food webs. Photoautotrophs harness the solar energy of the sun by converting it to chemical energy in the form of ATP (and NADP). The energy stored in ATP is used to synthesize complex organic molecules, such as glucose.
Chemoautotrophs are primarily bacteria that are found in rare ecosystems where sunlight is not available, such as in those associated with dark caves or hydrothermal vents at the bottom of the ocean (Figure $1$). Many chemoautotrophs in hydrothermal vents use hydrogen sulfide (H2S), which is released from the vents as a source of chemical energy. This allows chemoautotrophs to synthesize complex organic molecules, such as glucose, for their own energy and in turn supplies energy to the rest of the ecosystem.
Productivity within Trophic Levels
Productivity within an ecosystem can be defined as the percentage of energy entering the ecosystem incorporated into biomass in a particular trophic level. Biomass is the total mass, in a unit area at the time of measurement, of living or previously living organisms within a trophic level. Ecosystems have characteristic amounts of biomass at each trophic level. For example, in the English Channel ecosystem, the primary producers account for a biomass of 4 g/m2 (grams per meter squared), while the primary consumers exhibit a biomass of 21 g/m2.
The productivity of the primary producers is especially important in any ecosystem because these organisms bring energy to other living organisms by photoautotrophy or chemoautotrophy. The rate at which photosynthetic primary producers incorporate energy from the sun is called gross primary productivity. An example of gross primary productivity is shown in the compartment diagram of energy flow within the Silver Springs aquatic ecosystem as shown (Figure $2$). In this ecosystem, the total energy accumulated by the primary producers (gross primary productivity) was shown to be 20,810 kcal/m2/yr.
Because all organisms need to use some of this energy for their own functions (like respiration and resulting metabolic heat loss) scientists often refer to the net primary productivity of an ecosystem. Net primary productivity is the energy that remains in the primary producers after accounting for the organisms’ respiration and heat loss. The net productivity is then available to the primary consumers at the next trophic level. In our Silver Spring example, 13,187 of the 20,810 kcal/m2/yr were used for respiration or were lost as heat, leaving 7,632 kcal/m2/yr of energy for use by the primary consumers.
Ecological Efficiency: The Transfer of Energy between Trophic Levels
As illustrated in Figure $2$, large amounts of energy are lost from the ecosystem from one trophic level to the next level as energy flows from the primary producers through the various trophic levels of consumers and decomposers.
The main reason for this loss is the second law of thermodynamics, which states that whenever energy is converted from one form to another, there is a tendency toward disorder (entropy) in the system. In biologic systems, this means a great deal of energy is lost as metabolic heat when the organisms from one trophic level consume the next level. In the Silver Springs ecosystem example, we see that the primary consumers produced 1103 kcal/m2/yr from the 7618 kcal/m2/yr of energy available to them from the primary producers. The measurement of energy transfer efficiency between two successive trophic levels is termed the trophic level transfer efficiency (TLTE) and is defined by the formula:
$\text{TLTE} = \dfrac{\text{production at present trophic level}}{\text{production at previous trophic level}} \times 100 \nonumber$
In Silver Springs, the TLTE between the first two trophic levels was approximately 14.8 percent. The low efficiency of energy transfer between trophic levels is usually the major factor that limits the length of food chains observed in a food web. The fact is, after four to six energy transfers, there is not enough energy left to support another trophic level. In the Lake Ontario example, only three energy transfers occurred between the primary producer, (green algae), and the apex consumer (Chinook salmon).
Ecologists have many different methods of measuring energy transfers within ecosystems. Some transfers are easier or more difficult to measure depending on the complexity of the ecosystem and how much access scientists have to observe the ecosystem. In other words, some ecosystems are more difficult to study than others, and sometimes the quantification of energy transfers has to be estimated.
Another main parameter that is important in characterizing energy flow within an ecosystem is the net production efficiency. Net production efficiency (NPE) allows ecologists to quantify how efficiently organisms of a particular trophic level incorporate the energy they receive into biomass; it is calculated using the following formula:
$\text{NPE} = \dfrac{\text{net consumer productivity}}{\text{assimilation}} \times 100 \nonumber$
Net consumer productivity is the energy content available to the organisms of the next trophic level. Assimilation is the biomass (energy content generated per unit area) of the present trophic level after accounting for the energy lost due to incomplete ingestion of food, energy used for respiration, and energy lost as waste. Incomplete ingestion refers to the fact that some consumers eat only a part of their food. For example, when a lion kills an antelope, it will eat everything except the hide and bones. The lion is missing the energy-rich bone marrow inside the bone, so the lion does not make use of all the calories its prey could provide.
Thus, NPE measures how efficiently each trophic level uses and incorporates the energy from its food into biomass to fuel the next trophic level. In general, cold-blooded animals (ectotherms), such as invertebrates, fish, amphibians, and reptiles, use less of the energy they obtain for respiration and heat than warm-blooded animals (endotherms), such as birds and mammals. The extra heat generated in endotherms, although an advantage in terms of the activity of these organisms in colder environments, is a major disadvantage in terms of NPE. Therefore, many endotherms have to eat more often than ectotherms to get the energy they need for survival. In general, NPE for ectotherms is an order of magnitude (10x) higher than for endotherms. For example, the NPE for a caterpillar eating leaves has been measured at 18 percent, whereas the NPE for a squirrel eating acorns may be as low as 1.6 percent.
The inefficiency of energy use by warm-blooded animals has broad implications for the world’s food supply. It is widely accepted that the meat industry uses large amounts of crops to feed livestock, and because the NPE is low, much of the energy from animal feed is lost. For example, it costs about 1¢ to produce 1000 dietary calories (kcal) of corn or soybeans, but approximately $0.19 to produce a similar number of calories growing cattle for beef consumption. The same energy content of milk from cattle is also costly, at approximately$0.16 per 1000 kcal. Much of this difference is due to the low NPE of cattle. Thus, there has been a growing movement worldwide to promote the consumption of non-meat and non-dairy foods so that less energy is wasted feeding animals for the meat industry.
Modeling Ecosystems Energy Flow: Ecological Pyramids
The structure of ecosystems can be visualized with ecological pyramids, which were first described by the pioneering studies of Charles Elton in the 1920s. Ecological pyramids show the relative amounts of various parameters (such as the number of organisms, energy, and biomass) across trophic levels.
Pyramids of numbers can be either upright or inverted, depending on the ecosystem. As shown in Figure $3$, typical grassland during the summer has a base of many plants and the numbers of organisms decrease at each trophic level. However, during the summer in a temperate forest, the base of the pyramid consists of few trees compared with the number of primary consumers, mostly insects. Because trees are large, they have great photosynthetic capability and dominate other plants in this ecosystem to obtain sunlight. Even in smaller numbers, primary producers in forests are still capable of supporting other trophic levels.
Another way to visualize ecosystem structure is with pyramids of biomass. This pyramid measures the amount of energy converted into living tissue at the different trophic levels. Using the Silver Springs ecosystem example, this data exhibits an upright biomass pyramid (Figure $3$), whereas the pyramid from the English Channel example is inverted. The plants (primary producers) of the Silver Springs ecosystem make up a large percentage of the biomass found there. However, the phytoplankton in the English Channel example make up less biomass than the primary consumers, the zooplankton. As with inverted pyramids of numbers, this inverted pyramid is not due to a lack of productivity from the primary producers but results from the high turnover rate of the phytoplankton. The phytoplankton are consumed rapidly by the primary consumers, thus, minimizing their biomass at any particular point in time. However, phytoplankton reproduce quickly, thus they are able to support the rest of the ecosystem.
Pyramid ecosystem modeling can also be used to show energy flow through the trophic levels. Pyramids of energy are always upright, and an ecosystem without sufficient primary productivity cannot be supported. All types of ecological pyramids are useful for characterizing ecosystem structure. However, in the study of energy flow through the ecosystem, pyramids of energy are the most consistent and representative models of ecosystem structure.
Consequences of Food Webs: Biological Magnification
One of the most important environmental consequences of ecosystem dynamics is biomagnification. Biomagnification is the increasing concentration of persistent, toxic substances in organisms at each trophic level, from the primary producers to the apex consumers. Many substances have been shown to bioaccumulate, including classical studies with the pesticide dichlorodiphenyltrichloroethane (DDT), which was published in the 1960s bestseller, Silent Spring, by Rachel Carson. DDT was a commonly used pesticide before its dangers became known. In some aquatic ecosystems, organisms from each trophic level consumed many organisms of the lower level, which caused DDT to increase in birds (apex consumers) that ate fish. Thus, birds accumulated sufficient amounts of DDT to cause fragility in their eggshells. This effect increased egg breakage during nesting and was shown to have adverse effects on these bird populations. The use of DDT was banned in the United States in the 1970s.
Other substances that biomagnify are polychlorinated biphenyls (PCBs), which were used in coolant liquids in the United States until their use was banned in 1979, and heavy metals, such as mercury, lead, and cadmium. These substances were best studied in aquatic ecosystems, where fish species at different trophic levels accumulate toxic substances brought through the ecosystem by the primary producers. As illustrated in a study performed by the National Oceanic and Atmospheric Administration (NOAA) in the Saginaw Bay of Lake Huron (Figure $4$), PCB concentrations increased from the ecosystem’s primary producers (phytoplankton) through the different trophic levels of fish species. The apex consumer (walleye) has more than four times the amount of PCBs compared to phytoplankton. Also, based on results from other studies, birds that eat these fish may have PCB levels at least one order of magnitude higher than those found in the lake fish.
Other concerns have been raised by the accumulation of heavy metals, such as mercury and cadmium, in certain types of seafood. The United States Environmental Protection Agency (EPA) recommends that pregnant women and young children should not consume any swordfish, shark, king mackerel, or tilefish because of their high mercury content. These individuals are advised to eat fish low in mercury: salmon, tilapia, shrimp, pollock, and catfish. Biomagnification is a good example of how ecosystem dynamics can affect our everyday lives, even influencing the food we eat.
Summary
Organisms in an ecosystem acquire energy in a variety of ways, which is transferred between trophic levels as the energy flows from the bottom to the top of the food web, with energy being lost at each transfer. The efficiency of these transfers is important for understanding the different behaviors and eating habits of warm-blooded versus cold-blooded animals. Modeling of ecosystem energy is best done with ecological pyramids of energy, although other ecological pyramids provide other vital information about ecosystem structure. | textbooks/bio/Introductory_and_General_Biology/Principles_of_Biology/03%3A_Chapter_3/26%3A_Ecosystems/26.02%3A_Energy_Flow_through_Ecosystems.txt |
Energy flows directionally through ecosystems, entering as sunlight (or inorganic molecules for chemoautotrophs) and leaving as heat during the many transfers between trophic levels. However, the matter that makes up living organisms is conserved and recycled. The six most common elements associated with organic molecules—carbon, nitrogen, hydrogen, oxygen, phosphorus, and sulfur—take a variety of chemical forms and may exist for long periods in the atmosphere, on land, in water, or beneath the Earth’s surface. Geologic processes, such as weathering, erosion, water drainage, and the subduction of the continental plates, all play a role in this recycling of materials. Because geology and chemistry have major roles in the study of this process, the recycling of inorganic matter between living organisms and their environment is called a biogeochemical cycle.
Water contains hydrogen and oxygen, which is essential to all living processes. The hydrosphere is the area of the Earth where water movement and storage occurs: as liquid water on the surface and beneath the surface or frozen (rivers, lakes, oceans, groundwater, polar ice caps, and glaciers), and as water vapor in the atmosphere. Carbon is found in all organic macromolecules and is an important constituent of fossil fuels. Nitrogen is a major component of our nucleic acids and proteins and is critical to human agriculture. Phosphorus, a major component of nucleic acid (along with nitrogen), is one of the main ingredients in artificial fertilizers used in agriculture and their associated environmental impacts on our surface water. Sulfur, critical to the 3–D folding of proteins (as in disulfide binding), is released into the atmosphere by the burning of fossil fuels, such as coal.
The cycling of these elements is interconnected. For example, the movement of water is critical for the leaching of nitrogen and phosphate into rivers, lakes, and oceans. Furthermore, the ocean itself is a major reservoir for carbon. Thus, mineral nutrients are cycled, either rapidly or slowly, through the entire biosphere, from one living organism to another, and between the biotic and abiotic world.
The Water (Hydrologic) Cycle
Water is the basis of all living processes. The human body is more than 1/2 water and human cells are more than 70 percent water. Thus, most land animals need a supply of fresh water to survive. However, when examining the stores of water on Earth, 97.5 percent of it is non-potable salt water (Figure $1$). Of the remaining water, 99 percent is locked underground as water or as ice. Thus, less than 1 percent of fresh water is easily accessible from lakes and rivers. Many living things, such as plants, animals, and fungi, are dependent on the small amount of fresh surface water supply, a lack of which can have massive effects on ecosystem dynamics. Humans, of course, have developed technologies to increase water availability, such as digging wells to harvest groundwater, storing rainwater, and using desalination to obtain drinkable water from the ocean. Although this pursuit of drinkable water has been ongoing throughout human history, the supply of fresh water is still a major issue in modern times.
Water cycling is extremely important to ecosystem dynamics. Water has a major influence on climate and, thus, on the environments of ecosystems, some located on distant parts of the Earth. Most of the water on Earth is stored for long periods in the oceans, underground, and as ice. Figure $2$ illustrates the average time that an individual water molecule may spend in the Earth’s major water reservoirs. Residence time is a measure of the average time an individual water molecule stays in a particular reservoir. A large amount of the Earth’s water is locked in place in these reservoirs as ice, beneath the ground, and in the ocean, and, thus, is unavailable for short-term cycling (only surface water can evaporate).
There are various processes that occur during the cycling of water, shown in Figure $3$. These processes include the following:
• evaporation/sublimation
• condensation/precipitation
• subsurface water flow
• surface runoff/snowmelt
• streamflow
The water cycle is driven by the sun’s energy as it warms the oceans and other surface waters. This leads to the evaporation (water to water vapor) of liquid surface water and the sublimation (ice to water vapor) of frozen water, which deposits large amounts of water vapor into the atmosphere. Over time, this water vapor condenses into clouds as liquid or frozen droplets and is eventually followed by precipitation (rain or snow), which returns water to the Earth’s surface. Rain eventually permeates into the ground, where it may evaporate again if it is near the surface, flow beneath the surface, or be stored for long periods. More easily observed is surface runoff: the flow of fresh water either from rain or melting ice. Runoff can then make its way through streams and lakes to the oceans or flow directly to the oceans themselves.
Rain and surface runoff are major ways in which minerals, including carbon, nitrogen, phosphorus, and sulfur, are cycled from land to water. The environmental effects of runoff will be discussed later as these cycles are described.
The Carbon Cycle
Carbon is the second most abundant element in living organisms. Carbon is present in all organic molecules, and its role in the structure of macromolecules is of primary importance to living organisms. Carbon compounds contain especially high energy, particularly those derived from fossilized organisms, mainly plants, which humans use as fuel. Since the 1800s, the number of countries using massive amounts of fossil fuels has increased. Since the beginning of the Industrial Revolution, global demand for the Earth’s limited fossil fuel supplies has risen; therefore, the amount of carbon dioxide in our atmosphere has increased. This increase in carbon dioxide has been associated with climate change and other disturbances of the Earth’s ecosystems and is a major environmental concern worldwide. Thus, the “carbon footprint” is based on how much carbon dioxide is produced and how much fossil fuel countries consume.
The carbon cycle is most easily studied as two interconnected sub-cycles: one dealing with rapid carbon exchange among living organisms and the other dealing with the long-term cycling of carbon through geologic processes. The entire carbon cycle is shown in Figure $4$.
The Biological Carbon Cycle
Living organisms are connected in many ways, even between ecosystems. A good example of this connection is the exchange of carbon between autotrophs and heterotrophs within and between ecosystems by way of atmospheric carbon dioxide. Carbon dioxide is the basic building block that most autotrophs use to build multi-carbon, high-energy compounds, such as glucose. The energy harnessed from the sun is used by these organisms to form the covalent bonds that link carbon atoms together. These chemical bonds thereby store this energy for later use in the process of respiration. Most terrestrial autotrophs obtain their carbon dioxide directly from the atmosphere, while marine autotrophs acquire it in the dissolved form (carbonic acid, H2CO3). However carbon dioxide is acquired, a by-product of the process is oxygen. The photosynthetic organisms are responsible for depositing approximately 21 percent oxygen content of the atmosphere that we observe today.
Heterotrophs and autotrophs are partners in biological carbon exchange (especially the primary consumers, largely herbivores). Heterotrophs acquire the high-energy carbon compounds from the autotrophs by consuming them and breaking them down by respiration to obtain cellular energy, such as ATP. The most efficient type of respiration, aerobic respiration, requires oxygen obtained from the atmosphere or dissolved in water. Thus, there is a constant exchange of oxygen and carbon dioxide between the autotrophs (which need the carbon) and the heterotrophs (which need the oxygen). Gas exchange through the atmosphere and water is one way that the carbon cycle connects all living organisms on Earth.
The Biogeochemical Carbon Cycle
The movement of carbon through the land, water, and air is complex, and in many cases, it occurs much more slowly geologically than as seen between living organisms. Carbon is stored for long periods in what are known as carbon reservoirs, which include the atmosphere, bodies of liquid water (mostly oceans), ocean sediment, soil, land sediments (including fossil fuels), and the Earth’s interior.
As stated, the atmosphere is a major reservoir of carbon in the form of carbon dioxide and is essential to the process of photosynthesis. The level of carbon dioxide in the atmosphere is greatly influenced by the reservoir of carbon in the oceans. The exchange of carbon between the atmosphere and water reservoirs influences how much carbon is found in each location, and each one affects the other reciprocally. Carbon dioxide (CO2) from the atmosphere dissolves in water and combines with water molecules to form carbonic acid, and then it ionizes to carbonate and bicarbonate ions (Figure $5$)
The equilibrium coefficients are such that more than 90 percent of the carbon in the ocean is found as bicarbonate ions. Some of these ions combine with seawater calcium to form calcium carbonate (CaCO3), a major component of marine organism shells. These organisms eventually form sediments on the ocean floor. Over geologic time, the calcium carbonate forms limestone, which comprises the largest carbon reservoir on Earth.
On land, carbon is stored in soil as a result of the decomposition of living organisms (by decomposers) or from weathering of terrestrial rock and minerals. This carbon can be leached into the water reservoirs by surface runoff. Deeper underground, on land and at sea, are fossil fuels: the anaerobically decomposed remains of plants that take millions of years to form. Fossil fuels are considered a non-renewable resource because their use far exceeds their rate of formation. A non-renewable resource, such as fossil fuel, is either regenerated very slowly or not at all. Another way for carbon to enter the atmosphere is from land (including land beneath the surface of the ocean) by the eruption of volcanoes and other geothermal systems. Carbon sediments from the ocean floor are taken deep within the Earth by the process of subduction: the movement of one tectonic plate beneath another. Carbon is released as carbon dioxide when a volcano erupts or from volcanic hydrothermal vents.
Carbon dioxide is also added to the atmosphere by the animal husbandry practices of humans. The large numbers of land animals raised to feed the Earth’s growing population results in increased carbon dioxide levels in the atmosphere due to farming practices, respiration, and methane production. This is another example of how human activity indirectly affects biogeochemical cycles in a significant way. Although much of the debate about the future effects of increasing atmospheric carbon on climate change focus on fossil fuels, scientists take natural processes, such as volcanoes and respiration, into account as they model and predict the future impact of this increase.
The Nitrogen Cycle
Getting nitrogen into the living world is difficult. Plants and phytoplankton are not equipped to incorporate nitrogen from the atmosphere (which exists as tightly bonded, triple covalent N2) even though this molecule comprises approximately 78 percent of the atmosphere. Nitrogen enters the living world via free-living and symbiotic bacteria, which incorporate nitrogen into their macromolecules through nitrogen fixation (conversion of N2). Cyanobacteria live in most aquatic ecosystems where sunlight is present; they play a key role in nitrogen fixation. Cyanobacteria are able to use inorganic sources of nitrogen to fix nitrogen. Rhizobium bacteria live symbiotically in the root nodules of legumes (such as peas, beans, and peanuts) and provide them with the organic nitrogen they need. Free-living bacteria, such as Azotobacter, are also important nitrogen fixers.
Organic nitrogen is especially important to the study of ecosystem dynamics since many ecosystem processes, such as primary production and decomposition, are limited by the available supply of nitrogen. As shown in Figure $6$, the nitrogen that enters living systems by nitrogen fixation is successively converted from organic nitrogen back into nitrogen gas by bacteria. This process occurs in three steps in terrestrial systems: ammonification, nitrification, and denitrification. First, the ammonification process converts nitrogenous waste from living animals or from the remains of dead animals into ammonium (NH4+) by certain bacteria and fungi. Second, the ammonium is converted to nitrites (NO2) by nitrifying bacteria, such as Nitrosomonas, through nitrification. Subsequently, nitrites are converted to nitrates (NO3) by similar organisms. Third, the process of denitrification occurs, whereby bacteria, such as Pseudomonas and Clostridium, convert the nitrates into nitrogen gas, allowing it to re-enter the atmosphere.
Human activity can release nitrogen into the environment by two primary means: the combustion of fossil fuels, which releases different nitrogen oxides, and by the use of artificial fertilizers in agriculture, which are then washed into lakes, streams, and rivers by surface runoff. Atmospheric nitrogen is associated with several effects on Earth’s ecosystems including the production of acid rain (as nitric acid, HNO3) and greenhouse gas (as nitrous oxide, N2O) potentially causing climate change. A major effect of fertilizer runoff is saltwater and freshwater eutrophication, a process whereby nutrient runoff causes the excess growth of microorganisms, depleting dissolved oxygen levels and killing ecosystem fauna.
A similar process occurs in the marine nitrogen cycle, where the ammonification, nitrification, and denitrification processes are performed by marine bacteria. Some of this nitrogen falls to the ocean floor as sediment, which can then be moved to land in geologic time by the uplift of the Earth’s surface and thereby incorporated into terrestrial rock. Although the movement of nitrogen from rock directly into living systems has been traditionally seen as insignificant compared with nitrogen fixed from the atmosphere, a recent study showed that this process may indeed be significant and should be included in any study of the global nitrogen cycle (Morford, Houlton, & Dahlgren, 2011).
The Phosphorus Cycle
Phosphorus is an essential nutrient for living processes; it is a major component of nucleic acid and phospholipids, and, as calcium phosphate, makes up the supportive components of our bones. Phosphorus is often the limiting nutrient (necessary for growth) in aquatic ecosystems (Figure $7$).
Phosphorus occurs in nature as the phosphate ion (PO43−). In addition to phosphate runoff as a result of human activity, natural surface runoff occurs when it is leached from phosphate-containing rock by weathering, thus sending phosphates into rivers, lakes, and the ocean. This rock has its origins in the ocean. Phosphate-containing ocean sediments form primarily from the bodies of ocean organisms and from their excretions. However, in remote regions, volcanic ash, aerosols, and mineral dust may also be significant phosphate sources. This sediment then is moved to land over geologic time by the uplifting of areas of the Earth’s surface.
Phosphorus is also reciprocally exchanged between phosphate dissolved in the ocean and marine ecosystems. The movement of phosphate from the ocean to the land and through the soil is extremely slow, with the average phosphate ion having an oceanic residence time between 20,000 and 100,000 years.
Excess phosphorus and nitrogen that enters these ecosystems from fertilizer runoff and from sewage causes excessive growth of microorganisms and depletes the dissolved oxygen, which leads to the death of many ecosystem fauna, such as shellfish and finfish. This process is responsible for dead zones in lakes and at the mouths of many major rivers (Figure $8$).
A dead zone is an area within a freshwater or marine ecosystem where large areas are depleted of their normal flora and fauna; these zones can be caused by oil spills, dumping of toxic chemicals, and other human activities. The number of dead zones has been increasing for several years, and more than 400 of these zones were present as of 2008. One of the worst dead zones is off the coast of the United States in the Gulf of Mexico, where fertilizer runoff from the Mississippi River basin has created a dead zone of over 8463 square miles. Phosphate and nitrate runoff from fertilizers also negatively affect several lake and bay ecosystems including the Chesapeake Bay in the eastern United States.
Everyday Connection – Chesapeake Bay
The Chesapeake Bay has long been valued as one of the most scenic areas on Earth. It is now in distress and is recognized as a declining ecosystem. In the 1970s, the Chesapeake Bay was one of the first ecosystems to have identified dead zones, which continue to kill many fish and bottom-dwelling species, such as clams, oysters, and worms. Several species have declined in the Chesapeake Bay due to surface water runoff containing excess nutrients from artificial fertilizer used on land. The source of the fertilizers (with high nitrogen and phosphate content) is not limited to agricultural practices. There are many nearby urban areas and more than 150 rivers and streams empty into the bay that are carrying fertilizer runoff from lawns and gardens. Thus, the decline of the Chesapeake Bay is a complex issue and requires the cooperation of industry, agriculture, and everyday homeowners.
Of particular interest to conservationists is the oyster population; it is estimated that more than 200,000 acres of oyster reefs existed in the bay in the 1700s, but that number has now declined to only 36,000 acres. Oyster harvesting was once a major industry for Chesapeake Bay, but it declined 88 percent between 1982 and 2007. This decline was due not only to fertilizer runoff and dead zones but also to overharvesting. Oysters require a certain minimum population density because they must be in close proximity to reproduce. Human activity has altered the oyster population and locations, greatly disrupting the ecosystem.
The restoration of the oyster population in the Chesapeake Bay has been ongoing for several years with mixed success. Not only do many people find oysters good to eat, but they also clean up the bay. Oysters are filter feeders, and as they eat, they clean the water around them. In the 1700s, it was estimated that it took only a few days for the oyster population to filter the entire volume of the bay. Today, with changed water conditions, it is estimated that the present population would take nearly a year to do the same job.
Restoration efforts have been ongoing for several years by non-profit organizations, such as the Chesapeake Bay Foundation. The restoration goal is to find a way to increase population density so the oysters can reproduce more efficiently. Many disease-resistant varieties (developed at the Virginia Institute of Marine Science for the College of William and Mary) are now available and have been used in the construction of experimental oyster reefs. Efforts to clean and restore the bay by Virginia and Delaware have been hampered because much of the pollution entering the bay comes from other states, which stresses the need for inter-state cooperation to gain successful restoration.
The new, hearty oyster strains have also spawned a new and economically viable industry—oyster aquaculture—which not only supplies oysters for food and profit, but also has the added benefit of cleaning the bay.
The Sulfur Cycle
Sulfur is an essential element for the macromolecules of living things. As a part of the amino acid cysteine, it is involved in the formation of disulfide bonds within proteins, which help to determine their 3-D folding patterns, and hence their functions. As shown in Figure $9$, sulfur cycles between the oceans, land, and atmosphere. Atmospheric sulfur is found in the form of sulfur dioxide (SO2) and enters the atmosphere in three ways: from the decomposition of organic molecules, from volcanic activity and geothermal vents, and from the burning of fossil fuels by humans.
On land, sulfur is deposited in four major ways: precipitation, direct fallout from the atmosphere, rock weathering, and geothermal vents (Figure $10$). Atmospheric sulfur is found in the form of sulfur dioxide (SO2), and as rain falls through the atmosphere, sulfur is dissolved in the form of weak sulfuric acid (H2SO4). Sulfur can also fall directly from the atmosphere in a process called fallout. Also, the weathering of sulfur-containing rocks releases sulfur into the soil. These rocks originate from ocean sediments that are moved to land by the geologic uplifting of ocean sediments. Terrestrial ecosystems can then make use of these soil sulfates (SO42−), and upon the death and decomposition of these organisms, release the sulfur back into the atmosphere as hydrogen sulfide (H2S) gas.
Sulfur enters the ocean via runoff from land, atmospheric fallout, and underwater geothermal vents. Some ecosystems rely on chemoautotrophs using sulfur as a biological energy source. This sulfur then supports marine ecosystems in the form of sulfates.
Human activities have played a major role in altering the balance of the global sulfur cycle. The burning of large quantities of fossil fuels, especially coal, releases larger amounts of hydrogen sulfide gas into the atmosphere. As rain falls through this gas, it creates the phenomenon known as acid rain. Acid rain is corrosive rain caused by rainwater falling to the ground through sulfur dioxide gas, turning it into weak sulfuric acid, which causes damage to aquatic ecosystems. Acid rain damages the natural environment by lowering the pH of lakes, which kills many of the resident fauna; it also affects the man-made environment through the chemical degradation of buildings. For example, many marble monuments, such as the Lincoln Memorial in Washington, DC, have suffered significant damage from acid rain over the years. These examples show the wide-ranging effects of human activities on our environment and the challenges that remain for our future.
Summary
Mineral nutrients are cycled through ecosystems and their environment. Of particular importance are water, carbon, nitrogen, phosphorus, and sulfur. All of these cycles have major impacts on ecosystem structure and function. As human activities have caused major disturbances to these cycles, their study and modeling is especially important. A variety of human activities, such as pollution, oil spills, and other events have damaged ecosystems, potentially causing global climate change. The health of Earth depends on understanding these cycles and how to protect the environment from irreversible damage. | textbooks/bio/Introductory_and_General_Biology/Principles_of_Biology/03%3A_Chapter_3/26%3A_Ecosystems/26.03%3A_Biogeochemical_Cycles.txt |
In the 1980s, biologists working in Lake Victoria (Figure \(1\)) in Africa discovered one of the most extraordinary products of evolution on the planet. Located in the Great Rift Valley, Lake Victoria is a large lake about 68,900 km2 in area (larger than Lake Huron, the second largest of North America’s Great Lakes). Biologists were studying species of a family of fish called cichlids. They found that as they sampled for fish in different locations of the lake, they never stopped finding new species, and they identified nearly 500 evolved types of cichlids. But while studying these variations, they quickly discovered that the invasive Nile Perch was destroying the lake’s cichlid population, bringing hundreds of cichlid species to extinction with devastating rapidity.
27: Conservation Biology and Biodiversity
Traditionally, ecologists have measured biodiversity, a general term for the variety present in the biosphere, by taking into account both the number of species and their commonness. Biodiversity can be estimated at a number of levels of organization of living things. These estimation indexes, which came from information theory, are most useful as a first step in quantifying biodiversity between and within ecosystems; they are less useful when the main concern among conservation biologists is simply the loss of biodiversity. However, biologists recognize that measures of biodiversity, in terms of species diversity, may help focus efforts to preserve the biologically or technologically important elements of biodiversity.
The Lake Victoria cichlids provide an example through which we can begin to understand biodiversity. The biologists studying cichlids in the 1980s discovered hundreds of cichlid species representing a variety of specializations to particular habitat types and specific feeding strategies: eating plankton floating in the water, scraping and then eating algae from rocks, eating insect larvae from the bottom, and eating the eggs of other species of cichlid. The cichlids of Lake Victoria are the product of an adaptive radiation. An adaptive radiation is a rapid (less than three million years in the case of the Lake Victoria cichlids) branching through speciation of a phylogenetic tree into many closely related species; typically, the species “radiate” into different habitats and niches. The Galápagos finches are an example of a modest adaptive radiation with 15 species. The cichlids of Lake Victoria are an example of a spectacular adaptive radiation that includes about 500 species.
At the time biologists were making this discovery, some species began to quickly disappear. A culprit in these declines was a species of large fish that was introduced to Lake Victoria by fisheries to feed the people living around the lake. The Nile perch was introduced in 1963, but lay low until the 1980s when its populations began to surge. The Nile perch population grew by consuming cichlids, driving species after species to the point of extinction (the disappearance of a species). In fact, there were several factors that played a role in the extinction of perhaps 200 cichlid species in Lake Victoria: the Nile perch, declining lake water quality due to agriculture and land clearing on the shores of Lake Victoria, and increased fishing pressure. Scientists had not even cataloged all of the species present—so many were lost that were never named. The diversity is now a shadow of what it once was.
The cichlids of Lake Victoria are a thumbnail sketch of contemporary rapid species loss that occurs all over Earth and is caused by human activity. Extinction is a natural process of macroevolution that occurs at the rate of about one out of 1 million species becoming extinct per year. The fossil record reveals that there have been five periods of mass extinction in history with much higher rates of species loss, and the rate of species loss today is comparable to those periods of mass extinction. However, there is a major difference between the previous mass extinctions and the current extinction we are experiencing: human activity. Specifically, three human activities have a major impact: the destruction of habitat, the introduction of exotic species, and over-harvesting. Predictions of species loss within the next century, a tiny amount of time on geological timescales, ranging from 10 percent to 50 percent. Extinctions on this scale have only happened five other times in the history of the planet, and they have been caused by cataclysmic events that changed the course of the history of life in each instance. Many scientists believe Earth is now entering a sixth mass extinction.
Types of Biodiversity
Scientists generally accept that the term biodiversity describes the number and kinds of species in a location or on the planet. Species can be difficult to define, but most biologists still feel comfortable with the concept and are able to identify and count eukaryotic species in most contexts. Biologists have also identified alternate measures of biodiversity, some of which are important for planning how to preserve biodiversity.
Genetic diversity is one of those alternate concepts. Genetic diversity or variation is the raw material for adaptation in a species. A species’ future potential for adaptation depends on the genetic diversity held in the genomes of the individuals in populations that make up the species. The same is true for higher taxonomic categories. A genus with very different types of species will have more genetic diversity than a genus with species that look alike and have similar ecologies. If there were a choice between one of these genera of species being preserved, the one with the greatest potential for subsequent evolution is the most genetically diverse one. It would be ideal not to have to make such choices, but increasingly this may be the norm.
Many genes code for proteins, which in turn carry out the metabolic processes that keep organisms alive and reproducing. Genetic diversity can be measured as chemical diversity in that different species produce a variety of chemicals in their cells, both the proteins as well as the products and byproducts of metabolism. This chemical diversity has potential benefits for humans as a source of pharmaceuticals, so it provides one way to measure diversity that is important to human health and welfare.
Humans have generated diversity in domestic animals, plants, and fungi. This diversity is also suffering losses because of migration, market forces, and increasing globalism in agriculture, especially in heavily populated regions such as China, India, and Japan. The human population directly depends on this diversity as a stable food source, and its decline is troubling biologists and agricultural scientists.
It is also useful to define ecosystem diversity, meaning the number of different ecosystems on the planet or in a given geographic area. Whole ecosystems can disappear even if some of the species might survive by adapting to other ecosystems. The loss of an ecosystem means the loss of interactions between species, the loss of unique features of coadaptation, and the loss of biological productivity that an ecosystem is able to create. An example of a largely extinct ecosystem in North America is the prairie ecosystem. Prairies once spanned central North America from the boreal forest in northern Canada down into Mexico. They are now all but gone, replaced by crop fields, pasture lands, and suburban sprawl. Many of the species survive, but the hugely productive ecosystem that was responsible for creating the most productive agricultural soils is now gone. As a consequence, soils are disappearing or must be maintained at greater expense.
Current Species Diversity
Despite considerable effort, knowledge of the species that inhabit the planet is limited. A recent estimate suggests that the eukaryote species for which science has names, about 1.5 million species, account for less than 20 percent of the total number of eukaryote species present on the planet (8.7 million species, by one estimate). Estimates of numbers of prokaryotic species are largely guesses, but biologists agree that science has only begun to catalog their diversity. Even with what is known, there is no central repository of names or samples of the described species; therefore, there is no way to be sure that the 1.5 million descriptions is an accurate number. It is a best guess based on the opinions of experts in different taxonomic groups. Given that Earth is losing species at an accelerating pace, science is very much in the place it was with the Lake Victoria cichlids: knowing little about what is being lost. Table \(1\) presents recent estimates of biodiversity in different groups.
Table \(1\): Estimates of the Numbers of Described and Predicted Species by Taxonomic Group
Mora et al. 2011 Chapman 2009 Groombridge & Jenkins 2002
Described Predicted Described Predicted Described Predicted
Animalia 1,124,516 9,920,000 1,424,153 6,836,330 1,225,500 10,820,000
Chromista 17,892 34,900 25,044 200,500
Fungi 44,368 616,320 98,998 1,500,000 72,000 1,500,000
Plantae 224,244 314,600 310,129 390,800 270,000 320,000
Protozoa 16,236 72,800 28,871 1,000,000 80,000 600,000
Prokaryotes 10,307 1,000,000 10,175
Total 1,438,769 10,960,000 1,897,502 10,897,630 1,657,675 13,240,000
There are various initiatives to catalog described species in accessible ways, and the internet is facilitating that effort. Nevertheless, it has been pointed out that at the current rate of species description, which according to the State of Observed Species Report is 17,000 to 20,000 new species per year, it will take close to 500 years to finish describing life on this planet (IISE, 2011). Over time, the task becomes both increasingly impossible and increasingly easier as extinction removes species from the planet.
Naming and counting species may seem an unimportant pursuit given the other needs of humanity, but it is not simply an accounting. Describing species is a complex process by which biologists determine an organism’s unique characteristics and whether or not that organism belongs to any other described species. It allows biologists to find and recognize the species after the initial discovery and allows them to follow up on questions about its biology. In addition, the unique characteristics of each species make it potentially valuable to humans or other species on which humans depend. Understanding these characteristics is the value of finding and naming species.
Patterns of Biodiversity
Biodiversity is not evenly distributed on Earth. Lake Victoria contained almost 500 species of cichlids alone, ignoring the other fish families present in the lake. All of these species were found only in Lake Victoria; therefore, the 500 species of cichlids were endemic. Endemic species are found in only one location. Endemics with highly restricted distributions are particularly vulnerable to extinction. Higher taxonomic levels, such as genera and families, can also be endemic. Lake Huron contains about 79 species of fish, all of which are found in many other lakes in North America. What accounts for the difference in fish diversity in these two lakes? Lake Victoria is a tropical lake, while Lake Huron is a temperate lake. Lake Huron in its present form is only about 7,000 years old, while Lake Victoria in its present form is about 15,000 years old. Biogeographers have suggested these two factors, latitude and age, are two of several hypotheses to explain biodiversity patterns on the planet.
Biogeography is the study of the distribution of the world’s species—both in the past and in the present. The work of biogeographers is critical to understanding our physical environment, how the environment affects species, and how environmental changes impact the distribution of a species; it has also been critical to developing evolutionary theory. Biogeographers need to understand both biology and ecology. They also need to be well-versed in evolutionary studies, soil science, and climatology.
There are three main fields of study under the heading of biogeography: ecological biogeography, historical biogeography (called paleobiogeography), and conservation biogeography. Ecological biogeography studies the current factors affecting the distribution of plants and animals. Historical biogeography, as the name implies, studies the past distribution of species. Conservation biogeography, on the other hand, is focused on the protection and restoration of species based upon known historical and current ecological information. Each of these fields considers both zoogeography and phytogeography—the past and present distribution of animals and plants.
One of the oldest observed patterns in ecology is that species biodiversity in almost every taxonomic group increases as latitude declines. In other words, biodiversity increases closer to the equator (Figure \(1\)).
It is not yet clear why biodiversity increases closer to the equator, but hypotheses include the greater age of the ecosystems in the tropics versus temperate regions that were largely devoid of life or drastically impoverished during the last glaciation. The idea is that greater age provides more time for speciation. Another possible explanation is the increased energy the tropics receive from the sun versus the decreased energy that temperate and polar regions receive. It is not entirely clear how greater energy input could translate into more species. The complexity of tropical ecosystems may promote speciation by increasing the heterogeneity, or number of ecological niches, in the tropics relative to higher latitudes. The greater heterogeneity provides more opportunities for coevolution, specialization, and perhaps greater selection pressures leading to population differentiation. However, this hypothesis suffers from some circularity—ecosystems with more species encourage speciation, but how did they get more species to begin with? The tropics have been perceived as being more stable than temperate regions, which have a pronounced climate and day-length seasonality. The tropics have their own forms of seasonality, such as rainfall, but they are generally assumed to be more stable environments and this stability might promote speciation.
Regardless of the mechanisms, it is certainly true that all levels of biodiversity are greatest in the tropics. Additionally, the rate of endemism is the highest, and there are more biodiversity hotspots. However, this richness of diversity also means that our knowledge of species is lowest, and there is a high potential for biodiversity loss.
Conservation of Biodiversity
In 1988, British environmentalist Norman Myers developed a conservation concept to identify areas rich in species and at significant risk for species loss: biodiversity hotspots. Biodiversity hotspots are geographical areas that contain high numbers of endemic species. The purpose of the concept was to identify important locations on the planet for conservation efforts, a kind of conservation triage. By protecting hotspots, governments are able to protect a larger number of species. The original criteria for a hotspot included the presence of 1500 or more endemic plant species and 70 percent of the area disturbed by human activity. There are now 34 biodiversity hotspots (Figure \(2\)) containing large numbers of endemic species, which include half of Earth’s endemic plants.
Biodiversity Change through Geological Time
The number of species on the planet, or in any geographical area, is the result of an equilibrium of two evolutionary processes that are ongoing: speciation and extinction. Both are natural “birth” and “death” processes of macroevolution. When speciation rates begin to outstrip extinction rates, the number of species will increase; likewise, the number of species will decrease when extinction rates begin to overtake speciation rates. Throughout Earth’s history, these two processes have fluctuated—sometimes leading to dramatic changes in the number of species on Earth as reflected in the fossil record (Figure \(3\)).
Paleontologists have identified five strata in the fossil record that appear to show sudden and dramatic (greater than half of all extant species disappearing from the fossil record) losses in biodiversity. These are called mass extinctions. There are many lesser, yet still dramatic, extinction events, but the five mass extinctions have attracted the most research. An argument can be made that the five mass extinctions are only the five most extreme events in a continuous series of large extinction events throughout the Phanerozoic (since 542 million years ago). In most cases, the hypothesized causes are still controversial.
The Five Mass Extinctions
The fossil record of the mass extinctions was the basis for defining periods of geological history, so they typically occur at the transition point between geological periods. The transition in fossils from one period to another reflects the dramatic loss of species and the gradual origin of new species. These transitions can be seen in the rock strata. Table \(2\) provides data on the five mass extinctions.
Table \(2\): the names and dates for the five mass extinctions in Earth’s history.
Mass Extinctions
Geological Period Mass Extinction Name Time (millions of years ago)
Ordovician–Silurian end-Ordovician O–S 450–440
Late Devonian end-Devonian 375–360
Permian–Triassic end-Permian 251
Triassic–Jurassic end-Triassic 205
Cretaceous–Paleogene end-Cretaceous K–Pg (K–T) 65.5
The Ordovician-Silurian extinction event is the first recorded mass extinction and the second largest. During this period, about 85 percent of marine species (few species lived outside the oceans) became extinct. The main hypothesis for its cause is a period of glaciation and then warming. The extinction event actually consists of two extinction events separated by about 1 million years. The first event was caused by cooling, and the second event was due to the subsequent warming. The climate changes affected temperatures and sea levels. Some researchers have suggested that a gamma-ray burst, caused by a nearby supernova, is a possible cause of the Ordovician-Silurian extinction. The gamma-ray burst would have stripped away the Earth’s ozone layer causing intense ultraviolet radiation from the sun and may account for climate changes observed at the time. The hypothesis is speculative, but extraterrestrial influences on Earth’s history are an active line of research. Recovery of biodiversity after the mass extinction took from 5 to 20 million years, depending on the location.
The late Devonian extinction may have occurred over a relatively long period of time. It appears to have affected marine species and not the plants or animals inhabiting terrestrial habitats. The causes of this extinction are poorly understood.
The end-Permian extinction was the largest in the history of life. Indeed, an argument could be made that Earth nearly became devoid of life during this extinction event. The planet looked very different before and after this event. Estimates are that 96 percent of all marine species and 70 percent of all terrestrial species were lost. It was at this time, for example, that the trilobites, a group that survived the Ordovician–Silurian extinction, became extinct. The causes for this mass extinction are not clear, but the leading suspect is extended and widespread volcanic activity that led to a runaway global-warming event. The oceans became largely anoxic, suffocating marine life. Terrestrial tetrapod diversity took 30 million years to recover after the end-Permian extinction. The Permian extinction dramatically altered Earth’s biodiversity makeup and the course of evolution.
The causes of the Triassic–Jurassic extinction event are not clear and hypotheses of climate change, asteroid impact, and volcanic eruptions have been argued. The extinction event occurred just before the breakup of the supercontinent Pangaea, although recent scholarship suggests that the extinction may have occurred more gradually throughout the Triassic.
The causes of the end-Cretaceous extinction event are the ones that are best understood. It was during this extinction event about 65 million years ago that the dinosaurs, the dominant vertebrate group for millions of years, disappeared from the planet (with the exception of a theropod clade that gave rise to birds). Every land animal that weighed more than 25 kg became extinct. The cause of this extinction is now understood to be the result of a cataclysmic impact of a large meteorite, or asteroid, off the coast of what is now the Yucatán Peninsula. This hypothesis, proposed first in 1980, was a radical explanation based on a sharp spike in the levels of iridium (which rains down from space in meteors at a fairly constant rate but is otherwise absent on Earth’s surface) at the rock stratum that marks the boundary between the Cretaceous and Paleogene periods (Figure \(4\)). This boundary marked the disappearance of the dinosaurs in fossils as well as many other taxa. The researchers who discovered the iridium spike interpreted it as a rapid influx of iridium from space to the atmosphere (in the form of a large asteroid) rather than a slowing in the deposition of sediments during that period. It was a radical explanation, but the report of an appropriately aged and sized impact crater in 1991 made the hypothesis more believable. Now an abundance of geological evidence supports the theory. Recovery times for biodiversity after the end-Cretaceous extinction are shorter, in geological time, than for the end-Permian extinction, on the order of 10 million years.
The Pleistocene Extinction
The Pleistocene Extinction is one of the lesser extinctions and a recent one. It is well known that the North American, and to some degree Eurasian, megafauna, or large animals, disappeared toward the end of the last glaciation period. The extinction appears to have happened in a relatively restricted time period of 10,000–12,000 years ago. In North America, the losses were quite dramatic and included the woolly mammoths (last dated about 4,000 years ago in an isolated population), mastodon, giant beavers, giant ground sloths, saber-toothed cats, and the North American camel, just to name a few. The possibility that the rapid extinction of these large animals was caused by over-hunting was first suggested in the 1900s. Research into this hypothesis continues today. It seems likely that over-hunting caused many pre-written history extinctions in many regions of the world.
In general, the timing of the Pleistocene extinctions correlated with the arrival of humans and not with climate-change events, which is the main competing hypothesis for these extinctions. The extinctions began in Australia about 40,000 to 50,000 years ago, just after the arrival of humans in the area: a marsupial lion, a giant one-ton wombat, and several giant kangaroo species disappeared. In North America, the extinction of almost all of the large mammals occurred 10,000–12,000 years ago. All that are left are the smaller mammals such as bears, elk, moose, and cougars. Finally, on many remote oceanic islands, the extinction of many species occurred coincident with human arrivals. Not all of the islands had large animals, but when there were large animals, they were lost. Madagascar was colonized about 2,000 years ago and the large mammals that lived there became extinct. Eurasia and Africa do not show this pattern, but they also did not experience a recent arrival of humans. Humans arrived in Eurasia hundreds of thousands of years ago after the origin of the species in Africa. This topic remains an area of active research and hypothesizing. It seems clear that even if climate played a role, in most cases human hunting precipitated the extinctions.
Present-Time Extinctions
The sixth mass extinction (also called the Holocene extinction) appears to have begun earlier than previously believed and has mostly to do with the activities of Homo sapiens. Since the beginning of the Holocene period, there are numerous recent extinctions of individual species that are recorded in human writings. Most of these are coincident with the expansion of the European colonies since the 1500s.
One of the earlier and popularly known examples is the dodo bird. The dodo bird lived in the forests of Mauritius, an island in the Indian Ocean. The dodo bird became extinct around 1662. It was hunted for its meat by sailors and was easy prey because the dodo, which did not evolve with humans, would approach people without fear. Introduced pigs, rats, and dogs brought to the island by European ships also killed dodo young and eggs.
Steller’s sea cow became extinct in 1768; it was related to the manatee and probably once lived along the northwest coast of North America. Steller’s sea cow was first discovered by Europeans in 1741 and was hunted for meat and oil. The last sea cow was killed in 1768. That amounts to 27 years between the sea cow’s first contact with Europeans and the extinction of the species.
In 1914, the last living passenger pigeon died in a zoo in Cincinnati, Ohio. This species had once darkened the skies of North America during its migrations, but it was hunted and suffered from habitat loss through the clearing of forests for farmland. In 1918, the last living Carolina parakeet died in captivity. This species was once common in the eastern United States, but it suffered from habitat loss. The species was also hunted because it ate orchard fruit when its native foods were destroyed to make way for farmland. The Japanese sea lion, which inhabited a broad area around Japan and the coast of Korea, became extinct in the 1950s due to fishermen. The Caribbean monk seal was distributed throughout the Caribbean Sea but was driven to extinction via hunting by 1952.
These are only a few of the recorded extinctions in the past 500 years. The International Union for Conservation of Nature (IUCN) keeps a list of extinct and endangered species called the Red List. The list is not complete, but it describes 380 extinct species of vertebrates after 1500 AD, 86 of which were driven extinct by overhunting or overfishing.
Estimates of Present-Time Extinction Rates
Estimates of extinction rates are hampered by the fact that most extinctions are probably happening without observation. The extinction of a bird or mammal is likely to be noticed by humans, especially if it has been hunted or used in some other way. But there are many organisms that are of less interest to humans (not necessarily of less value) and many that are undescribed.
The background extinction rate is estimated to be about one per million species per year (E/MSY). For example, assuming there are about ten million species in existence, the expectation is that ten species would become extinct each year (each year represents ten million species per year).
One contemporary extinction rate estimate uses the extinctions in the written record since the year 1500. For birds alone, this method yields an estimate of 26 E/MSY. However, this value may be underestimated for three reasons. First, many species would not have been described until much later in the time period, so their loss would have gone unnoticed. Second, the number of recently extinct species is increasing because extinct species now are being described from skeletal remains. And third, some species are probably already extinct even though conservationists are reluctant to name them as such. Taking these factors into account raises the estimated extinction rate closer to 100 E/MSY. The predicted rate by the end of the century is 1500 E/MSY.
A second approach to estimating present-time extinction rates is to correlate species loss with habitat loss by measuring forest-area loss and understanding species-area relationships. The species-area relationship is the rate at which new species are seen when the area surveyed is increased. Studies have shown that the number of species present increases as the size of the island increases. This phenomenon has also been shown to hold true in other habitats as well. Turning this relationship around, if the habitat area is reduced, the number of species living there will also decline. Estimates of extinction rates based on habitat loss and species-area relationships have suggested that with about 90 percent habitat loss an expected 50 percent of species would become extinct. Species-area estimates have led to species extinction rate calculations of about 1000 E/MSY and higher. In general, actual observations do not show this amount of loss and suggestions have been made that there is a delay in extinction. Recent work has also called into question the applicability of the species-area relationship when estimating the loss of species. This work argues that the species-area relationship leads to an overestimate of extinction rates. A better relationship to use may be the endemics-area relationship. Using this method would bring estimates down to around 500 E/MSY in the coming century. Note that this value is still 500 times the background rate.
Summary
Biodiversity exists at multiple levels of organization and is measured in different ways depending on the goals of those taking the measurements. These measurements include numbers of species, genetic diversity, chemical diversity, and ecosystem diversity. The number of described species is estimated to be 1.5 million with about 17,000 new species being described each year. Estimates for the total number of species on Earth vary but are on the order of 10 million. Biodiversity is negatively correlated with latitude for most taxa, meaning that biodiversity is higher in the tropics. The mechanism for this pattern is not known with certainty, but several plausible hypotheses have been advanced.
Five mass extinctions with losses of more than 50 percent of extant species are observable in the fossil record. Biodiversity recovery times after mass extinctions vary, but have been up to 30 million years. Recent extinctions are recorded in written history and are the basis for one method of estimating contemporary extinction rates. The other method uses measures of habitat loss and species-area relationships. Estimates of contemporary extinction rates vary, but some rates are as high as 500 times the background rate, as determined from the fossil record, and are predicted to rise. | textbooks/bio/Introductory_and_General_Biology/Principles_of_Biology/03%3A_Chapter_3/27%3A_Conservation_Biology_and_Biodiversity/27.01%3A_The_Biodiversity_Crisis.txt |
It may not be clear why biologists are concerned about biodiversity loss. When biodiversity loss is thought of as the extinction of the passenger pigeon, the dodo bird, and even the woolly mammoth, the loss may appear to be an emotional one. But is the loss practically important for the welfare of the human species? From the perspective of evolution and ecology, the loss of a particular individual species is unimportant (however, the loss of a keystone species can lead to ecological disaster). Extinction is a normal part of macroevolution. But the accelerated extinction rate means the loss of tens of thousands of species within our lifetimes, and it is likely to have dramatic effects on human welfare through the collapse of ecosystems and in added costs to maintain food production, clean air and water, and human health.
Agriculture began after early hunter-gatherer societies first settled in one place and heavily modified their immediate environment. This cultural transition has made it difficult for humans to recognize their dependence on undomesticated living things on the planet. Biologists recognize the human species is embedded in ecosystems and is dependent on them, just as every other species on the planet is dependent. Technology smoothes out the extremes of existence, but ultimately the human species cannot exist without its ecosystem.
Human Health
Contemporary societies that live close to the land often have a broad knowledge of the medicinal uses of plants growing in their area. Most plants produce secondary plant compounds, which are toxins used to protect the plant from insects and other animals that eat them, but some of which also work as medication. For centuries cultures around the globe have organized knowledge about the medical uses of plants into ceremonies and traditions. Humans are not the only species to use plants for medicinal reasons: the great apes, orangutans, chimpanzees, bonobos, and gorillas have all been observed self-medicating with plants.
Modern pharmaceutical science also recognizes the importance of these plant compounds. Examples of significant medicines derived from plant compounds include aspirin, codeine, digoxin, atropine, and vincristine (Figure \(1\)). Many medicines were once derived from plant extracts but are now synthesized. It is estimated that, at one time, 25 percent of modern drugs contained at least one plant extract. That number has probably decreased to about 10 percent as natural plant ingredients are replaced by synthetic versions. Antibiotics, which are responsible for extraordinary improvements in health and lifespans in developed countries, are compounds largely derived from fungi and bacteria.
In recent years, animal venoms and poisons have excited intense research for their medicinal potential. By 2007, the FDA had approved five drugs based on animal toxins to treat diseases such as hypertension, chronic pain, and diabetes. Another five drugs are undergoing clinical trials, and at least six drugs are being used in other countries. Other toxins under investigation come from mammals, snakes, lizards, various amphibians, fish, snails, octopuses, and scorpions.
Aside from representing billions of dollars in profits, these medicines improve people’s lives. Pharmaceutical companies are actively looking for new compounds synthesized by living organisms that can function as medicine. It is estimated that 1/3 of pharmaceutical research and development is spent on natural compounds and that about 35 percent of new drugs brought to market between 1981 and 2002 were from natural compounds. The opportunities for new medications will be reduced in direct proportion to the disappearance of species.
Agricultural Diversity
Since the beginning of human agriculture more than 10,000 years ago, human groups have been breeding and selecting crop varieties. This crop diversity matched the cultural diversity of highly subdivided populations of humans. For example, potatoes were domesticated beginning around 7,000 years ago in the central Andes of Peru and Bolivia. The potatoes grown in that region belong to seven species and the number of varieties likely is in the thousands. Each variety has been bred to thrive at particular elevations and soil and climate conditions. The diversity is driven by the diverse demands of the topography, the limited movement of people, and the demands created by crop rotation for different varieties that will do well in different fields.
Potatoes are only one example of human-generated diversity. Every plant, animal, and fungus that has been cultivated by humans has been bred from original wild ancestor species into diverse varieties arising from the demands for food value, adaptation to growing conditions, and resistance to pests. The potato demonstrates a well-known example of the risks of low crop diversity: the tragic Irish potato famine when the single variety grown in Ireland became susceptible to a potato blight, wiping out the crop. The loss of the crop led to famine, death, and mass emigration. Resistance to disease is a chief benefit to maintaining crop biodiversity, and lack of diversity in contemporary crop species carries similar risks. Seed companies, which are the source of most crop varieties in developed countries, must continually breed new varieties to keep up with evolving pest organisms. These same seed companies, however, have participated in the decline of the number of varieties available as they focus on selling fewer varieties in more areas of the world.
The ability to create new crop varieties relies on the diversity of varieties available and the accessibility of wild forms related to the crop plant. These wild forms are often the source of new gene variants that can be bred with existing varieties to create varieties with new attributes. Loss of wild species related to a crop will mean the loss of potential in crop improvement. Maintaining the genetic diversity of wild species related to domesticated species ensures our continued food supply.
Since the 1920s, government agriculture departments have maintained seed banks of crop varieties as a way to maintain crop diversity. This system has flaws because, over time, seed banks are lost through accidents, and there is no way to replace them. In 2008, the Svalbard Global Seed Vault (Figure \(2\)) began storing seeds from around the world as a backup system to the regional seed banks. If a regional seed bank stores varieties in Svalbard, losses can be replaced from Svalbard. The seed vault is located deep into the rock of an arctic island. Conditions within the vault are maintained at ideal temperature and humidity for seed survival, but the deep underground location of the vault in the arctic means that failure of the vault’s systems will not compromise the climatic conditions inside the vault.
Crop success is largely dependent on the quality of the soil. Although some agricultural soils are rendered sterile using controversial cultivation and chemical treatments, most contain a huge diversity of organisms that maintain nutrient cycles—breaking down organic matter into nutrient compounds that crops need for growth. These organisms also maintain soil texture that affects water and oxygen dynamics in the soil that are necessary for plant growth. If farmers had to maintain arable soil using alternate means, the cost of food would be much higher than it is now. These kinds of processes are called ecosystem services. They occur within ecosystems, such as soil ecosystems, as a result of the diverse metabolic activities of the organisms living there, but they provide benefits to human food production, drinking water availability, and breathable air.
Other key ecosystem services related to food production are plant pollination and crop pest control. Over 150 crops in the United States require pollination to produce food. One estimate of the benefit of honeybee pollinations within the United States is \$1.6 billion per year. Other pollinators contribute up to \$6.7 billion more.
Many honeybee populations are managed by apiarists who rent out their hives’ services to farmers. Honeybee populations in North America have been suffering large losses caused by a syndrome known as colony collapse disorder, whose cause is unclear. Other pollinators include a diverse array of other bee species and various insects and birds. Loss of these species would make growing crops requiring pollination impossible, increasing dependence on other crops.
Finally, humans compete for their food with crop pests, most of which are insects. Pesticides control these competitors; however, pesticides are costly and lose their effectiveness over time as pest populations adapt. They also lead to collateral damage by killing non-pest species and risking the health of consumers and agricultural workers. Ecologists believe that the bulk of the work in removing pests is actually done by predators and parasites of those pests, but the impact has not been well studied. A review found that in 74 percent of studies that looked for an effect of landscape complexity on natural enemies of pests, the greater the complexity, the greater the effect of pest-suppressing organisms. An experimental study found that introducing multiple enemies of pea aphids (an important alfalfa pest) increased the yield of alfalfa significantly. This study shows the importance of landscape diversity via the question of whether a diversity of pests is more effective at control than one single pest; the results showed this to be the case. Loss of diversity in pest enemies will inevitably make it more difficult and costly to grow food.
Wild Food Sources
In addition to growing crops and raising animals for food, humans obtain food resources from wild populations, primarily fish populations. For approximately 1 billion people, aquatic resources provide the main source of animal protein. But since 1990, global fish production has declined. Despite considerable effort, few fisheries on the planet are managed for sustainability.
Fishery extinctions rarely lead to the complete extinction of the harvested species, but rather to a radical restructuring of the marine ecosystem in which a dominant species is so over-harvested that it becomes a minor player, ecologically. In addition to humans losing the food source, these alterations affect many other species in ways that are difficult or impossible to predict. The collapse of fisheries has dramatic and long-lasting effects on local populations that work in the fishery. In addition, the loss of an inexpensive protein source to populations that cannot afford to replace it will increase the cost of living and limit societies in other ways. In general, the fish taken from fisheries have shifted to smaller species as larger species are fished to extinction. The ultimate outcome could clearly be the loss of aquatic systems as food sources.
Psychological and Moral Value
Finally, it has been argued that humans benefit psychologically from living in a biodiverse world. A chief proponent of this idea is entomologist E. O. Wilson. He argues that human evolutionary history has adapted us to live in a natural environment and that built environments generate stressors that affect human health and well-being. There is considerable research into the psychological regenerative benefits of natural landscapes that suggests the hypothesis may hold some truth. In addition, there is a moral argument that humans have a responsibility to inflict as little harm as possible on other species.
Summary
Humans use many compounds that were first discovered or derived from living organisms as medicines: secondary plant compounds, animal toxins, and antibiotics produced by bacteria and fungi. More medicines are expected to be discovered in nature. Loss of biodiversity will impact the number of pharmaceuticals available to humans.
Crop diversity is a requirement for food security, and it is being lost. The loss of wild relatives to crops also threatens breeders’ abilities to create new varieties. Ecosystems provide ecosystem services that support human agriculture: pollination, nutrient cycling, pest control, and soil development and maintenance. Loss of biodiversity threatens these ecosystem services and risks making food production more expensive or impossible. Wild food sources are mainly aquatic, but few are being managed for sustainability. Fisheries’ ability to provide protein to human populations is threatened when extinction occurs.
Biodiversity may provide important psychological benefits to humans. Additionally, there are moral arguments for the maintenance of biodiversity. | textbooks/bio/Introductory_and_General_Biology/Principles_of_Biology/03%3A_Chapter_3/27%3A_Conservation_Biology_and_Biodiversity/27.02%3A_The_Importance_of_Biodiversity_to_Human_Life.txt |
The core threat to biodiversity on the planet, and therefore a threat to human welfare, is the combination of human population growth and resource exploitation. The human population requires resources to survive and grow, and those resources are being removed unsustainably from the environment. The three greatest proximate threats to biodiversity are habitat loss, overharvesting, and the introduction of exotic species. The first two of these are a direct result of human population growth and resource use. The third results from increased mobility and trade. A fourth major cause of extinction, anthropogenic climate change, is predicted to become significant during this century. Global climate change is also a consequence of the human population’s need for energy and the use of fossil fuels to meet those needs (Figure \(1\)). Environmental issues, such as toxic pollution, have specific targeted effects on species, but they are not generally seen as threats at the magnitude of the others.
Habitat Loss
Habitat loss is a major threat to biodiversity. Remove the entire habitat within the range of a species and, unless they are one of the few species that do well in human-built environments, the species will become extinct. Human destruction of habitats accelerated in the latter half of the twentieth century. Consider the exceptional biodiversity of Sumatra: it is home to one species of orangutan, a species of critically endangered elephant, and the Sumatran tiger, but half of Sumatra’s forest is now gone. The neighboring island of Borneo, home to the other species of orangutan, has lost a similar area of forest. Forest loss continues even in protected areas of Borneo. The orangutan in Borneo is listed as endangered by the International Union for Conservation of Nature (IUCN), but it is simply the most visible of thousands of species that will not survive the disappearance of the forests of Borneo. The forests are removed for timber and to plant palm oil plantations (Figure \(2\)). Palm oil is used in many products including food products, cosmetics, and biodiesel in Europe. A five-year estimate of global forest cover loss for the years 2000–2005 was 3.1 percent. In the humid tropics where forest loss is primarily from timber extraction, 272,000 km2 was lost out of a global total of 11,564,000 km2 (or 2.4 percent). In the tropics, these losses certainly also represent the extinction of species because of high levels of endemism.
Preventing Habitat Destruction with Wise Wood Choices
Most consumers do not imagine that the home improvement products they buy might be contributing to habitat loss and species extinctions. Yet the market for illegally harvested timber is huge, and the wood products often find themselves in building supply stores in the United States. One estimate is that 10 percent of the imported timber stream in the United States, which is the world’s largest consumer of wood products, is potentially illegally logged. In 2006, this amounted to \$3.6 billion in wood products. Most of the illegal products are imported from countries that act as intermediaries and are not the originators of the wood.
How is it possible to determine if a wood product, such as flooring, was harvested sustainably or even legally? The Forest Stewardship Council (FSC) certifies sustainably harvested forest products, therefore, looking for their certification on flooring and other hardwood products is one way to ensure that the wood has not been taken illegally from a tropical forest. Certification applies to specific products, not to a producer; some producers’ products may not have certification while other products are certified. While there are other industry-backed certifications other than the FSC, these are unreliable due to lack of independence from the industry. Another approach is to buy domestic wood species. While it would be great if there was a list of legal versus illegal wood products, it is not that simple. Logging and forest management laws vary from country to country; what is illegal in one country may be legal in another. Where and how a product is harvested and whether the forest from which it comes is being maintained sustainably all factor into whether a wood product will be certified by the FSC. It is always a good idea to ask questions about where a wood product came from and how the supplier knows that it was harvested legally.
Habitat destruction can affect ecosystems other than forests. Rivers and streams are important ecosystems and are frequently modified through land development and from damming or water removal. Damming of rivers affects the water flow and access to all parts of a river. Differing flow regimes can reduce or eliminate populations that are adapted to these changes in flow patterns. For example, an estimated 91 percent of river lengths in the United States have been developed: they have modifications like dams, to create energy or store water; levees, to prevent flooding; or dredging or rerouting, to create land that is more suitable for human development. Many fish species in the United States, especially rare species or species with restricted distributions, have seen declines caused by river damming and habitat loss. Research has confirmed that species of amphibians that must carry out parts of their life cycles in both aquatic and terrestrial habitats have a greater chance of suffering population declines and extinction because of the increased likelihood that one of their habitats or access between them will be lost.
Overharvesting
Overharvesting is a serious threat to many species, but particularly to aquatic species. There are many examples of regulated commercial fisheries monitored by fisheries scientists that have nevertheless collapsed. The western Atlantic cod fishery is the most spectacular recent collapse. While it was a hugely productive fishery for 400 years, the introduction of modern factory trawlers in the 1980s and the pressure on the fishery led to it becoming unsustainable. The causes of fishery collapse are both economic and political in nature. Most fisheries are managed as a common (shared) resource even when the fishing territory lies within a country’s territorial waters. Common resources are subject to an economic pressure known as the tragedy of the commons in which essentially no fisher has a motivation to exercise restraint in harvesting a fishery when it is not owned by that fisher. The natural outcome of harvests of resources held in common is their overexploitation. While large fisheries are regulated to attempt to avoid this pressure, it still exists in the background. This overexploitation is exacerbated when access to the fishery is open and unregulated and when technology gives fishers the ability to overfish. In a few fisheries, the biological growth of the resource is less than the potential growth of the profits made from fishing if that time and money were invested elsewhere. In these cases—whales are an example—economic forces will always drive toward fishing the population to extinction.
For the most part, fishery extinction is not equivalent to biological extinction—the last fish of a species is rarely fished out of the ocean. At the same time, fishery extinction is still harmful to fish species and their ecosystems. There are some instances in which true extinction is a possibility. Whales have slow-growing populations and are at risk of complete extinction through hunting. There are some species of sharks with restricted distributions that are at risk of extinction. The groupers are another population of generally slow-growing fishes that, in the Caribbean, includes a number of species that are at risk of extinction from overfishing.
Coral reefs are extremely diverse marine ecosystems that face peril from several processes. Reefs are home to 1/3 of the world’s marine fish species—about 4,000 species—despite making up only 1 percent of marine habitat. Most home marine aquaria are stocked with wild-caught organisms, not cultured organisms. Although no species is known to have been driven extinct by the pet trade in marine species, there are studies showing that populations of some species have declined in response to harvesting, indicating that the harvest is not sustainable at those levels. There are concerns about the effect of the pet trade on some terrestrial species such as turtles, amphibians, birds, plants, and even the orangutan.
Bush meat is the generic term used for wild animals killed for food. Hunting is practiced throughout the world, but hunting practices, particularly in equatorial Africa and parts of Asia, are believed to threaten several species with extinction. Traditionally, bush meat in Africa was hunted to feed families directly; however, recent commercialization of the practice now has bush meat available in grocery stores, which has increased harvest rates to the level of unsustainability. Additionally, human population growth has increased the need for protein foods that are not being met from agriculture. Species threatened by the bush meat trade are mostly mammals including many primates living in the Congo basin.
Exotic Species
Exotic species are species that have been intentionally or unintentionally introduced by humans into an ecosystem in which they did not evolve. Such introductions likely occur frequently as natural phenomena. For example, Kudzu (Pueraria lobata), which is native to Japan, was introduced in the United States in 1876. It was later planted for soil conservation. Problematically, it grows too well in the southeastern United States—up to a foot a day. It is now a pest species and covers over 7 million acres in the southeastern United States. If an introduced species is able to survive in its new habitat, that introduction is now reflected in the observed range of the species. Human transportation of people and goods, including the intentional transport of organisms for trade, has dramatically increased the introduction of species into new ecosystems, sometimes at distances that are well beyond the capacity of the species to ever travel itself and outside the range of the species’ natural predators.
Most exotic species introductions probably fail because of the low number of individuals introduced or poor adaptation to the ecosystem they enter. Some species, however, possess preadaptations that can make them especially successful in a new ecosystem. These exotic species often undergo dramatic population increases in their new habitat and reset the ecological conditions in the new environment, threatening the species that exist there. For this reason, exotic species are also called invasive species. Exotic species can threaten other species through competition for resources, predation, or disease.
Lakes and islands are particularly vulnerable to extinction threats from introduced species. In Lake Victoria, the intentional introduction of the Nile perch was largely responsible for the extinction of about 200 species of cichlids. The accidental introduction of the brown tree snake via aircraft (Figure \(3\)) from the Solomon Islands to Guam in 1950 has led to the extinction of three species of birds and three to five species of reptiles endemic to the island. Several other species are still threatened. The brown tree snake is adept at exploiting human transportation as a means to migrate; one was even found on an aircraft arriving in Corpus Christi, Texas. Constant vigilance on the part of airport, military, and commercial aircraft personnel is required to prevent the snake from moving from Guam to other islands in the Pacific, especially Hawaii. Islands do not make up a large area of land on the globe, but they do contain a disproportionate number of endemic species because of their isolation from mainland ancestors.
It now appears that the global decline in amphibian species recognized in the 1990s is, in some part, caused by the fungus Batrachochytrium dendrobatidis, which causes the disease chytridiomycosis (Figure \(4\)). There is evidence that the fungus is native to Africa and may have been spread throughout the world by transport of a commonly used laboratory and pet species: the African clawed toad (Xenopus laevis). It may well be that biologists themselves are responsible for spreading this disease worldwide. The North American bullfrog, Rana catesbeiana, which has also been widely introduced as a food animal but which easily escapes captivity, survives most infections of Batrachochytrium dendrobatidis and can act as a reservoir for the disease.
Early evidence suggests that another fungal pathogen, Geomyces destructans, introduced from Europe is responsible for white-nose syndrome, which infects cave-hibernating bats in eastern North America and has spread from a point of origin in western New York State (Figure \(5\)). The disease has decimated bat populations and threatens the extinction of species already listed as endangered: the Indiana bat, Myotis sodalis, and potentially the Virginia big-eared bat, Corynorhinus townsendii virginianus. How the fungus was introduced is unclear, but one logical presumption would be that recreational cavers unintentionally brought the fungus on clothes or equipment from Europe.
Climate Change
Climate change, and specifically the anthropogenic (meaning, caused by humans) warming trend presently underway, is recognized as a major extinction threat, particularly when combined with other threats such as habitat loss. Scientists disagree about the likely magnitude of the effects, with extinction rate estimates ranging from 15 percent to 40 percent of species committed to extinction by 2050. Scientists do agree, however, that climate change will alter regional climates, including rainfall and snowfall patterns, making habitats less hospitable to the species living in them. The warming trend will shift colder climates toward the north and south poles, forcing species to move with their adapted climate norms while facing habitat gaps along the way. The shifting ranges will impose new competitive regimes on species as they find themselves in contact with other species not present in their historic range. One such unexpected species contact is between polar bears and grizzly bears (Figure \(6\)). Previously, these two species had separate ranges. Now, their ranges are overlapping and there are documented cases of these two species mating and producing viable offspring. Changing climates also throw off species’ delicate timing adaptations to seasonal food resources and breeding times. Many contemporary mismatches to shifts in resource availability and timing have already been documented.
Range shifts are already being observed: for example, some European bird species ranges have moved 91 km northward. The same study suggested that the optimal shift based on warming trends was double that distance, suggesting that the populations are not moving quickly enough. Range shifts have also been observed in plants, butterflies, other insects, freshwater fishes, reptiles, and mammals.
Climate gradients will also move up mountains, eventually crowding species higher in altitude and eliminating the habitat for those species adapted to the highest elevations. Some climates will completely disappear. The rate of warming appears to be accelerated in the arctic, which is recognized as a serious threat to polar bear populations that require sea ice to hunt seals during the winter months: seals are the only source of protein available to polar bears. A trend to decreasing sea ice coverage has occurred since observations began in the mid-twentieth century. The rate of decline observed in recent years is far greater than previously predicted by climate models.
Finally, global warming will raise ocean levels due to melt water from glaciers and the greater volume of warmer water. Shorelines will be inundated, reducing island size, which will have an effect on some species, and a number of islands will disappear entirely. Additionally, the gradual melting and subsequent refreezing of the poles, glaciers, and higher elevation mountains—a cycle that has provided freshwater to environments for centuries—will also be jeopardized. This could result in an overabundance of salt water and a shortage of fresh water.
Summary
The core threats to biodiversity are human population growth and unsustainable resource use. To date, the most significant causes of extinctions are habitat loss, introduction of exotic species, and overharvesting. Climate change is predicted to be a significant cause of extinctions in the coming century. Habitat loss occurs through deforestation, damming of rivers, and other activities. Overharvesting is a threat particularly to aquatic species, while the taking of bush meat in the humid tropics threatens many species in Asia, Africa, and the Americas. Exotic species have been the cause of a number of extinctions and are especially damaging to islands and lakes. Exotic species’ introductions are increasing because of the increased mobility of human populations and growing global trade and transportation. Climate change is forcing range changes that may lead to extinction. It is also affecting adaptations to the timing of resource availability that negatively affects species in seasonal environments. The impacts of climate change are greatest in the arctic. Global warming will also raise sea levels, eliminating some islands and reducing the area of all others. | textbooks/bio/Introductory_and_General_Biology/Principles_of_Biology/03%3A_Chapter_3/27%3A_Conservation_Biology_and_Biodiversity/27.03%3A_Threats_to_Biodiversity.txt |
Preserving biodiversity is an extraordinary challenge that must be met by greater understanding of biodiversity itself, changes in human behavior and beliefs, and various preservation strategies.
Measuring Biodiversity
The technology of molecular genetics and data processing and storage are maturing to the point where cataloguing the planet’s species in an accessible way is close to feasible. DNA barcoding is one molecular genetic method, which takes advantage of rapid evolution in a mitochondrial gene present in eukaryotes, excepting the plants, to identify species using the sequence of portions of the gene. Plants may be barcoded using a combination of chloroplast genes. Rapid mass sequencing machines make the molecular genetics portion of the work relatively inexpensive and quick. Computer resources store and make available the large volumes of data. Projects are currently underway to use DNA barcoding to catalog museum specimens, which have already been named and studied, as well as testing the method on less studied groups. As of mid 2012, close to 150,000 named species had been barcoded. Early studies suggest there are significant numbers of undescribed species that looked too much like sibling species to previously be recognized as different, which can now can be identified with DNA barcoding.
Numerous computer databases now provide information about named species and a framework for adding new species. However, as already noted, at the present rate of description of new species, it will take close to 500 years before the complete catalog of life is known. Many, perhaps most, species on the planet do not have that much time.
There is also the problem of understanding which species known to science are threatened and to what degree they are threatened. This task is carried out by the non-profit IUCN which, maintains the Red List—an online listing of endangered species categorized by taxonomy, type of threat, and other criteria (Figure \(1\)). The Red List is supported by scientific research. In 2011, the list contained 61,000 species, all with supporting documentation.
Changing Human Behavior
Legislation throughout the world has been enacted to protect species. The legislation includes international treaties as well as national and state laws. The Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) treaty came into force in 1975. The treaty, and the national legislation that supports it, provides a legal framework for preventing approximately 33,000 listed species from being transported across nations’ borders, thus protecting them from being caught or killed when international trade is involved. The treaty is limited in its reach because it only deals with international movement of organisms or their parts. It is also limited by various countries’ ability or willingness to enforce the treaty and supporting legislation. The illegal trade in organisms and their parts is probably a market in the hundreds of millions of dollars. Illegal wildlife trade is monitored by another non-profit: Trade Records Analysis of Flora and Fauna in Commerce (TRAFFIC).
Within many countries, there are laws that protect endangered species and regulate hunting and fishing. In the United States, the Endangered Species Act (ESA) was enacted in 1973. Species at risk are listed by the Endangered Species Act; the U.S. Fish & Wildlife Service is required by law to develop management plans that protect the listed species and bring them back to sustainable numbers. The Endangered Species Act, and others like it in other countries, is a useful tool, but it suffers because it is often difficult to get a species listed, or to get an effective management plan in place once it is listed. Additionally, species may be controversially taken off the list without necessarily having had a change in their situation. More fundamentally, the approach to protecting individual species rather than entire ecosystems is both inefficient and focuses efforts on a few highly visible and often charismatic species, perhaps at the expense of other species that go unprotected. At the same time, the Endangered Species Act has a critical habitat provision outlined in the recovery mechanism that may benefit species other than the one targeted for management.
The Migratory Bird Treaty Act (MBTA) is an agreement between the United States and Canada that was signed into law in 1918 in response to declines in North American bird species caused by hunting. The Migratory Bird Treaty Act now lists over 800 protected species. It makes it illegal to disturb or kill the protected species or distribute their parts (much of the hunting of birds in the past was for their feathers).
The international response to global warming has been mixed. The Kyoto Protocol, an international agreement that came out of the United Nations Framework Convention on Climate Change that committed countries to reducing greenhouse gas emissions by 2012, was ratified by some countries, but spurned by others. Two important countries in terms of their potential impact that did not ratify the Kyoto Protocol were the United States and China. The United States rejected it as a result of a powerful fossil fuel industry and China because of a concern it would stifle the nation’s growth. Some goals for reduction in greenhouse gasses were met and exceeded by individual countries, but worldwide, the effort to limit greenhouse gas production is not succeeding. The intended replacement for the Kyoto Protocol has not materialized because governments cannot agree on timelines and benchmarks. Meanwhile, climate scientists predict the resulting costs to human societies and biodiversity will be high.
The private non-profit sector plays a large role in the conservation effort both in North America and around the world. The approaches range from species-specific organizations to the broadly focused IUCN and TRAFFIC. The Nature Conservancy takes a novel approach. It purchases land and protects it in an attempt to set up preserves for ecosystems. Ultimately, human behavior will change when human values change. At present, the growing urbanization of the human population is a force that poses challenges to the valuing of biodiversity.
Conservation in Preserves
The establishment of wildlife and ecosystem preserves is one of the key tools in conservation efforts. A preserve is an area of land set aside with varying degrees of protection for the organisms that exist within the boundaries of the preserve. Preserves can be effective in the short term for protecting both species and ecosystems, but they face challenges that scientists are still exploring to strengthen their viability as long-term solutions.
How Much Area to Preserve?
Due to the way protected lands are allocated (they tend to contain less economically valuable resources rather than being set aside specifically for the species or ecosystems at risk) and the way biodiversity is distributed, determining a target percentage of land or marine habitat that should be protected to maintain biodiversity levels is challenging. The IUCN World Parks Congress estimated that 11.5 percent of Earth’s land surface was covered by preserves of various kinds in 2003. This area is greater than previous goals; however, it only represents 9 out of 14 recognized major biomes. Research has shown that 12 percent of all species live only outside preserves; these percentages are much higher when only threatened species and high quality preserves are considered. For example, high quality preserves include only about 50 percent of threatened amphibian species. The conclusion must be that either the percentage of area protected must increase, or the percentage of high quality preserves must increase, or preserves must be targeted with greater attention to biodiversity protection. Researchers argue that more attention to the latter solution is required.
Preserve Design
There has been extensive research into optimal preserve designs for maintaining biodiversity. The fundamental principle behind much of the research has been the seminal theoretical work of Robert H. MacArthur and Edward O. Wilson published in 1967 on island biogeography (MacArthur & Wilson, 1967). This work sought to understand the factors affecting biodiversity on islands. The fundamental conclusion was that biodiversity on an island was a function of the origin of species through migration, speciation, and extinction on that island. Islands farther from a mainland are harder to get to, so migration is lower and the equilibrium number of species is lower. Within island populations, evidence suggests that the number of species gradually increases to a level similar to the numbers on the mainland from which the species is suspected to have migrated. In addition, smaller islands are harder to find, so their immigration rates for new species are lower. Smaller islands are also less geographically diverse so there are fewer niches to promote speciation. And finally, smaller islands support smaller populations, so the probability of extinction is higher.
As islands get larger, the number of species accelerates, although the effect of island area on species numbers is not a direct correlation. Conservation preserves can be seen as “islands” of habitat within “an ocean” of non-habitat. For a species to persist in a preserve, the preserve must be large enough. The critical size depends, in part, on the home range that is characteristic of the species. A preserve for wolves, which range hundreds of kilometers, must be much larger than a preserve for butterflies, which might range within ten kilometers during its lifetime. But larger preserves have more core area of optimal habitat for individual species, they have more niches to support more species, and they attract more species because they can be found and reached more easily.
Preserves perform better when there are buffer zones around them of suboptimal habitat. The buffer allows organisms to exit the boundaries of the preserve without immediate negative consequences from predation or lack of resources. One large preserve is better than the same area of several smaller preserves because there is more core habitat unaffected by edges. For this same reason, preserves in the shape of a square or circle will be better than a preserve with many thin “arms.” If preserves must be smaller, then providing wildlife corridors between them so that individuals and their genes can move between the preserves, for example along rivers and streams, will make the smaller preserves behave more like a large one. All of these factors are taken into consideration when planning the nature of a preserve before the land is set aside.
In addition to the physical, biological, and ecological specifications of a preserve, there are a variety of policy, legislative, and enforcement specifications related to uses of the preserve for functions other than the protection of species. These can include anything from timber extraction, mineral extraction, regulated hunting, human habitation, and nondestructive human recreation. Many of these policy decisions are made based on political pressures rather than conservation considerations. In some cases, wildlife protection policies have been so strict that subsistence-living indigenous populations have been forced from ancestral lands that fell within a preserve. In other cases, even if a preserve is designed to protect wildlife, if the protections are not or cannot be enforced, the preserve status will have little meaning in the face of illegal poaching and timber extraction. This is a widespread problem with preserves in areas of the tropics.
Limitations on Preserves
Some of the limitations on preserves as conservation tools are evident from the discussion of preserve design. Political and economic pressures typically make preserves smaller, never larger, so setting aside areas that are large enough is difficult. If the area set aside is sufficiently large, there may not be sufficient area to create a buffer around the preserve. In this case, an area on the outer edges of the preserve inevitably becomes a riskier suboptimal habitat for the species in the preserve. Enforcement of protections is also a significant issue in countries without the resources or political will to prevent poaching and illegal resource extraction.
Climate change will create inevitable problems with the location of preserves. The species within them will migrate to higher latitudes as the habitat of the preserve becomes less favorable. Scientists are planning for the effects of global warming on future preserves and striving to predict the need for new preserves to accommodate anticipated changes to habitats; however, the end effectiveness is tenuous since these efforts are prediction based.
Finally, an argument can be made that conservation preserves reinforce the cultural perception that humans are separate from nature, that humans can exist outside of nature, and that humans can only operate in ways that damage biodiversity. There is concern that creating wildlife preserves reduces the pressure on human activities outside the preserves to be sustainable and non-damaging to biodiversity. Ultimately, the political, economic, and human demographic pressures will degrade and reduce the size of conservation preserves if the activities outside them are not altered to be less damaging to biodiversity.
Habitat Restoration
Habitat restoration holds considerable promise as a mechanism for restoring and maintaining biodiversity. Of course, once a species has become extinct, its restoration is impossible. However, restoration can improve the biodiversity of degraded ecosystems. Reintroducing wolves, a top predator, to Yellowstone National Park in 1995 led to dramatic changes in the ecosystem that increased biodiversity. The wolves (Figure \(2\)) function to suppress elk and coyote populations and provide more abundant resources to the guild of carrion eaters. Reducing elk populations has allowed revegetation of riparian areas, which has increased the diversity of species in that habitat. Decreasing the coyote population has increased the populations of species that were previously suppressed by this predator. The number of species of carrion eaters has increased because of the predatory activities of the wolves. In this habitat, the wolf is a keystone species, meaning a species that is instrumental in maintaining diversity in an ecosystem. Removing a keystone species from an ecological community may cause a collapse in diversity. The results from the Yellowstone experiment suggest that restoring a keystone species can have the effect of restoring biodiversity in the community. Ecologists have argued for the identification of keystone species where possible and for focusing protection efforts on those species; likewise, it also makes sense to attempt to return them to their ecosystem if they have been removed.
Other large-scale restoration experiments underway involve dam removal. In the United States, since the mid-1980s, many aging dams are being considered for removal rather than replacement because of shifting beliefs about the ecological value of free-flowing rivers and because many dams no longer provide the benefit and functions that they did when they were first built. The measured benefits of dam removal include restoration of naturally fluctuating water levels (the purpose of dams is frequently to reduce variation in river flows), which leads to increased fish diversity and improved water quality. In the Pacific Northwest, dam removal projects are expected to increase populations of salmon, which is considered a keystone species because it transports key nutrients to inland ecosystems during its annual spawning migrations. In other regions such as the Atlantic coast, dam removal has allowed the return of spawning anadromous fish species (species that are born in fresh water, live most of their lives in salt water, and return to fresh water to spawn). Some of the largest dam removal projects have yet to occur or have happened too recently for the consequences to be measured. The large-scale ecological experiments that these removal projects constitute will provide valuable data for other dam projects slated either for removal or construction.
The Role of Captive Breeding
Zoos have sought to play a role in conservation efforts both through captive breeding programs and education. The transformation of the missions of zoos from collection and exhibition facilities to organizations that are dedicated to conservation is ongoing. In general, it has been recognized that, except in some specific targeted cases, captive breeding programs for endangered species are inefficient and often prone to failure when the species are reintroduced to the wild. Zoo facilities are far too limited to contemplate captive breeding programs for the numbers of species that are now at risk. Education is another potential positive impact of zoos on conservation efforts, particularly given the global trend to urbanization and the consequent reduction in contacts between people and wildlife. A number of studies have been performed to look at the effectiveness of zoos on people’s attitudes and actions regarding conservation; at present, the results tend to be mixed.
Summary
New technological methods such as DNA barcoding and information processing and accessibility are facilitating the cataloging of the planet’s biodiversity. There is also a legislative framework for biodiversity protection. International treaties such as CITES regulate the transportation of endangered species across international borders. Legislation within individual countries protecting species and agreements on global warming have had limited success; there is at present no international agreement on targets for greenhouse gas emissions. In the United States, the Endangered Species Act protects listed species but is hampered by procedural difficulties and a focus on individual species. The Migratory Bird Act is an agreement between Canada and the United States to protect migratory birds. The non-profit sector is also very active in conservation efforts in a variety of ways.
Conservation preserves are a major tool in biodiversity protection. Presently, 11 percent of Earth’s land surface is protected in some way. The science of island biogeography has informed the optimal design of preserves; however, preserves have limitations imposed by political and economic forces. In addition, climate change will limit the effectiveness of preserves in the future. A downside of preserves is that they may lessen the pressure on human societies to function more sustainably outside the preserves.
Habitat restoration has the potential to restore ecosystems to previous biodiversity levels before species become extinct. Examples of restoration include reintroduction of keystone species and removal of dams on rivers. Zoos have attempted to take a more active role in conservation and can have a limited role in captive breeding programs. Zoos also may have a useful role in education. | textbooks/bio/Introductory_and_General_Biology/Principles_of_Biology/03%3A_Chapter_3/27%3A_Conservation_Biology_and_Biodiversity/27.04%3A_Preserving_Biodiversity.txt |
• Agricultural Biotechnology and Gene Therapy
We will discuss some general background, on mutations and recombination. This will lead to work on genetically modified plants and animals -- and gene therapy for humans. We began to talk about gene modification. We started with the natural processes of mutation and recombinat
• Bird Flu
The current news on bird flu is important because it is possible for very serious human flu viruses to develop from bird flu viruses. At this point, it appears that some people have been infected with the bird flu, and some have died from it. So far, the evidence is that transmission of the bird flu from human to human is very limited. This is only slightly reassuring; the real concern is that the virus will change (e.g., mutate) to allow efficient transmission between humans.
• Case Studies: Diseases
• Cloning and stem cells
Cloning (in this context) involves growing a new organism from a single cell of an old organism. In part, this requires that the cell used for cloning be able to revert to the "primitive" state typical of an egg cell -- able to replicate and differentiate. This is particularly a challenge if the cell used for cloning is already differentiated.
• DNA and the genome
A major news story over recent years has been the announcement of the genome sequence for humans. In fact, this project reached a symbolic completion point in April 2003. But this human genome work is just part of a much bigger story -- which includes a list of many completed genomes, for microbes, plants and animals. All this genome work is just the beginning; genome information alone does not solve anything in particular; it is a big resource that will make further biological work easier.
• Prions
Prion diseases have long fascinated biologists, because of the unusual nature of the infectious agent. Recently, prion diseases have become a major news story because of the emergence of the bovine (cow) prion disease BSE, which can be transmitted to humans as the disease vCJD.
Supplemental Modules (Molecular Biology)
Why are GM foods and gene therapy shown as one topic? Because they are fundamentally the same. Both involve the intentional and directed modification of an organism's genome. In general, one might carry out such a modification either by changing a gene within the organism, or by delivering a new gene to the organism. In the latter case, the new gene may either replace an original version of the gene that was within the organism, or may add into the genome.
Introduction
You might suggest that delivering a new gene, which then replaces the original, would be considered changing the original gene. Fair enough. But there also are procedures being considered that result in changing a gene without delivery/replacement in the usual sense, so there is still some distinction worth keeping.
Most work on genetic modification of higher organisms is currently done by adding a gene, rather than changing or replacing. Why do these genetic modifications? One major use is in research. Such genetic modifications have long been used to help us understand gene function in microbes. The techniques were then extended to study gene function in some higher organisms. Now we are in the era of practical genetic modifications -- where the intent is to create a modified organism. One class of such modifications is to make crop plants with "improved" properties (such as resistance to a pest). Another class is to repair a defect in an organism -- to treat a disease. The use of gene therapy to treat a disease in humans, such as SCID (severe combined immune deficiency), is an example.
An aside... A "knockout mouse". In all seriousness, knockout mice are important research tools. Techniques have been developed that allow one to change a particular gene in the mouse genome. One type of change that is often made is simply to inactivate (knock out) the gene. Mice are then grown without this gene product. This is one useful tool for figuring out what the function of a gene is. Unfortunately, the techniques for doing this have not been widely adapted for other organisms.(Figure source lost. Anyone have any information?)
For a general description of how to make knockout mice, see http://www.bio.davidson.edu/courses/genomics/method/homolrecomb.html. Caution... it is rather complex! (This is from Malcolm Campbell's site, which is listed as a general BITN resource for molecular biology methods, under Web sites.)
The 2007 Nobel prize in Medicine or Physiology was awarded to Mario R Capecchi, Martin J Evans and Oliver Smithies "for their discoveries of principles for introducing specific gene modifications in mice by the use of embryonic stem cells" -- that is, for their pioneering work in developing the knockout mouse and related procedures. Nobel site: http://www.nobelprize.org/nobel_prizes/medicine/laureates/2007/index.html.
One other distinction among types of genetic modification is important. Some modifications are hereditary, and will be passed on to the offspring of the individual that was treated. Some are not hereditary, and will affect only the treated individual. The former is called "germ line" treatment, and the latter "somatic" (body) treatment. All work with human gene therapy is somatic at this time. (The use of knockout mice, above, leads to germ line treatment.)
What is controversial? The heart of the controversy is evaluation of what the benefits and risks are of making such modifications. For example, I suggested above that a pest-resistant plant would be an "improvement". That statement is subject to debate about how much or how useful an improvement it is, and we need to consider what the risks are. In the field of human gene therapy, a current clinical trial involving treating SCID seemed to be showing benefit to the patients. Then it was found that two of the patients have developed leukemia, quite possibly a side effect of the gene therapy.
Overview
This topic was discussed in the BITN class, Fall 2003. This overview section summarizes the class presentation. The original web materials were designed as a supplement to that class presentation.
Genetic modification. We will discuss some general background, on mutations and recombination. This will lead to work on genetically modified plants and animals -- and gene therapy for humans.
We began to talk about gene modification. We started with the natural processes of mutation and recombination. The former creates new genetic information and the latter rearranges existing information. A generic procedure for gene modification involves getting (finding or making) a new gene, getting it into the desired cell, and getting it to function. All of these steps have many variations, depending both on the specific goal and the organism being modified. I showed examples involving bacteria, tobacco and mice. I showed slides which are equivalent to Figures 7-4, 8-36, and 8-38 from Lodish et al, Molecular Cell Biology (4th edition, 2000). A link to a very nice animation of part of the recombination process is below under New Links.
We discussed the gene therapy trial for X-SCID in some detail. We briefly discussed the nature of the disease, and then the general approach of the gene therapy treatment. The basic result is a very high level of treatment success: most of the treated patients have developed immune systems that seem good, and are now living substantially normally. However, two of the patients developed leukemia. The leukemia itself was treatable, so the benefit seems to outweigh the side effect in this case. The leukemia is now understood to be due to how the gene therapy vector integrated. How to avoid this side effect is a subject of active work. An important question, which can be answered only over time, is whether more patients will develop the leukemia side effect. Despite the side effect, this is the best success for gene therapy so far, after two decades or so of work. Two articles in The Scientist on this gene therapy trial are listed for the topic.
We then discussed some issues of GMO crops. I emphasize that formulating questions is the critical step here; good questions can -- ultimately -- be answered. The big problem is with "uneasy feelings" that are not formulated as answerable questions. I also emphasize that you do not need to accept my "biases" (predicted likely answers) for things that have not yet been tested.
Article mentioned in class, about trying to predict which crop modifications are more or less likely to be environmental problems: J F Hancock, A framework for assessing the risk of transgenic crops. BioScience 53:512; 5/03. In reading this, I think it is more important at this point to follow his general plan, rather than to agree with him on specifics.
Agricultural biotechnology (GM food)
Transgenic crops: An Introduction and resource guide. A wide range of basic information, including many individual projects. For example, there is a section on "golden rice" -- rice with a high content of vitamin A. http://cls.casa.colostate.edu/TransgenicCrops/index.html. Also in Spanish. (This site is not being updated, since December 2004. Nevertheless, it is a fine archive of useful material.)
Biotech Primer, from a leading company in the field. www.monsanto.co.uk/primer/primer.html. Also see the section Knowledge Center (from top menu). Caution... Remember, this is not a site for unbiased information about the pro and con issues in the field. Then again, few sites are unbiased. It is best to read a variety of sources, being aware of their biases.
Maize & Biodiversity - The effects of transgenic maize in Mexico. www.cec.org/maize/index.cfm. From the Commission for Environmental Cooperation (CEC) for North America. Also in French & Spanish, reflecting the tri-national nature of the Commission. The CEC site (see "Home page" link at top or bottom) includes many issues.
European views. There is major resistance to GM foods in Europe, and especially in Britain. It is interesting to watch their attempts to rationally analyze the issue, and to see what impact their work has both on the general public, and ultimately on the regulatory systems.
GM Science Review. An extensive review of GM foods by an independent panel appointed by the British government. http://www.gmsciencedebate.org.uk. This link leads to two reports (July 2003 and January 2004), plus a news release for each, giving the highlights.
Farm scale evaluations. Several reports of experimental work on ecological impacts of GM crops, including gene flow, are available from the UK Department for Environment, Food and Rural Affairs (DEFRA). archive.defra.gov.uk/environm.../crops/fse.htm. The reports are mainly from 2002-2005, plus some background materials.
Public Perceptions of Agricultural Biotechnologies in Europe. European Commission, May 2002. http://csec.lancs.ac.uk/archive/pabe/index.htm. Some documents here are also available in French, Italian.
Africa. R J Blaustein, The green revolution arrives in Africa. BioScience 58:8, 1/08. Article is free online: www.bioone.org/doi/abs/10.1641/B580103.
Nature has a web focus site on GM crops. http://www.nature.com/nature/focus/gm/index.html. (October 2003)
The Pew Initiative on Food and Biotechnology, http://www.pewtrusts.org/our_work_detail.aspx?id=442.Topics include:
* "Issues in Science and Regulation of Transgenic Fish" (January 2003). Transgenic salmon (salmon with modified growth hormone, intended for faster farming production).
* "A Snapshot of Federal Research on Food Allergy: Implications for Genetically Modified Food" (June 2002). Allergens in plants; note that this issue is not restricted to GMOs, but is a general concern.
* "Harvest on the Horizon: Future Uses of Agricultural Biotechnology" (September 2001).
* Monarch butterflies.
* Labeling of GM foods.
The Safety of Genetically Modified Foods Produced Through Biotechnology. A "Position Paper" from the (US) Society of Toxicology (Sept 2002). 209.183.221.234/AI/GM/GM_Food.asp. The tone of the report is generally favorable, but of course there is much meat in it, on issues such as methodology and philosophy of how novel products should be evaluated.
Approved GM plants:
* A database of GM plants approved in the US. Includes extensive information about the approval. From various US government agencies. usbiotechreg.nbii.gov
* GM Crop Database, including information on their regulatory status in two dozen countries. Includes a bibliographic database. http://www.cera-gmc.org/?action=gm_crop_database, From the Center for Environmental Risk Assessment (CERA).
Plantstress. A web site on stresses that affect plants, including the use of genetic modification to produce stress-resistant crops: http://www.plantstress.com
Biological Confinement of Genetically Engineered Organisms, a report from the National Academy of Science, 2004. http://www.nap.edu/catalog.php?record_id=10880. One concern with GMO is the spread of engineered genes to the non-engineered relatives in the field. Thus considerable effort is being expended to explore methods to prevent such gene transfer. A simple example is to make the GMO plant sterile, so that it can not cross with its relatives.
The books listed below are also listed on my page Books: Suggestions for general reading.
Book: Pamela G Ronald & Raoul W Adamchak, Tomorrow's Table - Organic farming, genetics, and the future of food. Oxford, 2008. ISBN 978-0-19-530175-5. A little book on the role of genetic engineering -- "GM" (genetic modification) as it is often called -- in organic farming. It is written by a plant geneticist who does GM and an organic farmer -- who are wife/husband. The organic farming movement has typically objected to GM, but the authors here suggest they should be more open to considering it. They suggest that GM is a good tool to achieve the underlying objectives of organic farming. This is a short and sometimes rambling book. It does not really answer questions, but its purpose is more to raise questions, to get people to look anew at the issues of what GM is and what its role might be. Importantly, it emphasizes that each individual use of GM should be considered on its own merit. I certainly encourage those who might be skeptical of GM to try this book -- not to change your mind, but simply as an opener to further discussion.
Book: Nina V Fedoroff & Nancy Marie Brown, Mendel in the Kitchen - A scientist's view of genetically modified foods. Joseph Henry (National Academies Press), 2004. The book can be purchased online, pdf file or print: http://www.nap.edu/catalog.php?record_id=11000; the page also has more information about the book. Fedoroff is a scientist who has worked on GM (biotechnology) foods, so brings some authority and knowledge -- and of course bias -- to the table. One strength of the book is the extensive discussion of conventional plant breeding, including its risks. This is interesting history, and also serves to put modern GM technologies in proper historical perspective. Another strength is that Fedoroff takes the time to analyze several particular cases in some detail, including good analyses of arguments made against specific developments. (Occasionally, I think she spends too much time on some topics -- a minor problem.) A must read if you want to understand the development of GM plants. In controversial areas, no one book can be trusted to provide a complete view, but this one should be one important part of understanding the GM story.
Book: D. Charles, Lords of the harvest - Biotech, big money, and the future of food. Perseus, 2001. ISBN 0-7382-0291-6. (Paperback: ISBN 0-7382-0773-X.) A journalist tells the story of "GMOs" -- the application of biotechnology to agriculture. The book is intended for the general audience, and avoids scientific detail while presenting all the basic logic. The book is widely regarded as being a fair presentation of a range of views on the subject. I enjoyed reading it.
Gene therapy
Gene therapy tutorial. The Molecular Medicine in Action series (listed as a general resource for BITN, under web sites) includes a tutorial on gene therapy. www.iupui.edu/~wellsctr/MMIA/htm/animations.htm. Click on "other" to get to the Gene Therapy item. Some parts of this are not entirely clear, but overall, it is a useful introduction to both techniques and issues.
NIH Genetic Modification Clinical Research Information System (GeMCRIS). This site, from the US National Institutes of Health and cooperating agencies, is a gene therapy database. It gives information on US gene therapy trials. It includes reports of adverse events. www.gemcris.od.nih.gov.
Gene therapy for SCID and other immune disorders. One major story of recent years was the development of a gene therapy treatment that cured (?) several young boys of X-SCID (severe combined immunodeficiency, due to a mutation on the X-chromosome). Some of the boys also developed leukemia (and one died); scientists have come to understand that this was due to certain specifics of the treatment. Good review of this and other developments during the first decade of the century: A Aiuti & M G Roncarolo, Ten years of gene therapy for primary immune deficiencies. Hematology 2009:682, 2009. http://asheducationbook.hematologylibrary.org/cgi/content/abstract/2009/1/682.
Gene therapy and stem cells: How are they related?
The short answer is that they are distinct techniques, but they can be combined. Gene therapy involves changing the genetic information in a cell. Stem cells are cells that can divide and differentiate into the desired cell type. It is possible to do gene therapy on stem cells. One approach used in the work on treating muscular dystrophy in dogs was of this type. That work is described on my stem cell page: Muscular dystrophy in dogs. This section is included on both my pages for stem cells and for gene therapy (this page).
Gene therapy in China
China has launched gene therapy products aimed at cancer treatment. Cultural and language barriers mean that we know relatively little of the details. Science ran a "news focus" on gene therapy in China -- an interesting article. J Guo & H Xin, Chinese gene therapy: Splicing out the west? Science 314:1232, 11/24/06. Online at http://www.sciencemag.org/content/31...3/1232.summary.
The article referred to (in the above Science article) as an English-language summary of the Chinese work is: Z Peng, Current status of gendicine in China: Recombinant human Ad-p53 agent for treatment of cancers. Human Gene Therapy 16:1016-1027, 9/05. Online at http://www.liebertonline.com/doi/abs...m.2005.16.1016. It is accompanied by an editorial: J M Wilson, Gendicine: The first commercial gene therapy product. Human Gene Therapy 16:1014, 9/05. Online at http://www.liebertonline.com/doi/abs...m.2005.16.1014. The editorial is also available there in Chinese.
There is more in the October 2006 issue of Human Gene Therapy, focusing on regulation and approval. Article: H Yin, Regulations and procedures for new drug evaluation and approval in China. Human Gene Therapy 17:970-974, 10/06. Online at http://www.liebertonline.com/doi/abs...um.2006.17.970. Accompanying editorial: J M Wilson, Regulation of gene therapy in China. Human Gene Therapy 17:969, 10/06. Online at http://www.liebertonline.com/doi/abs...um.2006.17.969.
Miscellaneous (other books, web sites, comments)
The Electronic Journal of Biotechnology (EJB). See more detailed information on the EJB.
Recombination. Animated gif. Recombination is one of the underlying processes in genetics -- both natural and lab work. The page listed here shows what we think is happening with one of the best understood recombination processes, in the bacterium Escherichia coli. Nice picture! And it illustrates the idea of molecular motors. The protein is moving along the DNA, fueled by ATP. For details and link, see my page of Molecular Biology - Internet Resources, for the Recombination chapter.
Recent items, briefly noted
CAUTION. A single report does not a truth make. People are trying various things. I will note here some interesting reports. But these are not final answers. Sometimes such reports turn out to not be reproducible, or not due to what the original authors thought. Or even if true, they may not work in humans. Etc etc. This is all part of the normal process of developing new things. Each breakthrough begins with a simple preliminary step. Some of these hold up, some do not. So, here are some news stories -- of various steps along the way.
Added August 9, 2011. My Musings newsletter contains posts on gene therapy. For example... Gene therapy: Curing an animal using a ZFN (August 9, 2011).
High-calcium carrots. A Texas group has genetically modified carrots to take up calcium better. In the new work, reported here, they show that the higher calcium content of the carrots is indeed bioavailable, for both mice and humans. This is an example of modifying a food crop for an improvement in a nutritional characteristic. In this case, if further work shows this works well, consumption of high-calcium carrots could allow reduced consumption of dairy products. News story: Scientists unveil 'supercarrot'. January 2008. http://news.bbc.co.uk/2/hi/health/7188969.stm. The paper is: J Morris et al, Nutritional impact of elevated calcium transport activity in carrots. PNAS 105(5):1431-5, 2/15/08. Online at: http://www.pnas.org/content/105/5/1431.abstract.
Parkinson's disease. A gene therapy trial for Parkinson's disease was just reported. It was a small Phase I trial; the main purpose of this stage is to look for general safety, and the trial is not blinded. The main conclusion, then, is that the treatment seemed quite safe; some patients have been followed for over three years so far. Intriguingly, there were signs of efficacy, with most patients showing some improvement. Clearly, this work deserves follow-up. News story from Cornell: First gene therapy clinical trial for Parkinson's disease improves patients' motor skills with no major side effects, 8/8/07. http://www.news.cornell.edu/stories/...arkinsons.html. The paper is M G Kaplitt et al, Safety and tolerability of gene therapy with an adeno-associated virus (AAV) borne GAD gene for Parkinson's disease: an open label, phase I trial. Lancet 369:2097, 6/23/07. There is an accompanying commentary, on p 2056; this is probably a good place to start.
Making cottonseed non-toxic. Gossypol is a toxic polyphenol terpenoid found in cotton plants. The high levels of this toxic compound in the seed limit the use of this abundant resource for human food. Previously, scientists were able to develop mutant cotton plants that lack gossypol; the problem was that they were highly susceptible to insects, thus showing the natural protective role of this chemical. Now, K S Rathore and colleagues at Texas A&M have developed a cotton that lacks gossypol only in the seeds, but has normal levels elsewhere. The basic strategy for doing this makes use of two kinds of knowledge. First, they develop a RNAi (interfering RNA) that is specific for a key gene needed for making gossypol. Second, they target this RNAi to the seed, by using a seed-specific promoter. The results are encouraging, suggesting that the plant makes enough gossypol to protect itself, yet produces seeds that contain minimal levels of the toxic compound. A news story: "Toxic seed becomes hope for the hungry. Scientists reengineer cottonseed. Now, they aim to turn more poisonous plants into human food." November 27, 2006. http://www.csmonitor.com/2006/1127/p03s02-usgn.html. The paper is G Sunilkumar et al, Engineering cottonseed for use in human nutrition by tissue-specific reduction of toxic gossypol. PNAS 103:18054-9, 11/29/06. Online at: http://www.pnas.org/content/103/48/18054.abstract. For some background on RNAi, see my section RNAi (RNA interference or silencing).
Selenium decontamination. UC Berkeley scientists, headed by Dr Norman Terry, have been studying decontamination of soils that contain high levels of selenium. They have developed GM plants with enhanced ability to decontaminate such soils. A news story about a field trial of these plants was in the Feb 3, 2005, issue of the Berkeleyan. "New GMO technique really cuts the mustard. Engineered to absorb high levels of selenium, and tested with great caution, these plants may aid in toxic cleanup." Online at: http://www.berkeley.edu/news/berkeleyan/2005/02/02_GMO.shtml.
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The current news on bird flu is important because it is possible for very serious human flu viruses to develop from bird flu viruses. At this point, it appears that some people have been infected with the bird flu, and some have died from it. So far, the evidence is that transmission of the bird flu from human to human is very limited. This is only slightly reassuring; the real concern is that the virus will change (e.g., mutate) to allow efficient transmission between humans.
General points to consider in thinking about "bird flu"
In an effort to help the reader sort through the confusing news on this topic, here are some general points to consider. Most of the points here are probably fairly well accepted, though not necessarily completely firm. I hope that this dialog will give you a framework for exploring this topic further, and for following the news.
Current status in birds
There is a type of bird flu that is spreading around the world rapidly. This "bird flu" is of the H5N1 type. Note that H5N1 is a type of virus, not a specific virus. That is, simply knowing that a virus is H5N1 does not in itself tell us much about properties of interest.
• The current H5N1 bird flu is extremely virulent in a wide range of birds, including domestic poultry. Therefore, regardless of any other concerns about this virus, it has serious economic consequences, simply for its effect on the poultry industry.
• The current H5N1 bird flu is spreading around the world. At least one reason for its spread is that it infects migratory birds. Known migration routes are being used to predict the spread of bird flu.
Despite those generalities above, we should also note:
• The virulence of H5N1 flu viruses in birds varies widely. Some H5N1 strains grow in some birds with no apparent ill effect. This actually has an important implication... Healthy infected birds (i.e., asymptomatic birds) are perhaps more of a threat for transmission of the virus over large distances. After all, sick birds don't fly much.
• Although migratory birds are suspected as one major source of long distance transmission of the virus, the clear facts on the matter are usually minimal. Trade -- both legal and illegal -- is also suspect.
• "H5N1" is not really synonymous with "bird flu". Many types of flu virus grow in birds. The two terms are sometimes -- and perhaps carelessly -- used synonymously in the current context, where a particular bird flu virus, of the H5N1 type, is of concern.
Current status in humans
The current H5N1 bird flu can infect humans. However, it seems that very few humans have been infected by it; most who are infected have had very close contact with infected birds.
• The current virus is poorly (rarely) transmitted from one human to another.
• The mortality rate for humans who do get infected by it is very high -- perhaps well over 50%.
• With "common" flu, mortality is greatest among the elderly and others in weakened condition. For the bird flu, this is not the case; people who are young and healthy die from it. We should note that this characteristic was also true of the famed 1918 flu virus.
• Where is a caveat in the information about bird flu in humans. It is hard to know how many people might have been infected that we do not know about -- people with mild symptoms or perhaps no symptoms at all. It is possible that many many have been infected, but that we are only aware of the severe cases. There is a way to test for this (by testing many people in bird flu areas for antibodies to the virus); to my knowledge, there is no answer yet.
An update. Once again, bird flu seemed quiet -- until the end of the year. A burst of cases near year end reminds us that it has not gone away, and that we remain unable to predict its course. News story: New bird flu cases revive fears of human pandemic, January 4, 2009. http://articles.latimes.com/2009/jan/04/world/fg-birdflu4.
An update. 2007 has come and gone, without a major bird flu impact on humans. Reported cases of bird flu in humans were actually down a bit for the year -- though no one knows how much these reported numbers underestimate what actually happened. Does this mean that the bird flu problem is over? No, not at all. The virus is still out there in birds; the risk of it mutating to become a pandemic virus are probably not much different than before. Anyway, some flu virus will become a serious pandemic threat at some point, so the general attempt to become prepared is good. News story: A pandemic that wasn't but might be, January 22, 2008. http://www.nytimes.com/2008/01/22/science/22flu.html.
Winter 2007-8 flu problem? You may be hearing about this being a bad winter for flu. Does this mean that the bird flu has arrived? No, it is another issue. This year's flu vaccine turns out to be not very good. Each year, a flu vaccine is designed based on a "best guess" as to which strains of flu will likely be prevalent. Usually these guesses are fairly close, but this year they missed on one. So, there will be probably be more flu this winter than expected -- but it will be the usual types of flu, not the feared bird flu.
Summary: Current concerns
Based on what is stated above, the current H5N1 bird flu is a serious problem for birds. It is also a problem for those whose living is based on birds (economic impact). It is also somewhat of a health risk for those in close contact with infected birds. It does not seem to be of much risk to the general public -- those not in direct contact with birds that are likely to be infected.
So why is there is so much said about the health risk?
Influenza viruses change rapidly. To some extent this is a common property of viruses, but there are aspects of flu virus biology that make this case worse. We are aware of the rapid change in flu viruses simply from the need to design a new flu vaccine each year. The big concern is that the current bird flu virus will acquire the ability to transmit well to humans, and in particular to transmit well from one human to another. If this happens, the number of people infected with this flu virus could increase dramatically -- from "very few" (now) to "almost everyone". If the virus that adapted to humans had the same virulence we think the current bird flu virus does, that could be very serious.
How likely is it that the bird flu virus will change so that it efficiently infects humans?
The short answer is that we don't know. However, the more widespread the bird virus is, the more chance there is for the change to happen.
If the bird flu virus acquires the ability to efficiently infect humans, will it have the high mortality in humans that it now seems to have?
Again, the short answer is that we don't know.
So, if we don't know the answers to the previous two questions, why is there so much concern?
Because we don't know the answers. If we don't know, it is prudent to consider a range of possibilities, including "worst case" scenarios. It is plausible that the virus might mutate to efficiently infect humans, and with high mortality. We do know that new strains of the flu arise regularly (that's why we have a new vaccine each year), and we know that very serious new strains arise from time to time. There are some features of the current bird flu virus that make it a good candidate to develop into a serious challenge to humans. These include its widespread distribution and its current high mortality in humans. Further, it is a type of flu virus to which people have not been generally exposed, so there is little or no immunity among humans.
Do all those working on flu viruses agree that the current bird flu virus is a serious threat to humans?
No. But even those who are most skeptical agree that a serious flu virus will emerge again at some point. So they do agree that the current effort, stimulated by the H5N1 bird flu, to better understand flu virus changes and virulence, and to plan how we would deal with a major flu pandemic, are worthwhile efforts -- even if this virus is not "the one".
What about predictions that fifty million people (choose your number) will die from the bird flu pandemic?
These numbers come from models of how a virus may spread and kill. Each number comes from a specific model, using a specific set of assumptions. That is, each number really means that, if such and such happens, then the following consequences will occur. The models are useful to public health officials, because it helps them to understand how a virus spreads, and therefore what are the most important places to try to intervene. That is, what is most important to the scientists is to see how the models make different predictions as the assumptions are varied. Making "worst case" scenarios is useful to those trying to understand what might happen and to those planning how we might respond. It is somewhat unfortunate that these numbers are quoted without the context of how they were estimated. One should not take any such number as a prediction in the sense that someone really thinks it will happen, and is "wrong" if it does not. What the numbers do is to illustrate the potential danger, if a pandemic happens and we do not respond well.
No one knows how many people died from the 1918 flu. Estimates are in the range 20-100 million. The current world population is 3-4 fold greater than then. Flu viruses are now able to travel around the world at speeds unknown in 1918 (on jet planes). Yes, we now have vaccines and drugs, but we are not sure how effective they would be against a novel flu strain that moves fast. These brief comments should show that we do not know how bad a new flu pandemic would be, but that it plausibly could kill not only 50 million, but far more.
What about vaccines and drugs?
Questionable. These are complex topics, and I don't want to spend much time on them now. However, neither helps much in the short term. Conventional flu vaccines are made for specific strains. So we can't make a (conventional) vaccine against a strain that has not yet emerged, and it takes several months to make a new vaccine. (There is some effort to make generic H5N1 vaccines, and this may prove to be useful experience. However, there can be no claim that any such vaccine prepared in advance would actually be useful against a new strain that emerges.) There are a few drugs that are of some use against flu virus. Oseltamivir is perhaps the best known -- by the Roche brand name Tamiflu. These drugs are quite expensive, and useful only in the very early stages of the infections. They may be useful in a local area to stop spread of the virus. One should not expect too much from them.
Drug notes
Tamiflu no longer works for dominant flu strain. This news story (February 7, 2009) is about an odd -- and discouraging-- finding: One of the major strains circulating this season has become resistant to one of the major drugs used. No one knows why; it does not seem related to use -- or overuse -- of the drug. It just happened. Of course, most important is whether such resistance will spread to or emerge in other strains. Time will tell. The story is at http://articles.latimes.com/2009/feb/07/science/sci-flu7.
Vaccine developments. There have been several recent announcements of progress with flu vaccines, including ones specifically intended for possible use in a pandemic. Some examples of these announcements follow. These are all "progress" -- and "good news". But it is also important to understand that the problems have not been "solved". All of these stories are incomplete, and many are untested or incompletely tested.
Antibodies Could Radically Alter Approach to Flu. This news story (February 23, 2009) discusses a new paper with a new approach to developing broad-range antibodies to influenza virus. In this work they develop monoclonal antibodies that target a highly conserved critical region of the H (hemagglutinin) protein, responsible for proper fusion of the virus with the membrane. They show that these antibodies are effective against a considerable range of flu viruses, and that they are effective both in preventing and treating flu in mice. They provide some evidence that the virus cannot easily mutate to avoid these antibodies, because of their critical function. The story is at http://www.medpagetoday.com/InfectiousDisease/URItheFlu/12994. The bottom of the story identifies the paper and an accompanying news story in the journal (shown as "Primary source" and "Additional source"), with links. That news story is particularly good at putting the work in perspective, including dealing with its limitations.
GE, Novavax team up on pandemic flu vaccine. A press release from two companies, December 10, 2007. They propose use of a "generic" vaccine -- rather than one against a specific strain. They propose use of cell culture, rather than the traditional egg method for vaccine production. And they propose use of inexpensive disposable reactors for growing the vaccine-producing cells. There is much new here. That means it is potentially very interesting, and may lead to vaccine production that is both faster and cheaper. However, it is unproved. The press release is at http://www.reuters.com/article/2007/12/10/idUSN1041110520071210.
New vaccine may give long-term defense against deadly bird flu and its variant forms. A press release from Purdue Univ, April 17, 2008. They have developed a vaccine with a couple of useful features. First, it is not made in eggs. Whatever the usual reservations are about the traditional system of making flu vaccine in eggs, it will be particularly problematic when growing a vaccine strain that is active in birds. Second, the vaccine appears to be active against a group of H5N1 viruses, not just a single strain. They thus suggest that this vaccine could be stockpiled in anticipation of an outbreak, even though a more specific vaccine might be developed when the outbreak occurs. So far, testing of this vaccine is only with mice. Nevertheless, this is an encouraging development, which will be followed up. The press release gives a good overview of the flu vaccine issues, and includes abstracts of a couple of recent papers on the work. The press release is at http://news.uns.purdue.edu/x/2008a/080417MittalBirdflu.html.
A new vaccine has been approved for possible emergency (but not routine) use in the US. As you read the news story, note that it is of rather limited effectiveness. News story: First Vaccine Against H5N1 Avian Flu Approved In The US, April 18, 2007. http://www.medicalnewstoday.com/articles/68109.php. There is a link at the end to more information from the FDA.
Is it safe to eat poultry and poultry products (e.g., eggs)?
Probably. But it is good to understand the reasons behind that conclusion, so you can re-evaluate at some point if things change. There are three reasons why eating poultry should be safe. First, in terms of the American food supply, there is no H5N1 bird flu virus in the system at this point. Second, proper cooking will kill the flu virus. (Remember, there are other things you can get from poultry, such as Salmonella. So proper food hygiene is an issue anyway. We also know that not everyone follows "best practice".) Third, the flu virus probably does not infect humans by oral ingestion. Some have suggested that this is not known for sure, but so far there is no reason to believe it is infectious orally. On balance, I'm inclined to suggest that this is not a problem, at least now. One of the links below is on food safety issues regarding bird flu.
The new 2009 flu
This section started in April 2009, as a new flu strain emerged. It quickly became known as the swine flu, for better or worse. Things moved fast. I can't capture all that here, but the goal is to simply point to some resources.
Here is a short message that I received from ASM (American Society for Microbiology). It offers a key resource that I am sure will be kept quite up to date. It also offers a key piece of practical advice. (Links have been updated.)
"The ASM is closely following the swine flu outbreak and wants to make you aware of current information and educational resources that you may find helpful. For general information please go to CDC site on the new flu. The CDC site contains information in print, podcast and Spanish translation for your use. In all infectious disease outbreaks, handwashing is one of the first and most important lines of defense against disease spread. The ASM has long been a leader in increasing awareness of the importance of handwashing and also has public education resources on handwashing for download and distribution at Don't Get Caught Dirty Handed."
In general terms, much of what is discussed on this page for bird flu is similar for the new 2009 swine flu. In fact, the new flu was a chance to test some of the flu preparedness ideas that had developed in preparation for the bird flu.
More information (web resources, articles)
Added May 28, 2011. There are numerous Musings posts on various flu issues. Most are listed on the supplementary page: Musings: Influenza.
New, December 22, 2010. What makes a flu virus virulent? Comparison of the genes in various flu viruses, including the 1918 pandemic virus and the 2009 virus, allows one to ask which features are important for virulence in humans. The work offers clues, but not simple answers. This article is a readable overview, written for a general audience. It discusses the viruses and their genes, and the various experimental systems. Recommended. J A Belser & T M Tumpey, What We Learned from Reconstructing the 1918 Influenza Pandemic Virus. Microbe 5:477, 11/10. It is online, free access, at microbemagazine.org/index.php...pandemic-virus.
Why winter? It is common knowledge that flu is a disease of winter. Why this is so has been unclear, with various ideas being considered. Now, a new report shows that the virus transmits best at low absolute humidity (rather than relative humidity). The humidity effect may reflect the stability of the virus under various conditions. The paper is: J Shaman et al, Absolute humidity and the seasonal onset of influenza in the continental United States. PLoS Biology 8:e1000316, 2/10. It is online, free access, at http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000316. For a brief introduction to the work, see an announcement from the NIH: Dry air may spur flu outbreaks (3/8/10). http://www.nih.gov/researchmatters/march2010/03082010flu.htm.
Google tracks the flu. You may have heard about this in the news. Google, in collaboration with the CDC, says they can track the flu by the frequency of searches on flu symptoms and such. The idea is not new, but their implementation of it is more advanced than prior efforts. The big advantage is the speed at which the information becomes available. See http://www.google.org/flutrends/. That page shows what is happening. The page also links to more information, which includes the paper published in the Feb 19 issue of Nature.
Antibodies from 1918. Researchers studied 32 survivors from the 1918 flu epidemic -- and found that all had antibodies to the 1918 flu strain. They were able to isolate antibody-producing memory cells from some of these survivors -- a testament to how long immunological memory can survive. They then used these cells to develop some potent monoclonal antibodies to the 1918 virus. This work has no direct impact on current issues, but is fascinating general information about our immune system. A news story about this work... 1918 Flu Antibodies Resurrected From Elderly Survivors, August 17, 2008: http://www.mc.vanderbilt.edu/news/releases.php?release=83. The paper is X Yu et al, Neutralizing antibodies derived from the B cells of 1918 influenza pandemic survivors. Nature 455:532, 9/25/08.
What determines virulence? We know that viruses differ in their ability to infect, and in the severity of disease (virulence) if they do infect. One difference between bird flu and human flu viruses is in the specific structure they recognize on the cell surface. Simply, the common H5N1 flu virus just doesn't do very well at getting into human cells, at least in the "usual" part of the respiratory tract. But if it does, then what? A recent paper compared two H5N1 bird flu strains, one of which was rather virulent to mice and the other of which was not. They were able to show that a specific amino acid change was responsible for this difference -- and that it probably acts through the host defense system. Implication? Well, for now, it is mainly one piece of information that helps us understand the picture better. It is possible that the protein involved would be a good target for anti-viral therapy. The paper is: P Jiao et al, A Single-Amino-Acid Substitution in the NS1 Protein Changes the Pathogenicity of H5N1 Avian Influenza Viruses in Mice. Journal of Virology 82:1146-1154, 2/08. It is online, with free access to at least the abstract, at http://jvi.asm.org/cgi/content/abstract/82/3/1146.
H5N1 overview. Article: R G Webster et al, H5N1 influenza continues to circulate and change. Microbe 1:559, 12/06. "As the H5N1 viruses continue to expand their range and behave in unexpected ways, they remain a serious threat to birds and humans." Microbe, the news magazine of the American Society for Microbiology, is free online; this item is at forms.asm.org/microbe/index.asp?bid=47152 (HTML) or forms.asm.org/ASM/files/ccLib...1206000559.pdf (PDF).
Avian Influenza (Bird Flu): Implications for Human Disease. http://www.cidrap.umn.edu/cidrap/content/influenza/avianflu/biofacts/avflu_human.html. Excellent. This is part of the CIDRAP site. Other flu pages here include "General Influenza and Flu Vaccine Information" and "Pandemic Influenza"; see the menu bar at the left of their page. I also list CIDRAP as a good general source of information on Emerging diseases.
Reassortment. The flu virus has a segmented genome -- rather analogous to the way humans have 23 separate chromosomes. (This is different from most viruses, which have only one "chromosome".) A concern is that an avian flu virus and a human flu virus infecting the same cell could "reassort" their segments, producing progeny with all sorts of combinations of flu and human segments. In the worst case, one or more such "reassortants" might have the worst properties of each -- virulence of the avian virus and transmission characteristics of the human virus. It is thought that the virus for some recent flu pandemics did arise this way, at least in part. A recent report showed that many of the simple reassortants one might get do not have any particularly bad properties. It should be emphasized that this does not preclude that reassortment will be a problem; it simply excludes certain things they have tested. A news story in Science a couple years ago is a good discussion of the background for such work -- including concern about the ethics of doing an experiment which might well make a dangerous virus. M Enserink, Virology: Tiptoeing around Pandora's box. Science 305:594, 7/30/04.
The article on the reassortants is T R Maines et al, Lack of transmission of H5N1 avian-human reassortant influenza viruses in a ferret model. PNAS 103:12121, Aug 8, 2006. Online at http://www.pnas.org/content/103/32/12121.abstract.
The April 21, 2006, issue of Science contains a Feature section on Influenza. Topics include patterns of flu virus spread, issues of host specificity, drugs, and vaccines. Many of the articles should be readable by the general audience. The following link is to the introduction: http://www.sciencemag.org/content/312/5772/379.short. This introductory article briefly describes and links to the other articles of this Feature section, and also other materials that are available in Science. This reference is also listed on my page of Further reading: Medical topics.
Nature web sites on influenza:
www.nature.com/swineflu/ Swine Flu. (Spring 2009; Nature updates it.)
www.nature.com/avianflu/index.html Avian flu news. (Spring 2007 to February 2009.)
http://www.nature.com/nature/focus/a...flu/index.html Warnings of a Flu Pandemic. (2005-6.)
http://www.nature.com/nature/focus/1918flu/index.html 1918 influenza pandemic. (October 2005; Nature updates it.)
http://www.nature.com/nature/focus/birdflu/index.html Bird Flu. (August 2004)
Access to Nature web sites may be incomplete, unless you have a subscription. If you use a UC library terminal, you will have full access. In any case, even partial access is probably "useful".
Avian flu: food safety issues, from the World Health Organization (WHO): www.who.int/foodsafety/micro/avian/en/. At this point, most transmission of the bird flu to humans is in cases where people are substantially exposed to infected flocks. Contact with an occasional infected dead chicken might, though is not likely to, transmit the flu. Ordinary cooking would inactivate the virus. Also available in French.
Vaccine development. A news story: FDA, producers moving toward mammalian cell-based flu vaccines. Microbe 1:54, 2/06. Microbe, the news magazine of the American Society for Microbiology, is free online; this item is at forms.asm.org/microbe/index.asp?bid=40620.
The 1918 influenza pandemic killed 20 million people over the course of a couple years. Can it happen again -- worse this time? Well, if a new strain emerges with high virulence and we have limited protection against it, sure. One of the problems with influenza is that new strains arise regularly, and move rapidly. The US government is making plans to deal with a new flu pandemic. The Pandemic Influenza Plan, from the US Dept of HHS, November 2005: www.hhs.gov/pandemicflu/plan/. (This is part of a larger Pandemic Flu site, from the Dept HHS: http://www.pandemicflu.gov/.)
UC Berkeley Pandemic Flu Preparedness. www.uhs.berkeley.edu/pandemicflu/. In the event of a real problem, this site would provide useful local information. But beyond that, it is good general information, intended to be read and used by real people.
Also see the section on Vaccines (general). Although the page listed there about thimerosal is general, it of particular interest regarding the flu vaccine.
Contributors
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Aging (including Alzheimer's disease)
C Rundel, Genes, aging, and the future of longevity. Engineering & Science LXV #4, 12/02, p 36. A delightful essay on some issues of aging, written by a Caltech undergraduate as part of a science writing class -- and then published in the Caltech magazine. The article is available online at http://eands.caltech.edu/articles/LXV4/longevity.html. The article discusses some genes that are known to affect aging in simple model organisms, and even a drug which seems to extend the life of fruit flies.
An intriguing result has recently been published: A team at Scripps Research Institute (La Jolla, California) has engineered mice to have a slightly lower core body temperature (by about 0.5 degree Celsius). These mice lived longer (by about 15%) than the "normal" mice. How did they lower the body temperature? By engineering the mice to make a heat-producing protein (uncoupling protein) in the hypothalamus -- where the body senses and regulates its temperature. The cooler mice ate and exercised normally, had somewhat higher weight (since they were producing less heat from the same food) -- and lived longer. Interestingly, one effect of severe caloric restriction, which is known to increase lifespan, is lowering the body temperature. So this work may give us one more piece of a complex puzzle. Its practical significance for now is purely speculative: there is no known way to reduce human body temperature, and of course we know nothing about what the side effects might be. The paper is B Conti et al, Transgenic mice with a reduced core body temperature have an increased life span. Science 314:825, 11/3/06. The paper is accompanied by a "perspective" article: C B Saper, Biomedicine: Life, the universe, and body temperature. Science 314:773, 11/3/06. These are online at http://www.sciencemag.org/content/314/5800/773.summary (perspective, probably the best place to start) and http://www.sciencemag.org/content/314/5800/825.abstract (article).
SAGE KE, the Science of Aging Knowledge Environment Archive Site, from Science magazine. "From October 2001 to June 2006, Science's SAGE KE provided news, reviews, commentaries, disease case studies, databases, and other resources pertaining to aging-related research. Although SAGE KE has now ceased publication, we invite you to search and browse the article content on this archive site." http://sageke.sciencemag.org/.
Nature web focus sites on aging:
Book. Stephen S Hall, Merchants of Immortality - Chasing the dream of human life extension. Houghton Mifflin, 2003. ISBN 0-618-09524-1. Available in Berkeley Public Library. For more about this book, see the listing of it under Cloning and stem cells. The "aging" parts of the book largely deal with telomerase, a fascinating scientific topic which probably is not a key limiting factor in human aging. In fact, much of the book deals with the hype surrounding telomerase -- and attempts to commercialize telomerase technologies.
Book. Lenny Guarente, Ageless Quest - One scientist's search for genes that prolong youth. Cold Spring Harbor Lab Press, 2003. ISBN 0-87969-652-4. Available in UC Berkeley Library. Guarente is a biologist at MIT. In this short book, he talks about finding a gene that extends the life of simple yeast -- and of worms. The question, then, is whether it is relevant to aging in higher organisms, including humans. He discusses evidence that it may be, though conclusive evidence is not yet available. This story is a good testimonial to the importance of basic research -- how studying simple model systems leads to insights that guide work in more complex systems. It is also a good story of how scientists develop and pursue leads -- some of which work out and some of which do not; that is how science works. It is an optimistic book -- perhaps too optimistic, since the gap between what has been shown and what is needed is still quite large. Enjoy the story, and Guarante's enthusiasm. But be careful to distinguish what turns out to work from the exciting discussions of what might be.
Anthrax
Anthrax vaccine immunization program. One place where the anthrax vaccine is actually used with high frequency is in the US military. This is their site about the vaccine and the program. Be alert for bias (as with any source!), but there is actually a lot of good info here. www.anthrax.osd.mil.
Researchers, including a group from UC Berkeley, have explored the tricks that the anthrax bacteria use to get the iron they need for growth. They found that these bacteria make two chemicals designed to steal iron from their host; such chemicals are generically called siderophores. One of these is attacked by the human immune system; however, the other -- the more novel one -- evades it, and actually succeeds in supplying iron to the bacteria. They suggest that this novel siderophore might be a good target for anti-anthrax drugs, or simply a marker for detection of this pathogen. The work was featured in the student newspaper, December 8, 2006: Researchers Find Possible Way to Block Anthrax, http://archive.dailycal.org/article/22576/_i_science_technology_i_br_researchers_find_possib. It was also discussed in a nice article in the student publication BSR: N Keith, Double Trouble - Anthrax has two tricks for stealing iron. Berkeley Science Review, Issue 12, p 15, Spring 2007. BSR is free online; this item is at sciencereview.berkeley.edu/ar...ticle=briefs_5. The work was published as R J Abergel et al, Anthrax pathogen evades the mammalian immune system through stealth siderophore production. PNAS 103:18499, 12/5/06. Online at http://www.pnas.org/content/103/49/18499.abstract. This work is also briefly noted on my Intro Chem Internet Resources page under solutions.
Book. For some interesting history, see the listing for Thomas D Brock, Robert Koch - A Life in Medicine and Bacteriology (1988) on my page Books: Suggestions for general reading. One major story is the first clear elucidation of the life cycle of a pathogenic bacterium -- anthrax. Those interested in bacteria, especially as agents of disease, will enjoy this fascinating tale of the origins of modern medical microbiology.
Antibiotics
Bacterial 'battle for survival' leads to new antibiotic -- Holds promise for treating stomach ulcers. A press release from MIT, Feb 2008, on a new approach for discovering new antibiotics. Briefly, they force bacteria not known to make antibiotics to compete with other bacteria. One possible response is for them to develop the ability to make antibiotics. This should be considered interesting lab work at this point. The potential of the new antibiotics is unknown. web.mit.edu/newsoffice/2008/a...tics-0226.html.
Alliance for the Prudent Use of Antibiotics. www.tufts.edu/med/apua/. This site has "an agenda" -- trying to reduce "inappropriate" use of antibiotics. A particular concern is the use of vast amounts of antibiotics with farm animals, sometimes with minimal justification. The site also contains a lot of general information about antibiotics, aimed at the consumer and at doctors.
A local angle. The July 24, 2003, issue of the Berkeleyan (a campus newspaper for staff) published part of an interview with science writer and UCB journalism professor Michael Pollan on the subject of antibiotics in beef farming, with a focus on McDonald's announcement of favoring suppliers that use less antibiotics. The article title is Prof has a beef with McDonald's antibiotics announcement. The entire interview is online at http://www.berkeley.edu/news/media/releases/2003/07/01_pollan.shtml. Very readable, with a useful general overview of why antibiotics are used in commercial production of animals. Pollan also expresses reservations about how significant the policy announcement will be.
Art
The DNA double helix has become a popular icon, known well beyond the circles of those who know anything about biology. And of course, some artists are attracted to social issues. Thus it should not be surprising that DNA and genes and genomes and related issues have become the subject of artistic efforts.
John Sulston was the head of the British lab working on the human genome. Provocatively and/or appropriately, artist Marc Quinn did a "portrait" of Sulston -- using his DNA. For a news article on this, which includes the "portrait", see http://www.guardian.co.uk/culture/2001/sep/22/art. If you have access to Nature, see Martin Kemp's article about the portrait in the October 25, 2001, issue (413:778). (The printed article and the online PDF file contain the "portrait"; however the online HTML file does not.) This article is part of Nature's regular series, Science and Culture; art historian Kemp is a regular contributor.
Sulston shared the 2002 Nobel prize for his work on development in the worm Caenorhabditis elegans. In the course of that work, he played a key role in discovering the phenomenon of programmed cell death, now called apoptosis. http://www.nobelprize.org/nobel_priz...aureates/2002/.
England issued a coin to commemorate the 50th anniversary of the DNA structure (which was developed at Cambridge Univ in England); it shows a DNA double helix on one side. (The other side shows the Queen, who coincidentally is celebrating her 50th anniversary as monarch.) For pictures of the coin, plus some information: http://www.taxfreegold.co.uk/2003two...dsdnagold.html.
Also see L Gamwell, Science in culture: Art after DNA. Nature 422:817, 4/24/03. http://www.nature.com/nature/journal...l/422817a.html. The subtitle notes "The double helix has inspired scientists and artists alike."
Bio-inspiration (biomimetics)
Book. Peter Forbes, The Gecko's Foot - Bio-inspiration: Engineering new materials from nature. Norton, 2005. The lotus leaf is easily rinsed clean; the gecko can climb a glass wall. Why? And, can we make use of the principles that Nature has used to achieve these remarkable accomplishments? Those are just two of the topics in this delightful book -- one of which is reflected in its title. The theme is bio-inspiration (sometimes called biomimetics), in which we look to Nature for an idea about how to do something. The hook-and-loop fastener, popularly known by the tradename Velcro, is an example of old, but the field has now taken on an identity that reflects a more focused effort to discover and exploit what Nature has already learned. Forbes emphasizes work at the "nano" level, where recent advances in instrumentation, such as the scanning electron microscope (SEM), helped us unlock Nature's secrets. Commercial importance? Well, products based on the self-cleaning lotus leaf and the sticky gecko foot are on the market. They are not yet big successes; perhaps that will take time, or perhaps there is less here of commercial importance than we would like to believe. In any case, the book is delightful biology, delightfully presented. It is suited for the scientific novice, but even biologists are likely to find it rewarding. This book is listed on my Book suggestions page, and as further reading for Intro Chem Ch 15, re intermolecular forces, and for Organic/Biochem Ch 15, re spider silk. In fact, it was reading this book that prompted me to start this BITN section.
From the University of Reading:
• Centre for Biomimetics. www.reading.ac.uk/biomim/home.htm.
• BIONIS: The Biomimetics Network for Industrial Sustainability. www.reading.ac.uk/bionis/.
From University of California, Berkeley
• Biomimetic Millisystems Lab. "The goal of the Biomimetic Millisystems Lab is to harness features of animal manipulation, locomotion, sensing, actuation, mechanics, dynamics, and control strategies to radically improve millirobot capabilities. Research in the lab ranges from fundamental understanding of mechanical principles to novel fabrication techniques to system integration of autonomous millirobots. The lab works closely with biologists to develop models of function which can be tested on engineered and natural systems. The lab's current research is centered on fly-size flapping flight, and all-terrain crawling using nanostructured adhesives." The "Current Research Projects" listed in January 2008 include: Micromechanical Flying Insect, Biologically Inspired Synthetic Gecko Adhesives, Millirobot Rapid Prototyping, Micro-Robots and Microassembly. http://robotics.eecs.berkeley.edu/~ronf/Biomimetics.html. This page is from Ronald Fearing, in EECS (Electrical engineering and computer science). However, a glance at the people shows that this is a collaboration that also includes the Departments of Integrative Biology and Chemical Engineering.
• CIBER. The Center for Interdisciplinary Bio-inspiration in Education & Research. A new center at Berkeley, headed by Dr Robert Full, of Integrative Biology. http://ciber.berkeley.edu. From "Objectives": CIBER "will innovate methods to extract principles in biology that inspire novel design in engineering and train the next generation of scientists and engineers to collaborate in mutually beneficial relationships. ... Biologists working with engineers, computer scientists and mathematicians are discovering general principles of nature from the level of molecules to behavior at an ever-increasing pace. Now more than ever before, nature can instruct us on how to best use new materials and manufacturing processes discovered by engineers, because these human technologies have more of the characteristics of life. This effort will require unprecedented integration among disciplines that include biology, psychology, engineering, physics, chemistry, computer science and mathematics." Choose Publications & Journals for good information on the work going on.
* Robot Flea Circus - Berkeley engineers build bionic bugs, by Tracy Powell. Berkeley Science Review, Fall 2007, p 22. Studying insect locomotion leads to ideas for designing robots. sciencereview.berkeley.edu/ar...cle=bionicbugs.
* News story in the Daily Cal, the student newspaper, February 12, 2008. Mimicking the geckos' ability to defy gravity - From geckos to humans to robots: new adhesive tape makes the vertical horizontal. http://archive.dailycal.org/article/100353/mimicking_the_geckos_ability_to_defy_gravity.
* News release: Engineers create gecko-inspired high-friction micro-fibers, August 2006. http://www.berkeley.edu/news/media/releases/2006/08/22_microfiber.shtml. As you read the item, note that they are not making synthetic gecko feet, but rather using some of what they learned about gecko feet to help them design a new material.
'Gecko foot' band-aids could promote healing. A news story in New Scientist, February 19, 2008, about the development of a new type of adhesive tape, which may be suitable for not only band-aids but also sutures. It is based in part on the structure of the gecko foot. Importantly, the work does not simply mimic the gecko foot, but builds on it, to develop a material suitable for the intended use. The story is online at http://www.newscientist.com/article/dn13347. The work referred to is published as: A Mahdavi et al, A biodegradable and biocompatible gecko-inspired tissue adhesive. PNAS 105:2307, 2/19/08. There is a link to the article at the end of the news story.
Posts on my Musings pages on biomimetics include...
* New, April 18, 2011. Why don't woodpeckers get headaches? Designing better shock absorbers (April 18, 2011).
* New, February 27, 2011. Robots should learn to crawl first, then walk (February 27, 2011).
* Added December 15, 2010. Armor (February 5, 2010).
Brain (autism, schizophrenia)
There is evidence to suggest that infection of the mother during pregnancy may increase the chances of some brain diseases, including autism and schizophrenia. The effects seem to be due not to the infectious agent per se, but to the host response. Now, work with a mouse model system points to one specific component, the cytokine IL-6, as promoting the brain mis-development. Remember, this is with mice; the work generates some leads that must be followed up to see if they are relevant to humans. A press release about this work: "Researchers discover link between schizophrenia, autism and maternal flu", Oct 1, 2007: media.caltech.edu/press_releases/13039. The paper is: S E P Smith et al, Maternal immune activation alters fetal brain development through interleukin-6. Journal of Neuroscience, 27:10695-10702, 10/3/07.
Cancer
Some general educational resources...
New, November 29, 2010. Inside Cancer. Educational materials, for the general public. Sections include: hallmarks, causes and prevention, diagnosis and treatment, pathways. Some materials are specifically for teachers. www.insidecancer.org. This is from the Dolan DNA Learning Center, Cold Spring Harbor Laboratory: http://www.dnalc.org/websites/. Other parts of the Dolan DNA Learning Center are referred to under BITN Resources: DNA and the genome and Molecular Biology Internet Resources: Methods.
Understanding Cancer. A series of informational web pages for the general public, from the National Cancer Institute. www.cancer.gov/cancertopics/U...standingCancer. Also in Spanish.
Cancer Quest, a broad informational resource, largely organized as a tutorial, from G Orloff, Emory Univ. Topics range from the basic underlying biology to clinical issues. Special pages offer guidance to patients, educators, students, and health professionals. http://www.cancerquest.org. Also available in Chinese, Italian, Russian, Spanish.
Other...
Personalized cancer vaccine made in plants. This work deals with a cancer of the immune system, called follicular B cell lymphoma. An important characteristic of this cancer is that each case expresses a unique antigen, reflecting its development from a single immune system cell. The goal is to make a vaccine that targets this particular antigen. Here, they show that they can do this in a plant system -- which is both faster and cheaper than animal systems previously tried. The resulting vaccines do elicit an immune response in [most of] the patients, though no therapeutic benefit was seen in this small early study. The work is of note both for the special approach of making a personalized vaccine, and for the broader issue of making vaccines in plants. News story, from Stanford: Plants can be factories making vaccine to treat cancer, July 23, 2008. http://news.stanford.edu/news/2008/july23/med-plants-072308.html. The paper: A A McCormick et al, Plant-produced idiotype vaccines for the treatment of non-Hodgkin's lymphoma: Safety and immunogenicity in a phase I clinical study. PNAS 105:10131, 7/22/08. Free online: http://www.pnas.org/content/105/29/10131.
Drug targeting. A group from UC Berkeley and San Francisco reported making a new drug delivery system. The active drug is attached to a large molecule called a dendrimer. Because the blood system in tumors tends to be leaky, the large drug complex is taken up by the tumor selectively, and then hydrolyzed. They report promising results in a mouse model system. Both the article and the story about it discuss some of the logic of the system. There is a good news story about the work in BSR, a student publication: N Parghi, Right on target - Reducing chemotherapy's collateral damage. Berkeley Science Review, issue 12, p 12, Spring 2007. Free online: sciencereview.berkeley.edu/ar...ticle=briefs_3. The paper: C C Lee et al, A single dose of doxorubicin-functionalized bow-tie dendrimer cures mice bearing C-26 colon carcinomas. PNAS 103:16649, 11/7/06. Free online: http://www.pnas.org/content/103/45/16649.
Irreversible electroporation. UC Berkeley scientists, led by B Rubinsky, are working on a new approach to treating solid tumors. A new paper is on the use of the method with pigs, the first large animal tests. The method is a variation of the common electroporation used in laboratory work to make transient membrane pores that can allow uptake of drugs or even DNA. The key difference is that the conditions are chosen so that the pores do not quickly reseal; thus the cells "leak to death". In this method, the electrical pulse is delivered directly to tumor cells, in a surgical procedure. News story, "A breakthrough treatment for tumors? New medical technique uses electrical pulses to punch holes in target cell membrane." February 14, 2007. Online: http://www.berkeley.edu/news/berkele...reatment.shtml.
The Carcinogenic Potency Database (CPDB). A database of carcinogens, based on testing in animals. From Lois Swirsky Gold, Bruce Ames, and colleagues at UC Berkeley. potency.berkeley.edu/.
Book. J Michael Bishop, How to win the Nobel prize - An unexpected life in science. Harvard Univ Press, 2003. ISBN 0-674-00880-4. Bishop is a local story -- long time scientist at UCSF, now Chancellor there. Bishop's work on cellular genes that become cancer genes earned the Nobel Prize for him and his UCSF colleague Harold Varmus. (And a few days after the Nobel announcement he was at Candlestick Park for the World Series game that did not happen.) The book is based on a series of lectures, and has the informal breezy style of talks for a general audience. It is more generally about the nature of science, and about baseball, music and the human Michael Bishop, than about cancer in particular. One chapter does indeed give a good, not-too-technical introduction to the nature of cancer -- and his own contributions. The final chapter is about the future of science, and its role in society. All-in-all, a fairly light but interesting read.
Diabetes
J Diamond, The double puzzle of diabetes. Nature 423:599, 6/5/03. Feature. Nature's blurb for this article: "Why is the prevalence of type 2 diabetes now exploding in most populations, but not in Europeans? The genetic and evolutionary consequences of geographical differences in food history may provide the answer." The article gives an overview of the types of diabetes, and their incidence. The main purpose is to propose an explanation of why diabetes is not rampant among Europeans. As you read this, remember that he is proposing a hypothesis -- and some tests of it; be careful about remembering his "answer" as if it were true. Reading the article for its background information can be good. Online at http://www.nature.com/nature/journal...l/423599a.html.
Ebola and Marburg
Ebola and Marburg are related viruses. Ebola has been observed to emerge "from the jungle" from time to time. A major -- and important -- mystery is where is it "hiding". That is, what is the "reservoir" (likely an animal) from which the virus emerges? Now there is evidence that bats may be the culprit.; the bats carrying the virus show no symptoms. It is important to emphasize that this is a new finding, subject to further work. Even if correct, it only shows that the bats are a part of the story; there may be more to it. The article is: E M Leroy et al, Fruit bats as reservoirs of Ebola virus. Nature 438:575, 12/1/05. The abstract is at http://www.nature.com/nature/journal...s/438575a.html. Here are two news stories on this finding: http://www.innovations-report.com/ht...ort-53574.html and http://news.bbc.co.uk/2/hi/health/4484494.stm.
Now there is a report of Marburg virus being detected in bats. The work is published: J S Towner et al, Marburg virus infection detected in a common African bat. PLoS ONE 2(8):e764, 8/22/07. There is a news story, August 2007: Scientists detect presence of Marburg virus in African fruit bats, at: http://www.eurekalert.org/pub_releas...-sdp082107.php. This has a link to the article, which is freely available.
Progress with efforts to control Ebola, Marburg viruses. Microbe 1:217, 5/06. Microbe, the news magazine of the American Society for Microbiology, is free online; this item is at forms.asm.org/microbe/index.asp?bid=42381. Discusses both vaccines and drugs.
Emerging diseases (general)
In the Spring of 2003, as I started to put together a BITN web site, one dominant news story was a new illness, called SARS (severe acute respiratory syndrome). Our fears of SARS are enhanced by our ignorance. And that is not just the ignorance of the general public, but also the ignorance of the medical and scientific communities. SARS is a new disease. At least at the start, we do not know what causes it, how it is transmitted, how to contain or treat it -- even how to diagnose or define it, or what its risks are. Of course, over time, answers to some of these questions are developed. It is actually quite amazing how fast some of the answers come in. On the other hand, not all the answers we hear are correct. (For example, three different organisms were quickly "identified" as the cause of SARS. Obviously, two of those were likely to be incorrect.)
By mid-summer, we may have the disease under control. Yet, we still have little idea how the disease started -- and if/when it may return.
SARS is an example of an emerging disease -- a new disease. Other diseases that have emerged over the last 30 years include Legionnaire's diseases, AIDS, toxic shock syndrome, Ebola, West Nile Virus -- and perhaps a new strain of Influenza each year. Both SARS and the broader topic raise lots of questions about how we deal with a disease that has emerged, and how we might predict or prevent new emerging diseases.
M E J Woolhouse, Where Do Emerging Pathogens Come from? Microbe 1:511, 11/06. microbemagazine.org/index.php...gens-come-from. A discussion of the factors involved in the emergence of new diseases.
J L Fox, Cats with MRSA, elephants with TB are parts of a "microbial storm". Microbe 3:451, 10/08. Microbe, the news magazine of the American Society for Microbiology, is free online; this item is at microbemagazine.org/images/st...1008000448.pdf (scroll down to page 4 of the file for this item -- or just look for the elephants). "Emerging diseases" is a two-way street. Diseases may pass from humans to other animals, too. This news story discusses some examples and concerns.
The following sites track emerging diseases
• Center for Infectious Disease Research and Policy (Univ Minnesota). http://www.cidrap.umn.edu. I list specific CIDRAP sections on my pages for Influenza (Bird flu) and Prions (BSE, CJD, etc). Other topic areas here include: Bioterrorism, Biosecurity (e.g., food), Food safety (foodborne illnesses, irradiation), and a miscellaneous section that includes SARS, West Nile, Monkeypox, Chemical Terrorism. Useful for the general audience.
• Healthmap, a "Global disease alert map", presents disease reports by country. You can click on a map or chose from a list of countries. http://www.healthmap.org/. From J Brownstein, Harvard Medical School. Also in Arabic, Chinese, French, Portuguese, Russian, Spanish. Caution: loads very slowly.
• ProMED-mail is aimed at medical professionals, informing them about emerging diseases; it is one of the major primary sources underlying the sites listed above. Includes announcements and maps of outbreaks, as well as general information. From the International Society for Infectious Diseases. http://www.promedmail.org. Parts of the site are also available in Chinese, Japanese, Portuguese, Russian, Spanish.
• US government sites with information on emerging diseases:
• CDC. www.cdc.gov/ncidod/diseases/e...ease_sites.htm.
• NIH. http://www.niaid.nih.gov/topics/emerging/.
• Book. See the listing for Dorothy H Crawford, Deadly Companions - How microbes shaped our history (2007) on my page Books: Suggestions for general reading. This book is about the relationship between microbes and man. It starts with a discussion of SARS, and discusses many emergences of the past. Good perspective.
• Posts on my Musings pages on emerging diseases include...
Ethical and social issues
As noted in the introductory materials, I intend the main emphasis here to be the scientific issues. Of course, other issues are important parts of the overall story. Some of the topic-specific resources listed include ethical and social issues. But occasionally, I may want to list a site that focuses on these matters.
Bloodlines: Technology Hits Home. The web site http://www.pbs.org/bloodlines/ was written to accompany a PBS show. It broadly deals with issues arising from reproductive and genetic technologies, and includes interactive questions which you can try to evaluate for yourself.
Bioethics Web. "BioethicsWeb is a gateway to evaluated, high quality Internet resources relating to biomedical ethics, including ethical, social, legal and public policy questions arising from advances in medicine and biology, issues relating to the conduct of biomedical research and approaches to bioethics." Subtopics include: Biomedicine, Clinical practice, Environment/agriculture/foods, Ethics: theory and concepts, Research conduct, Society/policy/law, and more.
HIV (AIDS)
aidsinfo.nih.gov. A broad source of HIV information, from NIH. It includes a section on vaccine trials, as well as drug treatments and other research areas.
The 2008 Nobel prize in Physiology or Medicine was awarded to Harald zur Hausen, "for his discovery of human papilloma viruses causing cervical cancer" and Francoise Barre-Sinoussi and Luc Montagnier, "for their discovery of human immunodeficiency virus". See the Nobel site: http://www.nobelprize.org/nobel_priz...aureates/2008/. This item is listed on this page for HIV and HPV.
Hormone replacement therapy
A major and continuing news story for 2002-3 was based on some long term studies of the use of replacement hormones by post-menopausal women. The results were not at all what had been commonly expected. One important general point from the story is the problem of knowing what long term effects of a treatment are, especially the smaller effects -- without doing long term studies with large numbers of patients. Lots of info, with regular updates, is available at the home page for the Women's Health Initiative: http://www.whi.org. "The Women's Health Initiative (WHI) is a long-term national health study that focuses on strategies for preventing heart disease, breast and colorectal cancer and fracture in postmenopausal women. This 15-year project involves over 161,000 women ages 50-79, and is one of the most definitive, far reaching programs of research on women's health ever undertaken in the U.S. The purpose of this site is to provide WHI participants [and] others interested in the WHI findings a way of obtaining information about research results directly from the study."
And now, after five more years of data, the advice changes again. It is more detailed, more nuanced. This is common, and emphasizes that we must be cautious about over-interpreting any data set. News story, June 21, 2007, from Brigham and Women's Hospital and Harvard Medical School: "Estrogen Therapy and Coronary Artery Calcification. Women aged 50-59 who took estrogen show a reduced risk of coronary plaque buildup." www.brighamandwomens.org/abou...b=0&PageID=272.
For an introduction to the use of testosterone supplements in men, see a page from the US National Institute on Aging: Frequently Asked Questions About Testosterone and the IOM Report, 11/12/03. www.nia.nih.gov/NewsAndEvents...eIOMReport.htm.
HPV (Human papillomavirus)
A new vaccine was announced recently. It is widely known by its trade name, Gardasil. It acts to prevent infection by some strains of the human papillomavirus, which cause cervical cancer and genital warts. The vaccine itself is indeed a product of modern biotechnology: it contains only viral proteins (produced in yeast), with no viral genome; thus it cannot grow at all. Here are some materials from the CDC about this vaccine:
* "Questions and Answers about HPV Vaccine Safety". www.cdc.gov/vaccinesafety/Vac.../hpv_faqs.html
* A more technical report: "Quadrivalent Human Papillomavirus Vaccine -- Recommendations of the Advisory Committee on Immunization Practices (ACIP)", by L E Markowitz et al, dated March 23, 2007. It provides background about the type of virus and its effects, and the nature of the vaccine. http://www.cdc.gov/mmwr/preview/mmwrhtml/rr5602a1.htm
Notes...
There are many strains of HPV. Only some of them cause cancer or warts. The vaccine is effective against four of these strains. Data so far suggests that the vaccine is extremely effective against those four strains, but it is important to realize that strains other than those in the vaccine are responsible for some cancer. One might be confused by hearing that the virus is "100%" effective or "70%" effective. The former number refers to the apparent effectiveness against the strains included in the vaccine; the latter number refers to the overall effectiveness against cervical cancer, given that the current vaccine works against only some of the relevant strains.
Long term issues about this new vaccine are, of course, not known. For example, how long is it effective?
The May 10, 2007, issue of the New England Journal of Medicine contains several articles on this new vaccine -- with more data and perspectives. I suggest that readers start with two editorials, with differing views. Both are freely available online.
Here is another approach to making an HPV vaccine. This one seeks to treat a person who is infected; it is thus a therapeutic vaccine. It targets a protein that is part of the viral life cycle in an infected cell -- and which is actually responsible for causing and maintaining cancer. This vaccine is still in testing. News story: Experimental HPV Vaccine Helps in Treating Mice with Cervical Cancer, Microbe 3:318, 7/08. Free online: microbemagazine.org/images/st...0708000314.pdf. Scroll down to page 5 of the file for this item.
The 2008 Nobel prize in Physiology or Medicine was awarded to Harald zur Hausen, "for his discovery of human papilloma viruses causing cervical cancer" and Francoise Barre-Sinoussi and Luc Montagnier, "for their discovery of human immunodeficiency virus". See the Nobel site: http://www.nobelprize.org/nobel_priz...aureates/2008/. This item is listed on this page for HIV and HPV. It is also noted in a Musings post: Nobel prizes (October 8, 2008).
The main emphasis with HPV and cancer has been cervical cancer. However, there is increasing evidence that these viruses, probably the same strains, may cause other cancers. Here is one news story on this: HPV-Linked Oral Cancer In Men Increasing, Feb 4, 2008. http://www.medicalnewstoday.com/articles/96053.php.
The traditional method of screening for cervical cancer is the pap smear, which looks for abnormal cells; in poor countries, little or no screening may be done. A new study suggests that it might be better to screen for the virus that causes the cancer. Their extensive testing shows that the test for the viral DNA is more effective than the pap smear. They argue that it is also likely to become inexpensive enough to be practical -- and worthwhile -- in poorer countries. A news story on this work: DNA Test Outperforms Pap Smear; April 6, 2009. www.nytimes.com/2009/04/07/he...virus.html.The paper is: R Sankaranarayanan et al, HPV Screening for Cervical Cancer in Rural India. N Engl J Med 360:1385, April 2, 2009. Freely available at http://www.nejm.org/doi/full/10.1056/NEJMoa0808516. The article is accompanied by an editorial: M Schiffman & S Wacholder, From India to the World - A Better Way to Prevent Cervical Cancer. N Engl J Med 360:1453, April 2, 2009. Freely available at http://www.nejm.org/doi/full/10.1056/NEJMe0901167. The editorial is a good overview of many issues surrounding cervical cancer.
Malaria
Malaria is one of the world's great killers. Recent years have seen the analysis of the genome of both the malaria parasite itself and its mosquito vector. Nature has posted a "web focus" on the diverse aspects of this disease, 2008. http://www.nature.com/nature/focus/malaria/index.html
A UC Berkeley group led by Jay Keasling is working on production of artemisinin, a new type of anti-malarial drug, in microbes (bacteria and yeast).
Malaria Vaccine Initiative (MVI). http://malariavaccine.org/. For a short news story on malaria vaccines, including the role of the MVI: Money, Technology, and Fresh Ideas Converge on Malaria. Microbe 3:9, 1/08. Microbe, the news magazine of the American Society for Microbiology, is free online; this item is at forms.asm.org/microbe/index.asp?bid=55316.
Measles
In some ways measles would seem to be a good target for eradication. It occurs only in humans, so there is no need to worry about animal reservoirs. A good vaccine is available. Yet measles remains a major killer. One key reason is that the virus is highly infectious, thus a very high level of population immunity is needed to block its transmission. The following article is a good readable discussion of the issues of measles, its vaccine, and the difficulty of eradicating this disease. D E Griffin & W J Moss, Can We Eradicate Measles? Microbe 1:409, 9/06. It is at microbemagazine.org/images/st...0906000409.pdf.
Polio
Whatever happened to polio?. A history site from the Smithsonian Institution, posted to coincide with the 50th anniversary of the first polio vaccine. http://americanhistory.si.edu/polio/. Includes information on the current effort to eradicate polio.
A report from the Institute of Medicine (IOM)... K Stratton et al, Immunization safety review: SV40 Contamination of Polio Vaccine and Cancer, October 2002. http://www.nap.edu/catalog.php?record_id=10534. Some early batches of the original polio vaccine (the Salk vaccine, with killed virus) were later found to be contaminated with the virus SV40 (which was not killed by the treatment used to kill the poliovirus). SV40 may be a cancer-causing virus. So, inadvertently, we have been running a big test on whether it causes cancer in humans. A long enough time has passed that it is rather clear there is no big problem. Some data has suggested increases in certain very rare cancers. This report analyzes what is known. One of the frustrations, inherent in an accidental test, is that the data is not kept very well. This is an interesting story, but I do suggest you read it for the message about how things should be done, and not try to make SV40 into a big problem.
Nature web focus: http://www.nature.com/nature/focus/polio/index.html. End of polio - the final assault. (September 2004)
Protein Folding -- and diseases
This topic was suggested by a student. It was stimulated in part by the Sept 8, 2003, issue of The Scientist, including a feature article by P Hunter, Protein Folding: Theory meets disease, p 24: http://classic.the-scientist.com/art...display/14060/. It is also related to the topic Prions (BSE, CJD, etc.).
There are several issues here. The general topic of how proteins fold has long fascinated -- and frustrated -- biologists. But the topic has taken on greater significance with the increasing recognition of how relevant the protein folding problem is to disease. In fact, a good place to start with the Hunter article, listed above, is the side-bar on p 25, "Miss a fold, prompt a disease." Many cases are now known where we realize that the main effect of a mutation that causes a disease is to interfere with protein folding. For example, the major mutation found in cystic fibrosis is of this type. Once/if the mutant protein manages to fold, it works fine, but the mutation greatly slows the folding process.
Another type of folding-disease connection is illustrated by the prions. Although our understanding of prions is still incomplete, it seems that the prion proteins have two stable forms. One is the normal form of the protein, in your cells, and the other form causes disease. See the Prions (BSE, CJD, etc.) page for more.
A classic experiment in the history of studying protein folding was done by Christian Anfinsen, around 1960. Anfinsen showed that a protein could fold up properly in vitro, without any external source of "information" on how to fold. This established the paradigm that the 3D shape of a protein follows from its amino acid sequence. Although there are some nuances, this still underlies our modern understanding of protein folding. Anfinsen shared the 1972 Nobel prize for Chemistry "for his work on ribonuclease, especially concerning the connection between the amino acid sequence and the biologically active conformation". See the Nobel site: http://www.nobelprize.org/nobel_priz...aureates/1972/.
RNAi (RNA interference or silencing)
Natural small RNA molecules act as gene regulators. Similarly, synthetic small RNA molecules may be useful to biologists to probe gene function -- and may be useful as therapeutic agents. This is a new field. Particularly with regard to actual therapeutic use, there is much promise but little information. Two articles in the March 29, 2004, issue of The Scientist provide a good introduction and overview. The articles are A Adams, RNAi inches toward the clinic (p 32), and A Constans, Concocting a knock-out punch for HIV-1 (p 28). http://classic.the-scientist.com/art...display/14559/ & http://classic.the-scientist.com/art...display/14552/.
The Scientist for Sept 13, 2004 (Vol 18 #17) has the feature topic of RNAi, with multiple articles: classic.the-scientist.com/2004/9/13/. Again, an excellent introduction and overview.
The idea of using an inhibitory RNA as a therapeutic is simple enough, but there are many technical hurdles. Here is a report of targeting an siRNA (small interfering RNA) to the brain -- by using a protein from rabies virus. Rabies infects the nervous system, and the scientists exploit one part of that virus to deliver the therapeutic RNA across the blood brain barrier. The therapeutic RNA attached to the rabies virus delivery system protects the mice from an experimental viral infection of the brain. Press release, from NIH, June 17, 2007: Blood-Brain Barrier Breached by New Therapeutic Strategy. http://www.niaid.nih.gov/news/newsre...inbarrier.aspx. The work was published: P Kumar et al, Transvascular delivery of small interfering RNA to the central nervous system . Nature 448:39, 7/5/07. Accompanying news story: E M Cantin & J J Rossi, Molecular medicine: Entry granted. Nature 448:33, 7/5/07.
The 2006 Nobel prize for physiology or medicine was awarded to Andrew Z Fire and Craig C Mello for their discovery of "RNA interference - gene silencing by double-stranded RNA". http://www.nobelprize.org/nobel_priz...aureates/2006/.
See the BITN page Prions (BSE, CJD, etc): Treatment for a paper on the possible use of RNAi to treat a prion disease.
See the BITN page Agricultural biotechnology (GM foods): Recent items for a paper on the use of RNAi, targeted to the seeds, to reduce production of a toxic chemical in cotton seeds.
Nature has a web focus site on this topic. Of particular interest may be a set of animations of how the process works: www.nature.com/focus/rnai/ani...ons/index.html.
SARS (Severe acute respiratory syndrome)
See Emerging diseases section, above, for perspective.
The web site of the US Centers for Disease Control (CDC) is a good site to keep abreast of SARS -- and of course of other diseases. The CDC SARS page: www.cdc.gov/ncidod/sars/
The CDC site has links to all local and state public health departments, and also includes travel advisories.
Nature magazine's "web focus" on SARS: http://www.nature.com/nature/focus/sars/index.html. This set seems to be freely available.
In July, Nature published a "news feature" called "SARS - What have we learned?" It is in the form of a series of questions, with answers, about various aspects of the SARS story. Among the questions... Was the fuss overblown? Are we prepared for the next viral threat? Where did the SARS virus come from? What about a vaccine? Very readable overview and update. Nature 424:123, 7/10/03; also available at the top of their web focus page, listed above.
A free online SARS "textbook", maintained by B S Kamps & C Hoffmann: http://www.sarsreference.com. Also available in Chinese, French, Greek, Italian, Portuguese, Romanian, Spanish, Vietnamese.
Smallpox
www.bt.cdc.gov/agent/smallpox/index.asp. The site provides a wide range of information, including much history. Some materials are also available here in Spanish.
Sudden Oak Death
http://www.suddenoakdeath.org. A range of information, both for the consumer and the scientist. The site is from UC Berkeley.
Sudden larch death (SLD) is due to the same pathogen. Some information on the spread of SLD in Europe is included at this site. Just search on larch.
Synthetic biology
A nice overview of the field of synthetic biology. M Stone, Life redesigned to suit the engineering crowd. Microbe 1:566, 12/06. Microbe, the news magazine of the American Society for Microbiology, is free online; this item is at forms.asm.org/microbe/index.asp?bid=47155 (HTML) or forms.asm.org/ASM/files/ccLib...1206000566.pdf (PDF).
Craig Venter, of genome sequencing fame, plans to make new organisms. One key step along the way was to take a small bacterium, and determine how many of its -- already small -- gene set are really needed. This sets the stage for making artificial genomes -- and then for designing new organisms to do specific tasks. News has been coming fast and furious from the Venter lab; I list some of the news coverage and some of their own press releases below.
Good news stories:
* Venter Institute team builds M. genitalium genome from scratch (Microbe magazine, April 2008). microbemagazine.org/images/st...0408000162.pdf.
* Countdown to a synthetic lifeform (7/11/07). http://www.newscientist.com/article/mg19526114.000.
* Genetic engineers who don't just tinker (7/8/07). http://www.nytimes.com/2007/07/08/we...ew/08wade.html.
* Tycoon's team finds fewest number of genes needed for life (6/8/07). http://www.guardian.co.uk/science/20...etics.research.
Press releases from the J Craig Venter Institute:
* First Self-Replicating Synthetic Bacterial Cell (5/20/10). www.jcvi.org/cms/press/press-...te-researcher/. Since the terms "synthetic" or "artificial" cells are ambiguous and subject to hype, we should be clear what is accomplished here. They made a synthetic genome; that is, they assembled a new genome without using any natural DNA. They then transplanted this into an existing cell, and the new genome "took over". In this case, the synthetic genome is (substantially) identical to a known genome. That is, this work is proof of principle that a new genome can be made and used.
* Synthetic bacterial genome (1/24/08). www.jcvi.org/cms/research/pro...press-release/.
* JCVI scientists publish first bacterial genome transplantation changing one species to another (6/28/07). www.jcvi.org/cms/press/press-...es-to-another/.
Jay Keasling's work, at UC Berkeley, to develop a cheaper way to make the anti-malarial drug artemisinin is noted in the Malaria section of this page. The work involves making major changes in the metabolic capabilities of the microbes, and is considered synthetic biology.
TGN1412: The clinical trial disaster
March 2006. The news media carried a story of a clinical trial gone terribly wrong. Within an hour or so of receiving a drug, all recipients were seriously ill. What happened? Was there some mix-up -- perhaps the wrong drug used? Was the trial not properly planned or executed? Or was this just "one of those things" -- showing why we start with a small test in humans? So far, the evidence suggests that the last possibility is correct. Everything seems to have been done properly. However, given the severe result in this case, people are questioning whether "properly" was good enough. Was there reason to have been more cautious in this case -- more cautious than just following standard procedure? Perhaps -- and people are debating this. The drug was of a new type, one about which we know little, and about which some are very concerned -- despite the good data from animal tests. It is clear that even a simple precaution, of giving the drug to one patient at a time, and watching them for an hour or two, would have been much better in this case.
As to the nature of the drug, it is hard to describe briefly. But a simple start would be that it was designed to stimulate the immune system -- and the problem is that it did so inappropriately in the human subjects.
The analysis of the incident is still in progress. However, some information is now appearing in the literature, so it seems appropriate to share that here. I do encourage people to be cautious in reaching conclusions at this point.
The New England Journal of Medicine published three articles in the September 7 issue on this topic. In the order listed below: one is a perspective (an overview discussion of the topic), one is the main scientific report, and one is a commentary. All are freely available online. For most people, the first item listed below -- the perspective -- may be the best place to start.
* A H Sharpe & A K Abbas, Perspective: T-Cell Costimulation � Biology, Therapeutic Potential, and Challenges. New England Journal of Medicine 355:973, 9/7/06. http://www.nejm.org/doi/full/10.1056/NEJMp068087.
* G Suntharalingam et al, Cytokine Storm in a Phase 1 Trial of the Anti-CD28 Monoclonal Antibody TGN1412. New England Journal of Medicine 355:1018, 9/7/06. http://www.nejm.org/doi/full/10.1056/NEJMoa063842.
* J M Drazen, Commentary: Volunteers at Risk. New England Journal of Medicine 355:1060, 9/7/06. http://www.nejm.org/doi/full/10.1056/NEJMe068175.
There is also a government report on the incident. I might cynically comment that it reads like a government report. Nevertheless, browsing it may be useful, at least as a guide to the questions that get raised. The final report (December 2006) is at www.dh.gov.uk/en/Publications...ance/DH_063117. (The link to the preliminary version of the report at the end of the Drazen article listed above is now a dead link.)
Vaccines (general)
A general comment and caution... Vaccines seem to be the subject of many controversies. But be particularly careful with any arguments that appear to make criticism of vaccines in general. The diseases against which we have vaccines are diverse, and the vaccines are diverse. Most real vaccine issues are specific to a particular vaccine or type of vaccine.
This section is mainly for sources about vaccines in general, or sources with info about many vaccines. Also see sections for individual diseases for info about specific vaccines. For example, the sections on Anthrax, Ebola, HIV (AIDS), HPV (Human papillomavirus), Malaria, Measles, Polio, Smallpox, and West Nile Virus contain info on vaccines for those diseases. An item listed under Cancer deals with making personalized vaccines in plants.
Added September 21, 2011. VIOLIN -- the Vaccine Investigation and Online Information Network. A broad-based vaccine resource, from the University of Michigan Medical School... http://www.violinet.org.
Added September 8, 2011. A report from the Institute of Medicine (IOM)... Adverse Effects of Vaccines: Evidence and Causality, August 25, 2011. www.iom.edu/Reports/2011/Adve...Causality.aspx. The report addresses numerous possible side effects of vaccines, and tries to analyze whether evidence supports a causal relationship between vaccine and effect. You can download a pdf file of a "Report Brief", or read the report online.
Making a wimpy virus. One approach to making vaccines is to use an attenuated strain of the infectious agent -- one that can induce an immune response, but not cause disease. Scientists at Stony Brook have developed a new approach to making an attenuated virus for use in a vaccine. They re-code the virus so that it uses codons that are poorly translated. They made a few hundred changes in the poliovirus genome, each one making it harder for the genome to function. The result was a virus that seemed to work well as a vaccine strain in mouse tests. A nice feature of this approach is that it would seem to be of general applicability, though of course it needs to be tested in each case. Press release, summarizing the story: "SBU Team Designs Customized "Wimpy" Polioviruses, A Method That Could Be A New Path To Vaccines. Reported in Science, the 'Save' Computer-driven Method Creates a Weakened Synthetic Virus"; June 26, 2008. commcgi.cc.stonybrook.edu/am2...Vaccines.shtml. The paper is: J R Coleman et al, Virus attenuation by genome-scale changes in codon pair bias. Science 320:1784, 6/27/08.
Thimerosal in vaccines. Thimerosal is an organic mercury compound, used as a preservative -- including in vaccines. As with any mercury compound, it is toxic. Of course, the fact that it is toxic is why it is used as a preservative. The intent is that it is more toxic to bacteria and fungi than to humans. The available information suggests that the risks from exposure to mercury from thimerosal are quite small. (Exposures from eating fish and from coal-fired power plants are likely to be larger.) As a precaution -- in the US and Europe -- thimerosal is now rarely used in vaccines intended for children; the common Influenza vaccine is the one prominent exception. Note points of uncertainty, especially regarding children (which is why extra precautions are taken with children), but also note that there is really no data suggesting any problem with thimerosal as used in vaccines.
* This FDA web page is a good overview of the use of thimerosal. It should serve as a good framework for further discussion. http://www.fda.gov/BiologicsBloodVac...fety/UCM096228.
* A new study shows that ethyl mercury, the form of mercury from thimerosal, is eliminated from the body much faster than methyl mercury. (Methyl mercury is a more common toxic form of mercury, and has been used as a frame of reference for discussing thimerosal in the absence of more direct information.) Children getting many vaccines containing thimerosal (in Argentina) do not show elevated blood level of mercury. A press release from the University of Rochester accompanying publication of this work: Babies Excrete Vaccine-Mercury Quicker than Originally Thought, January 30, 2008. http://www.urmc.rochester.edu/news/s...ex.cfm?id=1848. The paper is M E Pichichero et al, Mercury Levels in Newborns and Infants After Receipt of Thimerosal-Containing Vaccines. Pediatrics 121:e208-e214, 2/08. It is freely available at http://pediatrics.aappublications.or.../e208.abstract.
* I have posted a page showing the chemical structure of thimerosal and some related compounds, including aspirin: thimerosal.
* This topic is also listed under Introductory Chemistry Internet Resources: Thimerosal and Introduction to Organic and Biochemistry Internet Resources: Alcohols, ethers, sulfur compounds.
Growing vaccines in plants. Oral, Plant-Based Vaccine against Shiga Toxin Effective in Mice. A news story about this new approach, in Microbe 1:311, 7/06. Microbe, the news magazine of the American Society for Microbiology, is free online; this item is at forms.asm.org/microbe/index.asp?bid=43695.
The article this news story refers to is S X Wen et al, A plant-based oral vaccine to protect against systemic intoxication by Shiga toxin type. PNAS 103:7082, May 2, 2006. Online at http://www.pnas.org/content/103/18/7082.abstract.
National Network for Immunization Information (NNii). An excellent general resource on immunizations. Articles address individual vaccines, and some of the news stories you may hear about them (see Immunization Issues). http://www.immunizationinfo.org/. From their introduction: "The mission of the National Network for Immunization Information (NNii) is to provide the public, health professionals, policy makers, and the media with up-to-date, scientifically valid information related to immunization to help them understand the issues and to make informed decisions. The National Network for Immunization Information (NNii) is an affiliation of the Infectious Diseases Society of America, the Pediatric Infectious Diseases Society, the American Academy of Pediatrics, the American Nurses Association, the American Academy of Family Physicians, the National Association of Pediatric Nurse Practitioners, the American College of Obstetricians and Gynecologists and the University of Texas Medical Branch."
Financing Vaccines in the 21st Century: Assuring Access and Availability, a report from the Institute of Medicine, August 2003. This report discusses policy issues regarding vaccines. The economics of vaccine production are complex, and in some cases not very good. What role should the government play is assuring vaccine availability even when "ordinary economics" might seem to argue otherwise? www.iom.edu/Reports/2003/Fina...ilability.aspx. As with all IOM reports, you can read it online, or purchase it; a short summary is also available online.
The Jordan Report: Accelerated Development of Vaccines, from the NIAID (National Institute of Allergy and Infectious Diseases). 2007. The purpose of the Jordan Report is "to inform policy-makers, researchers and the public about recent accomplishments and future trends in vaccine research." http://www.niaid.nih.gov/topics/hivaids/research/vaccines/reports/Pages/default.aspx; the report is listed near the top, under "Vaccines Reports and Articles - General Reports".
A report from the Institute of Medicine (IOM)... K Stratton et al, Immunization safety review: Multiple immunizations and immune dysfunction, February 2002. http://www.nap.edu/catalog.php?record_id=10306. A short summary is that they found no evidence of vaccine-induced problems, but they also note areas where the evidence is insufficient to reach a conclusion and further study is needed.
West Nile Virus
The Contra Costa Mosquito & Vector Control District (CCMVCD) has a short flier, which it distributes to all county residents, about West Nile Virus. It is written, of course, for the general public, and contains a range of useful information -- about the disease, the virus, and prevention measures. They also have a website, with much useful information: http://www.ccmvcd.dst.ca.us. See menu bar at left for items about West Nile Virus.
California West Nile Virus (and dead bird surveillance) web site, from the state Department of Health Services: http://westnile.ca.gov.
Yellow Fever Virus-based West Nile vaccine edges others protecting horses. Microbe 3:11, 1/08. A news story on vaccine development. A similar West Nile vaccine for humans is under development. Microbe, the news magazine of the American Society for Microbiology, is free online; this item is at: forms.asm.org/microbe/index.asp?bid=55322.
Some scientists now suggest that the West Nile Virus has "settled in" in North America, and probably peaked. That is, they suggest it is likely to stay, but at the generally low levels now observed. Their view is not entirely accepted at this point. A brief summary, West Nile Virus Settled in, but Perhaps No Longer Expanding in the U.S., is in Microbe (Vol 2, p 167, April 2007); it refers to the primary publication. Microbe, the news magazine of the American Society for Microbiology, is free online; this item is at: forms.asm.org/microbe/index.asp?bid=49483.
Case Studies: Diseases
Each of the organisms discussed here challenges our simple views of the microbial world. Many are accommodated easily enough by simply broadening our view a bit. Some may perhaps raise some important questions. Most of these organisms were discovered recently (or at least the key points of interest were discovered recently). That should be a clue that more surprises are likely.
Introduction
This page was written in collaboration with Borislav Dopudja, a third-year science student at the University of Zagreb. It grew out of some casual but extensive discussions we were having exploring some of the oddities of the microbial world, things that don't quite fit with our common views. It seems worthwhile to share some of these. There is no attempt here to be profound, but rather to have some fun enjoying the diversity of the microbial world. Borislav's web site is: www.pluff-sky.net/. I have also listed it, with more information, on my page of Internet resources: Biology Miscellaneous in the Biology: other section.
Terminology
What are "microbes"? Microbes (or microorganisms) are small organisms. For our purposes, that means single-celled organisms. The single cells may be prokaryotic or eukaryotic. The prokaryotic microbes include the bacteria and the archaea (or the eubacteria and archaebacteria, by older terminology). The eukaryotic microbes include the protists (protozoa), the fungi and at least the unicellular algae. The terms are not always used consistently, especially in older literature. Whether viruses should be included is a matter of taste, and I won't be entirely consistent there; for the most part, we will discuss cellular organisms.
Sources
Most of the links below are to web sites that are suitable for "the general audience". A few links to articles from the regular scientific literature are given in small type. In particular, in some cases I have included links to the first reports of these organisms or of key features.
Many links are to Microbe magazine -- or to its precursor, ASM News. Microbe is the news magazine of the American Society for Microbiology. Microbe is written for microbiologists, but written to be enjoyed by a wide range of non-specialists. Both the news stories and feature articles can serve well as readable material with serious scientific content, yet not too technical. Microbe is now freely available online. Links to individual items are given as they come up. If you would like to browse Microbe magazine -- recommended! -- go to http://www.microbemagazine.org/. The current issue will come up; for more, see "Explore Microbe" at the left.
Some links are given to original articles or news stories in Science magazine. Some of these are freely available online, though you may need to create a free registration before getting access to the full text. In general, Science releases research articles -- but not news stories -- for free access 12 months after publication; their file goes back to about 1997. (Those with institutional subscription access, such as those using university computers at UC Berkeley, have full access, and will not be asked to register or log on.) The home page for Science magazine: http://www.sciencemag.org.
Big bacteria
One of the most characteristic properties of bacteria is that they are small. Microscopic. Barely visible under the microscope: we can tell their general shape, but can generally see very little structure. Typical dimensions are on the order of 1 micrometer (1 μm). So, have a look at Epulopiscium and Thiomargarita -- bacteria big enough to be seen with the naked eye. These bacteria -- at least the larger specimens -- approach 1 millimeter (1 mm) in size. One of these was first reported in 1985 -- but not understood to be a bacterium until 1993; the other was first reported in 1999.
Epulopiscium
Epulopiscium grows in the gut of certain fish. It has a complex life cycle, which is coordinated with the daily rhythm of its host. This complex -- and unusual -- life cycle qualifies Epulopiscium for another section of this page: Bacteria that give birth to live young.
• http://microbewiki.kenyon.edu/index.php/Epulopiscium. From the Microbe Wiki.
• www.microbelibrary.org/index....ium-fishelsoni. From the Microbe Library at ASM.
• www.accessexcellence.org/LC/ST/st12bg.php. "Epulopiscium fishelsoni, Big bug baffles biologists!", an essay on this unusual bug, from Peggy E Pollak & W Linn Montgomery, both early investigators of Epulos. (Another Access Excellence page is listed on this page, in the section The biggest microbe?. The Access Excellence site is listed as a general resource on my page of Miscellaneous Internet Resources, under Of local interest... -- since it had its origins near here.)
Cornell researchers study bacterium big enough to see -- the Shaquille O'Neal of bacteria. Press release (May 6, 2008) on new work showing that an Epulopiscium cell contains 100,000 or so copies of its genome, thus has many times more DNA than a human cell. This site is worth it for the pictures alone. The upper picture is a classic, showing an Epulo, a paramecium and an ordinary E. coli bacterium. http://www.news.cornell.edu/stories/...cteria.kr.html. The paper, from Angert's lab at Cornell and collaborators in Australia and New Zealand, is: J E Mendell et al, Extreme polyploidy in a large bacterium. PNAS 105:6730-6734, 5/6/08. Online: http://www.pnas.org/content/105/18/6730.abstract.
The first report of Epulopiscium, describing it as a large and peculiar cigar-shaped organism, presumably a protist: L Fishelson et al, A unique symbiosis in the gut of tropical herbivorous surgeonfish (Acanthuridae: Teleostei) from the Red Sea. Science 229:49, 7/5/85. The abstract is freely available at http://www.sciencemag.org/content/22...08/49.abstract. You may or may not be able to get the full article at that site. If not and you have an institutional subscription to JStor, such as at UCB, try www.jstor.org/stable/1695432.
The definitive report that Epulopiscium is really a bacterium: E R Angert et al, The largest bacterium. Nature 362:239, 3/18/93. http://www.nature.com/nature/journal.../362239a0.html.
Thiomargarita
Thiomargarita can be quite big, but it "cheats". It is mostly vacuole. Why? Well, it is quite like a deep sea diver carrying an oxygen tank. Thiomargarita uses nitrate ions in its respiration, rather than oxygen gas; the vacuole is a supply of nitrate that lets the bug continue to respire at great depths.
Is Life Thriving Deep Beneath the Seafloor? An article from the Woods Hole Oceanographic Institute (WHOI). http://www.whoi.edu/oceanus/viewArticle.do?id=2497. To focus on Thiomargarita, scroll down to "The world's largest bacterium". The article is by WHOI oceanographer Carl Wirsen, April 2004. WHOI microbiologist Andreas Teske was part of the team that discovered Thiomargarita; he is a co-author of the Science paper listed below as the original report.
H N Schulz, Thiomargarita namibiensis: Giant microbe holding its breath. ASM News 68:122, 3/02. The news magazine ASM News -- now called Microbe -- is free online; this item is at newsarchive.asm.org/mar02/feature2.asp (HTML) or newsarchive.asm.org/mar02/images/f2.pdf (PDF). The figure at the right is "Figure 1" from that article. Note the scale bar (which is for part "A" of the Figure); the cells shown are over a half millimeter across.
The original report on Thiomargarita: H N Schulz et al, Dense populations of a giant sulfur bacterium in Namibian shelf sediments. Science 284:493, 4/16/99. It is accompanied by a news story: B Wuethrich, Microbiology: Giant sulfur-eating microbe found. Science 284:415, 4/16/99. The article is freely available at: http://www.sciencemag.org/content/28...3/493.abstract.
Small bacteria
Scientists from UC Berkeley, led by Dr Jill Banfield, have found an archaeon smaller than any cellular organism previously known. It is about 200 nm (0.2 μm) diameter. It is so small that it is very near the "limit" of what people think might be the smallest possible organism. In fact, some people think it might be below that limit! Time will tell whether the new claim is valid. An important issue is whether this is a "complete" organism, or a parasite of some kind that is absolutely dependent on other cells to provide basic functions. This is part of their work on the acidic mine drainage from the Richmond Mine at Iron Mountain, Calif.
Shotgun sequencing finds nanoorganisms. A news release from UC Berkeley, December 2006, on this discovery: http://www.berkeley.edu/news/media/releases/2006/12/21_microbes.shtml. The original report on this tiny organism: B J Baker et al, Lineages of acidophilic archaea revealed by community genomic analysis. Science 314:1933, 12/22/06. http://www.sciencemag.org/content/31.../1933.abstract.
There is another story of small bacteria, a story that has been around for several years but has not really been confirmed. The basic idea is a claim that there are tiny bacteria involved in such processes as calcification of your arteries. These bacteria, which have been termed nanobacteria, are alleged to be even smaller than those discussed above -- far below any reasonable limit of what is "possible" for a living cell. Since these alleged organisms really do not fit in any modern understanding of what cells are, solid evidence is needed -- and is lacking. Two new papers appeared in early 2008 with rather strong evidence that these "things" are not alive. They appear to be some calcium minerals, complexed with protein. They may well be interesting, and they may still be involved in disease processes, but they are not bacteria. The Wikipedia entry is a good introduction to these "nanobacteria" (or "calcifying nanoparticles"), including the uncertainties that surround them. It notes these 2008 papers, and has links to them, and to one good news story on the new findings. http://en.Wikipedia.org/wiki/Nanobacterium.
Bacteria that give birth to live young
Bacteria divide by binary fission: they grow bigger, and then divide in two. But there are exceptions. An interesting type of exception occurs when bacteria seem to give birth to live young. That is, they develop new cells inside, and then liberate these daughter cells. One of the first cases where this type of bacterial reproduction was seen was with Epulopiscium, discussed in the section on Big bacteria. Then it was found in the bacterium Metabacterium -- but in a form that was easier to understand. It has long been known that some bacteria make spores. Specifically, bacteria of the genera Bacillus and Clostridia make "endospores": each cell makes one spore, a resistant structure that is capable of long term survival. Such spore formation does not increase the population, because each cell makes one spore. It merely results in a new type of cell, the resistant spore. But Metabacterium makes multiple spores per cell -- and rarely undergoes the more "ordinary" process of binary fission. Thus a variation of ordinary endospore formation has become the primary means of reproduction. With Epulopiscium, it would seem that this process has been modified further, so that what is produced is not spores but rather ordinary cells -- baby cells.
Thus both Metabacterium and Epulopiscium "give birth to live young" -- a process that can be thought of as a variation of ordinary endospore formation.
Esther Angert, Beyond binary fission: Some bacteria reproduce by alternative means. Microbe 1:127, 3/06: forms.asm.org/microbe/index.asp?bid=41230 (HTML) or forms.asm.org/ASM/files/ccLib...0306000127.pdf (PDF). Angert, at Cornell, works with both Metabacterium and Epulopiscium. She was the first to recognize that Epulopiscium was actually a bacterium.
Metabacterium with four daughter spores. The figure at the right shows a single Metabacterium polyspora cell containing four spores, with the bright appearance that is typical of bacterial endospores. The individual spores are several μm long. The figure is a trimmed version of a figure at: author.cals.cornell.edu/cals/...abacterium.cfm. That page discusses the life cycle of Metabacterium, and how it relates to the natural environment for this organism. It is part of Esther Angert's web site; the home page is author.cals.cornell.edu/cals/...-lab/intro.cfm.
More links for Epulopiscium are in the section on Big bacteria.
Square bacteria
What is the shape of bacteria? Round. Or roundish -- such as rods with rounded ends. Certainly not square, with sharp corners. Imagine then the surprise of the scientist who, in 1980, found square bacteria with sharp corners, in concentrated salt solutions. They are not only square, but very thin -- about 200 nm (0.2 μm) thick. They seem to grow as two dimensional objects, increasing the size of their squares, but not their thickness. Square bacteria caught in the act of division look like a sheet of postage stamps.
Their thinness increases their surface to volume ratio; this may be important in helping them to maintain a proper intracellular environment. They probably spend much energy pumping ions out!
It is not known why they are square or how they achieve their squareness. The square bacteria are archaea. (That was recognized in the original report; at that time, the archaebacteria were considered a type of bacteria, whereas we now consider them a distinct group from the bacteria per se.) They have been named Haloquadratum walsbyi.
The following two links both include good pictures of the square bacteria. The figure at the right is a variation of one shown at the second site, Dyall-Smith's web site.
• Square bacteria grown in the laboratory. Press release, from the University of Melbourne, announcing the first successful growth of the square bacteria in the lab, October 2004. uninews.unimelb.edu.au/news/1855/.
• Web site for Dr Mike Dyall-Smith, group leader for that work: http://www.haloarchaea.com/. The broad topic of the site is Haloarchaea and Haloviruses.
Edwin Abbott would have loved them. http://www.ibiblio.org/eldritch/eaa/FL.HTM. A good read!
Genome paper: H Bolhuis et al, The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity. BMC Genomics 7:169, 7/4/06. Free online: http://www.biomedcentral.com/1471-2164/7/169.
The original report of these organisms: A E Walsby, A square bacterium. Nature 283:69, 1/3/80. It's a delightful little paper, a brief report of a quite unexpected observation. Online: http://www.nature.com/nature/journal.../283069a0.html. Even reading the opening lines, which are freely available there, gives a nice hint of the literary quality of this paper. However, it probably requires subscription for full access.
Microbes with too much DNA
The organism with the largest known genome? Amoeba dubia, a protist. 670 billion base pairs of DNA. That is about 200 times more than we have. What is the significance of this finding? It's not at all clear. In fact, it is hard to even find the source of the number. Is this really a measure of the haploid genome size? Or is it simply based on the cellular DNA content, with the assumption that the cell is diploid? Not only is the original source hard to pin down, there seems to be no modern work following it up. But the number is oft-quoted, so we quote it too. Someday we may understand what it means.
For a nice discussion of genome sizes, see http://www.genomesize.com/statistics.php. Scroll down to the section "A comment on the overall animal range", and what follows, including a nice graph summarizing genome sizes over all types of organisms. This is from T Ryan Gregory, Univ Guelph. Regardless of the ultimate verdict on the Amoeba dubia genome, many organisms have genomes much larger than ours.
In the web page referred to above, Gregory gives genome size in picograms (pg). Biologists often give genome sizes in base pairs (bp). 1 picogram of DNA is about 109 (one billion) base pairs. For example, the human genome contains about 3.5 billion bp, and weighs about 3.5 pg.
Gregory's genome size site is also referred to on my Internet resources - Molecular Biology page, under Genomes, and in the Musings post Who is #1: the most DNA? (March 7, 2011).
Microbes with too many genes
The human genome project brought us the revelation that we have only about 22,000 genes -- not all that many more than a worm (Caenorhabditis elegans, 20,000 genes) or a fruit fly (Drosophila melanogaster, 14,000 genes). Now, Trichomonas vaginalis - a common sexually-transmitted protist (protozoan)... Its genome sequence was reported in January 2007. Preliminary analysis suggests about 60,000 genes.
Don't make too much of this. Gene counts are notoriously difficult, as we learned from the human genome project. Identification of genes simply by looking at DNA sequences is something of an art. In fact, the report offers multiple numbers for the gene count, using different criteria. Of course, I chose the higher one for this note. Further, the significance of the gene count is unclear. We now understand that many proteins can be made from a "single" gene (for example, by alternative splicing). Nevertheless, this stands, at least for now: the most genes known in any microbe, in fact, in any organism. Glossary entry: Alternative splicing.
News story in Microbe, 4/07: "Peculiar" T. vaginalis parasites are jam-packed with genes. forms.asm.org/microbe/index.asp?bid=49481.
Scientists Crack the Genome of the Parasite Causing Trichomoniasis. The press release from the New York Univ School of Medicine, one of the lead institutions for this work. January 11, 2007. http://communications.med.nyu.edu/ne...trichomoniasis.
The report of the Trichomonas genome: J M Carlton et al, Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science 315:207, 1/12/07. Online: http://www.sciencemag.org/content/315/5809/207.short.
Bacteria with "atypical" chromosomes
In the early days, it was very difficult to observe bacterial chromosomes. Bacteria are small, and their chromosomes are quite tiny by comparison with eukaryotic chromosomes. Further, bacterial chromosomes do not condense into more compact and more easily visible bodies, again in contrast to eukaryotic chromosomes. So, information about bacterial chromosomes emerged slowly, with various -- and mostly indirect -- techniques.
The early work suggested that bacteria have only one chromosome, and that it is circular. In one case, one E coli chromosome was even observed -- a circle. Other work seemed consistent with this, so the generality emerged: bacteria have only one chromosome, and it is circular. Both of these features served to distinguish bacteria from the eukaryotes. And that was nice: bacteria are supposedly "simpler", and having only one chromosome is certainly "simpler". Further, having a circular chromosome avoided the difficulties of replicating linear DNA, and could also be considered "simpler".
Alas, it is not really so. Neither feature is universal among bacteria. This web site discusses bacterial chromosomes, and has a table showing the number and type of chromosomes found in many bacteria. http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/chroms-genes-prots/chromosomes.html. From Stanley Maloy, San Diego State University. It is part of a larger site on the broader topic of microbial genetics: http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/.
The following site is from a discussion of bacterial genetics in an online microbiology textbook. I include it here particularly because it contains a nice copy of a very famous figure, which I referred to above. Go to http://www.ncbi.nlm.nih.gov/books/NBK7908/; scroll down to Fig 5.2. This shows a single chromosome of one E coli cell, in the act of replicating. It is clearly circular.
That site is from Chapter 5, Genetics, by R K Holmes & M G Jobling, of the online book Medical Microbiology, 4th edition, edited by S Baron. This online book is listed in the Microbiology: books section of my page of Internet resources: Biology - Miscellaneous. The figure is from John Cairns, Cold Spring Harbor Symposia on Quantitative Biology 28:44, 1963.
Bacteria that can count -- and talk
Some bacteria can emit light -- more or less as fireflies do. The phenomenon is called bioluminescence. But the light from a single bacterial cell would be too dim to be of any use. So, isolated bacteria do not emit light. They only emit light when there are many of them together, so that -- together -- they give off a substantial amount of light. Clearly, bacteria can count how many neighbors they have.
How do bacteria count their population size? The basic logic of how they do it is actually rather simple. To make light, they need an "inducer" -- a substance that turns on the light-producing system. They make an inducer, and secrete it into the external environment. They then take it up from the environment. What does this accomplish? Well, imagine a simple situation of bacteria growing in a test tube. If there are only a few bacteria, there will be little inducer in the tube. When the bacteria try to take up inducer from the environment, they find very little -- and thus they do not emit light. But if the bacteria grow, so that there are many many bacteria in the tube, all making and secreting inducer, then the bacteria find a high level of inducer in the environment; they take it up, and emit light. Thus the bacteria sense their population size by responding to the level of inducer in the medium; as a result, they emit light only when the population size is large.
Is that artificial situation of a test tube of bacteria relevant to the bacteria in nature? Indeed it is. Some fish cultivate these bacteria in a special pouch, called a light organ. The light organ emits light only when it contains enough bacteria to do so usefully.
The phenomenon discussed above is often called quorum sensing. That is, the bacteria check to see if a quorum is present before emitting light. The details of this are now quite well understood. And as the system was being studied, it became clear that it was simply one example of a much wider phenomenon: bacteria communicating to each other, for a range of purposes. In this case, the bacteria are communicating their population size to their own kind. But more broadly, bacteria are signaling their presence -- and numbers -- to other types of bacteria too.
How hot?
What is the highest temperature at which life is possible? We all know that many of the molecules in living systems are quite sensitive to heat; the ease of cooking an egg reminds us of that regularly.
When I was in college, the highest temperature reported for life was around 60° C (degrees Celsius), the maximum temperature (Tmax) for growth of the bacterium Bacillus stearothermophilus. Since then, the known maximum has increased to at least 113° C, and perhaps even to 121° C. This increase came along with the discoveries of an entirely new class of microorganism, the archaea, and of a new geological phenomenon, the deep sea thermal vent; both discoveries date from 1977. Thus the increase in known Tmax for life is not simply an abstract story of some biological limit, but is part of a broad series of major advances in both biology and geology.
Thermus aquaticus has a maximum growth temperature of about 80° C. It was isolated from hot springs in Yellowstone National Park, and was reported in 1969. Thermus aquaticus is perhaps the organism that ushered in the new era of the commercialization of enzymes from thermopiles -- useful precisely because of their heat stability; the "Taq" DNA polymerase made the polymerase chain reaction -- PCR -- practical.
As noted above, 1977 brought the separate discoveries of archaea and deep sea thermal vents. Over the following years, these stories converged, and a succession of hyperthermophilic archaea were discovered near the vents. 1997 brought Pyrolobus fumarii, which grows up to 113° C; this archaeon has been widely accepted as having the highest known Tmax. 2003 brought a report of an archaeon that could grow at 121° C -- the normal operating temperature of an autoclave commonly used to kill even the most resistant forms of life, or so we thought. This organism has been dubbed simply Strain 121 for now.
These continuing discoveries of organisms with ever higher Tmax, maybe even up to the common operating temperature of an autoclave, raise some questions: ... [more]
Derek Lovley's web page (Univ Massachusetts) on the work that led to Strain 121: www.geobacter.org/Life-Extreme.
The first report of Strain 121. K Kashefi & D R Lovley, Extending the upper temperature limit for life. Science 301:934, 8/15/03. Online at http://www.sciencemag.org/content/301/5635/934.full.
For more about Lovley's lab, see "Electricigenic bacteria" in either the Redox section of the page for Internet resources for Intro Chem or the Carbohydrates section of the page for Internet resources for Intro Organic/Biochem.
For an update, see a summary of the Ninth International Conference on Thermophiles (Bergen, Norway, September 2007). T Satyanarayana, Meeting report: Thermophiles 2007. Current Science 93(10):1340, 11/25/07. Current Science, published by the Indian Academy of Sciences is freely available online. This article is at: http://www.ias.ac.in/currsci/nov252007/1340.pdf . The article contains a number of interesting tidbits. They suggest that the finding that strain S121 grows at 121° C has been questioned; they also suggest that another microbe has been shown to grow at 122° C at high pressure. It is normal enough that such claims are questioned. Time will tell. None of these details change the general perspective on high temperature microbes presented here.
Bacteria that know where north is
A microbiologist looks at a sample under the microscope. He notices that the bacteria seem to be moving over to one side of the microscope slide. Why? Perhaps they are responding to the light. So he adjusts the lighting, and it has no effect. After numerous such observations and tests, the conclusion is inescapable: the bacteria go north. Now, that is novel! He looks at the bacteria further, and finds that they contain tiny magnets -- iron oxide magnets, just like simple toy magnets. And that is how magnetic bacteria were discovered -- by Richard Blakemore in 1975.
Why do these bacteria use a magnet to guide their swimming? A common idea -- not entirely accepted -- is that these bacteria benefit from following the earth's magnetic lines of force. Doing that leads them "down" into the mud, which seems good for their lifestyle. Consistent with this, it was soon found that -- for some types of magnetic bacteria -- those in the northern hemisphere swim north, whereas those in the southern hemisphere swim south.
Magnetic Microbes, by Sandi Clement. commtechlab.msu.edu/Sites/dlc.../caOc96SC.html.
Magnetosomes. The figure at the right is from Richard Frankel's page: Magnetotactic Bacteria Photo Gallery. www.calpoly.edu/~rfrankel/mtbphoto.html. The figure shows a single cell of the bacterium Magnetospirillum magnetotacticum, with a chain of magnetosomes. Each individual magnetosome in the chain is approximately 45 nm across, and surrounded by a membrane. The Gallery page listed has many more figures, showing the diversity of magnetic bacteria. And for more, go to Frankel's home page, at Cal Poly San Luis Obispo: www.calpoly.edu/~rfrankel/. Scroll down to Research Interests, then Magnetotactic Bacteria.
R B Frankel & D A Bazylinski, Magnetosome mysteries. ASM News 70:176, 4/04. The news magazine ASM News -- now called Microbe -- is free online; this item is at forms.asm.org/microbe/index.asp?bid=26445.
C N Keim et al, Magnetoglobus, Magnetic aggregates in anaerobic environments. Microbe 2:437, 9/07. Microbe, the news magazine of the American Society for Microbiology is free online; this item is at forms.asm.org/microbe/index.asp?bid=52638. An article about a type of magnetic bacterium that normally occurs in multicellular aggregates. Should this be considered a multicellular bacterial organism? Considering that question gives insight into what multicellularity is about. This article is also listed in the section Multicellular bacteria.
W Hansen, This End Up -- Magnetic organelles point bacteria in the right direction. Berkeley Science Review, Issue 14, Spring 2008, p 8. A brief introduction to work on magnetic bacteria being done by Arash Komeili at UCB. Berkeley Science Review (BSR), published by UCB graduate students, is free online; this item is at sciencereview.berkeley.edu/ar...ticle=briefs_1.
The first report of magnetic bacteria: R Blakemore, Magnetotactic bacteria. Science 190:377-379, 10/24/75. The abstract is freely available at http://www.sciencemag.org/content/190/4212/377.abstract. You may or may not be able to get the full article at that site. If not and you have an institutional subscription to JStor, such as at UCB, try Access to Blakemore article through JStor.
Bacteria that eat other bacteria
The story of predatory bacteria starts with Bdellovibrio, a type of bacterium that obligatory lives within other bacterial cells. Since they kill the bacteria that they infect, Bdellovibrios form clear regions on a lawn of dense bacterial growth, much like bacterial viruses form plaques. But they are not viruses. They are cellular, with rather ordinary bacterial cells. It's just that they grow in a way that we find unusual. Well, it's not the "way" that is unusual as much as it is the "where". They burrow into a bacterial cell, and grow there.
E Jurkevitch, Predatory behaviors in bacteria -- diversity and transitions. Microbe 2:67, 2/07. Microbe, the news magazine of the American Society for Microbiology, is free online; this item is at forms.asm.org/microbe/index.asp?bid=48203.
At the end of the article listed above, Jurkevitch raises an interesting speculation about the possible role of predatory bacteria in the origin of the eukaryotic cell. Biologists agree that the mitochondrion arose from a bacterium that got inside another cell. But how did it get there? Bacteria do not show phagocytosis -- do not engulf other cells. However, predatory bacteria such as Bdellovibrio offer an alternative. Perhaps mitochondria originated by a predation event that led to symbiosis. There is no evidence on this point, so it must be regarded as speculation for now. At least it is a plausible view of how one of the great events of biological history might have occurred.
Multicellular bacteria
Single cells. Grow, and then divide into two. That is our simple image of bacteria. However, as we learn more about this vast group of organisms, we find that bacteria can be more complex. The myxobacteria probably have the most complex bacterial life cycle. They spend part of their life as free-living individual bacterial cells, then aggregate to form a fruiting body, an organized multicellular structure visible to the naked eye. In fact, their life cycle is rather similar to that of the cellular slime molds, such as Dictyostelium -- the myxomycetes.
Myxobacteria web page: http://myxobacteria.ahc.umn.edu/. In particular, step through the section What are the Myxobacteria? for a good introduction with some wonderful pictures. From Dr Martin Dworkin, with the help of Tim Leonard, at the University of Minnesota.
The figure above shows three examples of Myxobacteria fruiting bodies. Each is just under one millimeter tall. The figure is Fig 1 from the Microbe article listed below, and is also shown at the Myxobacteria web page listed above (What Are Myxos? : Part 2). The photos are attributed at both places to Dr Hans Reichenbach.
M Dworkin, Lingering Puzzles about Myxobacteria. Microbe 2:18, 1/07. Dworkin's "puzzles" include:
• How the cells construct the multicellular, macroscopic fruiting body
• The biochemical basis of myxospore morphogenesis
• The mechanism and function of individual cellular motility
• The regulation of directionality of social movement
• The mechanism of the cells' ability to perceive physical objects at a distance
• The role of the myxobacteria in nature.
Microbe, the news magazine of the American Society for Microbiology, is free online; this item is at forms.asm.org/microbe/index.asp?bid=47794 (HTML) or forms.asm.org/ASM/files/ccLib...0107000018.pdf (PDF).
C N Keim et al, Magnetoglobus, Magnetic aggregates in anaerobic environments. Microbe 2:437, 9/07. Microbe, the news magazine of the American Society for Microbiology is free online; this item is at forms.asm.org/microbe/index.asp?bid=52638. An article about a type of magnetic bacterium that normally occurs in multicellular aggregates. Should this be considered a multicellular bacterial organism? Considering that question gives insight into what multicellularity is about. This article is also listed in the section Bacteria that know where north is. Other topics on this page introduce other ways in which some bacteria are more complex that we might have thought. These include:
A huge virus
Ordinary organisms are based on cells. The organisms reproduce by the cells growing and dividing. Viruses are different. Viruses are small and simple. Viruses do not grow and divide. They reproduce by infecting a cell, disassembling, and then directing the production of new "parts", which then assemble into new virus particles.
Small and simple? Well, usually. The smallest viruses have one millionth or so the amount of genome (DNA or RNA) we do. Some have only a handful of genes. Some have only a piece of DNA (or RNA) and a simple protein coat -- no machinery for making anything, and no enzymes.
Some viruses are not so small and not so simple. Biologists have still been able to make a clear distinction between viruses and cells, primarily by looking at their basic strategy for reproduction. Cells grow and divide; viruses disassemble and reassemble.
The most recent challenge to the simplicity of viruses is the mimivirus, which grows in the protozoan Acanthamoeba polyphaga. It has about three times more genetic material (DNA) than any previously known virus -- more DNA than some bacteria. It is bigger than some bacteria -- about 400 nm (0.4 μm) diameter. And it is quite complex, with a collection of enzymes that are supposedly not to be found in viruses. For example, mimivirus codes for several enzymes used in protein synthesis -- genes never before found in any virus. Yet its life style (and structure) make it clear that this is a virus. It was characterized as a virus only in 2003.
2008 brings new developments that make the story of mimivirus even more fascinating. First, a new mimivirus, even bigger than the first. They call it mamavirus. But perhaps more importantly, a satellite virus: a virus that can grow only in cells infected by mimivirus. A news story about this satellite virus, dubbed Sputnik: 'Sputnik' Virus Orbits, Hijacks Other Viruses, Aug. 13, 2008. dsc.discovery.com/news/2008/0...s-sputnik.html.
Discussions about mimivirus and Sputnik inevitably seem to wander onto topics such as "What is a virus?" or even "What is life?" These are fun to discuss, but a caution: they need not have simple answers, or even any answers at all beyond our common definitions. Use such questions to provide a framework for your knowledge and understanding, but forcing simple answers to complex questions is not fruitful. Mimivirus has its own website: http://www.giantvirus.org.
The organism now known as mimvirus was found in 1992. The first paper that identified it as a virus: B La Scola et al, A giant virus in Amoebae. Science 299:2033, 3/28/03. Online: http://www.sciencemag.org/content/299/5615/2033.short.
The report of the Sputnik satellite virus: B La Scola et al, The virophage as a unique parasite of the giant mimivirus. Nature 455:100, 9/4/08. There is a good news story about this finding: Biggest known virus yields first-ever virophage. Microbe 3:505, 11/08. Free online: microbemagazine.org/images/st...1108000502.pdf. Scroll down to the story, on page 4 of the file.
The biggest microbe?
Probably the unicellular green alga Acetabularia, whose cells can be several centimeters long. Because of the large size, Acetabularia was a favorite organism for studying the relationship between nucleus and cytoplasm. The following links introduce the organism and some classic experimental work.
• en.Wikipedia.org/wiki/Acetabularia. Basic introduction to Acetabularia.
• www.accessexcellence.org/RC/V...mmerling_s.php. Classic work on the role of nucleus and cytoplasm in determining cell development, done by J Hammerling in the 1930s. The large cells of Acetabularia allowed a simple but novel transplantation to be done; the results revealed the key role of the nucleus. This item is given as a link at the end of the previous one. (Another Access Excellence page is listed on this page, in the section Big bacteria. The Access Excellence site is listed as a general resource on my page of Miscellaneous Internet Resources, under Of local interest... -- since it had its origins near here.)
Briefly noted
This section is something of a "miscellany" -- a place to briefly note some other unusual aspects of microbial life. In some cases, I may make only a single small point or note only a single paper, Perhaps some of these will grow into "full-blown" topics at some point, or perhaps we will just keep a section of "miscellany".
G forces? Humans don't do well with g forces a few times normal gravity. Microbes do better, it seems. A recent paper shows that several microbes studied, bacteria and yeast, grew in an ultracentrifuge tube with accelerations many thousands of times g. Two of the bacterial grew at the highest accelerations tested, over 400,000 x g. They have no information about what limits the growth as the g force increases; they speculate that it has something to do with sedimentation within the cell. That organisms vary might allow them to pursue finding what is important. It is also unclear why this is of interest. After all, such high g forces are found in nature only under extreme conditions, such as the shock waves of supernovae. For now, this paper is basically just a cute finding. It will be interesting to see where it leads.
Where is the inside? Some bacteria, such as the gram negatives, have a double membrane system. It is the inner membrane that is energized, and used to make ATP. Now we have a discovery of the first double membrane system of an archaeon -- and it is the outer membrane that is energized. The archaeon, Ignicoccus hospitalis, is closely associated with Nanoarchaeum equitans -- which relies on the Ignicoccus for its energy; is this energy parasitism dependent on the unusual energy system of the Ignicoccus? The authors even wonder whether Ignicoccus might be an ancestor of the eukaryotic cell. Clearly, this is an unusual and intriguing finding -- still quite incomplete.
For a fine introduction to this novel system, see the ASM blog entry by Moselio Schaechter... Of Archaeal Periplasm & Iconoclasm (February 11, 2010): http://schaechter.asmblog.org/schaechter/2010/02/of-archaeal-periplasm-iconoclasm.html.
The paper... U Küper et al, Energized outer membrane and spatial separation of metabolic processes in the hyperthermophilic Archaeon Ignicoccus hospitalis. PNAS 107:3152, 2/16/10. Online at: http://www.pnas.org/content/107/7/3152.
Arsenic. There are bacteria that can oxidize arsenic compounds, and there are bacteria that can reduce arsenic compounds. Now there is a report of bacteria that can use arsenite -- AsO33-, containing As(III) -- as the electron donor for photosynthesis. (The most common electron donor is water -- with oxygen gas being evolved. The most common electron donor in anaerobic systems is sulfide, often with sulfur granules being produced.) Analysis of this process suggests that arsenic metabolism is quite ancient, and that it is an important part of the arsenic cycle in nature. News story: In Lake, Photosynthesis Relies on Arsenic, August 18, 2008. http://www.nytimes.com/2008/08/19/science/19obarsenic.html.
The paper... T R Kulp et al, Arsenic(III) Fuels Anoxygenic Photosynthesis in Hot Spring Biofilms from Mono Lake, California. Science 321:967, 8/15/08. Online at: http://www.sciencemag.org/content/321/5891/967.abstract.
Microbes survive the cold. Scientists have recovered DNA and even viable bacteria from ancient ice samples in the Antarctic (and other places). The idea is that bacteria were trapped in the ice, perhaps in pockets of liquid water just big enough for the one cell. The bacteria may have carried out maintenance reactions, perhaps only a few chemical reactions per day, to survive. Even with quibbling about how old each sample really is, this is still a fascinating insight into survival of life in extreme conditions. News story: Eight-million-year-old bug is alive and growing, August 7, 2007. http://www.newscientist.com/article/dn12433.
Here are a couple of papers, both of which should be freely available. The first goes with the news story listed above, and is generally about the isolation of the old bacteria and their DNA. The second, from UC Berkeley, is about how the bacteria may metabolize and survive in the ice.
K D Bidle et al, Fossil genes and microbes in the oldest ice on Earth. PNAS 104:13455, 8/14/07. Free online at: http://www.pnas.org/content/104/33/13455.abstract.
R A Rohde & P B Price, Diffusion-controlled metabolism for long-term survival of single isolated microorganisms trapped within ice crystals. PNAS 104:16592, 10/16/07. Free online at: http://www.pnas.org/content/104/42/16592.abstract.
A lonely bug. Organisms live in complex communities. Seems pretty basic in our modern understanding of biology. Certainly, we expect to find bacteria in complex communities. So, it is striking when we find a report of the discovery of a bacterial growth in a South African goldmine that seems to contain only one species. Of course, it is hard to exclude some very low level of other organisms, but the analysis shows that the main bacterium, called Candidatus Desulforudis audaxviator, is at least 99.9% of the culture.
What is it growing on down there? Well, seems likely that it is using the energy from uranium decay as its main energy source. So this loner is also a nuclear-powered bug.
The paper is: D. Chivian et al, Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth . Science 322:275, 10/10/08. Free online at: http://www.sciencemag.org/content/322/5899/275.abstract. For a good news story about this work, see Journey Toward The Center Of The Earth: One-of-a-kind Microorganism Lives All Alone, 10/10/08: http://http://www.sciencedaily.com/releases/2008/10/081009143708.htm.
More "Curious microbes"
While looking for some nice web sites to include in the various sections above, I came across Sandi Clement's page on Magnetic Microbes listed for Bacteria that know where north is. Turns out that is part of a larger site with a theme rather similar to this one -- and written by students in a class on Extreme and Unusual Microbes taught by Dr. Rick Martin at the Center for Microbial Ecology, Michigan State Univ. The site is called The Curious Microbe - Essays of the Extreme and the Unusual: commtechlab.msu.edu/Sites/dlc...us/cindex.html.
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Introduction
Abbreviations: ESC = embryonic stem cell(s). iPSC = induced pluripotent stem cell(s). Note: usage varies as to whether the C is included with the abbreviation for stem cell terms. That is, some people will say ESC and some will say ES cells.
Why are cloning and stem cells shown as one topic? Because they are closely related in some ways. Both involve dealing with the progress of cells as an organism develops. A fertilized egg cell develops into a complete organism; that egg cell has the capability to replicate -- and to "differentiate" (change) into different kinds of specialized cells (e.g., heart and kidney). These specialized cells are typically unable to replicate much, if at all.
Stem cells are cells that can replicate and can turn into any of some variety of cells. Potentially, stem cells may be useful in replenishing missing or defective cell populations in an organism.
Cloning (in this context) involves growing a new organism from a single cell of an old organism. In part, this requires that the cell used for cloning be able to revert to the "primitive" state typical of an egg cell -- able to replicate and differentiate. This is particularly a challenge if the cell used for cloning is already differentiated. The common form of cloning that is discussed involves "nuclear transfer"; only the nucleus of the cell to be cloned is used, and it is transferred to an egg cell that has been deprived of its own nucleus. That same nuclear transfer procedure has been used in some procedures for making stem cells -- specifically for making embryonic stem cells.
The word "cloning" has various meanings in biology. The general meaning is to make an identical copy of something. Some organisms, such as bacteria, normally reproduce by cloning; they get bigger, then divide in two, producing two identical daughter cells. Some plants can reproduce from pieces of an old plant -- a type of cloning. Those working with DNA refer to cloning a gene -- making many copies of it outside its normal environment. Note that the "nuclear transfer" type of cloning actually does not clone the donor cell, but only its nucleus.
Overview: The view in 2003
This topic was discussed in the BITN class, Fall 2003. This overview section summarizes the class presentation. The original web materials were designed as a supplement to that class presentation. Although the field has advanced -- spectacularly in some cases -- this overview still seems useful. Much of the basic outline is still germane, and it is fun to compare the current scene with this one from only a few years ago.
We started with a general perspective on what stem cells, regeneration, and cloning are about. We discussed how a single cell, a fertilized egg cell, develops into a complex organism, by the dual processes of cell division and differentiation. Both of these processes are highly regulated. It is as important that cells stop dividing as that they divide. We showed an example of how growth factors interact with a receptor that spans the cell membrane to regulate cell growth. (In fact, such a growth factor receptor is the target of the cancer drugs Gleevec and Herceptin, which we discussed last time.) It is a useful generality that cells tend to lose the ability to divide as they become differentiated. Stem cells are a supply of undifferentiated (or partly differentiated) cells that can still divide. Thus stem cells can replenish missing differentiated cells. That happens naturally. The goal of stem cell work, broadly, is to allow us to use stem cells for medical treatment. We discussed one example of stem cell work, which has turned out to be less positive than the initial results suggested. It is important to realize that we are very early in stem cell work. The negatives we talk about do not diminish the potential of the field, but they should make you cautious about simplified summary headlines about stem cell work.
Some of the figures I showed are from Lodish et al, Molecular Cell Biology (4th edition, 2000), or are similar to figures from that book. This book is available online at the PubMed Bookshelf: http://www.ncbi.nlm.nih.gov/sites/entrez?db=Books. Relevant figures include: Fig 8-32 (Preparation of embryonic stem cells); Fig 14-7 (Production of differentiated cells from stem cells; diagram); Fig 24-8 (Formation of differentiated blood cells from hematopoietic stem cells in the bone marrow). For more about this site, which includes a number of free books, see my Internet - Misc; Books section. (If you are already at the PubMed site, choose Books.)
The big news story of the week was the nuclear transplant work from China, done to circumvent a type of infertility due to cytoplasm problems. The basic procedure here is similar to that used for cloning, although "common cloning" uses nuclei from adult cells. A student brought another example of the use of gene chips (arrays) to classify cancer, in this case, breast cancer.
We discussed more of the complexity of the real world of stem cells. We spent much of our time on two examples of how very promising work reported with stem cells has turned out to be more complicated than one might have guessed from the initial report, and certainly from the headlines about the initial report. I emphasize again that I do not mean my presentation on stem cells to be negative about their potential. But I do hope I have de-hyped the work some. There is very little that is well accepted yet, in this rather new field. There is much that is fascinating and exciting.
We then discussed cloning. The area of interest is cloning of mammals from adult cells. We outlined the general procedure of nuclear transfer. We then discussed some recent work which showed problems with cloning. Gene function in developing clones is abnormal, apparently due to failure to achieve proper reprogramming of the transferred adult cell nucleus. Cloning of primates has failed so far; most work has been with rhesus monkeys. Recent work has shown that cell division in this case is quite abnormal, and that this problem is due to certain proteins being missing. These proteins are normally found in the egg nucleus in primates -- and this nucleus is discarded. This same problem is thought to occur with humans; thus we predict that human cloning would not work with current technology. Note that things identified as problems may at some point be solved.
Terminology
Stem cells are commonly classified two ways: by their origin, and by their potency (capability).
Stem cell origin. The most common terms, perhaps, have long been embryonic stem cells and adult stem cells. These terms clearly point to the origin of the cells. The term embryonic stem cells usually refers to a specific procedure for getting stem cells from a particular stage of embryonic development -- one that has been shown to work well. In contrast, the term adult stem cells is general, and encompasses a variety of types of cells. For example, hematopoietic (blood-forming) stem cells and nerve stem cells are both examples of adult stem cells. As these examples illustrate, the "origin" terms are fairly straightforward descriptors. The caution is that the term per se does not imply the characteristics, and we must always be careful to remember that our common views of them may or may not be completely correct. In particular, we should not expect various kinds of adult stem cells to behave similarly.
Stem cell potency. This type of term describes what the cells can do. Common terms include pluripotent, multipotent, and unipotent. These terms represent a hierarchy, from having a wide range of capabilities to having only one possible fate. Pluripotent stem cells can become most anything. Unipotent stem cells are restricted to becoming only one special type of cell. Multipotent cells are somewhere in between. As an example, hematopoietic stem cells may become any of various kinds of blood cells, but not other types of cells.
Relationship between origin and potency. The common view is that embryonic stem cells, from early in development, are undifferentiated, and therefore pluripotent. As development continues, cells differentiate to one or another fate, and become of lower potency. Thus adult stem cells are generally thought to have restricted potency, being either multipotent or unipotent, depending on the specific case.
Differentiation. The broad view in biology is that an organism starts as an undifferentiated (unspecialized) cell (the fertilized egg). As development proceeds, individual cells become progressively more differentiated (specialized). Differentiation is usually thought to be primarily unidirectional, especially in higher organisms. Dedifferentiation refers to the process of becoming less specialized; this is probably uncommon in real life, but we will see that it is an important process in stem cell work. Trans-differentiation refers to the hypothetical process in which a cell that is specialized to be one type changes to become specialized of another type. Whether trans-differentiation actually occurs, either in the animal or in the lab, is a controversial issue.
Caution. Stem cells terms are descriptive. Do not take them as definitive. For example, we have said above that adult stem cells have restricted potency. This fits with our general understanding of how differentiation occurs, and agrees with most of our experiences. But it would be improper to conclude that it must always be so. In fact, people are still exploring and debating the properties of adult stem cells -- in part because there are many types. As always in biology, we must take care to not get trapped in our terminology. Biological phenomena often do not classify as cleanly as we would like, or as early work might suggest.
Gene therapy and stem cells: How are they related?
The short answer is that they are distinct techniques, but they can be combined. Gene therapy involves changing the genetic information in a cell. Stem cells are cells that can divide and differentiate into the desired cell type. It is possible to do gene therapy on stem cells. One approach used in the work on treating muscular dystrophy in dogs was of this type. That work is described below: Muscular dystrophy in dogs.
This section is included on both my pages for stem cells (this page) and for gene therapy.
Induced pluripotent stem cells (iPSC)
The hot new kid on the stem cell block is the induced pluripotent stem cell (iPSC). To understand why this development is so exciting, we need to look at the pro and con of embryonic stem cells (ESC). The big plus of ESC is their versatility -- their pluripotency. They can become any kind of cell -- naturally in ordinary development of the embryo into an adult animal, or in the lab. The big minus is that they are hard to get. Getting ESC requires getting a young embryo or newly fertilized egg. In humans, this is technically demanding, and ethically controversial.
So what are iPSC? Briefly, they are cells with ESC capabilities (pluripotency -- the plus side of ESC), but produced without an egg or embryo (thus avoiding the minus side of ESC).
How are iPSC made? The basic idea is to take cells from an adult -- fully differentiated cells such as skin cells, grow then in the lab and treat them, to induce them to dedifferentiate to an ESC-like state.
Why did people think to try that? Because we know it works. Procedures such as the cloning that created Dolly the sheep do something like this. The nucleus of an adult cell is transferred into an unfertilized egg. The new hybrid cell develops into a new organism, a clone of the animal that donated the nucleus. This process is called somatic cell nuclear transfer (SCNT). We understand that the adult nucleus must first have dedifferentiated into an embryonic-like state. If it can happen in an egg, then maybe we can make it happen outside of an egg -- in the lab.
How is it done? And how did people figure it out? Well, the first thing they did was to examine gene expression in ESC. This gave some hints about which genes were likely to be important. Those genes were then checked more carefully. Turns out, adding about four gene products to the adult cells induces them to become ESC-like -- what we now call induced pluripotent stem cells, or iPSC. It's all fairly new, and there are various procedures that work. People are now trying to refine the procedures.
The original procedures used to make iPSC were not particularly efficient, and some aspects of the procedures were undesirable. For example, one of the genes used to induce iPSC was an oncogene -- a gene known to cause cancer. Interestingly, the initial reports from different labs used somewhat different procedures. So, despite the weaknesses, the procedure seems better than isolating ESC from embryos. Even in the few months since the initial reports of iPSC, there have been reports of work on understanding why it works, why it is inefficient, and developing improved procedures.
Are iPSC really just like ESC? That is still an open question. They seem to be quite similar. In particular, they can be made to produce many cell types, as with ESC. On the other hand, they do not seem exactly like ESC when their gene expression patterns are examined. Remember, not all ESCs are the same. It is probably best at this point to be very cautious. The development of iPSC is an exciting new development, but its potential remains to be seen.
Bottom line, are induced pluripotent stem cells the magic answer we have all been waiting for? Whoa. Patience. It is too early to know. We know only a little about them so far. As noted above, they do seem to have some key characteristics of ESC, but are not identical to ESC. The significance of the differences remains to be understood. Further, one of the early procedures for making iPSC used one gene product that may well cause cancer. Better ways to make them are needed -- and are being worked out. So, let's take this as an exciting development, a good story to follow.
Here are a few papers from the iPSC field. They are in reverse chronological order; if you want to read this group of references in historical order, start at the end of this section.
The difference between iPSC and ESC. Although iPSC show many of the key characteristics of "true" ESC, they usually show some differences, and are variable. This paper does a detailed comparison of iPSC and ESC, and shows that transcription of a particular chromosome region is key to the difference, and that this difference is due to imprinting. This would seem to open the door to understanding the iPSC process better, and also to recognizing "better" iPSC lines. A news story: Gene Silencing May Be Responsible for Induced Pluripotent Stem Cells' Limitations (Science Daily, 4/29/10); http://www.sciencedaily.com/releases/2010/04/100425151134.htm. The paper is M Stadtfeld et al, Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells. Nature 465:175, 5/13/10.
Making human iPSC that cure a disease. They take skin cells from patients with a genetic defect, cure the genetic deficit, and make iPSC. They then show that these stem cells can form hematopoietic (blood forming) cells. They do not yet carry out the final step, showing that these can be used to treat the patient. Press release from the Salk Institute: Genetic Re-disposition: Combined stem cell-gene therapy approach cures human genetic disease in vitro. June 01, 2009. http://www.salk.edu/news/pressrelease_details.php?press_id=360. The paper is A Raya et al, Disease-corrected haematopoietic progenitors from Fanconi anaemia induced pluripotent stem cells. Nature 460:53, 7/2/09.
Making iPSC using only one factor. A German group has shown that a single factor seems to be both necessary and sufficient for making induced pluripotent stem cells -- in one particular case. This is a good step forward both in its practical implications (simplicity, and in avoiding the oncogene factors), and in understanding. Its generality remains to be seen. A news story: Single Factor Converts Adult Stem Cells Into Embryonic-Like Stem Cells. February 5, 2009. www.stemcellresearchnews.com/...asp?a=1571&z=9. The paper is J B Kim et al, Oct4-Induced Pluripotency in Adult Neural Stem Cells. Cell 136:411, 2/6/09.
Disease-specific stem cells. A group at the Harvard Stem Cell Institute (HSCI) used the iPSC technique to make stem cell lines from a number of individuals with a range of genetic diseases, both simple and complex. For now, these lines will be for research. But of course, the dream is that some day it may be possible to make therapeutic cell lines based on disease-specific, or even patient-specific, stem cell cultures. Their press release is: Daley and colleagues create 20 disease-specific stem cell lines - Lines to be part of new HSCI iPS collection available to researchers. August 7, 2008. http://news.harvard.edu/gazette/story/2008/08/daley-and-colleagues-create-20-disease-specific-stem-cell-lines-2/. The paper is I-H Park et al, Disease-specific induced pluripotent stem cells. Cell 134:877, 9/5/08. The PubMed listing, with abstract, is at http://www.ncbi.nlm.nih.gov/pubmed/18691744; a copy of the final manuscript is freely available there.
Understanding and improving the process of making iPSC. The procedure for making iPSC certainly has advantages over the original procedure for making ESC. However, it has its own problems. It is inefficient, and at least some versions of the procedure use a gene that may cause cancer. So, there has been an active effort to understand what is going on during reprogramming, and to find improved procedures. Work at Harvard has made progress. The ease of making iPSC at all has certainly facilitated the work. In this work, they examined the state of the genome and its expression during the reprogramming. As a result of their explorations, they try using a particular drug to aid with the formation of iPSC -- and indeed find that it improves the efficiency. This is rather complex stuff, not easy to read. The main point -- and simple bottom line -- is that they are making progress improving the iPSC procedure. That is very encouraging. Their press release is: Genomic analysis gives new insights into cellular reprogramming - Research uncovers critical events on reverse path from adult to stem cell state. May 28, 2008. http://news.harvard.edu/gazette/story/2008/05/genomic-analysis-gives-new-insights-into-cellular-reprogramming/. The paper is T S Mikkelsen et al, Dissecting direct reprogramming through integrative genomic analysis. Nature 454:49, 7/3/08. There is an accompanying news story by J F Costello, p 45. The PubMed listing for the paper, with abstract, is at http://www.ncbi.nlm.nih.gov/pubmed/18509334; a copy of the final manuscript is freely available there.
Stem cells from skin -- human. The item below this one is about making a type of stem cell with properties similar to those of embryonic stem cells (ESC) starting with skin cells. With mice. Now, similar results have indeed been reported with human skin cells. One group reporting this is the lab of human stem cell pioneer James Thomson, Univ of Wisconsin. Their press release is: UW-Madison scientists guide human skin cells to embryonic state, November 20, 2007. http://www.news.wisc.edu/14474. A news story in Science discusses the Thomson work, plus the similar work from the Yamanaka lab at Univ Kyoto, which was one of the labs that did the mouse work in the next item: G Vogel & C Holden, Developmental biology: Field leaps forward with new stem cell advances. Science 318:1224, 11/23/07. The paper: J Yu et al, Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells. Science 318: 1917, 12/21/07. http://www.sciencemag.org/content/318/5858/1917.abstract.
Stem cells from skin. An announcement that has attracted much attention: three groups reported that they can make a type of stem cell with properties similar to those of embryonic stem cells (ESC) starting with skin cells. If this holds up, it would allow production of the versatile ESC without use of embryos. But a big caution... The work is with mice, and no one yet knows whether it will work with humans. Further, it remains to be seen how well these skin-derived cells really work. That is, the work reported here is an exciting finding, but it is only a "step 1" in what is inevitably a long and complex process. One of the news stories reporting this work: Scientists Use Skin To Create Stem Cells - Discovery Could Recast Debate. June 7, 2007. www.washingtonpost.com/wp-dyn...060601345.html.
Trans-differentiation
The idea of trans-differentiation was introduced in the section above on Terminology. Briefly, it refers to converting one type of differentiated cell directly to another type of differentiated cell. I also noted there that it is controversial. Interestingly, in the month or so since I wrote that section, it has perhaps become less controversial -- in one way.
There is no problem with the idea of trans-differentiation. It is only a matter of showing that it has occurred. And frankly, until recently, preliminary reports of trans-differentiation just did not seem to hold up.
So, what is new? In the previous section, on Induced pluripotent stem cells (iPSC), we noted that they were developed by a specific procedure. The first step was to explore gene expression in the two cell types of interest. In that case, they were the adult cell used to start and the embryonic stem cell, which was the goal. This analysis then prompted some specific work to see which of the differences observed were key to making the cell change from one to the other. A similar approach seems to have led to trans-differentiation. They analyzed gene expression in the two cell types of interest: the starting type of differentiated cell and the desired final type of differentiated cell. They then tested to see which of those differences were key. It worked.
This seems to be an exciting development. However, some cautions are in order -- beyond the simple obvious one that this is a first report, and needs to be confirmed.
* Lest the procedure discussed above sound simple, I should caution that it is not. The list of gene expression differences is not short or simple. It is a lot of work, some of it trial and error, to sort out what is important. Still, the list of gene expression differences is a huge step compared to knowing nothing about the two cell types. Further, as experience is gained, people will begin to predict which differences are more likely to be critical.
* The specific problem addressed was perhaps a simple one: the two cell types involved were related: both pancreatic cells. It remains to be seen how well the approach extends to other cases. On the other hand, the case dealt with here is quite interesting and hopefully useful.
HSCI researchers see major breakthrough. Press release from Harvard, September 11, 2008. http://news.harvard.edu/gazette/story/2008/09/hsci-researchers-see-major-breakthrough/. In this work, they induced one type of pancreatic cell from mice to differentiate to insulin-producing islet cells. The paper is: Q Zhou et al, In vivo reprogramming of adult pancreatic exocrine cells to β-cells. Nature 455:627, 10/2/08.
Blood stem cells (bone marrow, cord blood)
One type of stem cell therapy has been around for a while. Bone marrow transplantation involves treatment with stem cells from the hematopoietic (blood-forming) system, to form a new blood-forming system in the recipient. In modern terminology, this is a use of adult stem cells -- stem cells not only taken from an adult, but which are partly specialized: they are stem cells for the blood system, and they do not change that basic character in this treatment. The method is not without problems, mostly related to the role of the immune system, but it is a long-standing and well-accepted use of stem cells. The work on developing bone marrow transplantation was recognized in the awarding of the 1990 Nobel Prize in Physiology or Medicine to E Donnall Thomas (along with Joseph E Murray) "for their discoveries concerning organ and cell transplantation in the treatment of human disease". See the Nobel site: http://www.nobelprize.org/nobel_priz...990/index.html.
Cord blood. One source of blood stem cells that is becoming very interesting is the umbilical cord. Harvesting of blood from the umbilical cord (or placenta) at birth may provide a source of blood stem cells that the individual can use later in life. These stem cells may also be useful in treating other individuals. One source of good information about cord blood is the National Cord Blood Program Website, from the New York Blood Center. http://www.nationalcordbloodprogram.org/.
Cancer stem cells
Stem cells, broadly, are cells that can divide and then go on to become "something else". Could one have "cancer stem cells" -- cells that can divide, and which are destined to go on to become cancer cells. This possibility is being considered, and is now thought likely to be true for at least some cancers. One implication is that successful treatment must, somehow, remove not only the cancer but the cancer stem cells -- those cells not yet part of the cancer, but destined to take that route. The picture is complicated; some -- but not all -- cancers do seem to have stem cells. And there is some evidence that the presence of stem cells does affect treatment.
A news article about some aspects of cancer stem cells... "Killing Cancer Stem Cells - A new screening method identifies drugs that selectively target these elusive cells in tumors. " (8/13/09.) www.technologyreview.com/biomedicine/23222/.
NIH: Educational sites and reports
Creating a Cloned Sheep Named Dolly -- an introduction to Dolly and to cloning, from the NIH Science Education pages: science-education.nih.gov/hom...hlight=0,dolly. The page also discusses cloning monkeys from embryonic cells -- a result announced at about the same time as Dolly. There are flow charts showing the main steps in the two cloning procedures. For the monkey cloning, the flow chart shows the donor nucleus coming from embryonic cells. The key difference with Dolly is that the donor nucleus came from a cell from an adult animal. The general flow of the cloning procedure is otherwise the same. However, use of adult cells turns out to be a major difference, because of the differentiated state of these cells.
Stem Cell Information -- The National Institutes of Health resource for stem cell research. An educational site on stem cells, from the NIH. http://stemcells.nih.gov/. To start, you might choose Info Center from the top menu bar, near left; then choose Stem Cell Basics.
There are also two NIH Reports listed at the Info Center noted above:
* Regenerative Medicine, 2006. "Written by experts in stem cell research, this report describes advances made since 2001 and outlines the expectations for future developments. It discusses current stem cell biology, not limited to NIH-funded research. Authors explain research using cells from embryos, fetal tissue, and adult tissues."
* Stem Cells: Scientific Progress and Future Research Directions, 2001. Basic background, and discussion of how stem cells might be used.
Human cloning?
In January 2004 we once again hear reports claiming to have cloned humans, or that such work is in progress.
In my opinion, it is extremely unlikely that any of these reports are correct. Further, I believe that is the broad view of the biomedical community.
Why do we take reports of human cloning with such disbelief?
First, as scientists, we find that absolutely no evidence has been presented that any such cloning has occurred. Scientific work progresses by presenting and analyzing evidence. News conferences are not scientific reports. It would be a relatively simple matter to show that a child is a clone of a specified individual, by analysis of the genome. No such analysis, at any level, has been offered.
Second, there are many scientific reasons why cloning work on humans is unlikely. Although several mammals have been cloned, it is still a very difficult process. It is not that the actual operations are difficult, but rather that it is difficult to obtain success. Overall, only around 1% of cloning attempts are successful. Further, cloned animals often show some degree of abnormality. The low efficiency of success and high frequency of abnormalities combine to mean that the chances of producing a normal clone, in any mammal, are extremely low. They also tell us that we lack understanding of some key parts of the process.
In particular, attempts to clone other primates (monkeys) -- still have had only limited success.
Overall, it seems that cloning is a high risk procedure, with more barriers in primates. With that background, it is extremely unlikely that cloning would work with humans (using current procedures). Further, most scientists would argue that there is no basis for even attempting such work with humans.
The idea of human cloning raises ethical questions. It is important to note that there really are two distinct ethical questions here. One is the general question of whether one should clone humans at all. The second is whether there is sufficient knowledge about cloning at this point to allow extension of the procedure to humans. My usual approach at this site is to emphasize the scientific issues, not the ethical issues. However, a reasonable interpretation of my discussion above of the scientific background is that it would be inappropriate to do cloning experimentation on humans at this point, given what we know about the process.
Human cloning: can it be made safe? An article by S M Rhind et al, Nature Reviews Genetics 4:855, 11/03. An overview of issues concerning human cloning; the authorship includes Ian Wilmut, head of the pioneering team that made Dolly. Some of the content is too technical for the general audience, but browsing it should yield much that is accessible and of interest. It includes some nice figures, including a flowchart comparing therapeutic cloning and reproductive cloning.
Scientific and Medical Aspects of Reproductive Cloning. Report from the National Academy of Sciences (NAS); 2002. http://www.nap.edu/catalog.php?record_id=10285
Human Cloning and Human Dignity: An Ethical Inquiry. Report from The President's Council on Bioethics (the Kass commission, on stem cell research); July 2002. Now archived at: http://bioethics.georgetown.edu/pcbe/reports/cloningreport/
Beyond Therapy: Biotechnology and the Pursuit of Happiness. Report from The President's Council on Bioethics (the Kass commission, on stem cell research); October 2003. Now archived at: http://bioethics.georgetown.edu/pcbe/reports/beyondtherapy/.
Book. Leon Kass (then head of President Bush's bioethics commission; see above) has written a book: Life, liberty and the defense of dignity - The challenge for bioethics. Encounter Books, 2002. ISBN 1-893554-55-4. I have not seen the book, but there is a review of it in Science 298:2335, 12/20/02, by O O'Neill. The review gives an idea of the issues that Kass presents. For those with subscription access, the review is online at http://www.sciencemag.org/content/29...2335.1.summary.
Miscellaneous (books, web sites, comments)
I have thought about trying to subdivide the following collection. But the topics are so interrelated that it is really hard to do so. So, browse! Stem cell work is mixed here with cloning work -- and some involves both. Some resources here emphasize scientific issues, some emphasize ethical issues, and many consider both.
Most books listed here are also listed on my page Books: Suggestions for general reading.
Book. Michael Bellomo, The Stem Cell Divide: The facts, the fiction, and the fear driving the greatest scientific, political, and religious debate of our time. Amacom, 2006. ISBN 978-0-8144-0881-0. A short overview of the stem cell issues. The emphasis is on the broad picture, both in terms of the biology and the social perspective. The book is new enough to deal with the California Stem Cell Initiative and the fall of Hwang. This may be a good place to start for some people looking to get a sense of the stem cell landscape. Also see Sott, 2006 (next item), for more, especially on the biology.
Book. Christopher Thomas Scott, Stem Cell Now - From the Experiment That Shook the World to the New Politics of Life. Pi Press, 2006. ISBN 0-13-173798-8. A stem cell primer, for the general audience. It starts with basic biology, and describes the types of stem cells. It then describes some of the types of work being done with stem cells, and finally the moral and political debate. Scott is obviously an advocate of stem cell work, but strives for balanced presentation of controversies. The best part of the book, for many, will be the basic biology in the first chapters. Also see Bellomo, 2006 (just above); Bellomo may be a less technical introduction to stem cells.
Book. Ian Wilmut & Roger Highfield, After Dolly: The Uses and Misuses of Human Cloning. Norton, 2006. ISBN 0-393-06066-7. Ian Wilmut was the head of the team that cloned Dolly the sheep. Here Wilmut teams with a science journalist to tell two interwoven stories. One is the story of how Dolly came to be, and the other is Wilmut's views of the social issues he has encountered -- and those that are in front of us, especially with regard to human cloning. The story of Dolly is superb -- told by a person who was at the center of it. Wilmut includes the historical background on which the Dolly work built. I found Wilmut's discussion of the social issues somewhat less interesting. He raises good questions, but tends to provide the simple pat answers one might expect from a scientist who is pioneering in the field. That's fine, but it does not add much. Certainly one should not go away simply accepting Wilmut's answers -- or those of any single individual. Perhaps his views will stimulate serious thought on the matter by some. Fortunately (for me), the bulk of the book was on the Dolly story and its background. The level is suitable for general reading.
Book. Stephen S Hall, Merchants of Immortality - Chasing the dream of human life extension. Houghton Mifflin, 2003. ISBN 0-618-09524-1. This is a book by a journalist, not a scientist. It tells the story -- or is it stories? -- of developments in the related fields of aging (especially the hype about telomerase), cloning and stem cells. Much of it focuses on Michael West and a couple of his companies -- including the Bay Area company Geron, a pioneer in aging work. The book has little scientific depth, but the science is rather good so far as it goes. The subject matter of the book has been major grist for news over recent years, and the social issues remain unresolved. In fact, the scientific issues largely remain unresolved. Hall takes the story into 2001 and even 2002. I think this book can be a good introduction to cloning and stem cells, with a little science and a good sense of the public debate. This book is also noted in the section for the topic Aging.
Article. J B Gurdon & J. A. Byrne, The first half-century of nuclear transplantation. Proc Natl Acad Sci 100:8048, 7/8/03. Free online at: http://www.pnas.org/content/100/14/8048.abstract. A short overview of the history.
An informational site on stem cells from the Univ of Michigan. The tutorials will introduce you to the types of stem cells, and to potential applications. http://www.umich.edu/stemcell/
Upon the death of Dolly, Nature put up a special "web focus" site, Dolly the sheep. It includes all relevant publications in Nature journals. http://www.nature.com/nature/dolly/index.html
Nature also has special web sites on stem cells.
http://www.nature.com/stemcells/index.html (2009)
http://www.nature.com/nature/focus/s...ars/index.html. 25 years of Embryonic Stem Cells. (June 2006)
http://www.nature.com/nature/focus/m...lls/index.html. Making Stem Cells. (October 2005)
http://www.nature.com/nature/focus/s...lls/index.html. Riches in stem-cell niches: Bone marrow niches, Neural stem cell niches, Drosophila germ cells. (June 2005)
http://www.nature.com/nature/stemcells/index.html (June 2002)
Access to Nature web sites may be incomplete, unless you have a subscription (perhaps through your university). In any case, even partial access is probably "useful".
Do No Harm, from The Coalition of Americans for Research Ethics. A site from an organization opposed to research on embryonic stem cells. http://www.stemcellresearch.org
Tissue engineering - and stem cells. Tissue engineering is the construction of artificial tissues. Stem cells might be one source of cells for getting started. There is a nice intro to this in The Scientist for Oct 6, 2003 (Vol 17 #19): A Constans, Body by science, p 34. http://classic.the-scientist.com/art...display/14154/
Then, on Oct 28 the following news story showed up in my daily news feed, Science in the News, from Sigma Xi:
STEM CELLS GROWN INTO TISSUES from The Boston Globe
MIT scientists today reported the first known success in using human embryonic stem cells to grow primitive versions of human organs and tissues. They say this represents a promising step toward the development of lab-engineered tissues that could one day eliminate some organ shortages.
The researchers, led by Robert Langer, created structures resembling young cartilage, liver, and neural tissues by growing cells on biodegradable polymer scaffolds -- spongelike structures that resemble the shape of the organ to be created. The scientists also exposed the cells to several hormones that normally stimulate the growth of these organs during embryonic development.
The newly forming tissues were implanted in mice whose blood vessels began to grow into the lab-made tissues, supplying oxygen and nutrients needed for further growth. http://www.boston.com/news/nation/ar..._into_tissues/
Guidelines for Human Embryonic Stem Cell Research, from the National Academies Press, 2005: http://www.nap.edu/catalog.php?record_id=11278. Includes a link for a 2007 "Amendment".
California Institute for Regenerative Medicine, California's new home for stem cell research not supported by the usual procedures of federal funding: http://www.cirm.ca.gov/. (The CIRM was established by the voters of California, in Proposition 71, November 2004.)
Vet-Stem.Inc, a company for "Regenerative Veterinary Medicine"; they provide stem cell treatments for horses. http://www.vet-stem.com. I post this as something of a curiosity, without any judgment on how well documented their technologies are. They do post a reference list, with abstracts, but I have not tried to evaluate how close their services are to what has been shown to be useful.
The original paper on human embryonic stem cells -- from 1998: J A Thomson et al, Embryonic stem cell lines derived from human blastocysts. Science 282:1145, 11/6/98. Free online at: http://www.sciencemag.org/content/28.../1145.abstract.
Recent items, briefly noted
CAUTION. A single report does not a truth make. Stem cells are an area of active work. Many people are trying many things. I will note here some interesting reports. But these are not final answers. Sometimes such reports turn out to not be reproducible, or not due to what the original authors thought. Or even if true, they may not work in humans. Etc etc. This is all part of the normal process of developing new things. Each breakthrough begins with a simple preliminary step. Some of these hold up, some do not. So, here are some news stories -- of various steps along the way.
Cloning of a camel. A cloned camel was born recently. News story... Scientist: First cloned camel born in Dubai. April 14, 2009. www.signonsandiego.com/news/2.../?zIndex=82237.
Cloning of an extinct animal. Cloning can be done from a dead animal -- if genetic material is available. Simplest is to have well-preserved cells from the donor. In this case, the animal was not only dead, but extinct. The donor cells were from the last known specimen of the animal; samples had been taken the year before its death. Cloning "worked"; a live specimen was born. However, it died a few minutes after birth, due to a birth defect. Such defects are not uncommon in cloning, and are probably due to imperfect reprogramming of the genome during the cloning process. Nevertheless, the work is symbolically of interest. News story: Extinct ibex is resurrected by cloning -- An extinct animal has been brought back to life for the first time after being cloned from frozen tissue. Feb 4, 2009. http://www.telegraph.co.uk/science/s...y-cloning.html.
Cloning of prize horses. A Texas company, ViaGen, in collaboration with Texas A&M University, has cloned a prize show horse. The clone will be used as stud, not as a performer. Thus the clone will pass on the genes of the prize horse. An interesting development. (Apparently, use of clones is forbidden for thoroughbred race horses, by regulation.) News story: Cloned horses could offer insight into DNA possibilities; January 2009. It appeared originally in The Philadelphia Inquirer, and is now available at http://www.physorg.com/news152115527.html.
Myelination of nerve cells. Myelin is the coating around nerve cell axons; it serves as a type of insulation. Numerous diseases, in man and mouse, involve defective myelin formation. Here, they treat mice that have a myelin deficiency with a special population of nerve stem cells, isolated from human fetal tissue. The treated mice show improvement at two levels. At the cellular level, there is myelin formation. However, even more importantly, at the animal level, there is improved survival of the mice. The survival is an improvement over previous such work, and they attribute the improvement to various specific technical improvements. Still, fewer than 1/4 of the treated mice survived. Thus the work shows both improvement and limitation; much more is to be done before trials with human children. A press release from the University of Rochester, June 4, 2008: Human Stem Cells Show Promise Against Fatal Children's Diseases. http://www.urmc.rochester.edu/news/s...ex.cfm?id=2025. The work is published: M S Windrem, Neonatal Chimerization with Human Glial Progenitor Cells Can Both Remyelinate and Rescue the Otherwise Lethally Hypomyelinated Shiverer Mouse. Cell Stem Cell 2:553-565, 6/08.
Insulin-producing cells. An obvious target for stem cell work has long been to make insulin-producing cells to treat Type 1 diabetes. But it has proved difficult. Here, a group at Novocell (now Viacyte) reports significant progress: they use insulin-producing cells derived from human embryonic stem cells to successfully treat mice, in a model system. As always, it remains to be seen whether this work translates to real humans. Their press release is: Novocell Reports Successful Use of Stem Cells to Generate Insulin in Mice, February 20, 2008. www.viacyte.com/news/press/2008-2-20.html. The work is published: E Kroon et al, Pancreatic endoderm derived from human embryonic stem cells generates glucose-responsive insulin-secreting cells in vivo. Nature Biotechnology 26:443, 4/08.
Jose Cibelli, Developmental biology: A decade of cloning mystique. Science 316:990, 5/18/07. A nice overview of the field, on the occasion of the tenth anniversary of Dolly. For those with subscription access, it is online at http://www.sciencemag.org/content/31...27/990.summary. A general conclusion is that the process is still very inefficient and often produces animals with abnormalities; we don't know why.
Mice with neurodegenerative disease. The work here is on Sandhoff disease -- or rather a mouse model of it. This is a serious neurodegenerative disease, of the type commonly called lysosomal storage diseases. In the mouse model, they show that mouse neural stem cells provide some benefit to the mouse patient. They also show that human neural stem cells, ether primary or based on embryonic stem cells, work in the mice. A news story: Burnham team is successful in stem cell study. legacy.signonsandiego.com/uni..._1m12stem.html. The work was published: J-P Lee et al, Stem cells act through multiple mechanisms to benefit mice with neurodegenerative metabolic disease. Nature Medicine 13(4):439, 4/07.
Muscular dystrophy in dogs. Duchenne muscular dystrophy is a muscle weakness, caused by loss of functional dystrophin protein. A dog model of the disease is available. A European collaboration, led by Dr Giulio Cossu of the Univ of Milan, has shown some promising results treating the dogs with stem cells. They use a special type of stem cell, isolated from blood vessels, that is capable of differentiating into muscle cells. They take two approaches. In one approach, they use stem cells from a healthy donor; in this case, the stem cells contain a normal copy of the dystrophin gene, but immunosuppression is required. In the other approach, they use stem cells from the afflicted dog, and use gene therapy to provide these stem cells a new dystrophin gene. The latter approach avoids the problem of immunological rejection. However, the dystrophin gene is huge, and it is currently possible by gene therapy to provide only a fragment of the protein; that fragment has only partial function. Both approaches show some encouraging results -- and limitations. Logically, the approaches might reasonably work with humans, but that remains to be tested. A news story... Muscular Dystrophy: Stem Cell Help? Stem Cell Treatment Shows Potential in Lab Tests on Dogs. http://www.webmd.com/parenting/news/20061115/stem-cell-help-for-muscular-dystrophy. The work was published: M Sampaolesi et al, Mesoangioblast stem cells ameliorate muscle function in dystrophic dogs. Nature 444:574, 11/30/06. Accompanying news story: J S Chamberlain, Stem-cell biology: A move in the right direction. Nature 444:552, 11/30/06. Online: http://www.nature.com/nature/journal...ture05282.html and http://www.nature.com/nature/journal...ture05406.html.
Stem Cell Experiment Yields Heart Valves. "Scientists for the first time have grown human heart valves using stem cells from the fluid that cushions babies in the womb - a revolutionary approach that may be used to repair defective hearts in the future. The idea is to create these new valves in the lab while the pregnancy progresses and have them ready to implant in a baby with heart defects after birth." The procedure uses fetal stem cells isolated from the amniotic fluid. From Simon Hoerstrup, University of Zurich. Press release, November 17, 2006, based on a meeting presentation: http://www.nytimes.com/2006/11/18/he...erland&emc=rss. The work was later published as: D Schmidt et al, Prenatally fabricated autologous human living heart valves based on amniotic fluid-derived progenitor cells as single cell source. Circulation 116:I-64, 9/11/07.
Stretching bone marrow stem cells pushes them towards becoming blood vessels, a UC Berkeley press release (Oct 23, 2006) about work from the lab of Dr Song Li and his students, in the Dept of Bioengineering and Center for Tissue Engineering. Their goal is to take stem cells and get them to differentiate in vitro into muscle tissue, which can then be used to repair damaged blood vessels. They explore the effect of physical stresses on the fate of stem cells. In particular, they show that the direction of stretching forces can affect how the cells develop. The press release is at: http://www.berkeley.edu/news/media/releases/2006/10/23_stretch.shtml. The publication referred to is K Kurpinski et al, Anisotropic mechanosensing by mesenchymal stem cells. PNAS 103:16095-16100, 10/31/06. Online at: http://www.pnas.org/content/103/44/16095.abstract.
A fascinating story about repair of damaged hearts has been developing over the last few years. This may be a good stem cell story -- or it may not be. Briefly... Injection of bone marrow cells (stem cells from the blood-forming system) into a damaged heart leads to a small improvement in heart function. Results from work with model animals were sufficiently encouraging that trials with humans have been done. One interpretation is that the bone marrow cells are changing to become heart muscle cells (more precisely, are changing to allow heart muscle cells to develop). Unfortunately, attempts to show that this happens have all failed. Yet the effect remains -- maybe. It is a very small effect, and is not seen in all experiments. So we have a tantalizing mystery. There seems to be something good happening -- though even that is not entirely for sure. And why it is happening is not clear at all. The following article is an editorial accompanying three reports of clinical trials in humans: A Rosenzweig, Cardiac Cell Therapy - Mixed Results from Mixed Cells. N Engl J Med 355:1274, 9/21/06. Free online at: http://www.nejm.org/doi/full/10.1056/NEJMe068172.
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A major news story over recent years has been the announcement of the genome sequence for humans. In fact, this project reached a symbolic completion point in April 2003. But this human genome work is just part of a much bigger story -- which includes a list of many completed genomes, for microbes, plants and animals. All this genome work is just the beginning; genome information alone does not solve anything in particular; it is a big resource that will make further biological work easier.
Introduction
Two major news stories of 2003 set the background for this discussion. One is the 50th anniversary of the announcement of the double helical structure of DNA. The other is the announcement of the completed DNA sequence for the human genome. We discussed the development of the DNA structure. A key idea that emerged from this is the complementarity of the two DNA strands. This complementarity immediately suggests how DNA replicates -- by the two strands separating and each serving as a template for a new strand. The resulting "daughter" DNA molecules have one "old" strand and one "new" strand. A physical test of replicated DNA, showing this characteristic, was key in "proving" the basic DNA model. There is much chemical complexity to DNA and much biochemical complexity to how DNA really replicates, but the basic logic of a double stranded structure held together by complementarity still holds.
We then discussed DNA sequencing. We started by looking at some simple DNA sequencing results -- and showed how easy it is to actually read the sequence. Of course, what we looked at is the end step of a lengthy series of steps. We discussed an example of how one might generate the pattern we saw on the sequencing film; our example was not what is actually done, but was a simpler variation to illustrate the logic. The main problem with this basic sequencing procedure is that it works for only about 500 bases. Thus sequencing larger genomes requires some additional work, but it is still based on the same classical procedure that we started with. For large genomes, the process is highly automated, including the use of lasers to read dye-coded bases. Further, tremendous computer capability is needed to keep track of the data from the millions of pieces of DNA that are individually sequenced.
We discussed the gene count for humans. It is rather low -- and also uncertain. It is uncertain because we actually have considerable difficulty recognizing genes simply from DNA sequences, especially for complex organisms. The low gene count is forcing us to emphasize complexities in gene function, such as splicing and editing, that allow more than one protein to be made from a gene. We then discussed applications of genome information, especially of genome differences between individuals. These include applications such as forensic testing and paternity testing, which were developed some time ago. We discussed some drugs which are chosen based on specific genetic characteristics -- either of the individual, or even of the particular cancer. We then discussed more recent work, using gene chips (microarrays), where analysis of many genes allows leukemia (or leprosy) sub-types to be recognized. The specific figure that I showed was from a recent supplement to The Scientist: New Frontiers in Cancer Research, Sept 22, 2003. One topic that came up during general discussion was prions; I now have a page on prions.
An introduction to DNA: basic structure and how it replicates
The human genome is made of DNA -- as is the genome of almost all organisms. (A few viruses use the closely related chemical, RNA, for their genome; RNA operates by the same basic principles as DNA in this role.) A major milestone in the history of DNA is being celebrated in 2003 (the year this page was started)... It was fifty years ago, April 1953, that Watson & Crick announced that they had determined the structure of DNA -- a structure that in fact "made clear" how it works.
The Fig at the left is a diagram of the general structure of DNA. It shows the famous overall double helix. And it shows the four bases (A, T, G and C) -- which are the "information". At each rung along the DNA ladder is a base pair. Each pair is either A with T or G with C; that is, one strand precisely determines the other strand -- and that indeed is the key to how DNA replicates. See next Fig.
This Fig is from the Glossary of the NIH genome site, www.genome.gov/glossary/index.cfm?. Choose deoxyribonucleic acid (DNA). Also see next Fig.
The Fig at the left is a diagram of DNA replicating. The top of the Fig shows a "parental" DNA molecule; the bottom shows two "daughters". During DNA replication, the two parental strands separate, and each serves as the template for a new strand, which is made by those simple base pairing rules (A-T and G-C), which were mentioned with the Fig above.
In this Fig, the "replication fork" (the site and apparatus for making new DNA) is moving upward.
This Fig is also from the Glossary of the NIH genome site, www.genome.gov/glossary/index.cfm?. Choose DNA replication.
Good overview of DNA, by David Goodsell. This is a "Molecule of the Month" feature at the Protein Data Bank. http://www.rcsb.org/pdb/101/motm.do?momID=23. For more, see ndbserver.rutgers.edu/education/index.html. This is from the educational resources of The Nucleic Acid Database Project at Rutgers.
Commemorations of the 50th anniversary of the Watson-Crick DNA structure
The double helix structure was published by Watson and Crick in 1953 in the journal Nature. 2003 is the 50th anniversary of that landmark, and there are many commemorations. The January 23, 2003, issue of Nature has a big feature on this. It includes an introductory article (Nature 421:310), copies of the original papers on DNA structure, and many articles discussing various aspects of the DNA story. And then there is more in the April 24, 2003, issue. This includes an article (Nature 422:835) by Francis Collins et al on the future of the human genome project. Fig 1 of that article is a fold-out timeline "Landmarks in Genetics and Genomics"; this is available as a pdf file from the Nature web site. At least some of this material could be usefully read or browsed by those with little background in the field.
* Nature is available online at http://www.nature.com/index.html.
* The Nature "web focus" Double helix: 50 years of DNA ... http://www.nature.com/nature/dna50/index.html.
* A Nature News Special on the DNA Anniversary ... http://www.nature.com/news/specials/dna50/index.html.
Among other web sites that resulted from the commemoration of the DNA anniversary...
• The Cold Spring Harbor Laboratory (long headed by Watson) proclaimed itself the Official Site of the 50th Anniversary of the DNA Double Helix. They no longer maintain the anniversary celebration page, but they have much about DNA... Go to the Dolan DNA Learning Center: http://www.dnalc.org/websites/. Sections of interest there include DNA from the Beginning and DNA Interactive -- and more (from "websites" list at the left). Also, choose the "Resources" section (top menu) and find The Biology Animations Library, with DNA methods such as PCR and Southern blotting. DNA from the Beginning is also available in Chinese, Danish, French, Icelandic, Italian, Portuguese (with German, Spanish promised soon); it is also listed for Molecular Biology Resources: Methods. Another section, Inside Cancer, is listed for BITN Resources: Miscellaneous -- Cancer.
• And from our local Exploratorium: http://www.exploratorium.edu/origins/. Choose Cold Spring - DNA.
The human genome
The human genome was officially announced in February 2001 by two groups.
The main genome articles are probably too technical for most, but the issues contain many news stories dealing with various aspects of the project.
The Human Genome. A genome site from the Burroughs Wellcome Trust, which supported much of the British part of the genome project. genome.wellcome.ac.uk/. Includes a range of information at various levels, including for the general public.
Nature: Human Genome Collection. http://www.nature.com/nature/supplements/collections/humangenome/index.html. Links to all human genome work from Nature journals. Much consists of the technical articles, but there are also news stories and discussions.
Neandertal genome. February 2009 brings the announcement of a genome sequence from a 38,000 year old Neandertal. It is actually fairly rough at this point, but it is a remarkable achievement to get this far. There is little to conclude for now, except that the genome evidence so far provides no evidence for interbreeding between Neandertals and modern man (Homo sapiens).
Genome results are so important and fascinating that rodents have been seen scrutinizing their genome data. http://news.bbc.co.uk/2/hi/science/nature/424076.stm. (My main purpose in giving this link is for the Figure, for fun. But the work described there is an example of moving a gene from one organism to another, and using that as a tool to learn about the characteristics of an organism.)
Examples of how genome information is useful
As noted earlier, the genome is just data. It is not the magic solution to anything in particular. Because the genome data is fairly new, in fact few practical advances can be directly attributed to it. So, much of what I do here is to show how genome info might be used.
Pharmacogenomics and nutrigenomics. Traditional recommendations about proper nutrition and medicine assume that the population is uniform. Data is collected about population averages and this is used to guide medical treatments and nutritional advice. But we are not all the same. In fact, some examples of genetic differences in how we respond to drugs or nutrients have been found, more or less accidentally, in the past. The availability of complete genome information will allow such knowledge to come more rapidly. Briefly, pharmacogenomics is the customization of drug usage depending on an individual's genetic makeup; nutrigenomics is the analogous customization of nutrition information depending on an individual's genetic makeup.
The following two items are major nutrigenomics sites:
* The Center of Excellence for Nutritional Genomics at UC Davis, supported by the NCMHD (National Center for Minority Health and Health Disparities, part of the NIH) : nutrigenomics.ucdavis.edu.
* The European Nutrigenomics Organisation (NuGO): www.nugo.org/everyone/. In particular, see their page www.nugo.org/nip/ for the Nutrigenomics Information Portal, then choose Research. Also, they have an electronic newsletter. You can read it online, or sign up to receive it by email; choose NutriAlerts from the "NuGO sites" menu at the left (of either of those pages).
The two sites above are also listed on my page Further reading: Medical topics, under Web Sites. A specific page of the NuGO site, on Adipose Tissue, is listed for Organic/Biochemistry Internet resources, under Lipids.
The Future of Nutrigenomics - From the Lab to the Dining Room. A brochure for the general public, from the Institute for the Future. March 2005. www.iftf.org/node/773.
Cancer. Two articles on work to classify cancers by gene expression patterns. This work has implications for customizing treatment. A Gianella-Borradori et al, Reducing risks, maximizing impact with cancer biomarkers and B A Maher, The makings of a microarray prognosis. The Scientist Mar 15, 2004, pp 8 & 32.
Race. Is "race" a useful criterion for guiding medical treatment? The important point for us here is that genomics is offering new insight into this socially-charged question. At this point, genetic analysis suggests that there are some genes that reflect "geographical origin", but that the variability of human genomes within any "race" is far more than the genetic differences between "races". Of course, this information will be of more practical use as details emerge.
The following New York Times article discusses a clinical trial of a drug that is being targeted to and tested with only one racial group -- with the approval of the FDA. U.S. to Review Heart Drug Intended for One Race, June 2005. http://www.nytimes.com/2005/06/13/bu.../13cardio.html.
The following two short essays are by scientists discussing the race issue:
• M W Feldman et al, A genetic melting-pot. Nature 424:374, 7/24/03. A "Concept essay".
• S B Haga & J C Venter, Genetics: FDA races in wrong direction. Science 301:466, 7/25/03. "Policy forum". This article explicitly addresses -- and questions -- FDA guidelines for collecting racial data in clinical trials.
Personalized medicine. There are now companies that will take your DNA (and some money) and report back to you your risk for certain diseases. A good idea in principle, but how good is it in practice. Genome pioneer Craig Venter and colleagues have evaluated a couple of these companies, and offer some suggestions. As a general perspective, they think the companies are doing high quality work, technically, but the quality and usefulness of the information is questionable. It is true that your DNA contains information about disease susceptibility, but current knowledge of that is limited -- more limited than the companies want to admit. The paper is: P C Ng et al, An agenda for personalized medicine. Nature 461:724, 10/8/09. The paper seems to be freely available via the web site of the Venter Institute. Go to their page of press releases: www.jcvi.org/cms/press/press-releases/. Scroll down to the item for October 7, 2009. Click on its link; it takes you directly to the article at Nature. This probably means that the article is freely available directly from Nature.
Added May 7, 2011. There are many Musings posts in the broad area of personalized medicine. One of the first was: Personalized medicine: Getting your genes checked (10/27/09). It links to several others in the area.
Miscellaneous (books, web sites, comments)
An Introduction to Genomics: The Human Genome and Beyond, and related educational materials on the how and why of sequencing. From the Joint Genome Institute, a US DOE lab in Walnut Creek, CA. http://www.jgi.doe.gov/education/index.html.
Genetics Home Reference, an educational site on genetic diseases in humans; from the National Library of Medicine. http://ghr.nlm.nih.gov.
Book. J D Watson (with A Berry), DNA - The Secret of Life. Knopf, 2003. Watson has played a major role in the DNA story, most famously as co-discoverer of the DNA double helical structure and as the first head of the US Human Genome Project. Here he discusses the history and future of the human genome project. He is a fine writer -- clear, and provocative enough to be fun. This book is for the general public. The science in it is good, and well-explained, with helpful artwork. The history is broadly good. And it is Watson's style to tell you what he thinks about controversial issues; agree or disagree, he makes for lively reading. For two -- very different -- reviews: Lindee, Science 300:432, 4/18/03; Singer, Nature 422:809, 4/24/03. Lindee concludes that "[Watson's] latest promotional brochure is not worth anyone's time." Singer says that the public and even scientists "can learn a great deal from the book, and enjoy doing so." I recommend it -- without endorsing all of his opinions.
Online video. A conversation with Jim Watson. Go to the Caltech theater listings for Science and Technology: http://today.caltech.edu/theater/lis...ry%5fcount=end. Scroll down the list to this item, dated May 5, 2003. The conversation is with David Baltimore, (then) president of Caltech and himself a Nobel prize winner (for his discovery of the enzyme reverse transcriptase, the enzyme that copies RNA into DNA).
Book. B Maddox, Rosalind Franklin - The dark lady of DNA. Harper/Collins, 2002. One of the dark parts of the DNA story is the lack of recognition of the role of Rosalind Franklin, who made the very fine X-ray pictures that Watson & Crick used as part of developing the double-helix structure. This lack of recognition was magnified by Watson's poor treatment of Franklin, especially in his earlier book, The Double Helix. Brenda Maddox's new biography has received wide praise as being fair and accurate; she had access to many materials that were previously unavailable. This is a biography, not a science book -- though you will certainly get a good sense of how the DNA story was developed. Highly recommended, but don't expect to come away declaring winners and losers; it's not that simple, but it is a good story, and it certainly enhances our understanding of an important scientist. (One part of the controversy, to some, is why Franklin did not share in the Nobel prize for the DNA work. It is a sufficient answer to that question that she died a few years before the DNA Nobel, 1962; posthumous Nobels are not allowed. Note that this point does not address the merits of her contributions, but does address one question which often comes to the forefront.)
There is a short essay about Franklin, in the general spirit of the book, online in the Mill Hill collection: K Rittinger & A Pastore, Rosalind Franklin - The dark lady of DNA... www.nimr.mrc.ac.uk/mill-hill-...rk-lady-of-dna. For more about the Mill Hill essays, see the note on the BITN main page, under Web sites.
Recent items, briefly noted
Coumadin (warfarin) is a widely prescribed medication to reduce blood clotting. The dosage must be carefully controlled, and people vary in how they respond. The FDA has announced a new labeling of coumadin that encourages testing the patient for two known genetic factors that affect the metabolism of the drug. A brief version of the announcement is at www.fda.gov/Safety/MedWatch/S.../ucm152972.htm.
A small trial has been reported showing that such testing is beneficial. So far, all we have is a news story summarizing the key findings. Gene test cuts complications from blood thinner warfarin (3/16/10). http://www.usatoday.com/news/health/...rin-gene_N.htm.
Sequencing technology -- and cost. The human genome project cost about \$3 billion. Much technology was developed along the way; as the project wrapped up, it was estimated that one could sequence a person's genome for a few million dollars. There is a dream -- and goal -- of sequencing an individual's genome for a thousand dollars. That may still be a way off, but the cost of sequencing has been declining, in large part due to fundamentally new approaches to sequencing. 2009 brings a report of a complete human genome for \$50,000. A news story on this: Cost of Decoding a Genome Is Lowered. A Stanford engineer has invented a new technology for decoding DNA and used it to decode his own genome for less than \$50,000. August 10, 2009. http://www.nytimes.com/2009/08/11/science/11gene.html.
Using genetic information to assess risk and guide screening. Most genes that affect disease susceptibility have only a small effect. How do we use such information? A paper in the New England Journal of Medicine lays out a model. Although there is probably much to quibble with, the model is clear enough, and may be a useful reference point for discussion. They start with the current UK recommendation that women be screened for breast cancer starting at age 50. Accepting this as the starting point, they note that this is the point at which a woman has a 2.3% chance of breast cancer within the next 10 years. They then argue that by a simple test for some known genetic variants, they can mark some women for screening at age 40 -- because with their genetic makeup that is the age at which they now have a 2.3% risk of breast cancer within 10 years. Similarly, women with other genetic variants have lower risk, and their screening can be delayed. The result is the same use of resources, but more effectively deployed. A news story about this work: Cancer gene test 'for all women', June 26, 2008. Online: http://news.bbc.co.uk/2/hi/health/7475312.stm. The paper is P D P Pharoah et al, Polygenes, Risk Prediction, and Targeted Prevention of Breast Cancer. N Engl J Med 358:2796, 6/26/08. Free online: http://www.nejm.org/doi/full/10.1056/NEJMsa0708739.
Tradeoff. We sometimes dream of finding "the gene" that causes a particular disease -- so we can counteract that gene. But among the complications... It may be that the same gene is good in one way and bad in another. Recent work suggests such a tradeoff may occur between diabetes and prostate cancer. In fact, two genes with this tradeoff have been found. News story: Genetic variants may be 'trading' one illness with another using new genes, Oxford research shows. Online: http://www.timesonline.co.uk/tol/new...cle3649020.ece.
Genome ethics. Genome work is raising a new set of ethics questions -- especially since there is so much uncertainty what the genome information means at this point. A group of bioethicists has proposed a set of guidelines for doing genome research, published as: T Caulfield et al, Research Ethics Recommendations for Whole-Genome Research: Consensus Statement. PLOS Biology 6, e73, 3/08. The paper is free online: http://www.plosbiology.org/article/i...l.pbio.0060073.
Ancestry. An interesting subject is tracing human lineages by genetic tests. This is indeed a proper area of study, and has yielded insights into human migrations. It has also entered the popular arena. There are commercial tests that claim to reveal your ancestry. Unfortunately, the quality of this testing is questionable at this point. A "Policy Forum" article about this appeared in Science, and a news story about the work and that article appeared in the UC Berkeley news. The Science article: D A Bolnick et al, Genetics: The science and business of genetic ancestry testing. Science 318:399, 10/19/07. The UC Berkeley news story, featuring co-author Kimberly TallBear: Researchers caution against genetic ancestry testing; October 18, 2007. http://www.berkeley.edu/news/media/releases/2007/10/18_genetictesting.shtml.
Craig Venter is one of the pioneers of genome work. He is also the first person to have his entire DNA -- the diploid chromosome set -- completely sequenced and reported. Importance? Well, for now it is a technical milestone and something of a curiosity. However, as more complete genomes become available -- and as the cost comes down -- the usefulness will increase. For example, they note how he has specific alleles that both favor and disfavor heart disease. At this point, that is too little info to be useful. At some point, with more information, it will be useful. I doubt that many will want to read this in detail, but simply browsing the Introduction and Discussion sections will give the flavor. And it is a historic paper. The paper -- by Venter, about Venter, and from the Venter Institute -- is: S Levy et al, The Diploid Genome Sequence of an Individual Human. PLoS Biol 5(10): e254. 9/4/07. It is open access at http://www.plosbiology.org/article/i...l.pbio.0050254.
M May, Pharmacogenetics lurches forward. The Scientist 8/2/04, p 26. This article discusses several specific examples of how drugs may affect individuals differently, depending on their genetics. It includes the recent genetic analysis of why Iressa works for some patients and not others.
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Prion diseases have long fascinated biologists, because of the unusual nature of the infectious agent. Recently, prion diseases have become a major news story because of the emergence of the bovine (cow) prion disease BSE, which can be transmitted to humans as the disease vCJD.
Introduction
Prions are infectious agents that long defied some of our basic ideas of biology. They appear to behave like other infectious organisms, yet they lack any of the most fundamental features of organisms. In particular, they lack any genetic material (DNA or RNA). Over time, work on prions has suggested that the "infectious agent" is actually a misfolded protein -- which causes a normal cellular protein to change its shape to the misfolded form.
Prion diseases and prions are so unusual and so fascinating that they have been the subject of two Nobel prizes in Physiology or Medicine. In 1976 Carleton Gajdusek shared the Nobel prize for his work showing that the human disease kuru was similar to the well known sheep disease scrapie. In 1997 Stanley Prusiner, at UCSF, was the sole recipient of the prize; Prusiner was responsible for developing the modern prion model.
As diseases, prion diseases are quite rare and difficult to transmit. But they are also quite scary, because they are progressive neurodegenerative diseases, with no cure or treatment. They also have the mystique of being strange, due to the poor understanding of what prions are and how they work.
The prion disease most in the news is BSE (bovine spongiform encephalopathy), often called mad-cow disease. It is rather likely that the BSE agent can be transmitted to humans, and cause vCJD (variant Creutzfeldt-Jakob disease). The number of known vCJD cases in humans is under 200, but there are so many unknowns, including a possible incubation period of many many years, that this mysterious disease strikes fear -- at least much uncertainty.
As we learn more about prion diseases, a new part of the story is emerging. It is possible that a number of neurodegenerative diseases long considered quite distinct may share some underlying features. These include Alzheimer's disease, Parkinson's disease, Huntington disease, and the prion diseases. The common thread may be that all involve misfolded proteins. The reason for the misfolding and the details of the disease development vary, and there is no implication here that all of these are infectious. In fact, not all prion diseases are infectious.
Prion diseases
Prion diseases are typically slowly developing neurodegenerative diseases. The classic prion diseases are found in mammals. However, prion-type phenomena have been found in yeast, as discussed below. Thus we should be open to the possibility of finding prion phenomena, good or bad, that are different from the neurodegenerative diseases that we usually discuss.
Here are some of the more common prion diseases you are likely to hear about. In general, these diseases are fairly specific to one type of animal, so they are listed by animal.
Sheep
• Scrapie is the "classic" prion disease and the subject of most early work on this type of disease. Sheep are not very good lab animals, so progress was slow. Scrapie has been adapted to small lab animals, including mice and hamsters; much lab work is done with mouse scrapie or hamster scrapie.
Cattle
• BSE (bovine spongiform encephalopathy) is the big one in the news
Humans
• Kuru
• CJD (Creutzfeldt-Jakob Disease)
• vCJD (variant Creutzfeldt-Jakob Disease). This is a distinct disease from CJD; it is almost certainly caused by the agent that causes BSE in cattle.
• Less common but reasonably well-characterized prion diseases in humans include: FFI (fatal familial insomnia) and GSS (Gerstmann-Straussler-Scheinker syndrome)
Elk and deer
• CWD (chronic wasting disease)
The prion: the infectious agent
Some prion disease appear to be infectious. That is, one can isolate something from an infected individual, give it to another individual and that individual will get the disease and make more of the infectious material. This is the behavior one expects for an infectious agent, such as a virus or bacterium. (Microbiologists would say that the prion infectious agent satisfies Koch's postulates, a set of groundrules used to show that one has an infectious agent.)
So what kind of an infectious agent is it? This is the step at which the biologists get very fascinated with the prion. The properties of the infectious agent do not correspond to those of any known agent. In particular...
* The prion agent is not inactivated by a wide range of treatments that should inactivate viruses or bacteria.
* The prion agent, so far as we can tell, contains no nucleic acid -- no genome.
Now, prion infectious material is not easy to handle, and early experiments showing these properties were subject to challenge. However, further work continued to support these properties. Thus it seemed that the prion agent was not an ordinary agent. In fact, it almost seemed that the prion agent was a self-replicating protein. The problem is that "a self-replicating protein" does not fit with our modern understanding of proteins. "A self-replicating protein" would be a major violation of the "Central Dogma", which says that only nucleic acids can "self-replicate". This is why biologists have been fascinated by the prion agent. If it really did what it seemed to do, it would reveal a major weakness in our understanding of genes and proteins.
Two major developments have served to bring some clarity to the nature of the prion agent. We discuss these in the following two sections. At that point, we will present the current working model for the nature of the prion agent -- a model which is now widely accepted, yet has still not been clearly shown to be correct.
The prion gene
At some point the gene that codes for the prion protein was found. Where? In the host. That is, the prion gene -- the gene for the prion protein -- is a normal host gene. When a sheep gets a prion disease (scrapie), the sheep's own gene for the prion protein codes for any new prion protein that is produced.
A direct test showing the importance of the host prion gene for the prion disease came with mice, where it is "easy" to delete a specific gene. Mice lacking the gene for the prion protein cannot be infected with prions. (The method used to make such a "knockout mouse" is discussed briefly on the BITN page Agricultural biotechnology (GM foods) and Gene therapy - Introduction.)
Finding the prion gene solves one problem in the prion mystery. The protein does not truly self-replicate. It is coded for by a gene, a normal gene -- in fact, by a host gene. Thus the feature of the prion model which most seriously challenged our common understanding of genes and proteins is no longer a problem. Attention now turns to the question of how this host protein turns "toxic", and how its toxic form can be infectious.
So what is the normal purpose of this prion gene in your cells? The work with the mice lacking that gene (above) gave a clue: Those mice appeared quite normal. That is, it seemed that the prion gene has no normal role -- that it is non-essential. However, this may not be the complete story. The prion gene is highly conserved among mammals, which suggests it is there for a reason. And there are reports of subtle differences between mice with and without the normal prion gene. In particular, there is evidence that the normal prion protein is involved in regulation of sleep. (Interestingly, one prion disease in humans involves abnormal sleep.) Thus at this point we really do not know what the normal prion protein is for, and it is even possible that it is unnecessary. We will return to this point when we discuss Genetic susceptibility -- and resistance -- to prions.
A paper published in November 2007 offers evidence for a role for the normal form of the prion protein. They suggest that it is involved in immune responses; specifically, they show that the normal prion protein acts to control endogenous retroviruses. It will be interesting to see how this finding holds up, and what its implications are. The paper is: M Lotscher et al, Induced Prion Protein Controls Immune-Activated Retroviruses in the Mouse Spleen. PLoS ONE 2(11): e1158, 11/7/07. The paper is free online at: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001158.
Shadoo. New work is leading to a new view on the role of the prion gene. Another gene that is related to the prion gene has been found; it is called Shadoo. The key result is that loss of both Shadoo and the prion gene is lethal, while loss of either one alone is not. This suggests that we have two related proteins with overlapping function; either one can compensate for the other -- though perhaps imperfectly. This finding will open up new approaches to studying prion function. The new paper is: R Young et al, The prion or the related Shadoo protein is required for early mouse embryogenesis. FEBS Letters 583:3296-3300, 9/14/09.
A tentative model
From the work described above -- and of course much more -- a tentative model for the prion began to develop. At this point, the model is that the toxic protein is an altered form of a normal cellular protein. Extensive data has failed to show any difference in the composition of the two forms. And some data has shown that the two forms are different folded forms -- called "conformations". That is, the normal prion protein folds up to a certain 3D structure, whereas the toxic prion protein folds up differently. Then, says the model, the toxic form can cause the normal form to refold into the toxic form.
That proteins may have more than one stable or useful conformation is well within our common understanding of biochemistry. Proteins are flexible, and shape changes are part of their normal function and regulation. Proteins commonly interact with each other, and of course cause conformational shifts when they do so. Nevertheless, the specifics of the prion model -- that one form causes the other form to refold "in its own image" -- is novel.
Yeast prions
Yeast? How did we get from neurodegenerative diseases to yeast? Well, it is a complicated story, so just a few notes here with some highlights. Yeast biologists had noticed that certain novel properties did not show normal inheritance. After some sleuthing, they showed that the behavior was very much like that of the postulated prion of mammals. The novel property was due to an altered folding of a normal protein, and the abnormal protein could induce abnormal folding of normal molecules.
So what the yeast work did was to establish a simple model system for one key aspect of the prion story. The basic idea of a protein inducing a shape change in its brethren, causing a new cellular property to occur, could be experimented with rather easily in the yeast system. This induced shape change is the heart of the prion model, and so these yeast proteins became known as yeast prions.
It is important to stress that the yeast work did not prove what mammalian prions are. What is important is that the yeast prions provided a model; they showed that proteins could do what was proposed in the mammalian system. The yeast work progressed rapidly because yeast prions are relatively easy to work with. It remained to be seen how much the yeast prion model actually fit the mammalian prions. As we shall see below, the answer is that the basics of yeast prions do carry over to the mammalian prions.
Genetic susceptibility -- and resistance -- to prions
There are two broad reasons why some organisms might be more/less resistant to getting prion diseases, for genetic reasons. One would be "general" -- that something in the general genetic nature of the organism affects some aspect of the prion disease. The other is more specific: since the prion protein is now known to be coded by a host gene, variations in this gene might cause variations in disease.
So far as I know, there is no evidence yet for "general" genetic factors that affect prion disease in animals. One might expect that some will be found at some point, so we should not make much of this point, one way or the other. (In yeast, a chaperone protein is essential for the prion effect; hence its gene would be such a general genetic factor. I suspect that such factors will be found in animals.)
On the other hand, there is abundant evidence that variations in the prion gene affect prion disease.
The most dramatic example is that absence of the prion gene makes the animal resistant to the disease. This was noted above, as evidence for the key role of the host prion gene.
It was also noted that the animals that lack the prion gene seemed quite normal. Thus one might wonder whether a practical way to combat prion disease, at least with farm animals, would be to breed them to lack the prion gene. In fact, work is being done along this line. Whether it proves useful remains to be seen.
In December 2006 it was announced that researchers had finally succeeded in making cows that lack the prion gene. Preliminary evidence suggests that these cows are indeed resistant to prion diseases, but more definitive work is in progress. The cows also appear to be quite normal so far. The paper is J A Richt et al, Production of cattle lacking prion protein. Nature Biotechnology 25:132, 1/07. Online: http://www.nature.com/nbt/journal/v2...s/nbt1271.html. (Access beyond the abstract is probably restricted to subscribers.) A news story: "Mad Cow Breakthrough? Genetically Modified Cattle Are Prion Free"; January 1, 2007. It is at http://www.sciencedaily.com/releases/2007/01/070101103354.htm.
Could this approach be extended to humans? Well, the common approaches used to make genetic variants of farm or lab animals are not applicable to humans -- at least at this point. However, one might also wonder whether a drug targeted at reducing activity of the prion gene would help. Again, this is under investigation, but it is not an easy problem (partly because it is difficult to get drugs to the brain).
There are natural variations ("polymorphisms") found in the prion gene in humans. The frequency of prion diseases is different for people with different versions of the prion gene. Thus it seems that some versions of the prion protein are more likely to convert to the disease state than other versions.
Transmission and other "causes" of prion diseases
Most of our attention has been focused on the idea that prion diseases are "transmissible" (or infectious, at least in a general sense of the word). That is why we are concerned about BSE; it seems that the BSE prion can be transmitted to humans (albeit probably inefficiently). However, we also now understand that the prion protein itself is a normal part of the body. So can it somehow cause a "disease" -- without any "transmission"? Yes, indeed.
Several prion diseases are known in humans. The most common is Creutzfeldt-Jakob Disease -- the original CJD. It occurs at a frequency of about one in a million, per year -- thus making it a rare disease, but certainly not unknown. It seems likely that it is due to a random event of the normal prion protein misfolding into the disease form. It is conceivable that some event triggers the disease event, but so far there is no evidence on the matter. This "background", apparently spontaneous, CJD is sometimes known as "sporadic CJD", or sCJD".
In a very few cases prion diseases have been found to run in families. Modern analyses of such families shows that the family carries a mutant form of the prion gene. Apparently, the mutation increases the chance of the disease form of the prion forming.
Thus we have three broad "causes" of prion disease:
• Transmission: acquiring a defective prion from the outside;
• Spontaneous or sporadic: one's own prion protein turning to the disease form;
• Genetics: having a higher chance of one's own prion protein turning to the disease form.
All of these causes of prion disease can be accounted for in the current version of the prion model.
Routes of Prion Transmission
We have said that prions can be transmitted from one infected animal to another. What are the routes of transmission?
In common discussion, we are often talking about oral transmission. vCJD is transmitted to humans by eating infected beef -- meat from cows carrying BSE. Further, it is likely that BSE was transmitted from cow to cow by feeding the cows material containing products from infected cows. Kuru was transmitted from human to human by ritual cannibalism -- eating the brains of infected people.
However, oral transmission is only one possible route. In fact, oral transmission is not particularly efficient, and is not well understood. Generally, proteins ingested orally are degraded. Somehow, the stable toxic prion manages to survive the usual digestion process -- at least at some low level.
In laboratory work, transmission is often accomplished by direct injection into the brain. This is probably the most efficient transmission known. It might seem irrelevant to the real world, but unfortunately that is not entirely true. There are known cases where prion disease has been transmitted on surgical instruments, or by use of infected tissues. These cases are extremely rare, but they are clear, and they do help in understanding the transmission process. CJD transmitted by medical procedures is known as iatrogenic CJD.
It used to be thought that the risk of prion transmission was associated only with nervous system tissue. However, this seems to be an over-simplification. As work continues, it seems that other tissues -- including body fluids such as blood or saliva -- can transmit prions, at least in some cases.
How do prions cause disease? Relevance of prion diseases to other protein-folding diseases.
The short answer is that we do not know.
An interesting story is emerging, however. It is now clear that there are several neurodegenerative diseases of higher animals, including humans, which share a common feature: production of an aggregate of insoluble proteins in the affected cells. These diseases include Alzheimer disease, Huntington disease, and Parkinson disease, as well as the prion diseases. How the altered protein that produces the aggregate is made varies with the disease. Only the prion diseases appear to involve a transmissible protein. Now, there is no assurance that all of these protein aggregates cause damage the same way, but at least the broad issue of the effects of these excessive aggregating proteins is being studied in several systems.
There is some evidence that Alzheimer disease can be transmitted by direct injection of the disease form of the protein into the brain. The work was done in model systems in mice. To my knowledge, there is no evidence for transmission of Alzheimer, or any of the other non-prion protein-folding diseases, by "ordinary" means.
The paper showing transmission of Alzheimer disease in the mouse model is: M Meyer-Luehmann et al, Exogenous induction of cerebral β-amyloidogenesis is governed by agent and host. Science 313:1781, 9/22/06. It is free online at: http://www.sciencemag.org/content/313/5794/1781.abstract.
One theme that is beginning to develop is that it may well not be the aggregate itself that causes disease, but rather something about the high level of the protein. A variation of this is the possibility that a very early stage of aggregation is the toxic agent. For example, an aggregate of only a few protein molecules -- called an oligomer -- may still be soluble, and able to cause damage; in contrast, the more prominent large aggregates may be more side effects than important in their own right. A consequence of this model is that effort to disaggregate the large aggregates may be misguided; doing that may create more of the smaller and more toxic oligomers.
New work with Alzheimer disease has yielded some interesting clues. The work involved purifying different forms of the Alzheimer protein, and injecting them into rat brains. A key result was that the soluble dimer of the protein was most active. In particular, the monomer was not active, and insoluble plaque material was not active. This provides direct support for the idea that a small soluble form is the active form, not the more readily observed plaque material. Of course, this result is for this disease and this model system; its generality remains to be seen. The system also allows them to begin to see how the active protein causes disease.
A press release announcing this work: "Scientists isolate a toxic key to Alzheimer's disease in human brains -- Soluble Beta-Amyloid Protein Fragments May Damage Brain Cell." June 23, 2008. Online: http://news.harvard.edu/gazette/story/2008/06/scientists-isolate-a-toxic-key-to-alzheimers-disease-in-human-brains. The paper is: G M Shankar et al, Amyloid-β protein dimers isolated directly from Alzheimer's brains impair synaptic plasticity and memory. Nature Medicine 14:837, 8/08. The PubMed listing, with abstract, is at http://www.ncbi.nlm.nih.gov/pubmed/18568035; a copy of the full article is freely available there.
Treatment of prion diseases
The short answer is that there is no treatment or cure available.
As understanding of the prion improves, there is work on trying to find agents that might interfere with either the formation of the "bad" form or with its action, or possibly even "dissolve" preexisting prion material. There is some interesting work, and even some anecdotal promising results. But so far, proper testing has not validated any treatment.
Testing an agent against prion disease in humans is very difficult. For one thing, such diseases are quite rare. Further, much of the lab work suggests that treatment would be most effective very early in the course of the disease; however, diagnosis of prion diseases in humans usually occurs when the case is well established.
Some work on developing treatments for prion diseases...
Congo red derivatives. Congo red is a dye that binds to prion proteins. It is used to detect prions, but it is too toxic to be used therapeutically. Here they explore some derivatives of Congo red, with two interesting results. One is that they develop a compound that is effective in clearing cultured cells of prions, and seems worth testing in animal models. Second, comparison of the compounds suggests that a key property is that the effective compounds allow degradation of the prion protein. More specifically, the drug may keep the prion from inhibiting the protein-degrading machinery -- the proteasome. A news story about this work is: Congo dye derivatives free proteosome [sic] to rid cells of prions, Microbe 2:524, 11/07. Microbe, the news magazine of the American Society for Microbiology, is free online; this item is at forms.asm.org/microbe/index.asp?bid=54023. The paper itself is: S Webb et al, Mechanistic insights into the cure of prion disease by novel antiprion compounds. Journal of Virology 81:10729-41, 10/07. Free online at: http://jvi.asm.org/cgi/content/abstract/81/19/10729.
RNAi treatment. RNAi stands for RNA interference; the idea is to make a short RNA molecule that can bind to the mRNA (messenger RNA) for a gene, and interfere with its function. An interesting article made news in December 2006. In the new work, they used RNAi to reduce production of the prion protein. They demonstrated the principle using mouse cells in lab culture. Then, using a viral vector to deliver the gene for the RNAi, they showed an effect in a mouse model system. Emphasize that this result -- certainly very interesting -- is a clue that needs to be followed up. The logic is good, but the effect is fairly modest at this point -- and all the work is with mice. The world of drug development is littered with good ideas that showed promise in an animal system, then did not work in humans. Nevertheless, this is an interesting item, and the Commentary article shown below is a good overview of the field (including other treatment options being tried) as well as the particular work. The Commentary: Q Kong, RNAi: a novel strategy for the treatment of prion diseases. Journal of Clinical Investigation 116(12):3101, 12/06. It is free online at: http://www.jci.org/articles/view/30663. The Commentary links to the research article. This item is also briefly noted under the BITN topic RNAi (RNA interference or silencing).
Reversal. The symptoms of a prion disease can be reversed if continued prion replication is prevented, according to work reported in February 2007. The work was done in mice, using a genetic trick that would not be applicable to humans. Nevertheless, the work offers some hope, a "proof of principle." It is likely that such treatment would be most effective early in the disease, thus raising the problem of early diagnosis. The paper is G R Mallucci et al, Targeting cellular prion protein reverses early cognitive deficits and neurophysiological dysfunction in prion-infected mice, Neuron 53:325, 2/1/07. A news story about the work: "Scientists 'reverse' vCJD signs. Prion diseases affect the brain. Symptoms of prion diseases, such as the human form of mad cow disease vCJD, can be reversed, a study of mice suggests." February 1, 2007. http://news.bbc.co.uk/2/hi/health/6314877.stm.
My opinion/advice about BSE risks
At the top of the page, I cautioned that my background is not medical, and that my purpose here is not medical advice. I have been interested in the prion story long before BSE -- long before the word prion or the name Prusiner became known. Prions are fascinating.
Nevertheless, having gotten this far, I do want to state how I evaluate the current BSE situation in the United States. I will try to give my reasons, so you can analyze those, not just take my bottom line. From my understanding, I think there is a very low risk of getting vCJD from eating beef. There are several considerations that go into reaching this conclusion. Each of these reasons has limitations, but overall, I see little reason to be concerned.
Reasons to not worry too much about BSE-infected beef:
• There is no reason to believe that there is any significant number of BSE-infected cows in the US. Of course, one limitation of this is that rather few are tested, so one can be somewhat leery of the actual data. However, there is almost no evidence of any cows with signs of disease, and steps to prevent transmission of BSE have been in place for several years. Remember that the BSE-cow in the news (Jan 2004) was born before key steps to break transmission were put into place. This cow has re-focused attention on the subject, and additional measures to reduce BSE transmission have been implemented.
• Acquiring the disease from an infected animal requires eating tissue that contains the prion. To the best of our knowledge, this is largely brain and nervous system tissue. These are parts that do not commonly enter the human food chain. Muscle, the part of the cow most commonly eaten, has little or no prion.
• Transmission of the agent from cows to humans is probably not very efficient. In Great Britain, which had a huge number of BSE-infected cows, fewer than 200 people have developed vCJD. Of course, we do not know whether more will develop it later; after all, this is a type of disease with a notoriously long latent period. However, the accumulating evidence is showing no signs of a major increase -- at least so far.
External Links
• Book: Warwick Anderson, The Collectors of Lost Souls -- Turning kuru scientists into whitemen. Johns Hopkins University Press, 2008. ISBN 978-0-8018-9040-6. Kuru is a neurodegenerative disorder, a spongiform encephalopathy rather like what we refer to as mad cow disease (or BSE or CJD). It was the first large cluster of this type of disease, which was endemic to the Fore tribe of New Guinea. This book is the story of kuru, and the work of scientists in the late 1950s to learn about this unusual disease. In particular, it is the story of Carleton Gajdusek, who received the Nobel prize for showing that kuru was transmitted by ritual cannibalism among the Fore. Later work would lead to the understanding of the transmittable agent as a prion -- and to another Nobel prize, to Stan Prusiner. The book is the story of disease, but also of culture: the culture of the Fore, and the culture of the scientists. For example, there is a discussion of the nature of cannibalism, including a comparison with the doctors' practice of doing an autopsy and collecting brains. Much is made of the competition between various groups studying the Fore, and of changing styles in science in the US. It is interesting that, despite all the dedicated efforts to figure out kuru, what really made the difference was a casual comment by a veterinarian -- which Gajdusek was wise enough to follow. The book concludes on an inevitable down note, with Gajdusek's fall, and imprisonment. But that is part of the story, and it is handled gracefully. Author Anderson is a doctor and science historian, so he understands the content, and he writes well. All in all, this is an enjoyable book at multiple levels.
• Book: P Yam, The Pathological Protein: Mad cow, chronic wasting, and other deadly prion diseases. Copernicus, 2003. ISBN 0-387-95508-9. An excellent overview of the prion story, for the general audience, from a science journalist. This book presents the range of prion diseases, in animals and humans, and the relationships between them. It develops our current understanding of what prions are and how they work, with a good consideration of uncertainties in the story. A good place to start, if you want to know what prions are about; probably a good overview for many scientists, as it brings together a lot of information into one fairly short and very readable book.
• Prion Diseases. www.microbiologybytes.com/virology/Prions.html. Good overview. It is part of a broader site, Microbiology Bytes.
• BSE and vCJD News. http://www.cidrap.umn.edu/cidrap/content/other/bse/index.html. From CIDRAP; I also list CIDRAP as a good general source of information on Emerging diseases.
• Chronic wasting disease (CWD). wildlifedisease.nbii.gov/dise...agemode=submit. From the National Biological Information Infrastructure (NBII). CWD is a prion disease of deer and elk, which is becoming a serious problem in the US. The implications for human health are unclear. So far, there is no evidence for transmission to humans (e.g., deer hunters), but it is hard to make a strong argument that there is no risk.
• Bovine Spongiform Encephalopathy (BSE). From the USDA FAS (Foreign Agricultural Service). "This page provides sources of information on the effects of BSE on trade. Provided are links to related documents such as regulations, reports, and press briefings, as well as main BSE pages for various government and organization sites." www.fas.usda.gov/dlp/BSE/bse.html. This page may be too technical for most use, but is a great source when you want information about governmental regulations.
• S Seethaler, In the face of uncertainty -- Batty bovines and empty blood banks. (Also titled: What do mad cows have to do with my blood? Connecting the dots: Batty bovines, empty blood banks, and groceries for a song.) Berkeley Science Review, Spring 2003, p 40. BSR is a free publication by UC Berkeley graduate students, usually highlighting work from Berkeley. This article is available online at sciencereview.berkeley.edu/ar...le=perspective. It focuses on the new restriction that those who have spent much time in England cannot be blood donors. At the time this came out, there was almost no evidence that prions can be transmitted by blood; however, more recent evidence has increased the concern a bit. In part, the article is based on discussion with Dr Kate O'Neill, Professor of Environmental Science, Policy and Management.
• Nobel prize sites:
• Gajdusek: http://www.nobelprize.org/nobel_priz...aureates/1976/.
• Prusiner : http://www.nobelprize.org/nobel_priz...aureates/1997/.
• Prusiner's page, at UCSF: Molecular Biological, Genetic and Protein Structural Studies of Prion Disease. www.neuroscience.ucsf.edu/neu.../prusiner.html. | textbooks/bio/Introductory_and_General_Biology/Supplemental_Modules_(Molecular_Biology)/Prions.txt |
Recently many people have been making a huge fuss about cleaning up our oceans and climate change. They talk about all of these different things: ocean warming, ocean acidification, overfishing, pollution, and coral bleaching. They tell us the oceans are in grave danger. So, yeah, all of this sounds really bad but honestly what does it all mean? More importantly, why should it matter to you?
Physical Map of the World under CC 4.0
Looking at a map you can tell that the ocean takes up the majority of our planets surface area, and when calculated it covers a whopping 72% of the earths surface! The ocean also provides over 50% of the earth’s oxygen and stores 50 times more carbon dioxide than the atmosphere. It also plays a huge role in regulating our planet’s climate and weather patterns. If you want to read a little more about all of this check this article out.
If all of that doesn’t convince you of the importance of the ocean, think about all the fun that people can enjoy involving the ocean and the beach. There’s swimming, surfing, boating, parasailing, cruises, the list goes on and on! Okay, so maybe you’re not a beach person, I mean the sand does get everywhere.
The ocean also plays a pretty big part of the economies of the world. You also may not realize how important the ocean is for coastal communities in developing countries. For example just in the United States the ocean produces about 282 million dollars per year and creates about 3 million jobs. It also provides a mode for 90% of all trade transportation in the world. Lastly, we use the ocean for a large portion of our protein source.
People swimming and diving in the water by GoodFreePhotos CC by 2.0
The biodiversity of oceans is critical. Coral reefs (a tropical marine ecosystem) are often considered the “tropical rainforest of the seadue to their diversity in marine life and varying animal species. There is still a lot to discover about the ocean, however we do know it’s important to maintain because it’s the largest ecosystem we have on the planet. This ecosystem maintains homeostasis via regulation by abioticand biotic factors. The oceans are often overlooked especially since we don’t see the dynamics between marine organisms and our own environment as we don’t share this habitat.
In tropical marine ecosystems, biotic factors include sea plants, algae, bacteria, and animals. Abiotic factors are similar to those on land such as sunlight, temperature, and soil nutrients. However, since the ocean is water, pH and salinity are also considered important abiotic factors that influence and sustain healthy and productive organisms. Oceans function just like land ecosystems, but they have far more area and depth. Both aquatic and terrestrial ecosystems have complicated food webs that distribute energy, and the main biotic components are a variety of primary producers, consumers and decomposers. Marine food webs contain primary producers such as phytoplankton which undergo photosynthesis and provide consumers with the nutrients they need. Click here for a cool video from Khan Academy to learn more about about food chains and trophic levels. Trophic pyramids for aquatic ecosystems are inverted compared to terrestrial ecosystems due to the fact that the short life span and rapid consumption of autotrophic phytoplankton means the biomass of heterotrophs at any given time might be greater than autotrophs (the opposite of what you usually see in terrestrial systems).
Although the ocean is somewhat overlooked it is a truly remarkable ecosystem. Unfortunately, there has been a rise in ecological crisis in aquatic ecosystems mostly at the hands of humans. For example, overfishing can alter predator/prey balance, and pollution can significantly impact the health of the environment. If the oceans continue to be in crisis at a global level, it could result in mass species extinction. Therefore, it is really important to care for our oceans. We hope this chapter gives you a little more perspective on why the ocean is so important for a healthy environment, global economy and for civilizations around the world.
The information in this chapter is thanks to content contributions from Marisa Benjamin, Maddie Ouellette, and Allie Tolles | textbooks/bio/Marine_Biology_and_Marine_Ecology/01%3A_Coral_Reefs_and_Diversity/01.1%3A_Why_do_the_Oceans_Matter.txt |
What are corals you ask? “ A little bit algae, a little bit rock, and a lot animal.” Corals are close cousins to sea anemones and jellyfish, meaning they all belong to the same phylum of Cnidarians. Coral is a marine invertebrate that is composed of simple structures known as polyps. The polyp has one opening which is the coral’s mouth that is surrounded by a ring of tentacles. These tentacles have stinging cells called cnidocytes, used for food and protection. These cells fire tiny toxic barbs called nematocysts when they are touched to ward off predators or capture food. Inside the polyp are reproductive and digestive tissues. Coral can live as an individual polyp, but most corals exist as large colonies of interconnected polyps.
Coral Polyp” by Wikimedia Commons under CC by 2.0
How do Corals Survive?
Sunlight: Corals grow in shallow water where the sunlight can reach them. The algae that live inside of them, zooxanthellae, need sunlight to survive, since the coral animal depends on the zooxanthellae, corals need sunlight to survive.
Clear Water: Clear water is needed for corals to survive because it lets the sunlight in. When the water is opaque the corals will not thrive.
Warm Water Temperature: Most corals, though not all, require warm waters to grow and survive. Corals general live in water temperature of 68-90°F
Clean Water: Corals are very sensitive to pollution and sediments that can be in the sea. Sediments can create cloudy water conditions which won’t allow for sunlight to get through which will harm the polyps. Corals do not typically do well in environments where there is little sunlight, except for the deep-sea corals. Another issue that may arise is the addition of too many nutrients. An overflow of nutrients in the water can cause things such as algae to grow, in turn taking over the reef. Sediments and pollutants can also cause direct harm to coral tissue.
Salt Water: Corals require a certain balance between the concentration of salts and water (salinity).
Nutrients: Though zooxanthellae do provide some nutrients, the coral animals still need to receive other sources of nutrition. Corals can also grab passing nutrients (like zooplankton) by using their tentacles to snag passing organisms flowing by.
Coral Reef Functions:
Protection: Functions as a form of protection for the shores from harsh waves and storms
Habitat: Provides shelter and safety for many organisms
Nutrients: Many forms of heterotrophic marine life are supported from the primary production of the coral zooxanthellae. Carbon and nitrogen-fixing is an important part of the marine food chain. Nutrient cycling within the coral polyps is very efficient and contributes to the high production of reefs.
How do Corals Reproduce?
Some species have distinct male or female polyps while other coral can alternate gender. Many coral reef species only reproduce once or twice a year. For some coral that only have single-gender polyps, certain events (i.e. full moon) trigger the polyps to release massive amounts of sperm or eggs that flood into the seas, where the gametes eventually come together. Most coral species spawn by releasing eggs and sperm into the water; but the period of spawning depends on the type of coral. When an egg and sperm meet, the fertilized egg eventually develops into a larva called planula. Planula can form by two different ways, either fertilized within the body of a polyp or fertilized outside the polyp, externally in the water. Fertilization of an egg within the body of the coral polyp happens when sperm that is released through the mouth of another polyp, is taken in by a polyp with an egg. When the larva is matured enough the mother will spit it out via the mouth. If fertilization is external, corals will eject large amounts of egg and sperm into the water which eventually find each other. The release of larvae or gametes is known as coral spawning. Most species also reproduce asexually, budding new polyps or fragments, that grow either on an older polyp or drift around before landing on a new surface.
The information in this chapter is thanks to content contributions from Haley Zanga, Marisa Benjamin, and Haley Fantasia | textbooks/bio/Marine_Biology_and_Marine_Ecology/01%3A_Coral_Reefs_and_Diversity/01.2%3A_Coral_Reefs%3A_An_Introduction.txt |
What Types of Coral Exist?
When people think about coral they often think about the stony calcified coral they get at a gift shop during a vacation to a tropical island. However, these are only the skeletons of stony corals, and are only one type of coral that exists. There are also deep water and soft corals. Each of these types of corals is unique structurally and in how they interact with their surroundings. There are over two thousand different types of coral which form colonies that play a key role in marine environments.
1. Hard Corals
“Hard Corals” by Amal FM under CC BY-SA 2.0.
Hard coral is a fundamental part of building the coral reef. The polyps of hard corals secrete skeletons of calcium carbonate (Limestone), that will eventually become rock. Hard coral includes species such as brain coral and elkhorn coral. Hard coral are considered to be hermatypes, which are reef-building corals. These corals require a certain type of algae called zooxanthellae that live within their tissues, this important mutualism is necessary for their survival. These organisms are what give corals their colors, which is dependent upon where they are living. The shape and appearance of each coral are dependent upon its species type, location, depth, water movement, and many other factors. Hard coral polyps are very similar to sea anemones, as they also have stinging cells called cnidocytes. Hard coral species can be found in all of the world’s oceans, yet their populations are expected to decrease due to global changes and ocean acidification.
As mentioned earlier, hard corals build coral reefs. A coral reef begins when the coral polyp attaches itself to a rock on the seafloor. This one coral polyp then begins to divide or bud into thousands and thousands of clones of itself. Polyps and their calcareous skeletons connect to one another which creates a colony that will act as one. As this colony grows over hundreds and thousands of years it will join with other colonies and become a reef. Read more in our chapter on coral reef formation.
Maldives reef” by Alexander Semenov under CC by 2.0
2. Soft Corals
“SOFT CORALS” BY NAJIM ALMISBAH UNDER CC BY-SA 2.0
Soft corals often resemble plants and trees. They are soft and bendable so they do not have stony skeletons like hard coral. For protection and support, they grow woodlike cores for stability. These cores are made of structural proteins such as gorgonin and other protein similar to those of nails and horns of other animals. These types of coral are referred to as Ahermatypes(non-reef building corals). Examples of soft coral in the Bahamas and Caribbean include sea fingers or sea whips. This type of coral also does not always have a symbiotic relationship with zooxanthellae. Though many utilize their presence, soft corals will typically eat any type of passerby out of the water column. These types of corals do not produce calcium carbonate, rather they contain spiny skeletal sclerites. These give the softer corals some protection and support. Soft species also prefer to live in nutrient-rich waters with less intense light. In other parts of the world, fleshy true soft corals have no rigid internal skeleton at all.
3. Deep-Sea Corals
Deep-sea coral can be found in the dark depths of up to 6,000 m (20,000 ft) below the surface of the ocean. These corals live in icy cold water with little to no sunlight. These corals, like shallow species, can exist as single polyps or multiple, living in complex colonies made up of different species. Since these species do not require sunlight or warm water, they are able to grow in a vast array of waters around the world. They have even been found in waters as cold as -1-degree celsius. Since these corals live without sunlight they contain no zooxanthellae. This means these corals must obtain their energy and nutrients elsewhere. They do this by trapping tiny organisms in passing currents. The main reason many scientists had no idea of the existence of these deep-sea corals, is because, for many years, the oceans deep depths were inaccessible. In addition to being surprisingly diverse, scientists have also discovered that deep-sea corals are amongst the oldest marine organisms on record. Since corals are constantly growing, regenerating new polyps, some coral reefs have been actively growing for almost 40,000 years. To your and my surprise, scientists have identified nearly as many deep-sea corals as shallow-water species.
The information in this chapter is thanks to content contributions from Haley Zanga, Marisa Benjamin, Haley Fantasia, and Melissa Wydra | textbooks/bio/Marine_Biology_and_Marine_Ecology/01%3A_Coral_Reefs_and_Diversity/01.3%3A_Different_Types_of_Corals.txt |
Have you ever wondered how coral reefs are formed? It has been established by the scientists in the Tropical Marine Biology field that coral reefs can be divided into three types: Fringing reefs, Barrier reefs, and Atolls which all require very specific conditions to develop. Coral reefs begin to form when free-swimming coral larvae attach to a rock or other submerged object on the edges of islands. As the corals grow, over very long periods of time, they form into a reef. The three types of reef represent stages in development of a coral reef over time.
1. Fringing Reefs:
Fringing reefs grow near the coastline around islands and continents. These types of reefs are the most common type we see and are considered to be the youngest of the 3 types of coral reefs. They are separated from the shore by shallow lagoons. The first stage of the formation is when the coral larvae attach itself to rocks or soil near the coasts. In certain parts of the world, they tend to form where volcanoes have also formed due to the shallow sloped walls being ideal to make shore reefs. The larvae become polyps and excrete calcium carbonate, which forms their exoskeleton. The secreted calcium carbonate sediments on the rocks and provides a substrate for more polyps coming to attach themselves. As more and more polyps attach, and layer over time, they create a coral reef. Calcareous Algae also add their sediments to the structure. Other organisms with calcareous skeletons, also add their own remains to the reef as they die and sink. Since fringing reefs are the youngest and grow onshore, they tend to have less diversity of species within that ecosystem. Some locations of these reefs include Kenya, Australia and other parts of Africa shores.
Fringing Reef in Eilat, Israel
Photo by: Mark A. Wilson [CC by 2.0]
2. Barrier Reefs:
As the name states, these reef types border along coastlines with a very wide and deep lagoon separating the two structures. The term “barrier” comes from the more shallower coral that sticks out of the water and creates a barrier or wall-like structure. One of the most famous and largest barrier reefs is “The Great Barrier Reef” in Australia. This reef is around 1200 miles and consists of many complex reefs making it up. This type of reef is formed when the fringing reefs slowly combine with each other and form a borderline along the coast. The calcium carbonate structures attract more polyps and the spaces are filled up. It forms a line along the coast and a ring around an island. Large barrier reefs are the rarest type of coral reef and only seen in a select few places on earth such as Belize and parts of the southern Pacific Ocean. Smaller barrier reefs are seen in places where islands are in an earlier stage of becoming submerged.
Great Barrier Reef by Studio Sarah Lou by Flickr
Most of the reefs surrounding the Turks and Caicos Islands are barrier reefs that formed from the precipitation of CaCO3 on the remnants of continental debris resulting from the separation of North America from South Africa 200 million years ago (continental drift). Dissolved minerals in the seawater form small particles called ooids that become cemented together to form oolite rock which makes up most of the Turks and Caicos islands and bank.
3. Atoll Reefs:
An Atoll Reef is a ring-like shaped coral reef or small islands of reefs in a circle with a lagoon in the middle and are usually located in the middle of the sea. These types of reefs are formed when an island has sunk completely (or nearly) in the middle of the ocean from rising sea levels around a pre-existing structure (these islands are often the tops of underwater volcanoes). Most atoll reefs can be found in the Pacific ocean where the waters are warm and salty. They can grow between the sizes of 12.6 km2 (Great Chagos Bank) and as small as 1.5 km2 (Ontong Java reef). More animals are found in an atoll than in earlier stage reefs. Over a million species can live in one square kilometer of coral reef. The three types of reef from fringing to barrier to atoll, form in this sequential order and represent stages of development of a reef.
Formation of Coral” by NOAA Ocean Service Education via Wikimedia Commons
Below is a link to a video created by three undergraduates at Keene State College who discuss more about the different types of coral reefs:
A YouTube element has been excluded from this version of the text. You can view it online here: http://pb.libretexts.org/marine/?p=35
4. Patch reefs
Patch reefs are small, isolated reefs that grow from the open bottom of the island platform or continental shelf. They usually occur between fringing reefs and barrier reefs. They vary in size and rarely reach the surface of the water.
The information in this chapter is thanks to content contributions from Haley Zanga and Emily Michaeles | textbooks/bio/Marine_Biology_and_Marine_Ecology/01%3A_Coral_Reefs_and_Diversity/01.4%3A_Reef_Types_and_How_Coral_Reefs_are_Formed.txt |
When you first see this picture below of a coral reef landscape, you are captivated. Captivated by the beautiful, bright, elegant colors popping through the clear blue water. But why? Why do these coral reefs have such bright, bold colors? The colors found in colorful corals are mostly due to three things – photosynthetic pigments, fluorescent proteins, and non-fluorescent chromoproteins.
Coral Polyps
In order to understand why corals get their color, it is important to first learn the structure of the coral polyps. The majority of polyps have clear, transparent bodies over their hard, white skeletons. Millions of zooxanthellae live inside the tissues of these polyps. These zooxanthellae produce pigment, and because they reside in the clear tissue of the polyp, the pigments are visible, and the corals get their beautiful colors.
Light Intensity Dependency
Zooxanthellae are photosynthetic algae, and in order to ensure there is a continuous amount of nutrients being delivered to the coral, the coral regulates the number of zooxanthellae cells, as well as the amount of chlorophyll in them. Because zooxanthellae is a photosynthetic algae, zooxanthellae are sensitive to light intensity, which can ultimately alter the color and overall health of the coral. Too much light intensity can release some zooxanthellae, or the amount of chlorophyll will be decreased. In the presence of harsh light intensity, it can potentially be detrimental to the coral reef by excess oxygen production, causing it to accumulate and have toxic effects on the coral. If the light intensity is insufficient, the zooxanthellae will not be able to provide enough nutrients for the host coral, and thus the number of zooxanthellae and amount of chlorophyll will increase. When the zooxanthellae cells use light to produce large organic compounds, oxygen is also released. The brighter the color of the coral, the more photosynthesis and oxygen production. Corals can decrease or increase the chlorophyll production from the zooxanthellae cells, depending on environmental requirements. They can also expel zooxanthellae when under stress.
So, what does this mean? Essentially, the number of zooxanthellae and the amount of chlorophyll affect coral coloration. Because zooxanthellae cells range in color from a golden-yellow to brown, and when there is a large number of zooxanthellae cells present the coral color appears brown, it suggests that the light intensity affects the number of zooxanthellae and the amount of chlorophyll.
Why are some more colorful than others?
Corals are home to different types, or clades of zooxanthellae, that vary in light intensity sensitivity and temperature. While zooxanthellae color can range from a golden-yellow to a brown pigment, zooxanthellae can also fluoresce deep red color under certain circumstances. For example, Phycoerythrin is a photosynthetic pigment that fluoresces a bright orange color that’s found in zooxanthellae. In addition, there are about 85 more fluorescent pigment colors produced by colorful corals, typically cyan, green, yellow, and red, and they can even glow in the right lighting! These proteins absorb light of one color (wavelength) and emit (fluoresce) a different (lower energy wavelength) color. There are also other pigments produced by the coral called chromoproteins, they are non-fluorescent, or reflective, and there are about 24 chromoproteins found in corals. Of the 24 chromoproteins, the pigments can appear as purple, red, blue, to name just a few.
Coral Reef by Jan-Mallander via Pixabay [CC 2.0]
What Are the Roles of the Corals Colors?
It is thought that these fluorescent compounds may help corals survive, however, the role is not yet well understood. A few possibilities are that they may serve as a “sunscreen” protecting corals by filtering out harmful ultraviolet rays. Corals can manipulate the zooxanthellae cells in response to light. Only recently have scientists begun to comprehend the relationship between color-producing light and how it appears at different depths. Wavelengths of light become diluted the deeper down they have to travel. UV light rays are naturally filtered out by water in deeper oceanic regions. That’s why shallow-water reefs are bright with color and deeper coral tend to appear more gray-like. It has also been shown thatinjured corals often form colorful patches. This is due to the fact that the coral is makingfluorescent molecules that act as antioxidants, capturing toxic oxygen radicals that threaten to damage cells.
The information in this chapter is thanks to content contributions from Jaime Marsh and Haley Zanga | textbooks/bio/Marine_Biology_and_Marine_Ecology/01%3A_Coral_Reefs_and_Diversity/01.5%3A_Coral_Reef_Colors.txt |
Coral reefs are home for many organisms such as sponges, fish including large nurse sharks and reef sharks to groupers, clownfish, eels, snappers, and parrotfish, jellyfish, anemones, crustaceans, other invertebrates and algae. So, how do coral reefs support such a huge weight on their shoulders? It is the symbiotic relationship that is formed when two different species interact with each other. These interactions create a balance within the ecosystem because at least one of the species is gaining from it. The other species may also gain from the relationship, be unaffected or even get harmed from the relationship. Symbiotic relationships are very common in the ocean, especially near coral reefs. There are three main types of symbiotic relationships. They are mutualism, parasitism, and commensalism. Mimicry is also frequently seen amongst coral reef organisms.
Types of Mutualism:
There are two primary types of mutualism: obligate mutualism and facultative mutualism.
Mutualism, or a mutualistic relationship, by definition, is when two organisms of different species work together so that each is benefiting from the relationship.
An example of obligate mutualism is the relationship between ants and Acacia plants. While the plant provides shelter and food for the ants, the ants actually defend the plant from organisms such as other herbivores that may eat the plant, as well as remove any other species of plants that may limit the plant’s growth.
A more specific example of obligate mutualism that is more related to this topic would be the relationship between hard coral and algae (zooxanthellae). The relationship between coral and zooxanthellae (algae), is one of the most important mutualistic relationships within the coral reef ecosystem. Zooxanthellae are microscopic, photosynthetic algae that reside inside the coral. The hard coral provides protection, as well as compounds needed for photosynthesis to occur. In return for their protection for herbivores and other organisms, zooxanthellae photosynthesize organic compounds from the sun, and then pass the nutrients, glucose, glycerol, and amino acids, which are the products of photosynthesis, to their coral hosts, essentially giving the coral reefs their beautiful colors. The corals then use those nutrients to produce proteins, fats, carbohydrates, and calcium carbonate. This is so important, in fact, approximately 90% of the nutrients produced during the photosynthesis in zooxanthellae is transferred to the coral for their use. Zooxanthellae also aid in the excretion, or removal of waste such as carbon dioxide and nitrogen. Ultimately, without algae, coral would starve to death (coral bleaching), and if algae didn’t have protection, they would be more vulnerable to several herbivores and other organisms. This relationship is so important, that if this mutualistic relationship did not exist, it would be very likely coral reefs would not even exist. Therefore, making this relationship obligate mutualism, as mentioned before.
CORAL POLYP ” BY EMAZE
The mutualistic relationship between anemones and clownfish is also another commonly known relationship. Clownfish are found in warmer waters of the Indian and Pacific oceans. Of the over 1,000 anemone species that live in the ocean, only 10 species coexists with the 26 species of tropical clownfish. Within these species, only select pairs of anemone and clownfish are compatible. Sea anemones are actually predators, with stinging polyps, that attach themselves to rocks, the ocean floor, or even coral. They patiently wait for fish to swim by close enough to get entangled in their poisonous tentacles. The toxins paralyze their prey, and the tentacles guide the prey into the anemone’s mouth. However, clownfish are the exception and actually call the anemone home. Clownfish are coated with a mucus layer that essentially makes them immune to the deadly sting of the anemone. Therefore, clownfish are able to live within the anemone’s tentacles, while also gaining protection from predators, and the clownfish helps feed the anemone by either letting them eat their leftovers, or by also luring fish over to the anemone, so that the anemone can catch them with their poisonous tentacles, and eat them for dinner (or maybe lunch).
“Clownfish and Sea Anemone” by Samuel Chow under Flickr
• Facultative mutualism the other type of mutualism, is when species benefit from one another, but do not necessarily fully depend on one another.
An example of facultative mutualism is the relationship between certain types of our gut bacteria, or the bacteria that live in our digestive tracts, and us humans. When we eat food, bacteria use some of the nutrients from that food we are actually digesting, and in return, they help us digest our food.
Again, a more specific example of facultative mutualism that is more so related to the coral reef ecosystem, is the relationship between shrimp or smaller fish and large marine organisms. The shrimp or cleaning fish remove materials, such as parasites, off of the larger marine organisms, in which they get a meal from, and the larger marine organisms have potentially harmful parasites removed!
As mentioned before, earlier on in the post, smaller fish or cleaner shrimp, such as the Bluehead Wrasse or Spanish Hogfish remove parasites and other materials off larger marine organisms such as fish, sharks, and rays. In most cases, these smaller fish would typically be the larger marine organism’s prey, however, in this case, these larger organisms gain the benefit of having these parasites removed, that could potentially cause harm, while the smaller fish or shrimp get a meal.
Cleaner fish and larger fish share a mutualistic relationship. This is because the cleaner fish eats harmful parasites and other small sources of food off of the large fish. This gives the cleaner fish a meal, the larger fish is helped because it no longer has these parasites on them. Often times larger fish wait in “cleaning stations” for the cleaner fish to come and get these things off of them. Some small shrimp can also be cleaners. The picture below shows a cleaner shrimp cleaning a large fish at a cleaning station that would normally eat the shrimp if it wasn’t for this mutualism.
DANGEROUS DINING” BY CHRIS LEWIS UNDER VIMEO
Another facultative mutualistic relationship is between the root-fouling sponge called Tedania inis, and red mangrove called Rhizophora mangle. In this relationship, the red mangrove provides the sponge with carbon that was produced by the mangrove, and the nitrogen the sponge releases gets eaten up by the mangrove to enhance growth.
Mutualism also occurs between spider crabs and algae. This relationship benefits both of these species because the greenish-brown algae live on the spiders back, which helps the spider crab blend into the shallow areas of the ocean floor where they live. In return, the algae benefit from a good place to live.
JAPANESE SPIDER CRAB” BY (OVO) UNDER FLICKR
Another example is the relationship between the Boxer Crab and anemones. In this relationship, the Boxer Crab carries around two anemones that sting and it uses them for protection. The anemones are benefited because since the crab carries them around, it allows them to be mobile which increases their options for finding food.
BOXING (POM POM) CRAB” BY LIQUIDGURU UNDER VIMEO
One last mutualistic relationship is the relationship between a goby (Nes Longus and Ctenogobius saepepallens) and a snapping shrimp (Alpheus floridanus). The shrimp dig a decent sized burrow in the floor of the ocean, and the goby will then live in the entrance of that burrow. When the shrimp exits the burrow, it will stay in contact with the goby through its antennae, and depending on the species of the goby, it will either signal to the shrimp of approaching predators by darting headfirst back into the burrow or by flicking its caudal tail. Ultimately, the goby gets a free place to live and hide from potential predators, while in return the shrimp gets a look-out individual while it hunts for food!
Parasitism:
Parasitism is not a mutualistic relationship because only one of the species is benefited. The parasite gains from the relationship while the other species involved is harmed. Ectoparasites live on the outside of the host body, whereas endoparasites live inside the host.
One example of a ectoparasitic relationship is between fish lice and small fish hosts. The fish can be killed if there are too many fish lice attached to it. The lice benefit from the fish by feeding off of their bodily fluids.
Isopods can also cause be involved in a parasitic relationship. Some isopods will eat the fishes tongue and then live in the fishes mouth so they can eat whatever the fish is attempting to eat.
“BETTY IN MOUTH” BY UNIVERSITY OF SALFORD PRESS OFFICE UNDER FLICKR
Commensalism:
Commensalism is a relationship where one species benefits from another species. The other species is neither harmed nor helped in this relationship. There are many examples of commensalism in the ocean.
One example of commensalism among marine life is jellyfish and small fish. The small fish will typically hide inside of the jellyfish’s stinging tentacles if the stinging does not affect them. The tentacles provide protection for the fish from larger predators. This relationship has no effect on the jellyfish.
“BABY FISH TAKE SHELTER IN JELLYFISH” BY EARTH TOUCH NEWS NETWORK
Another relationship is between shrimp and a featherstar. The shrimp will blend in with the featherstar and use it for protection. As you can see in the picture below, it is very difficult to find the shrimp hiding in there.
“Shrimp in Featherstar” by prilfish under Flickr
Mimicry:
One type of Mimicry is when one organism that is harmless evolves to look similar to another organism that is poisonous. This stops predators from eating them because they think they are the poisonous species. They can also use mimicry to appear larger than they really are.
The four-eye butterflyfish uses a large eyespot in order to appear larger to predators.
“CHAETODON CAPISTRATUS1” BY CHRIS HUSS UNDER PUBLIC DOMAIN
Another example of mimicry is between the Sabre-tooth Blenny and Cleaner Wrasses. The Cleaner Wrasse have a mutualistic relationship with larger fish so they don’t get eaten, and the Sabre-tooth Blenny takes advantage of this relationship by evolving to look very similar to the Cleaner Wrasse. Instead of cleaning the larger fish, the Sabre-tooth Blenny will take a bite out the the large fish’s flesh and swim away. This is an example of aggressive mimicry.
“BLUESTREAK CLEANER WRASSE” BY NEMO’S GREAT UNCLE UNDER FLICKR “SABRE-TOOTH BLENNY” BY FISH INDEX
On the top, there is a Bluestreak cleaner wrasse and on the bottom is a sabre-tooth blenny. You can see how similar they look and how fish could mistake them.
What’s the Big Deal?
Mutualistic relationships, whether obligate or facultative mutualism, are an integral part of sustaining a coral reef ecosystem, and without them, the coral reefs would simply not exist. These mutualistic relationships define a largely intricate number of connections and relationships which deeply rely on one other, and where one could start to deteriorate, another could as well. It is more important now than ever that we sustain healthy coral reefs to support these intricate relationships, communities, and ecosystems.
The information in this chapter is thanks to content contributions from Jaime Marsh, Christian Paparazzo, and Alana Olendorf | textbooks/bio/Marine_Biology_and_Marine_Ecology/01%3A_Coral_Reefs_and_Diversity/01.6%3A_Symbiotic_Relationships_in_Coral_Reef_Ecosystem.txt |
Why Are Reefs Important?
Coral reefs are very complex ecosystems that provide valuable habitat for fish and other animals with their beautiful and unique structures. These structures provide shelter for many organisms such as fish, marine worms, clams and many other animals and plants that all play a vital role in the coral reef ecosystem. Coral reefs are important for a variety of reasons which we will discuss below.
Coral Outcrop Flynn Reef by Toby Hudson via Wikimedia [CC by 2.0]
Biodiversity:
Coral reefs are often thought of as a busy city; the buildings being made of coral and the thousands of organisms inhabiting this city acting like the humans interacting with each other and performing daily jobs. Coral reefs provide protection and shelter to nearly one-quarter of all known marine species and have evolved into one of the largest and most complex ecosystems known to humans. Coral reefs are home to over 4,000 species of fish, 700 species of coral and thousands of other plants and animals. This diversity of species provides a large gene pool giving communities more resilience during extreme environmental conditions and climate change. This is important to the overall health of an ecological community. With greater species diversity, the impact of losing any one species to extinction will be less. The enormous diversity of coral reef organisms also provides potential for new medicines or other products that may be developed from biochemicals that these organisms produce. Most coral reef organisms have not been studied for their potential benefits to medicine and industry.
Coastal Protection:
Coral reefs act as a natural barrier protecting coastal beaches, cities, and communities from the waves of the ocean. Nearly 200 million people depend on coral reefs to protect them from storm surges and waves. Without coral reefs, many buildings would become vulnerable to storm damage.
Reefs Protect Costallines by NOAA via Flicker [CC by 2.0]
Food:
Coral reefs are an important food source for the people who live near the reefs and are crucial for worlds fisheries providing them with a significant source of protein. In developing countries, the reef is said to contribute to one-quarter of the total fish catch providing food resources for tens of millions of people.
Commercial Fisherman” by NOAA [CC by 2.0]
Medicine:
Many of the compounds now being used in human medicines are found on the coral reef with the potential of more to be discovered. A number of organisms found on reefs produce chemical compounds that have been isolated for human applications. Scientists have developed treatments for a variety of illnesses such as cardiovascular diseases, skin cancer, ulcers, and leukemia. Other compounds can help with reducing inflammation, kill viruses and relax muscles. Not only do the organisms inhabiting the coral reef provide medical treatments but the coral’s unique skeletal structure has been used for bone-grafting material.
Tourism:
Coral reef ecosystems are among the most biologically diverse and economically valuable ecosystems on Earth, as they not only support local but global economies. Through tourism (i.e. snorkeling, scuba diving, swimming) and fisheries, coral reefs generate billions of dollars, as well as jobs in more than 100 countries around the world. The annual value of the ecosystem services provided by coral reefs to millions of people is estimated to be over \$375 billion. The coral reefs can indirectly bring economic value to these countries by letting visitors enjoy beaches, eat local seafood, paddleboard and sail. All of this is possible due to coral reefs acting as a buffer against waves, storms, and floods. The downside is when tourism harms the coral reefs it not only affects the organisms and the coral reefs, but local people and their economy who rely on the income from tourism.
Snorkel by Angelique800326 via Wikimedia [CC by 2.0]
A good example can be found in Bonaire, a small Caribbean island. Bonaire earns about \$23 million (USD) annually from coral reef activities, yet managing its marine park costs less than \$1 million per year. A study conducted in 2002 estimated the value of coral reefs at \$10 billion, with direct economic benefits of \$360 million per year. For residents of coral reef areas who depend on income from tourism, reef destruction creates a significant loss of employment in the tourism, marine recreation, and sport fishing industries. This large amount of money of revenue generated is being threatened by the degradation of coral reefs. As you can see there is a positive feedback loop occurring because of this situation. Many components of tourism, including recreational activities, are the cause of damage to the reefs but ironically it has been shown that ecotourism is as well.
The information in this chapter is thanks to content contributions from | textbooks/bio/Marine_Biology_and_Marine_Ecology/01%3A_Coral_Reefs_and_Diversity/01.7%3A_Importance_of_Coral_Reefs.txt |
Coral Reefs as Ecosystems
An ecosystem includes all of the living organisms (biotic) in a given area, interacting with each other, and also with their non-living components and environmental factors (abiotic). In an ecosystem, each species has its own niche or role to play. All of the aspects of the coral reef act together in a unit called an ecosystem. Coral reefs are a very high functioning ecosystem and are home to thousands of species of marine life. Algae, fish, echinoderms and many other species depend on the reef for their habitat and food too. The number of species is directly proportional to the mass of the coral reef. Mesophotic coral ecosystems (MCEs), are a common type of ecosystem that are home to light-dependent life, such as corals and their zooxanthellae. MCEs are typically at depths of 30-40 m and can extend over 150 m in tropical and subtropical regions.
Roles of Marine Organisms
The biotic portion of the marine ecosystem includes three main groups called producers, consumers, and decomposers. The organisms in these groups all play a key role in contributing to a functioning ecosystem.
Producers– These are autotrophic organisms which make their food through photosynthesis. Green plants, algae, and chemo-synthetic bacteria are all examples of producers in marine habitats.
Consumers– These organisms obtain food from other organisms or organic matter and are animals, zooplankton, and heterotrophs. Consumers are broken down into primary, secondary, tertiary, and quaternary categories. Primary consumers feed on producers and are herbivores. These organisms include sea turtles, zooplankton, and sea urchins. The secondary level feed on the primary producers and are organisms like rays and fish. The last levels are tertiary and quaternary, which feed on the secondary consumers and are the large fish, sharks, and sea lions.
Detritivores and Decomposers– These organisms feed on dead organic matter. Crustaceans like crabs and lobsters which shred and consume dead animals are examples of detritivores. Bacteria and fungi are decomposers that gain energy by breaking down dead organic matter into nutrients such as nitrates, nitrites, phosphates, and carbon dioxide. These are released back into the surrounding environment along with heat energy.
A Vimeo element has been excluded from this version of the text. You can view it online here: http://pb.libretexts.org/marine/?p=49
O-BIO-15 Energy Pyramid” by eLearn.Punjab via Vimeo
The health, abundance, and diversity of the organisms that make up a coral reef are directly linked to other surrounding terrestrial and marine environments. Mangroves and seagrass beds are two of the most important associated habitats of the greater coral reef ecosystem.
Mangroves:
Mangroves are salt-tolerant trees that grow along tropical and subtropical coasts. They provide protection by stabilizing the coastline with their complex root system. They protect uplands from erosion, wind, waves, and floods. They also act as carbon storage systems, and help produce nutrients and filter out pollutants. Their complex root system serves as breeding and feeding grounds for marine organisms such as fish, invertebrates, and others. They are especially important as nursery grounds for juvenile and larval reef organisms, many of the animals raised in mangroves migrate to coral reefs.
There are around 80 different species of mangrove trees that live in many places around the world. In Florida, the Bahamas and the Caribbean, there are three main types of mangrove. Red mangroves grow on the ocean’s edge, black mangroves occur a bit upland from the reds, and white mangroves are found at the highest elevations furthest upland.
The schematic mangrove zonation done by Tom Vierus on www.livingdreams.tv.
In Mumbai, the shores once used to be covered in mangroves but those forests were severely degraded from housing developments encroaching on the edge of the land and mismanagement of waste disposal. Mumbai alone has lost about 40% of its mangrove forests in just a few decades from being destroyed for houses to be built or also from the wastes left behind which can clog the roots of the trees preventing them from getting oxygen and filtering the freshwater they need.
Mission Mangroves, a project run by NGO United Way Mumbai, is making changes towards protecting the remaining mangroves and planting new ones. Every month volunteers partake in a clean up of the wetlands and twice a week there are planting sessions to restore the forests. At the time of this writing, they have already planted 55,000 new trees. United Way Mumbai’s director of community impact, Ajay Govale, stated that “the mission is to green 20 acres of wetland by planting mangroves, and to educate thousands of Mumbai people about the importance of mangroves.”
India is at the top for countries that are the worst at mismanaging plastic wastes and Mumbai is one of the worst cities for air pollution. The destruction of mangroves has contributed to this problem as they help filter pollutants out of the air and can absorb four times more carbon than tropical forests. The loss of mangrove forests also impacts other parts of the ecological community. Since they serve as shelter and breeding grounds for marine wildlife, this affects local fisheries and communities reliant on these marine animals. The loss of the mangrove forests also leaves the coastlines more vulnerable to be affected by rising sea levels from global climate change.
Seagrasses:
Seagrass – Seagrasses are flowering plants that often form meadows between mangrove habitats and coral reefs. They provide nutrients to organisms such as sea turtles, sea urchins and thousands of other species. Seagrasses also provide protection and shelter for crustaceans like crabs and lobsters, as well as fish such as snappers. Similar to mangroves, they also function as nursery grounds for juveniles, perform water filtration , release oxygen necessary for most marine life, and prevent seabed erosion.
Seagrass Meadows by U.S. Department of Agriculture via Flicker
The information in this chapter is thanks to content contributions from Marisa Benjamin,Haley Zanga and Emma Verville | textbooks/bio/Marine_Biology_and_Marine_Ecology/01%3A_Coral_Reefs_and_Diversity/01.8%3A_Coral_Reefs_are_Complex_Ecosystems.txt |
Many marine organisms have at least a single larval stage . The reproductive adults will release many offspring into a water column. These free-swimming larvae will then become part of the zooplankton , being carried mostly by currents. This life stage is very important to some species, who as adults are benthic . Once the larvae settle, they are there for life. There are three methods of larval dispersion and development:
1. Direct development or crawl-away larvae have a low dispersal potential. The young usually hatch from the egg looking very similar to the adults of the species.
2. Lecithotropic larvae have more of a dispersal potential than crawl-away larvae. One thing that characterizes this type is that they are provided with a yolk sac, or some other form of nutrition. This finite source of nutrition only allows for a certain amount of time to disperse and settle before this nutrition source runs out.
3. Planktotrophic larvae have the greatest dispersal potential. they can survive as pelagic larvae longer than the other types of larvae. This is because they are able to feed on smaller zooplankton and phytoplankton. Most sessile invertebrates have planktotrophic larvae.
There are many settlement cues, all of which vary from species to species.
Chemical cues are common and heavily studied. These cues are biological compounds created by another individual that larvae pick up on and use as a way to tell if a location is safe to settle in. These cues can be from adults of the same species, which ensures it is a safe place to settle, or from predators, which ensures its not a safe place to live. Raymond C. Highsmith studied the induced settlement in sand dollars, Dendraster excentricus. He found that the larvae of D. excentricus showed a preference for adult-associated sand or sand with adults present. He also found that the type of substrate didn’t matter, as long as adults were present, thus proving a chemical cue. The preference for this settlement cue is most likely due to the absence of micro predators that feed on metamorphizing larvae, such as Leptochelia dubai, from areas where adults are present. The reworking of the substrate by the adult sand dollars makes it impossible for these micro-predators to live there, leaving it a safe place to settle.
Sand Dollar by mosaikweb Via Pixabay
Physical settlement cues are also important for some species. Some larvae may only settle in areas with certain substrate types. Fish larvae are commonly seen to use physical cues as they prefer certain habitat types. Whalan et al. looked at this largely ignored cue. They studied five types of sessile marine invertebrates found on coral reefs, two species of scleractinian coral and three species of sponge. They found that both of the coral and one sponge species had significantly higher settlement on tiles with microtopography that included divots that closely matched the larval width. This proves that physical cues also play a role in the settlement.
Previously there have been observations about where coral reef fish larvae are orientated when they swim offshore. They require orientation cues. A study done by Jack O’Connor and Rachel Muheim examined the effects of magnetic fields on the orientation of coral reef fish. During the observations, coral-reef fish larvae revealed remarkably consistent orientation behavior while swimming offshore, requiring large-scale orientation cues. However, the mechanisms causing this behavior are still being investigated. One potential large-scale cue for orientation is the Earth’s geomagnetic field. Here, they examined the effect of magnetic field manipulations on the orientation behavior of coral-reef fish during the pelagic larval phase. In the absence of visual cues, individual larvae responded to a 90-degree shift of the horizontal component of the magnetic field within a Helmholtz coil with a comparable shift in orientation. This shows that they use a magnetic compass for orientation. Their findings suggest that geomagnetic field information guides the swimming behavior of larval fish in the pre-settlement phase. The ability to use large-scale sensory cues allows location-independent orientation of swimming, a behavior that influences dispersal and connectivity of fish populations, which has important ecological implications for anthropogenic development of marine areas.
The information in this chapter is thanks to content contributions from William Trautman | textbooks/bio/Marine_Biology_and_Marine_Ecology/01%3A_Coral_Reefs_and_Diversity/01.9%3A_Larval_Dispersal_and_Settlement.txt |
The fish species Holocentrus adscensionis, also known commonly as the squirrelfish or soldierfish, is found in the family Holocentridae. There are around 70 different species of the tropical reef squirrelfish. They have large eyes to help them see at night, are colorful (typically red and gold) with spiny elongated fins. While they can grow up to two feet in total length, they commonly do not surpass 10 inches. Squirrelfish are found distributed throughout the warm tropical waters of the Atlantic Ocean around the Caribbean, Bahamas, Florida, Bermuda, Turks and Caicos, and the Gulf of Mexico, where they typically remain at depths four feet to 40 feet where the waters are still warm but can go up to around 250 meters deep.
Squirrelfish have all five fins, a see-through pectoral fin, ventral, anal, and elongated dorsal and caudal tail fins. They also have fin spines along their spine with horizontal striped white lines along their back below them. In some species of squirrelfish, they have spines on their gill covers that are venomous that they use for self-protection. When the squirrelfish are juveniles they have more iridophores, cells that reflect light, which give them a silvery shimmer. When they transition into adults is when the red pigments of the chromatophores are more prominent distinguishing the young from the adults. The red orangey color helps them to blend in with the corals they sleep in during the day. The IUNC red list has classified squirrelfish globally as a species of least concern when they were assessed in January of 2013 but, global warming may have changed this trend as the corals are being bleached from being stressed as a result from warming ocean waters.
Squirrelfish are nocturnal carnivorous fish that hide in crevices of the coral reefs during the day to avoid predation. At night they swim through the reefs through seagrass beds hunting meroplankton, larvae and small crustaceans with the occasional small fish. When these fish are young, they tend to group together with one another which helps with protection and hunting, while adults prefer to establish their own territory and be alone. They are also able to communicate intra-specifically by producing sounds with their swim bladders. They make these sounds through vibrations to warn off predators or define their territory.
02.10: Bull Sharks
Bull sharks are commonly found in warm, coastal areas in freshwater or saltwater. They are well known for their aggressive behavior and can be a big risk for humans since they are known for living in high density near the shoreline. Many experts consider Bull sharks to be the most dangerous shark in the world. They are among one of 3 species most likely to attack humans.
Parts of a shark. photo by Chris_huh via public domain, March 7th 2007.
They are shorter than other sharks with a blunt nose that they occasionally use to head butt prey before attacking. They are gray on top and white below and have dark tip fins. This allows them to hunt better because prey below them see white from above masked with the light from the sun and animals above them see gray which can be hard to see blending in with the ocean floor. This is known as countershading. The bull shark is diadromous, meaning they can swim between salt and freshwater with no issues. The reason for this is due to a bottleneck effect where groups of bull sharks were separated during the last ice age. This bottleneck effect allowed bull sharks to adapt to both freshwater and saltwater. Bull sharks blood is naturally salty to allow them to live in saltwater. When moving from saltwater to freshwater where the salt levels are much lower they increase the level of osmosis in their gills to make up for the loss of sodium and chlorine. They also have a number of organs that can regulate the amount of saltwater in their body to allow them to easily live in freshwater, organs like, rectal gland, kidneys, liver, and gills. Although Bull sharks can live in freshwater it may not be advantageous for them to do so, mainly because their main source of prey is located in saltwater areas.
A Caribbean reef shark photographed at Roatan, Honduras.
CC BY 2.5
Bull sharks mainly eat bony fish. However, they are not picky eaters. They will eat dolphins, turtles, stingrays, even other Bull sharks. Humans are not necessarily on their menus but they have been known to bite humans out of confusion for other prey or curiosity. They use a technique called the bump and bite attack. After the first initial contact, they continue to bite and tackle prey until they are unable to flee.
Bull sharks mate during the late summer and autumn seasons. They can have anywhere from 1-13 live young after gestating for 12 months. Gestation is the process of the development of a fetus inside the body of viviparous animals.
The information in this chapter is thanks to content contributions from Bryce Chouinard
02.11: Longfin Damselfish
Coral reefs are home to more than 35,000 marine species. These species range from simple plankton all the way up to complex reef sharks. One little fish that I have found to be extremely interesting is the Longfin Damselfish. Every living organism in the world has a common name and a scientific name. The scientific name of Longfin Damselfish is Stegates diencaeus in the family Pomacentridae.
Adult Longfin Damselfish reach a length of 12.5 cm when they become full grown. Adults are commonly a blackish-grey color and their snout and nape of the neck have a yellowish-brown tint. On their anal fin, you can see a bright blue coloring just on the outer most part of their fin. Their head is generally small and contains a small row of sharp front teeth. Their dorsal fin is singular and continuous with 12 spines and 14-17 rays. Their anal fin also contains rays and 2 spines. Just like humans, juveniles and adults look much different. When Longfin Damselfish are younger, their bodies are bright yellow. There are two purple-blue stripes that start at their head and continue all the way back to their anal fins. Once the stripe gets to the anal fin, it ends with a large black dot just at the base of their anal fin.
Longfin Damselfish juvenile by zsispeo via Flickr
Longfin Damselfish by zsispeo via Flickr
Longfin Damselfish can be found in the Atlantic Ocean, mainly in southern Florida, Bahamas, Mexico and the Carribean. They like to make their homes in coral and rocky reefs. They are a very territorial species and will spend most of their lives by themselves or with their mate. It is unknown at what points during the year Longfin Damselfish mate, but, we do know that they always spawn at dawn. When the mating season begins, the male and female engage in a “mating dance” with rapid swimming and fin movements. During this time, the males will turn a shade or two darker and some display white blotches. Once the female picks her mate, she lays a ton of sticky eggs that stick to the nest. The male then comes and fertilizes the eggs. After fertilization, the male will protect the eggs until they are hatched. This usually takes roughly 2-3 days.
Longfin Damselfish consume mostly algae, plankton, and benthic invertebrates. This puts them in the category of secondary feeders. The only natural known predator that they have is the Lion Fish. While this predator is an invasive species with no known predators of their own, the Longfin Damselfish species is nowhere near endangered. Longfin Damselfish are also caught for the aquarium trade. Fishermen have to use nets and traps to catch the Longfin damselfish. They are known as nibblers so they can not be caught with hook and line. While they are caught by humans for sale, it does not appear to be globally affecting their populations.
The information in this chapter is thanks to content contributions from Morgan Tupper | textbooks/bio/Marine_Biology_and_Marine_Ecology/02%3A_Common_Fish_in_the_Coral_Reef/02.1%3A_Squirrel_Fish.txt |
Parrotfish are colorful fish found throughout the world’s coral reefs. There are about 90 species of parrotfish, including Stoplight, Queen, and Princess Parrotfish common in tropical and subtropical parts of the western Atlantic Ocean and the Caribbean Sea. Parrotfish are characterized by a beak-like structure (fused teeth) that they use to feed. They are mostly herbivores and feed on algae, but also feed on corals and sponges. Their beak helps them scrape algae and crush the hard limestone of corals. They then excrete this undigested material as sand, which helps to create the white sandy beaches of the tropics.
Parrotfish are also known as sequential hermaphrodites. A sequential hermaphrodite is an animal that goes through an initial and terminal phase during its adult life. Each phase is characterized by being one gender. So, for example, some species of parrotfish start as female in their initial phase, then change to male in the terminal phase. This change usually takes place due to an environmental cue, such as the loss of the dominant male.
Probably the most interesting thing though about parrotfish is their role in coral reefs. Coral reefs face a number of stressors including ocean acidification, rising ocean temperatures, and changing ecosystem balance due to overfishing and bycatch. Interestingly, studies show that the number one thing we can do to protect the health of coral reefs is to limit the number of parrotfish we remove from the environment. In the Caribbean, parrotfishes are the primary herbivores on the reef at mid-depth, helping keep macroalgae in check. A shift to macroalgae dominated habitat would offer little value to fisheries, as most of the nutrients are lost to detrital pathways. Unfortunately, parrotfish are commonly fished in the Caribbean. A recent study suggests that if we implement a capture size restriction of less than 30cm there is a win: win outcome in the short term. This would have both ecological and economic benefits as it would also lead to an increase in coral reef health and production. Focusing on more long term benefits requires a more strict harvest limitation to combat the ever-increasing threats to coral reefs.
Parrotfish are also one of the primary grazers of sponges. Sponges (along with corals) are the primary habitat-forming organism on Caribbean reefs. Loh and Pawlik found that parrotfish, along with other spongivores, would graze on sponges that lacked chemical defenses over sponges that possess secondary metabolites. Due to this grazing, the palatable sponges tend to heal and grow faster, as well as have a higher rate of recruitment and reproduction. This allows them to compete with sponges that are left relatively untouched. They also determined that sponge species composition depended more on the abundance of spongivores instead of geographic location. A decrease in the number of these species would result in a top-down effect, leaving more of the faster spreading palatable sponges to out-compete the slower defended sponges and reef-building corals, worsening the state of these coral reef communities. Below is a figure from this paper which compares different sites and the percent of sponge communities and how it relates to an abundance of spongivores.
Figure 2 from the Loh and Pawlik paper
The information in this chapter is thanks to content contributions from William Trautman | textbooks/bio/Marine_Biology_and_Marine_Ecology/02%3A_Common_Fish_in_the_Coral_Reef/02.12%3A_Parrotfish.txt |
Hypoplectrus indigo, or the Indigo Hamlet as it is commonly known, is in the order Percoidea and the family Serranidae. Indigo Hamlets typically grow to be 3-5 inches (about 8-13 centimeters) in length and are known for their beautiful blue and white lateral “bar” striped bodies. They typically have blue colored ventral fins and opaque clear/white pectoral fins and caudal. The fin lines and dorsal fin range from blue to opaque clear/white in color, and they tend to mate with other Hamlets of similar color and stripe patterns.
Although the patterns of striping can differ a bit, all Indigo Hamlets possess the similar blue and white diagonal 5 stripe pattern throughout their life phases which are spent within the safety of the reef. Hamlets are small, oval-shaped fish that have sloping heads and tapered bodies. The Indigo Hamlet ranges throughout the Caribbean island reefs, from the Bay Islands to the Bahamas, Belize, the Cayman Islands. Hamlets are known to stay near the benthic region on and around the coral reefs between 3 and 45 meters, however, that is not to say that they are inactive, as they are often seen swimming around. They are relatively solitary fishes who tend to stick to themselves rather than swim in large schools and are described as highly resilient to the environment. Although they themselves are not a protected species, they do live in some protected reef areas. Hamlets are also simultaneous hermaphrodites, meaning that they have both male and female sexual organs and are able to act as both genders at the same time, which is incredibly rare for vertebrates. Although they do not self fertilize, they do take turns mating as both male and female.
The Hamlet is a carnivorous fish who feeds predominantly on other species of fish and is relatively territorial within its habitat. Because of this, it is possible that the Indigo Hamlet possesses its beautiful coloration for a number of reasons that are similar to other fish species. The patterns and coloration may announce territorial ownership to others, secondly, it may help with courting, and third, it is possible that the bright coloration would be useful for protecting their eggs and hunting grounds. By being brightly colored and patterned, mates will easily spot them as their own species. Furthermore, their bright color and aggressive behavior may draw others away from their territory and eggs.
The information in this chapter is thanks to content contributions from Suki Graham
02.2: Jackknife Fish
The Jack-knifefish (Equetus lanceolatus), is a black and white/silvery fish which belongs to the Sciaenidae family, the drums category. It is a Carribean reef fish and can be found in the Carribean, Bahamas, Florida, and the Gulf of Mexico.
Photo by Barry Peters is licensed under CC BY 2.0. This is a juvenile Jackknife fish.
Morphology
Morphology deals with the size, form, shape, and structure of organisms. The Jack-knifefish is a fairly small fish ranging from about 5-9 inches in size (12-23 cm). It has an elongated dorsal fin with a black band that runs from the tip of the dorsal fin to the end of the tail, which helps identify this exotic looking fish. They are an odd-shaped fish and have considerably long dorsal and caudal fins. The combination of those two fins resembles a jack-knife, giving it it’s a common name, the Jack-knifefish. This odd trait is more present in a juvenile jackknife fish than older jackknife fishes.
General description and Behavior
The Jackknife fish is a shy and graceful saltwater fish, so they require a peaceful environment with a sandy bottom and plenty of places/rocks to hide in. They feed on inhabitants of reefs like ornamental shrimps, polychaete worms, and even other small reef fishes; because of this, I think it’s safe to say that they are carnivorous benthic feeders.
The odd shape of the Jackknife fish actually serves as a kind of protection from predators by confusing them into thinking that it is two different fishes, rather than one. The coloration of the jackknife fish may also serve to hide the eyes so that predators cannot tell where the fish is looking, and even confuse the predators into thinking maybe it’s not even a fish.
The information in this chapter is thanks to content contributions from Malisa Rai | textbooks/bio/Marine_Biology_and_Marine_Ecology/02%3A_Common_Fish_in_the_Coral_Reef/02.13%3A_Indigo_Hamlet.txt |
Specific Name: Balistes Vetula
Genus: Balistes
Species: Vetula
Family: Balistidae
This beautiful Queen Triggerfish can be described to be a large oval shape that is laterally compressed. The eyes are located towards the top of its head. Their eyes have the ability to move independently of each other. They are about 8-16 inches long. The name ‘triggerfish” comes from the two spines on the anterior dorsal fins that lock the fish into crevices at night. How does she do this? Good question! The Queen Triggerfish uses the first fin to lock itself into the crevice and the second fin to unlock itself. This is a defensive mechanism to keep themselves from getting eaten by their predators. This isn’t the only way they protect themselves; these amazing fish can also produce a throbbing sound by using a specialized membrane located beneath their pectoral fin. This throbbing sound is a warning to their predators to stay away.
Coloration:
The back of the Queen Triggerfish is typically green or blue while its abdomen and the lower head are orange and yellow. One of the prettiest features of this fish is the bright blue bands that extend from the snout to the front and below the pectoral fins, the bands around its mouth, and the bands around the caudal peduncle and median fins. Both female and male have similar morphology. The difference in coloration differs in juveniles because the younger triggerfish are paler in color and have smaller fins.
Queen triggerfish by adam under CC by 2.0
Where can I find them?
The Queen Triggerfish can be found in depths of approximately 7-902 feet, typically over rocky bottoms and around reefs. They also form schools. Geographically they are located in the Caribbean, Bahamas, Florida, Bermuda and the Gulf of Mexico.
What’s for dinner?
The Queen Triggerfish are primarily carnivores but are also sometimes herbivorous as they occasionally eat algae. The majority of their diet consists of sea urchins, bivalves, crabs, starfish, sea cucumbers, shrimp and polychaetes.
The information in this chapter is thanks to content contributions from Jennifer Rosado
02.4: Blue Chromis
Geographic Location and Habitat
Chromis cyanea or Blue Chromis are located in the Western parts of the Atlantic Ocean including the Gulf of Mexico and the Caribbean Sea and are also found on the coast of Bermuda. They are most commonly seen swimming in reef habitats but can also be living in lagoons where food and shelter are prevalent. They are most commonly found swimming at depths of 10 meters to 20 meters. These fish rely greatly on the health of coral as they provide the Blue Chromis with a place to live, breed, feed and also protection from potential predators.
Description
This oval-shaped reef fish is about 13 to 15cm in length once fully grown in their adult life stage. These fish get their name from their bright blue body color. They also have a black striped dorsal fin, anal fin, and caudal fin. One fun fact about Blue Chromis is that they have dark eyes which are a great way for people to distinguish this species among other similar ones.
Threats
These fish face several threats in their everyday life, some of which are not often touched upon by many people and they slide under the radar. One of the most serious threats is the Chromis trade. Large numbers of Blue Chromis are collected for use in aquaria. Damselfish or Blue Chromis make up a very large portion of the life we see in aquariums around the globe, almost half in most portions of the world. Another, possibly less serious threat is predation from lionfish which are growing in number every day. These invasive fish consume small damselfish and other reef fishes in the Caribbean and Atlantic oceans. Finally, another large and growing problem is the loss of coral which occurs in all oceans. The coral reefs are what provide the structure for the entire ecosystem which the Chromis thrive in and spend almost all of their lives.
The information in this chapter is thanks to content contributions from Devon Audibert | textbooks/bio/Marine_Biology_and_Marine_Ecology/02%3A_Common_Fish_in_the_Coral_Reef/02.3%3A_Queen_Triggerfish.txt |
Honeycomb Cowfish (Acanthostracion polygonius) belong to the Ostaciidae family, typically known as boxfishes. The structure of fish in the family include many bones and are shaped like a square. They have small mouths and broom-like tails that help with swimming because the boxy shape weighs them down. The Honeycomb Cowfish, however, is a rare species and have heavy hexagonal scales that cover the whole body. One form of defense are the tiny horns that protrude over the eyes. They typically grow between the range of 7 to 15 inches and are commonly found in water depth of 20-60 ft, meaning they inhabitant the neritic zone.
HoneyComb Cowfish CC BY SA 2.0
Location:
The habitat of Honeycomb Cowfish is the western Atlantic Ocean. They are found as far up along the coast of New Jersey and as far south as southern Brazil, but are most typically found in the Caribbean and Gulf of Mexico. These diurnal animals prefer to reside in clear water with an average temperature of 22-270 C in coral reef habitatsand vicinity.
Anatomy:
A closer look at the biology of the fish shows the hexagonal scales are attached firmly to each other except around the head and tail of the fish. This allows for respiration and movement for the gills, fins, and eyes, and caudal peduncle. The color of the fish is also a unique characteristic; they are seen in blues and greens and yellows and browns. The dorsal edge has darker and/or irregular hexagons due to the opening of the scales. Juvenile fish are more brightly colored and have shorter dorsal fins. The honeycomb scales are used for protection. Honeycomb fish feed on marine invertebrates, mainly shrimp, tunicates, and sponges. The structure of the small mouth is used to suck in small food particles. Their food sources are mainly sessile which are easier to find, as honeycomb cowfish are not active hunters. They have a solitary nature and are never seen in groups of more than 3 individuals. Typically, when grouping, the small school will be comprised of one male and two females. Not much is known about their reproductive nature, but many scientists conclude this grouping may be significant. It is known that they are open water mating fish which means they swim to the surface quickly to release gametes and then swim back down immediately.
Cowfish Honeycomb By Amanderson2 CC BY SA
Like many fish, they undergo different life stages. For Honeycomb Cowfish they have two stages of juvenile and adult. Juveniles are rounder and brighter in color. They can also change color to protect themselves from predators. They do this by sending a signal via nerve impulse to Chromatophores, which are pigment cells in the scales. To learn more about this process watch this video.
Predators of Honeycomb Cowfish are larger fish, but usually cowfish are undesirable as food due to their external armor. As Honeycomb Cowfish grow into adulthood their colors fade and they become more triangular and rigid resulting in awkward swimming. One way they protect themselves is by use of camouflage by blending into the colorful surrounding of coral reefs. When stressed, adults can brighten their colors to be more effectively hidden. When using camouflage, they remain stationary for long periods of time.
Overall, Honeycomb Fish are very unusual fish and use honeycomb-shaped scales as protective armor. They can also use their bright colors to blend into coral reefs to hide from predators and the boxy shape makes them undesirable to natural predators. Unfortunately, these fish are used to a great extent commercially as pets which can damper population sizes. By choosing their habitat close to coral reefs, they have easy access to food and shelter. These fish are really interesting. If you want to learn more about boxfishes, watch this video.
The information in this chapter is thanks to content contributions from Maddison Oulette
02.6: Spotted Drum
The Spotted Drum can grow to be anywhere between six and ten inches and possesses a distinctive black and white pattern consisting of both dots and stripes and has an unusually long dorsal fin as can be seen on the adult pictured above. As juveniles, they are extremely elegant and beautiful, their patterning consists only of stripes, and they possess an extremely long dorsal fin that becomes shorter as they age.
There is not much in the literature about the purpose of their patterning specifically, but we can draw from information regarding other fish with similar patterns. For example, Angel Fish which are also solitary, possess a similar solid dark banded pattern. This pigment switch from light to dark is a mechanism to confuse predators during an attack.
This fish can also be classified as an odd-shaped swimmer. Odd-Shaped Swimmers are often characterized by a slow and awkward swimming technique. In character with this, Spotted Drums swim around in small repetitive circles. They are solitary fish and are often described as secretive- they are very rarely seen in groups. It does not seem as though they are aggressive or territorial fish because they are very easily approached by divers.
The Spotted Drums spend their days hiding in caves and crevices in reefs in the Bahamas, Bermuda, the Caribbean, and Florida. You will on occasion spot one swimming around the base of the reef during the day. Normally they only come out at night in order to feed on things like small crustaceans, worms, and shrimp. As for predators of the Spotted Drum, according to the literature they are threatened by very little.
The information in this chapter is thanks to content contributions from Allie Tolles | textbooks/bio/Marine_Biology_and_Marine_Ecology/02%3A_Common_Fish_in_the_Coral_Reef/02.5%3A_Honeycomb_Cowfish.txt |
Bothus lunatus, also known as the peacock flounder or plate fish is in the Lefteye Flounder (Bothidae) family. It is one of the most common flounders in coral reefs! They are usually 6 to 8 inches and thrive at a depth of 2 to 100 meters. They are found in the Bahamas, Caribbean, Bermuda, Gulf of Mexico, and Florida. Bothus lunatus is the Atlantic species of peacock flounder and Bothus mancus is the indo-pacific peacock flounder. This chapter is going to focus on the Atlantic species of peacock flounder, Bothus lunatus although there are many similarities between the two.
Peacock Flounder- Bothus lunatus by prilfish via Flickr
The peacock flounder is usually found in sandy areas in mangroves, seagrass meadows, and coral reefs. As a benthic organism as it spends most of its life on the ocean floor or slowly swimming slightly above.
They prey on small fish, which make up about 85.7% of its diet. However, it occasionally preys on octopi and small crustaceans such as marine shrimps and mollusks. They use their incredible camouflage to blend in with their surroundings to catch their meals. To catch their meals, they lie on the seabed partially submerged in the sediment and ambush their prey. When they aren’t on the seafloor, they remain close to the sediment and swim using short gliding motions with occasional bursts of fast motion when trying to avoid predators. As a diurnally active fish, they are most active during the day and typically rest at night.
Bothus lunatus (peacock flounder) (San Salvador Island, Bahamas) by James St. John via Wikimedia Commons
As juveniles, their eyes are on opposite sides of their head, and as they mature their right eye migrates towards the left. Having both eyes on the same side of the head helps when they lay down in the sand. They can see prey better as they have two eyes facing upwards and none facing the sand. They are great at camouflage and use their eyes to see their background and adjust their color to it. A problem arises if they have damaged sight when they try to camouflage because they can’t see the surroundings correctly. Their eyes are also spaced very far apart with males having an even wider gap between the left and right eyes.
When they are not camouflaged, their natural coloring is brown/grey/tan with bright blue, circular spots on their entire body, including their fins.
A colorful peacock flounder showing off its vibrant colors by Hectonichus Via Wikimedia Commons
Fun fact: it takes the peacock flounder somewhere between 2 to 8 seconds to completely blend into their background. Different ages of peacock flounder face different kinds of predators. Juvenile peacock flounder face predation from shrimp, crab, and other fish. Adult flounder are prey for a variety of animals; striped bass, cod, bluefish, groupers, moray eels, stingrays, sharks, and more. The peacock flounder can live up to 10 years and breeds year-round. They always mate just before sunset and the mating lasts for a quick 15 seconds, on average.
The peacock flounder has been evaluated by the IUCN and, as of 2012, is of least concern when it comes to extinction likelihood. However, the peacock flounder is eaten by humans and overfishing and by-catch could potentially push it into a near threatened or vulnerable status in the future. It is said that by 2048 there will be ‘fishless oceans‘. Now, ‘fishless’ doesn’t mean no fish at all, at least immediately, but instead refers to a ‘collapse’ of the species… A species collapse means that 90% of the species are gone. With a 90% reduction in organisms, eventually, the number will end up climbing to 100%. This is mostly due to the issue of overfishing and the impact of climate change on ocean ecosystems. As of 2018, fishing industries are taking in 2 to 3 times as much fish than the oceans are able to support. This has caused about 85% of the WORLDS fish populations to be driven to near extinction or put on a fast track to extinction.
The information in this chapter is thanks to content contributions from Sarah Larsen | textbooks/bio/Marine_Biology_and_Marine_Ecology/02%3A_Common_Fish_in_the_Coral_Reef/02.7%3A_Peacock_Flounder.txt |
Caribbean Reef Shark (Carcharhinus perezi) are in the family Carcharhinidae. They are most abundant in the South-Western Atlantic ocean, although they can be found from the coast of Georgia to the southern coast of Brazil.
Carribean Reef Shark by Leineabstiegsschleuse via Wikimedia Commons
Size, Shape, and Overall body form of Caribbean Reef Shark :
Size: 6ft – 10ft Adult Size Shark
Color: Silvery Grey and Greyish brown with a white underside.
Caribbean reef shark (Carcharhinus perezi). Illustration courtesy FAO, Species Identification and Biodata
Shape :
1. Snout is rounded defined by the short features
2. Pectoral fins are long in length and skinny in appearance
3. The dorsal fins are used to navigate and are short as well
Conservation status:
The Conservation of this species is monitored by International Union for Conservation of Nature. This organization rates the level of which a species is threatened in the wild.
Habitat and Behavior :
These sharks prefer to swim about the reef near the bottom hunting small boney fish in isolation. The Caribbean Reef Shark has evolved to hunt at the bottom depths having an extrasensory gland that allows these sharks to hear extra low frequency sounds making hunting for panicking fish easier. In Brazil, these sharks have been documented to hide in small caves to hunt prey and to rest. This is one of the only species of sharks that lie motionless to sleep versus counterpart species such as great white sharks that swim while sleeping.
Human interactions:
Caribbean Reef Sharks are not deadly to humans typically but will be if they feel threatened or are provoked. If you are more curious about the number of attacks each type of shark species has on humans and if they were deadly check out this link: Shark attack records
Tropical Role of Caribbean Reef Sharks :
Like many sharks, the Caribbean Reef Shark is an apex predator. They fear nothing and eat a healthy diet of cephalopods and small boney fish. They also have a mutualistic relationship with smaller fish that almost piggyback on the shark. They swim close to the bottom jaw and assist the sharks in sometimes finding prey and getting the scraps of the kill. In addition, surgeonfish, goby, and other cleaner fish will pick off algae or any type of parasites growing on the sharks when the sharks rest near sites containing these species.
Want to see these sharks in the wild check out this video on youtube of Caribbean Reef Sharks in the wild: Nature Habitat of Reef Sharks
The information in this chapter is thanks to content contributions from Tim Brodeur
02.9: Black Durgon
Black Durgons, along with other Triggerfish, are in the Balistidae family. Melichthys niger is commonly referred to as the Black triggerfish. They are most commonly known for their incredible opalescent brilliance in direct light. Despite this, in the absence of light, the organism may seem dark and black, much to its evolutionary advantage. Thus it has been labeled as the Black Durgon.
Melichthys Niger. Photo by John Martin Davies, July 25, 2007 (CC-BY-SA-3.0)
Melichthys niger from adolescence to adulthood may measure 6-14 in. and could be found at depths 10-200 ft. (Reefguide). Their distribution has been described as circumtropical. They express a small to medium-oval morphology with a pronounced dorsal and anal fin. There is typically seen a distinctive blue-silver lining along the connective length of the fin to the main body of the individual. Pectoral fins are small relative to the size of the species and express the shape of a seashell.
The habitat of Black Durgon is restricted to the Neritic zone, and they are known to be mostly mobile as well as solitary in their behavior, perhaps due to their aggressiveness. Maximum lifespans have been estimated up to 11 years (Environmental Biology of Fishes). Black Triggerfish favor temperatures between 72-78o Fahrenheit and a pH of 8.1-8.4 (slightly basic).
Black Durgon over a patch reef. Photo by James St. John, June 23, 2010 (CC-BY-2.0)
The home range of these individuals is about 20o north and south of the equator in tropical regions around the globe (Black Triggerfish). They are most common to Florida, the Bahamas and the Caribbean. The Black Durgon is known to be an omnivore. This species eats essentially anything that they can procure including but not limited to: other small fish, small cephalopods, zooplankton, algae, and plants. Intriguing aspects of Melichthys niger are reflected in their ability to undergo biochemical processes to change color and iridescence. Examples of individuals turning stark white from their typical black-opal shade have been recorded and was likely an event to match the fish to its surroundings. Conspicuous blue streaks and markings can also be seen around the heads of these animals (Rolling Harbour). There are no obvious distinctions between the males and females of the species. When triggerfish get together for mating periods it is thought to be dictated by the moon and other tidal factors. Males are territorial in nature at this time as they build nests adequate enough to house thousands of eggs produced by the females. During gestation, male and female triggerfish are known to share care responsibilities of their offspring, fanning the eggs to ensure proper oxygen supply (National Geographic). The population status of Black Durgon is not currently listed as critical. They are renowned for their frequency, beauty, and contribution as one of the lesser aggressive forms of triggerfish, making them pleasurable to study and observe.
The information in this chapter is thanks to content contributions from Jason Charbonneau | textbooks/bio/Marine_Biology_and_Marine_Ecology/02%3A_Common_Fish_in_the_Coral_Reef/02.8%3A_Caribbean_Reef_Shark.txt |
Plastics are an integral part of our modern lives. They are found everywhere from Home Goods to electronics, and are by far one of the most versatile and useful technologies humans have been able to harness. On top of their usefulness, plastics are easily re-purposed, with more than 40% of plastic being recycled. Although plastic helps us go about our everyday lives, it is having a serious effect on the ocean and marine life. In 1975 it was reported by the National Academy of Sciences that an estimated 14 billion pounds of garbage, much of it plastic, were being dumped into the oceans every year. Today, that number has shrunk to around 8 billion pounds a year thanks to public awareness.
So what are the effects plastic has on marine life?
For starters, ”…Plastic has been found in more than 60% of all seabirds and in 100% of sea turtle species…” according to the group Ocean Conservancy To a sea turtle, a plastic bag can look extremely similar to a jellyfish, which is a common food source for them. For other species such as seabirds, fish are a common food source. When smaller pieces of plastic get consumed by small fish, the plastic will move its way up the food chain to bigger fish and bigger fish until it is consumed by a seabird, or other marine animal. The accumulation of plastic in these species impacts their health in many ways including nutrient uptake, general fitness, and feeding efficiency.
While fish and turtles are motile animals, sessile species such as corals are not free from the effects of plastics in their environment either. A study has been done by Hall et al. that shows corals will consume micro-plastics at the same rate as their food. Micro-plastics are any piece of plastic under 5mm in size. The corals in this study were found to starve at a very slow rate because the plastic pieces that they were consuming overloaded their stomach and they were not getting the amount of nutrients that they needed. Corals are very non-selective feeders, but they are sensitive to their environment.
Although the oceans are huge, they are not big enough to disperse all of the plastic that winds up in them. It is estimated that there are between 15-51 trillion pieces of plastic in the worlds oceans, and due to ocean currents, millions of tons of plastics congregate in massive gyres in the ocean. There are 5 major subtropical gyres, each containing its own garbage patch. The most notorious of these is the Great Pacific Garbage Patch, an island of plastic waste 1.6 million kilometers squared in area, or three times the size of France. In this garbage patch, it is estimated that there is 6 times more plastic than plankton. Plankton is a necessary food source for some marine life. It is also up to 9 feet deep in some portions of the garbage patch. For more information on garbage patches, watch the video below:
A YouTube element has been excluded from this version of the text. You can view it online here: http://pb.libretexts.org/marine/?p=90
One of the questions this raises is how does it all get there? How does 8 million tons of plastic waste end up in the ocean each year? In the developed world, which contributes for roughly 10% of the worlds plastics problem, plastic enters our oceans through our sewer systems, and as consequences of storms and heavy rains. While the developed world contributes in part to the plastic problem, we are by no means the biggest culprit. According to the World Economic Forum, 90% of all plastic waste that pollutes our oceans comes directly from 10 rivers in China, Southeast Asia (Laos, Thailand, Vietnam, etc), Egypt, and Niger. What these areas have in common are massive populations centered around these rivers combined with poor waste management systems and general lack of education about environmental preservation.
So what is being done to combat this?
There have been a number of laws put in place in an attempt to stop the plastic pollution. The Act to Prevent Pollution from Ships (APPS) (PDF) was amended in 1987 by the Marine Plastic Pollution Research and Control Act. It is meant to reduce the amount of improperly disposed plastic that is released into the environment. It also studies the effects that this plastic is having on the environment.
The Marine Debris Research, Prevention, and Reduction Act (MDRPRA) (PDF) has established programs within the National Oceanic and Atmospheric Administration (NOAA) and the United States Coast Guard. Its goal is also to reduce the amount of plastic and trash that gets put into the marine environment.
The Shore Protection Act (SPA) is another Act that was put into place in order to stop this growing problem. This Act controls the transportation of waste in coastal waters.
One of the most important Acts put into place is the Marine Protection, Research, and Sanctuaries Act (MPRSA). It is also known as the Ocean Dumping Act and it prohibits the following:
• Transporting material from the United States with the intention of ocean dumping
• Transporting material from anywhere for the purpose of ocean dumping by U.S agencies or U.S flagged ships
• The dumping of material transported from outside the U.S into the U.S. territorial sea
Outside of the US, thanks to efforts by international and local organizations, agreements have been signed and efforts are being made to reduce plastic wastes across the globe. China for example has ordered 46 cities to recycle 35% of all plastics by the year 2020, and India has begun to ban disposable plastics in some cities.
The information in this chapter in thanks to content contributions from Andrew Fuhs and Alana Olendorf | textbooks/bio/Marine_Biology_and_Marine_Ecology/03%3A_Environmental_Threats/03.1%3A_Plastics_in_Our_Oceans.txt |
Human noise in the ocean is becoming a major concern. From sonar on our submarines to cargo ship traffic and even oil drilling rigs, we are filling our oceans up with lots of unnatural noise. This noise is linked to altering the calling, foraging, and migration patterns for many species. In extreme situations, scientists also believe it is a reason there have been so many beached whales.
Here is a video that shows what some different noises in the oceans sound like, and how loud they really are.
EFFECTS OF SOUND ON WHALES
It seems that whales and dolphins are the marine animals that are most affected by the noisy oceans. Although natural noise in the ocean from wind, waves or other marine animals is a common occurrence, they are not nearly as intense as noise from humans. This more intense and frequent noise can be causing stress to whales and contributing to them beaching themselves. One scientist has said that he has seen whales abandon a location because of noise. These locations sometimes contain a food source necessary for the whales survival.
Sound waves from military submarine sonar systems can get as loud as 235 decibels. They are able to travel hundreds of miles and can maintain the intensity of 140 decibels as far as 300 miles from the source.
Cargo Ships create what is known as ambient noise. This is particularly concerning for low-frequency great whales. Right whales are endangered and it has been proven that noise from cargo ships constantly crossing the ocean is causing them stress.
Here is a video on the process of deep water oil rigging. It would be hard to believe that these rigs don’t make a ton of noise. It is understandable that hearing noise from these rigs constantly could cause stress to a whale or confuse it considering they rely heavily on acoustics for survival.
RECENT BEACHED WHALE STORIES
On February 10th, 2017, New Zealand had over 600 Pilot whales wash ashore. Volunteers were able to save about 80 of the whales, who went on to join a nearby pod. After they were saved, later that night the pod that they joined got stranded on Farewell Spit. Although the cause of these whales stranding and beaching themselves is unknown, one theory is underwater noise. The loud sound waves that humans create can panic the whales into surfacing too quickly or swimming into the shallows.
In May 2016, more than 20 whales beached themselves near San Felipe, Mexico. According to one statement, there were no signs of injuries noted on the whales, but they seemed disoriented. Since the whales had no signs of injury, it is very reasonable to believe that sonar and loud ocean noise drove them out of deep water towards the beach.
Less than a year after 330 whales washed ashore on Patagonian Inlet, 70 whales were found on a beach in southern Chile. Although they are not the same species, this is a terrible trend that is happening. The whales were smaller this time and they had been dead for about 2 months before they were found.
Information in this chapter is thanks to contributions from Alana Olendorf | textbooks/bio/Marine_Biology_and_Marine_Ecology/03%3A_Environmental_Threats/03.2%3A_Noisy_Oceans.txt |
Ocean acidification is simply the decrease in the pH of all of the oceans on Earth. But is it really that simple? The answer is no, it is not that simple. The ocean absorbs about 25% of the atmosphere’s carbon dioxide or CO2, and as atmospheric CO2 levels increase, so does the amount of CO2 that the ocean absorbs. Therefore, as the amount of greenhouse gases increase, not only does the temperature of the ocean begin to rise, but the increase in CO2 levels causes the ocean’s pH levels to decrease. The rising acidic conditions cause a multitude of deleterious effects from limiting the formation of skeletons for marine organisms, to limiting coral growth, and corroding already existing coral skeletons.
While natural levels of carbon dioxide are fine, the excess CO2 that humans have managed to produce through burning fuels are the major problem. This is largely because when CO2 dissolves in the sea water, (CO2 + H2O-> H2CO3), it produces carbonic acid. While carbonic acid is not as strong of an acid, as say HCl, it still acts as an acid by donating protons, and interacting with surrounding molecules. Now, when excess acid is added to a solution, it causes the pH of that solution to drop, or become more acidic, and while H2CO3 is not considered a strong acid, it still has the potential to massively impact the entire chemical makeup of the ocean environment. The lower the pH of a solution gets, the higher the concentration of H+ ions in that solution. This has become a massive problem for many species.
Chemical reactions can be extremely sensitive to any fluctuation in pH levels, however, in the ocean, these pH changes can affect marine life through chemical communication, reproduction, as well as growth. In particular, the building of the skeletons in marine life is extremely sensitive to any change in pH. Thus, the current increase in CO2 levels that have caused a more acidic environment, have greatly and negatively impacted the growth of new shells.
This is because Hydrogen ions easily bond to carbonate (CO3 2-) molecules to create carbonic acid, and a marine animal’s shell consists of Calcium Carbonate (CaCO3). In order for marine animals to build shells, they take Calcium ions (Ca2+) with a carbonate molecule from the seawater surrounding it, to form the Calcium Carbonate needed to build their shells . So, instead of the carbonate giving all of it’s attention to Calcium so that the marine animal can build it’s shell, it now pays more attention to the Hydrogen ion. In addition, Hydrogen ions have a greater attraction to carbonate, than a Calcium ion does to carbonate, and when two Hydrogen ions bind to carbonate, it produces a bicarbonate ion, and a marine animal does not have the capability to extract only the carbonate ion . Ultimately, this limits marine animals from building any new shells for themselves, and even if the marine animal has the ability to build a new shell, it takes a lot of energy to do so, essentially taking away from other important processes and activities.
“Impacts of Ocean Acidification” by Wikimedia [CC BY SA 2.0]
Not only can this affect the formation of new shells, but in the right conditions, it can corrode already existing shells. When there are too many Hydrogen ions floating around, and not enough molecules for them to bind to, they can actually start breaking the already existing Calcium Carbonate molecules apart, ultimately breaking down the marine animal’s shell that already exists.
Another organism that feels the effects of ocean acidification are corals. Similar to other marine animals that build their homes with calcium carbonate, reef-building corals also use calcium carbonate to build their own bodies and structures. These reef-building corals are also home to other coral animals and other organisms. As mentioned before, the increased acidification greatly limits any further growth of new coral, as well as corrodes any pre-existing coral reefs. Even if a coral reef has surpassed all the odds, and has been able to grow, it will be a weaker reef that is subject to natural erosion. It has been predicted that by the middle of the century, healthy coral reefs will be eroding more quickly than can be reproduced.
This is bad news for the species that live in these coral reefs. If these species are not able to grow and develop in a safe settlement, such as the coral reef, these larvae will be unable to reach adulthood , thus being unable to reproduce. This will ultimately lead to a mass extinction in the future.
The information in this chapter in thanks to content contributions from Jaime Marsh and Morgan Tupper. | textbooks/bio/Marine_Biology_and_Marine_Ecology/03%3A_Environmental_Threats/03.3%3A_Ocean_Acidification.txt |
Ever been told to only eat shellfish during the months that have the letter “R”, (September-April)? Well this rule is actually pretty important for keeping the health of people safe and to allow for many species of shellfish to repopulate. But why are the other months of the year not safe for people to eat shellfish? In short its because of the algae that grow during this time of year and as ocean temperatures rise. During these specific months of warmer weather, billions upon billions of these microorganisms start to take over our oceans and can have many consequences for us.
Before going into what red tide is or how the populations of these microorganisms seem to be increasing significantly as oceans warm up, lets take a closer look at algae. Most species of algaeare single-celled organisms but some species can be multi-cellular as seen in the photo above. Algae are autotrophs, meaning they use photosynthesis as their means of producing energy for themselves. Though similar to plants in the way they are both producers, algae have no stems or leaves and are more closely related to other groups of protists. Habitatsfor algae include any bodies of water including fresh and salt water, or have extreme external environment factors. There are few cases where they have been found on land such as rocks, trees, hot springs, etc… Species of algae have been well documented to be able to survive many harsh environments and have been on earth far longer than most living organisms to this day. They contributed to the Earth being able to house life by producing oxygenthrough photosynthesis. Overall Algae species are very tough and can survive in a wide range of environments, which can be seen as both a positive and negative situation.
A YouTube element has been excluded from this version of the text. You can view it online here: http://pb.libretexts.org/marine/?p=96
The red tide occurs when the algae from algal blooms becomes so numerous that it discolors the water. It is also sometime referred to as a Harmful Algal Bloom or “HAB”. This is where the name “red tide”comes from. Some key factors involved in red tides forming are warm ocean surface temperatures, low salinity, high nutrient content, calm seas, and rain followed by sunny days during the summer months. Some effects of the red tide are that it could deplete the oxygen in the water and/or release toxins into the water. The toxins in the water could have negative effects on the health of humans and animals exposed to them. There are three types of algae that can release these harmful toxins, they are Alexandrium fundyense, Alexandrium catenella and Karenia brevis.
What is important to recognize about “Red tides” and Algal blooms is that it isn’t always obvious that algae growth is there. They are not always a red color. The photos above show two examples of Algal blooms from two very different parts of the world, yet both species are considered “Red Tide” and harmful to some shellfish and animals that eat the shellfish. Algae alone is not an issue and even during the time of the year where there seems to be an excess amount of growth, this is a natural occurrence. What becomes a problem or what classifies as a “Red Tide” are the algae that release toxins in the air and water when they grow. Very few algae species can produce this toxin but when a large enough group forms on shores it can have a negative effect on both the marine environment and humans. The toxins produced can often affect the respiratory and nervous systems of all life forms. Thus when smaller marine animals feed on the algae, the trophic level above them can become poisoned as well. Paralytic Shellfish Poisoning is typically found along the Pacific and Atlantic coasts of the United States and Canada. It can cause paralysis and in extreme cases death. Some of the toxins that cause Paralytic Shellfish Poisoning can be 1,000 times more potent than cyanide. Diarrhetic Shellfish Poisoning is another example of a harmful effect from eating contaminated shellfish. It is caused by Okadaic acid, which is produced by several species of dinoflagellates, and is usually non-deadly to humans. Small amounts of the okadaic acid usually do not have any harmful effects and only become an issue when large amounts are consumed. Amnesic Shellfish Poisoning is the third common poisoning that humans will get from eating contaminated shellfish. It can be life threatening and cause both gastrointestinal and neurological disorders. These disorders are caused by domoic acid. After an incident in Canada in 1987 where 4 people died from Amnesic Shellfish Poisoning, the levels of domoic acid in shellfish are now being monitored.
Algal Blooms can have serious effects on corals. Red algae, brown algae, and green algae are a few examples of macro-algae that can have a very negative effect on corals. They do this by outcompeting, overgrowing and eventually replacing sea-grasses and coral reef habitats. According to some research that is being done, harmful tropical algal blooms are increasing in frequency and intensity. This can have a significant impact on coral reefs.
Notable Red Tides:
1844: First recorded case off the Florida Gulf Coast.
1972: Red tides killed 3 children and hospitalized 20 adults in Papua New Guinea.
2005: The Canadian red tide was discovered to have come further south than it has in years prior by the ship (R/V) Oceanus, closing shellfish beds in Maine and Massachusetts. Authorities were also alerted as far south as Montauk to check their beds. The experts who discovered the reproductive cysts in the seabed warned of a possible spread to Long Island in the future. This halted the area’s fishing and shellfish industry.
2013: In January, a red tide occurred on the West Coast Sea of Sabah in the Malaysian Borneo. There were two fatalities reported after they consumed a shellfish that had been contaminated with the red tide toxin.
2015: In September, a red tide bloom occurred in the Gulf of Mexico, affecting Padre Island National Seashore along North Padre Island and South Padre Island in Texas.
Scientists have been able to help control the spread of the effects of harmful algal blooms by developing new technology to help track them better. Tracking these harmful algal blooms could help prevent people from eating contaminated shellfish and knowing which areas will be most effected by them. Some examples of the technology that can help with monitoring them are better and more advanced satellite imagery. Also the development of an antidote to the toxins produced is another way to reduce the harmful effects. Even though they are a natural occurrence, what is alarming some scientists is that they may start to last longer and occur more often during the year as ocean temperatures and CO2 levels rise.
The information in this chapter in thanks to content contributions from Emily Michaeles and Alana Olendorf | textbooks/bio/Marine_Biology_and_Marine_Ecology/03%3A_Environmental_Threats/03.4%3A_Harmful_Algal_Blooms.txt |
“Eco Cafe” by Phuket [CC by 2.0]
Coral bleaching is a phenomenon that occurs when coral turns white due to environmental stress. It is a reoccurring event that frightens marine biologists and raises a lot of concern for marine ecosystems all over the world. When the water is too warm, corals will expel the algae (zooxanthellae) living in their tissues. As a result, the coral loses its vibrant color and becomes more prone to developing disease. Corals have a mutualistic relationship with these algae. This means that the organisms depend on each other for survival. From their photosynthetic products, zooxanthellae give the coral the nutrients they need to survive while the coral in exchange give the zooxanthellae carbon dioxide and safe harbor. When they are lost, it is a huge loss for the coral because these symbiotic algae provide the coral with 90% of its energy through the process of photosynthesis. Without the zooxanthellae, the coral begins to lose its color and eventually has a bright white appearance, hence the term coral bleaching. In essence, the coral will starve and die without the needed nutrients from the zooxanthellae. Global warming is a big cause of coral bleaching but other environmental factors also play major roles.
The video below explains more about what coral bleaching is, what causes it and the effects that it is having!
A YouTube element has been excluded from this version of the text. You can view it online here: http://pb.libretexts.org/marine/?p=98
The corals may be able to survive for a short period of time without the zooxanthellae, but since the algae provides its primary food source it cannot survive for long. Once the coral has died, its begins to degrade. Another cause of coral bleaching is oxygen starvation. This is caused by an increase in the zooplankton population in a given area, most likely due to over-fishing. Another trigger that is less common but still notable is sedimentation. This occurs from silt runoff from land into the ocean via rain and other bodies of water leading into the ocean. Also, La Nina or EL Nino can also play a role by not only changing the temperature of the water but also by bringing some silt/sand along with nutrients up from the bottom of the ocean. The biggest cause of coral bleaching is from the stress created from warmer water temperatures due to global climate change.
Corals provide shelter for a number of marine organisms and they also protect shorelines. Without coral reefs, marine life would most likely leave the area which in turn, could cause harm to marine ecosystems. Coral reefs help to support approximately 25% of marine species. They are also a huge benefit to the fishing industry since they attract so much marine life.
There have been three major coral bleaching events recorded in history, the first occurred in 1998, an underwater heatwave spread, killing 16% of corals around the world. The second major coral bleaching event occurred in 2010, caused by an El Niño. The most recent coral bleaching event occurred in 2015, which was caused by ocean warming.
The warming of the ocean is a huge threat to coral reefs. As stated previously, ocean warming is the number one cause of coral bleaching. A shocking 93% of climate change heat is absorbed by the ocean.
But what is the underlying cause of all of this?
Global climate change is caused by increased greenhouse gases, primarily carbon dioxide, that are released into Earth’s atmosphere. The carbon dioxide and other gases trap heat in the atmosphere, causing the Earth to heat up. When the Earth heats up, water temperatures increase and result in coral bleaching.
Humans are the main source of greenhouse gases that are produced and released into the atmosphere due to the burning of fossil fuels. Vehicles are one of the many producers of Carbon Dioxide. Burning one gallon of gas produces approximately 24 pounds of Carbon Dioxide. Another way in which humans produce these gases is by burning coal for electricity. Burning wood to produce fire for cooking is also another every day activity that contributes to the emission of these gases. The other major factor that contributes to increase in greenhouse gases in Earth’s atmosphere is deforestation. For years, humans have been cutting down trees in large numbers to make room for the construction of buildings and also to use the wood as fuel. Trees are very important to our ecosystems because they absorb a lot of the carbon dioxide that is in the Earth’s atmosphere. By absorbing carbon dioxide, they are able to perform photosynthesis and release Oxygen as a byproduct. As trees are removed in large numbers, this sink for carbon dioxide is greatly reduced and the amount of carbon dioxide in the atmosphere continues to increase.
Most people don’t realize how important coral really is to not only marine life, but also to human life. For fish communities and other reef dwelling creatures, the coral is everything to them and they all rely on the coral structure in some way. The reefs provide shelter for smaller fish and can be a food source for others. Coral reefs are essential for life for a countless number of organisms and without the coral, a good number of these organisms will perish, leading to a much bigger problem. If the smaller fish can no longer survive without the coral reef, then that will lead to less food for the larger fish that feed on them.
Around 100 million people around the globe rely on coral reefs for survival. With a decrease in healthy coral ecosystems, there will be less fish which are an important food source for many humans. People also rely on coral reefs for other economic purposes such as tourism. The impact of coral reef loss on the tourism industry is estimated at around 10 to 40 billion dollars, followed by fisheries losing 7 to 23 billion dollars and biodiversity impacts resulting in losses of 6 to 22 billion dollars.
Marine Species Impacts:
Butterfly fish are fish that feed exclusively on coral polyps. With their food source disappearing. their chance of survival is small. Butterfly fish also keep algae from smothering corals and if this population decreases, the corals that are still living could end up dying because of too much algae.
Spiny lobsters need coral reefs for protection, especially when they are molting because that is when they are most vulnerable. These lobsters play a significant role in maintaining a balanced ecosystem. Spiny lobsters are predators of sea urchins, which feed on kelp forests and can destroy them if populations are not predator-controlled.
Dolphins and most whales are predatory animals and they are all carnivorous. They survive by eating fish that rely on coral reef habitats. Each species that is lost from coral bleaching has the potential to affect the rest of the ecosystem.
Hawksbill Sea turtles have become a critically endangered species and are very dependent on coral reefs for their food sources. Their diet mostly consists of sponges. Sea turtles play a very important role in their ecosystems by helping with nutrient cycling from ocean to land, maintaining healthy sea grass beds, and balancing food webs.
Studies have shown that whale shark populations have decreased in the 1980s and 1990s and this may be due to the destruction of corals. Many corals were destroyed in this time period from people and coral bleaching. Although it is not certain that these two are related to each other, the times frames suggest that they are.
Solutions:
There are many ways that people can help reduce the amount of coral bleaching that is occurring. One way that we can do it is by reducing fuel pollution by using alternative transportation methods such as running or biking instead of driving a motor vehicle, or kayaking and canoeing instead of using your boat. Not touching and breaking corals when diving or snorkeling can be a huge help since just touching a coral with your bare hand can have negative effects on it. Not using harmful fertilizers and pesticides in your yard and garden can also help a lot because they will eventually find their way to the ocean. Volunteering for a community reef and beach cleanup can also help keep trash out of the ocean which will keep it from getting into the reefs.
The information in this chapter is thanks to content contributed by Alana Olendorf, Simone McEwan, Haley Fantasia and Devon Audibert | textbooks/bio/Marine_Biology_and_Marine_Ecology/03%3A_Environmental_Threats/03.5%3A_Coral_Bleaching.txt |
When talking about the warming of our oceans, it’s important to first talk about global warming. Is global warming real?
This topic has been debated for years and even more so now with the new United States president. This topic has sparked a great debate among caring citizens, politicians, and news outlets on whether or not global warming is real or a hoax. However, scientists all over the world have scoured over all relevant data and facts and harmoniously agree the planet is indeed warming.
Many might ask, “well what exactly is global warming?”. Global warming is the term used to describe a gradual increase in the average temperature of the Earth’s atmosphere and its oceans; a change that is believed to be permanently changing the Earth’s climate.
There are cold hard facts that prove climate change is prevalent. The EPA has over forty data contributors from different government agencies that provide indicators of the cause and effects of climate change. These indicators effect the oceans in detrimental ways like thermal stress, (“stress in a body or structure due to inequalities of temperature”), and the warming of the oceans.
Greenhouse Effect
The greenhouse effect is the result of greenhouse gases trapping heat in the Earth’s atmosphere radiating from earth toward space, resulting in the warming of the oceans and melting glaciers. When the glaciers melt, it increases the sea level which adds to the ocean that is already expanding.
Examples of greenhouse gases are: carbon dioxide (CO2), methane (CH4), nitrous oxide (N2O), and water vapor (H2O). From 1990-2010 gas emissions caused by humans have increased by 35%. Electricity generation is the worlds largest contributer of emissions followed by transportation. Climate forcing, which is a change in the earth’s energy balance that results in a warming or a cooling effect on the climate. Over the past several years we have also steadily increased our use of fossil fuels, which has ultimately produced 5x more carbon dioxide emissions.The graph below shows how our use of fossil fuel emissions has skyrocketed in the last decade.
How is the warming ocean impacting the marine life?
One of the most vulnerable organisms to global warming is coral. Higher temperatures cause coral bleaching, which results in disease, lack of nutrients and even death of the coral. The zooxanthellae’s enzyme systems are effected from rising temperatures which makes it hard to protect the coral from toxicity. Even an increase of 1-2 degrees Celsius can cause bleaching. Coral Bleaching occurs when corals experience stress such as temperature change. This harms corals because they have a limited temperature range in which they can live. When water is above the corals ideal temperature, the coral expels the symbiotic algae that reside in its tissue and provide it with nutrients. This turns the reefs a ghostly white (thus the term ‘bleached’), and, while the coral is not exactly dead at that point, it is more susceptible to diseases which lead to death.
As humans burn fossil fuels and release carbon dioxide, those gases enter the atmosphere where they cause an increase in global temperature. However, did you know that not all of the carbon dioxide ends up in the atmosphere? In fact, about 40% is said to get absorbed by the ocean waters. The amount of carbon dioxide that the ocean can hold is dependent upon the temperature of the ocean. For example, colder water can absorb more carbon where warmer water absorbs less. Today, scientists believe that as the oceans warm they will become less and less capable of taking up and absorbing carbon dioxide. As a result, more of our carbon pollution will stay in the atmosphere and therefore further the contribution to global warming. For now, the oceans are considered our saviors by absorbing large amounts of our carbon pollution. This buys us some time to reduce our use of fossil fuels. However, there is always a consequence. The increased carbon uptake by the ocean means that the ocean waters will become acidic more rapidly than they otherwise would. This acidification threatens many components of the food chain.
When the ocean temperature increases, this can cause a bottleneck in the food chain, which can result in an interruption in the marine food web. The higher the temperature, the higher the growth of zooplankton. Zooplankton reproduce faster than the phytoplankton and end up eating all of the plankton in an area. This can have a drastic effect on any organism that feeds off of them.
Rising sea levels are a result of the ocean expanding from warming. When the sea levels rise, they interrupt ecosystems and habitats of thousands of organisms such as sea turtles and seals. A rise in sea level results in coastal flooding, which has increased in the United States on coastlines such as the Carolina’s, New Jersey, and Maryland. Floods are now 10 times more likely to happen than they were years ago. These floods are endangering species and ruining coastline habitats.
The information in this chapter in thanks to the content contributions from Haley Zanga and Marisa Benjamin | textbooks/bio/Marine_Biology_and_Marine_Ecology/03%3A_Environmental_Threats/03.6%3A_The_Warming_of_Our_Oceans.txt |
According to the National Oceanic and Atmospheric Association, there are thousands of oil and chemical spills each year. The Ocean Service’s Office of Response and Restoration is the first to come to the scene and assess the impacts that a spill may have, identify risks, and recommend different cleanup methods. However, when oil spills occur, the first organisms to come into contact with the oil are marine organisms. Many of the issues that occur for marine life are due to the bioaccumulation of oil components by organisms. Biological organisms lower in food chains such as zooplankton accumulate the oil’s chemicals within their tissues. When these zooplankton are consumed by organisms such as fish at higher trophic levels, the concentration of chemicals is magnified. With each successive trophic level, this biomagnification continues and the concentrations of the chemicals can be extremely dangerous especially for apex predators causing health and reproductive problems.
The effects of oil spills are varied across species, the distance from the spill, how big the spill is, and where the oil disperses. Organisms such as shellfish can be unaffected by oil or only slightly. This is because most of the oil floats within the water column and the amount that sinks to the ocean floor is limited, although there are still some circumstances where the oil spill has a large effect on the shellfish. Oil spills that are in shallow or confined waters are the most at risk for effects. Oxygen depletion can occur due to the formation of oil slicks at the surface of the water.
Oil slicks in deeper water can also have an effect. For example, the BP Oil spill in the Gulf of Mexico had well leaks at deep depths. Organisms such as shellfish that don’t move often or far and are filter-feeders, are unable to avoid exposure to oil. Juvenile and adult fish are much more mobile, are more selective in what foods they eat, and they also have a variety of enzymes that allow them to detoxify many oil compounds. As a result, they are often better suited to limited oil exposure and related impacts. In spite of this, many fish are killed as a result of light oils and petroleum in shallow water. Also, oil spills can completely kill or wipe out fish egg populations.
Effects of oil spills can be direct or indirect. Direct impacts include when oil directly touches, is consumed, or is injected through a cut in the skin. When these things happen they can deteriorate the thermal insulation of some organisms. They can also result in changes in the behavior and reproductive systems of those organisms that come into contact with the oil. Indirect effects of oil spills are those that result from consuming individuals who have direct contact with the oil as well as effects from the mass mortality and decomposition that occurs during oil spills such as oxygen depletion. Another indirect effect can be losing a major food source which could result in the death or extinction of one or more species.
Another factor that can affect marine organisms is the type of oil that is spilled. Light oils and petroleum products can cause acute toxicity in fish, but the toxic event is generally over fairly quickly. Heavier oils sometimes do not affect fish, however they can be detrimental to fish that are in the larval and spawning stages. The type of oil and the timing of the release influences the severity of oil effects on fish. Heavier oils can have great impacts on sea birds. This is because the feathers on birds are naturally waterproof, and in order to maintain this, the feathers on the birds bodies must be aligned. This is so the water cannot leak through the microscopic barbs, and barbules that are part of the vane of each feather. The bird, through a process referred to as preening, distributes natural oils on the feathers to keep the feathers in place. The oil floating in the ocean water sticks onto the birds feathers, causing it to become matted. The matting causes the feathers to separate ultimately making the feathers no longer waterproof. The bird then suffers from hypothermia or hyperthermia when it can no longer protect itself from extreme temperatures. Birds react to the presence of oil by preening, and by doing so the birds end up ingesting the oil that is toxic to them. During this time all of the birds energy is put into preening and they are left vulnerable and malnourished. Death, in most cases, is what the birds are facing without proper treatment. The washing treatment can not begin until the bird is at an acceptable weight, with good blood values while displaying active and alert behavior.
This information in this chapter is thanks to content contributions from Andrew Fuhs and Alana Olendorf. | textbooks/bio/Marine_Biology_and_Marine_Ecology/03%3A_Environmental_Threats/03.7%3A_Oil_Spills_and_Marine_Life.txt |
When we think about destroying the oceans, most people think of destruction via pollution. Although chemical dumping and plastics have a drastic effect on marine life and ecosystems, it is very important to consider another major issue that is causing detrimental effects on marine systems. This issue is destructive fishing methods. Destructive fishing includes practices that leave marine populations irreversibly damaged and can destroy entire habitats for fish and other organisms.
According to the World Wildlife Fund (WWF), there will be no more fish left in the oceans by 2048. This is because more than 30 percent of the world’s fisheries have been pushed beyond their biological limits. Therefore, we need stricter regulations and laws to prevent this disaster.
Destructive fishing is mostly done in underdeveloped countries which don’t have regulations for fishermen to follow. These methods are used because they are effective in getting a large amount of fish in a short period of time saving fishermen time and effort. Some dangerous methods include over-fishing, blast fishing, bottom trawling, and cyanide fishing.
Over-fishing
Over-fishing is when fish are captured before they can reproduce, which can significantly reduce population sizes for the future. This disrupts not only the species that was harvested, but also the other organisms that depend on those species and potentially the whole ecosystem.
– In just over 40 years there has been a decrease in recorded marine species by 39%.
– Around 93 million tons of fish were caught world-wide.
– Entire species, such as the Pacific Blue-fin tuna and swordfish, are highly endangered and are at an all-time low.
– Other marine species, such as whales, dolphins and turtles, are unintentionally killed as a result of over-fishing.
Causes:
A major issue is the open access to the ocean and the absent regulations and monitoring of the water. Due to the increased number of fisheries, management has begun to slack. Current rules and regulations are not strict and do not mark a limit of intake. More importantly, there is little to no international fishing regulations. Even if the nations did come together to fight this issue, we still face illegal fishing. To reduce the intake of fish it should be mandatory to report intake and there must be a maximum limit that is determined by biologists and not companies. Also, we need stronger monitoring of the ocean, which may be hard due to the number of fisheries and the huge surface area the ocean covers.
Impacts:
The WWF states that the populations that are mainly targeted are top predators in the ecosystem such as Billfish, Tuna, Salmon, and sharks. This is because of the economic and social demands of the fishing industry. Decreases in the top predator population can severely disrupt other marine populations. A prime example of this is increases in population sizes of smaller marine animals at the bottom of the food web that are fed on by top predators. This impacts other aspects of the marine ecosystem such as increases in algal overgrowth, which can be dangerous to coral reefs. Algae, although essential for the ecosystem, can have negative effects if there is a large abundance.
Another issue that is closely related to over-fishing is by-catch. By-catch refers to non-target animals such as turtles or dolphins that are captured or killed in fishing nets. This threat causes the loss of billions of fish and other animals such as sea turtles and cetaceans.
Watch this Tedtalk on over fishing here and a video on by-catching here.
Over-fishing causes a cascade of effects in marine communitiesthat can destroy habitats and result in the loss of biodiversity both in terms of overall abundance and species richness (Coleman, 2002). Not only does over-fishing destroy marine ecosystems, it also impacts food security for people. Humans that live in coastal communities rely largely on fish as a protein resource. Over-fishing decreases food security by threatening the long-term food supply, especially for individuals in developing countries.
Solutions:
There have been new movements to push fisheries to practice sustainable fishing. The WWF has helped develop and set environmental standards to help set a plan for sustainable fisheries. Approximately 15,000 seafood products hold to the standard of sustainable fishing, which is a great first step. There are other ways to help with over-fishing and one way is by influencing the market for fish. By reducing the need for fish products, less fish will be caught and hopefully it will allow some time for re-population.
Blast Fishing
Blast fishing or dynamite fishing is a practice outlawed in most of the world, but is still used in southeast Asia. It involves using explosions to stun or kill large schools of fish for easy collection. The explosions often destroy underlying ecosystems from the strength of the blast. Around 70,000 fishermen still use this practice. Researchers believe that destructive fishing practices like blast fishing are one of the biggest threats to coral reef ecosystems. Coral reefs are less likely to grow in places of constant disturbance. The damage done to coral reefs has an immediate negative effect on the fish population in the area. From a single blast, it takes a coral reef about 5-10 years to recover. From constant blast fishing it leaves coral reefs unable to grow leaving an ocean of rubble. To reduce the use of this method, enforcement officials patrol the seas to try to catch and reprimand offenders.
Bottom trawling
Bottom trawling is a method that uses a large net that scrapes against the ocean floor to collect large groups of fish. Global catch from bottom trawling has been estimated at over 30 million tons per year, an amount larger than any other fishing method. The trawl doors disturb the sea bed, create a cloud of muddy water which hides the oncoming trawl net and generates a noise which attracts fish. The fish begin to swim in front of the net mouth. As the trawl continues along the seabed, fish begin to tire and slip backwards into the net. Finally, the fish become exhausted and drop back, into the “cod end” and are caught. The problem with bottom trawling is that it is un-selective in the fish it catches and severely damages marine ecosystems. Many creatures end up mistakenly caught and thrown overboard dead or dying, including endangered fish and vulnerable deep-sea corals that can live for hundreds of years or more.
Cyanide fishing
Cyanide fishing is a fishing technique used to gather fish for aquaria. In this process, a cyanide solution is used to stun fish for easier collection. This method can kill neighboring fish communities and severely harm coral reefs. Recent studies have shown that the combination of cyanide use and stress of post capture handling results in mortality of up to 75% of the organisms within less than 48 hours of capture. With such high mortality numbers, a greater number of fish must be caught in order to supplement post-catch death.
The information in this chapter in thanks to content contributions from Maddison Ouellette and Bryce Chouinard. | textbooks/bio/Marine_Biology_and_Marine_Ecology/03%3A_Environmental_Threats/03.8%3A_Destructive_fishing_methods.txt |
The Current Coral Situation
With the current environmental crisis occurring on our planet, and the large amount of data we have to aid us in understanding the degree of the phenomenon, it is important now more than ever to utilize our knowledge to protect these ecosystems. Earth has a diverse array of natural habitats including Coral Reefs. It has been reported by the Global Reef Monitoring Network (GCRMN) that about 19% of the Earth’s coral reefs are now dead, with multiple factors to blame including rising sea temperatures and ocean acidification.
Table coral of genus Acropora by Yumi Yasutake via NOAA, 2008 under [CC BY 2.0].
Coral reef ecosystems and the accompanying organisms that depend upon them are in danger of disappearing if we do not take action to protect these reefs. Coral reefs make up only 0.2% of our oceans, but they are home to over 25% of all marine fish species. The United Nations predicts that the Earth is on the brink of a massive extinction event, with some studies even suggesting 25% of the planet’s species will be extinct by 2050. If we do not stop the effects of these factors we may lose a whole lot more than just the corals. The rapid decline of coral reefs will result in a significant number of social, economic and environmental tragedies around the world. We as humans must intervene knowing this current situation. In the US, the decline and danger from the loss of corals started to gain attention by the government in 1998. Since then, many reef protection organizations have emerged varying from government-funded to non-profits.
United States Coral Reef Task Force (USCRTF)
The USCRTF was established in 1998 by Bill Clinton who was President of the United States at that time. It’s mission is aimed to protect and conserve coral reefs.
The USCRTF accomplishes this mission by mapping and monitoring the U.S. coral reefs, as well as helping to identify the problems causing the decline in reefs. Their goals as a task force is to find solutions to these problems, and to promote conservation and the sustainable use of coral reefs to the public. By working together with other organizations they try to find the best possible strategies to save the reefs. The USCRTF is responsible for many tasks which include but are not limited to:
• Implementation of Executive Orders
• Developing efforts to map and monitor coral reefs
• Research the cause and find solutions to these causes of reef decline
• Reduce cord reef degradation from pollution, and over fishing
• Implementing strategies to promote conservation and education to the public internationally
In 2000, the USCRTF adopted the National Action Plan to Conserve Coral Reefs (National Action Plan). This was the first blueprint for U.S domestic and international actions to address the issues of coral reef decline. This plan consists of conservation strategies to address the challenges that reefs are facing today. Not long after, the USCRTF developed the U.S. Coral Reef National Action Strategy (National Action Strategy) to further regulate the National Action Plan. The National Action Strategy’s documents provide the framework for the priorities, strategies, and actions of the USCRTF and its members.
Similar to USCRTF there are many organizations out there trying to make a difference by saving coral reefs and the ecological communities that surround them. Below are four well known organizations trying similar tactics by identifying the problems and finding solutions for coral reef ecosystem protection.
Coral Reef Alliance (CORAL)
One organization working to protect our coral reefs is the Coral Reef Alliance (CORAL). They work with people from very different backgrounds: politicians, scientists, divers, and even fisherman. Their holistic conservation programs can be seen around the world, anywhere from Hawaii to Indonesia. After seeing the success of their programs many other communities and organizations have emulated their programs and efforts. Some of their work consists of creating healthy fisheries for reefs, assisting in ensuring clean water for reefs, protecting intact reef ecosystems, improving knowledge of the science of adaptation, among other things.
If you are interested in helping the Coral Reef Alliance there are many things that you can do. CORAL suggests a couple of things that can let you take action in your daily life such as traveling sustainably and working to educate others. If you want to take a more active role you can donate to their cause or even volunteer.
National Oceanic and Atmospheric Administration (NOAA)
NOAA by Wikimedia Commons under [CC BY 2.0]
A second organization working to protect the worlds coral reefs is the NOAA’s Coral Reef Conservation Program. This organization was founded in the year 2000 by the Coral Reef Conservation Act and they have four main pillars of work: Increase resilience to climate change, reduce land-based sources of pollution, improve fisheries’ sustainability, and to restore viable coral populations. In order to preserve the Coral Reefs they are working with many scientists involved in many different facets of NOAA. They believe that collaboration is the key to coral reef conservation. They partner with governments, academic institutions, and community groups to help save the coral reef environments. If you are interested in getting involved with the NOAA’s coral reef conservation efforts there are a few ways you can do that. You can join the U.S. Coral Reef Task Force. If you are interested in heading your own efforts for Coral Reef conservation here is some information on how to get funded through the NOAA’s grant programs. The NOAA also has job opportunities- here is a link to follow if you’re interested. You can follow them on Twitter to see how they are getting the word out to the public.
Ocean Conservancy
Ocean Conservancy is another organization whose goal is to conserve every part of the ocean and marine life that surrounds it. This organization promotes health and diverse ocean ecosystems and aims to stop/limit the practices that threaten marine and human life. They focus on some of the main problems threatening marine life such as ocean acidification, trash, and helping set up sustainable fisheries to prevent over-fishing and the harmful effects of tourism.
National Fish and Wildlife Foundation (NFWF)
NFWF was created by Congress in 1984 and since then has become one of the world’s largest conservation organizations. They work with both public and private sectors to help protect and restore the nation’s fish, wildlife and habitats that surrounds them. They support conservation efforts in all 50 states and U.S. territories. NFWF has a primary focus on bringing together parties, getting results, and finding better solutions to help the future world. NFWF leads conservation financially with a funding budget up to \$3.8 billion dollars.
Due to the major threats happening to coral reef ecosystems, NFWF has been responding to these problems by taking on multiple coral conservation initiatives in an aim to limit the threats, increase public awareness and find solutions to the problems of the decline of coral reefs both domestically and internationally.
To do this, NFWF works with many different partners to achieve these ideas for coral conservation. Some of these programs include programs that were discussed above such as managing the Coral Reef Programs with NOAA’s Coral Program and USDA-NRCS. NFWF specializes in bringing all parties together (i.e. individuals, government agencies, nonprofit organizations and corporations). This promotes a solid foundation to protect and restore species, promote healthy oceans, improve wildlife habitat, help with sustainable fisheries, and water conservation. To date, NFWF has supported projects for coral reef conservation totaling over \$34 million in about 39 countries giving them a global outreach.
Reef Check International
Reef Check International is an organization whose mission is to preserve the oceans and reefs emphasizing how critical they are to our survival. They work to not only protect tropical coral reefs but also California rocky reefs through education, research and conservation. Impressively, Reef Check has volunteer teams in more than 90 countries and territories.
The results of citizen science divers are used to improve the management of these critically important natural resources. Reef Check programs are notable for providing ecologically sound and economically sustainable solutions to save reefs, by creating partnerships among community volunteers, government agencies, businesses, universities and other nonprofits.
Dr. Karen Cangialosi of Keene State College is the Reef Check International Team Coordinator for the Turks and Caicos Islands. Read about her reef monitoring and youth education program here.
The information in this chapter in thanks to content contributions from Allie Tolles and Haley Zanga . | textbooks/bio/Marine_Biology_and_Marine_Ecology/04%3A_Reef_Conservation/04.1%3A_Protecting_the_Reefs%3A_Organizations.txt |
Uniqueness of Coral Reefs and their Structure
Coral reefs are home to an abundant number of organisms and many different highly specialized species. Many of these species are endemic to these reefs, meaning they are only found here. Coral reefs also act as a nursery to some species that may not spend their whole life there. Reefs provide structure that promote safety and initiate the settlement of larvae of some species. Not only do they provide valuable services to the marine world, but also act as protection against storm swells and beach erosion for the terrestrial world (to learn more about corals visit here). However, they are in rapid decline as they face many challenges including climate change, ocean acidification and coral bleaching. So, what can be done about this decline? One possible solution is to construct artificial reefs.
What are Artificial Reefs?
Artificial reefs are man-made structures that are designed to imitate natural reefs. They imitate the physical structure that these reefs provide. They can be made from pretty much anything. Some are unintentional, such as oil rigs or boats that have sank, while others are constructed exactly for this purpose. Some are made from concrete or rock, others are made of metal or tires, but the most common object used to make artificial reefs are old ships. One example includes artificial reefs made from sunken New York city subway cars.
Subway cars being pushed into the water by unknown source under [SC DNR, CC 3.0]
Structures are usually placed in open, featureless areas of ocean. These new structures act as a place for new coral polyps to settle, as well as larvae of many species. They can also act as a connection between different reef communities. Many marine organisms, including corals, have a planktonic larval stage. These larva have a set time and distance they can travel. If they don’t settle before then, they will die. Artificial reefs can help connect different populations by serving as points for dispersing organisms to settle. These connections would be multigenerational in most cases as settlement means that individuals don’t move from one reef to another, or in extreme cases, not at all. However, the offspring from one population could move to the next reef, and so on. Eventually, corals and sponges that are found in natural reefs take over and cover the man-made structures, and fish and invertebrates will be attracted to them like they are to natural reefs.
Biscayne National Park by US National Park Services under [CC open access].
Research on Artificial Reefs
A study done by Arena, et al. (2007) that took place off the coast of Florida looked at the differences between natural and artificial (vessel) reefs. They found greater fish abundance and biomass on the vessel reefs, as well as greater species richness. There were also many economically important fish species found on artificial reefs. However, different assemblages of fish were associated with the different reef types. The vessel reefs housed a much greater proportion of planktivores compared to the natural reef. Planktivores on the younger vessel reefs are lower in the food chain, they represent resources yet to be unlocked and transferred to higher trophic levels. Over time, artificial reefs are expected to transition to be more similar to natural reefs as they age.
Artificial reefs can provide a valuable solution to help with the threats that natural coral reefs face, but if things don’t change and stressors continue to increase, then artificial reefs won’t be sufficient.
There are many well known artificial reefs around the world primarily created from old machinery but there are also some that have been placed there initially for this purpose. “The Silent Evolution” by artist Jason de Caires Taylor, is a beautiful project where art sculptures were placed underwater to serve as artificial reefs. Visitors can enjoy the diverse underwater creatures but also take in the mystifying and magical art that is helping to protect Mexico’s rich beauty and important ecology.
Below is a video tour of “The Silent Evolution”
A Vimeo element has been excluded from this version of the text. You can view it online here: http://pb.libretexts.org/marine/?p=113
Below is a video about Artificial reefs by Texas Parks and Wildlife:
A YouTube element has been excluded from this version of the text. You can view it online here: http://pb.libretexts.org/marine/?p=113
It is worth mentioning that there are other types of reefs in the world besides coral reefs. Some, such as oyster reefs, can also be artificially made using simple materials such as oyster shells for spat (oyster larvae) to grow on and cement the loose materials into a solid reef structure. Many organizations such as The Elizabeth River Project and Chesapeake Bay Foundation work to restore oysters and reefs in the Chesapeake Bay and waterways of the US.
The information in this chapter is thanks to content contributions from William Trautman. | textbooks/bio/Marine_Biology_and_Marine_Ecology/04%3A_Reef_Conservation/04.2%3A_Artificial_Reefs.txt |
What is Bioremediation?
Bioremediation is a possible solution for the growing problem of pollution and global warming. Bioremediation involves using living microbes to clean waste. These microbes can naturally occur in the area or scientists can extract them and place them into areas that need them. When scientists place cultured microbes into an area for purposes of bioremediation it is called bioaugmentation.
In Situ Bioremediation” by Jørgensen, K. S. via in situ bioremediation under [CC BY-SA 4.0]
The Process of Bioremediation
Microbes in the environment break down organic material. Some microorganisms can degrade contaminants by breaking down these materials into harmless substances. Bioremediation is about creating an ideal environment for microbes that degrade pollution by providing these organisms with fertilizer, oxygen, and other conditions that encourage their rapid growth. Microbes often break down pollutants into small amounts of water and harmless chemicals like carbon dioxide.
Mechanisms involved in bioremediation of toxic compounds” by Timmer26, via bioremediation of oil spills [CC BY-SA 4.0]
In order for bioremediation to work successfully, conditions need to be ideal for cell growth. Adequate temperature and food must be present in the area. If conditions are not already ideal, amendments can be used. Amendments can consist of common materials like molasses or vegetable oil that increase the chance of survival for microbes by making conditions more suitable for their growth and enhancing their ability to break down contaminants. The process of bioremediation can be as short as a few months or as long as a few years. If the contamination concentration is high, or the contaminated area is very large, then clean up will take longer. Many people worry about the safety of using microbes. However, microbes are completely safe because they are already naturally occurring in the environment and are not harmful to humans. After the contaminants they needed for growth are depleted, the microbes from bioaugmentation will no longer have ideal living conditions and will not survive long. One downside of bioremediation includes creating noise pollution from the use of mixers and pumps that could be irritating to businesses and households.
Advantages of Bioremediation
Bioremediation is relatively cheap compared to other pollution cleanup methods. It is safe and can lead to cleaner water and soil in the area. Another advantage is that contaminated soil and groundwater are treated onsite without having to dig and transport materials elsewhere for treatment. One common example of a successful bioremediation process is composting. This video explains how bioremediation has been used to help clean up oil spills.
Information in this chapter is thanks to content contributions from Bryce Chouinard .
04.4: Biocontrol in Hawaiian Reefs
What is Biocontrol?
Biocontrol or Biological Control is the introduction of a natural predator into an environment in order to control a pest species. It is an important way to aid in the management of terrestrial and aquatic habitats that have been invaded by non-native species. Using natural methods is a great way to help troubled ecosystems without many of the negative impacts associated with chemicals and other non-natural interventions.
Here is a video by the Hawaiian Conservation Alliance of the work completed in the bay of Oahu, HI for the urchin biocontrol project.
Native Sea Urchin Biocontrol Example
Native sea urchins have been used as a form of biocontrol for algae overgrowth in Hawaiian coral reefs.
Two sea urchins in Hawaii by Opencage under [CC BY-SA 2.5]
A non-native species of algae was introduced to Hawaiian coral reefs in the 1970’s that quickly became invasive and invaded Oahu’s coral reefs. The algae grew so uncontrollably that it smothered out local flora and fauna and is still causing major issues for the Hawaii’s reef areas today. Herbivorous fish are highly impacted by this overgrowth. People spent up to 8 hours a day pulling algae from the reefs in attempts to control its growth to little avail.
Finally researchers discovered the idea that native sea urchins could be used to control the algae. Urchins are great at controlling algal growth because they graze on the algae. After the introduction of 100,000 urchins to the reefs, an 85% decrease of algae cover was observed after just 2 years!
Biocontrol Successes and Failures
Though there have been biocontrol failures highlighted in the media, such as the Cane Toad introduction to Australia, there have also been many great successes.
The information in this chapter is thanks to content contributions from Sarah Larsen . | textbooks/bio/Marine_Biology_and_Marine_Ecology/04%3A_Reef_Conservation/04.3%3A_Bioremediation_to_Clean_Our_Oceans.txt |
Recreational activity is one of the joys in life that so many people share. Various types of recreation get people outside in all conditions from the 10o F New England winter weather to the hot beaches of a Caribbean island. Some tropical island activities include: boating, kayaking, scuba diving, snorkeling, sailing, wind surfing, and wake boarding- but they all have one thing in common, that is they are located in the ocean. Although some take place in deeper water, many of these activities are performed in shallow waters full of coral reef habitats. We know how fragile and important these reefs are and we also know how easily us humans have caused damage to them. Coral reef ecosystems are among the most biologically diverse and economically valuable ecosystems on Earth. Worldwide precious coral reefs attract millions of tourists annually and yield a significant economic benefit to those countries and regions where they are located. According to the National Oceanic and Atmospheric Administration (NOAA ), recreation and tourism account for \$9.6 billion of the total global net profit of coral reefs. This large amount of revenue generated is being threatened by the degradation of coral reefs.
As you can see there is a positive feedback loop occurring because of this situation. Many components of tourism, including recreational activities, are the cause of damage to the reefs, but ironically it has been shown that ecotourism is damaging as well.
Ecotourism is defined as: “Responsible travel to natural areas that conserves the environment and improves the well-being of local people.”
A YouTube element has been excluded from this version of the text. You can view it online here: http://pb.libretexts.org/marine/?p=120
However, increased tourism to sensitive natural areas such as coral reefs, without appropriate planning and management, can threaten the integrity of ecosystems and local cultures. The increase of visitors to ecologically sensitive areas can lead to significant environmental degradation. Likewise, local communities and indigenous cultures can be harmed in numerous ways by an influx of foreign visitors and wealth. Mass tourism poses a threat to reefs and to the revenue generated from these ecosystems. Although branded under the word ecotourism many businesses and organizations are contributing to the increase in coral reef degradation. Once coral reefs are damaged, they are less able to support the many creatures that make their home on the reef and in turn lose value as a destination for tourists.
Little Venice quay flooded with tourists. Mykonos island. Cyclades, Agean Sea, Greece. Photo by Mstyslav Chernov. [CC BY-SA 3.0]
Most tourism in natural areas today is not ecotourism and is not, therefore, sustainable. Specifically, ecotourism possesses the following characteristics:
• Conscientious, low-impact visitor behavior
• Sensitivity towards, and appreciation of, local cultures and biodiversity
• Support for local conservation efforts
• Sustainable benefits to local communities
• Local participation in decision-making
• Educational components for both the traveler and local communities
What is ecotourism? Photo by Ron Mader via Flikr. [CC BY-SA 2.0]
“Tourism will never be completely sustainable, as every industry has impacts. However, it’s important to know if the revenue created from tourism is reinvested correctly in order to benefit the coral reefs and build a sustainable future. For ecotourism to be sustainable, companies must take responsibility and allocate revenue it generates from its eco-attractions into the protection of reefs instead of further investing in tourist structures and attractions that have negative impacts on the health of these ecosystems.”
• Breakage of coral colonies and tissue damage from direct contact such as walking, touching, kicking, standing, or gear contact
• Breakage or overturning of coral colonies and tissue damage from boat anchors
• Changes in marine life behavior from feeding or harassment by humans
• Water pollution
• Invasive species
• Trash and debris deposited in the marine environment
There are lessons to learn from the ecological destruction in Australia, Hawaii, Indonesia and other Pacific Islands where recreational activities are high in the bays of resort-filled areas and multiple-use marine parks.
In a study in Australia, activities such as diving, snorkeling, ski jets, and motor boats with surfing skis had high impacts on coral reef ecosystems. These activities can cause direct damage to the corals and increase pollution in the water. Surfing had less negative impact as it is superficial.
Some activities and their impacts are listed below.
[material below 1-4 is copied from How Does Tourism Affect Coral Reefs?]:
1.) Scuba Diving and Snorkeling
While most diving and snorkeling activities have little physical impact on coral reefs, physical damages to corals can and do occur when people stand on, walk on, kick, touch, trample, and when their equipment contacts corals. Coral colonies can be broken and coral tissues can be damaged when such activities occur. Divers and snorkelers can also kick up sediment that is damaging to coral reefs.
2.) Boating and Anchors
Boats grounding in coral reef habitat can damage corals, as can anchors. Anchors can cause a great deal of coral breakage and fragmentation, particularly from large boats like freighters and cruise ships. Heavy chains from large ships can break or dislodge corals. These damages to corals can last for many years.
Anchoring can also damage the habitats near reefs such as seagrasses that serve as nurseries and habitats for the juveniles of different coral reef organisms. Marinas may inappropriately dispose of oils and paint residues, polluting local waters, and additional pollution may occur during fueling.
3.) Fishing and Seafood Consumption
An abundance of tourist fishing and consumption of local fish stocks may lead to overexploitation and competition with local fishers. Inappropriate fishing techniques such as bottom trawling can cause physical damage to reefs.
4.) Cruises and Tour Boats
These vessels can cause physical damage to reefs through anchoring and grounding, as well as through the release of gray water and human waste into coral reef habitat. Chemicals added to paint used on boats and fishnets that are intended to discourage the growth of marine organisms can also cause pollution in coral reef waters.
The variety of marine life and protected beaches supported by coral reefs provide beautiful sights for sightseers, sunbathers, snorkelers. Healthy reefs support local and global economies. Through the tourism industry and fisheries, coral reefs generate billions of dollars, and millions of jobs, in more than 100 countries around the world. Studies show that on average, countries with coral reef industries derive more than half of their gross national product from them. A good example can be found in Bonaire, a small Caribbean island. Bonaire earns about \$23 million (USD) annually from coral reef activities, yet managing its marine park costs less than \$1 million per year. A study conducted in 2002 estimated the value of coral reefs at \$10 billion, with direct economic benefits of \$360 million per year. For residents of coral reef areas who depend on income from tourism, reef destruction creates a significant loss of employment in the tourism, marine recreation, and sport fishing industries.
As we all know, coral reefs are undergoing major stress-related side effects because of human impacts. Through over-use, direct damage and ill-considered tourist operations, the World Wildlife Fund predicts that 24% of the world’s reefs are under imminent risk of collapse through human pressures; and a further 26% are under a longer term threat of collapse. Another significant anthropogenic problem facing coral reefs is sedimentation. Sedimentation (losing soil from upland areas) is an extremely important cause of coral reef destruction. Coastal construction and shoreline development (back to the ecotourism concept) often result in heavy sediment loading. Watersheds cleared of their forests and other vegetation cover is vulnerable to erosion and flooding, resulting in increased levels of sediments reaching the reefs. Excessive sedimentation also exceeds the clearing capacity of some filter feeders and smothers the substrate. It reduces light penetration and can alter the vertical distribution of plants and animals on reefs. Sediments can also absorb and transport other pollutants.
When tourists accidently touch, pollute or break off parts of the reef, corals experience stress. The coral organisms try to fight off the intrusion, but this process often leads to coral bleaching—when corals react in a stressed way to expel the brightly colored algae that live in them this in turn, starves themselves and eventually become completely white. Once corals are bleached, they die and can no longer contribute to the biodiversity of the reef community. Since the disruption of one ocean system impacts all the others, sea grass and mangroves—shallow-water plant species vital to the health of the marine ecosystem—are also threatened by coral stress. Many of these events of accidental coral destruction are caused by recreational activities.
One study examined diver behavior at several important coral reef dive locations within the Philippines and also assessed how diver characteristics and dive operator compliance with an environmentally responsible diving program, known as the Green Fins approach, affected reef contacts. The role of dive supervision was assessed by recording dive guide interventions underwater, and how this was affected by dive group size. Of the 100 recreational divers followed, 88 % made contact with the reef at least once per dive. Divers from operators with high levels of compliance with the Green Fins program exhibited significantly lower reef contact rates than those from dive operators with low levels of compliance.
Although it’s difficult for an individual to stop the entire coral reef dilemma it’s easy to take small but powerful steps in the right direction.
Some of these steps include:
• Don’t touch living coral and don’t pick up wildlife for souvenirs, including shells, coral rubble and plants.
• Be conscious of what you bring with you, for example, reusable water bottles instead of plastic bottles and a backpack for your trash in case there isn’t an area nearby to dispose of waste properly.
• Take the bus instead of a car, and if possible, do your research on the hotels or hostels where you stay.
• Try to stay at hotels that are environmentally friendly. Many coastal hotels dump their graywater—wastewater from laundry, cooking and household sinks—into the ocean, contributing to sedimentation and the contamination of coral reefs.
So, the message of this post is to be aware of corals and precious ecosystems when recreating! Also, try to vacation more sustainably by researching and traveling more eco-friendly. Some places that offer eco-tourism travel are green loons. Travel Tips for eco-traveling can be found below.
A YouTube element has been excluded from this version of the text. You can view it online here: http://pb.libretexts.org/marine/?p=120
The information in this chapter in thanks to content contributions from Audrey Boraski. | textbooks/bio/Marine_Biology_and_Marine_Ecology/04%3A_Reef_Conservation/04.5%3A_Ecotourism%2C_Recreation%2C_and_Reefs.txt |
The decline in coral reefs causes major problems. Coral reefs make up only 0.2% of our ocean however they are home to over 25% of marine fish species and other organisms. They play many roles including protection of shorelines from major storms. The loss of coral reefs can disrupt many other ecosystems in and around the ocean.
Although the destruction of coral reefs have been caused by human activity, it is also humans that are saving these systems and finding solutions using technological advancements. Scientists from all over are exploring different technologies aimed at protecting coral reef ecosystems.
1. UNDERWATER ROBOTS THAT MIMIC OCEAN LIFE
Underwater robots may be a key in helping us understand coral reef systems. Underwater robots were recently developed by researchers at Scripps Institution of Oceanography at the University of California San Diego. This new tool can offer a new way to study ocean currents as well as the creatures that are in the ocean. Right now the goal of these underwater robots is to use them to help answer questions about the most abundant form of life in the ocean: plankton.
The researchers at Scripps have designed and built these underwater explorers to study small scale environmental processes that are taking place in the ocean. These robots include probes that are equipped with temperature and other sensors to measure ocean conditions by swimming up and down or by maintaining a constant depth. These small robots could potentially be deployed in the hundreds to thousands to capture a multi-dimensional view of the interactions between the physical ocean and marine life.
During a study using these robots, scientists wanted to test theories behind how plankton form dense patches under the ocean surface, which then later leads them to rise to the surface as red tides. These robots were the perfect way to mimic the underwater swimming behavior of plankton and examine the organisms’ movements with the ocean currents.
This was the first time that a mechanism like this has ever been tested underwater. The biggest advancement is that these small robots are made inexpensively and are able to be tracked continuously underwater. What this means is that these robots could potentially be used as a small army and be deployed in a swarm. This swarm-sensing approach opens up a new world of ocean exploration. These small, low cost robots with cameras would allow for the photographic mapping of things such as corals. This technique could be huge in identifying the problem as well as seeing the effects of coral bleaching in almost real time.
You can check out the video and experiment that went along with this study HERE
2. ELECTRICAL BIOROCK STIMULATES CORAL GROWTH
To help preserve and restore coral, scientists are using an innovative technology called biorock. Biorock is a piece of technology that has a low-voltage direct current which is run through steel. This electricity can then interact with minerals in the seawater and cause solid limestone to grow on the structure. It uses the same principles as electrolysis, where the electric current causes a chemical reaction to occur that wouldn’t normally happen. Coral fragments from other reefs can than be translocated to the biorock structure where they can grow due to the natural mineral crystals that were formed.
This type of technology is being used as conservation measures for coral reefs. This is because this type of technology can speed up the normal processes of coral growth. When a diver sees an injured coral they can move them to these structures so that they can continue to grow and heal. The coral then have 50% greater chance of survival then they had before. Biorocks have also helped fish and lobster populations, especially juveniles who shelter in the structures.
3. 3D MAPPING AND BATHYMETRY TO MONITOR REEFS
Coral reef mapping and monitoring have helped scientists gather data on these habitats. With this technique scientists can collection biological, socioeconomic and climatic data needed to evaluate the conditions of the coral reefs and the surrounding area.
Monitoring operations include the National Coral Reef Monitoring Program (NCRMP), a new integrated and monitoring effort that will provide a precise picture of the U.S. coral reefs condition. To learn more about the NCRMP click here.
Mapping underwater coral reefs with 3D mapping allows volunteers and researchers to spend more time studying fish and invertebrates in water, while still getting the data needed from the reef. Cameras are used to take a multitude of underwater images and specialized software is used to analyze those images. More precise numeric data can be obtained with this technology. Before the use of technology such values could only be estimated by expert divers. Another advantage of this technology is its non-invasiveness, allowing the study of an environment in the office with less stressful field operations and coral extractions. The ease of repetitive surveys will make an amazing database for following coral reef changes over time, with the possibility to quantify all changes in near-real-time.
4. 3D PRINTED CORAL ENCOURAGES REEF RESTORATION
3D Printing Could Potentially Save our Coral Reefs: Check out this video showing the work being done to create artificial reefs
A YouTube element has been excluded from this version of the text. You can view it online here: http://pb.libretexts.org/marine/?p=122
As coral reefs are declining at fast rates, scientists are struggling to find effective and innovative ways to save them. One of the new ways they are doing this is by 3D printing. 3D printing has become a common way to construct many things such as human organs. 3D printing of portions of reefs can replace lost pieces of coral. These “fake” reefs are thought to be less vulnerable to climate change and more resilient to changing environmental conditions. Scientists are using 3D printing technology that helps them to create fake reefs to mimic the texture and structure of the natural reefs in an effort for restoration.
These experimental 3D printed reefs have already been implemented in the Mediterranean, the Caribbean, the Persian Gulf, and Australia. If they succeed, it will allow for new habitat for fish, but also baby coral polyps to attach themselves and multiply to grow into new reefs.
Artificial reefs have also been used to provide habitat and act as an ecosystem by mimicking a coral reef. They have been made of sunken shipwrecks, plastic, concrete blocks, old tires, and old cars—all heaped onto the ocean floor in hopes that fish and other marine life will come to call them home. However, many of these reefs fail because they do not fit in. A 3D printed reef is a better option since it can recreate the small spaces needed to protect the species that live in the community, it can act as a passageway and door. It can also provide angles that cast light or shades in a certain directions enabling fish to avoid predation. Since this technology is so new there are still so many questions behind it like how well will they actually work? How sustainable are these structures? Can they withstand harsh storms?
As the years go on scientists will be able to determine the effectiveness of these structures. This technology is a step in the right direction to trying to find alternative ways to save coral reefs.
OTHER TECHNOLOGIES BEING USED:
The information in this chapter in thanks to content contributions from Haley Zanga. | textbooks/bio/Marine_Biology_and_Marine_Ecology/04%3A_Reef_Conservation/04.6%3A_How_Technology_is_Saving_the_World%E2%80%99s_Coral_Reefs.txt |
The People and the Location
Native peoples living near coral reefs have been displaced for centuries for many reasons some including tourism, agriculture, and conquering of land. Today, nearly 40% of the world’s 6,000-8,000 indigenous groups encompass coastal ocean and island regions within their homelands, territories, and nations.
Below is a list of some native populations that live/lived near reefs around the world
• The Ciboney and Carib peoples from mainland America inhabited some land the West Indies.
• Giraavaru people were the ancient owners and rulers of the Maldives.
• The Taíno were an Arawak people who were the indigenous people of the Caribbean and Florida.
• Aboriginal people and Torres Strait Islander people belong to Australia and are connected with the Great Barrier Reef.
• Sentinelese people an indigenous people who inhabit North Sentinel Island in the Bay of Bengal in India. They are considered one of the world’s last uncontacted peoples.
• The many tribes of Papuans living on Papua New Guinea.
• Malagasy people of Madagascar make up many different groups.
Below is a map of coral building reefs around the world. As seen they are located along the tropics where high densities of human populations live.
Climate Change Threats
Many inescapable threats besides displacement affect indigenous cultures today. One heavily discussed is Climate Change. Climate change is impacting many indigenous communities by endangering sacred and traditional living sites, cultural practices, local forests and ecosystems, traditional foods and water quality. In response to this crisis, scientists in the US are attempting to work with coastal communities to study the impacts of climate change on the health and vitality of the social, economic and natural systems of these communities.
As climate change affects coral reefs intensely, these impacts influence the people that live near and depend on these ecosystems. Two studies in Hawai`i are exploring climate change impacts on coral reefs and in particular the flooding of coastal communities from rising sea water levels. It is agreed widely by scientists that climate change poses the greatest long-term threat to coral reefs and among other impacts, climate change is expected to result in more frequent severe tropical storms and severe coral bleaching events. Coral bleaching is caused by environmental stress from warm water which causes corals to expel their symbiotic algae from their tissues, turn white and eventually the afflicted coral may die. Threats from increasing storms, rising sea level and direct effects of ocean warming will continue to have devastating impacts on coastal ecosystems and their human communities.
6M Sea Level Rise” by NASA under [public domain]
Indigenous Solutions
Scientists, along with members of Washington State’s Swinomish Indian Tribal Community, are addressing climate change threats to the Tribe’s land, wildlife, culture and community health. As sea levels rise, coastal erosion intensifies which lead to many negative side affects on land and in the ocean. One important part of preparing for climate change is identifying a full range of potential impacts from declining natural resources such as fish, to damaged infrastructure such as roads and buildings, to compromised community health. The Swinomish fishing tribe in Seattle WA are taking action to build community resilience by implementing the Swinomish Climate Change Initiative. With funding from the Northwest Climate Science Center and the North Pacific Landscape Conservation Cooperative, the Swinomish have conducted a pioneering study to combine assessments of ecological health with newly developed community health indicators to identify priority adaptation tactics. For more information watch a webinar about the project here. Other funding has been granted towards these areas such as from the Interior Department which recently claimed to make \$8 million available to fund projects that promote tribal climate change adaptation and ocean and coastal management planning through its Tribal Climate Resilience Program.
On the island of Maui scientists are developing a tool to help coral reef managers make science-based decisions; this tool can map, assess, value and simulate changes in the coral reef ecosystems under different climate change scenarios. Hawai`i’s coral reefs provide seafood, areas for recreation and tourism, coastal protection and support the traditional lifestyles and values of the state’s native cultures. The research will show potential climate change impacts and help land and coastal managers make informed decisions to create resilient coral reefs and coastal communities.
Divers from the Commonwealth of the Northern Marianas Islands reef resiliency team conduct assessments of reef resilience in the Marianas archipelago by USGS licensed under [public domain].
The Battle of Good VS Good
Traditionally native peoples were displaced due to other nations conquering the land and many now assume it is all over. Unfortunately, this problem still occurs today with a strange and complicated twist. Many indigenous people are being pushed out of their homes in the name of conservation because governments can acquire money for conservation projects like setting aside land. When the economic priority is to generate revenue from conservation, humans get pushed away from the protected areas so they can become “protected for nature”. Most of the world’s 6,000 national parks and 100,000 protected places have been created by the removal of tribal peoples. Hundreds more parks are being created every year as countries commit to meeting the UN’s goal to protect 17% of land by 2020. And the human toll is rising accordingly.
Resist tug of war: by author unknown via Pixabay, July 9, 2019. [Simplified Pixabay License].
Misc. Resources
• MinorityRights.org provides information on indigenous peoples in all countries and regions on the world.
• Reefbase.org is a coral reef database full of information open to all
The information in this chapter in thanks to content contributions by Audrey Boraski. | textbooks/bio/Marine_Biology_and_Marine_Ecology/04%3A_Reef_Conservation/04.7%3A_Indigenous_People_and_Conservation.txt |
What is Volunteering?
There are countless people and organizations working around the world at this moment to help protect coral reef ecosystems. Many of these people are unpaid volunteers and realize the importance of coral reef conservation and its effects on everyone around the world. Volunteering is an amazing form of work that anyone can do anywhere in the world, within any area. It is simply helping out or working without compensation other than self-satisfaction. According to Nationalservice.org the 2018 Volunteering in America report found that 77.34 million adults (30.3 percent) volunteered through an organization last year. Altogether, Americans volunteered nearly 6.9 billion hours, worth an estimated \$167 billion in economic value, based on the Independent Sector’s estimate of the average value of a volunteer hour for 2017. Millions more are supporting friends and family (43.1 percent) and doing favors for their neighbors (51.4 percent), suggesting that many are engaged in acts of “informal volunteering”. There are so many different environmental organizations one can volunteer with and below is a list of just a few that involve coral reef projects.
Organizations and information from their websites:
Mission: Our mission is to change the face of volunteer travel. Established in 2007, we have grown to become the world’s leading volunteer travel company, working in over 40 destinations around the world and placing thousands of volunteers abroad every year.
We believe in a future where any traveler, anywhere in the world is empowered to make a meaningful difference in the community they are visiting, and we take pride in making this happen.
We’re focused on providing affordable volunteer travel experiences that are responsible, safe and high quality. Our programs heighten global awareness and cultural understanding through the skills and expertise taken by volunteers to their host communities, and through the experiences and lessons that volunteers take back to their own countries and cultures.
Price: Fees from \$1010 for 1 week
Time Commitment: 1-4 weeks
Tasks you would do!:
Volunteers on the Marine Conservation project in Australia have the opportunity to join a variety of important conservation efforts focused on the protection of Great Barrier Reef ecosystem.
When volunteering in Australia, you will work in collaboration with a number of oceanographic organizations to gather vital raw data and support the protection of the Great Barrier Reef through a range of initiatives, including:
Reef Monitoring – This portion of the Marine Conservation project involves snorkeling within an assigned area to collect data on the species living in the Great Barrier Reef. You do not require any previous reef surveying experience to participate, as you will be trained in the methodology of in-water surveying during your program orientation. A full-length lycra suit will be supplied and volunteers are just required to bring their own snorkel and waterproof watch.
Name: GVI
Mission: 20 years later, GVI has engaged over 35,000 participants, set up 600 community partnerships, and currently runs 21 programs in 13 countries worldwide. Richard and Ben’s vision to not only facilitate global citizenship and leadership skills in young adults, but to allow them to have a truly positive impact on local communities and environment is very much alive.
Price: \$4,965, \$6,125, \$7,285, \$9,605
Time Commitment: 4, 6, 8, 12 weeks
Tasks you would do!: Travel to the crystal clear waters of the Indian Ocean as a member of an expedition and work on critical marine conservation projects amongst the beautiful islands of the Seychelles.
You will contribute towards various conservation-related surveys aimed at providing data to the local government on coral reef research, fish, and invertebrate surveys and assist with the development of an environmental education and awareness program as well as marine plastic pollution cleanups and surveys.
You will spend the majority of your time on this expedition scuba diving and as such you need to be qualified to at least PADI Open Water, or equivalent. For non-divers wishing to attend, we can recommend local dive centers that will help you qualify before your intended start date.
Name: Earth Watch
Mission: Earthwatch engages people worldwide in scientific field research and education to promote the understanding and action necessary for a sustainable environment.
Price: \$1550
Time Commitment: 5+ days
Tasks you would do!: On this expedition, participants can get involved through scuba or snorkel activities. You will assist researchers in making baseline measurements of environmental conditions, actively removing algae, deploying coral recruitment (settlement) tiles, and assessing fish and invertebrate diversity and abundance. By joining this expedition, you’ll be at the forefront of active reef restoration science. You will assist researchers in experiments that aim to develop best practice methods for removing this macroalgae and allowing coral to regrow. You will be directly involved in filling in the gaps that will enable reef managers to make evidence-based decisions about active interventions that support the recovery of the Great Barrier Reef, and reefs all over the world.
Name: OPERATION WALLACEA
Mission: Operation Wallacea is a network of academics from European and North American universities, who design and implement biodiversity and conservation management research expeditions.
Research is supported by students who join the programme, to strengthen their CV or resume or collect data for a dissertation or thesis. Academics benefit from funding for high quality fieldwork enabling them to publish papers in peer reviewed journals. This model enables the collection of large temporal and spatial datasets used for assessing the effectiveness of conservation management interventions.
Price: \$5,925.00 (\$2,370.00)
Time Commitment: 8 weeks
Tasks you would do!: IVHQ’s affordable Sea Turtle and Marine Conservation volunteer projects offer international volunteers with the opportunity to provide vital support to ocean conservation organizations around the world that are focused on the protection of fragile ecosystems and threatened marine species.
Benefits of Volunteering
With busy lives, it can be hard to find time to volunteer. However, the benefits of volunteering can be enormous. Volunteering offers vital help to people in need, worthwhile causes, and the community, but the benefits can be even greater for you, the volunteer. Giving to others can also help protect your mental and physical health. It can reduce stress, combat depression, keep you mentally stimulated, and provide a sense of purpose. While it is true that the more you volunteer, the more benefits you’ll experience, volunteering does not have to involve a long-term commitment or take a huge amount of time out of your busy day. Giving in even simple ways can help those in need and improve your health and happiness.
Just a few benefits of volunteering are listed below
1. Connects you to others
2. Good for your mind and body
3. Advance your career
4. Brings fun and fulfillment to your life
5. Doing things you would not do otherwise
The information in this chapter in thanks to content contributions by Audrey Boraski. | textbooks/bio/Marine_Biology_and_Marine_Ecology/04%3A_Reef_Conservation/04.8%3A_Volunteer_to_be_Victorious.txt |
Tropical Marine Biology Class
The Tropical Marine Biology Class taught by Dr. Karen Cangialosi at Keene State College, allows undergraduate students the opportunity to investigate topics such as tropical marine ecology, biodiversity, coral reef biology, conservation, and environmental issues. The course incorporates a rich field trip experience to the Turks and Caicos Islands where students get direct hands-on experience diving and snorkeling to observe marine life. Students also learn the methods of reef monitoring and learn much about the local culture of the islands. Tropical Marine Biology students continue to play an important role as instructors in the September Reef Education Program.
Beyond the Classroom by Jaime Marsh
Picture this: you sign up for a class, on the first day you take a seat in a generic, over-sized lecture hall alongside 20 other classmates, you open your textbook to the first chapter, the professor walks in and shortly begins lecture. With the exception of a few monotonous exams, this is how the next 15 weeks of the semester will be. This is how the majority of classrooms have operated throughout our middle school, high school, and college years. For many of us, we do not know any differently, however a new wave of an open education based curriculum is slowly approaching that is very quickly changing the way we learn.
For me, it started in a Tropical Marine Biology course I enrolled in, in my junior year at Keene State College. We began the first day of class in the most non-traditional way possible, by being asked one simple question: ‘what do you all want to do this semester?’ While we still had some traditional components to the course like lectures, it rapidly evolved into something much larger- from something we learned, to something we could apply, to something we created, to something that I love. While the series of identification quizzes at the start of the semester provided me a solid base to apply my knowledge of certain species and marine ecosystems, they did not prepare me for the depth and wealth of my actual experiences on the May 2017 trip. For many reasons, this trip to the Turks and Caicos Islands forever changed me.
First and foremost, it provided me the opportunity to return to TCI in September 2018 to participate in the Coral Reef Monitoring and Youth Education Program under the direction of Dr. Karen Cangialosi and Dr. Scott Strong (read more about this below).
Once there, my classmate Alana and I assisted in the collectionof data for the Reef Check International database, as well as helped run a small after-school snorkeling program for a few of the local high school girls. With my first trip to TCI under my belt, I was confident and excited to not only share my knowledge of the coral reef system, but to also share my passion for the ocean and all of its’ wonders. However, to say it was a humbling experience would be an understatement. Dr. Cangialosi had previously stated that many of the Turks Islanders do not know how to swim, and in fact, many have never even been in the ocean because they are scared of it or have been discouraged from swimming. When we asked the girls if any of them knew how to swim, most of them timidly answered ‘yes,’ however once in the water, their lack of experience was evident. For the first few days we focused largely on teaching the girls not only how to swim and float, but also teaching them the basics of the coral reef system and species identification. The majority of the time they clung to us; my hand had never been so numb. Several times I was pulled underwater, or hit in the face by flailing arms and flippers, all while treading water for over an hour. Over the course of a week we watched them become more comfortable, not just with the ocean and the water, but also with themselves. They slowly let go of our hands, and before you know it heads were popping up out of the water yelling to us in pure excitement that they had just seen a Queen Parrotfish, a Spotted Eagleray, or their favorite-a Sea Turtle. It was incredibly rewarding to see these girls begin to excel so quickly at something they were at first so afraid of.
I felt that our time with this group of girls went beyond what we originally set out to do. The goal was to teach them how to snorkel and give them information regarding the coral reefs; but within this short period of time, the moments that mattered the most were the small victories that each girl accomplished. One girl floated for the first time all by herself, another swam for 50 meters without stopping, and all of them were identifying the different species that comprise the coral reef system. We also listened to their hopes and dreams, their plans after high school, and encouraged them to go to university. I would like to think that we instilled them with confidence to go forth in life and follow any dreams big or small. And while I would love for any of them to continue to snorkel and identify the different species, and even share their knowledge with others, I do not believe that this was the biggest take away. They learned to not only trust themselves, but to trust a complete stranger, to be independent but to lean on others when you need to, and most importantly I think they learned how to believe in themselves when faced with a challenge.
Girls in Keene State College-TCI Reef Education Program, photo by Scott Strong, copyright.
That being said, it would be naïve of me to say that they did not have a similar impact on me because while this experience was humbling, it was also rewarding. The number one lesson I learned was that there are just some things that you can’t learn in a classroom. Yes, in the classroom I learned how to identify at least a hundred different types of marine life, but now knowing that I can actually apply it outside in the real world puts many things into perspective. To begin with, a classroom can’t teach you that everyone comes from a different background, and it is likely different than what we see on the surface or what we imagine. A classroom can’t teach you that it’s important to find the joy and happiness in all moments, no matter how big, small, sad, or happy they may be. A classroom can’t teach you what you love, just so you can do it, you have to experience it-whether it is medicine, marine biology, teaching, or all of the above. A classroom can’t teach you that it is alright to go down a path to find out it’s not where you want to be-sometimes you just have to travel down it. Some lessons are meant to be learned outside of the classroom, even if it happens to be in the middle of the ocean, 60 meters underwater. In the famous words of Jacques Cousteau, “The sea, once it casts its spell, holds one in its net of wonder forever.”
Field Trip May 2017
See some of the reflections on a field trip to Providenciales in the Turks and Caicos Islands from May 9 to May 19, 2017.
A YouTube element has been excluded from this version of the text. You can view it online here: http://pb.libretexts.org/marine/?p=133
Coral Reef Monitoring, Youth Education in the Turks and Caicos Islands
Photo by Scott Strong (copyright, use with permission)
In 2008, Dr. Karen Cangialosi and Dr. Scott Strong, established a coral reef monitoring program off the shores of Providenciales, in the Turks and Caicos Islands (TCI). On an annual basis habitat quality, measures of the physical environment, and invertebrate and fish diversity along a linear 100M transect on a small patch reef in Grace Bay are collected for data using the protocols of Reefcheck International. Each year the data is submitted to the Reefcheck International database, an Open Dataset available to the public. The data that is collected is also submitted to and used locally by the TCI Department of Environmental and Maritime Affairs. Over the years, they have established strong relationships with many individuals on Provo including business owners/operators, government officials, teachers, and school administrators. Dr. Karen Cangialosi serves as the Reef Check Team Coordinator for the Turks and Caicos Islands.
Integral to this project, they also run a small-scale Reef Education Program (REP) with resident students affiliated with the Gartland Youth Centre on Providenciales (Provo). This program is designed to help youth develop an understanding of the marine environment and emphasizes that sustainable practices can ensure not just the health of TCI’s reefs, but lead to healthier and more equitable living for its people. REP participants (14 to 17-yr-olds) are recruited primarily from Clement Howell High School, which has approximately 350 students including local Turks Islanders (Belongers), and expatriates primarily from Haiti, Jamaica, and the Dominican Republic. Participants learn snorkeling, marine life identification, behavior, diversity, and ecology of coral reefs, while also focusing on issues central to reef conservation. This program has been very successful in contributing to increased environmental awareness, internships, jobs, university admission and other opportunities for our Turks Islander REP participants.
Modified slightly from “Coral Reef Monitoring, Youth Education in the Turks and Caicos Islands” by Karen Cangialosi.
“Tropical Marine Biology Class and Field Trip May 2017” by Audrey Boraski and Haley Zanga
“Beyond the Classroom” By Jaime Marsh | textbooks/bio/Marine_Biology_and_Marine_Ecology/04%3A_Reef_Conservation/04.9%3A_Keene_State_College_Outreach.txt |
Porifera
Sponges are unique creatures. They are in the Phylum Porifera and there are about 5,000 different known species. They are one of the simplest forms of multi-cellular animals and come in a variety of different colors, shapes, and sizes. Sponges lack organs and a nervous system. They are sessile organisms, attached to reef surfaces via a holdfast. They get their food through filter feeding when the ocean currents go through their pores. There are 4 different classes of sponges; Calcarea (calcareous- has spicules*), Hexactinellida (horn sponges), Demospongiae (coralline), and Sclerospongiae (glass sponges). Each class of sponge is composed of different organic materials. If you want to learn more about sponges and their structure, this is a really informative article about them!
Spicules are “sharp spikes made of calcium carbonate located in the mesohyl. Spicules form the skeleton of many sponges”. Spicules can be a form of defense for the sponges to deter or hurt predators.
Sponges are some of the oldest organisms on earth having been around up to 500 million years! Each individual cell in a sponge can transform to do any function within the sponge. This is a unique and helpful trait to have. An article from Oceana.org even says that “a sponge destroyed in a blender can reform itself as the cells swim back together and take on the form and job needed for recovery”.
Most sponges are also hermaphrodites meaning that each adult can act as either male or female in the reproductive process. Some sponges can also go through asexual reproduction to produce clones when a piece of sponge breaks off and grows in another location!
Sponge fibers help filter water through the organism. This is important because they filter feed on plankton and bacteria while attached to the ocean floor
There are many different types of rope sponge. Row Pore Rope Sponge, Scattered Pore Rope Sponge, Thin Rope Sponge, and so on. They are a tropical sponge that come in a variety of colors, sizes, and depth ranges. This Marine Species Identification portal has some amazing information on marine species.
Tube sponges are another type of tropical sponge. They have a tube shape and also come in a variety of colors, shapes, and sizes. Below is the Yellow Tube Sponge, also known as Aplysina fistularis. The Yellow Tube Sponge has a large opening at the top of it and is attached at the bottom. If they are exposed to the atmosphere, they will turn purple and black and die.
The Barrel Sponge is another common type of tropical sponge. They are called Barrel Sponges because of the way they look. They are bowl shaped and have very large openings (osculum) at the top of them. They grow to be at least 6 feet wide, making them one of the largest sponge species in their habitats. They are homes for a variety of marine life such as shrimps, crabs, gobies, and cardinalfishes.
Fun fact: Giant tube sponges can live up to 2000 years old!!
Sponges are home to an array of microorganisms. Green algae, cyanobacteria, archaea, cryptophytes, red algae, dinoflagellates, heterotrophic bacteria, and diatoms are known to inhabit a range of sponge species. Most microorganisms that regularly inhabit sponges live in symbiosis with the sponges, however parasitic and pathogenic organisms can also affect them. Some microorganisms give corals their vibrant colors. Multiple microorganisms may live in the same sponge at the same time as well. The symbiotic relationship can be either commensalistic or mutualistic, and the types of microorganisms found in and on sponges can have an effect on the sponges growth and development, as well as its color.
The information in this chapter is thanks to content contributions from Sarah Larsen | textbooks/bio/Marine_Biology_and_Marine_Ecology/05%3A_Major_Marine_Phyla/05.1%3A_Phylum_Porifera.txt |
Cnidarians are organisms found exclusively in aquatic habitats. Of the over 10,000 aquatic Cnidarian species discovered, most inhabit marine environments. Cnidarians exhibit two major body forms, polyp or medusae. Polyps consist of a body stalk with a tubular shape with a single opening and multiple tentacles that surround this opening which serves as a mouth and anus. Polyps point upward for filter-feeding. The tentacles are covered with cnidocytes (stinging cells). Cnidocytes are the most important characteristic that distinguishes organisms as belonging to the Cnidarian phylum.Polyps are sessile and remain attached to a substrate. The medusa form is most notably observed in the umbrella like form of jellies. Similar to polyps, they consist of a body with a single opening surrounded by tentacles, but the gelatinous layer is much thicker and the mouth is usually oriented towards the substrate when swimming. Many Cnidarians have the ability to switch between these two morphs over the course of their life.
Class Hydrozoa
Hydrozoans can be found in both the medusae and polyp form in equal abundance. Compared to other cnidarians hydromedusea have a thinner and more delicate mesoglae (gelatinous) layer. In the polyp phase, most hydrozoans live colonially and often have polyps that bud from other polyps. They have a shared gastrovascular (GV) cavity and are genetically identical. Since the GV cavity is shared if one polyp is actively carrying out its function, such as feeding, the product of digestion (acquisition of nutrients) can be distributed among the other polyps. Each polyp can have a different function in the colony. Although they are all genetically identical different genes are expressed to vary the function of the individuals. Individual polyps are known as zooids. Gastrozooids, gonozooids, and dactylozooids respectively function for digestion, reproduction and defense1.
Hydras are hydrozoans that are unique in several respects. Unlike almost all other hyrdrozoans, they are solitary, live in fresh water and lack a medusa phase. Like many Cnidarians, Hydras can contain endosymbiotic algae or Zooxanthellae.
Some benefits of being an individual within a colony are protection, resource sharing, and even the passing of signal impulse. If one individual is stimulated by a threat, the signal will be sent throughout the colony, initiating a retraction across the whole colony.
Class Anthozoa
Anthozoans only occur in the polyp body form. Their polyps are more complex than the other Cnidarian classes, and the colonies can grow to enormous sizes. Anthozoans include the hard corals, gorgonians, soft corals and sea anemones. Read more about corals in chapter 3.
When analyzing the “skeleton” of corals, there are distinct factors that you should pay special attention to. When they grow, coral polyps deposit CaCO3 which is constantly accumulated around the living organisms throughout the course of their life-cycles. The live polyps are housed within the calcareous cups that they secrete, these serve a skeletal function and for protection. Analyzing the ‘skeletons’ left behind after the death of these organisms, you can see how they lived and developed over time. All of the perforations that might be observed in the dead skeleton were once home to a live polyp that made up the actual live being of a coral.
The photo below depicts a living hard coral polyp with its cnidocyte-covered tentacles protruding from the calcareous cup.
Class Scyphozoa
Scyphozoans are found predominately in the medusae form, but also have polyp phases in their life cycles. The spectacular variety of jellies are in this class. Check out the Monterey Bay Aquarium’s fantastic Live Jelly Cam!
Sea Nettle (Chrysaora fuscescens) Jellyfish in captivity in the Monterey Bay Aquarium [CC BY SA 2.5]
Reference
[1] Brusca, R.C., & Brusca, G.J.(2003). Invertebrates. Sunderland, MA: Sinauer Associates, Inc.
The information of this chapter in thanks to content contributors from Jessica Comeau and Jason Charbonneau | textbooks/bio/Marine_Biology_and_Marine_Ecology/05%3A_Major_Marine_Phyla/05.2%3A_Phylum_Cnidaria.txt |
Annelids
The Phylum Annelida is defined by its morphology as segmented worms. They express closed circulatory systems in the same fundamental manner that Homo sapiens do. Annelids are categorized taxonomically into many classes. A few of these classes are: Class Polychaeta, Class Clitellate and Class Echiuran. Common organisms in the Class Clitellate include Oligochaeta (earthworms) and Branchiobdellida ad Hirudinea (leeches). Ecologically, Annelids are subdivided into two classifications. Errent polychaetes express a multitude of parapodia appendages, defined heads complete with proboscis and are able to extend their bodies in order to have a greater physical surface area for gas exchange. The latter group being Sessile Tube Dwelling Annelids. These organisms contain the segmented part of their bodies within an external tube. The portion of their being that is extended is a feeding appendage that filters through the water. A great example of a Sessile Tube Dwelling Annelid is the Christmas-tree worm. Each Christmas-tree worm has two feeding appendages to filter through the water. They also have the ability to retract quickly when the worm feels threatened. Some are even photosensitive, which means when natural light is obscured by a potential predator, they automatically retreat. Sessile annelids are also inclusive of medusa worms and deep-sea thermal vents.
Split-crown feather dusters also live in reefs like the Christmas-tree worm. They have two semi-circle crowns of radioles which form a crown with a split down the center. These worm don’t just live on the reef, they live in tubes that the worm builds from particles of sand and a “glue” that is excreted from the worms body. The crown of radioles act as gills and that capture plankton and other microscopic organisms that the worm can feed from. When threatened, feather dusters will quickly retreat back into their tubes.
In the Turks and Caicos and other locations where they are found, there is an incredible phenomenon that takes place with the Odontosyllis enopla, otherwise known as the Bermuda Fireworm. This is a small, polychaete worm found in the western Atlantic Ocean. Since they are polychaetes, their bodies consist of multiple segments, each with a pair of parapodia. Their heads have two pairs of eyes at the sides each with lenses. Each pair of eyes is orientated in a different plane. Females can grow up to 20mm while males grow up to about 12mm. Their nickname comes from the fact that they are bioluminescent when they rise to the surface during the mating period. The Bermuda Fireworm typically lives in protected rocky bottoms and they swim to the surface 2 to 3 days after each full moon to spawn. These worms are only bioluminescent during mating times. They also follow a lunar periodicity pattern, which is why the swim to the surface to mate around the time of a full moon. Lunar periodicity is typically seen in response to changes in light intensity from the sun to light intensity from the stars. Typically, the female worm appears first, swimming up from the rocky bottom to make circles at the surface. The females then give off a green glow, looking like “marine fireflies”. The glowing, though amusing for human spectators, is designed to attract the attention of males at the bottom. If you look closely, you can see the males rush up to the surface to meet the females. When the males fly up to the surface, they immediately fertilized the released eggs.
The information of this chapter in thanks to content contributions from Melissa Wydra and Jason Charbonneau
05.4: Phylum Arthropoda
Arthropoda
All members of the Phylum Arthropoda have a distinct, rigid exoskeleton of chitin. Arthropoda are also known as the most taxonomically diverse phylum on the planet. They occupy nearly every known habitat on earth. Estimates state that there are anywhere from 30-100 million different species in this phylum. The segmentation of Arthropod bodies is different from that of Annelids in that they consist of subsections composed of fused segments referred to as tagmatization. Tagmata are the specific sections (i.e. Head, Thorax, Abdomen), which may vary from species to species. Some important features of arthropods are their open circulatory system, molting, coelomate, protostome and the fact that they live in almost all habitats on earth. Arthropods will molt their exoskeletons, this process of molting is also called ecdysis. Their exoskeletons have three main functions: protection from predators, prevention from desiccation, and locomotion (attachment sites for mussels). Sclerotization is the hardening of the procuticle after molting (also called tanning). Arthropods are also commonly noted for their jointed appendages. Examples of marine Arthropods include lobster, banded coral shrimp, cleaner shrimp. barnacles, horseshoe crabs, copepods, and other microcrustaceans that form the zooplankton.
The most important difference that is noticed between certain Arthropods such as crayfish and crabs is the morphology of and arrangements of body parts. Crabs and crayfish both have chelipeds, but crabs have a distinguishable single structure prosoma. As with all Arthropods, both types of creatures are contained by chitinous exoskeletons that they are able to shed and regrow throughout their life-cycles.
Barnacles are interesting, even among the variant Phylum of life that is Arthropods. As with all other Arthropods, they are distinguished by a chitinous exoskeleton, however unlike many of their relatives, a barnacle also has an outer cup made of calcium carbonate that resembles a tiny volcano in structure. Barnacles also have internal calcareous plates that can close. This is not only for protection from predators, but also to keep the barnacles from drying out if they are not submerged in the water. There are over 1,400 known species of barnacles, most of which have the notable characteristics of secreting a natural ‘glue’ that allows them to adhere to the various surfaces that they inhabit. The incredible part is, through scientific observation and testing, the tensile strength of these natural epoxies have been measured at over 5,000 lbs/in2. The manner in which barnacles feed is through cirri. This is a ‘feather-like’ appendage that combs through the water for zooplankton and other microorganisms that they can capture and ingest.
The information in this chapter in thanks to content contributions from Jason Charbonneau and Alana Olendorf | textbooks/bio/Marine_Biology_and_Marine_Ecology/05%3A_Major_Marine_Phyla/05.3%3A_Phylum_Annelida.txt |
Molluscs
The phylum Mollusca is defined by several special characteristics. These defining characteristics include a mantle with a mantle cavity, a shell (except where lost), visceral mass, foot, and radula. The odontophore is in the mouth of most mollusks and it supports the radula (a ribbon of teeth). In many molluscs, it moves forward while the radula contacts the food, allowing the mollusc to feed. Mollusca can be found in freshwater, marine and terrestrial habitats. More features of molluscs include bilateral symmetry, soft or unsegmented bodies, respiration via ctenidium, ganglia/nerve comprised nervous system, haemocoel body cavity, etc. [1].
Although when most people think of a mollusc they imagine a typical clam or snail with the shell on the exterior of the organism, there are actually variations of these characteristics. One example of this is the Flamingo Tongue. The Flamingo Tongue is a small marine snail. It is a fascinating organism, in that their mantle, when they are at rest, covers the outer shell on the exterior of the organism. When threatened the Flamingo Tongue will retract all of the exposed tissue back into the shell in a very interesting manner.
Polyplacophorans
Chitons are the common name for species in the Class Polyplacophora. Chitons are considered more primitive in relation to other groups within the phylum such as bivalves or cephalopods. There are 8 dorsal plates lining the dorsal surface of these organisms. There are many primitive species of the class Polyplacophora that are still extant. However, only a few species of Monoplacophorans still exist in the world today.
Gastropods
Gastropoda is a very diverse class of molluscs. The subclass Prosobranchia, are often identified by their coiled, cone shaped or tubular shells [1]. The mantel cavity is typically located on the anterior of the organism. Important distinctions of these organisms are the variations or the absence of radula. These organisms utilize Nephridia for excretion of nitrogenous waste. One characteristic of gastropods is the presence of a calcareous operculum. This structure acts as a shielded plate that protects the organism by covering the opening when it is retracted into its shell.
In the photo below, the dark oval in the center is the operculum. They are calciferous and rough to the touch, protecting the opening to the shell like a man-hole cover.
Nudibranchs
Nudibranchs are typically categorized as sea snails which lack shells. Often they are richly colored and captivating to the eye. Their magnificent beauty is the result of aposematism which is the bright coloration exhibited by these organisms that warns predators that they are toxic, distasteful or dangerous. The toxicity of these organisms differentiates from species to species, with some being exponentially more dangerous than others. Their toxicity is usually contingent upon their evolutionary specialization and their genus’s specific niche.
Bivalves
Class Bivalvia consists of molluscs that have two connected shells such as Oysters, Clams, Mussels, Scallops and many more. Most bivalves are enjoyed as delicacies, despite the fact that they are benthic level filter-feeders. As others in the phylum Mollusca, bivalves have a shell that is made up of deposits of Calcium Carbonate. These deposits are derived from substances in the water and harden over-time.
Visible among the many aspects of an open clam are the posterior and anterior adductor muscles. The function of these muscles is to hold the shell closed as a defense from predators. The strength of these muscles given their relative size is immense. The mantle is a layer of tissue that overlays the visceral mass of these organisms and is directly connected to the shell. The foot of the bivalve is directly responsible for its movement. The muscular foot will emerge when the shell is opened and pushes the organism along or into the benthos or substrate.
Cephalopods
Cephalopods exhibit several similarities but also distinguishable differences from other molluscs. They sometimes exhibit a calcium carbonate shell. Squids and Octopus lack this feature, but the more primitive Nautilus does have this feature. Species in the Class Cephalopoda contain a large closed circulatory system and prehensile arms/tentacles that encompass a mouth, complete with a beak and radula. One of the most important evolutionary aspects of these organisms are their large complex eyes. These eyes are specialized for improved sight at depths where little ambient light reaches. The mantle of these organisms forms a sizable ventral cavity containing ctenidia. A portion of the mantle also forms a muscular funnel. Water is taken up and forced through these chambers under pressure creating a unique form of jet propulsion. There are over 900 living species of cephalopods that inhabit the world today.
References
1. Brusca, Gary J., Brusca, Richard C. 2003, Invertebrates 2nd ed. ISBN 0-87893-097-3
The information in this chapter in thanks to content contributions from Alana Olendorf and Jason Charbonneau | textbooks/bio/Marine_Biology_and_Marine_Ecology/05%3A_Major_Marine_Phyla/05.5%3A_Phylum_Mollusca.txt |
Echinodermata
The Phylum Echinodermata is distinguished by characteristics such as spiny-skin, pentaradial symmetry, and an endoskeleton composed of calcareous ossicles. Given that all species in this phylum are exclusively marine dwellers, they also evolved a specialized water-vascular system. This includes several canals, that comprise part of a hydraulic system for functions such as the extension of limbs, movement, nutrient distribution, gas exchange and feeding [4]. Another fascinating aspect of Echinoderms is that the water vascular system also includes the tube feet with powerful suction capability. Due to the structural makeup of these organisms, largely in part to their calcareous plates, they dry and preserve well as both specimens and fossils.
Asteroidea
The photo below features a dried sea star. Sea star is a broad ecological term that refers to the entire Class Asteroidea. Sea stars typically have five arms, which they rely upon for movement; these animals also utilize their limbs and the various forms of tube feet on them for the capture and drawing in of prey. Their diet includes but is not limited to: gastropods, bivalves and many annelid worms. Interestingly enough, most Asteroidea in nature protrude their stomach outside of the body through the mouth to digest prey externally. This allows them to digest organisms they have captured and rest on top of. The aboral surface of the specimen shows the spiky-skin described above, jutting out from calcareous plated dermis. The small white structure, slightly off center to the left is the sieve plate or madreporite. This structure is the exterior opening to the water-vascular system of the sea star.
The oral surface shows many interesting distinctions. Among them, ambulacral grooves lining the arms. Lining the ambulacral groove are several dozen podia, which are also called tube feet. These podia are the primary mechanism for movement and predation. In the aboral view shown below, the tube feet as the tiny black structures that appear sunken into the organism (this is due to the fact that this specimen is long dead).
Ophiuroidea
The class Ophiuroidea (brittle stars and basket stars) is related to the asteroids but they are more morphologically slender, the arms do not contain tube feet, and they are distally stretched from the central disc. In the case of the basket stars, the structure of their limbs is highly branched, resembling capillary systems, or an entire conglomeration of roots. The complexity of these limbs may be attributed to evolutionary advantages from an increase in the surface area to volume ratio for gas exchange and feeding. The ability to reach out and capture large zooplankton prey without excess expenditure of energy is favorable to these organisms. The brittle star on the other hand exhibits an almost-serpentine like movement of the arms, giving them the nickname serpent stars. The diet of these organisms is very generalist, as they will consume essentially anything that they can come in contact with.
A special note in the story of the brittle star comes from recent reports that some brittle star species may actually share a symbiotic relationship with corals. An observational study in 2010 showed deep sea corals in the Gulf of Mexico covered in a substance called floc, which is speculated to be an odd combination of trace amounts of oil, dispersants, and excess mucus from stressed or sickly corals. Brittle stars were observed brushing off this substance which would have likely otherwise lead to the death of some very old coral reef colonies [ Smithsonian-Ocean ]. The extent and mechanism of this relationship is still not fully understood.
Echinoidea
Echinoidea is the class of Echinoderms that includes sea urchins, sand dollars, sea biscuits and others. The spines observed on these organisms are actually mobile, which serves to enhance protection, feeding, and aid in movement. Echinoidea are encased in an endoskeleton commonly called a test. Much like other endoskeleton exhibiting marine dwellers, the test is comprised of calcium carbonate [3]. Other morphological characteristics to note are that sea urchins exhibit longer spines than other members of the class such as heart urchins and sand dollars where the latter are very short relative to the organism’s size [4].
Holothuroidea
Sea cucumbers are a unique, divergent class from the rest of the Echinodermata. Unlike their counterparts, their ‘skeletal’ structure is greatly reduced, resulting in a soft body that is malleable and has many captivating traits. Without any arms, class Holothuroidea relies on small tentacles that surround the mouth. They prey on minuscule food items that are afloat in the oceans or that rest on the benthic level of the ocean floor [4].
Some unique aspects of sea cucumbers lie in their rather interesting defense mechanisms. If touched or squeezed, they will rapidly shrink in size and project water from several pores all over their body which hardens as they shrink. They can also expel all of their internal organs allowing predators to feed on them, but later they can regenerate these parts which is nothing short of astonishing. They also have mutable connective tissue and can quickly change the shape and texture of their body.
Crinoidea
The Class Crinoidea includes the feather stars and sea lilies. The defining characteristic of this class is that they anchor themselves to a substrate through the use of cirri. These cirri are attached to a long stalk which keeps them in place, as most of the species comprising this phylum are sessile. There is an exception to this general rule in the case of Analcidometra armata, commonly called the swimming crinoid. This is a rare group of Crinoids that may be observed across the Caribbean; they use their ten arms to gently manipulate water as a medium in order to become mobile [Marine Species Identification Portal]. These Crinoids are threatened species and if seen they should not be touched!
References
1. De Klujiver, M., Gijswijt, G., De Leon, R., & Da Cunda, I. (2019). Swimming crinoid (Analcidometra armata). Developed by ETI BioInformatics
2. Hall, D. (2018, May 10). A Brittle Star May Be a Coral’s Best Friend.
3. Hyman, L. H. 1955. The Invertebrates. Volume IV: Echinodermata. McGraw-Hill, New York.
4. Peachey, Donna & Gordon, The Biocam Museum of Life Series. Kelowna, B.C. Canada VIY 7N8 Box 417 PBC,
The information in this chapter in thanks to content contributions from Jason Charbonneau | textbooks/bio/Marine_Biology_and_Marine_Ecology/05%3A_Major_Marine_Phyla/05.6%3A_Phylum_Echinodermata.txt |
Four diagnostic features characterize species in the phylum Chordata: 1) The notochordis a malleable rod running the length of the organism’s body, to which the rest of the skeletal structure relies upon for foundational support; 2) the presence of a tail extending past the anus; 3) a hollow, dorsal nerve cord (becomes the spinal cord in humans!); and 4) pharyngeal gill slits, with the ability to be modified for specialized functions in mature vertebrates. Though this might sound outlandish, but since we are chordates, even all human fetuses early in development have gills!
There are many classes that comprise the phylum Chordata. These classifications and their relationships are constantly reassessed with taxonomic research and our continued development of our understanding of life on Earth. This chapter will focus primarily on the marine chordates.
Urochordata
The subphylum Urochordata includes the tunicates, otherwise known as ‘sea squirts’. They are exclusively found in marine environments and it seems strange that they are in the same category as vertebrates. Even more interesting is their manner of nutrient collection and waste expulsion. It is a rather simple system, there is an incoming siphon, that draws in water and food particulates that may be floating in the water. These nutrient particulates are then passed down to the intestine where they are processed for sustenance. The excess water and waste products are expelled through the other siphon known as the excurrent siphon. Even more surprising is the fact that these animals only show all traits of Chordates when they are in larval stage. Urochordata often occur in colonial form as adults as seen below.
Cephalochordata
The subphylum Cephalochordata (lancelets) exhibit all the traits of Chordata as adults. Like Urochordata, they are also marine organisms and may be found world wide in shallow waters. They are often observed in benthic environments, where they burrow themselves into the sediment but leave their anterior exposed as a foraging mechanism [1]. The anterior portion of these organisms resembles that of the face of shrimp or of a praying mantis. Their manner of feeding is through the filtration of nutrient rich waters around them. Cephalochordata have been described as ‘fishlike’ in comparison to their Urochordata counterparts. The species that comprise this subphylum are relatively small ranging from 5-15 cm in length. And though they possess a closed circulatory system, they have no heart. Instead, their blood is oxygenated via their gill slits and recycled throughout. Their dorsal nerve runs throughout their body, however the anterior end does not form a brain complex.
Agnatha
Moving into the vertebrate category, it is important to start off with the superclass Agnatha, more commonly known as the jawless fish. Two of the classes comprising Agnatha are Cyclostomata (lampreys) and Myxini (hagfishes). It is commonly accepted that the evolution of vertebrates began with the segmentation of a vertebral column. This gave rise to a ‘backbone’ [1]. This vertebral column typically incorporates and/or replaces the primitive notochord. Further vertebrate adaptations include the development of sensory organs, a complex neural system, and a brain encased in a skull. Vertebrate Chordates also exhibit bilateral symmetry, having a closed circulatory system with a chambered heart. The degree to which the heart is chambered (i.e. one, two, three and four chambered hearts), varies with taxonomic class.
Lampreys (Cyclostomata) are jawless fish that are parasitic on other fish. As juveniles they derive their nutrition from filter feeding on plankton and particles floating in fresh water. Lamprey juveniles wait until maturity to migrate into salt water environments. In the ocean, lampreys may often be observed attached to larger reef fish and megafauna. They press their mouth to their host and using a tongue, they draw blood and tissue out of their victims.
The Myxini Class are commonly known as hagfish and reside solely in marine environments. They are similar in structure to eels and are jawless. Myxini can be either consumers or detritivores, feeding on the flesh of weakened or already dead fish. They have also been known to prey upon small invertebrates. Just like the lamprey, hagfish tongues resemble a rasp, and are similar to serrations on a knife. One of the defense mechanisms exhibited by the Class Myxini resembles that of many amphibians in that when threatened, they will release mass amounts of high-viscosity fluids. These fluids help to distract, escape from, confuse or deter potential predators [1].
Osteichthyes and Chondrichthyes
Fish can be divided into the two main groups, Osteichthyes and Chondrichthyes. Osteichthyes, traditionally considered as an taxonomic class, is now known to be a paraphyletic group. As their name suggests, they are boney fish that dwell in both fresh water and salt water around the globe. Boney fish are comprised of a hard calcareous skeleton and are coated in slippery, sometimes sharp scales. An important feature of boney fish is their lateral line. This is a zone that runs horizontally along the body of the fish and is predominantly used in the detection of vibrations. The lateral line has been attributed to the coordinated and navigational success of schools of fish, in which mass quantities of individuals conglomerate for various reasons. There are currently over 34,000 known species of fish on the planet, and that number is both growing and shrinking [ fishbase ]. Many fish populations are threatened by egregious over-fishing practices which has caused species diversity and abundance in various ecosystems to move into a downward spiral.
The skeletons of Chondrichthyes are comprised of cartilage rather than bone. Cartilaginous fish include the Rays, Sharks and Chimaeras. The vast majority of sharks are predators, much of their power and deadliness comes from their evolutionary adaptations in their physiology. Their streamlined and highly muscular body lends to their high proficiency as consumers. The flattened bodies of rays contributes to their free-flowing nature through water. Often times rays consume invertebrates that are found in the benthos of the ocean, however they are highly diverse in size, morphology and behavior. Giant Manta Rays can get up to 7m in width and filter feed on masses of zooplankton, whereas the southern stingray may only be a few dozen centimeters in width and feed on the bottom in sandy flats near coral reefs [ NOAA ].
Chimaera
The Chimaera are an interesting group of organisms that inhabit the deep sea. Their physiology is atypical and they possess a cross of several characteristics as their name suggests. Rather than a jawline filled with teeth Chimaeras have a flat dental plate. Origins of Chimaeroid marine species can be traced back upwards to 280 million years, predating the earliest dinosaurs of the Triassic period.
A January 2017 discovery of a fossilized Dwykaselachus oosthuizeni skull showed that there are few structural differences in ancient Chimaeras compared to modern Chimaeras. CT scans of the fossil showed significant cranial nerves, inner-ear structure, and nostrils, which are all exhibited by modern Chimaeras [ UChicago Medicine ]. An incredible aspect of this would pertain to Earth’s projected geological history. The presence of modern-day Chimaeras with little difference from ancient species means that these organisms survived two mass extinction events, showing the perseverance of the beings that dwell in the ocean depths.
In Text Reference: 1. Peachey, Donna & Gordon, The Biocam Museum of Life Series. Kelowna, B.C. Canada VIY 7N8 Box 417 PBC, 2000
The information in this chapter in thanks to content contributions from Jason Charbonneau | textbooks/bio/Marine_Biology_and_Marine_Ecology/05%3A_Major_Marine_Phyla/05.7%3A_Phylum_Chordata.txt |
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
Contributors and Attributions
• Dr. Gary Kaiser (COMMUNITY COLLEGE OF BALTIMORE COUNTY, CATONSVILLE CAMPUS)
Exercises: Microbiology (Kaiser)
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
1.1: Introduction to Microbiology
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. List 5 basic groups of microbes. (ans)
2. State 3 of the many benefits from microbial activity on this planet. (ans)
3. State 2 of the harmful effects associated with microbial activities. (ans)
4. Briefly describe two different beneficial things the human microbiome does for the normal function of our body. (ans)
1.2: Cellular Organization: Prokaryotic and Eukaryotic Cells
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. An electron micrograph of a cell shows a rigid cell wall, cytoplasmic membrane, nuclear body without a nuclear membrane, and no endoplasmic reticulum or mitochondria. Explain why it is or is not each of the following.
1. a bacterium (ans)
2. a yeast (ans)
3. a virus (ans)
4. an animal cell (ans)
2. Match the descriptions below with the best type of cellular organization.
_____ no nuclear membrane, circular chromosome of DNA, no mitosis (ans)
_____ capable of endocytosis, sterols in membrane, 80S ribosomes (ans)
_____ mitochondria, Golgi apparatus, endoplasmic reticulum (ans)
_____ cell wall contains peptidoglycan (ans)
1. eukaryotic
2. prokaryotic
3. Multiple Choice (ans)
1.3: Classification: The Three Domain System
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Matching
_____ Eukaryotic cells. They have membranes composed of straight fatty acid chains attached to glycerol by ester linkages.If they possess cell walls, those walls contain no peptidoglycan. (ans)
_____ Prokaryotic cells. They have membranes composed of branched hydrocarbon chains attached to glycerol by ether linkages and have cell walls that contain no peptidoglycan. They often live in extreme environments. (ans)
_____ Prokaryotic cells. They have membranes composed of straight fatty acid chains attached to glycerol by ester linkages and have cell walls containing peptidoglycan. (ans)
1. Archaea
2. Bacteria
3. Eukarya
2. Matching
_____ Simple, predominately unicellular eukaryotic organisms. Examples includes slime molds, euglenoids, algae, and protozoans. (ans)
_____ Multicellular organisms composed of eukaryotic cells. The cells are organized into tissues and lack cell walls. They do not carry out photosynthesis and obtain nutrients primarily by ingestion. (ans)
_____ Multicellular organisms composed of eukaryotic cells. The cells are organized into tissues and have cell walls. They obtain nutrients by photosynthesis and absorption. (ans)
1. Fungi Kingdom
2. Protista Kingdom
3. Plantae Kingdom
4. Animalia Kingdom
3. Multiple Choice (ans)
02.E: The Prokaryotic Cell: Bacteria (Exercises)
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
Fundamental Statements for this Learning Object:
1. Physical control includes such methods of control as high or low temperature, desiccation, osmotic pressure, radiation, and filtration.
2. Chemical control refers to the use of disinfectants, antiseptics, antibiotics, and chemotherapeutic antimicrobial chemicals.
3. Sterilization is the process of destroying all living organisms and viruses.
4. Disinfection is the elimination of microorganisms, but not necessarily endospores, from inanimate objects or surfaces.
5. Decontamination is the treatment of an object or inanimate surface to make it safe to handle.
6. A disinfectant is an agents used to disinfect inanimate objects but generally to toxic to use on human tissues.
7. An antiseptic is an agent that kills or inhibits growth of microbes but is safe to use on human tissue.
8. A sanitizer is an agent that reduces microbial numbers to a safe level.
9. An antibiotic is a metabolic product produced by one microorganism that inhibits or kills other microorganisms.
10. Synthetic chemicals that can be used therapeutically.
11. An agent that is cidal in action kills microorganisms.
12. An agent that is static in action inhibits the growth of microorganisms.
13. Selective toxicity means that the chemical being used should inhibit or kill the intended pathogen without seriously harming the host.
14. A broad spectrum agent is one generally effective against a variety of Gram-positive and Gram-negative bacteria.
15. A narrow spectrum agent generally works against just Gram-positives, Gram-negatives, or only a few bacteria.
2.1: Sizes, Shapes, and Arrangements of Bacteria
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Match the following descriptions with the best answer.
_____ Division in one plane; cocci arranged in pairs (ans)
_____ Division in one plane; cocci arranged in chains (ans)
_____ Division in two planes; cocci arranged in a square of four (ans)
_____ Division in one plane; rods completely separate after division. (ans)
_____ Division in one plane; rods arranged in chains. (ans)
_____ A comma shaped bacterium. (ans)
_____ A thin, flexible spiral. (ans)
_____ A thick, rigid spiral. (ans)
1. bacillus
2. streptobacillus
3. spirochete
4. spirillum
5. vibrio
6. streptococcus
7. staphylococcus
8. diplococcus
9. tetrad
10. sarcina
2. A Gram stain of discharge from an abcess shows cocci in irregular, grape-like clusters. What is the most likely genus of this bacterium? (ans)
3. State the diameter of an average-sized coccus-shaped bacterium. (ans)
4. Multiple Choice (ans) | textbooks/bio/Microbiology/Exercises%3A_Microbiology_(Kaiser)/01.E%3A_Fundamentals_of_Microbiology_%28Exercises%29.txt |
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
3.1: Horizontal Gene Transfer in Bacteria
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Define horizontal gene transfer. (ans)
2. State three mechanisms of horizontal gene transfer in bacteria. (ans)
3. Briefly describe the mechanisms for transformation in bacteria. (ans)
4. Briefly describe the mechanism of generalized transduction in bacteria. (ans)
5. Briefly describe the following mechanisms of horizontal gene transfer in bacteria:
1. Transfer of conjugative plasmids in gram-negative bacteria (ans)
2. F+ conjugation (ans)
6. Describe R-plasmids, R-plasmid conjugation, and the significance of R-plasmids to medical microbiology. (ans)
7. Multiple Choice (ans)
3.2: Bacterial Quorum Sensing, Pathogenicity Islands, and Secretion Systems (Injectosomes)
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Define pathogenicity. (ans)
2. Define virulence. (ans)
3. Even though a microorganism may be considered pathogenic, it still may not be able to cause disease upon entering the body. Discuss why. (ans)
4. Define and briefly describe the overall process of quorum sensing in bacteria and how it may enable bacteria to behave as a multicellular population. (ans)
5. Multiple Choice (ans)
3.3: Enzyme Regulation
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Matching
_____ Regulatory proteins that block transcription of mRNA by binding to a portion of DNA called the operator that lies downstream of a promoter. (ans)
_____ A molecule that alters the shape of the regulatory protein in a way that blocks its binding to the operator and thus permits transcription. (ans)
_____ Regulatory proteins that promote transcription of mRNA. (ans)
_____ A molecule that alters the shape of the regulatory protein to a form that can bind to the operator and block transcription. (ans)
_____ Producing antisense RNA that is complementary to the mRNA coding for the enzyme. When the antisense RNA binds to the mRNA by complementary base pairing, the mRNA cannot be translated into protein and the enzyme is not made. (ans)
_____ The induction or repression of enzyme synthesis by regulatory proteins that can bind to DNA and either block or enhance the function of RNA polymerase. (ans)
_____ The inhibitor is the end product of a metabolic pathway that is able to bind to a second site (the allosteric site) on an enzyme. Binding of the inhibitor to the allosteric site alters the shape of the enzyme's active site thus preventing binding of the first substrate in the metabolic pathway. (ans)
_____ The inhibitor is the end product of an enzymatic reaction. That end product is also capable of reacting with the enzyme's active site and prevents the enzyme from binding its normal substrate. (ans)
_____Regulatory proteins that bind to DNA located some distance from the operon they control by working with DNA-bending proteins that enable RNA polymerase can to bind to a promoter and initiate transcription. (ans)
1. activators
2. competitive inhibition
3. corepressors
4. genetic control
5. inducer
6. non-competitive inhibition
7. repressors
8. translational control
9. enhancers
2. Describe how the lac operon in E. coli functions as an inducible operon. (ans) | textbooks/bio/Microbiology/Exercises%3A_Microbiology_(Kaiser)/03.E%3A_Bacterial_Genetics_%28Exercises%29.txt |
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
4.1: An Overview to Control of Microorganisms
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Matching:
_____ An agent that kills the organism. (ans)
_____ An agent that inhibits the organism's growth long enough for body defenses to remove it. (ans)
_____The chemical agent being used should inhibit or kill the intended pathogen without seriously harming the host. (ans)
_____ A chemical agent that generally works against just gram-positives, gram-negatives, or only a few bacteria. (ans)
_____ A chemical agent that is generally effective against a variety of gram-positive and gram-negative bacteria. (ans)
_____ Antimicrobial drugs synthesized by chemical procedures in the laboratory. (ans)
_____ Metabolic products of one microorganism that inhibit or kill other microorganisms. (ans)
_____ The process of destroying all living organisms and viruses. (ans)
_____ The elimination of microorganisms, but not necessarily endospores, from inanimate objects or surfaces. (ans)
_____ An agent that kills or inhibits growth of microbes but is safe to use on human tissue. (ans)
1. selective toxicity
2. broad spectrum agent
3. narrow spectrum agent
4. cidal
5. static
6. sterilization
7. antibiotic
8. chemotherapeutic synthetic drug
9. antiseptic
10. disinfection
11. disinfectant
4.2: Ways in which Chemical Control Agents Affect Bacteria
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Matching:
_____ Alter bacterial 30S ribosomal subunits blocking translation. (ans)
_____ Inhibit peptidoglycan synthesis causing osmotic lysis. (ans)
_____ Alter bacterial 50S ribosomal subunits blocking translation. (ans)
_____ Inhibit nucleic acid synthesis. (ans)
1. macrolides(erythromycin, azithromycin, clarithromycin, dirithromycin, troleandomycin, etc.), oxazolidinones (linezolid), and streptogramins
2. penicillins, monobactams, carbapenems, cephalosporins, and vancomycin
3. fluoroquinolones (norfloxacin, lomefloxacin, fleroxacin, ciprofloxacin, enoxacin, trovafloxacin, etc.), sulfonamides and trimethoprim, and metronidazole
4. aminoglycosides (streptomycin, neomycin, netilmicin, tobramycin, gentamicin, amikacin, etc.) and tetracyclines (tetracycline, doxycycline, demeclocycline, minocycline, etc.)
2. Describe 4 different ways antibiotics or disinfectants may affect bacterial structures or macromolecules and state how this ultimately causes harm to the cell.
3. Multiple Choice (ans)
4.3: Ways in which Bacteria May Resist Chemical Control Agents
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Name 2 bacteria that have low-permeability membrane barriers and are thereby intrinsically resistant to many antibiotics. (ans)
2. Briefly describe 3 different mechanisms as a result of genetic changes in a bacterium that may enable that bacterium to resist an antibiotic.
3. State what the following stand for:
1. MRSA (ans)
2. VRE (ans)
3. CRE (ans)
4. Briefly describe R plasmids and state their significance in our attempts to treat infections with antibiotics. (ans)
5. Multiple Choice (ans) | textbooks/bio/Microbiology/Exercises%3A_Microbiology_(Kaiser)/04.E%3A_Using_Antibiotics_and_Chemical_Agents_to_Control_Bacteria_%28Exercises%29.txt |
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
5.0: virulence factors that promote bacterial colonization of the host
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. List 6 virulence factors that promote bacterial colonization of the host.
5.1: The Ability to Use Motility and Other Means to Contact Host Cells
Questions
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. State why it might be of an advantage for a bacterium trying to colonize the bladder or the intestines to be motile. (ans)
2. Briefly describe how the spirochete Treponema pallidum that causes syphilis uses its motility to disseminate from the initial infection site to other parts of the body. (ans)
3. Give a brief description of how a bacterium may use toxins to better disseminate from one host to another. (ans)
4. Multiple Choice (ans)
5.2: The Ability to Adhere to Host Cells and Resist Physical Removal
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Briefly describe 3 different mechanisms by which bacteria can adhere to host cells and colonize. Name 2 bacteria that utilize each mechanism and name an infection that each bacterium causes.
2. Define biofilm and state 5 benefits associated with bacteria living as a community within a biofilm. (ans)
3. By activating different genes, Neisseria gonorrhoeae is able to rapidly alter the amino acid sequence of the adhesive tip of its pili. Why might this be an advantage? (ans)
4. Multiple Choice (ans)
5.3: The Ability to Invade Host Cells
Questions
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Briefly describe a mechanism by which invasins enable certain bacteria to enter host cells. (ans)
2. Briefly describe how a type 3 secretion system might be used to invade and survive inside host cells. (ans)
3. Multiple Choice (ans)
5.4: The Ability to Compete for Nutrients
Questions
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. State why the ability to compete for iron is important for bacteria to cause disease. (ans)
2. Multiple Choice (ans)
5.5: The Ability to Resist Innate Immune Defenses
Questions
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Describe unenhanced attachment as it relates to phagocytosis. (ans)
2. Describe enhanced attachment as it relates to phagocytosis. (ans)
3. Describe ingestion as it relates to phagocytosis. (ans)
4. Describe destruction as it relates to phagocytosis. (ans)
5. State 4 different body defense functions of the body's complement pathways. (ans)
6. Multiple Choice (ans)
5.5B
Questions
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Briefly describe 3 ways capsules may enable bacteria to resist phagocytic engulfment. (ans)
2. State 2 mechanisms other than capsules that certain bacteria might use to resist phagocytic engulfment. (ans)
3. The vaccine for Haemophilus influenzae type b contains capsular material from this bacterium. The body recognizes this capsular material as foreign and produces antibodies against it. One part of the antibody is able to bind to the capsular material while another part has a shape that fits a receptor on phagocytic cells. Why might this protect the person from infection with this bacterium? (ans)
4. Multiple Choice (ans)
Questions
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. State 4 different ways bacteria might be able to resist phagocytic destruction once engulfed. (ans)
5.6: The Ability to Evade Adaptive Immune Defenses
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. State 4 four ways the antibody molecules made during adaptive immunity protect us against bacteria. (ans)
2. Briefly describe 3 ways a bacterium might evade our immune defenses and name a bacterium that does each.
3. Multiple Choice (ans) | textbooks/bio/Microbiology/Exercises%3A_Microbiology_(Kaiser)/05.E%3A_Virulence_Factors_that_Promote_Colonization_%28Exercises%29.txt |
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. List 3 general categories of virulence factors that damage the host.
07.E: The Eukaryotic Cell (Exercises)
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
7.1: The Cytoplasmic Membrane
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Match the following descriptions with the best answer.
_____ The movement of water across a membrane from an area of higher water concentration (lower solute concentration) to lower water concentration (higher solute concentration). (ans)
_____ The net movement of gases or small uncharge polar molecules across a phospholipid bilayer membrane from an area of higher concentration to an area of lower concentration. No metabolic energy is required. (ans)
_____ A transport where the cell uses transport proteins such as antiporters or symporters and metabolic energy to transport substances across the membrane against the concentration gradient. (ans)
_____ If the net flow of water is out of a cell, the cell is in ________________ environment. (ans)
_____ If the net flow of water is into a cell, the cell is in ________________ environment. (ans)
_____ Theingestion of dissolved materials by endocytosis whereby the cytoplasmic membrane invaginates and pinches off placing small droplets of fluid in a vesicle. (ans)
_____ The process by which a cell releases waste products or specific secretion products by the fusion of a vesicle with the cytoplasmic membrane. (ans)
1. active transport
2. passive diffusion
3. osmosis
4. exocytosis
5. pinocytosis
6. phagocytosis
7. a hypotonic
8. a hypertonic
9. an isotonic
7.2: The Cell Wall
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. State which eukaryotic organisms possess a cell wall and which lack a cell wall. (ans)
2. The function of the cell wall in those eukaryotic cells that possess one is to ____________________. (ans)
7.5: Ribosomes
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Briefly describe and state the function of eukaryotic ribosomes. (ans)
7.6: The Cytoskeleton
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. State 3 different functions associated with the cytoskeleton of eukaryotic cells. (ans)
7.8: The Endosymbiotic Theory
1. Parallel membranous tubules and flattened sacs with ribosomes attached. Functions in protein synthesis, production of new membrane, and transport of these proteins and membrane to other locations within the cell. This best describes the:
A. the Golgi apparatus.
B. smooth endoplasmic reticulum.
C. rough endoplasmic reticulum.
D. the nucleus.
2. Consists of 3-20 flattened and stacked saclike structures called cisternae. Modifies certain proteins and lipids received from the ER and packages these molecules into vesicles for transport to other parts of the cell or secretion from the cell. This best describes:
A. the Golgi apparatus.
B. smooth endoplasmic reticulum.
C. rough endoplasmic reticulum.
D. the nucleus.
3. Surrounded by two membranes. The outer membrane forms the exterior of the organelle while the inner membrane is arranged in a series of folds called cristae . Produces ATP through oxidative phosphorylation . This describes:
A. the Golgi apparatus.
B. mitochondria.
C. chloroplasts.
D. the endoplasmic reticulum.
4. Membrane-enclosed spheres that contain powerful digestive enzymes that function to digest materials that enter by endocytosis. This best describes:
A. peroxisomes.
B. mitochondria.
C. proteasomes.
D. lysosomes.
5. A fluid phospholipid bilayer embedded with proteins and glycoproteins. Determines what goes in and out of the cell. This best describes the:
A. cell wall.
B. cytoplasmic membrane.
C. endomembranesystem.
D. cytoskeleton.
6. Long and few in number and consisting of 9 fused pairs of protein microtubuleswith side arms of the motor molecule dynein. Originate from a centrioleand function in locomotion. This best describes:
A. cilia.
B. flagella.
C. the cytoskeleton.
Solution
1=C; 2=A; 3=B; 4=D; 5=B; 6=B | textbooks/bio/Microbiology/Exercises%3A_Microbiology_(Kaiser)/06.E%3A_Virulence_Factors_that_Damage_the_Host_%28Exercises%29.txt |
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
8.1: Overview of Fungi
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. A fungal infection is termed a _________________. (ans)
8.2: Yeasts
Questions
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Briefly describe a typical yeast and state how it reproduces asexually. (ans)
2. Match the following:
_____ Reproductive spores produced by yeast by budding. (ans)
_____ Thick walled survival spores produced by the yeast Candida. (ans)
_____Long, continuous fungal filaments produced by dimorphic yeast. (ans)
1. hyphae
2. blastoconidia (blastospores)
3. chlamydoconidia (chlamydospores)
3. Name 3 potentially pathogenic yeasts and state an infection each causes.
4. Multiple Choice (ans)
8.3: Molds
Questions
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Define mold. (ans)
2. Match the following:
_____ The hyphae that grow up in the air and produce asexual reproductive spores. (ans)
_____ Large asexual reproductive mold spores coming of of vegetative hyphae and often produced by dermatophytes. (ans)
_____ Asexual reproductive mold spores produced inside a sac or sporangium at the end of an aerial hypha. (ans)
_____ The hyphae that anchor a mold and absorb nutrients. (ans)
_____ Asexual reproductive mold spores produced in chains at the end of an aerial hypha. (ans)
_____ A branching tubular structure of a mold that is usually divided into cell-like units by crosswalls called septa. (ans)
_____ Asexual reproductive mold spores produced by fragmentation of vegetative hyphae. (ans)
1. hypha
2. macroconidia
3. vegetative mycelium
4. aerial mycelium
5. sporangiospores
6. arthrospores
7. conidiospores
3. Define dermatophyte. (ans)
4. List 2 genera of dermatophytes.
5. Name 3 dermatophytic infections. (ans)
6. Describe what is meant by the term "dimorphic fungus", name 2 systemic infections caused by dimorphic fungi, and state how they are initially contracted. (ans)
7. Multiple Choice (ans)
8.4: Fungal Pathogenicity
Exercise
1. Name at least 3 fungal virulence factors that promote fungal colonization.
2. Name 2 fungal virulence factors that damage the host.
8.5: Chemotherapeutic Control of Fungi
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Briefly describe 2 different ways antifungal chemotherapeutic agents may affect fungi and give an example of an antibiotic for each way.
09.E: Protozoa (Exercises)
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
9.1: Characteristics of Protozoa
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Match the following:
_____ Multiple fission. The nucleus divides many times before the cell divides. The single cell then separates into numerous daughter cells. (ans)
_____ Division in which one cell splits in two. (ans)
_____ Division in which a cell pinches off of the parent cell. (ans)
_____ The vegetative, reproducing, feeding form of a protoaoan. (ans)
_____ A protective form that enables protozoa to survive harsh environments. (ans)
1. trophozoite
2. cyst
3. fission
4. schizogony
5. budding
9.2: Medically Important Protozoa
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Matching
_____ Moves by flagella; transmitted by ingesting cysts via the fecal-oral route; causes an intestinal infection. (ans)
_____ Moves by cilia; transmitted by ingesting cysts via the fecal-oral route; causes an intestinal infection. (ans)
_____ Moves by flagella; transmitted by an infected tsetse fly; causes African sleeping sickness. (ans)
_____ Nonmotile in the body; reproduces sexually and asexually; transmitted by an infecteded Anopheles mosquito; causes malaria. (ans)
_____ Moves by flagella; transmitted sexually; causes vaginitis. (ans)
_____ Nonmotile in the body; reproduces sexually and asexually; transmitted by eating infected meat or inhaling or ingesting cysts from cat feces. (ans)
1. Entamoeba histolytica
2. Acanthamoeba
3. Giardia lamblia
4. Trichomonas vaginalis
5. Trypanosoma brucei-gambiens
6. Balantidium coli
7. Plasmodium species
8. Toxoplasma gondii
9. Cryptosporidium
2. Multiple Choice (ans) | textbooks/bio/Microbiology/Exercises%3A_Microbiology_(Kaiser)/08.E%3A_Fungi_%28Exercises%29.txt |
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
10.1: General Characteristics of Viruses
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. State 2 living characteristics of viruses.
2. State 2 nonliving characteristics of viruses.
3. List 3 criteria used to define a virus.
4. A virus that infects only bacteria is termed a ___________________. (ans)
5. State why viruses can't replicate on environmental surfaces or in synthetic laboratory medium. (ans)
10.2: Size and Shapes of Viruses
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1. Compare the size of most viruses to that of bacteria. (ans)
2. List 4 shapes of viruses.
10.3: Viral Structure
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1. Briefly describe the structure of most viruses that infect humans. (ans)
2. Define the following:
1. capsid (ans)
2. capsomeres (ans)
3. nucleocapsid (ans)
3. Describe how most animal viruses obtain their envelope. (ans)
4. State why some bacteriophages are more complex than typical polyhedral or helical viruses. (ans)
5. Multiple Choice (ans)
10.5: Other Acellular Infectious Agents: Viroids and Prions
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Small, circular, single-stranded molecules of infectious that cause of a few plant diseases such as potato spindle-tuber disease,cucumber pale fruit, citrus exocortis disease, and cadang-cadang (coconuts) are called ____________. (ans)
2. Infectious protein particlesthought to be responsible for a group of transmissible and/or inherited neurodegenerative diseases including Creutzfeldt-Jakob disease, kuru, and Gerstmann-Straussler- syndrome in humans as well as scrapie in sheep and goats are called ______________. (ans)
3. Name 3 other neurological protein misfolding diseases that apprear to be initiated by prions. (ans)
10.7: Bacteriophage Life Cycles: An Overview
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1. Name the 2 types of bacteriophage life cycles and state what the bacteriophage capable of each is called.
10.7A: The Lytic Life Cycle of Bacteriophages
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1. Describethe 5 steps involved in the lytic life cycle of bacteriophages.
2. Multiple Choice (ans)
10.7B: The Lysogenic Life Cycle of Bacteriophages
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1. Describehow the lysogenic life cycle of temperate bacteriophages differs from the lytic life cycle of lytic bacteriophages. (ans)
2. What is spontaneous induction as it relates to the lysogenic life cycle? (ans)
3. When a bacteriophage inserts its DNA into the DNA of the host bacterium, this form of the virus is called a ________________. (ans)
4. The host bacterium for a bacteriophage is called a ________________. (ans)
5. A virus capable of the lysogenic life cycle is called a __________________. (ans)
6. Multiple Choice (ans)
10.8: Pathogenicity of Animal Viruses
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1. Briefly describe 4 ways viruses can damage infected host cells.
2. Briefly describe 2 different ways viruses can evade host immune defenses and give an example of a virus that uses each mechanism.
3. Multiple Choice (ans)
10.9: Bacteriophage-Induced Alterations of Bacteria
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1. Describe how a bacteriophage may in some cases enable a bacterium to become virulent and state 2 examples. (ans)
10.10: Antiviral Agents
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1. Explain why the antibiotics we use to treat bacterial infections are not effective against viral infections. (ans)
2. Match the following drugs with the viral infections they are used against:
_____ amantadine, rimantidine, zanamivar, and oseltamivir (ans)
_____ acyclovir, famciclovir, penciclovir, and valacyclovir(ans)
_____ foscarnet, gancyclovir, cidofovir, valganciclovir, and fomivirsen(ans)
_____ AZT (ZDV), didanosine, zalcitabine, stavudine, nevirapine, delavirdine, saquinavir, and ritonavir (ans)
1. HIV infection and AIDS
2. influenza A
3. severe CMV infections such as retinitis
4. HSV and VZV infections
3. Match the following:
_____ These are drugs that bind to the active site of an HIV-encoded protease and prevent it from cleaving the long gag-pol polyprotein and the gag polyprotein into essential proteins essential to the structure of HIV and to RNA packaging within its nucleocapsid. As a result, viral maturation does not occur and noninfectious viral particles are produced. (ans)
_____ These drugs chemically resemble normal DNA nucleotides, the building block molecules for DNA synthesis. They bind to the active site of the reverse transcriptase which, in turn, inserts it into the growing DNA strand in place of a normal nucleotide. Once inserted, however, new DNA nucleotides are unable to attach to the drug and DNA synthesis is stopped. This results in an incomplete provirus. (ans)
1. nucleoside reverse transcriptase inhibitors
2. non-nucleoside reverse transcriptase inhibitors
3. protease inhibitors
4. entry inhibitors
4. Multiple Choice (ans)
10.11: General Categories of Viral Infections
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Match the following:
_____ Viral infections in which the infectious agents gradually increase in number over a very long period of time during which no significant symptoms are seen. (ans)
_____ Viral infections of relatively short duration with rapid recovery. (ans)
_____ Viral infections where the virus can be demonstrated in the body at all times and the disease may be present or absent for an extended period of time. (ans)
_____ Viral infections where the virus remains in equilibrium with the host for long periods of time before symptoms again appear, but the actual viruses cannot be detected until reactivation of the disease occurs. (ans)
1. acute viral infection
2. chronic viral infection
3. latent viral infection
4. slow viral infection
2. Give an example of of a virus causing each of the following:
1. acute viral infection (ans)
2. chronic viral infection (ans)
3. latent viral infection (ans)
4. slow viral infection (ans)
3. Multiple Choice (ans) | textbooks/bio/Microbiology/Exercises%3A_Microbiology_(Kaiser)/10.E%3A_Viruses_%28Exercises%29.txt |
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
11.1: The Innate Immune System: An Overview
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1. Describe what is meant by the following:
1. innate immunity (ans)
2. adaptive (acquired) immunity (ans)
2. Define the following:
1. antigen (ans)
2. pathogen-associated molecular patterns or PAMPs (ans)
3. epitope (ans)
3. Multiple Choice (ans)
11.2: Defense Cells in the Blood: The Leukocytes
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1. What is the difference between a CBC and a leukocyte differential count? (ans)
2. A person has an elevated white blood cell count with anelevated number of band-form neutrophils. What is the significance of this? (ans)
3. Match the following descriptions and functions with the type of leukocytes:
_____ Important phagocytes; 54%-75% of the leukocytes; granules stain poorly; produce enzymes for the synthesis of bradykinins and prostaglandins that promote inflammation. (ans)
_____ Capable of phagocytosis but primarily kill microorganisms and parasitic worms extracellularly; 1%-4% of the leukocytes; large granules stain red; secrete leukotriens and prostaglandins to promote inflammation. (ans)
_____ Not important in phagocytosis; large granules stain a purplish blue; 0%-1% of the leukocytes; release histamine, leukotriens, and prostaglandins to promote inflammation. (ans)
_____ Important in phagocytosis and aid in the adaptive immune responses; produce cytokines; 4%-8% of the leukocytes; differentiate into macrophages and dendritic cells when they leave the blood and enter the tissue. (ans)
_____ Mediate humoral immunity (antibody production); have B-cell receptors (BCR) on their surface for antigen recognition; differentiate into antibody-secreting plasma cells. (ans)
_____ Regulate the adaptive immune responses through cytokine production; have CD4 molecules and TCRs on their surface for antigen recognition. (ans)
_____ Carry out cell-mediated immunity; have CD8 molecules and TCRs on their surface for antigen recognition; differentiate into cytotoxic T-lymphocytes (CTLs). (ans)
_____ Lymphocytes that lack B-cell receptors and T-cell receptors; kill cells to which the antibody IgG has attached as well as human cells lacking MHC-I molecules on their surface. (ans)
1. B-lymphocytes
2. T4-lymphocytes
3. T8-lymphocytes
4. NK cells
5. basophils
6. neutrophils
7. eosinophils
8. monocytes
4. State what type of cell monocytes differentiate into when they enter tissue. (ans)
5. Multiple Choice (ans)
11.3: Defense Cells in the Tissue: Dendritic Cells, Macrophages, and Mast Cells
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. State 3 different functions of macrophages in body defense.
1. (ans)
2. (ans)
3. (ans)
2. Name the cells in the tissue whose primary function is to present antigen to naive T-lymphocytes. (ans)
3. Name the cells in the tissue whose primary function is to present antigen to effector T-lymphocytes. (ans)
4. State the primary function of mast cells in body defense. (ans)
5. Multiple Choice (ans)
11.3: Immediate Innate Immunity
11.3A: Antimicrobial Enzymes and Antimicrobial Peptides
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Matching
____ Found in in tears, mucous, saliva, plasma, tissue fluid, etc.; breaks down peptidoglycan. (ans)
____ A protein produced by skin and mucosal epithelial cells. The two peptides produced upon cleavage of this protein are directly toxic to a variety of microorganisms. (ans)
____ An enzyme that penetrates the bacterial cell wall and hydrolizes the phospholipids in the bacterial cytoplasmic membrane. (ans)
____ Short cationic peptides that are directly toxic by disrupting the cytoplasmic membrane of a variety of microorganisms causing leakage of cellular needs. They also activate cells for an inflammatory response. (ans)
1. lysozyme
2. phospholipase A2
3. defensins
4. cathelicidins
5. lactotransferrin and transferrin
11.3B: The Complement System
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1. Briefly describe how the classical complement pathway is activated. (ans)
2. Match the following:
_____ Complement proteins that trigger inflammation (ans)
_____ Complement proteins that chemotactically attracting phagocytes to the infection site. (ans)
_____ Complement proteins that promote the attachment of antigens to phagocytes (enhanced attachment or opsonization. (ans)
_____ Complement proteins that cause lysis of Gram-negative bacteria and human cells displaying foreign epitopes. (ans)
1. the membrane attack complex (MAC)
2. C5a. and to a lesser extent, C3a and C4a.
3. C3b, and to a lesser extent, C4b.
4. C5a
3. Briefly describe how the lectin complement pathway is activated. (ans)
4. Briefly describe how the alternative complement pathway is activated. (ans)
5. Multiple Choice (ans)
11.3C: Anatomical Barriers to Infection, Mechanical Removal of Microbes, and Bacterial Antagonism by Normal Body Microbiota
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Describe what is meant by anatomical barriers to infection. (ans)
2. List 4 ways in which the body can physically remove microorganisms or their products. (ans)
3. Describe how bacterial antagonism by normal microbiota acts as a nonspecific body defense mechanism. (ans)
4. Multiple Choice (ans)
11.4: Early Induced Innate Immunity
11.3A: Pathogen-Associated Molecular Patterns (PAMPs) and Danger-Associated Molecular Patterns (DAMPs)
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1. State the function of pathogen-associated molecular patterns as they relate to innate immunity. (ans)
2. Name at least 5 PAMPS associated with bacteria. (ans)
3. Name at least 2 PAMPS associated with viruses. (ans)
4. Define DAMP. (ans)
5. Multiple Choice PAMPs and DAMPs (ans)
11.3B: Pattern-Recognition Receptors (PRRs)
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1. State the function of the following as they relate to innate immunity.
1. pathogen-associated molecular patterns (ans)
2. pattern recognition receptors (ans)
3. endocytic pattern recognition receptors (ans)
4. signaling pattern recognition receptors (ans)
5. danger-associated molecular patterns
6. danger recognition receptors (ans)
7. inflammasome (ans)
2. Briefly describe the major difference between the effect of the cytokines produced in response to PAMPs that bind to cell surface signaling PRRs and endosomal PRRs. (ans)
3. Multiple Choice (PRRs) (ans)
11.3C: Cytokines Important in Innate Immunity
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Match the following:
_____ Cytokines that promote inflammation by enabling white blood cells to adhere to the inner surface of blood vessels, migrate out of the blood vessels into the tissue, and be chemotactically attracted to the injured or infected site. (ans)
_____ Cytokines that prevent viral replication, activate a variety of cells important in body defense, and exhibit some anti-tumor activity. (ans)
_____ A wide variety of intercellular regulatory proteins produced by many different cells in the body that ultimately control every aspect of body defense. Cytokines activate and deactivate phagocytes and immune defense cells, increase or decrease the functions of the different immune defense cells, and promote or inhibit a variety of nonspecific body defenses. (ans)
1. lysozyme
2. chemokines
3. cytokines
4. interferons
5. human beta-defensins
2. Describe specifically how type-I interferons are able to block viral replication within an infected host cell. (ans)
3. Multiple Choice (ans)
11.3D: Harmful Effects Associated with Abnormal Pattern-Recognition Receptor Responses, Variations in Innate Immune Signaling Pathways, and/or Levels of Cytokine Production
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Briefly describe two specific examples of how an improper functioning PRR can lead to an increased risk of a specific infection or disease.
1. (ans)
2. (ans)
Questions I
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Briefly describe the role of the following as they relate to phagocytosis:
1. inflammation (ans)
2. lymph nodules (ans)
3. lymph nodes (ans)
4. spleen (ans)
2. Multiple Choice (ans)
Questions II
1. Describe the following steps in phagocytosis:
1. activation (ans)
2. chemotaxis (ans)
3. attachment (both unenhanced and enhanced) (ans)
4. ingestion (ans)
5. destruction (ans)
2. State what happens when either phagocytes are overwhelmed with microbes or they adhere to cells to large to be phagocytosed. (ans)
3. Most of the tissue destruction seen during microbial infections is do to ______________________. (ans)
4. Multiple Choice (ans)
11.3F: Natural Killer Cells (NK Cells) and Invariant Natural Killer T-Lymphocytes (iNKT Cells)
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Matching
_____ Recognize stress induced molecules such as MICA and MICB on the surface of tumor cells or infected cells. (ans)
_____ Recognize MHC-I molecules usually present on all nucleated cells of the body. (ans)
_____ Mechanism by which NK cells kill tumor cells and infected cells. (ans)
1. Apoptosis, a programmed cell suicide
2. Killer-activating receptors
3. Killer-inhibitory receptors
2. Epitopes of glycolipid antigens are recognized by iNKT lymphocytes by way of their _______. (ans)
3. iNKT cells promote both innate and adaptive immunity and may also regulate immune responses by way of the ____________ they produce once activated. (ans)
4. Multiple Choice (ans)
11.3G: Inflammation
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Describe the following in termsof inflammation:
1. mechanism for inflammation (ans)
2. benefits of plasma leakage (ans)
3. benefits of diapedesis (ans)
4. healing (ans)
2. Briefly describe the process of diapedesis, indicating the role of the following:
1. P-selectins (ans)
2. integrins (ans)
3. adhesion molecules (ans)
3. Briefly describe the problems that arise from chronic inflammation. (ans)
4. Multiple Choice (ans)
11.3H: Nutritional Immunity
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. State three different ways the body deprives microorganisms of iron.
1. (ans)
2. (ans)
3. (ans)
11.3I: Fever
1. Describe the mechanism behind fever. (ans)
2. State 2 benefits of fever.
1. (ans)
2. (ans)
11.3J: The Acute Phase Response
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Briefly describe the mechanism behind the acute phase response. (ans)
2. An acute phase protein that binds to phospholipids in microbial membranes, sticks the micobe to phagocytes, and activates the classical complement pathway is ___________________. (ans)
3. An acute phase protein that binds to mannose in microbial walls, sticks the micobe to phagocytes, and activates the lectin pathway is ___________________. (ans)
4. Multiple Choice (ans)
11.3K: Intraepithelial T-lymphocytes and B-1 cells
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
_____ These cells have a limited diversity of antigen receptors that initially produce a class of antibody molecule called IgM against common polysaccharide and lipid antigens of microbes and against PAMPs of bacteria that invade body cavities. (ans)
_____ These cells have a limited diversity of antigen receptors that recognize molecules associated with epithelial cells but expressed only when those cells arestressed or infected. They kill those cells by inducing apoptosis, a programmed cell suicide. (ans)
1. gamma:delta T-lymphocytes
2. alpha:beta T-lymphocytes
3. B-1 cells
4. marginal zone B cells | textbooks/bio/Microbiology/Exercises%3A_Microbiology_(Kaiser)/11.E%3A_Innate_Immunity_%28Exercises%29.txt |
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
12.1: An Overview of Innate and Adaptive Immunity
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Describe what is meant by the following:
1. innate immunity (ans)
2. adaptive (acquired) immunity (ans)
2. Define the following:
1. antigen (ans)
2. immunogen (ans)
3. epitope (ans)
4. humoral immunity (ans)
5. cell-mediated immunity (ans)
12.2: Antigens and Epitopes
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Match the following:
_____ Asubstance that reacts with antibody molecules and antigen receptors on lymphocytes. (ans)
_____ An antigen that is recognized by the body as non-self and stimulates an adaptive immune response. (ans)
_____ The actual portions or fragments of an antigen that react with receptors on B-lymphocytes and T-lymphocytes as well as with free antibody molecules. (ans)
_____ An antibody molecule composed of 4 glycoprotein chains whose Fc portion is anchored to the membrane of certain lymphocytes; able to recognize epitopes on protein and polysaccharide antigens. (ans)
_____ A molecule composed of 2 glycoprotein chains anchored to the membrane of certain lymphocytes; able to recognize peptide epitopes from protein antigens presented by the body's own cells by way of MHC molecules. (ans)
_____ Antigens are proteins found within the cytosol of human cells such as viral proteins, proteins from intracellular bacteria, and tumor antigens. (ans)
_____ An organism’s own antigens (self-antigens) that stimulate an autoimmune reaction. (ans)
_____ Antigens that enter from outside the body, such as bacteria, fungi, protozoa, and free viruses. (ans)
1. B-cell receptor
2. T-cell receptor
3. immunogen
4. hapten
5. epitope
6. antigen
7. autoantigens
8. endogenous antigens
9. exogenous antigens.
2. Briefly describe how the body recognizes an antigen as foreign. (ans)
3. In terms of infectious diseases, describe 2 categories of microbial materials that may act as an antigen.
1. (ans)
2. (ans)
4. Describe 3 groups of noninfectious materials that may act as an antigen.
1. (ans)
2. (ans)
3. (ans)
5. Multiple Choice (ans)
12.3: Major Cells and Key Cell Surface Molecules Involved in Adaptive Immune Responses
12.3B: Antigen-Presenting Cells (APCs)
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Match the following in terms of antigen-presenting dendritic cells presenting antigens to naive T4-lymphocytes:
_____ Dendritic cells engulf ____________ antigens. (ans)
_____ Once engulfed by dendritic cells, protein antigens are degraded into peptides by organelles called ____________. (ans)
_____ Dendritic cells bind peptides to grooves in _________________. (ans)
_____ The dendritic cell then presents the MHC/peptide complex to the ___________________. (ans)
_____ Dendritic cells produce co-stimulatory signals after pathogen-associated molecular patterns bind to ___________________. (ans)
1. TCR of T4-lymphocytes
2. TCR of T8-lymphocytes
3. MHC-I molecules
4. MHC-II molecules
5. exogenous
6. endogenous
7. toll-like receptors
8. lysosomes
9. proteasomes
10. cytosol
2. Match the following in terms of ntigen-presenting dendritic cells presenting antigens to naive T8-lymphocytes:
_____ Dendritic cells engulf ____________ antigens. (ans)
_____ Once engulfed by dendritic cells, protein antigens are degraded into peptides by organelles called ____________. (ans)
_____ Some proteins escape from phagosomes and phagolysosomes into the ____________. (ans)
_____ Once in the cytosol, protein antigens are degraded into peptides by organelles called ____________. (ans)
_____ Dendritic cells then bind peptides to grooves in _________________. (ans)
_____ The Dendritic cell then presents the MHC/peptide complex to the ___________________. (ans)
1. TCR of T4-lymphocytes
2. TCR of T8-lymphocytes
3. MHC-I molecules
4. MHC-II molecules
5. exogenous
6. endogenous
7. toll-like receptors
8. lysosomes
9. proteasomes
10. cytosol
3. Name the primary type of cell that functions as an antigen-presenting cell to naive T4-lymphocytes and naive T8-lymphocytes. (ans)
4. State the role of T4-effector cells in activating macrophages (ans) .
5. State the role of T4-effector cells in the proliferation and differentiation of activated B-lymphocytes. (ans)
6. Multiple Choice (ans)
12.3C: T4-Lymphocytes (T4-Cells)
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Match the following in terms of activation and function of T4-lymphocytes:
_____ Epitopes of antigens are recognized by T4-lymphocytes by way of their ____________. (ans)
_____ The TCR/CD4 molecules of T4-lymphocytes recognize ________________________ on antigen-presenting cells (APCs) such as dendritic cells, macrophages, and B-lymphocytes. (ans)
1. peptides from exogenous antigens bound to MHC-II molecules
2. peptides from endogenous antigens bound to MHC-I molecules
3. MHC-I molecules
4. toll-like receptors
5. B-cell receptors
6. T-cell receptors
7. plasma cells
8. lysosomes
9. proteasomes
2. Matching
_____ Promote cell-mediated immunity against intracellular pathogens; enhance the killing ability of macrophages, promote diapedesis and chemotaxis of macrophages, and promote the production of opsonizing antibodies. (ans)
_____ Help to limit immune responses and prevent autoimmunity by suppressing T-lymphocyte activies, promote immune memory, help to sustain pregnancy, and control established inflammation. (ans)
_____ Promote a local inflammatory response to stimulate a strong neutrophil response and promote the integrity of the skin and mucous membranes. (ans)
_____ Promote the production of the antibody isotype IgE in response to helminthsand allergens, attract and activate eosinophils and mast cells, promote the production of antibodies that neutralize microbesand toxins, and promote the removal of microbes in mucosal tissues. (ans)
1. CD4 TH2 cells
2. CD4 TH1 cells
3. CD4 Treg cells
4. CD4 TH17 cells
5. CD4 TFH cells
3. Multiple Choice (ans)
12.3D: T8-Lymphocytes (T8-Cells)
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Match the following in terms of activation and function of T8-lymphocytes:
_____ Epitopes of antigens are recognized by T8-lymphocytes by way of their ____________. (ans)
_____ The TCR/CD8 molecules of naive T8-lymphocytes recognize ________________________ on antigen-presenting dendritic cells. (ans)
_____ After activation, T8-lymphocytes proliferate and differentiate into _____________________ (ans)
1. peptides from exogenous antigens bound to MHC-II molecules
2. peptides from endogenous antigens bound to MHC-I molecules
3. MHC-I molecules
4. toll-like receptors
5. B-cell receptors
6. T-cell receptors
7. plasma cells
8. cytotoxic T-lymphocytes (CTLs)
9. natural killer cells (NK cells)
2. State the overall function of activated T8-lymphocytes in adaptive immunity. (ans)
3. Multiple Choice (ans)
12.3E: Invarient Natural Killer T-Lymphocytes (iNKT Cells)
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Epitopes of glycolipid antigens are recognized by iNKT lymphocytes by way of their _______. (ans)
2. The TCR molecules of iNKT lymphocytes recognize ________________________ on antigen-presenting dendritic cells. (ans)
3. iNKT lymphocytes can also be activated by the cytokine __________ (ans) produced by activated dendritic cells.
4. iNKT cells promote both innate and adaptive immunity and may also regulate immune responses by way of the ____________ they produce once activated. (ans)
12.3F: B-Lymphocytes (B-Cells)
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Match the following in terms of activation of B-lymphocytes by T-dependent antigens:
_____ Epitopes of antigens are recognized by B-lymphocytes by way of their ____________. (ans)
_____ Once engulfed by APCs, protein antigens are degraded into peptides by organelles called ____________. (ans)
_____ B-lymphocytes bind peptides to grooves in _________________. (ans)
_____ The B-lymphocyte then presents the MHC/peptide complex to the ___________________. (ans)
_____ B-lymphocytes eventually differentiate into antibody-secreting cells called ___________________. (ans)
1. TCR of T4-lymphocytes
2. TCR of T8-lymphocytes
3. MHC-I molecules
4. MHC-II molecules
5. B-cell receptors
6. CD4 molecules
7. plasma cells
8. lysosomes
9. proteasomes
2. State the overall function of B-lymphocytes in adaptive immunity. (ans)
3. Multiple Choice (ans)
12.3G: Natural Killer Cells (NK Cells)
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Briefly describe how NK cells bind to and kill infected cells and tumor cells through ADCC. (ans)
2. Briefly describe how NK cells recognize and kill infected cells and tumor cells that suppress MHC-I production. (ans)
12.3A: Major Histocompatibility Complex (MHC) Molecules
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Match the following:
_____ Produced by all nucleated cells in the body. (ans)
_____ Produced primarily by antigen-presenting cells such as macrophages, dendritic cells, and B-lymphocytes. (ans)
_____ Primarily bind peptides from exogenous antigens. (ans)
_____ Primarily bind peptides from endogenous antigens. (ans)
_____ Recognize peptides bound to MHC-II molecules. (ans)
_____ Recognize peptides bound to MHC-I molecules. (ans)
1. TCR of T4-lymphocytes
2. TCR of T8-lymphocytes
3. MHC-I molecules
4. MHC-II molecules
2. State the role of proteasomes in binding of peptides from endogenous antigens by MHC-I molecules. (ans)
3. State the role of lysosomes in binding of peptides from exogenous antigens by MHC-II molecules. (ans)
4. Multiple Choice (ans)
12.4: The Lymphoid System
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Match the following with the BEST answer:
_____ Contain antigen-presenting cells, such as macrophages and dendritic cells, and ever changing populations ofB-lymphocytes and T- lymphocytes. Examples include the tonsils, the appendix, Peyer's patches, MALT, SALT, lymph nodes, and the spleen. (ans)
_____ Produce B-lymphocytes and T-lymphocytes. The bone marrow and the thymus. (ans)
_____ The fluid surrounding cells in the body. (ans)
_____ The liquid portion of the blood. (ans)
_____ A diffuse system of small concentrations of lymphoid tissue found in various sites of the body such as the gastrointestinal tract, respiratory tract, eye, and skin. It is populated by loose clusters of T-lymphocytes, B-lymphocytes, plasma cells, activated TH cells, and macrophages. (ans)
_____ The liquid found in lymph vessels. (ans)
_____ Expose antigens found in the lymph to dendritic cells, B-lymphocytes, and T-lymphocytes. (ans)
_____ Expose antigens found in the blood to dendritic cells, B-lymphocytes, and T-lymphocytes. (ans)
1. plasma
2. lymph
3. tissue fluid
4. primary lymphoid organs
5. secondary lymphoid organs
6. the spleen
7. lymph nodes
8. MALT
2. Briefly describe the importance of the lymphoid system in adaptive immune responses. (ans)
3. Multiple Choice (ans)
12.5: An Overview of the Steps Involved in Adaptive Immune Responses
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. State where antigens may encounter APCs, B-lymphocytes, and T-lymphocytes if they enter the following:
1. the blood (ans)
2. tissues (ans)
3. the respiratory tract (ans)
4. the gastrointestinal tract (ans)
5. the genitourinary tract (ans)
2. Match the following:
_____ Use lysosomes to degrade exogenous antigens into peptides, bind them to MHC-II molecules, and present them to naive T4-lymphocytes. (ans)
_____ Uses BCR to recognize epitopes of antigens; a few antigens are recognized by toll-like receptors. (ans)
_____ Uses TCR and CD4 to recognize peptide epitopes from exogenous antigens bound to MHC-II molecules of antigen-presenting dendritic cells, macrophages, and B-lymphocytes. (ans)
_____ Uses TCR and CD8 to recognize peptide epitopes from endogenous antigens bound to MHC-I molecules of cells. (ans)
_____ Cells that allow for a heightened secondary response upon subsequent exposure to the same antigen. (ans)
_____ Once activated itself, secretes cytokines that enable activated B-lymphocytes and T-lymphocytes to proliferate and differentiate. (ans)
_____ Use proteasomes to degrade endogenous antigens into peptides, bind them to MHC-I molecules, and present them to naive T8-lymphocytes. (ans)
_____ Differentiate into antibody secreting plasma cells. (ans)
_____ Differentiate into cytotoxic T-lymphocytes (CTLs). (ans)
1. T4-lymphocytes
2. T8-lymphocytes
3. dendritic cells
4. B-lymphocytes
5. memory cells
3. State the overall function of T4-effector lymphocytes and the importance behind rapid proliferation of activated lymphocytes. (ans)
4. The ability of the body to initiate and direct adaptive immune responses against antigenic molecules foreign to the body but not against antigenic molecules that are a normal component of the body is called ____________________________. (ans)
5. Multiple Choice (ans) | textbooks/bio/Microbiology/Exercises%3A_Microbiology_(Kaiser)/12.E%3A_Introduction_to_Adaptive_Immunity_%28Exercises%29.txt |
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
13.1: Antibodies (Immunoglobulins)
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Define antibody. (ans)
2. In terms of infectious disease, state what humoral immunity is most effective against. (ans)
13.2: Ways That Antibodies Help to Defend the Body
• List 9 ways that antibodies help to defend the body.
13.3: Naturally and Artificially Acquired Active and Passive Immunity
1. Define the following:
1. active immunity
2. passive immunity
2. Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1.Matching
_____ Antibodies made in another person or animal enter the body and the immunity is short-lived. (ans)
_____ Antigens enter the body and the body responds by making its own antibodies and B-memory cells. (ans)
1. active immunity
2. passive immunity
13.3A: Naturally Acquired Immunity
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1. Give an example of naturally acquired active immunity. (ans)
2. Give two examples of naturally acquired passive immunity.
3. State why naturally acquired passive immunity is important to newborns and infants. (ans)
4. Multiple Choice (ans)
13.3B: Artificially Acquired Immunity
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Define and give an example of artifically acquired passive immunity. (ans)
2. Define and give an example of artifically acquired active immunity. (ans)
3. List 3 different forms of antigen that may be used for artificially acquired active immunity and state 2 common examples of each.
4. A patient with a deep puncture wound who has never received a DTP vaccinationis given both Td and TIG. Another patient with an identical wound and who had 4 DTP vaccinationsas a child and a Td booster 3 years ago is given nothing. Discuss the reasoning behind this. (hint: see Fig. 1) (ans)
5. Multiple Choice (ans)
14.E: Cell-Mediated Immunity (Exercises)
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
14.1: Cell-Mediated Immunity: An Overview
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. State three different ways by which cell-mediated immunity protects the body.
2. Define gene translocation. (ans)
3. Relate gene translocation to each T-lymphocyte being able to produce a T-cell receptor with a unique shape. (ans)
4. Define the following:
1. combinatorial diversity (ans)
5. In terms of humoral immunity, discuss what is meant by anamnestic response. (ans)
6. Briefly describe why there is a heightened secondary response during anamestic response. (ans)
14.2: Activating Antigen-Specific Cytotoxic T- Lymphocytes
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. The role of cytotoxic T-lymphocytes (CTLs) in body defense.
1. State from what cells cytotoxic T-lymphocytes are derived. (ans)
2. Describe how they can react with and destroy virus-infected cells, cells containing intracellular bacteria, and cancer cells without harming normal cells. (Indicate the role of following: TCR, CD4, MHC-I, and peptides from endogenous antigens.) (ans)
3. State the mechanism by which cytotoxic T-lymphocytes kill the cells to which they bind. (Indicate the role of the following: perforins, granzymes, caspases, and macrophages in the process.) (ans)
2. Multiple Choice (ans)
14.3: Activating Macrophages and NK Cells
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Viruses and malignant transformation can sometimes interfere with the ability of the infected cell or tumor cell to express MHC-I molecules. This enables them to resist destruction by cytoyoxic T-lymphocytes. However the body is still able to kill these infected cells and tumor cells. Describe how. (ans)
2. Describe how TH1 effector cells are able to interact with and activate macrophages. (ans)
3. Multiple Choice (ans)
14.4: Stimulating Cells to Secrete Cytokines
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Name 4 cytokines that regulate adaptive immune responses. (ans)
2. Name 3 cytokines that regulate innate immune responses by triggering an inflammatory response. (ans)
3. Name 2 cytokines that stimulate hematopoiesis. (ans)
4. Name the group of cytokines that regulates innate immunity by preventing translation of viral mRNA and by degrading both viral and host cell RNA. (ans) | textbooks/bio/Microbiology/Exercises%3A_Microbiology_(Kaiser)/13.E%3A_Humoral_Immunity_%28Exercises%29.txt |
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
15.1: Primary Immunodeficiency
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Match the following:
_____ Rare but severe primary immunodeficiencies occuring as the result of a rare recessive genetic defect in the immune responses that involves the development of B-lymphocytes, T-lymphocytes, or both and results in multiple, recurrent infections during infancy. (ans)
_____ Common, less severe primary immunodeficiencies involving just one or more of the huge number of genes involved in the immune responses. They involve the decreased ability to combat just a single type of infection or a narrow range of infections and relate to an individual’s own unique genetics. (ans)
_____ There may be greatly decreased humoral immunity but cell-mediated immunity remains normal. X-linked agammaglobulinemia and selective IgA deficiency are examples. May be treated with artificially-acquired passive immunization. (ans)
_____ Primary immunodeficiencies that affect both humoral immunity and cell-mediated immunity. There is a defect in both B-lymphocytes and T-lymphocytes, or just T-lymphocytes in which case the humoral deficiency is due to the lack of T4-helper lymphocytes. (ans)
1. B-lymphocyte disorder
2. combined B-lymphocyte and T-lymphocyte disorder
3. novel primary immunodeficiency
4. conventional primary immunodeficiency
2. Infants born with a nonfunctional thymus develop frequent and severe infections. Explain. (ans)
15.2: Secondary Immunodeficiency
Study the material in this section and then write out the answers to these questions. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. State what is meant by secondary immunodeficiency and list 4 possible contributing factors. (ans)
2. Briefly give three mechanisms of HIV-induced immunodeficiency. (ans)
16.E: Hypersensitivities (Exercises)
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
17.E: Bacterial Growth and Energy Production (Exercises)
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
17.1: Bacterial Growth
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Match the following:
_____ A population doubles every generation time. (ans)
_____ One cell splits in two. (ans)
_____ The time it takes for a population of organisms to double in number. (ans)
1. binary fission
2. generation time
3. geometric progression
2. If you started with 1000 E. coli with a generation time of 30 minutes, how many bacteria would you have after 3 hours? (ans)
3. Match the following:
_____ Phase where the population grows slowly or stops growing because of decreasing food, increasing waste, and lack of space. The rate of replication is balanced out by the rate of inhibition or death. (ans)
_____ Phase where the population dies exponentially from the accumulation of waste products, although the rate of death depends on the degree of toxicity and the resistance of the species. (ans)
_____ Phase where growth is relatively flat and the population appears either not to be growing or growing quite slowly. During this phase the newly inoculated cells are adapting to their new environment and synthesizing the molecules they will need in order to grow rapidly. (ans)
_____ Phase where the population increases geometrically as long as there is sufficient food and space for growth. (ans)
1. Lag phase
2. Exponential (log) growth phase
3. Stationary phase
4. Death (decline) phase
17.2: Factors that Influence Bacterial Growth
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1. Matching
_____ Bacteria that grow best at moderate temperatures. Their optimum growth temperature is between 25C and 45C. (ans)
_____ Cold-loving bacteria. Their optimum growth temperature is between -5C and 15C. They are usually found in the Arctic and Antarctic regions and in streams fed by glaciers. (ans)
_____ Organisms that grow with or without oxygen, but generally better with oxygen. (ans)
_____ Organisms that grow onlyin the absense of oxygen and, in fact, are often inhibited or killed by its presense. (ans)
_____ An environment where the water concentration is greater outside the cell and the solute concentration is higher inside. Water goes into the cell. (ans)
_____ Organisms that use the oxidation and reduction of chemical compounds as their primary energy source. (ans)
_____ Organisms that use light as an energy source and carbon dioxideas their main carbon source. (ans)
_____ Organisms that use organic compounds as both an energy source and a carbon source. (ans)
_____ Organisms that use lightas an energy source but cannot convert carbon dioxide into energy. Instead they use organic compounds as a carbon source. (ans)
1. photoautotrophs
2. photoheterotrophs
3. chemolithoautotrophs
4. chemooganoheterotrophs
5. phototroph
6. heterotroph
7. hypertonic
8. hypotonic
9. obligate aerobe
10. facultative anaerobe
11. obligate anaerobe
12. psychrophile
13. mesophile
14. thermophile
17.4: Cellular Respiration
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. An exergonic processes by which energy released by the breakdown of organic compounds such as glucose can be used to synthesize ATP, the form of energy required to do cellular work. This best describes:
1. anabolism (ans)
2. catabolism (ans)
2. Intermediate molecules that link catabolic and anabolic pathways; can be either oxidized to generate ATP or can be used to synthesize macromolecular subunits such as amino acids, lipids, and nucleotides. (ans)
3. Define cellular respiration. (ans)
4. Pathways that do not require oxygen are said to be:
1. aerobic (ans)
2. anaerobic (ans)
5. Name an exergonic pathway that requires molecular oxygen (O2). (ans)
6. Name two anaerobic exergonic forms of cellular respiration. (ans) | textbooks/bio/Microbiology/Exercises%3A_Microbiology_(Kaiser)/15.E%3A_Immunodeficiency_%28Exercises%29.txt |
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
18.3: Aerobic Respiration
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Briefly describe aerobic respiration. (ans)
2. Give the overall chemical reaction for aerobic respiration. (ans)
3. During aerobic respiration, glucose is __________ to carbon dioxide.
1. oxidized (ans)
2. reduced (ans)
4. During aerobic respiration, oxygen is __________ to water.
1. oxidized (ans)
2. reduced (ans)
5. Name the four stages of aerobic respiration. (ans)
18.3A: Glycolysis
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1. Briefly describe the function of glycolysis during aerobic respiration and indicate the reactants and products. (ans)
2. State the reactants in glycolysis. (ans)
3. State the products in glycolysis. (ans)
4. Does glycolysis require oxygen? (ans)
5. Is the following statement true or false?
In eukaryotic cells, glycolysis takes place in the mitochondria. (ans)
6. Steps 1 and 3 of glycolysis are:
1. exergonic (ans)
2. endergonic (ans)
7. State why one molecule of glucose is able to produce two molecules of pyruvate during glycolysis. (ans)
8. The two net ATP produced in glycolysis are generated by:
1. oxidative phosphorylation (ans)
2. substrate-level phosphorylation (ans)
9. State the total number and the net number of ATP produced by substrate-level phosphorylation during glycolysis. (ans)
10. During aerobic respiration, state what happens to the 2 NADH produced during glycolysis. (ans)
11. During aerobic respiration, state what happens to the two molecules of pyruvate produced during glycolysis. (ans)
18.3B: Transition Reaction
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Briefly describe the function of transition reaction during aerobic respiration. (ans)
2. State the reactants in the transition reaction. (ans)
3. State the products in the transition reaction. (ans)
4. Is the following statement true or false?
In eukaryotic cells, the transition reaction occurs inside the mitochondria. (ans)
5. During aerobic respiration, state what happens to the two molecules of Acetyl-CoA produced during the transition reaction. (ans)
18.3C: Citric Acid (Krebs) Cycle
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Briefly describe the function of the citric acid cycle during aerobic respiration. (ans)
2. State the reactants for the citric acid cycle. (ans)
3. State the products for the citric acid cycle. (ans)
4. Is the following statement true or false?
In eukaryotic cells, the citric acid cycle occurs in the cytoplasm. (ans)
5. State the total number of ATP produced by substrate-level phosphorylation for each acetyl-CoA that enters the citric acid cycle. (ans)
6. State the total number of NADH and FADH2 produced for each acetyl-CoA that enters the citric acid cycle. (ans)
7. During aerobic respiration, state what happens to the NADH and the FADH2 produced during the citric acid cycle. (ans)
18.3D: Electron Transport Chain and Chemisomosis
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Briefly describe the function of the electron transport chain during aerobic respiration. (ans)
2. Describethe chemiosmotic theory of generation of ATP as a result of an electron transport chain. In the process, describe proton motive force and indicate the function of ATP synthase. (ans)
3. State whether the following statement is true or false.
In eukaryotic cells, the electron transport chain is located in the inner membrane of the mitochondria. (ans)
4. State the final electron acceptor and the end product formed at the end of aerobic respiration. (ans)
18.3E: Theoretical ATP Yield
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1. Fill in the blanks.
One molecule of glucose oxidized by aerobic respiration in prokaryotes yields the following:
Glycolysis:
_____ net ATP (ans) from substrate-level phosphorylation
_____ NADH (ans) yields _____ ATP (assuming 3 ATP per NADH) by oxidative phosphorylation (ans)
Transition Reaction:
_____ NADH (ans) yields _____ ATP (assuming 3 ATP per NADH) by oxidative phosphorylation (ans)
Citric Acid Cycle:
_____ ATP from substrate-level phosphorylation (ans)
_____ NADH (ans) yields _____ ATP (assuming 3 ATP per NADH) by oxidative phosphorylation (ans)
_____ FADH2 (ans) yields _____ ATP (assuming 2 ATP per FADH2) by oxidative phosphorylation (ans)
Total Theoretical Maximum Number of ATP Generated per Glucose in Prokaryotes
_____ ATP (ans): _____ from substrate-level phosphorylation (ans); _____ from oxidative phosphorylation (ans).
In eukaryotic cells, the theoretical maximum yield of ATP generated per glucose is _____ to _____. (ans)
18.4: Anaerobic Respiration
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1. Define anaerobic respiration. (ans)
2. State the pathways involved in anaerobic respiration. (ans)
3. State whether the following statement is true or false.
All organisms are capable of anaerobic respiration. (ans)
18.5: Fermentation
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Define fermentation. (ans)
2. All the ATP generated by fermentation are produced by:
1. substrate-level phosphorylation (ans)
2. oxidative phosphorylation (ans)
3. State the reactants for fermentation. (ans)
4. State the products for fermentation. (ans)
5. Compare the maximum yield of ATP from one molecule of glucose for aerobic respiration and for fermentation. (ans)
18.6: Precursor Metabolites: Linking Catabolic and Anabolic Pathways
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Define precursor metabolites and indicate their importance in metabolism. (ans)
18.7A: Introduction to Photosynthesis
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1. Organisms that absorb and convert light energy into the stored energy of chemical bonds in organic molecules through a process called photosynthesis best describes:
1. anoxygenic photoautotrophs (ans)
2. oxygenic photoautotrophs (ans)
2. Name the two stages of photosynthesis. (ans)
3. Define photon. (ans)
4. Describe what happens when photons of visible light energy strike certain atoms of pigments during photosynthesis and how this can lead to the generation of ATP. (ans)
5. Fill in the blank.
The inner membrane of a chloroplast encloses a fluid-filled region called the __________ (ans) that contains enzymes for the light-independent reactions of photosynthesis. Infolding of this inner membrane forms interconnected stacks of disk-like sacs called __________ (ans), often arranged in stacks called __________ (ans).
6. Name three different types of pigments that play a role in photosynthesis by absorbing light energy. (ans)
7. State the reactants and the products for photosynthesis and indicate which are oxidized and which are reduced. (ans)
18.7B: Oxygenic Photosynthesis: Light-Dependent Reactions
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1. Briefly describe the overall function of the light-dependent reactions in photosynthesis. (ans)
2. Where in the chloroplasts do the light-dependent reactions occur?
1. In the thylakoids. (ans)
2. In the stroma. (ans)
3. The parts of a photosystem that are able to trap light and transfer energy to a complex of chlorophyll molecules and proteins called the reaction center are called _____________. (ans)
4. In Photosystem II, the electrons lost by chlorophyll P680 molecules are replaced by:
1. the electrons traveling down the electron transport system of Photosystem I (ans)
2. the electrons released by the splitting of water (ans)
5. The primary function of Photosystem II is to produce:
1. ATP (ans)
2. NADPH (ans)
6. Briefly describe how ATP is generated by chemiosmosis during the light-dependent reactions of photosynthesis. (ans)
7. In Photosystem I, the electrons lost by chlorophyll P700 molecules are replaced by:
1. the electrons traveling down the electron transport system of Photosystem II (ans)
2. the electrons released by the splitting of water (ans)
8. The primary function of Photosystem I is to produce:
1. ATP (ans)
2. NADPH (ans)
9. Involves only Photosystem I and generates ATP but not NADPH. This best describes:
1. cyclic photophosphorylation (ans)
2. noncyclic photophosphorylation (ans)
18.7C: Oxygenic Photosynthesis: Light-Independent Reactions
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Briefly describe the overall function of the light-independent reactions in photosynthesis. (ans)
2. Where in the chloroplasts do the light-independent reactions occur?
1. In the thylakoids. (ans)
2. In the stroma. (ans)
3. State how the light-dependent and light-independent reactions are linked during photosynthesis. (ans)
4. Briefly describe the following stages of the Calvin cycle:
1. CO2 fixation (ans)
2. production of G3P (ans)
3. regeneration of RuBP (ans)
5. State the significance of glyceraldehyde-3-phosphate (G3P) in the Calvin cycle. (ans)
18.7D: C4 and CAM Pathways in Plants
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1. Is the following statement true or false?
During the C4 pathway for fixing CO2, CO2 from the air combines with ribulose bisphosphate to begin the Calvin cycle. (ans)
2. Plants that live in very dry condition and, unlike other plants, open their stomata to fix CO2 only at night best describes: (ans)
1. C4 plants
2. C3 plants
3. CAM plants
3. C4 and CAM pathways evolved for plants that live in _____________________ climates. (ans)
1. hot, humid
2. cold, dry
3. hot, dry | textbooks/bio/Microbiology/Exercises%3A_Microbiology_(Kaiser)/18.E%3A_Microbial_Metabolism_%28Exercises%29.txt |
These are homework exercises to accompany Kaiser's "Microbiology" TextMap. Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
19.1: Polypeptides and Proteins
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1. Describe an amino acid and state what all amino acids have in common. (ans)
2. State what makes one amino acid different from another. (ans)
3. Describe how amino acids are joined by peptide bonds. (ans)
4. Compare the terms peptide, polypeptide, and protein. (ans)
5. Due to hydrogen bonds that form between the oxygen atom of one amino acid and the nitrogen atom of another, this gives the protein or polypeptide the two-dimensional form of an alpha-helix or a beta-pleated sheet. This best describes:
1. the primary structure of a protein (ans)
2. the secondary structure of a protein (ans)
3. the tertiary structure of a protein (ans)
4. the quaternary structure of a protein (ans)
6. In some cases, such as with antibody molecules and hemoglobin, several polypeptides may bond together to form a quaternary structure. This best describes:
1. the primary structure of a protein (ans)
2. the secondary structure of a protein (ans)
3. the tertiary structure of a protein (ans)
4. the quaternary structure of a protein (ans)
7. The actual order of the amino acids in the protein that is determined by DNA. This best describes:
1. the primary structure of a protein (ans)
2. the secondary structure of a protein (ans)
3. the tertiary structure of a protein (ans)
4. the quaternary structure of a protein (ans)
8. In globular proteins such as enzymes, the long chain of amino acids becomes folded into a three-dimensional functional shape. This is because certain amino acids with sulfhydryl or SH groups form disulfide (S-S) bonds with other amino acids in the same chain. Other interactions between R groups of amino acids such as hydrogen bonds, ionic bonds, covalent bonds, and hydrophobic interactions also contribute to this structure. This best describes:
1. the primary structure of a protein (ans)
2. the secondary structure of a protein (ans)
3. the tertiary structure of a protein (ans)
4. the quaternary structure of a protein (ans)
9. Define gene. (ans)
10. Describe how the order of nucleotide bases in DNA ultimately determines the final three-dimensional shape of a protein or polypeptide. (ans)
19.2: Enzymes
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Define enzyme and state how enzymes are able to speed up the rate of chemical reactions. (ans)
2. Fill in the blanks.
Many enzymes require a nonprotein cofactor to assist them in their reaction. In this case, the protein portion of the enzyme, called an _______________ (ans), combines with the cofactor to form the whole enzyme or ____________ (ans). Some cofactors are ions such as Ca++, Mg++, and K+; other cofactors are organic molecules called _____________ (ans) which serve as carriers for chemical groups or electrons. Anything that an enzyme normally combines with is called a _____________ (ans).
3. Briefly describe a generalized enzyme-substrate reaction, state the function of an enzyme's active site, and describe how an enzyme is able to speed up chemical reactions. (ans)
4. State four characteristics of enzymes. (ans)
5. State how the following will affect the rate of an enzyme reaction.
1. increasing temperature (ans)
2. decreasing temperature (ans)
3. pH (ans)
4. salt concentration (ans)
19.3: Deoxyribonucleic Acid (DNA)
Questions
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. State the 3 basic parts of a deoxyribonucleotide. (ans)
2. State which nitrogenous bases are purines.
1. cytosine and thymine (ans)
2. adenine and guanine (ans)
3. In the complement base pairing of nucleotides, adenine can form hydrogen bonds with ____________ (ans) and guanine can form hydrogen bonds with ____________ (ans).
4. State what is meant by the 3' (3-prime) and 5' (5-prime) ends of a DNA strand. (ans)
5. State why DNA can only be synthesized in a 5' to 3' direction. (ans)
6. What is a nucleosome? (ans)
7. State whether the following characteristics are seen in prokaryotic or eukaryotic DNA.
1. linear chromosomes (ans)
2. no nuclear membrane (ans)
3. presence of nucleosomes (ans)
4. no mitosis (ans)
5. produce gametes through meiosis (ans)
19.4: DNA Replication in Prokaryotic Cells
Questions
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1. Briefly describe the process of DNA replication. (ans)
2. State what enzyme carries out the following functions during DNA replication.
1. Unwinds the helical DNA by breaking the hydrogen bonds between complementary bases. (ans)
2. Synthesizes a short RNA primer at the beginning of each origin of replication. (ans)
3. Adds DNA nucleotides to the RNA primer. (ans)
4. Digests away the RNA primer and replaces the RNA nucleotides of the primer with the proper DNA nucleotides. (ans)
5. Links the DNA fragments of the lagging strand together. (ans)
3. The DNA strand replicated in short fragments called Okazaki fragments is called the:
1. lagging strand (ans)
2. leading strand (ans)
19.5: DNA Replication in Eukaryotic Cells and the Eukaryotic Cell Cycle
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Briefly describe the process of DNA replication. (ans)
2. State which cell type has multiple origins of replication in its genome.
1. prokaryotic (ans)
2. eukaryotic (ans)
3. Identify the following stages of mitosis.
1. During this final stage of mitosis, the nuclear membrane and nucleoli reform, cytokinesis is nearly complete, and the chromosomes eventually uncoil to chromatin. (ans)
2. Refers to all stages of the cell cycle other than mitosis. During this phase, cellular organelles double in number, the DNA replicates, and protein synthesis occurs. The chromosomes are not visible and the DNA appears as uncoiled chromatin. (ans)
3. During this phase of mitosis, the nuclear membrane fragmention is complete and the duplicated chromosomes line up along the cell's equator. (ans)
4. During the first stage of mitosis, the chromatin condenses and the chromosomes become visible. Also the nucleolus disappears, the nuclear membrane fragments, and spindle fibers are assembled. (ans)
5. During this phase of mitosis, diploid sets of daughter chromosomes move toward opposite poles of the cell and cytokinesis (cytoplasmic cleavage) begins. (ans)
19.6: Ribonucleic Acid (RNA)
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. State the 3 basic parts of a ribonucleotide. (ans)
2. State 3 ways RNA differs from DNA. (ans)
3. Copies the genetic information in the DNA by complementary base pairing and carries this "message" to the ribosomes where the proteins are assembled. This best describes:
1. tRNA (ans)
2. mRNA (ans)
3. rRNA (ans)
4. Picks up specific amino acids, transfers the amino acids to the ribosomes, and insert the correct amino acids in the proper place according to the mRNA message. This best describes:
1. tRNA (ans)
2. mRNA (ans)
3. rRNA (ans)
19.7: Polypeptide and Protein Synthesis
Questions: Transcription
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Define transcription. (ans)
2. Match the following with their role in transcription.
_____ The end of a strand of nucleic acid that has a hydroxyl (OH) group on the number 3 carbon of the deoxyribose or ribose and is not linked to another nucleotide. (ans)
_____ The covalent bond that links ribonucleotides together to form RNA. (ans)
_____ The portion of DNA that contains the actual message for protein synthesis. (ans)
_____ A molecule synthesized by complementary base pairing of ribonucleotides with deoxyribonucleotides to match a portion of one strand of DNA coding for a polypeptide or protein. (ans)
_____ A series of three consecutive mRNA bases coding for one specific amino acid. (ans)
_____ A segment of DNA that determines what region of the DNA and which strand of DNA will be transcribed into RNA. (ans)
_____ The enzyme that initiates transcription, joins the RNA nucleotides together, and terminates transcription. (ans)
_____ A "stop" signal at the end of a gene that causes the completed mRNA to drop off the gene. (ans)
1. mRNA
2. 3' end
3. 5' end
4. RNA polymerase
5. phosphodiester bond
6. promoter
7. leader sequence
8. coding sequence
9. transcription terminator
10. codon
3. Match the following with their role in transcription in eukaryotic cells.
_____ The RNA synthesized after RNA polymerase copies both the exons and the interons of a gene. (ans)
_____ The RNA produced after non-protein coding regions (introns) are excised and coding regions (exons) are joined together by complexes of ribonucleoproteins called spliceosomes. (ans)
_____ An unusual nucleotide, 7-methylguanylate, that is added to the 5' end of the pre-mRNA early in transcription. It helps ribosomes attach for translation. (ans)
_____ Non-protein coding regions of DNA that are not part of the code for the final protein that are interspersed among the coding regions of DNA in most genes of higher eukaryotic cells. (ans)
_____ The coding regions of DNA in most genes of higher eukaryotic cells that actually code for the final protein. (ans)
_____ A series of 100-250 adenine ribonucleotides that is added to the 3' end of the pre-mRNA. This series of nucleotides is thought to help transport the mRNA out of the nucleus and may stabilize the mRNA against degradation in the cytoplasm. (ans)
1. introns
2. exons
3. precurser mRNA
4. cap
5. poly-A tail
6. mature mRNA
4. What amino acid sequence would the DNA base sequence 5' ATAGCCACC 3'code for? Hint: see Figure 8. (ans)
Questions: Translation
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Define translation. (ans)
2. Match the following with their role in translation.
_____ A series of three tRNA bases complementary to a mRNA codon. (ans)
_____ The ribozyme that forms peptide bonds between amino acids during translation. (ans)
_____ The ribosomal subunit that binds to mRNA to form the initiation complex. (ans)
_____ The ribosomal site where an aminoacyl-tRNA first attaches during translation. (ans)
_____ The ribosomal site where the growing amino acid chain is temporarily being held by a tRNA as the next codon in the mRNA is being read. (ans)
_____ A complex of an amino acid and a tRNA molecule. (ans)
_____ The sequence of bases on mRNA to which a 30S or 40S ribosomal subunit first attaches. (ans)
_____ A series of three mRNA bases coding for no amino acid and thus terminates the protein chain: UAA, UAG, UGA. (ans)
_____ A complex consisting of a 30S or 40S ribosomal subunit, a tRNA having the anticodon UAC and carrying an altered form of the amino acid methionine (N-formylmethionine or f-Met), and proteins called initiation factors. (ans)
_____ A three-dimensional, inverted cloverleaf-shaped molecule about 70 nucleotides long to which a specific amino acid can be attached; transports amino acids to the ribosome during translation. (ans)
1. 30S or 40S ribosomal subunit
2. ribosome binding site
3. initiation complex
4. 50S or 60S ribosomal subunit
5. tRNA
6. aminoacyl-tRNA
7. anticodon
8. P-site of ribosome
9. A-site of ribosome
10. peptidyl transferase
11. nonsense (stop) codon
12. release factors
13. start cocon
3. What amino acid sequence would the DNA base sequence AAAGAGCCT code for? Hint: see Fig. 2. (ans)
19.8: Enzyme Regulation
Questions
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Matching
_____ Regulatory proteins that block transcription of mRNA by binding to a portion of DNA called the operator that lies downstream of a promoter. (ans)
_____ A molecule that alters the shape of the regulatory protein in a way that blocks its binding to the operator and thus permits transcription. (ans)
_____ Regulatory proteins that promote transcription of mRNA. (ans)
_____ A molecule that alters the shape of the regulatory protein to a form that can bind to the operator and block transcription. (ans)
_____ Producing antisense RNA that is complementary to the mRNA coding for the enzyme. When the antisense RNA binds to the mRNA by complementary base pairing, the mRNA cannot be translated into protein and the enzyme is not made. (ans)
_____ The induction or repression of enzyme synthesis by regulatory proteins that can bind to DNA and either block or enhance the function of RNA polymerase. (ans)
_____ The inhibitor is the end product of a metabolic pathway that is able to bind to a second site (the allosteric site) on an enzyme. Binding of the inhibitor to the allosteric site alters the shape of the enzyme's active site thus preventing binding of the first substrate in the metabolic pathway. (ans)
_____ The inhibitor is the end product of an enzymatic reaction. That end product is also capable of reacting with the enzyme's active site and prevents the enzyme from binding its normal substrate. (ans)
1. activators
2. competitive inhibition
3. corepressors
4. genetic control
5. inducer
6. noncompetitive inhibition
7. repressors
8. translational control
2. Describe how the lac operon in E. coli functions as an inducible operon. (ans)
19.9: Mutation
Study the material in this section and then write out the answers to these question. Do not just click on the answers and write them out. This will not test your understanding of this tutorial.
1. Match the following:
_____The sequence of deoxyribonucleotide bases in the genes that make up a organism's DNA. (ans)
_____ An error during DNA replication that results in a change in the sequence of deoxyribonucleotide bases in the DNA. (ans)
_____ Alternate forms of a gene. (ans)
_____ Mutations caused by mutagens, substances that cause a high rate of mutation. (ans)
_____ The physical characteristics of an organism. (ans)
1. genotype
2. phenotype
3. allele
4. mutation
5. spontaneous mutation
6. induced mutation
2. Describe 2 different mechanisms of spontaneous mutation. (ans)
3. Match the following:
_____ This is usually seen with a single substitution mutation and results in one wrong codon and one wrong amino acid (ans)
_____ If the change in the deoxyribonucleotide base sequence results in transcription of a stop, the protein is terminated at that point in the message. (ans)
_____ This is sometimes seen with a single substitution mutation when the change in the DNA base sequence results in a new codon still coding for the same amino acid. (ans)
_____ This is seen when a number of DNA nucleotides not divisible by three is added or deleted and all of the codons and all of the amino acids after that addition or deletion are usually wrong. (ans)
1. sense mutation
2. nonsense mutation
3. frameshift mutation
4. missense mutation
4. Briefly describe 3 ways chemical mutagens work. (ans)
5. Compare ultraviolet radiation and gamma radiation in terms of how they induce mutation. (ans)
6. As a result of a substitution mutation, a DNA base triplet AGA is changed to AGG. State specifically what effect this would have on the resulting protein (see Figure 9). (ans)
7. A third triplet in a bacterial gene is TTT. A substitution mutation changes it to ATT. State specifically what effect this would have on the resulting protein (see Figure 9). (ans) | textbooks/bio/Microbiology/Exercises%3A_Microbiology_(Kaiser)/19.E%3A_Review_of_Molecular_Genetics_%28Exercises%29.txt |
What is Biosafety?
Microbiology is a science that investigates the biology of microscopic organisms. Although individual cells of these organisms may be directly observed with a microscope, and their shapes and activities observed, to investigate other characteristics such as metabolism or genetics, growing cells in populations (called cultures) is the preferred approach. For many types of experiments, all of the cells in the population must be essentially the same; such populations are called purecultures. A set of techniques, mostly developed in the late 19th century by Robert Koch, Louis Pasteur, and their collaborators, permitted the isolation of bacteria from their natural environments and separation into pure cultures for further study. Probably more than anything else, these are the techniques that define microbiology as a scientific field of study.
It has been estimated that less than 1% of bacteria can be grown in culture in a laboratory. However, many types can be, and those are the ones on which we will focus. Microbiologists culture bacteria by providing them with food, water, and other growth requirements in an environment with a constant and comfortable growth temperature. These requirements vary, depending on the natural growth conditions for the microbial populations under study.
Food is provided in the culturemedia we use. Media may be in the form of a liquid (called a “broth”) or solid or semi-solid forms, either in tubes or in culture dishes (Petri plates). The choice of media depends on what you want to do or need to know about the bacteria in your cultures.
To ensure that we culture only the specific bacteria we want, and nothing else from the environment, microbiologists use a set of strict aseptictechniques, which protects us from the bacteria in the cultures, and also protects our cultures from contaminants in the environment. These methods will be demonstrated in class. In addition, specific laboratory rules must be followed for containment of microbial cultures in the laboratory, for the safety of all. For this laboratory, these practices are listed below.
Laboratory Safety Practices and Procedures
1. Remember that all bacteria are potential pathogens that may cause harm under unexpected or unusual circumstances. If you as a student have a compromised immune system or a recent extended illness, you should share those personal circumstances with your lab instructor.
2. Know where specific safety equipment is located in the laboratory, such as the fire extinguisher and the eyewash station.
3. Recognize the international symbol for biohazards, and know where and how to dispose of all waste materials, particularly biohazard waste. Note that all biohazard waste must be sterilized by autoclave before it can be included in the waste stream.
1. Keep everything other than the cultures and tools you need OFF the lab bench.
2. All of the equipment and supplies used in experiments involving bacterial cultures should be sterilized. This includes the media you use and also the tools used for transferring media or bacteria, such as the inoculating instruments (loops and needles) and pipettes for liquid transfer.
3. Transfer of liquid cultures by pipette should NEVER involve suction provided by your mouth.
4. Disinfect your work area both BEFORE and AFTER working with bacterial cultures.
5. In the event of an accidental spill involving a bacterial culture, completely saturate the spill area with disinfectant, then cover with paper towels and allow the spill to sit for 10 minutes. Then carefully remove the saturated paper towels, dispose of them in the biohazard waste, and clean the area again with disinfectant.
6. Wear gloves when working with cultures, and when your work is completed, dispose of the gloves in the biohazard garbage. Safety glasses or goggles are also recommended.
7. Long hair should be pulled back to keep it away from bacterial cultures and open flame.
8. Make sure that lab benches are completely cleared (everything either thrown away or returned to storage area) before you leave the lab.
Bacteria pose varying degrees of risk both in a controlled laboratory environment and in their natural settings. Therefore, the level of containment necessary for working safely with bacterial cultures also varies according to a system that classifies microbes into one of four biosafety levels (BSL), which provides minimum standards for safe handling of microbes at each level. BSLs are defined and containment practices are detailed by the Centers for Disease Control and Prevention (CDC) for laboratories in the United States. The full document, “BiosafetyinMicrobiologicalandBiomedicalLaboratories,” can be viewed in its entirety at http://www.cdc.gov/biosafety/publications/bmbl5/index.htm.
Prior to the first meeting of the laboratory, navigate to the following web page to review the BSL guidelines as outlined by the CDC, which includes an interactive quiz:
http://www.cdc.gov/training/Quicklearns/biosafety/
Most of the bacterial cultures we will be working with are classified as BSL-1. Below, list three practices that should be used while you are working with BSL-1 bacteria:
1. __________________________________________________________________________
2. __________________________________________________________________________
3. __________________________________________________________________________
In a few of the labs, we will be working with bacteria that are classified as BSL-2. What additional safety practices should you employ when you work with these bacteria?
1. __________________________________________________________________________
2. __________________________________________________________________________
3. __________________________________________________________________________
After your instructor has discussed any additional safety procedures for your lab, complete the biosafety concept assessment on the following page (or one provided by your instructor) and sign the affirmation. Return the completed document to your instructor.
Microbiology Laboratory Biosafety Guidelines
Complete the following questions by writing the letter of the correct answer on the line.
___ 1. Biological agents are assigned to Biosafety Levels (BSLs) based on
a. whether they are bacteria, viruses, or other microorganisms.
b. their susceptibility to laboratory disinfectants.
c. the risk they pose to human health and the environment.
d. the amount of the agent that will be used in the lab.
___ 2. BSL 1 practices, equipment, and facilities are used when working with which type of microorganism?
a. Bacteria that are well characterized and not known to consistently cause disease in healthy adult humans.
b. Bacteria that are considered moderate-risk agents present in the community and associated with human diseases.
c. Indigenous or exotic bacteria with potential for aerosol transmission and associated with human disease.
d. Dangerous/exotic agents with a high risk of life-threatening disease.
___ 3. The primary hazards to people working in a BSL 1 or 2 laboratory relate to
a. accidental skin punctures caused by mishandling of sharp lab tools.
b. mucous membrane exposure due to accidental splashing of cultures.
c. accidental ingestion of infectious material.
d. All of the above are primary hazards in a BSL 1 or 2 lab.
___ 4. Which of the following is required when working with BSL 2 agents?
a. Biohazard warning signage on doors and lab areas where agents are kept or used.
b. Self-closing, double door access to the lab facility.
c. Clothing change when entering or leaving the lab.
d. There are no special precautions needed for a BSL 2 lab.
___ 5. What is the appropriate disposal method for a bacterial culture grown on an agar plate?
a. Throw the culture away in any one of the several garbage containers in the room.
b. Throw the culture away in the garbage container marked with a biohazard sign.
c. Allow the agar to dehydrate in the incubator and then discard in any garbage.
d. Bacteria grown on an agar plate medium should never be disposed of.
Microbiology Laboratory Biosafety Affirmation
By signing your name below, you affirm that:
• Potential hazards in the microbiology laboratory have been identified and explained.
• You understand that the bacterial cultures used in lab require either BSL 1 or BSL 2 containment procedures.
• Safety practices for BSL 1 and 2 have been explained and/or demonstrated to you.
• You fully understand the hazards associated with BSL 1 and 2 bacterial cultures and are willing to assume the risk.
• You are responsible for your own actions while working in a laboratory with potentially hazardous materials.
PRINT your FULL NAME __________________________________________________________
SIGN your name __________________________________________ Date _________________ | textbooks/bio/Microbiology/Microbiology%3A_A_Laboratory_Experience_(Ahern)/01%3A_Chapters/1.01%3A_Biosafety_Practices_and_Procedures_for_the_Microbiology_Laboratory.txt |
The Compound Microscope
There would be little to do in a microbiology laboratory without a microscope, because the objects of our attention (bacteria, fungi, and other single celled creatures) are otherwise too small to see. Microscopes are optical instruments that permit us to view the microbial world. Lenses produce the magnified images that allow us to visualize the form and structure of these tiniest of living beings.
To use this important piece of equipment properly, it is helpful to know how a microscope works. A good place to begin is to learn the name and function of all of the various parts, because when we talk about the ways to improve microscopic images, terms like “ocular lenses” and “condenser” always come up.
Based on the picture of the binocular, compound light microscope in Figure 1, match the name of the major part (listed below) with its location on the microscope, and give a very brief description of what each is used for:
Ocular lenses _________________________________ Locate the parts on the microscope that allow you to:
• Move the stage (stage adjustment knobs)
• Adjust the condenser lens
• Adjust the light intensity
• Adjust the iris diaphragm
• Adjust the distance between the ocular lenses
Objective lenses _________________________________
(Revolving) Nosepiece _________________________________
Stage and stage clips _________________________________
Course and fine focus knobs _________________________________
Condenser lens _________________________________
Iris diaphragm _________________________________
Making Images
With a bright-field microscope, images are formed as a result of the interplay between light waves, the object, and lenses. How images of biological objects are formed is actually more physics than biology. Since this isn’t a physics course, it’s more important to know how to create exceptional images of the object than it is to know precisely how those images are formed.
Light waves that pass through and interact with the object may speed up, slow down, or change direction as they travel through “media” (such as air, water, oil, cytoplasm, etc.) of different densities. For example, light passing through a thicker or denser part of a specimen (such as the nucleus of a cell) may be reflected or refracted (“bend” by changing speed or direction) more than those waves passing through a thinner part. This makes the thicker part appear darker in the image, while the thinner parts are lighter.
For a compound microscope, the optical path leading to a detectable image involves two lenses – the objective lens and the ocular lens. The objective lens magnifies the object and creates a real image, which will appear to be 4, 10, 40, or 100 times larger than the object actually is, depending on the lens used. The ocular lens further magnifies the real image by an additional factor of 10, to produce a vastly larger virtual image of the object when viewed by you.
Light from an illuminator (light source) below the stage is focused on the object by the condenser lens, which is located just below the stage and adjustable with the condenser adjustment knob. The condenser focuses light through the specimen to match the aperture of the objective lens above, as illustrated in Figure 2.
Appropriate use of the condenser, which on most microscopes includes an iris diaphragm, is essential in the quest for a perfect image. Raising the condenser to a position just below the stage creates a spotlight effect on the specimen, which is critical when higher magnification lenses with small apertures are in use. On the other hand, the condenser should be lowered when using the scanning and low power lenses because the apertures are much larger, and too much light can be blinding. For creating the best possible contrast in the image, the iris diaphragm can be opened to make the image brighter or closed to dim the light. These adjustments are subjective and should suit the preferences of the person viewing the image.
When the light waves that have interacted with the specimen are collected by the lenses and eventually get to your eye, the information is processed into dark and light and color, and the object becomes an image that you can see and think more about.
Magnification
The microscope you’ll be using in lab has a compound system of lenses. The objective lens magnifies the object “X” number of times to create the real image, which is then magnified by the ocular lens an additional 10X in the virtual image. Therefore, the total magnification, or how much bigger the object will actually appear to you when you view it, can be determined by multiplying the magnification of the objective lens by 10.
The magnifying power of each lens is engraved on its surface, followed by an “X.” In the table below, find the magnification, and then calculate the total magnification for each of the four lenses on your microscope.
Magnification of objective lens Total magnification of viewed object
Scanning Lens
Low Power Lens
High Power Lens
Oil Immersion Lens
Let’s say you wanted to look at cells of Bacilluscereus, which are rod-shaped cells that are about 4 µm long. If you were observing B. cereus with a microscope using the high power lens, how big would the cells appear to be when you look at them? ___________________________
Resolution Limits Magnification
So the microscope makes small cells look big. But why can’t we just use more or different lenses with greater magnifying power until the images we see are really, really big and easier to see?
The answer is resolution. Consider what happens when you try to magnify the fine print from a book with a magnifying glass. As you move the lens away from the print, it gets larger, right? But as you keep moving the lens, you notice that while the letters are still getting larger, they are becoming blurry and hard to read. This is referred to as “empty magnification” because the image is larger, but not clear enough to read. Empty magnification occurs when you exceed the resolving power of the lens.
Resolution is often thought of as how clearly the details in the image can be seen. By definition, resolution is the minimum distance between objects needed to be able to see them as two separate entities. It can also be thought of as the size of the smallest object that we can clearly see.
The ability of a lens to resolve detail is ultimately limited by diffraction of light waves, and therefore, the practical limit of resolution for most microscopes is about 0.2 µm. Therefore, it would not be practical to try to observe objects smaller than 0.2 µm with a standard optical microscope. In addition, cells of all types of organisms lack contrast because many cellular components refract light to a similar extent. This is especially true of bacteria. To overcome this problem and increase contrast, biological specimens may be stained with selective dyes.
The Oil Immersion Objective
The lens with highest magnifying power is the oil immersion lens, which achieves a total magnification of 1000X with a resolution of 0.2 µm. This lens deserves special attention, because without it our time in lab would be frustrating.
The resolving power of this lens is dependent on “immersing” it in a drop of oil, which prevents the loss of at least some of the image-forming light waves because of refraction. Refraction is a change in the direction of light waves due to an increase or decrease in the wave velocity, which typically occurs at the intersection between substances through which the light waves pass. This is a phenomenon you can see when you put a pencil in a glass of water. The pencil appears to “bend” at an angle where the air and water meet (see Figure 3). These two substances have different refractive indices, which means that light passing through the air reaches your eye before the light passing through the water. This makes the pencil appear “broken.”
The same thing happens as the light passes through the glass slide into the air space between the slide and the lens. The light will be refracted away from the lens aperture. To remedy this, we add a drop of oil to the slide and slip the oil immersion objective into it. Oil and glass have a similar refractive index, and therefore the light bends to a lesser degree and most of it enters the lens aperture to form the image.
It is important to remember that you must use drop of oil whenever you use the oil immersion objective or you will not achieve maximum resolution with that lens. However, you should never use oil with any of the other objectives, and you should be diligent about wiping off the oil and cleaning all of your lenses each time you use your microscope, because the oil will damage the lenses and gum up other parts of the instrument if it is left in place.
Using the Microscope
If you are new to microscopy, you may initially feel challenged as you try to achieve high quality images of your specimens, particularly in the category of “Which lens should I use?” A simple rule is: the smaller the specimen, the higher the magnification. The smallest creatures we observe are bacteria, for which the average size is a few micrometers (μm). Other microscopic organisms such as fungi, algae, and protozoa are larger, and you may only need to use the high power objective to get a good view of these cells; in fact, using the oil immersion objective may provide you with less information because you will only be seeing a part of a cell.
This brings us to two additional concepts related to microscopy—working distance and parfocality. Working distance is how much space exists between the objective lens and the specimen on the slide. As you increase the magnification by changing to a higher power lens, the working distance decreases and you will see a much smaller slice of the specimen. Also, once you’ve focused on an object, you should not have to make any major adjustments when you switch lenses, because the lenses on your microscope are designed to be parfocal. This means that something you saw in focus with the low power objective should be nearly in focus when you switch to a high power objective, or vice versa. Thus, for viewing any object and regardless of what lens you will ultimately use to view it, the best practice is to first set the working distance with a lower power lens and adjust it to good focus using the coarse focus knob. From that point on, when you switch objectives, only a small amount of adjustment with the fine focus knob should be necessary.
Here is a final consideration related to objective lenses and magnification. Look at the lenses on your microscope, and note that as the magnification increases, the length of the lens increases and the lens aperture decreases in size. As a result, you will need to adjust your illumination to compensate for a darkening image. There are essentially three ways to vary the brightness; by increasing or decreasing the light intensity (using the on/off knob), by moving the condenser lens closer to or farther from the object using the condenser adjustment knob, and/or by opening/closing the iris diaphragm. Don’t be afraid to experiment to create the best image possible.
Guidelines for safe and effective use of a microscope:
1. Carry the microscope to your lab table using two hands, and set it down gently on the bench. Once placed on the bench, do not try to slide it around on its base, because this is extremely jarring to the optical system.
2. Clean all of the lenses with either lens paper or Kimwipes (NOT paper towels or nose tissues) BEFORE you use your microscope, AFTER you are done, and before you put it away.
3. When you are finished with the microscope, check the stage to make sure that you don’t leave a slide clipped in the stage. Make sure to switch the microscope OFF before you unplug it. Gently wrap the cord around the base and cover your microscope with its plastic cover.
4. Return the microscope to the cabinet before you leave the lab. Make sure that the ocular lenses are facing IN.
Method
Together we will review how to effectively achieve an exceptional image using a standard optical microscope. This will include not only locating and focusing on the object, but also using the condenser lens and iris diaphragm to achieve a high degree of contrast and clarity.
Rectal Smear
We’ll start by looking at a prepared slide of a “rectal smear,” which is quite literally a smear of feces on a slide stained with a common method called the Gram stain. You will observe several different types of bacterial cells in this smear that will appear either pink or purple. While the main purpose of this is to develop proficiency in use of the oil immersion objective lens, it also provides the opportunity to look at bacteria, observe the differences in cell shapes and sizes, and note that when Gram stained they turn out to be either purple or pink.
When you have achieved an exceptional image of the fecal bacteria at 1000X, consider the following questions.
• In a single field, approximately what proportion of the bacterial cells are circular (the microbiology term for circular bacterial cells is “cocci”)? _____________________________
• Among the cells that are cocci, can you see any specific types of arrangements, like chains of cocci (called “streptococci”) or clusters (called “staphylococci”)? Sketch examples in the space below:
• In a single field, approximately what proportion of the bacterial cells are rod-like (the microbiology term for rod-shaped cells is “bacilli”)? _________________________________
• Among the cells that are bacilli, can you see any specific types of arrangements, like pairs (diplobacilli), chains (streptobacilli) or parallel clusters (palisades)? Sketch examples in the space below:
• Based on the shape/arrangement of the bacterial cells, and now including color (whether they are pink or purple), estimate how many different types of bacteria you are able to see in a single microscopic field. ___________________________________________________
What’s in YOUR Mouth?
The human mouth is home to numerous microbes, which persist no matter how many times you brush your teeth and use mouthwash. Since these microbes generally inhabit the surface layers of the oral mucosa, we humans have evolved ways to keep their numbers under control, including producing antibacterial chemicals in saliva and constantly turning over the outer layer of epithelial cells that line the inside of the mouth.
Obtain a prepared slide labeled “mouth smear.” On this slide you will see large cells with a nucleus, clearly visible with both the low power and high power objective lenses. These are squamous epithelial cells that form the outermost layer of the oral mucosa. At high power, you should start to see small cells on the surface of the larger epithelial cells. With the oil immersion objective lens, you will be able to tell the smaller cells are bacteria.
Locate and focus on a single squamous epithelial cell with obvious bacteria on its surface. Create a sketch of the “cheek” cell (as squamous epithelial cells are sometimes called) in the circle provided. Then label the cell membrane, cytoplasm, and nucleus of the “cheek” cell, which should be easily observed.
Add to your illustration the bacterial cells which you should see on or near the larger larger cheek cells. Try to keep the size of the bacterial cells to scale with the size of the cheek cell.
• How would you describe the shape and arrangement of the bacterial cells (using the microbiology terms you used to describe the bacteria in the rectal smear)?
• The nucleus of a squamous epithelial cells is approximately 10 µm in size. Compare the size of the cell’s nucleus with the size of the bacterial cells. Based on this comparison, what is the approximate size of the bacterial cells in the image?
Once you’ve looked at the prepared slide, obtain a glass slide and a sterile swab. Collect a sample of your oral mucosa by gently rubbing the swab over the inside of your cheek. Smear the swab over the surface of the slide (this is known as making a “smear” in microbiology). Allow the smear to dry, and then heat fix by passing the slide through the flame of a Bunsen burner, as demonstrated. Discard the swab in the biohazard waste.
Once the sample is heat fixed, stain it with safranin. This is a pinkish-red colored stain, and all cells (both bacterial and your mouth cells) will take up the stain and increase the contrast in the image.
Observe your mouth smear with the microscope. When you get to the oil immersion objective, locate and focus on a single cheek cell. As you did with the prepared slide, sketch the larger cheek cell in the circle provided and label the membrane and nucleus . Add the bacterial cells to your sketch, and try to keep the size scale accurate.
• Below, describe the shape and arrangement of the different types of bacterial cells you observe in the smear.
Will Yogurt Improve your Health?
Yogurt is produced when lactic acid (homolactic) bacteria that naturally occur in milk ferment the milk sugar lactose and turn it into lactic acid. The lactic acid accumulates and causes the milk proteins to denature (“curdle”) and the liquid milk becomes viscous and semi-solid.
Within the past few years, positive health benefits have been correlated with eating fermented foods containing “live” cultures. Although several types of bacteria are known to ferment milk and produce yogurt, two genera in particular, Lactobacillus and Bifidobacterium, have been singled out as promoting good digestive health and a well-balanced immune response. Both of these are bacilli arranged in pairs or short chains. Streptococcusspp., which are cocci arranged in chains, are also usually involved in the process of making the milk into yogurt, but these are not directly associated with positive health benefits to the person who eats the yogurt.
Obtain a prepared slide labeled “yogurt smear” and view it with the microscope. The milk proteins in the yogurt will be visible as lightly stained amorphous blobs. By now you should have a pretty good idea of what bacteria look like, so locate and focus on areas where you see bacterial cells.
• Using microbiology terms, describe the shape and arrangement of the different types of bacterial cells you see in the smear
Once you’ve made the observations using the prepared slide, obtain a glass slide and a sterile swab. Collect a sample from the container of commercially prepared yogurt by swirling the swab in the yogurt, then scraping of the excess on the edge of the container. Smear this over the surface of the slide, making sure that you leave only a thin film of yogurt on the surface. Make a second smear from the container of freshly prepared homemade yogurt, if available. Allow both smears to air dry, and then heat fix them.
Once the sample(s) are heat fixed, stain them with crystal violet. This is a purple colored stain, and although both the milk proteins and cells will stain this color, the milk stains faintly and the bacteria will appear dark purple. Keep in mind that the probiotic bacteria are bacilli. Below, sketch a representative field as seen with the oil immersion objective for each of the yogurt samples.
Move your stage so you observe 10 different microscope fields. Keep track of the number of different types of bacterial cells you encounter during your survey, and record that information below:
• Cell Count of Bacteria in Commercial Yogurt:
• Number of cocci in 10 microscope fields: ____________
• Number of bacilli in 10 microscope fields: ___________
• Cell Count of Bacteria in Homemade Yogurt:
• Number of cocci in 10 microscope fields: ____________
• Number of bacilli in 10 microscope fields: ___________
• Does the container of commercially prepared yogurt state that there are “live, active cultures” in the yogurt? If the container lists the name(s) of the bacteria, write them below, followed by whether they should be bacilli or cocci.
____________________________________________________________________
____________________________________________________________________
• Considering the relative number and type(s) of bacteria you saw in the stained smear of the commercially prepared yogurt, what do you conclude about the health benefits of eating products such as this as a probiotic?
• Considering the relative number and type(s) of bacteria you saw in the homemade yogurt, what do you conclude about the health benefits of eating a fresh, homemade type of yogurt as a probiotic? | textbooks/bio/Microbiology/Microbiology%3A_A_Laboratory_Experience_(Ahern)/01%3A_Chapters/1.02%3A_The_Microscopic_World.txt |
The Birth of Bacteriology
While perhaps best known to us as a cause of human disease, bacteria really should be far more famous for their positive contributions than for their negative ones. Below, list three positive things that bacteria do for you.
1. ______________________________________________________________________
2. ______________________________________________________________________
3. ______________________________________________________________________
Bacteria were first observed by Anton von Leeuwenhoek in the late 17th century, but didn’t become the objects of serious scientific study until the 19th century, when it became apparent that some species caused human diseases. The methods devised by Robert Koch, Louis Pasteur, and their associates during the “Golden Age” of microbiology, which spanned from the mid-1800s to early 1900s, are still widely used today. Most of these methods involved isolating single bacteria derived from a natural source (such as a diseased animal or human) and cultivating them in an artificial environment as a pure culture to facilitate additional studies.
During the middle of the twentieth century, when we believed we had defeated them at their disease-causing game, bacteria became popular subjects of empirical study in fields such as genetics, genetic engineering, and biochemistry. With the evolution of antibiotic-resistant strains and our increased knowledge of bacterial stealth attack strategies such as biofilms and intracellular growth, medical researchers have refocused their attention on disease-causing bacteria and are looking for new ways to defeat them.
Growing bacteria in pure culture is still one of the most widely used methods in microbiology. Many bacteria, particularly those that cause diseases and those used in scientific studies, are heterotrophic, which means that they rely on organic compounds as food, to provide energy and carbon. Some bacteria also require added nutritional components such as vitamins in their diet. An appropriate physical environment must be created, where important factors such as temperature, pH, and the concentration of atmospheric gases (particularly oxygen) are controlled and maintained.
The nutritional needs of bacteria can be met through specialized microbiological media that typically contain extracts of proteins (as a source of carbon and nitrogen), inorganic salts such as potassium phosphate or sodium sulfate, and in some cases, carbohydrates such as glucose or lactose. For fastidious bacteria (meaning, those that are picky eaters) vitamins and/or other growth factors must be added as well.
Bacteriological culture media can be prepared as a liquid (broth), a solid (plate media or slant media), or as a semi-solid (deeps) as illustrated in Figure 1. Solid and semi-solid media contain a solidifying agent such as agar or gelatin. Agar, which is a polysaccharide derived from red seaweed (Rhodophyceae) is preferred because it is an inert, non-nutritive substance. The agar provides a solid growth surface for the bacteria, upon which bacteria reproduce until the distinctive lumps of cells that we call colonies form.
Koch, Pasteur, and their colleagues in the 19th and early 20th centuries created media formulations that contained cow brains, potatoes, hay, and all sorts of other enticing microbial edibles. Today, bacteriological media formulations can be purchased in powdered form, so that all the preparer has to do is to measure out the correct amount, add the right amount of water, and mix. After the basic formula has been prepared, the medium is sterilized in an autoclave, which produces steam under pressure and achieves temperatures above boiling. Once sterilized media has cooled, it is ready to be used.
Growing Bacteria in Culture
A population of bacteria grown in the laboratory is referred to as a culture. A pureculture contains only one single type; a mixed culture contains two or more different bacteria. If a bacterial culture is left in the same media for too long, the cells use up the available nutrients, excrete toxic metabolites, and eventually the entire population will die. Thus bacterial cultures must be periodically transferred, or subcultured, to new media to keep the bacterial population growing.
Microbiologists use subculturing techniques to grow and maintain bacterial cultures, to examine cultures for purity or morphology, or to determine the number of viable organisms. In clinical laboratories, subculturing is used to obtain a pure culture of an infectious agent, and also for studies leading to the identification of the pathogen. Because bacteria can live almost anywhere, subculturing steps must be performed aseptically, to ensure that unwanted bacterial or fungal contamination is kept out of an important culture.
In microbiology, aseptic techniques essentially require only common sense and good laboratory skills. First, consider that every surface you touch and the air that you breathe may be contaminated by microorganisms. Then think about the steps you can take to minimize your exposure to unwanted invisible intruders. You should also be thinking about how to prevent contamination of your bacterial cultures with bacteria from the surrounding environment (which includes you).
To maintain an aseptic work environment, everything you work with should be initially free of microbes. Thus, we begin with pre-sterilized pipettes, culture tubes, and glassware. Inoculating loops and needles made of metal wire can be used to transfer bacteria from one medium to another, such as from the surface of an agar plate to a broth. Metal tools may be sterilized by heating them in the flame of a Bunsen burner. Glass tools or metal spreaders or forceps that can’t be sterilized by direct heat are dipped in alcohol followed by a brief pass through the flame to speed the evaporation process. Standard aseptic techniques used for culturing bacteria will be demonstrated at the beginning of lab.
One very important method in microbiology is to isolate a single type of bacteria from a source that contains many. The most effective way to do this is the streak plate method, which dilutes the individual cells by spreading them over the surface of an agar plate (see Figure 2). Single cells reproduce and create millions of clones, which all pile up on top of the original cell. The piles of bacterial cells observed after an incubation period are called colonies. Each colony represents the descendants of a single bacterial cell, and therefore, all of the cells in the colonies are clones. Therefore, when you transfer a single colony from the streak plate to new media, you have achieved a pure culture with only one type of bacteria.
Different bacteria give rise to colonies that may be quite distinct to the bacterial species that created it. Therefore, a useful preliminary step in identifying bacteria is to examine a characteristic called colonial morphology, which is defined as the appearance of the colonies on an agar plate or slant. Ideally, these determinations should be made by looking at a single colony; however, if the colonial growth is more abundant and single colonies are absent, it is still possible to describe some of the colonial characteristics, such as the texture and color of the bacterial growth.
Describing Colonial Morphology of Bacteria
By looking closely at the colonial growth on the surface of a solid medium, characteristics such as surface texture, transparency, and the color or hue of the growth can be described. The following three characteristics are readily apparent whether you’re looking at a single bacterial colony or more dense growth, without the aid of any type of magnifying device.
Texture—describes how the surface of the colony appears. Common terms used to describe texture may include smooth, glistening, mucoid, slimy, dry, powdery, flaky etc.
Transparency—colonies may be transparent (you can see through them), translucent (light passes through them), or opaque (solid-appearing).
ColororPigmentation—many bacteria produce intracellular pigments which cause their colonies to appear a distinct color, such as yellow, pink, purple or red. Many bacteria do not produce any pigment and appear white or gray.
As the bacterial population increases in number, the colonies get larger and begin to take on a shape or form. These can be quite distinctive and provide a good way to tell colonies apart when they are similar in color or texture. The following three characteristics can be described for bacteria when a single, separate colony can be observed. It may be helpful to use a magnifying tool, such as a colony counter or dissecting microscope, to enable a close-up view of the colonies. Colonies should be described as to their overall size, their shape or form, what a close-up of the edges of the colony looks like (edge or margin of the colony), and how the colony appears when you observe it from the side (elevation).
Figure 4 shows a close-up of colonies growing on the surface of an agar plate. In this example, the differences between the two bacteria are obvious, because each has a distinctive colonial morphology.
Using microbiology terms, describe fully the colonial morphology of the two colonies shown above. A full description will include texture, transparency, color, and form (size, overall shape, margin, and elevation).
Colony 1
Colony 2
Now describe the colonial morphology of Micrococcus luteus, using the TSA plate culture of this bacterium provided to your group at the beginning of lab:
Size: ___________________________________________________________________
Texture: ________________________________________________________________
Transparency: ___________________________________________________________
Pigmentation: ___________________________________________________________
Form (shape, margin, elevation): ____________________________________________
Media Considerations
A culture medium must contain adequate nutrients to support bacterial growth. Minimally, this would include organic compounds that can provide the building blocks necessary for cellular reproduction. In many cases, predigested protein, such as hydrolyzed soy protein, serves this purpose and will support the growth of many different bacteria. These media formulations are generally referred to as complex media, to indicate that it is a mixture with many components.
Many media contain additional substances such as an antibiotic that may be selective for a particular type of bacteria by inhibiting most or all other types. Differential media will have additional compounds that permit us to distinguish among bacterial types based on differences in growth patterns. We will eventually use selective and differential media in our experiments, but the focus of this lab is to learn the basic culturing techniques, and therefore, the media used will be Tryptic Soy medium, a complex medium formulated with hydrolyzed soy protein.
The media you use in this lab and in all of the future labs will have already been prepared, but it is important for you as a budding microbiologist to understand and appreciate how culture media is prepared. With this in mind, your instructor may have you watch a brief video that demonstrates the art of media making.
Liquid media
Pre-sterilized glass or plastic graduated pipettes (Figure 5) are used to transfer specific volumes of sterile liquids accurately. It is important that you learn how to use these tools correctly, since it may be necessary to transfer sterile and sometimes contaminated liquids among various bottles and tubes. Their appropriate use will be discussed and demonstrated in lab. Some tips to remember:
• The pipette and the media are sterile; there should never be any direct contact with your hands, skin, or lab surfaces.
• Caps or lids on tubes or bottles should never be set down on lab surfaces.
• Tubes or bottles should be held at an angle during the transfer process, to minimize the potential for airborne contaminants to make their way into the opening.
• Passing the opening of the tube or bottle briefly through a flame before and after the transfer process will discourage airborne contaminants from getting into the sterile liquid.
Pipette practice:
• Obtain water in a small beaker, a 10 ml sterile graduated pipette, and a pipette aid (pipump). Take a minute to note the divisions on the pipette and to understand what volume each mark represents. Use of the pipette to transfer liquids will be demonstrated. Before trying to pipette a sterile liquid, practice drawing up 5 ml of water from the beaker, and releasing it back into the beaker in 1 ml increments. Continue until you feel comfortable holding the pipette and using the pipump. Then practice it again with water in a capped media bottle using aseptic techniques.
A portion of a 10 mL graduated pipette is shown in Figure 6. What is the volume of liquid in this pipette?
Volume:________________________________
Solid and semi-solid media
Growing cultures of bacteria on solid media (agar plate or slant) permits us to view and identify colonial characteristics, and also provides a way to separate bacteria in a mixed culture. Cultures grown on agar plates usually don’t survive for long, since Petri dish lids are not tight fitting and the media (and bacteria) dehydrate. Cultures grown on agar plates should always be handled “bottom-up” to prevent condensation—which often accumulates on the lid of the dish during incubation—from dripping down on the culture.
Bacteria may be grown in agar slant or stab media in tubes if the purpose is to maintain them in a longer term culture. Generally, bacteria grown on slants will remain viable for a few weeks to a few months, and sometimes longer if stored in a refrigerator.
In this laboratory, you will be introduced to aseptic techniques and basic lab skills needed to grow and maintain bacteria in culture. You will be applying these skills often, so mastery is important.
Method
A volunteer from your lab bench should obtain one of each of the following cultures:
• TSA streak plate culture of Micrococcusluteus and Enterococcusfaecalis
What BSL containment level practices should be used?
M. luteus__________________
E. faecalis__________________
• A “mixed culture” in TSB that contains two different bacteria
Below, write the names of the two bacteria in the mixed culture and the appropriate BSL, as specified by your instructor:
Mixed culture bacterium 1 ____________________________________________________
Mixed culture bacterium 2 ____________________________________________________
The techniques needed will first be demonstrated by your instructor. After the demonstration, perform the following tasks, and record your observations/results.
Broth Subculture
Obtain 2 sterile glass culture tubes, a bottle of Tryptic Soy Broth (TSB) and a test tube rack. With small pieces of colored tape, label each tube with your name and either “S” for subculture, or “C” for control. Using aseptic technique, use a 10 ml graduated pipette to transfer 2 ml of broth to each tube.
As demonstrated, use a flame-sterilized inoculating loop to pick up from the surface of the M. luteus streak plate culture, a single colony (if small) or a part of a colony (if large) and transfer it to the broth in the tube labeled “S.” Add nothing to the second tube “C” which will serve as a sterility control. Note how the broths look immediately after you inoculate them (they should still look mostly clear). Bacterial growth in broths is indicated by the development of a cloudy appearance. If the newly inoculated broth looks cloudy at the start, you will have no way to determine if this is due to bacterial growth during the incubation period. If your broth looks cloudy, discard it and make another broth using less bacteria.
Place the broth subcultures in an incubator at the temperature and time specified by your instructor.
Streak Plate
Separation of a mixed culture into individual colonies that can be subcultured to make pure cultures depends on how well the streak plate is prepared. The goal of streak plate method is to dilute the cells by spreading them out over the surface of the agar. This is accomplished in stages, as will be demonstrated in lab before you try it yourself.
Use the simulated agar surface below to practice the streak pattern using a pen or pencil.
Obtain two TSA plates, and write your name on the bottom half (the half containing the media) around the edge and following the curve (so the writing won’t hide your view of the bacterial colonies once they grow). Also write M. luteus on one plate (the name of the bacteria you will subculture to this plate). On the other, write “mixed” to indicate that you’re subculturing from the mixed culture broth to this plate.
As demonstrated, use a sterilized inoculating loop to pick up one M. luteus colony (or a piece of a colony) and transfer it to the surface of the agar plate. Spread the bacteria over approximately a quarter of the plate, edge to edge. Consider this step 1.
Flame the loop and cool it in the agar. Overlap the step 1 streak 3-4 times to pull out a reduced number of bacteria, and spread them out down the side of the plate. Consider this step 2.
Flame the loop and cool it in the agar. Overlap the step 2 streak 3-4 times and spread over the surface. Continue this process, flaming the loop in between each step, until the entire surface of the agar plate is covered.
After performing this with the M. luteus culture for practice, repeat the process with a drop of the mixed culture broth that you transfer to the plate with a sterile inoculating loop.
Place the streak plate subcultures in an incubator at the temperature and time specified by your instructor.
Slant Subculture of M. luteus
Obtain one slant tube containing TSA, and label it using a small piece of tape with your name and culture name (M. luteus). Using a sterilized inoculating loop, pick up a bacterial colony (or piece of a colony) from the surface of the plate culture of M. luteus, and inoculate the surface of the slant. Place the slant subculture in an incubator at the temperature and time specified by your instructor.
Stab or Deep Tube Subculture of E. faecalis
Obtain one stab tube containing semisolid TSA, and label it using a small piece of tape with your name and culture name (E. faecalis). Using a sterilized inoculating needle, pick up a bacterial colony (or piece of a colony) from the surface of the plate culture of E. faecalis, and inoculate the media by stabbing the needle into the center of the agar in the tube,and pushing it down to the bottom. Withdraw the needle carefully and try to remove it by following the same stab line that you made pushing the needle down. Place the stab subculture in an incubator at the temperature and time specified by your instructor.
A note about incubation temperatures
As you will learn, bacteria have preferred growth temperatures where their reproduction rate is the greatest. All of the bacteria we work with in lab are mesophilic, which means that they grow at temperatures between 20–40°C. However, some prefer body temperature (37°C), while others grow best at room temperature (approximately 25°C). This lab is equipped with incubators set at either temperature.
How long you plan to leave your cultures in an incubator should also be a consideration. Growing cultures at the higher temperature may speed their rate of growth, but it also causes dehydration of the media and an earlier demise to the bacteria in the culture.
As a general rule, for bacteria that grow best at body temperature, if you intend on returning to lab within 24 to 36 hours (highly recommended), then incubate them at 37°C. If you cannot return to lab during an “open lab” period, then incubate them at room temperature, or arrange to have your cultures transferred to a refrigerator after they grow, so that the culture won’t die out before you can finish your experiments. Bacteria that grow best at room temperature should always be incubated at room temperature, and growth may take a little longer.
Primary culture from an environmental source—you!
With your introduction to basic bacteriological culturing techniques complete, it’s time to apply those skills. Today is the beginning of The Human Skin Microbiome Project, which starts with the primary culture of bacteria from your skin on TSA medium. It is important that you read the project description (in the next chapter) so that you understand the goals and the scope of the project.
To begin, you will take a sample from your skin. Your first decision will be what part of your skin do you want to sample? Note: ONLY external skin surfaces are permitted.
Obtain a sterile swab and a tube of sterile distilled water, and label a TSA plate with your name and the date. Remove the wrapping from the swab and soak it in sterile water, using aseptic technique.
Rub the wet swab back and forth firmly over the area of skin you have chosen to sample. Then rub the swab over approximately a third of the surface of the TSA agar plate.
Sterilize an inoculating loop, and complete the rest of the streak plate pattern using the loop. Incubate this plate at room temperature for up to a week.
After incubation, look to see if isolated colonies have developed on the plate. If there are no colonies or no isolated colonies, you will need to make another streak plate with the advice of your instructor on how to proceed. If there are isolated colonies, transfer the plate to the refrigerator. From this plate you will ultimately choose one single colony and prepare a pure culture. The criteria for colony selection and next steps are described in the next chapter, “The Human Skin Microbiome Project.”
To complete the lab , the bacteria in the cultures have to grow . Therefore , the following observations are made AFTER the cultures have had time to grow .
Observations and Outcomes
Broth subcultures
Look at the broth subculture tubes, and describe what you expected to see, and how they appear in terms of how “cloudy” they look—cloudiness is an indication of bacterial growth.
Cloudiness of broth before incubation Predicted appearance of broth after incubation Actual appearance of broth after incubation
M. luteus subculture (“S”)
Sterility Control (“C”)
Streak plate subcultures
Look at the streak plate subcultures that you made. Conduct a self-assessment of how well you performed the technique. What you hope to see are individual colonies, well separated from each other. On the streak plate of the mixed culture, you should be able to see two distinctly different types of colonies.
M. luteus streak plate:
• Are the colonies well separated?
• How many different types of colonies do you see?
• Describe in full the colonial morphology of the bacteria on this plate:
Streak plate of the mixed culture :
• Are the colonies well separated?
• Could you make a pure culture of both bacteria from this plate? If you think you can, subculture a single colony of each type to one half of a TSA plate, divided by drawing a line with a marker on the bottom of the plate, as shown below. Incubate the plate, and then observe to see if you successfully separated the two bacteria in the mixed culture into two pure cultures. Use this self-analysis to consider improvements you might make in the technique you applied to making the streak plate.
• Describe in full the colonial morphology of both of the bacteria from the mixed culture:
Colony Type 1 Colony Type 2
Size
Texture
Transparency
Pigmentation
Whole Colony
TSA slant subculture
Examine the subculture of M. luteus you prepared on the TSA slant.
• Describe the texture, transparency, and pigmentation of the bacterial growth on the slant. Only these characteristics can be described for a slant culture, since there should be no discreet colonies on the slant, only an area of dense growth along the streak line.
• Does your description match what was noted for the M. luteus colonies when you described the colonial morphology previously?
• Do you see evidence of any other type of bacteria (meaning a different colonial morphology) on the slant?
• Is this a pure culture?
TSA stab subculture
Look closely along the stab line in the media in the tube. Do you see evidence of bacterial growth? If yes, describe and/or sketch how it appears.
Semisolid agar of the type used in this exercise can be used as a way to evaluate if a bacteria is motile, meaning in possession of one or more flagella that facilitates movement through liquids or semisolids. The way to evaluate motility is to look closely at the line of inoculation you created when the tube was stabbed. Nonmotile bacteria will grow along the stab line only. If they are motile, they will be able to move through the semisolid agar (like swimming through jello), and you won’t be able to see a distinct line in the agar—just cloudiness surrounding the stab line.
• Based on your observation of the bacteria in the stab culture, is there evidence that the bacteria are motile?
• For bacteria, the ability to move (motility) requires that they have which specific cellular structure? | textbooks/bio/Microbiology/Microbiology%3A_A_Laboratory_Experience_(Ahern)/01%3A_Chapters/1.03%3A_Bacteriological_Culture_Methods.txt |
Project Goals and Objectives
The Human Skin Microbiome Project is an application of the principles and practices of classic microbiological investigation. During this project, which will take several weeks to complete, you will survey the microbial inhabitants of the human skin (yours). Then, you will apply an expanding array of microbiology laboratory skills to grow and investigate the colonial, cellular, and metabolic properties of one of the bacterial species from your skin culture.
More specifically, you will:
• prepare a primary culture from your skin, and observe the colonial and cellular properties of the bacteria that grow on it;
• identify one skin isolate that you would like to investigate further, and maintain it in a pure culture for an extended period of time;
• use microbiological methods to investigate the cellular and metabolic properties of your skin isolate;
• understand basic principles of taxonomy and how to apply the information in Bergey’s Manual of Determinative Bacteriology to presumptively identify your skin isolate.
Biosafety Considerations
While it may seem somewhat ironic that bacteria you have been carrying around on your skin forever are now going to be classified as a potential biohazard and subjected to risk assessment and laboratory containment practices, it is nonetheless an important consideration.
Of the various types of bacteria that might be encountered during the primary culture stage of this project, most are BSL-1, and some BSL-2. To minimize the risks of working with bacteria of unknown identity, this project will be limited to only Grampositive bacteria, and BSL-2 practices will be employed while working with cultures of your isolate.
Bergey’s Manual
The definitive reference book for bacterial taxonomy and identification is Bergey’s Manual. There are two versions: the manual of Systematic Bacteriology, which is concerned with issues of bacterial taxonomy and systematics (arranging bacteria into taxa according to similarities/differences in DNA), and the manual of Determinative Bacteriology, which deals specifically with the identification aspects of bacterial taxonomy. The latter book will be our primary resource for this project. For an overview of the manual and how to use it, read Chapters I, II, III, IV, and V.
The Human Skin Microbiome
The bacteria and other microbes that live on human skin are those that are best adapted to survive the prevailing conditions. Regions of the human body can be thought of as different ecosystems. Exposed, dry areas of the skin, such as the forearm, are akin to an arid desert environment, which is a preferred environment for many Gram-positive bacteria. Skin sites that are generally dark, warm, and moist, such as the underarm or perineum, are similar to temperate or tropical ecosystems; they tend to harbor more microbes in general and are more likely to have a larger percentage of Gram-negative bacteria.
The quantitative differences found at these sites may relate to the amount of moisture, body temperature, and varying concentrations of skin surface lipids. Most microorganisms live in the superficial layers of the skin (the stratum corneum) and in the upper parts of the hair follicles. Some bacteria, however, reside in the deeper areas of the hair follicles, where they may be beyond the reach of ordinary disinfection procedures (like washing your face with soap/water or an antibacterial product). These out-of-reach bacteria serve as a reservoir for recolonization of the skin environment after the surface bacteria are removed.
Figure 1 illustrates the types of bacteria that are commonly found on various regions of the human skin. Not all of these bacteria are culturable, because the growth conditions necessary for their survival are difficult to replicate in an artificial environment. Using the culture conditions established for this laboratory, the bacteria grown in your primary culture will most likely be Actinobacteria (Micrococcus, Corynebacterium, Mycobacterium), Firmicutes (Staphylococcus or other Gram-positive bacteria), or Proteobacteria (Gram negative bacteria).
The skin microbiome may include fungi such as yeasts and molds as well as bacteria. While interesting, these eukaryotic microorganisms are outside of the scope of this project. Molds form very distinctive colonies that will be easy to identify as fungal in origin, and thus, easy to avoid. Yeasts, however, produce colonies that resemble those of bacteria, although typically smaller and different in color. When you select the colony and make a pure culture, avoid colonies that have the appearance of either a mold (furry, fuzzy, or powdery) or a yeast (very small, very slow growing—only appearing after a week or more of incubation, and brightly colored—red, orange, pink, or even bright white colonies).
Over the course of several weeks, you will maintain your bacterial strain in pure culture while performing tests to determine its colonial, cellular, and metabolic properties, and ultimately its “presumptive” identity. The term “presumptive” is used because phenotypic methods are less exact than those that rely on a direct analysis of DNA.
Record all observations, test outcomes, and interpretations on the Human Skin Microbiome Project Worksheets, according to the instructions provided by your instructor.
Identification of an Unknown Bacterium
Bergey’s Manual contains an enormous amount of information about the characteristics of all known bacterial species, mostly presented in table form. You will use the information in these tables to determine the identity of your skin isolate. To aid in this process, and as a way to demonstrate how you ruled out all other possible bacterial species, a taxonomic tool called a dichotomous key (also called a diagnostic key or sequential key) will be used to narrow down the possibilities.
A dichotomous key is a sequence of questions with two possible mutually exclusive answers (a “couplet,” such as yes or no, positive or negative, cocci or bacilli). Starting with a large group of bacteria (in this case, all of the possible Gram-positive bacteria that can be found on the human skin), the first question should relate to an observable characteristic for which there are two choices, followed by additional questions until the possibilities are narrowed to a single choice. A brief example is shown in Figure 2.
Bergey’s Manual of Determinative Bacteriology is designed to facilitate identification, and not classification, of bacteria based primarily on phenotypic observations. In Bergey’s, the broadest grouping is represented by the four Major Categories. The primary criterion to establish the Major Category for your skin microbe will be the nature of its cell wall. Remember that you are being limited to choosing a bacterium that is Gram positive; therefore, the starting point for this project will be bacteria that are in Major Category II: Gram-positive eubacteria that have cell walls. Because of the culture methods and conditions we will employ in this project, it is highly unlikely that your isolate would be from Categories III (eubacteria lacking cell walls) or IV (archaeobacteria); thus, those are excluded.
At this point, you have narrowed your options down from all bacteria to only those classified as Category II. The next step is to identify the Group, within the Major Category, to which your isolate belongs. Chapter V in Bergey’s provides a list and brief summary of the bacteria in the Groups within each Category; Table V.2 refers specifically to Category II bacteria. Cellular morphology (for example, cell shape and presence of endospores) and physiology (particularly with regard to your isolate’s physiological oxygen requirements and relative results) will help you decide on a Group. Once you made that decision, you can follow the directions given in Table V.2 to find the first page of the identification tables in Bergey’s.
Continue to narrow your choices down to a single Genus within the Group, and once you’ve decided on a genus, locate and refer to the identification table that specifies the different Species within that genus. The tables also list the laboratory tests routinely performed to differentiate among the species, and the expected outcomes of those tests for each bacterial species in the genus.
You may not be able to conduct all of the tests listed in Bergey’s. Different tests may be available for you to perform, depending on the laboratory in which you work. For the purpose of identifying your skin microbe, below is a list of the tests that are available for you to use in the ID process.
• Gram stain and endospore stain
• 7.5% salt tolerance (MSA)
• Mannitol fermentation (MSA for salt-tolerant bacteria)
• Bile tolerance and esculin hydrolysis (BE)
• Hemolysis on blood agar
• Glucose fermentation (MR; VP; TSI)
• Lactose/sucrose fermentation (TSI)
• Fermentation of other carbohydrates (see instructor)
• Susceptibility or resistance to antibiotics
• Acetoin production (VP)
• Catalase
• Oxidase
• Production of H2S (TSI; SIM)
• Indole (SIM)
• Motility (SIM)
• Citrate utilization
• Nitrate reduction
• Coagulase (for staphylococci ONLY)
• Urease
Other tests may be available, as indicated by your instructor.
Observations, Outcomes, and Next Steps
The following tasks will be performed over the course of several weeks:
Project Step 1: Make a primary culture from your skin on a TSA plate and incubate it for up to a week at room temperature.
Project Step 2: After incubation, the TSA plate that contains the primary culture from your skin will very likely hold many, hopefully well isolated, colonies.
From among these, choose 3 colonies for subculture and further examination. Remember to avoid colonies that appear to be a mold (typically large, green or brown, and fuzzy) or yeast (very small and vibrantly white or a shade of red). With a sterile inoculation loop, subculture each colony to a section of a TSA plate, to create a pure culture, as you did previously and illustrated in Figure 3. Incubate the plate at RT until bacterial growth is abundant.
Project Step 3: Gram stain each of the three pure cultures. Choose one that is Gram-positive (bacilli or cocci) as your project bacterium (your skin microbe, or HSM). Subculture your HSM to a TSA slant and incubate it. Once there is abundant growth on the surface, store the TSA slant culture in the refrigerator. Make sure the slant is clearly labelled with your name.
Complete the Colonial and Cellular Morphology (CCM) Worksheet.
Project Step 4: From the observations you’ve made and the results of lab tests,use Bergey’s Manual as a reference to determine the Major Category, Group and then Genus of your HSM.
Complete the Genus Identification (GID) Worksheet.
Project Step 5: Once you’ve narrowed your options down to a single genus, locate the specific table in Bergey’s Manual for identification of individual species. Based on the information in the table, compile a list of appropriate tests that will facilitate species identification. Select those that are available for you to perform, as specified by your lab instructor. Perform the appropriate tests and record the results.
Project Step 6: Compare your results with the expected test outcomes from Bergey’s Manual to determine the Species of your human skin microbe.
Complete the Species Identification (SID) Worksheet.
HSMP Worksheet 1: Colonial and Cellular Morphology
Name __________________________________________ Date due _________________
Record the observations/results obtained so far below. NOTE: your instructor may make this worksheet available to you electronically through a course management system, and may request that you type your answers into the worksheet before printing and handing it in.
1. Name the region of your body from which you obtained the specimen for the primary culture.
2. Based on colony appearance, approximately how many different types of bacteria from your skin are represented on the TSA streak plate of your primary culture?
3. Based on the appearance of an isolated colony and using appropriate microbiology terminology, describe the colonial morphology of each of the three bacterial subcultures.
Colony Type 1
Colony size
Texture
Transparency
Pigmentation
Form (shape, margin, elevation)
Colony Type 2
Colony size
Texture
Transparency
Pigmentation
Form (shape, margin, elevation)
Colony Type 3
Colony size
Texture
Transparency
Pigmentation
Form (shape, margin, elevation)
4. For each of the three bacterial pure cultures, describe the outcome of the Gram stain using appropriate microbiology terminology:
Gram Stain Outcome Cell shape Arrangement
Colony 1
Colony 2
Colony 3
5. Of the three bacteria you investigated, choose one that is Gram-positive as your project bacterium. Below, indicate which of the three you chose and restate the Gram staining result.
Colony # and Gram stain result (including cell shape and arrangement):
_____________________________________________________________________
6. Compare and contrast the chemical composition and structure of the cell wall of a Gram-positive bacterium such as your isolate, with the cell wall of a Gram negative bacterium.
7. Briefly discuss why Gram-positive cells appear purple, and Gram-negative cells appear pink, after the Gram stain process is applied.
8. Briefly discuss how bacterial cells produce “arrangements” that we can observe with a microscope.
9. State whether it will be necessary for you to perform an endospore stain on your isolate, and give a specific reason to explain why you should, or should not, use this staining method to identify your isolate.
10. Briefly explain why it is necessary to include a mixture of iodine and potassium iodide (Gram’s Iodine) in the overall Gram stain procedure.
In addition to this worksheet, you may also be asked to prepare and provide to your instructor a Gram stained slide of a smear prepared from your environmental isolate to evaluate your technique. If evaluated, the following criteria will be used: single layer of cells is achieved, cell morphology and arrangement are easily determined, all cells appear the same color, shape, and arrangement, and there are no visible contaminants.
Instructor Evaluation of Gram Stained Slide:
Gram stain result as observed by instructor: _______________________________________
Evaluation of technique: _______________________________________________________
Criteria: Single layer of cells is achieved; cell morphology and arrangement are easily determined; all cells appear the same color, shape, and arrangement; and there are no visible contaminants. Degree of concurrence with instructor’s description of cellular morphology will also be noted.
HSMP Worksheet 2: Genus Identification
Name __________________________________________ Date due _________________
1. From your CCM worksheet, restate the Gram stain results (reaction, morphology, and arrangement) for your skin isolate:
2. Taxonomic Classification: State the Domain and Phylum for your isolate, based on the evidence you have accumulated so far.
3. Report the results of the following physiological tests performed on your environmental isolate:
Test Describe in detail the outcomes of the following tests (meaning, what you directly observe: such as bubbles after H2O2 was added; red color on the slant and yellow on the butt with cracks; etc.) Interpretation of observed outcome (for example; pos or neg; K/A, gas, etc)
Catalase
Oxidase
TSI agar
Nitrate Reduction
4. From your observations of bacterial growth characteristics and physiological tests up to this point, state ALL energy metabolism pathway(s) used by your skin bacterium to make ATP. Then provide convincing evidence from among your observations and test results to support your determination.
Energy Metabolism pathway Do your observations and/or results of the tests above indicate that your EI uses this pathway? (YES or NO) STATE one observation and/or test result that provides scientific evidence for that pathway, and explain why/how the result indicates that your EI bacterium uses this pathway.
Aerobic respiration
Anaerobic respiration
Fermentation
5. Growth Category for Oxygen
Based on the observed growth patterns and test results above, state the physiological oxygen requirement (strict aerobe, microaerophile, strict anaerobe, facultative anaerobe, or aerotolerant anaerobe) for your EI bacterium.
6. Bergey’s Group
Table V in Bergey’s is divided into four sections, one for each Major Category of bacteria. Remember that you were directed to select a Gram-positive bacterium as your EI, so look at Table V.2 to determine to which Group, within Major Category II, your EI should be assigned. Based on the characteristics of your EI bacterium that you have observed up to this point:
(a) State the Group (group number and name) for your EI according to the Bergey’s Manual identification system.
(b)State TWO observations that provide scientific evidence to support your choice of Group designation from (a) above.
7. Tests to assign Genus
If necessary (and it may not be necessary at this point), perform additional tests to determine the genus of your environmental isolate. Describe those tests and their outcomes in the table below. If you can determine the genus without additional tests, don’t put anything in this table.
Test/Observation Describe in detail the outcomes of the following tests (meaning, what you directly observe): such as bubbles after H2O2 was added; red color on the slant and yellow on the butt with cracks; etc.) Interpretation of observed outcome (for example; pos or neg; K/A, gas, etc)
8. Genus ID Flowchart (dichotomous key)
A brief example of how to construct a dichotomous key was provided previously in this lab. Note that the key you develop will be used by your instructor to review the process and logic of your choice of genus.
Some advice on how to proceed: Remember that your goal is to RULE OUT genera that are not consistent with the characteristics you’ve observed for your EI bacterium. Start by listing ALL of the possible genera in the Bergey’s Group. Then look at the characteristics that distinguish the various genera from one another (such as cell shape, endospore production, growth on human skin, etc.). As your first couplet, choose a feature that your isolate exhibits and the majority of other genera lack. Then, for the genera that were not ruled out, choose as the next couplet a feature that again rules out as many genera as possible. Continue until there is only a single genus left that is consistent with all of your observations made up to this point.
State the presumptive genus of your EI bacterium: ____________________________________
HSMP Worksheet 3: Species Identification
Name ____________________________________________Date Due _______________
1. Review of observations/characteristics of your EI determined so far:
Pigmentation of colonies (color ONLY)
Gram stain reaction
Cellular morphology
Cellular arrangement
Endospores observed (yes or no)
Result of catalase test (+ or -)
Result of the oxidase test (+ or -)
Result of TSI
Result of nitrate reduction test (+ or -)
List ALL energy pathways indicated
Growth category for oxygen
Bergey’s Group (# and name)
Name of Genus
2. Tests for Species ID
Locate the specific Table in Bergey’s Manual that shows the species within the genus and the tests needed for the differentiation and identification of your isolate. Below, list the tests you will need to perform (in addition to those already done) to presumptively identify your isolate. Cross reference the list of tests available in your laboratory (provided previously by your instructor).
3. Complete the table below with the tests/outcomes you observed for your EI bacterium. The number of rows in the table is arbitrary – only do as many tests as needed to ID your isolate. Add additional rows, if necessary).
Name of test Direct observation of the outcome of test(s) (how did the media, slide, tube, etc. APPEAR when you looked at it?) Outcome/Result (pos or neg, K/A, etc.)
4. As you did previously, construct a dichotomous key to show the process and logic used to presumptively identify your environmental isolate. Begin by listing ALL species within the genus, below. Note that subspecies (if there are any) should be listed individually.
5. Complete EITHER A or B below:
A. If you were able to identify a single species after completing all possible tests: Write the full binomial name (using scientific nomenclature) for your environmental isolate below:
B. If you were NOT able to discriminate a single species after completing all your tests: Write the full binomial name of ALL remaining species and provide the reason why you were unable to assign a single species to your EI.
6. Growth Characteristics
Use biology/microbiology terminology to state the specific category related to the following growth characteristics for your EI. Provide your reasoning for the choice of each category, including specific examples of growth patterns observed for your isolate from among your observations and tests.
Physiological Category Supporting evidence from among your observations/test results
Nutritional
Temperature
Osmotic (salt) tolerance
7. Fully classify your isolate by providing the following information, using appropriate terminology and scientific nomenclature:
Taxon Classification for your skin isolate
Domain
Phylum
Class
Order
Family
Genus
Species | textbooks/bio/Microbiology/Microbiology%3A_A_Laboratory_Experience_(Ahern)/01%3A_Chapters/1.04%3A_The_Human_Skin_Microbiome_Project.txt |
Viewing Bacterial Cells
The microscope is a very important tool in microbiology, but there are limitations when it comes to using one to observe cells in general and bacterial cells in particular. Two of the most important concerns are resolution and contrast. Resolution is a limitation that we can’t do much about, since most bacterial cells are already near the resolution limit of most light microscopes. Contrast, however, can be improved by either using a different type of optical system, such as phase contrast or a differential interference contrast microscope, or by staining the cells (or the background) with a chromogenic dye that not only adds contrast, but gives them a color as well.
There are many different stains and staining procedures used in microbiology. Some involve a single stain and just a few steps, while others use multiple stains and a more complicated procedure. Before you can begin the staining procedure, the cells have to be mounted (smeared) and fixed onto a glass slide.
A bacterial smear is simply that—a small amount of culture spread in a very thin film on the surface of the slide. To prevent the bacteria from washing away during the staining steps, the smear may be chemically or physically “fixed” to the surface of the slide. Heat fixing is an easy and efficient method, and is accomplished by passing the slide briefly through the flame of a Bunsen burner, which causes the biological material to become more or less permanently affixed to the glass surface.
Heat fixed smears are ready for staining. In a simple stain, dyes that are either attracted by charge (a cationic dye such as methylene blue or crystal violet) or repelled by charge (an anionic dye such as eosin or India ink) are added to the smear. Cationic dyes bind the bacterial cells which can be easily observed against the bright background. Anionic dyes are repelled by the cells, and therefore the cells are bright against the stained background. See Figures 1 and 2 for examples of both.
Probably the most important feature made obvious when you stain bacterial cells is their cellularmorphology (not to be confused with colonial morphology, which is the appearance of bacterial colonies on an agar plate). Most heterotrophic and culturable bacteria come in a few basic shapes: spherical cells (coccus/cocci), rod-shaped cells (bacillus/bacilli), or rod-shaped cells with bends or twists (vibrios and spirilla, respectively). There is greater diversity of shapes among Archaea and other bacteria found in ecosystems other than the human body.
Often bacteria create specific arrangements of cells, which form as a result of binary fission by the bacteria as they reproduce. Arrangements are particularly obvious with non-motile bacteria, because the cells tend to stay together after the fission process is complete. Both the shape and arrangement of cells are characteristics that can be used to distinguish among bacteria. The most commonly encountered bacterial shapes (cocci and bacilli) and their possible arrangements are shown in Figures 3 and 4.
Differential Staining Techniques
In microbiology, differential staining techniques are used more often than simple stains as a means of gathering information about bacteria. Differential staining methods, which typically require more than one stain and several steps, are referred to as such because they permit the differentiation of cell types or cell structures. The most important of these is the Gram stain. Other differential staining methods include the endospore stain (to identify endospore-forming bacteria), the acid-fast stain (to discriminate Mycobacterium species from other bacteria), a metachromatic stain to identify phosphate storage granules, and the capsule stain (to identify encapsulated bacteria). We will be performing the Gram stain and endospore staining procedures in lab, and view prepared slides that highlight some of the other cellular structures present in some bacteria.
Gram Stain
In 1884, physician Hans Christian Gram was studying the etiology (cause) of respiratory diseases such as pneumonia. He developed a staining procedure that allowed him to identify a bacterium in lung tissue taken from deceased patients as the etiologic agent of a fatal type of pneumonia. Although it did little in the way of treatment for the disease, the Gram stain method made it much easier to diagnose the cause of a person’s death at autopsy. Today we use Gram’s staining techniques to aid in the identification of bacteria, beginning with a preliminary classification into one of two groups: Gram positive or Gram negative.
The differential nature of the Gram stain is based on the ability of some bacterial cells to retain a primary stain (crystal violet) by resisting a decolorization process. Gram staining involves four steps. First cells are stained with crystal violet, followed by the addition of a setting agent for the stain (iodine). Then alcohol is applied, which selectively removes the stain from only the Gram negative cells. Finally, a secondary stain, safranin, is added, which counterstains the decolorized cells pink.
Although Gram didn’t know it at the time, the main difference between these two types of bacterial cells is their cell walls. Gram negative cell walls have an outer membrane (also called the envelope) that dissolves during the alcohol wash. This permits the crystal violet dye to escape. Only the decolorized cells take up the pink dye safranin, which explains the difference in color between the two types of cells. At the conclusion of the Gram stain procedure, Gram positive cells appear purple, and Gram negative cells appear pink.
When you interpret a Gram stained smear, you should also describe the morphology (shape) of the cells, and their arrangement. In Figure 5, there are two distinct types of bacteria, distinguishable by Gram stain reaction, and also by their shape and arrangement. Below, describe these characteristics for both bacteria:
Gram positive bacterium: Gram negative bacterium:
Morphology
Arrangement
Acid Fast Stain
Some bacteria produce the waxy substance mycolicacid when they construct their cell walls. Mycolic acid acts as a barrier, protecting the cells from dehydrating, as well as from phagocytosis by immune system cells in a host. This waxy barrier also prevents stains from penetrating the cell, which is why the Gram stain does not work with mycobacteria such as Mycobacterium, which are pathogens of humans and animals. For these bacteria, the acidfaststaining technique is used.
To perform the acid-fast stain, a heat-fixed smear is flooded with the primary stain carbol fuchsin, while the slide is heated over a steaming water bath. The heat “melts” the waxy cell wall and permits the absorption of the dye by the cells. Then the slide is allowed to cool and a solution of acid and alcohol is added as a decolorizer. Cells that are “acid-fast” because of the mycolic acid in their cell wall resist decolorization and retain the primary stain. All other cell types will be decolorized. Methylene blue is then used as a counterstain. In the end, acid-fast bacteria (AFB) will be stained a bright pink color, and all other cell types will appear blue.
Staining Methods to Highlight Specific Cell Structures
Capsule: The polysaccharide goo that surrounds some species of bacteria and a few types of eukaryotic microbes is best visualized when the cells are negative stained. In this method, the bacteria are first mixed with the stain, and then a drop of the mixture is spread across the surface of a slide in the thin film. With this method, capsules appear as a clear layer around the bacterial cells, with the background stained dark.
Metachromaticgranulesorotherintracytoplasmicbodies: Some bacteria may contain storage bodies that can be stained. One example is the Gram positive bacilli Corynebacterium, which stores phosphate in structures called “volutin” or metachromatic granules that are housed within the cell membrane. Various staining methods are used to visualize intracytoplasmic bodies in bacteria, which often provide an identification clue when observed in cells.
Endospore Stain
Endospores are dormant forms of living bacteria and should not be confused with reproductive spores produced by fungi. These structures are produced by a few genera of Gram-positive bacteria, almost all bacilli, in response to adverse environmental conditions. Two common bacteria that produce endospores are Bacillus or Clostridum. Both live primarily in soil and as symbionts of plants and animals, and produce endospores to survive in an environment that change rapidly and often.
The process of endosporulation (the formation of endospores) involves several stages. After the bacterial cell replicates its DNA, layers of peptidoglycan and protein are produced to surround the genetic material. Once fully formed, the endospore is released from the cell and may sit dormant for days, weeks, or years. When more favorable environmental conditions prevail, endospores germinate and return to active duty as vegetative cells.
Mature endospores are highly resistant to environmental conditions such as heat and chemicals and this permits survival of the bacterial species for very long periods. Endospores formed millions of years ago have been successfully brought back to life, simply by providing them with water and food.
Because the endospore coat is highly resistant to staining, a special method was developed to make them easier to see with a brightfield microscope. This method, called the endosporestain, uses either heat or long exposure time to entice the endospores to take up the primary stain, usually a water soluble dye such as malachite green since endospores are permeable to water. Following a decolorization step which removes the dye from the vegetative cells in the smear, the counterstain safranin is applied to provide color and contrast. When stained by this method, the endospores are green, and the vegetative cells stain pink, as shown in Figure 7.
Although endospores themselves are resistant to the Gram stain technique, bacterial cells captured in the process of creating these structures can be stained. In this case, the endospores are seen as clear oval or spherical areas within the stained cell. Endospores can also be directly observed in cells by using phase contrast microscopy, as shown in Figure 8.
Method
Because many differential staining methods require several steps and take a long time to complete, we will not be performing all of the differential staining methods discussed above.
Pre-stained slides will be used to visualize bacterial capsules, metachromatic granules, and acid-fast bacilli. Obtain one slide of each of the three bacteria listed in the table below. As you view these slides, make note of the “highlighted” structures. Your environmental isolate may have one or more of these cellular features, and learning to recognize them will aid in identification. These should all be viewed using the oil immersion objective lens.
Bacterium Stain Description or sketch of cells with the specified feature
Flavobacterium capsulatum Capsule stain
Corynebacterium diphtheriae Methylene blue(metachromatic granules)
Mycobacterium tuberculosis Acid fast stain
Gram Stain
All staining procedures should be done over a sink. The Gram stain procedure will be demonstrated, and an overview is provided in Table 1.
Table 1. Gram stain procedural steps.
Step Procedure Outcome
Primary stain(crystal violet) Add several drops of crystal violet to the smear and allow it to sit for 1 minute. Rinse the slide with water. Both Gram-positive and Gram-negative cells will be stained purple by the crystal violet dye.
Mordant (iodine) Add several drops of iodine to the smear and allow it to sit for 1 minute. Rinse the slide with water. Iodine “sets” the crystal violet, so both types of bacteria will remain purple.
Decolorization (ethanol) Add drops of ethanol one at a time until the runoff is clear. Rinse the slide with water. Gram-positive cells resist decolorization and remain purple. The dye is released from Gram-negative cells.
Counterstain(safranin) Add several drops of safranin to the smear and allow it to sit for one minute. Rinse the slide with water and blot dry. Gram-negative cells will be stained pink by the safranin. This dye has no effect on Gram-positive cells, which remain purple.
A volunteer from your lab bench should obtain cultures of the bacteria you will be using in this lab, as directed by your instructor. One of the cultures will be a Gram positive bacterium, and the other will be Gram negative. Below, write the names of the bacteria you will be using, along with the BSL for each culture:
__________________________________________________________________________________
Obtain two glass slides, and prepare a smear of each of the two bacterial cultures, one per slide, as demonstrated. Allow to COMPLETELY air dry and heat fix. Stain both smears using the Gram stain method. Observe the slides with a light microscope at 1,000X and record your observations in the table below.
Name of culture Gram stain reaction Cellular morphology Arrangement
Gram Stain “Final Exam”: prepare a smear that contains a mixture of the Gram-positive AND Gram-negative bacteria by adding a small amount of each bacterium to a single drop of water on a slide. Heat fix the smear and Gram stain it. You should be able to determine the Gram stain reaction, cellular morphology and arrangement of BOTH bacteria in this mixed smear. Your instructor may ask to see this slide and offer constructive commentary.
Endospore Stain
Only a few genera of bacteria produce endospores and nearly all of them are Gram-positive bacilli. Most notable are Bacillus and Clostridium species, which naturally live in soil and are common contaminants on surfaces. The growth of Clostridium spp. is typically limited to anaerobic environments; Bacillus spp. may grow aerobically and anaerobically. Endospore-forming bacteria are distinct from other groups of Gram positive bacilli and distinguishable by their endospores.
An overview of the endospore stain procedure is provided in Table 2.
Table 2. Endospore stain procedural steps.
Step Procedure Outcome
Primary stain(malachite green) Add several drops of malachite green to the smear and allow it to sit for 10 minutes. If the stain starts to dry out, add additional drops. Vegetative cells will immediately take up the primary stain. Endospores are resistant to staining but eventually take up the dye.
Decolorization(water) Rinse the slide under a gentle stream of water for 10-15 seconds. Once the endospores are stained, they remain green. A thorough rinse with water will decolorize the vegetative cells.
Counterstain(safranin) Add several drops of safranin to the smear and allow it to sit for 1 minute. Rinse the slide and blot dry. Decolorized vegetative cells take up the counterstain and appear pink; endospores are light green.
After staining, endospores typically appear as light green oval or spherical structures, which may be seen either within or outside of the vegetative cells, which appear pink.
The shape and location of the endospores inside the bacterial cells, along with whether the sporangium is either distending (D) or not distending (ND) the sides of the cell, are important characteristics that aid in differentiating among species (see Figure 9).
1. Oval, central, not distended (ND)
2. Oval, terminal, ND (and parasporal crystal)
3. Oval, terminal, distended (D)
4. Oval, central, D
5. Spherical, terminal, D
6. Oval, lateral, D
Endospores are quite resistant to most staining procedures; however, in a routinely stained smear, they may be visible as “outlines” with clear space within. If you observe “outlines” or what appear to be “ghosts” of cells in a Gram stained smear of a Gram-positive bacilli, then the endospore stain should also be performed to confirm the presence or absence of endospores.
A volunteer from your lab bench should obtain bacterial cultures for endospore staining, as directed by your instructor. Note that these will all be species of Bacillus. Prepare smears and stain each using the endospore staining technique. Observe the slides and note the shape and location of the endospore and the appearance of the sporangium (swollen or not swollen) in the table below:
Name of culture Endospore Shape Location Sporangium
In addition, choose ONE of the cultures from above and Gram stain it. Record your results below in the spaces provided:
Name of Gram stained culture: __________________________________________________
Gram stain reaction and cellular morphology: ______________________________________
Are endospores visible in the Gram stained smear? _________________ If you see endospores, describe how they appear in the Gram stained preparation, and how this is similar to and different from what you see in the endospore stained preparation. | textbooks/bio/Microbiology/Microbiology%3A_A_Laboratory_Experience_(Ahern)/01%3A_Chapters/1.05%3A_Differential_Staining_Techniques.txt |
Metabolism
Like an animal or a plant, the life of bacteria involves a daily routine of thousands of chemical reactions, many devoted to the breakdown (catabolism) of substrates to extract energy or building materials. Other types of reactions utilize the energy and building blocks liberated during catabolism for synthesis reactions (anabolism). The term “metabolism” is an expression used to describe all of the chemical reactions that occur in a cell.
Bacteria rely on enzymes for their biochemistry, just as do other cell types. For bacteria, enzymes needed for metabolic reactions are either endoenzymes, which work within the cell, or exoenzymes, which are produced inside the cell and then transported to the outside where they facilitate the preliminary digestion of high molecular weight substrates that do not pass readily through the cell membrane.
All of this chemistry results in the production of biomolecules and waste, much of which is excreted by the cells into the surrounding environment. Detecting and identifying the biochemical products of metabolism provides us with a way to learn more about the physiologic and growth capabilities of bacteria, and also give us a way to differentiate among and/or identify species.
In BergeysManual, the definitive reference book on bacteria, determinations of identity or taxonomic group are based on many criteria. Gram stain reaction is usually the first criteria, followed by biochemical characteristics such as aerobic or anaerobic respiration, fermentation of various sugars, degradation of proteins and amino acids, and other cellular events. Intermediates or end products of these varied metabolic activities can be detected by performing biochemical assays on a bacterial culture. The results of these tests provide a biochemical profile, or “fingerprint,” that can be used to classify or even identify the bacterial species. The outcomes of laboratory tests can also provide insight into physiology and what is needed to encourage and support bacterial growth.
One of the goals of Koch and Pasteur and their many associates was to develop methods to isolate and identify pathogens as the cause of a human disease. Although the limitations of this approach are now well known, the methods developed during the Golden Age period are still widely used in research and in clinical microbiology laboratories. From clinical specimens, isolated cultures are subjected to a battery of morphological and biochemical fingerprinting tests and compared to known outcomes. In this way, it is possible to identify potentially pathogenic bacteria and distinguish them from the usually helpful symbiotic microbiota.
Morphological Evaluation of Bacterial Isolates
The bacteria we will examine in this lab include species in different genera; Staphylocccus, Micrococcus, Streptococcus, Enterococcus, and Neisseria. At the cellular level, the one characteristic common to all of them is cellular morphology—all are cocci. They differ, however, in many other characteristics.
A volunteer from your lab bench should obtain cultures from your instructor, who will provide you with the species names. Write the name and BSL for each of the cultures below:
_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
Colonial morphology
Although there are similarities, the bacteria we will examine in this lab have notable differences, starting with appearance of their colonies. For the bacteria listed in the table below, choose one species from each of the genera below to observe, and describe the colonial morphology of the bacteria in the table below. Note that up until about a decade ago, Streptococcus and Enterococcus were considered part of the same genus and are very similar with regard to both cellular and colonial morphology.
Bacterium Colonial Morphology
Staphylococcus saprophyticus
Micrococcus luteus
Enterococcus faecalis
Gram stain and cellular morphology
On a cellular level, all of the bacteria we will look at in this lab have a similar morphology, but there are significant differences in Gram stain reaction, cell size, and cellular arrangements. These differences help to target the particular genus of a bacterial sample.
Prepare smears of the three bacteria you examined (above) and Gram stain them. Also look at a prepared Gram stained slide of Neisseriagonorrhoeae (the causative agent of the STD gonorrhea) and describe what you see in the table below.
Bacterium(write in species name)Gram stain results(reaction, morphology, and arrangement)Staphylococcus _________________(also representative of other Staphylococcus spp.) Micrococcus luteus (also representative of other Micrococcus spp.) Enterococcus faecalis (representative of both Entercoccus and Streptococcus spp.) Neisseria gonorrhoeae(There is no culture of this – view the prepared slide)
Physiology and growth characteristics
Growing bacteria in culture requires consideration of their nutritional and physical needs. Food, provided in the media, is broken down by cells and used for energy and building biomass. Unlike eukaryotic cells, bacteria have options when it comes to making energy, which depend not only on the type of organic molecules in the food but also on the availability of oxygen as a final electron acceptor for respiration.
Respiration is the pathway in which organic molecules are sequentially oxidized to strip off electrons, which are then deposited with a final electron acceptor. Along the way, ATP is made. For many types of bacteria, oxygen serves as the final electron acceptor in respiration. Remarkably, oxygen is not always a requirement for respiration. For bacteria that live in environments with no air, alternative electron acceptors may take the place of oxygen.
Unlike the majority of eukaryotes, bacteria have options when it comes to making ATP. Aerobic respiration and anaerobic respiration generate ATP by chemiosmosis, and some bacteria may also ferment sugars, although the oxidation is not complete and energy is left behind. Chemical by-products and end products of these pathways are detectable and serve as the basis for many biochemical tests performed to identify bacteria.
Fermentation and anaerobic respiration are anaerobic processes—meaning that no oxygen is required for ATP production. Some bacteria have the capability (meaning they produce the appropriate enzymes) to use more than one, or even all three, of these pathways depending on growth conditions.
Based on whether oxygen is required for growth, bacteria can be considered to be either aerobes or anaerobes. However, because some bacteria may use more than one pathway, there are additional categories that describe a culture’s requirement for oxygen in the atmosphere. The three major categories are:
Strict aerobe—Bacteria that are strict aerobes must be grown in an environment with oxygen. Typically, these bacteria rely on aerobic respiration as their sole means of making ATP, but some may also ferment sugars.
Strict anaerobe—These bacteria live only in environments lacking oxygen, using anaerobic respiration or fermentation to survive. For these types of cells, oxygen can be lethal because they lack normal cellular defenses against oxidative stress (enzymes that protect cells from oxygen free radicals).
Facultative anaerobe—The most versatile survivalists there are. These bacteria typically have access to all three ATP-forming pathways, along with the requisite enzymes to protect cells from oxidative stress.
Additionally, overlapping categories include:
Microaerophile—As the name implies, these bacteria prefer environments with oxygen, but at lower levels than normal atmospheric conditions. Often, microaerophiles also have a requirement for increased levels of carbon dioxide in the atmosphere and may also be called capnophiles. These bacteria make ATP by aerobic respiration and may also ferment sugars aerobically.
Aerotolerant anaerobe—These bacteria make ATP by anaerobic respiration and may also be fermentive. However, they are “tolerant” of oxygen because they may have cellular defenses against oxygen free radicals.
Tests that detect either components or end-products of these pathways may be used to assess a culture’s overall oxygen requirement category. The following tests provide the information necessary to assess this growth characteristic.
The catalasetest detects the ability of bacteria to produce an enzyme called catalase which is found in cells that live where there is air. Various chemical reactions in electron transport pathways create oxygen free radicals, which are electron-scavenging chemical species that can oxidize and potentially damage biomolecules in cells. One of these is hydrogen peroxide (H2O2), the substrate of the catalase enzyme which converts hydrogen peroxide to water and oxygen. The catalase test is performed by mixing a small amount of a bacterial culture with a drop of hydrogen peroxide on a slide. If the bacteria have the catalase enzyme, the substrate will be split, forming water and oxygen which is observed as bubbling when the gas is released (see Figure 1). A positive test result indicates that the bacteria live aerobically, and are likely to produce ATP by aerobic respiration. Strict aerobes, facultative anaerobes and microaerophiles may be positive for this test. Anaerobes (strict or aerotolerant) will be negative).
The oxidasetest identifies bacteria that produce cytochrome oxidase or indophenol oxidases, which are redox enzymes in the electron transport system that shuttle electrons to oxygen. The cytochrome system is usually only present in aerobic organisms that use oxygen as the final electron acceptor in respiration. There are several ways in which this test may be performed, but one of the simplest is to use a commercial test system, such as the BBL DrySlide Oxidase test, which consists of a card saturated with a chemical reagent that is colorless in its reduced state and turns dark blue when oxidized. The cytochrome oxidase enzymes donate electrons to the reagent, changing the color of the card from colorless to blue for a positive test (see Figure 2). Aerobic bacteria with a cytochrome-based electron transport system (similar to what is found in the mitochondria of eukaryotic cells) will be positive for this test.
The nitratereduction test detects reduced forms of nitrate, which occurs when bacteria use nitrate (NO3) as a substitute for oxygen (O2) during respiration. In the biogeochemical cycle known as the nitrogen cycle, nitrate reduction is the first step in a series of reactions collectively referred to as denitrification (Figure 3).
On an ecosystem scale, denitrification decreases the levels of NO3 in soil and slows leaching of this substance into groundwater. On the other hand, denitrification may lead to an increase in N2O, a “greenhouse gas” in the atmosphere and depletes nitrate from soil, which deprives plants and other microbes of this important nutrient. On a cellular scale, some bacteria reduce nitrate as a substitute for oxygen when they are in anoxic environments, and therefore, nitrate respiration can be a useful test for discriminating among bacterial species. This test is performed by subculturing bacteria to nitrate broth, a medium containing food and a source of nitrate available to serve as a final electron acceptor (as a substitute for oxygen for anaerobically respiring bacteria).
Nitrate reduction is demonstrated by adding chemicals that react with nitrite and noting development of a red color, which will occur if the bacteria reduced nitrate to nitrite. No color change after the chemicals are added might mean either the bacteria did not reduce the nitrate at all, or it may also mean the bacteria fully reduced the nitrate to N2 (denitrification). This can be discriminated by adding zinc to cultures that do not change color when the reagents were added. Electrons donated by zinc will subsequently reduce any nitrate remaining in the broth to nitrite, and the broth will become red—therefore a negative test. If the bacteria already reduced all the nitrate to forms other than nitrite, no color change will occur, and this is considered a positive test. A positive nitrate reduction test is indication of an anaerobic lifestyle.
Triple Sugar Iron is a slant medium with two growth environments: aerobic (on the slant) and anaerobic (in the “butt”). The medium contains three sugars in varying concentrations and a pH indicator that turns yellow at pH measurements below 6.8, and a deeper red at pH measurements above 8.2. Bacteria that ferment typically produce one or more types of acid as a byproduct, therefore, fermentation (both aerobic on the slant and anaerobic in the butt) is noted as a change in the color of the media. The medium also identifies strict aerobes that only grow on the slant surface, and also bacteria that produce H2S, either as a way to produce ATP anaerobically using sulfur or sulfate as a final electron acceptor, or as a result of the breakdown of proteins that contain high numbers of sulfur-containing amino acids (cysteine or methionine).
The results of this test are reported as appearance of the slant/appearance of the butt, using A to indicate acid reaction (yellow color), K to indicate an alkaline reaction, and NC to indicate no change in the medium. H2S (detected as a blackening in the media) and the production of gas (CO2) as a byproduct of fermentation are also reported if observed (see Figure 4).
As an example, and for practice, the interpretation and outcomes for the 4 TSI tests shown are provided in the table below. Note that many other possible reactions may also occur so proper interpretation of this test is important.
Table 1. TSI reactions shown in the cultures in Figure 4, from left to right.
Outcome Interpretation
Uninoculated control For color comparison with inoculated samples
K/NC Aerobic respiration (dark red on the slant) only. Bacteria are strict aerobes.
A/A; gas Fermentation of all three sugars with CO2 produced. Bacteria are facultative anaerobes.
K/A; H2S Aerobic respiration (dark red on slant), fermentation of glucose (acid only in butt), anaerobic respiration (black in butt). Bacteria are facultative anaerobes.
K/A Aerobic respiration (dark red on the slant); fermentation of glucose (acid only in butt). Bacteria are facultative anaerobes.
How would you interpret the outcome of the TSI slant, the appearance of which is described below?
Appearance Outcome and Interpretation
Slant is a dark red color, butt is yellow with noticeable cracking and bubbling.
After inoculation and test procedures have been demonstrated, perform these tests on the bacteria listed in the table, and record the outcomes below:
Bacterium Catalase Oxidase Nitrate Reduction TSI
Staphylococcus (aureus OR epidermidis)
Micrococcus luteus
Enterococcus faecalis
For each bacterium, determine if the test results provide evidence of aerobic or anaerobic respiration or fermentation, and indicate why you reached that conclusion. Then, based on your observations, state the logical growth category related to oxygen for each.
Staphylococcus ______________(write in species you tested)State what evidence from test results indicates the bacteria use this pathway. If there is no evidence, write “none.”
Aerobic respiration
Anaerobic respiration
Fermentation
Oxygen Growth Requirement Category______________________________________________
Micrococcus luteus State what evidence from test results indicates the bacteria use this pathway. If there is no evidence, write “none.”
Aerobic respiration
Anaerobic respiration
Fermentation
Oxygen Growth Requirement Category______________________________________________
Enterococcus faecalis State what evidence from test results indicates the bacteria use this pathway. If there is no evidence, write “none.”
Aerobic respiration
Anaerobic respiration
Fermentation
Oxygen Growth Requirement Category______________________________________________
Differentiating Among Bacterial Species Based on Phenotypic Characteristics
All of the “volunteer” bacteria used for this experiment are in Bergey’s Group 17 (Gram-positive cocci). From a medical perspective, some are considered primary or opportunistic pathogens, and others are nonpathogens. To distinguish among the cocci in this group, preliminary colonial and cellular characteristics along with growth patterns may be applied, as illustrated in the dichotomous key in Figure 5.
Differentiating amongStaphylococcusspp.
There are a large number of laboratory tests that facilitate differentiation among individual Staphylococcus spp. Cultures of three species of Staphylococcus have been provided. The following tests permit the differentiation of these species from one another. Note that an overnight incubation period is required for completion of these tests.
Coagulasetest for differentiating S. aureus from other staphylococci
Staphylococcusaureus is known to cause several types of disease in human in addition to foodborne illness. Staphylococcal food poisoning may result from ingesting food contaminated with either the bacteria or a heat-stable enterotoxin produced by the bacteria.
S. aureus differs from most other species of staphylococci on the basis of its ability to produce the enzyme coagulase, which induces blood clot formation, along with other cell surface antigens such as Protein A. Bound coagulase is referred to as “clumpingfactor.” Coagulase and clumping factor can be identified using lab tests, and in a clinical laboratory this test is done routinely when Gram positive, catalase positive cocci are isolated from clinical specimens.
Because of the clinical significance, commercial kits are available to detect coagulase activity in bacterial cultures. One such kit is Staphaurex, a rapid test for the detection of clumping factor and protein A associated with Staphylococcusaureus. The kit includes a solution of white beads coated with fibrinogen and IgG, and special reaction cards that make the clumping of the beads obvious. When mixed with the reagent, coagulase-positive staphylococci induce the beads to rapidly form large clumps, which are easily seen against the black background of the card. The degree of clumping has to be interpreted by the observer, and this will be demonstrated in lab.
MannitolSaltAgar: This is a selective medium for staphylococci and other halotolerant bacteria because the high concentration of salt (7.5%) inhibits the growth of bacteria susceptible to the effects of osmotic stress. In addition, the medium contains mannitol, which is a fermentable substrate for some bacteria, and phenol red as an indicator for acid. For those halotolerant bacteria that can grow on this medium, it is also possible to determine whether or not they ferment mannitol, by looking for a color change from red to yellow in the medium. The test is performed by streaking the bacteria over the surface of an MSA plate and incubating. Positive (left side) and negative (right side) results for mannitol fermentation are shown on the MSA plate in Figure 6.
Hemolysis: Some bacteria are known to produce enzymes that break down phospholipids and cause the cell membranes of red blood cells to rupture. Hemolytic bacteria then scavenge the hemoglobin released from the cell, typically to utilize the iron or other “growth factors” from inside the cell. Hemolysis can be observed by streaking bacteria across the surface of a Blood Agar Plate (BAP), which contains intact red blood cells. The BAP plate shown in Figure 7 is an illustration of β-hemolysis (beta hemolysis), seen as a clear area around the bacterial colonies.
Figure 7 shows a BAP plate with colonies that are non-hemolytic. This is referred to as γ-hemolysis (gamma hemolysis). Not shown is a pattern of hemolysis called α-hemolysis (alpha hemolysis), which is not really a true lysis in that the red blood cell membrane is not ruptured, but merely “bruised.” The hemoglobin, which mostly remains in the cell, is reduced to methemoglobin, which is a green color that can be seen surrounding the colonies growing on the BAP.
Urease: Many bacteria have the ability to hydrolyze urea, and some can do it more quickly than others. The enzyme urease is needed, which hydrolyzes urea to ammonia (a basic substance) and CO2. Urease broth contains two buffers—urea, a tiny amount of food, and phenol red. This test is performed by inoculating bacteria into urease broth and incubating. If they produce urease rapidly, the urea in the broth is hydrolyzed and ammonia raises the pH of the broth. This process is detected by the pH indicator which turns deep pink, which is interpreted as a positive test. A positive (left tube) and a negative (right tube) urease test result are shown in Figure 9.
Obtain cultures of three species of Staphylococcus. Then, perform each of the tests above and record the outcomes in the table below, including both what the result looks like (color change, clear area around growth, etc.) and the interpretation of the outcome (positive, hemolysis, etc.). Note that these tests all require that the bacteria be incubated before the test can be completed.
Test S. aureus S. epidermidis S. saprophyticus
Coagulase by Staphaurex
Mannitol fermentation
Hemolysis
Urease
From the results of the tests you performed on the three Staphylococcus spp., develop a dichotomous key (in the blank space below) that demonstrates how these tests can be applied to distinguish among the three species of Staphylococcus you tested:
Differentiating among streptococcal species
Chain-forming cocci (streptococci) are common members of the mammalian microbiota and sometimes cause disease. Many species inhabit the oral cavity and upper respiratory tract, while others are found in the GI tract. Philosophically, these two diverse habitats prompted taxonomists to split the GI dwelling streptococci into a separate genus, Enterococcus. Those species that inhabit the mouth remain in the genus Streptococcus. Streptococci in general are aerotolerant anaerobes, and can be distinguished from other types of Gram-positive cocci based on their negative response to the catalase test.
Bacteria in these two genera have many common characteristics. Because of their habitat, enterococci are tolerant to higher concentrations of bile. Bile is a yellow-green compound made up of bile acids, cholesterol, phospholipids, and the pigment biliverdin. It is produced in the liver, concentrated and stored in the gallbladder, and released into the duodenum after food is eaten, where it functions as a biological detergent that emulsifies and solubilizes lipids to help in fat digestion. The detergent action of bile also confers a potent antimicrobial activity. Thus, to survive in such an environment, the enterococci not only withstand the antimicrobial effects of bile, but also play a role in secondary bile metabolism in their host.
Bile Esculin Agar is a medium used to isolate and identify enterococci. This medium contains bile salts, which makes it selective for the bile tolerant enterococci, and esculin, which is an organic compound that some of the enterococci are able to chemically break down to glucose and esculetin. The latter substance combines with ferric ions in the medium, and form a complex which turns the both the colonies and the surrounding medium brownish black.
In a clinical laboratory, the medically important streptococci are identified by serological typing into Lancefield groups, which correlate to types of hemolysis observed when the bacteria are grown on Blood Agar Plates. The Group A streptococci, such as the pathogenic Streptococcuspyogenes, are β-hemolytic, while the Group D enterococci are typically non-hemolytic (γ-hemolysis).
Once the procedure has been demonstrated, subculture the two bacteria below to a Blood Agar Plate and Bile Esculin Agar plate and after incubation, observe the differences between them. Record the results below.
Bile Esculin Agar Hemolysis on Blood Agar
Streptococcus pyogenes
Enterococcus faecalis
On a separate sheet of paper below, construct a dichotomous key to show how the tests you performed may be used to distinguish among the different cocci we experimented with in this lab.
Table 2. Summary of Test Methods.
Test Method
Catalase Transfer bacteria to slide and add H2O2; observe for bubbles.
Oxidase Smear bacteria to DrySlide oxidase card; watch for color change that occurs WITHIN 20 SECONDS.
Nitrate Reduction Transfer 2 ml of Nitrate broth to a sterile culture tube, inoculate with bacteria and incubate. After incubation, add Nitrate A and B reagents – red is positive. IF NO CHANGE, add zinc. Red after zinc confirms negative result.
TSI Stab butt and streak slant of TSI slant; incubate.
Coagulase Place a drop of Staphaurex reagent in a circle on the test card. Add bacteria to the drop and mix; then rock the card.
Mannitol Salt Agar Inoculate MSA plate and incubate.
Hemolysis on Blood Agar Inoculate Blood Agar plate and incubate
Urease Transfer 2 ml of Urease broth to a sterile culture tube; inoculate with bacteria and incubate.
Bile Esculin Inoculate BE plate and incubate. | textbooks/bio/Microbiology/Microbiology%3A_A_Laboratory_Experience_(Ahern)/01%3A_Chapters/1.06%3A_Metabolism_Physiology_and_Growth_Characteristics_of_Cocci.txt |
The Diversity of Bacilli
Previously, we studied the colonial, cellular, and chemical characteristics of a group of bacteria that had a common cellular morphology (they were cocci), but were quite diverse metabolically. To continue the investigation, we will use a similar approach to examine the cellular and metabolic characteristics of a second group of bacteria, this time all bacilli.
Bacilli show great diversity at the cellular level, beginning with the overall size and shape of the cells themselves. Some bacilli are short and plump little rods, while others are extremely slender and long. Curved and spiral shapes are common. A few species of bacilli produce endospores or other types of cellular inclusion bodies, such as metachromatic granules and parasporal crystals.
BergeysManual initially divides the bacilli according to Gram stain reaction. Gram positive bacilli are further subdivided according to whether they form endospores, have filamentous growth or hyphae, and if they are acid-fast. Gram-negative bacilli are typically distinguished by size, shape, motility, and oxygen growth categories.
The group of bacteria included in this lab includes both Gram positive and Gram negative species. Using previous methods and additional tests, we will develop profiles of the bacilli as a way to distinguish among the various species.
Once again, although they are morphologically similar, the bacteria who have “volunteered” for this week’s lab differ in many ways and can be distinguished from each other by observing morphological and physiological characteristics. And like last week, we will begin by observing colonial and cellular morphology.
Morphological Evaluation of Bacterial Isolates
The bacteria we will examine in this lab include both Gram positive and Gram negative species of bacilli, each in a different genus. Observable differences start at the cellular level.
A volunteer from your lab bench should obtain cultures from your instructor, who will provide you with the species names. Write the name and BSL for each of the cultures below:
_________________________________________________________________
_________________________________________________________________
_________________________________________________________________
_________________________________________________________________
Colonial morphology
Distinguishing among bacterial species begins with examining colonial morphology, which you will do using the cultures listed below:
Bacterium Colonial Morphology
Bacillus_____________________
(write in Species name)
Corynebacterium______________
(write in Species name)
Pseudomonas aeruginosa
Gram stain and cellular morphology
Among the bacteria in this group, there are significant observable differences in cellular morphology that can be observed by staining the cells, beginning with the Gram stain. For each culture listed, Gram stain a smear you prepare, and record the Gram stain reaction, cellular morphology, and arrangement. Also if you observe any other cellular features, specifically endospores or inclusion bodies in the Gram stained smear, include those observations in your description as well.
Bacterium Gram stain results
Bacillus _____________________ (write in Species name)
Corynebacterium _____________
(Write in Species name)
Pseudomonas aeruginosa
A major distinction among Gram positive bacilli is the production of endospores, which can be observed by endospore staining. For the two Gram positive species of bacteria, prepare a second smear and stain it using the endospore stain method. If endospores are observed, report the shape and location.
Bacterium Endospores present? (if yes, describe)
Bacillus______________________ (write in Species name)
Corynebacterium______________ (write in Species name)
Physiology and growth characteristics
As previously done with the cultures of cocci, evaluate energy metabolism and physiological oxygen requirements for the bacteria in the table below by performing the catalase, oxidase, Triple Sugar Iron (TSI), and nitrate reduction tests.
Bacterium
Catalase
Oxidase
Nitrate Reduction
TSI
Bacillus __________________
(write in Species name)
Pseudomonas aeruginosa
Salmonella________________
(write in Species name)
From the outcome of the tests above, determine if there is evidence of aerobic or anaerobic respiration or fermentation, and indicate why you reached that conclusion.
Bacillus ________________ State what evidence from test results indicates the bacteria use this pathway. If there is no evidence, write “none.”
Aerobic respiration
Anaerobic respiration
Fermentation
Oxygen Growth Requirement Category____________________________________________
Pseudomonas aeruginosa State what evidence from test results indicates the bacteria use this pathway. If there is no evidence, write “none.”
Aerobic respiration
Anaerobic respiration
Fermentation
Oxygen Growth Requirement Category____________________________________________
Salmonella _____________ State what evidence from test results indicates the bacteria use this pathway. If there is no evidence, write “none.”
Aerobic respiration
Anaerobic respiration
Fermentation
Oxygen Growth Requirement Category____________________________________________
Differentiating Among Bacterial Species
In a clinical laboratory, differentiating the nonpathogenic microbiota found in the GI tract from pathogenic species has historically relied on phenotypic tests. The small and large intestines are home to the largest number of bacterial species, which contribute greatly to human health and disease. Generally, Gram positive cocci and bacilli are considered “probiotic” because of the health promoting benefits associated with these bacteria, while Gram negative species are commensals that can induce inflammation if their proliferation is not kept in check.
Many of the Gram negative bacteria residing in the GI tract are members of the Family Enterobacteriaceae. Bacteria in this family are facultative anaerobes that are usually oxidase-negative and ferment glucose, which distinguishes them from aerobic species of Gram negative rods. To differentiate among them, a set of tests with the acronym IMViC, which stands for: Indole, Methyl red, Voges-Proskauer, and Citrate (with the lower-case “I” thrown in to make it easier to say). The TSI and urease tests and others may also be performed at the same time to improve the identification process.
Examples of IMViC results for some of the Enterobacteriaceae, which illustrate how these tests can be used to differentiate among the bacteria in this group, are given in Table 1. As evidenced by the results shown for the two species of Proteus, metabolic differences may even exist among individual species within the same bacterial genus.
Table 1
Species Indole Methyl Red Voges-Proskauer Citrate
Escherichiacoli Positive Positive Negative Negative
Shigella spp. Negative Positive Negative Negative
Klebsiella spp. Negative Negative Positive Positive
Proteusvulgaris Positive Positive Negative Negative
Proteus mirabilis Negative Positive Negative Positive
Sulfide–Indole–Motility(SIM)
This is another medium in which a number of different reactions may occur. In fact, this medium is used to determine if (1) the bacterium reduces sulfate and produces H2S, which is evidence of anaerobic respiration; (2) the culture oxidizes the amino acid tryptophan and produces indole, and (3) the bacterium is motile. The medium contains sulfur (as the oxidizing agent) and ferrous ions (for H2S detection), tryptophan (for indole detection), and is prepared in tubes referred to as stabs or deeps (because they are not slanted). The medium also has a lower concentration of agar and is semi-solid, to detect bacterial motility. Bacteria are inoculated in this medium with an inoculating needle (as opposed to a loop) and stabbing the bacteria deep into the soft agar.
After incubation, a positive test for sulfide turns the media black, just as for the TSI test. Tryptophan oxidation by the bacteria yields indole, which can be detected by adding a reactive chemical, which turns deep pink. Motility, which may be the hardest to determine, is noted by looking closely at the stab line. Motile bacteria swim through the semi-solid agar and the medium appears cloudy, obscuring the stab line. If the bacteria are not motile, the stab line is clearly visible. The outcomes for all three tests (sulfide, indole, and motility) should be noted. Figure 1 shows three SIM tubes, each showing different outcomes for the three tests. From left to right, the results are:
1. Sulfide negative, Indole negative, Motility positive
2. Sulfide negative, Indole positive, Motility positive
3. Sulfide positive, Indole negative, and Motility positive
How would you interpret the results for the bacteria inoculated in the SIM medium shown below?
Sulfide: _____________________________________
Indole: ______________________________________
Motility: _____________________________________
Methyl Red and Voges-Proskauer (MR-VP)
Fermentation of glucose by bacteria may produce one or more acids or alcohols. Probiotic lactic acid (homolactic) bacteria produce lactic acid as the major end product. Other fermentation pathways yield a combination of acids and/or alcohols. The organic end products of these pathways can be detected using chemical methods. The medium used for these tests, MR-VP broth is the same for both tests. The broth contains glucose as a fermentable substrate, and the end products are measured after incubation.
Methyl Red (MR)
Bacteria utilizing a mixed acid fermentation produce stable organic acid end products. After the bacteria grow, the pH indicator methyl red (which is red below pH 4) is added to the culture. If the broth is red after methyl red is added, the result is considered a positive test. For bacteria that produce alcohols and other less acidic metabolites, the indicator (and therefore the medium) turns orange to yellow, which is a negative result (see Figure 2a)
Voges-Proskauer (VP)
Some bacteria use a butanediol fermentation pathway when glucose is the fermented substrate. The end products of this type of fermentation include a variety of both acidic and non-acidic end products, including ethanol, butanediol, and acetoin. If acetoin is present, chemical reagents added to the broth will react with it and form a reddish-brown colored compound, which is considered a positive test result (see Figure 2b).
Citrate utilization
Some bacteria have an enzyme (citrate permease) that facilitates the transport of citric acid into the cell, and another enzyme, citrase, for citrate catabolism. These bacteria have the ability to grow on a medium (Simmons’ citrate agar) that contains nothing more than citric acid, the first intermediate in the Krebs cycle of aerobic respiration, as a food source. Metabolism of citric acid releases carbon dioxide, which reacts with sodium and water in the medium to form a compound with a basic (alkaline) pH. In the presence of a base, the pH indicator in the medium (bromothymol blue) changes color from green to blue, which is a positive result for this test. The Simmons’ citrate agar plate shown in Figure 3 illustrates both a positive (on the left) and negative (on the right) result for this test.
Table 2. Summary of Test Methods
Test Method
SIM With an inoculating loop, stab culture to the bottom of a SIM deep tube; incubate. AFTER INCUBATION, add 5 drops of indole (Kovac’s) reagent and observe for deep red color.
Methyl Red (MR) Transfer 2 ml of MR-VP broth to a sterile culture tube and inoculate with bacteria; incubate. AFTER INCUBATION, add 5 drops of methyl red reagent and observe for red color.
Voges–Proskauer (VP) Transfer 2 ml of MR-VP broth to a sterile culture tube and inoculate with bacteria; incubate. AFTER INCUBATION, add 5-10 drops of Reagent A followed by 5-10 drops of Reagent B. Allow the tube to sit for at least 20 minutes and observe for red color.
Citrate Inoculate the surface of a Simmons’ citrate agar plate and incubate. Observe for blue color change.
After the tests have been demonstrated, perform them on the four Enterobacteriaceae listed in the table below.
Species Indole Methyl Red Voges-Proskauer Citrate
Escherichia coli
Salmonella spp.
Citrobacter freundeii
Enterobacter aerogenes
Construction of a dichotomous key to differentiate among this group of bacteria
In the space below, construct a dichotomous key to show how the tests you performed may be used to identify ALL of the different bacilli we used in this lab. | textbooks/bio/Microbiology/Microbiology%3A_A_Laboratory_Experience_(Ahern)/01%3A_Chapters/1.07%3A_Metabolism_Physiology_and_Growth_Characteristics_of_Bacilli.txt |
Testing for Bacterial Contamination of Food
Bacteria are incredibly diverse and abundantly found in most of the natural world. The majority are beneficial to us in ways we may not fully realize or appreciate. A few, however, are not and will cause disease when we cross paths with them. Pathogenic (harm-causing) and potentially pathogenic bacteria may be found in unexpected places, such as in the food we eat, the water we drink or use for recreation, in soil, on surfaces in your home, and elsewhere.
Unfortunately for us, the things we eat and drink are fairly common vehicles for disease transmission. And, because food and drink pass through our digestive tract, the most common symptoms of a foodborne disease are abdominal discomfort or pain, nausea, diarrhea, and/or vomiting. Gastrointestinal illnesses caused by foodborne microbes range in severity from mild to extremely debilitating, even fatal. The biological agents responsible for this type of disease may be viruses, bacteria, fungi, protozoa, or helminthes.
To protect the public from disease, manufacturers and distributors of food consumed in the United States must prove that their food is pathogen-free before it can be offered for sale. Regulatory agencies at the local, state and federal levels (such as the Department of Agriculture and the Food and Drug Administration) require routine bacteriological testing to protect the public from acquiring a foodborne illness. Although many types of microbes may cause foodborne disease, the CDC and FDA currently considers the bacteria Bacillus cereus, Campylobacter jejuni, Clostridium spp., pathogenic strains of Escherichia coli, Listeriamonocytogenes, Salmonella spp., Shigella spp., Staphylococcus aureus, Vibrio spp., and Yersinia spp.; the parasites Cryptosporidium and Cyclospora; and the Norwalk virus (norovirus) (http://www.cdc.gov/foodnet/index.html) to be the most common and of the greatest concern in the United States.
Although there are “rapid” methods available to detect bacterial contaminants in food that rely on DNA and antibody testing, plating samples on differential and selective culture media is a tried and true method. The disadvantage is that culture methods take more time, but the advantages include the simplicity of the tests and a higher level of both specificity and sensitivity.
The relatively low number of bacteria present in a food sample limits the sensitivity of all of the various types of tests available to evaluate food safety, including those based on culture. A preliminary step called enrichment culture may be used to amplify the number of bacterial pathogens, by pre-incubating the food sample in a non-selective medium that promotes growth of any bacteria that might be in the sample.
Many standard methods include a two-stage enrichment culture. The first step, or pre-enrichment, involves adding a specific amount (determined by weight, typically 10–25 grams) of the food to be tested in a large (100–250 ml) volume of a non-selective broth medium. After an incubation period of 18–24 hours at 37°C, a small sample of the enrichment culture is transferred to one or more types of selective media designed to inhibit growth of competing microbes while allowing the target pathogen to multiply. Many such formulations are also differential, in that growth of the bacterial target will cause a characteristic chemical change in the appearance of the medium, thus “differentiating” the pathogen from other possible contaminants, such as spoilage organisms, that might also be in the food.
We will be conducting our own investigation of food safety using a modified and scaled down adaptation of the standard laboratory methods, beginning with a pre-enrichment culture of food samples, followed by plated on several types of selective and differential media. Our determination of food contamination will be based on (a) growth of bacteria on the selective media and (b) observation of a specific biochemical reaction (usually a color change) characteristic for a particular type of pathogen. Note that these methods are based on bacterial phenotypes (traits), and more than one species of bacteria may have the same selective/differential traits. Therefore, definitive identification of a bacterium isolated from food requires additional testing.
Numerous media formulations are available that permit the isolation and identification of pathogenic bacteria in food. Using the media described in Table 1, we will be testing food for contamination with EHEC (enterohemorrhagic E. coli) and other strains of E. coli, S. aureus, B. cereus, Salmonella, and Shigella.
Table 1
Medium Selective Agent(s) Differential Agent(s) Detection
MacConkey Agar
(MAC)
Bile salts and crystal violet inhibits the growth of most Gram positive, non-enteric bacteria. Lactose and pH indicator Gram negative enteric bacilli will grow; E. coli will produce pink colonies, Salmonella and Shigella spp. do not ferment lactose and colonies are colorless.
Sorbitol MacConkey Agar
(SMAC)
Bile salts and crystal violet inhibits the growth of most Gram positive, non-enteric bacteria. Sorbitol and pH indicator Gram negative enteric bacilli will grow; E. coli 0157:H7 does not ferment sorbitol and colonies are colorless
Mannitol Salt Agar
(MSA
7.5% sodium chloride inhibits the growth of most Gram negative bacteria Mannitol and pH indicator Salt tolerant bacteria grow; S. aureus ferments mannitol and colonies are yellow; B. cereus does not ferment mannitol and colonies are deep red.
Pre-enrichment to Promote Bacterial Growth
Note: this will require time in addition to your regular lab period to complete. Because both the presence and type of bacteria that may be in the food is unknown, BSL2 containment practices should be used throughout the entire procedure.
Samples of foods will be available in the laboratory up to a week before your scheduled lab period.
Transfer 5 ml of Tryptic Soy Broth to a disposable plastic culture tube. You should select one food sample for testing. Prepare an enrichment culture of the selected food item, by transferring a small amount of the food to the broth in the culture tube, using aseptic technique. Place a cap on the tube, mix the contents fully, and place in the incubator at 37°C.
A minimum of 18 hours after starting the enrichment culture (one day after the enrichment culture is started is preferred), and no later than the day before the scheduled period for this investigation, return to the lab, and use an inoculating loop to subculture samples from the enrichment culture to each of the three types of selective and differential media described in Table 1. Use the streak plate method for all of the plates, so isolated colonies will form. Appropriately dispose of the enrichment culture as a potential biohazard.
Return the streak plates to the incubator for observation and further investigation during the lab period.
Food sample tested _____________________________________________________________
Cooked or raw? ________________________________________________________________
How was this food item stored before testing? ________________________________________
Medium Growth on medium? (yes or no) Appearance of colonies/medium if growth occurred
MacConkey Agar (MAC)
Sorbitol MacConkey Agar (SMAC)
Mannitol Salt Agar (MSA)
For each of the selective and differential media on which bacterial colonies are observed, indicate what the appearance of the colonies indicates in terms of the possible type(s) of bacteria present in the food sample.
Medium Observations that indicate contamination of food sample with potential food borne pathogens
MacConkey Agar (MAC)
Sorbitol MacConkey Agar (SMAC)
Mannitol Salt Agar (MSA)
The growth and appearance of colonies on selective and differential media is an indicator of the presence of specific bacterial pathogens, but these results must be confirmed before reporting that food is contaminated and ingestion may initiate a foodborne disease. Therefore, perform additional tests to confirm that the colonies observed on the selective media are potentially pathogenic bacteria. These tests include:
• Gram stain of representative colonies (all)
• Coagulase test to confirm Staphylococcus aureus (S. aureus is coagulase +)
• Colonial morphology and endospore stain to confirm Bacillus cereus
• TSI test to confirm E. coli, Salmonella, and Shigella
Expected and Experimental Results
For each bacterium, indicate the EXPECTED outcome of the Gram and Endospore stains and TSI tests which would confirm the identity of the potential foodborne pathogen.
Expected Gram stain reactions:
E. coli ______________________ Salmonella spp. _____________________
S. aureus ___________________ Shigella spp. ________________________
B. cereus ___________________
Expected Endospore stain reactions:
B. cereus ________________________________________
Expected TSI reactions:
E. coli ________________ Salmonella spp. _______________ Shigella spp. _______________
For each type of colony found growing on the various types of selective and differential media, perform the appropriate confirmatory (or indicatory) tests, and record those results in the results table.
Results of Confirmatory Tests
Potential Pathogen Found on which medium? Additional test(s) Outcome of test(s) Present in Food Sample?
E. coli
E. coli 0157:H7
S. aureus
B. cereus
Salmonella spp.
Shigella spp.
Once you know whether the pathogens we tested for in the lab were present in the food sample you tested, compare your results with those of others in your lab who tested other types of food.
Approximately how many of the food samples that were tested by your lab group were contaminated with one or more of these bacteria? List the foods with contaminants below:
_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
Reflect on the significance of the outcome of this investigation, and write your thoughts below. Before the class ends you may be asked to share your reflection as part of a larger discussion on what it means to find bacteria (pathogenic or otherwise) in food you might eat.
_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________ | textbooks/bio/Microbiology/Microbiology%3A_A_Laboratory_Experience_(Ahern)/01%3A_Chapters/1.08%3A_Microbiological_Food_Safety.txt |
Kill Them Before They Kill You!
Since the Golden Age of microbiology, when the connections between bacteria and disease were first revealed and Semmelweis started washing his hands, Pasteur postulated the Germ Theory, and Lister promoted aseptic surgery, we have become obsessed with destroying microbes. As a result, companies that make products to “kill” microbes—whether to have a cleaner home or to cure bacterial infections—make a killing off of us as we rush to acknowledge the effectiveness of marketing campaigns that tell tales about “evil germs” that must be “killed on contact.”
In reality, promoting the need for humans to live in a germ-free world is misguided and in some cases perhaps even dangerous. The overwhelmingly beneficial nature of our microbiome and its metagenome is now well established. Overuse of personal and environmental hygiene products and antibiotics has resulted in the logical evolution of bacterial resistance to them. As Friedrich Nietzsche (and Kelly Clarkson) famously said, “That which does not kill us makes us stronger.” This certainly bears true for bacteria. Some bacterial pathogens are now resistant to every type of antibiotic available. Bacteria acquire antibiotic resistance through mutation and natural selection, and once such traits are acquired, they are shared with other bacteria by horizontal gene transfer. Infectious diseases once thought defeated, such as tuberculosis and pneumonia, are again climbing the ranks on the mortality charts.
We are destined to live in a microbial world. Prudent use of antimicrobial products is a necessity, particularly in healthcare settings where sanitation practices and infection control are essential. Available are a large number of chemical and physical agents that are used for sterilization (killing or removal of all microorganisms) and disinfection (reducing the numbers of microorganisms) that are widely used to control microbial growth. But how do you know if they work?
Chemicals used to kill microbes damage cell components through chemical reactions with proteins, membranes, or other parts of bacterial cells. Heat, cold, and radiation are physical agents that inhibit or inactivate microbes in food, on surfaces, and even in the air. Bacteria exhibit a wide range of susceptibilities to these agents. For example, Gram-positive bacteria can withstand higher heat and more radiation, while Gram-negative bacteria tend to be more resistant to chemical destruction. Microbial susceptibility to antibiotics varies widely.
Selective removal of pathogenic microbes that spares or minimally damages body cells has long been the goal of medicine. Paul Ehrlich was searching for just such a “magic bullet” when he found the first real antibiotic, the arsenic-based compound Salvarsan for treatment of syphilis, in 1910. Now we realize there can be no magic bullet, because to one extent or another, antibiotics wreak havoc on our bacterial symbionts as much as the targeted pathogen, and those bacteria are as much a part of us as are our own cells.
Some antibiotics are effective against a narrow spectrum (or range) of bacteria, such as the antibiotic isoniazid which is only used to treat infections caused by mycobacteria. Broad spectrum antibiotics work against a wide range of taxonomic groups. In medicine, the preferred approach is to minimize damage to the microbiota by applying a narrow spectrum drug first, which also decreases the risk of promoting antibiotic resistance. Testing pathogen susceptibility to several types of antibiotics while the bacteria grow in culture is the preferred way to evaluate which to use for chemotherapy of the infection.
Several culture-based methods have been developed for this purpose. One of the most widely used methods is the disk diffusion test, used to assess the antimicrobial activity of chemical agents. The Kirby-Bauer assay, used in clinical laboratories to evaluate which antibiotics are effective against a bacterial pathogen, is a standardized form of disk diffusion test that follows a strict protocol (e.g. type of medium used, temperature and time of incubation) so the results can be compared across labs.
Kirby-Bauer Disk Diffusion Assay for Antimicrobial Susceptibility
After the widespread use of antibiotics began in the 1950s, one of the first observations made was that they didn’t work for every infection. Thus test methods to evaluate susceptibility were developed. The earliest versions were based on broth dilution methods, which although very useful for determining the level of susceptibility to various concentrations of the drug, were time and labor-intensive to perform. And so the disk diffusion method was developed.
The disk diffusion method was widely adopted as the standard method for antimicrobial testing by clinical labs in the US by the end of the 1950s. Basic procedures were modified to suit the locally available resources and expertise, and interpretation of results began to vary widely by lab.
Kirby and colleagues (including Bauer) were the first to propose that standardization of the method was necessary for uniformity across labs, and developed the method that still bears their names: the Kirby-Bauer assay.
Of major importance to the success of this method is to inoculate test plates with approximately the same number of bacterial cells each time the test is performed. A relatively simple way to achieve a uniform number of cells in the inoculum is to first prepare suspensions of bacterial cells in sterile saline, which may then be compared, either using an instrument such as a spectrophotometer or by direct visual comparison, to an optical standard matching a known concentration of bacteria. Typically a 0.5 McFarland standard is used. This is equivalent to a bacterial suspension containing between 1 x 108 and 2 x 108 CFU/ml of E. coli.
Standardized cell suspensions are then inoculated onto the surface of a specific type of medium using a sterile swab. The plates are inoculated to completely cover the surface of the medium with bacterial cells, which then grow into a lush “lawn” of colonies. Once the lawn is “seeded,” a filter paper disk saturated with the antibiotic is placed on the lawn. The antibiotic diffuses into the medium at the same time that the bacteria are trying to grow. If the bacteria are susceptible, an area of clearing called the “zone of inhibition” will be seen in the lawn surrounding the disks at the end of the incubation period. The definition of susceptibility and resistance varies with the type of test—either the bacteria are observed to grow right up to the edge of the antibiotic disk, or a small zone of inhibition that falls within a measured size range is seen. The agar plate in Figure 1 shows variations in the size of the zones of inhibition for four antibacterial chemicals. For the Kirby-Bauer assay, the size of each zone must be carefully measured.
As demonstrated, prepare suspensions in sterile saline to match a 0.5 McFarland standard using the bacteria listed below. For each, also indicate if they are Gram-positive or Gram-negative.
Escherichia coli ___________________________________
Staphylococcus aureus ___________________________________
Pseudomonas aeruginosa _________________________________
Once made, the three standardized suspensions of these bacteria will be used again later in this lab, so do not immediately discard them.
For uniformity across labs, the same type of medium must be used by each lab. The standard method calls for Mueller-Hinton agar (MHA) plates, which is a special formulation prepared with a lower concentration of agar at a specific pH to facilitate diffusion of the antibiotics into the medium.
Obtain three MHA plates, and as demonstrated, inoculate each with one of the bacteria listed above, using a sterile swab soaked in the corresponding bacterial suspension.
Using forceps sterilized in alcohol, place one disk of each antibiotic to be tested on all three of the inoculated plates, far enough away from each other so that the potential zones of inhibition will not overlap.
The standard method calls for the plates to be incubated at a temperature range of 35°C ± 2°C for 18–24 hours. This may be modified to accommodate your laboratory schedule, as directed by your instructor. Make a note of the time and temperature for incubation if it is a modification of the standard method, below:
Incubation time and temperature: ____________________________________
The four antibiotics we will be testing have different cellular targets, and therefore bacterial responses to them will vary. The bacterial cell wall is often a target of disruption for antibiotics. Two of the bacteria above have the same Gram stain reaction, but Pseudomonas spp. generally have a broader range of resistance than other types of bacteria. Research, and then below, list two strategies employed by pseudomonad bacteria to resist destruction by antibiotics:
__________________________________________________________________________
__________________________________________________________________________
__________________________________________________________________________
__________________________________________________________________________
__________________________________________________________________________
Complete the table below with the mechanism of action for each of the antibiotics we’ll be testing. Also, use a website such as Drugs.com or Rxlist.com to research the medical use (indications for use) for the antibiotic, and include that information in the table.
Antibiotic Bacterial cell target/ Mechanism of action Indications for use Contraindications for use (including side effects)
Cefixime (Suprax)
Tetracycline (Panmycin)
Azithromycin (Zithromax)
Ciprofloxacin (Cipro)
After incubation, look for zones of inhibition around each disk in all three lawns. If a zone is observed, measure the diameter in mm using a metric ruler and record the measurement in the table below. Using the table of standard values (Table 1), compare the measured size of the ZOI and determine if the zone size indicates the bacteria are resistant, susceptible, or have an intermediate susceptibility to each of the antibiotics.
E. coli S. aureus P. aeruginosa
Antibiotic ZOI in mm Result ZOI in mm Result ZOI in mm Result
Cefixime
Tetracycline
Azithromycin
Ciprofloxacin
Based on what you learned about each antibiotic in terms of its medical uses and patterns of susceptibility, consider which of the four antibiotics tests you would prescribe for the following types of infections, if you were the medical professional in charge of the case:
A urinary tract infection (UTI) caused by E. coli
A wound infection caused by S. aureus ____________________________________________
A respiratory tract infection caused by P. aeruginosa __________________________________
Using the Disk Diffusion Method to Test Chemicals for Antibacterial Action
The basic principles of the Kirby-Bauer method can also be applied to investigate the antimicrobial properties of solutions with known or suspected actions against bacteria.
Disinfectants and antiseptics are chemicals used for microbial control in many settings. As with antibiotics, microorganisms differ substantially in their susceptibility to the chemical agents we use to reduce the number of microbes on inanimate surfaces (disinfectants) or living tissues (antiseptics). To evaluate their potency, effectiveness is compared to that of a standard disinfectant such as phenol, which was the chemical first used and endorsed by Joseph Lister for aseptic surgery. This type of comparison can be done using broth dilution methods, but may also be accomplished by disk diffusion assay, in which the effectiveness of a particular chemical agent is assessed in a direct comparison of the size of the zone of inhibition to a positive control like phenol, which has a known and powerful antibacterial effect.
Obtain three MHA plates and label each plate with the name of one of the test bacteria (E. coli, S. aureus, and P. aeruginosa). Using the 0.5 McFarland-adjusted cell suspensions made previously, prepare lawns of the three bacteria on the surface of the MHA plates.
Available in lab will be several samples of chemicals with known or suspected antimicrobial properties. Choose three that you would like to investigate, and list your choices below. If the agent is a commercial product, also list the “active ingredient” from the label of the product. Also, record the positive control you will be comparing your selections against, according to your instructor.
Chemical Agent Active Ingredient (if known)
Positive Control Active Ingredient
On the bottom of the Petri dish holding the bacterial lawns, use a marker to draw intersecting lines that divide the plate into four sections. Label one section (+) to represent the positive control. Label the three other sections with the name or abbreviation of the test chemicals you selected.
Using forceps sterilized in alcohol, remove a sterile filter paper blank disk from its container and soak it in the positive control solution. Remove it from the solution and allow the excess liquid to drip back into the container. Place the soaked disk in the center of the appropriately labeled section on one of the plates, and then repeat the process for the other two plates.
Once the positive control disks have been placed, soak blank disks in the test solutions you chose and place them on the three lawns. Use the same three test solutions on each of the lawns.
Incubate the plates (overnight at 37°C is preferred). After the incubation period, examine the disks in the lawns for a zone of inhibition. Measure the diameter of the ZOI for the positive control first, as this is the standard by which you will be assessing the effectiveness of the test solutions. Record your results in the table below.
Solutions tested (write name) E. coli S. aureus Ps. aeruginosa
Pos. control _______________________
Test 1 _________________________
Test 2 _________________________
Test 3 _________________________
List the chemical agents you tested that were at least as effective against each bacterium as the positive control:
Bacteria Effective test chemicals
E. coli ____________________________________________
S. aureus ____________________________________________
P. aeruginosa ____________________________________________
Of the chemical agents you tested, which one shows the greatest overall range of antibacterial action?
__________________________________________________________________________
__________________________________________________________________________
Which bacteria showed the greatest degree of resistance to the chemical agents tested?
__________________________________________________________________________
Were any of the results a “surprise” to you (for example, perhaps something you thought would be a good disinfectant was not, or one of the natural products tested was more effective than predicted?). Reflect below, and you may be asked to share your thoughts on this during a discussion of the results.
__________________________________________________________________________
__________________________________________________________________________
__________________________________________________________________________
__________________________________________________________________________
__________________________________________________________________________
Using Antibiotic Susceptibility for Bacterial ID
Browsing through Bergey’s Manual reveals that susceptibility or resistance to various antibiotics can be useful when it comes to discriminating between bacterial species. Two examples are the novobiocin resistance test for Staphylococcus spp. and the “Taxo A” or the bacitracin susceptibility test for Streptococcus spp.
Novobiocin resistance test
This test was originally developed as a test to identify S. saprophyticus, which is a coagulase-negative staphylococci and the second most common cause of urinary tract infections (after E. coli). After the procedure has been demonstrated, perform the test using the cultures of Staphylococcus aureus and Staphylococcus saprophyticus provided.
Prepare standardized suspensions of S. aureus and S. saprophyticus, by transferring 2 ml of sterile saline to a culture tube, then adding colonies until the turbidity (cloudiness) in the solution matches that of a 0.5 McFarland optical standard.
Obtain one Mueller-Hinton agar (MHA) plate, and on the bottom of the Petri dish, draw a line with a marker to divide the plate in half. Label each half with the name of one of the two staphylococci.
Soak a sterile swab in one of the bacterial suspensions, and transfer it to the appropriately labeled side of the divided plate. Spread the suspension to create a confluent layer of bacterial cells which will grow into a lawn of bacterial colonies. Repeat the process with the other bacterial suspension on the other half of the plate.
With forceps sterilized in alcohol, place one novobiocin disk (5 µg) in each of the two lawns. Incubate the plate for a minimum of 24 hours. After incubation, examine the lawn around each disk. If a zone of inhibition is noted, measure the diameter of the zone with a metric ruler, in mm. For this test, bacteria are considered positive for novobiocin resistance if there is no zone of inhibition, or if the zone size is less than 12 mm. Susceptibility is a negative test. Record your results below.
Bacteria ZOI diameter (mm) Susceptible or Resistant? Positive or Negative outcome
S. aureus
S. saprophyticus
Table 1. Table of Standard Values: Kirby-Bauer Disk Diffusion Test
Antibiotic Spectrum Disk Zone diameter nearest whole mm
Resistant Intermediate Susceptible
β-LACTAMS (penicillins)
Carbenicillin Pseudomonas 100 µg <13 14-16 >16
Gram negatives 100 µg <19 20-22 >23
Methicillin Staphylococci 5 µg <9 10-13 >14
Mezlocillin Pseudomonas 75 µg <15 >16
Other Gram negs 75 µg <17 18-20 >21
Penicillin Staphylococci 10 units <28 >29
Enterococci 10 units <14 >15
Piperacillin Pseudomonas 100 µg <17 >18
Other Gram negs 100 µg <17 18-20 >21
β-LACTAM/ β-LACTAMASE INHIBITOR COMBINATIONS
Amoxycillin/clavulanate Staphylococci 20/10 µg <19 >20
Other organisms 20/10 µg <13 14-17 >18
Piperacillin/tazobactam Pseudomonas 100/10 µg <17 >18
Other Gram negs 100/10 µg <17 18-20 >21
Staphylococci 100/10 µg <17 >18
CEPHALOSPORINS
Cefotaxime 30 µg <14 15-22 >23
Cefixime 30 µg <15 16-18 >19
Ceftriaxone 30 µg <13 14-20 >21
Cefuroxime oral 30 µg <14 15-22 >23
CARBAPENEMS
Imipenem 10 µg <13 14-15 >16
MONOBACTAMS
Aztreonam 30 µg <15 16-21 >22
GLYCOPEPTIDES
Vancomycin Enterococci 30 µg <14 15-16 >17
Other Gram pos 30 µg <9 10-11 >12
AMINOGLYCOSIDES
Gentamicin 10 µg <12 13-14 >15
Streptomycin 10 µg <11 12-14 >15
Tobramycin 10 µg <12 13-14 >15
MACROLIDES
Azithromycin 15 µg <13 14-17 >18
Clarithromycin 15 µg <13 14-17 >18
Erythromycin 15 µg <13 14-22 >23
TETRACYCLINES
Doxycycline 30 µg <12 13-15 >16
Minocycline 30 µg <14 15-18 >19
Tetracycline 30 µg <14 15-18 >19
QUINOLONES
Ciprofloxacin 5 µg <15 16-20 >21
Nalidixic acid 30 µg <13 14-18 >19
Norfloxacin 10 µg <12 13-15 >16
Ofloxacin 5 µg <12 13-15 >16
OTHERS
Chloramphenicol 30 µg <12 13-17 >18
Clindamycin 2 µg <14 15-20 >21
Nitrofurantoin 300 µg <14 15-16 >17
Rifampin 5 µg <16 17-19 >20
Sulfonamides 250/300 µg <12 13-16 >17
Trimethoprim 5 µg <10 11-15 >16
Trimethoprim/
sulfamethoxazole
1.25/
23.75 µg
<10 11-15 >16
Note Adapted from: Clinical Laboratory Standards Institute. (2006). Performance standards for antimicrobial disk susceptibility tests; Approved standard 9ed. CLSI document M2-A9. 26:1. Clinical Laboratory Standards Institute, Wayne, PA. | textbooks/bio/Microbiology/Microbiology%3A_A_Laboratory_Experience_(Ahern)/01%3A_Chapters/1.09%3A_The_War_on_Germs.txt |
Epidemiology is a science that studies the causes and effects of health-related events as they occur in populations. Disease, defined as a deviation from health, is one such health-related event of concern to epidemiologists, so in that regard, epidemiology is often thought of as the study of disease in populations.
Although the historical origins of epidemiology as a science are investigations of epidemics of infectious disease, modern epidemiology has expanded to not only include contagious diseases, but also environmental connections to disease states and even accidental injuries. Epidemiologists gather data on the frequency of various diseases in populations, and correlate risk factors associated with disease development.
The information compiled by epidemiologists provides the foundation for the concept of “public health.” The focus of public health is to prevent and manage diseases, injuries, and other conditions that threaten human helath. Keeping track of the number of people who acquire or have a particular health-related condition guides the deployment of interventions, distribution of grant funding for research on particular diseases, and development of public health policy.
In the United States, the Centers for Disease Control and Prevention (CDC) is the arm of the federal government responsible for promoting and protecting public health. On the infectious disease front, the CDC receives reports on the occurrence of certain infectious diseases, called notifiable diseases, from regions in the United States and its territories. The data received from state and local health agencies each week is compiled into a large searchable database called the National Notifiable Diseases Surveillance System (NNDSS) and published in the Morbidity and Mortality Weekly Report (MMWR), which is available in both print and electronic formats.
The data maintained within the NNDSS tables is available for retrospective analysis and also used to predict trends in disease occurrence in populations by time and place.
Two important measurements of disease occurrence and distribution are morbidity (illnesses due to a disease) and mortality (deaths due to a disease). The morbidity of a specific disease is defined as the number of susceptible people in a population that have the disease during a specific period of time, and is usually expressed as a rate. Mortality may also be expressed as a rate, and reflects the number of deaths due to a particular disease in a population over time.
Frequency of Disease in a Population
The frequency at which a disease occurs in a population is a way to assess risk and disease impact. One way to measure disease frequency is to simply count how many people are afflicted with it in a given period of time. However, using simple counts prevents comparison among populations, which may vary vastly in size. Therefore, disease frequency is usually expressed as a proportion of the number of people affected by the disease to the population size, over a specified time period.
Two specific statistical measures widely used in epidemiological investigations are incidence and prevalence. Incidence is a measure of the number of NEW cases of a disease during a specific time period. Incidence is used as a way to understand risk factors, such as the cause of a health-related event or concern for disease spread. Prevalence refers to the total number of both new and existing cases in a population over time, and provides an indication of the overall health of the population during a time period.
Both of these statistics are measures of disease over time. For this reason, they are often expressed as a rate:
Incidence rate = Number of new cases of a disease in a population ÷ Number of at-risk people during a time period
Prevalence rate =Number of cases of a disease in a population ÷ Number of at-risk people during a time period
Because the number of cases of any disease may be small, and the size of the population under study may be very large, the resulting number may be so exceptionally small that it is perceived to be of no consequence. Therefore, these measures are often expressed as a percent, or multiplied by a factor of 100, 1,000, or even 100,000 so that the rates are expressed in number of people per 100, 1,000, or 100,000 individuals, respectively. For example, if over the course of one year, five women in a study population of 200 women (5/200) develop breast cancer, then the calculated incidence of breast cancer in this population is 0.025. Such a small number might lead some people to presume their disease risk is also small. Therefore, the incidence may be expressed as a percent (2.5%), or a multiplier can be used to express the disease rate as 25 breast cancer cases per 1,000 women per year.
Prevalence estimates the likelihood that someone in a group will have a disease, and is often used as an indicator of the overall healthcare burden of a disease. Prevalence is highly dependent on the duration of the morbidity associated with the disease. The prevalence of chronic diseases will continually increase as the cases accumulate over time since it is a measure of both new and existing cases.
For example, a survey asking about personal experience with colon cancer was provided to 80,000 people, with 2,400 responding that they had been recently diagnosed with the disease, and 7,000 people responding that they’d had the disease for more than a year. The prevalence rate for colon cancer in this population can be determined by adding new and existing cases (9,400) and dividing by the size of the population (80,000). Therefore, the prevalence of cancer in this population is 0.1175, which can be expressed as 11.75%, or 118 colon cancer cases per 1,000 people.
Incidence and prevalence are two fundamentally different statistics. Keeping track of new cases of a disease requires an extensive network of reporting, while prevalence can be determined by surveying members of a population at a given point in time. Although there are limitations, if the disease is fairly stable in the population, has an average time of duration, and is not irreversible, incidence can be estimated using the prevalence data, and vice versa, using the following relationships (where Time refers to the average amount of time a person is sick with the disease):
Prevalence rate = Incidence x duration (in days, weeks, or months) of the disease
Incidence rate = Prevalence / duration (in days, weeks, or months) of the disease
Example: A prevalence survey conducted in upstate New York in 2013 revealed that 200 people in a study population of 16,000 Saratoga County residents were diagnosed with anaplasmosis, a bacterial disease transmitted to humans by ticks. For appropriately treated patients, the average amount of time that a person is sick with this disease is approximately four weeks.
1. What is the prevalence of anaplasmosis in Saratoga County, expressed per 1,000 people?
2. What is the estimated annual incidence of anaplasmosis per 1,000 Saratoga County residents? (Hint: Because this asks for the annual incidence, time should be expressed in years.)
3. In 2013, there were 223,865 people living in Saratoga County. Therefore, how many of those people would be expected to have anaplasmosis in 2013?
Measures of Association
Measuring the frequency of health-related events in populations is a useful way to assess and compare the health status of people in a population at one time, at different times, among subgroups of the population, or between populations. However, knowing how frequently a disease occurs in a single group does not indicate whether being a member of that group increases a person’s risk of experiencing a specific health-related event.
Therefore, identifying the cause of a health-related event in epidemiology usually includes comparing disease rates between groups of people who differ by exposure. By measuring and comparing the frequency of health related events between groups where one is exposed and one is not, it is possible to evaluate if there is an association between a particular risk factor (such as smoking) and a positive or negative impact on health (such as cardiovascular disease).
For cohort studies which involve a group of people who share the same experiences, epidemiologists may make comparisons of disease frequency by calculating ratios of the variables. The risk ratio (also known as relative risk) gives an indication of the strength of the association between a factor and a disease or other health outcome. To calculate the relative risk, the incidence of the health-related event in a group that was exposed to the condition or variable is divided by the incidence of the same variable in the group that was not exposed. In general, a calculated risk ratio equal to or close to one indicates that there is no difference in risk, because the incidence is approximately equal in both groups. Ratios greater than or less than one suggest higher or lower risk, respectively.
To calculate relative risk in a study involving a cohort, the conventional method is to organize the data in a format known in statistics as a “2 x 2” table. An example is shown in Table 1:
Table 1. Standard 2 x 2 table for relative risk calculation.
Outcome
Yes No Total Incidence of outcome
Exposed 16 108 124 16/124 = 0.13
Not Exposed 14 341 355 14/355 = 0.04
Relative risk is calculated by dividing the incidence of the health event for the exposed group by the incidence of the health event in the unexposed group:
RR = incidence of outcome in exposed group / incidence of outcome of non-exposed group
RR = 0.13/0.04 = 3.25
In this case, because the calculated value is more than one, there is an increased risk associated with exposure to the risk factor. Specifically, the people in the exposed group were 3.25 times more likely to have the health event than those in the non-exposed group.
Example: To determine if patients who take prophylactic antibiotics before surgery are more or less likely to develop a hospital-acquired infection (HAI) of the wound, two groups of surgery patients were compared. One group with eighty participants took an antibiotic prior to surgery, and a second group of seventy patients did not take the antibiotic. Six people in the antibiotic group developed an HAI after surgery, and nine people in the no antibiotic group ended up with an HAI. Calculate the relative risk for this health-related event.
Table 2. Relative Risk Example
Outcome
HAI No HAI Total Incidence of outcome
Antibiotic 6 74 80 6/80 = 0.075
No antibiotic 9 61 70 9/70 = 0.13
RR = incidence of HAI for exposed group / incidence for non-exposed group
RR = 0.075/0.13 = 0.58
Because the relative risk is less than one, there is a reduced risk for a patient of getting a hospital-acquired infection if they are given an antibiotic before surgery. Specifically, someone who gets a pre-surgery antibiotic has 0.58 times the risk of an HAI, meaning that taking a pre-surgery antibiotic cuts the risk of HAI by almost half.
Another option to compare frequencies of health events is to calculate the risk difference, in which the difference between the two measures is determined by subtraction. The risk difference provides a measure of the public health impact of the risk factor and indicates how the health event might be prevented if the risk factor were eliminated.
The cohort study above examined if prophylactic antibiotics reduced the risk of getting a hospital acquired infection for patients. Note that the incidence of HAI in the antibiotic group was 75 per 1,000 people, and the incidence of HAI in the no antibiotic group was 130 per 1,000. The difference between these two values (55) indicates the number of HAI cases that could be prevented through prophylactic antibiotics before surgery. In this case, HAI would be prevented for 55 people (per thousand) if they are given an antibiotic before surgery.
Example: To determine if people who take a proton-pump inhibitor to combat heartburn are more or less likely to develop gastroesophogeal reflux disease (GERD), two groups of patients were compared. One group with 43 participants took the PPI daily, and a second group with 39 patients did not. After 3 months, 6 people in the PPI group developed developed GERD, while 5 people in the no PPI group developed GERD. Calculate the risk difference and indicate whether taking a PPI reduces the risk for GERD.
Using a case-control (as opposed to a cohort) study, relative risk is also a way for epidemiologists to track risk factors associated with disease outbreaks and potentially assign a cause, such as during a sporadic outbreak of a food-borne disease.
Example: On February 12, 2014 a forty-three-year-old man in New York was hospitalized with a one-week history of diarrhea and vomiting followed by fever, neck pain, and headache. This was the first reported (index) case of a sporadic outbreak of listeriosis, a disease caused by the bacterium Listeria monocytogenes. Almost everyone who is diagnosed with listeriosis has an invasive infection, meaning that the bacteria spread from their intestines to their bloodstream or other body sites, including the central nervous system.
An epidemiological investigation of this event identified 630 laboratory confirmed listeriosis cases across 11 states. To identify the source of the bacteria, a case-control study was conducted to compare the foods eaten by 52 of the patients with confirmed cases, with a group of 48 healthy controls who were matched to the case patients by gender, age, and geographic location. All 100 people were asked to complete a questionnaire about the foods they had eaten just prior to the index case report. The data is illustrated in Table 3.
Table 3. Questionnaire data
Ate food Did not eat food
Food item: Sick Not Sick Sick Not Sick
Weiner brand hot dog 24 28 22 26
Raggle brand sausage 20 32 29 19
Dairydelish yogurt 38 14 13 35
Yummyum ice cream bar 28 24 23 25
So… which food was contaminated? Calculate the relative risk for each food, and the highest number wins. Start by calculating the incidence for each group (first food item is shown):
Weiner hot dogs Incidence exposed 24/52 = 0.46 RR: 0.46/0.5 = 0.92
Incidence not exposed 22/48 = 0.5
Raggle sausage Incidence exposed RR:
Incidence not exposed
Dairydelish Incidence exposed RR:
Incidence not exposed
Yummyum Incidence exposed RR:
Incidence not exposed
Based on your calculations, which food is associated with this food-borne outbreak of Listeria?
Epidemiology Problem
On July 30, 2013, the New York State Department of Health received a complaint from a person who said that he and his entire family had become very ill with vomiting and diarrhea after eating at a particular restaurant. He went on to say that his two-year-old son, Devin, became so dehydrated that he required hospitalization. After rehydration therapy, Devin was well enough to return home. A specimen taken from Devin’s stool was cultured on several types of media, including Sorbitol-MacConkey (SMAC) Agar, Salmonella-Shigella (SS) Agar, and Mannitol Salt Agar (MSA). Pink colonies grew on the SMAC plates, but no colonies appeared on the MSA plate. Pertinent results and additional tests are provided in Table 4, or your instructor may provide you with the actual media containing the cultures you should use in this analysis.
Table 4. Laboratory results for bacteria cultured from stool specimen.
Gram stain MacConkey Agar Catalase Oxidase TSI
Pink single bacilli Colonies were translucent and beige colored Bubbles formed when H2O2 was added No color change when smeared on a DrySlide Oxidase card K/A H2S gas
Based on the laboratory results, what bacterial genus is the most likely cause of Devin’s illness?
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What is the name of the gastrointestinal disease caused by infection with this bacterium?
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Over the next 10 days, the hospital where Devin had been treated saw an additional 19 cases of rapid-onset gastroenteritis in people who dined at the same restaurant as Devin and his family. The Department of Health initiated an investigation, which included interviewing restaurant staff and people who had eaten there at some point over the previous two weeks. Samples of food taken from the restaurant at the time of the interviews did not test positive for any harmful bacterial agents.
To determine what food item might have been contaminated, a case-control study was conducted with the 19 people who developed food poisoning after dining at the restaurant matched with 20 controls, who had eaten at the restaurant but did not get sick. The responses were compiled and the data is shown in Table 5.
Table 5. Data from the case-control study
Exposed Not Exposed
Food item: Sick Not Sick Sick Not Sick
Hamburger 8 11 9 11
Hot dog 7 12 8 12
Fried chicken 9 10 12 8
French fries 10 9 11 9
Potato salad 16 3 4 16
Soda 11 8 11 9
Water 9 10 6 14
Beer 10 9 10 10
Can a particular food item be associated with the occurrence of disease among the people that ate at the restaurant? If yes, which food?
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Epidemiologists were interested in knowing if this was a sporadic outbreak or an indication of a disease becoming more common in the upstate New York region. Therefore, a quick analysis was performed by comparing the incidence of this disease at 4 times throughout the year of 2013, at weeks 12, 26, 40, and 52. Retrieve this data from the NNDSS database (you can find it at cdc.gov → MMWR → State Health Statistics → NNDSS Tables → Search Morbidity Tables).
Week 12: Number of reported cases __________
Week 26: Number of reported cases __________
Week 40: Number of reported cases __________
Week 52: Number of reported cases __________
In this case, the size of the population would be considered the same for each of the weeks, therefore it is possible to compare the number of reported cases without calculating the incidence. From this data, what can you conclude overall about the occurrence of this disease in upstate New York? Is there any indication that we are on the verge of an epidemic of this disease?
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Hematopoiesis
Blood is a fluid that transports and delivers nutrients and oxygen to body cells, and removes metabolic waste to be excreted. In vertebrate animals such as ourselves, blood is composed of several different types of cells (the cellular components) suspended in a watery liquid called plasma which contains dissolved solutes and proteins (the humoral components), including immunoglobulin proteins called antibodies. Both the cellular and humoral components of blood are transported throughout the body via the cardiovascular and lymphatic systems.
Cell-mediated immunity
The production of blood cells is called hematopoiesis and occurs throughout our lifetime, primarily in the bone marrow and in the lymph nodes after birth. Blood cells originate as “stem cells,” which become committed to differentiate into mature cells along one of two different paths: myeloid or lymphoid.
Found most abundantly in blood are the erythrocytes (red blood cells), which derive from the myeloid cell line. These are highly specialized cells filled with hemoglobin designed to transport respiratory gases to and from the lungs. Another type of cell that derives from the myeloid line are megakaryocytes, which produce thrombocytes (platelets).
Leukocytes (white blood cells) are our primary cellular system of defense against disease. White blood cells circulate and patrol the blood and tissues, where they encounter and examine foreign entities invading the human body, sometimes engaging in mortal combat.
Leukocytes are derived from either the myeloid or lymphoid cell lines. In general, the cells in the myeloid cell line play a key role in the innate (also called “nonspecific”) immune response. Myeloid white blood cells include granulocytes (neutrophils, eosinophils, and basophils) and monocytes. These are primarily phagocytes that hunt down, engulf and destroy invading entities, while sending messages to other types of immune cells that an invasion has taken place. The innate response also includes humoral components, such as complement. The majority of bacterial infections that breach the security of our skin and mucous membrane barriers are dealt with swiftly and effectively by our innate immune response.
Cells in the lymphoid cell line, called lymphocytes, are activated via signals received from myeloid cells. Lymphocytes launch the adaptive (also called “specific”) immune response. Lymphoid cells differentiate into natural killer (NK) cells, T-cells and B-cells. When activated, B-cells differentiate into plasma cells which produce antibodies.
Cells involved in the adaptive immune response Cells involved in innate immune response
Humoral immunity
The term “humoral” refers to the liquid portion of the blood. Although both innate and adaptive immune responses have humoral components, use of this term is most closely associated with the production of antibodies as the culmination of the adaptive immune response.
Antibodies (also called immunoglobulins) are proteins that recognize and bind specifically to foreign structures associated with cells or objects, which are called antigens.
Antibodies have unique molecular structures designed to match with only one type of antigen. Antibodies bind to and neutralize antigens in several ways.
Antibodies are produced by B-cells after they are activated by signals from other immune cells. Activated B-cells undergo rapid growth and produce a clone of cells all producing one specific type of antibody molecule.
A subpopulation of the activated B-cells develop into memory cells, which “remember” the antigen. Memory cells are primed and ready if the antigen is encountered again. This provides the biological basis for vaccination, in which the immune system is artificially exposed to an antigen without triggering disease. Antibodies and memory cells are produced as if the exposure was to the actual antigen, and this provides future protection against the actual disease.
Antibody molecules persist in the blood and may continue to circulate for months to years after the antigen exposure occurred. Both the antibodies, and microbial antigens themselves, can be detected and measured in laboratory tests called immunoassays, which can aid in the diagnosis of an infectious disease.
The overall human immune response is exquisite and enormously complex, and is actually a course unto itself. Characteristics of each of the two “arms” of the human immune system are summarized in Table 1. Our goal in microbiology is to better understand the types of interactions that occur when the immune system encounters harm-causing microbes, but it’s also important to understand immunity from the perspective of the home team (our commensals) as well.
Table 1. The two arms of the human immune system. Components of the Human Immune System
Innate Immune Response Adaptive Immune Response
Response is non-specific Specific for pathogen or other antigen
Immediate maximum response Lag time before maximum response
Cellular and humoral components Cellular and humoral components
No immunological memory Exposure leads to immunological memory
Found in nearly all forms of life Found only in jawed vertebrates
Antibodies as an indirect indicator of an infectious disease
Serological tests for antibodies or antigens in blood are widely applied in clinical laboratories because they provide evidence of infection. Detecting antibodies in a patient sample is not necessarily a direct indication that the person has a disease, but rather shows past or present exposure to the disease-causing agent.
Infectious mononucleosis (IM), a disease that may follow infection with Epstein-Barr virus (Human herpesvirus 4) or Cytomegalovirus (Human herpesvirus 5), is an example of a fairly common disease often diagnosed on the basis of detection of antibodies in a person’s blood. One type of immunoassay for IM detects “heterophile” antibodies in a patient’s serum. These are weak, early, broad specificity IgM class antibodies produced against poorly defined antigens, which happens to include cow, pig, and horse red blood cells. The reaction between heterophile antibodies and animal red blood cells results in “hemagglutination,” or clumping of the red blood cells, which can be visibly observed.
For whatever reason, people with infectious mononucleosis and a few other infectious diseases (hepatitis and rubella) have elevated levels of heterophile antibodies. They sometimes cross-react with “self” antigens, and may also be found in people with autoimmune disease.
Use reliable internet sources to research the clinical signs and symptoms consistent with a diagnosis of infectious mononucleosis (IM) and compile a list below.
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We will be performing a commercially-available qualitative assay for detection of heterophile antibodies as an indicator of infectious mononucleosis. Your instructor will demonstrate how to perform the test, using positive and negative controls.
The method below corresponds to the Fisher HealthCare Sure-Vue Color Mono Test kit, but other kits may be substituted by your instructor. The Sure-Vue test kit uses specially treated horse red blood cells. If heterophile antibodies are present in the patient sample, the red blood cells will agglutinate which will appear as dark clumps against a colored background.
Clinical Scenario
A 16 year-old female patient reports symptoms that include a sore throat and feeling achy and overly tired. Clinical observations include a fever of 102°F and swollen lymph nodes in the neck region. The initial differential diagnosis made by the physician includes streptococcal infection (strep throat) and infectious mononucleosis. A blood sample is taken and tested using the Sure-Vue Mono Test.
To perform the test, you will need to obtain a test card, one patient serum sample, and a bottle of test “reagent” (a suspension of horse erythrocytes) from your instructor.
Place one drop of the patient sample inside the circle on the card. Shake the reagent bottle, and add one drop of the reagent next to the drop of patient sample.
Using a wooden toothpick, mix the two drops together thoroughly so that the combined drops completely cover the surface within the circle.
Rock the slide back and forth gently for 1 minute, then set it down on the lab bench and let it sit undisturbed for an additional 1 minute. Without moving the slide again, look at the circle to see if clumping is visible.
A positive reaction will have moderate-to-large sized dark clumps against a blue-green background, distributed uniformly over the surface of the test circle.
A negative result will show no clumping, although there may be a slightly graining appearance, against a greenish-brown background.
Was your patient sample positive or negative for this test? __________________
Based on the clinical signs and the result of the test, can the doctor be absolutely certain that the patient is infected by either EBV or CMV, and that the infection is causing infectious mononucleosis? Explain your answer.
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Blood cell counts as indicators of health and disease
One way to evaluate a person’s (or animal’s) state of health is to directly or indirectly examine cells or metabolites found in blood. In clinical laboratories, levels of various metabolites in plasma may be measured by chemical assay, and blood cells can be distinguished and counted using automated methods.
It is also possible to evaluate the cellular components in blood by directly observing them with a microscope. To be able to see individual cells, it is first necessary to create a very thin film of blood with a “feathered edge” (a single layer of cells) on a glass slide. Unstained and stained blood smears with a near perfect “feathered edge” are shown in Figure 4.
Once the blood smear is stained, the cells are visually inspected with a microscope. One of the most commonly used differential stains is the Wright-Giemsa stain, which stains red blood cells a pinkish-red color, and stains the nucleus and cytoplasm of white blood cells various shades of purple. Stained blood smears are examined to evaluate the appearance of the blood cells, and to count the number of different types of white blood cells present. Blood smears may also be examined to see if the blood contains any protozoal or bacterial pathogens associated with disease.
From an infectious disease perspective, the number of white blood cells and the relative percentages of different types of cells may indicate whether a person has a disease. This can be noted as a departure (either higher or lower) from established “normal” values.
Normal ranges, expressed as a percent of total white blood cells, are provided in Table 2—note that these values vary across age and gender and are therefore only approximations provided for the purpose of this lab. The absolute number of white blood cells generally considered “healthy” ranges from 3.5 to 11 x 109 cells/L.
Table 2. Normal ranges for white blood cells in peripheral blood.
White blood cell type Range of relative values for “normal”
Neutrophils 50–75%
Lymphocytes 15–35 %
Monocytes 3–10%
Eosinophils 1–7%
Basophils 0–2%
Deviations from these “normal” values can be an indication that an active infectious disease or a blood-associated disorder is ongoing.
For the types of white blood cells listed in the table below, research what disease conditions are associated with a relative increase or decrease in the numbers of that particular cell type:
White blood cell type Conditions associated with a relative increase Conditions associated with a relative decrease
Immature neutrophils, in which the nucleus looks like a single “band”
Lymphocytes
Eosinophils
Basophils
To determine the relative percentages of the different types of white blood cells found in a person’s blood, it’s important to first know what each cell type looks like and be able to tell them apart. These will be shown in the lab and/or provided as handouts before you start your investigation.
The Differential White Blood Cell Count (a “Diff”)
When a differential cell count is performed in a clinical lab, the technologist first makes a blood smear either manually or by machine, hoping to achieve that perfect feathered edge. Smears are routinely stained with Wright-Giemsa stain, and this is the staining method used to prepare the slides we will be viewing in this lab.
After staining, the smear is observed with a light microscope using the oil immersion objective lens. An initial scan to evaluate the appearance of the red blood cells and platelets is performed, followed by a more detailed analysis of the populations of white blood cells present.
To determine the relative number (percent) of each type of white blood cell, the smear is scanned using a pattern that prevents the observer from counting the same cells more than once. As each white blood cell is encountered, it is identified by cell type and recorded. A “tally” is kept and when the total number of cells observed reaches 100 the proportion of each type can be easily determined as the number of that cell type/100. The percent is calculated by multiplying by 100.
Obtain a prepared slide of a Wright stained blood smear from the front bench. Using the scanning pattern illustrated in Figure 5 and as demonstrated, scan the entire slide. Identify and count each white blood cell you see, until you have reached 100 cells.
Using a cell counter (if one is available in your lab) makes the tally process a little easier. Record your results in the table below:
White blood cell type Number of cells Percent
Neutrophils (including bands)
Lymphocytes
Monocytes
Eosinophils
Basophils
Based on the results of your differential cell count, provide an analysis in terms of how the blood compares to the “normal” values. What do the results suggest about the overall state of health of the patient? Provide at least three specific examples from among your results to support your opinion.
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Staining methods to detect pathogens in blood
Although blood is generally thought of as a “sterile” tissue, some viruses, bacteria, protozoa and helminthes may actually live in blood cells and circulate throughout the human cardiovascular system. Infections of the blood can range in severity from a transient bacteremia (bacteria in the blood) to septicemia, a “septic” state which may result in severe illness and death.
Invading microbes in blood are usually attacked, destroyed and removed by the immune system as quickly as possible. However, we know from research that some highly adapted microorganisms may survive and even reproduce within blood cells. To accomplish this feat, the microbes must “convince” the immune system to leave them alone by either evading or subverting the innate or adaptive responses.
Although parasitic blood infections such as malaria and heartworm are relatively well known, it is becoming increasingly obvious that bacteria also cause long term infections that can lead to chronic disease. Two examples of bacteria that infect and reproduce inside blood cells include Rickettsia spp. (Rocky Mountain Spotted Fever) and Bartonella spp., (best known for causing a disease referred to as “Cat Scratch Fever”). Both of these bacteria and several others are zoonotic diseases that have “spilled over” into humans. Most are transmitted to humans by insect vectors such as fleas, lice, and ticks.
To survive in blood, bacterial pathogens must first evade capture and destruction by phagocytic cells. One successful approach is for the pathogen to infect and then reproduce inside the very cells that were sent to destroy them. This and other strategies used by bacteria are referred to as “stealth pathogenesis.” Attack strategies employed by stealth pathogens are fundamentally different from those used by the better known “frontal” pathogens, whose major tactic is to breach the host perimeter, reproduce and spread as quickly as possible before the immune system can rally for a response. Table 3 compares and contrasts these two strategies for host invasion and infection.
Table 3. Characteristics of Frontal versus Stealth Pathogens
Frontal Pathogens Stealth Pathogens
Incubation period Short (hours to days) Long (months to years)
Symptoms Acute Chronic
Immunity Sterilizing Non-sterilizing
Transmission Direct Indirect (vector)
Reproduction Rapid Slow
Carrier state Uncommon Common
Note. Adapted from “Front and stealth attack strategies in microbial pathogenesis” by D. S. Merrell and S. Falkow, 2004, Nature, 430, p. 250-256. Copyright 2004 by Nature Publishing Group.
Using stealth tactics, some microorganisms are able to invade their hosts, disseminate to parts of the body that have poor immune surveillance, evade phagocytosis and disarm the adaptive immune response. Many stealth pathogens that infect blood cells also have the ability to infect multiple types of animals, and are transmitted among hosts by blood-sucking insects.
We will be looking for evidence of infection by stealth microbes that reproduce inside of various blood cell types, by examining Wright-Giemsa stained blood smears.
Anaplasma spp.
Anaplasma spp. are stealth bacteria that invade red and white blood cells. Examples include A. centrale in cows, which invade red blood cells, and A. phagocytophilum in humans and other animals, which reproduce inside phagocytic white blood cells.
Although bacteria are presumed to have relatively simple lives, Anaplasma and other stealth bacteria have complex life cycles. Humans and animals are infected through the bites of a tick, which carry Anaplasma as well as a mélange of other disease causing agents, including Borrelia (Lyme disease), Ehrlichia (ehrlichiosis), and viruses that cause encephalitis in some patients.
Once in the blood, A. phagocytophilum binds to surface proteins on neutrophils and other granulocytes. After phagocytosis, the bacteria send signals that inhibit the development of a phagolysosome, and then are free to reproduce inside the endocytic vacuole (called the endosome).
This forms an observable structure, called the morulae, inside the infected cell (indicated by arrows in Figure 6), which can be seen by a careful observer on a Wright-Giemsa stained blood smear.
Obtain a stained blood smear slide labelled Anaplasma. Scan the slide using the oil immersion objective lens and when you encounter a phagocytic cell type, look closely at the cytoplasm and determine if there are morulae, which will stain light purple against the darker blue of the cytoplasm.
Keep a tally of the number of phagocytes you observe, both with and without morulae. Record your results in the table below:
Morulae of Anaplasma observed? Number of cells with morulae Number of cells without morulae Percent of infected phagocytes
Babesia spp.
Babesia spp. are protozoa classified as Apicomplexa, a group that also includes the better known Plasmodium, which causes malaria, and Toxoplasma, which causes toxoplasmosis.
Babesia has a complex life cycle that includes more than one life stage cycling through multiple hosts, as illustrated in Figure 7. Ticks introduce sporozoites into their host when they attach to take a blood meal. Sporozoites invade red blood cells and develop first into trophozoites, then merozoites, which are released and infect nearby red blood cells to perpetuate the cycle.
The trophozoites and merozoites can be observed both inside and outside of the cells in a Wright-Giemsa stained blood smear. Inside the red blood cells, the developing trophozoites take the shape of “rings” or “crosses” that stain purple and generally stand out distinctly from the red cell background, which is a pinkish color. The merozoites appear as amorphous blobs with a dark purple dot, which is the nuclear material of the parasite.
Obtain a stained blood smear slide labelled Babesia. Scan the slide using the oil immersion objective lens, and look for evidence of Babesia infection, both inside and outside the red blood cells. Move to the thinnest part of the smear, where you can see a single layer of the red blood cells. Start counting the number of red blood cells, keeping track of the cells with obvious signs of trophozoite development and any extracellular merozoites. Continue to count until you’ve counted 100 cells. Use this data to estimate the level of parasitemia.
Number of red cells with Babesia trophozoites Number of merozoites observed Estimated level of parasitemia (trophozoites/merozoites observed per 100 cells counted)
According to a scholarly source (and cite the source), approximately what percentage of people in the United States are infected with Babesia, but may be asymptomatic or experiencing mild or chronic non-specific symptoms?
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Reflect on the implications this might have on the supply of blood for blood transfusions available in the United States.
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Dirofilaria
Dirofilaria are nematodes (roundworms) also known as heartworms. Dogs and cats are both known to be hosts for this type of parasitic worm, and heartworm control is a primary concern for pet owners and veterinarians alike.
Adult heartworms live in the right ventricle (one of the chambers) of the heart in dogs, and in the pulmonary arteries of cats. The adult worms produce microfilaria (“baby” heartworms) which can be seen in blood smears. Complications of an active heartworm infection in dogs range from nonexistent in early or mild infections to coughing, vomiting, trouble breathing and heart failure in advanced infections.
Obtain a stained blood smear slide of Dirofilaria. Scan the slide using the oil immersion objective lens, and look for the microfilaria worms which will be obviously larger than the blood cells. Figure 10 shows a picture of a single microfilaria in unstained blood as observed by bright field or phase contrast microscopy. In a Wright-Giemsa stained smear, the microfilaria look like worms, only stained blue and purple. Note the size of the microfilaria worm in relation to the red blood cells (which are approximately 10 µm in diameter). Adult heartworms may grow to be 20–30 cm long.
Scan the entire slide, and keep track of the number of microfilariae you see.
How many individual microfilariae did you find in the blood smear? ________________________
Consider that the drop of blood from which the smear was originally made had a volume of less than 10 µl. Dogs are estimated to have approximately 80–90 ml of blood per kg body weight.
For a dog that weighs 100 lbs (45 kg), estimate how many microfilariae would be found in its circulation, using a value of 85 ml of blood per kg body weight.
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The great enemy of the truth is very often not the lie, deliberate, contrived and dishonest, but the myth, persistent, persuasive and unrealistic. - John F. Kennedy
What is Truth?
Truth is a philosophical construct whose meaning has been debated since humans invented language. That’s not the focus of this endeavor.
This project is more about Reason, also a philosophical construct. Reason provides a path for pondering the truth. According to some, truth results when people apply reason appropriately about an issue at hand. This is the goal of science.
Maybe you have recently heard a claim about a nutritional supplement or seen an advertisement for a pharmaceutical drug touting amazing benefits if you take it, and wondered if you should. Or you thought about the health risks associated with getting a flu vaccine, or considered taking a probiotic because your cousin’s friend said you should? How can you know what would be best for you?
There exists a vast body of scientific studies conducted on an infinite number of topics in science and medicine that is published in scholarly journals and stored in searchable databases. By conducting an organized review of the published research on the topic and applying “appropriate reason,” you can decide for yourself what would be best for you, rather than relying on advice from ads or people you don’t know.
The conduct of scientific research is guided by practices collectively referred to as the scientific method, in which experiments are designed to answer questions about a hypothesis. In a perfect world, experiments are carefully designed to ensure that the data collected and the results derived from them are objective and without bias. If the results are significant, the science gets published in a journal as a way to communicate the findings to other interested people. Volumes of journals have historically been stored in libraries, where articles contained therein could be read and copied if relevant. It is no longer necessary to hunt through dusty “stacks” of print journals to find a scientific article, because a huge number are now “open access” or available electronically through a library interface.
There are differences between articles published in scholarly journals and those in other types of publications, and the major difference is peer-review. It’s important to note that use of the term “publication” includes papers published in electronic form as well as in print.
You should view a short video available at www.library.vanderbilt.edu/peabody/tutorial_files/scholarlyfree/, which explains how to tell the difference between a source reference from a scholarly publication and one published in the popular media.
Your instructor will be providing you with a microbiology-themed notion that you may have heard about before starting this project. Depending on the preferences of your instructor, you may investigate your assigned idea as a written assignment, or you may be asked to format the assignment in presentation software (such as PowerPoint) and make a formal presenation.
Before doing any research, reflect on and then write down your first impressions and personal views about the idea you’ve been provided. If you are unfamiliar with the idea, or even if you feel you understand it well, do a little background searching of the topic using popular sources (such as Google and Wikipedia) to gather background information before embarking on your scholarly search.
Debunk the Myths, Support the Truth
So much of what you hear on the evening news related to discovery in science and medicine comes from research conducted at universities and medical colleges. The funding for this research may come from government sources, and is therefore paid for by the taxpaying public. However, given the limited size of the pot, research is also conducted by private companies who then profit from research that culminates in a profit-bearing product. When research leads to publication in a “highly ranked” journal (ranked according to the journal’s “impact factor,” based on the number of times articles published in the journal are cited as a reference in other publications), a brief description of the study and its outcome are released to the popular media for reporting to the general public. Sometimes government policy is developed using published studies as a foundation for legislation.
Scholarly and non-scholarly reporting of scientific discovery means that people today have the unprecedented opportunity to make informed decisions about things that may affect their lives. However, it also provides fertile ground for the dissemination of information designed to “market” the idea to gain popular support. Once entrenched in the public conscience, misapplied “facts” may become “myths”—persistent, persuasive, and unrealistic. How do you tell the difference?
For this project, you will investigate whether a common microbiology idea is scientifically conceived and the degree to which it is “true,” by evaluating and reporting on research published in scholarly journals. The components to be included in your report or presentation are specified below.
1. Review popular opinion and develop a thesis
Once you know your Mythbuster subject, look for background information and opinions among sources that are not considered “scholarly.” This includes popular press sources such as newspapers, magazines, internet sources, or Great Aunt Martha who knows everything.
From your accumulated knowledge on the topic, develop a thesis on the topic, and assert what you think about it in a thesis statement—a one or two sentence prediction of what you believe to be true. The thesis statement should be focused and specific enough to be provable within the boundaries of your investigation.
As you search for the “reason” to back up the “truth,” you may find that your thesis can’t be supported by the available scientific evidence. However, you have to be flexible, objective, and honest when you construct and conduct your search of the scientific literature and not just look for ways to make your opinion seem true.
2. Search the scholarly literature
Scientists who think their research is significant communicate the results through publication in scientific journals. Most medical and scientific organizations publish journals related to a professional field—the American Society for Microbiology, for example, publishes several journals such as Applied and Environmental Microbiology and Journal of Clinical Microbiology, among others. Manuscripts submitted to scientific journals are sent to a panel of other scientists, who review them for scientific legitimacy and integrity. This insures that the data and results are obtained from carefully designed, reproducible experiments, and the conclusions are evidence-based. Once they are peer-reviewed and approved, they are incorporated into a volume of the journal and published.
It is important to consider that in a perfect world, using science and the scientific method to understand nature is a logical, objective, and totally unbiased process, that peer-reviewers are always honest, and that peer-reviewed articles represent the “truth.” As several recent high profile cases illustrate, in which published studies have been “retracted” due to fraud on the part of the researchers and/or their reviewers, the process isn’t perfect. This is particularly true when the financial or personal stakes are high.
Once you have developed your thesis statement, the next step is to look for published research studies pertaining to your topic. You can refer to http://www.wikihow.com/Find-Scholarly-Articles-Online/ for a concise overview of how to construct and conduct a search for scholarly articles on a topic of interest.
Many libraries at colleges and universities, such as the State University of New York library system, have access to huge databases containing millions of scholarly articles. Therefore, another excellent starting point is to enlist the assistance of a reference librarian in your college library, who can tell you what article databases are available and can help you construct your search. Reference librarians are particularly helpful when it comes to deciding on the right words or phrases, so that your search yields a manageable number of returns, not too few or too many.
Be objective when you decide on which articles to read further. Don’t limit yourself to only those that agree with your thesis 100%. Peruse the abstract, and if it sounds like the article will be relevant to your idea, download the entire article (full text) and read the full content.
3. Create an annotated bibliography of selected scholarly articles
At this point you have (hopefully) browsed through a large list of articles pertaining to your subject. For those that you decided to read in greater depth, prepare a bibliography using the citation format preferred by your instructor. Some of the databases will actually write the citation for you, and again, your reference librarian can help you locate and access the citation application if it exists for that database.
You should provide citations for all of the articles you selected. Of those you include in the bibliography, select three of the articles that you feel exemplify your idea, and write a brief annotation to accompany the citation. “Annotated” means that after the citation, write a brief one to two paragraph summary of the objectives and outcomes of the research presented in the article. The final sentence of the summary should discuss how the article relates to your thesis. An example of an annotated reference is shown below (the citation format is APA).
Fava, F., Lovegrove, J. A., Gitau, R., Jackson, K. G., & Tuohy, K. M. (2006) The gut microbiota and lipid metabolism: Implications for human health and coronary heart disease. Current Medicinal Chemistry, 13, 3005-3021.
Summary: Coronary heart disease (CHD) is the leading cause of mortality in Western society, affecting about one third of the population before their seventieth year. This article reviews the modifiable risk factors associated with CHD and discusses the hypothesis that diets rich in sources of dietary fiber and plant polyphenols promote better coronary health. Plant fibers are metabolized by the gut microflora, and are converted into biologically active compounds that are complementary to human metabolism. Metabolism of plant fibers by the gut microflora may prevent or otherwise beneficially impact impaired lipid metabolism and vascular dysfunction that typifies CHD and type II diabetes. Overall this article supports my thesis that the bacteria in the human gut make positive contributions to a person’s overall good health.
4. Write a summary and conclusion
Paper Option: In a paragraph (or two), summarize the scope of the project, the idea you are investigating, and restate your thesis. In two to four paragraphs, summarize the research that you discovered in your search of the scholarly literature, being sure to include the appropriate citation for each reference. In a final paragraph (or two), compare and contrast the non-scholarly information with what you learned from your search of the science, and discuss whether the scientific evidence was in support of your thesis, or if the evidence did not support your view. Consider whether you are sticking with your thesis or if you want to change it, and what amendments might be appropriate based on the scientific evidence.
Presentation Option: Using PowerPoint (or other presentation software), develop your report into a ten minute talk, which you may be scheduled to give as an oral presentation. | textbooks/bio/Microbiology/Microbiology%3A_A_Laboratory_Experience_(Ahern)/01%3A_Chapters/1.12%3A_Microbe_Mythbuster.txt |
Equipment, Supplies, and Cultures
The following is a list of equipment, supplies, cultures, and media needed to support this laboratory experience. Specific bacteria may be replaced with other cultures according to individual lab preferences or requirements. Amounts are not provided, because numbers will vary by section size. Best outcomes will be achieved if students work alone for labs in which new skills are introduced.
General Lab Equipment
• Microscopes and immersion oil
• Bunsen burners or sterilizers
• Inoculating loops and needles (metal or sterile disposable plastic)
• Metal forceps
• Pipette pumps
• Incubators set for body temperature and room temperature incubation
• Biohazard disposal container(s)
• Autoclave
• Refrigerator
Maintained Stock of Laboratory Supplies
The following should be readily available to students during lab and open lab times:
• Glass slides
• Clear plastic flexible laboratory metric rulers
• Kimwipes and/or lens paper
• Sterile 10 ml glass pipettes
• Sterile swabs
• Sterile wood applicator sticks
Replaced and refilled as needed each week:
• Staining “kits,” each kit containing stains in dropper bottles for Gram and Endospore staining procedures (Crystal violet, Gram’s iodine, 95% ethanol, Safranin, and Malachite Green)
• Spray bottles with laboratory disinfectant
• 70% ethanol for disinfecting forceps and spreaders, with beakers
• 4–6 racks (160–240 tubes) of sterile glass culture tubes, empty
• 2 racks (80 tubes) of tubes with sterile distilled water for making smears
• 2 sleeves (80 plates) of TSA plates
• 1 rack (40 tubes) of TSA slants
• 2 bottles (100 ml) of TSB
The recommended nonselective growth medium for routine culture is Tryptic Soy (TS), but other types could easily be substituted.
Lab 1: Biosafety Practices and Procedures
• Principles of Biosafety Evaluation and Student Affirmation form to assess understanding and document biosafety training.
Lab 2: The Microscopic World
Prepared slides (purchased, stained and mounted):
• Rectal (or fecal) smear (Gram stain)
• Mouth smear (Gram stain)
• Yogurt smear (Gram stained)
Cultures:
• Yogurt, store bought, any brand
• Yogurt, freshly made (prepared within a week of lab)
To make yogurt: Combine a large spoonful of yogurt (or a starter culture such as YoGourmet) with steamed milk in a glass pint canning jar with a lid. Stir vigorously to mix, then incubate at 38–40°C overnight. Refrigerate when milk has thickened into yogurt.
Lab 3: Bacteriological Culture Methods
Cultures:
• Overnight plate cultures of Micrococcus luteus and Enterococcus faecalis
• Overnight broth culture containing two bacteria
For broth cultures: Grow broth cultures of bacteria separately, combine in one tube right before the lab begins.
• For BSL-1 only: M. luteus, Micrococcus roseus in equal proportions
• For BSL-2: any combination of bacteria. Try to use bacteria which grow at a similar rate, or proportions added to the mixed culture can be adjusted to account for growth rate (for example, 2x as much Gram-positive to Gram-negative ratio)
Culture Media:
• Tryptic Soy Broth (or other nonselective general growth medium) in bottles
• Tryptic Soy Agar plates
• Tryptic Soy Agar slants in culture tubes
• Tryptic Soy deeps in culture tubes (semisolid agar: use 3.5 g agar per liter TSB)
Lab 4: The Environmental Isolate Project
Cultures:
• Bacteria cultured from skin and isolated in pure culture
Culture media (available in lab for the duration of the project):
• TSA plates and TSA slants for primary culture and pure culture maintenance
The media necessary to identify the genus and species of the isolated bacteria will vary each week. See media requirements and supplies for Growth Characteristics and Food Safety labs.
Lab 5: Differential Staining Techniques
Prepared slides (purchased already stained and mounted):
• Flavobacterium capsulatum, capsule stained (or other capsule-stained smear)
• Corynebacterium diphtheriae, methylene blue stain (or other stain for metachromatic granules)
• Mycobacterium tuberculosis, acid-fast stain
Cultures:
• Overnight TSA plate cultures of a Gram-positive bacterium and a Gram-negative bacterium (suggested are Escherichia coli and Staphylococcus saprophyticus)
• Overnight TSA plate cultures of two species of Bacillus, each with a different endospore appearance: suggested are B. subtilis OR B. cereus (with oval, central endospores) AND B. sphaericus OR B. globisporus (with spherical, terminal endospores)
Lab 7: Metabolism, Physiology, and Growth Characteristics of Cocci
Prepared slides (purchased, stained and mounted):
• Neisseria gonorrhoeae, Gram stain
Cultures:
• Overnight TSA plate cultures of Staphylococcus aureus, S. epidermidis, and S. saprophyticus, Micrococcus luteus, Enterococcus faecalis, Streptococcus pyogenes
Media and Test Reagents:
• Nitrate broth, in bottles
• Nitrate reagents A and B, stored at 4°C
• Urease broth, in bottles
• Triple Sugar Iron (TSI) agar slants
• Mannitol Salt Agar (MSA) plates
• Blood Agar Plates (BAP)
• Bile Esculin (BE) agar plates
• 3% hydrogen peroxide in dropper bottles (for catalase test)
• DrySlide Oxidase test cards (for oxidase test)
• Staphaurex (or other coagulase test kit) cards and reagent
Lab 8: Metabolism, Physiology, and Growth Characteristics of Bacilli
Cultures:
• Overnight TSA plate cultures of a Bacillus spp., Corynebacterium xerosis, Pseudomonas aeruginosa, Escherichia coli, a Salmonella spp., Citrobacter freundii, Enterobacter aerogenes
Media and Test Reagents:
• Nitrate broth, in bottles
• Nitrate reagents A and B, stored at 4°C
• MR-VP broth, in bottles
• Methyl Red reagent, and VP (Barritt’s) reagents A and B, stored at 4°C
• Triple Sugar Iron (TSI) agar slants
• Sulfide-Indole-Motility (SIM) agar stabs
• Indole (Kovac’s) reagent, stored at 4°C
• Simmon’s Citrate Agar plates or slants
• 3% hydrogen peroxide in dropper bottles (for catalase test)
• DrySlide Oxidase test cards (for oxidase test)
Lab 9: Microbiological Food Safety
Cultures:
• A selection of food items, such as ground beef, bagged lettuce, eggs, chicken, etc. (which may be “spiked” with bacteria). Students may be encouraged to include items of interest that they transport to lab with them.
Media and Test Reagents:
• Plastic disposable culture tubes with caps (to facilitate cleanup and disposal)
• Tryptic Soy Broth (TSB) in bottles
• MacConkey Agar (MAC) plates
• Sorbitol-MacConkey Agar (SMAC) plates
• Mannitol Salt Agar (MSA) plates
• TSI agar slants
• Staphaurex (or other coagulase test kit) cards and reagent
Lab 10: Germ Warfare
Cultures:
• Overnight TSA plate cultures of Staphylococcus aureus, S. saprophyticus, Escherichia coli, and Pseudomonas aeruginosa
Media and other supplies:
• 0.85% saline, sterile, in bottles
• 0.5 McFarland turbidity standards
• Mueller Hinton Agar (MHA) plates
• Antibiotic disks with: novobiocin, cefixime, azithromycin, ciprofloxacin, tetracycline
• Sterile blank filter paper disks
• Samples of a variety of known and potential disinfectants and antiseptics, such as a commercial home product, hand sanitizer, antibacterial dish soap, mouthwash, products made with essential oils, honey, etc.
Lab 11: Epidemiology and Public Health
Supplies:
• Calculators
• Access to the internet
Lab 12: Blood: the Good, the Bad, and the Ugly
Prepared slides and other supplies:
• Wrights-Giemsa stained blood smears (no pathology)
• Wrights-Giemsa or Giemsa stained blood smears of Anaplasma spp., Babesia spp., and Dirofilaria (microfilarial form)
• Blood cell counters (optional)
• Sure-Vue Mono Test kit (or other commercial test kit for Infectious Mononucleosis) | textbooks/bio/Microbiology/Microbiology%3A_A_Laboratory_Experience_(Ahern)/02%3A_Appendices/2.01%3A_Appendix_A.txt |
List of Potential Mythbusters Topics
The measles vaccine may cause vaccinated children to develop autism or other autism-related disorders like OCD and Asperger’s syndrome.
Taking a probiotic pill containing bacterial cultures will improve your immune system and therefore your ability to fight off colds and other infections.
Bottled water is “cleaner” (meaning won’t have any bacteria or viruses in it) and is therefore better for you to drink than regular tap water from a municipal source.
Getting an annual “flu shot” (influenza vaccine) means you will never have to worry about getting the flu.
If you drop something on the floor, it will still be safe to eat if you pick it up within 5 seconds of dropping it.
It is safe and economical to use a sponge in your kitchen for cleaning surfaces because they last for a long time.
Using a plastic cutting board in your kitchen to cut up food is safer than using a wooden cutting board.
Tuberculosis is a disease that we no longer have to worry about contracting here in the United States.
Children do not need to be immunized because most diseases preventable by vaccine (like mumps, measles, and polio) have been eliminated in the United States.
If you see any mold growing anywhere in your house, you should probably move out immediately because all molds are toxic.
Using hand soaps or household cleaning products labelled as “antibacterial” is healthier for you and your family.
Drinking lots of cranberry juice will prevent or cure urinary tract infections.
“Raw” or unpasteurized dairy products contain deadly microorganisms and should never be consumed by humans.
It’s OK to let your dog “kiss” you on the mouth because a dog’s mouth is cleaner than a human mouth.
Getting salad from a salad bar is perfectly safe because the plastic cover over the top protects the food from being contaminated.
You can catch genital herpes or chlamydia by sitting on a toilet seat in a public restroom.
Development of the symptoms of multiple sclerosis (MS) may be the result of an infection caused by bacteria or a virus.
Meat like ground beef and chicken should always be cooked “well done” because otherwise it is not safe to eat.
Using a product that contains zinc gluconate will shorten the duration of the common cold.
Using a product that contains the herb Echinacea will prevent you from getting a cold or the flu.
If you chew gum, your mouth will be “cleaner” (meaning, have fewer plaque-forming bacteria) than if you don’t chew gum.
If you pick up a toad and it pees on your hand, you’ll get a wart at the spot where the pee touches your skin.
2.03: Appendix C
Differentiation of Bacterial Cultures based on Morphological and Physiological Characteristics
Group 1: Aerobic and Anaerobic Cocci
Table 1. Aerobic cocci.
Gram stain Arrangement
Micrococcus spp. + tetrads
Neisseria gonorrhoeae diplococci
Table 2. Anaerobic cocci.
Catalase Oxidase Arrangement Oxygen
Staphylococcus spp (see Table 1) + clusters Facultative anaerobe
Streptococcus spp.
(see Table 4)
chains Aerotolerant anaerobe
Enterococcus spp.
(see Table 4)
chains Aerotolerant anaerobe
Table 3. Differentiation of Staphylococcus spp.
Staphylococcus aureus Staphylococcus epidermidis Staphylococcus saprophyticus
Coagulase 4+ 1–2+
Mannitol Salt Agar + +
Urease – or wk+ + +
Hemolysis Beta (β) – or wk +
Novobiocin resistance Susc. (-) Susc. (-) Res. (+)
Table 4. Differentiation of Streptococcus and Enterococcus spp.
Streptococcus pyogenes Enterococcus faecalis
Hemolysis on BAP Beta (β) Gamma (γ)
Bile Esculin No growth (-) Growth/black (+)
Gram positive bacilli
Endospore forming: Bacillus spp. (see Table 5)
Non-endospore forming: Corynebacterium xerosis
Table 5. Differentiation of Bacillus spp.
Endospore shape, location, sporangium
B. cereus Oval, central, sporangium not swollen
B. lentus Oval, terminal, sporangium swollen
Gram negative bacilli
Strictly aerobic: Pseudomonas aeruginosa
Facultatively anaerobic: Enterobacteriaceae (see Table 6)
Table 6. Differentiation of Enterobacteriaceae
TSI Sulfide/Indole/Motility Methyl Red VP Citrate
Escherichia coli A/A – /+/+ +
Enterobacter aerogenes A/A -/-/+ + +
Citrobacter freundii A/A -/-/+ + +
Klebsiella pneumoniae A/A -/-/- + +
Salmonella enteritidis K/A +/-/+ + + | textbooks/bio/Microbiology/Microbiology%3A_A_Laboratory_Experience_(Ahern)/02%3A_Appendices/2.02%3A_Appendix_B.txt |
Microbiology is a broad term which includes virology, mycology, parasitology, bacteriology, immunology, and other branches. A microbiologist is a specialist in microbiology and these related topics. Microbiological procedures usually must be aseptic and use a variety of tools such as light microscopes with a combination of stains and dyes. As microbes are absolutely required for most facets of human life (including the air we breathe and the food we eat) and are potential causes of many human diseases, microbiology is paramount for human society.
Thumbnail: A cluster of Escherichia coli bacteria magnified 10,000 times. (Public Domain; Eric Erbe, digital colorization by Christopher Pooley, both of USDA, ARS, EMU).
01: Introduction to Microbiology
Learning Objectives
• Explain the roles of microorganisms in ecosystems and biotechnology.
A microbe, or microorganism, is a microscopic organism that comprises either a single cell (unicellular); cell clusters; or multicellular, relatively complex organisms. The study of microorganisms is called microbiology, a subject that began with Anton van Leeuwenhoek’s discovery of microorganisms in 1675, using a microscope of his own design.
Microorganisms are very diverse; they include bacteria, fungi, algae, and protozoa; microscopic plants (green algae); and animals such as rotifers and planarians. Some microbiologists also include viruses, but others consider these as nonliving. Most microorganisms are unicellular, but this is not universal, since some multicellular organisms are microscopic. Some unicellular protists and bacteria, like Thiomargarita namibiensis, are macroscopic and visible to the naked eye.
Microorganisms live in all parts of the biosphere where there is liquid water, including soil, hot springs, on the ocean floor, high in the atmosphere, and deep inside rocks within the Earth’s crust. Most importantly, these organisms are vital to humans and the environment, as they participate in the Earth’s element cycles, such as the carbon cycle and the nitrogen cycle.
Microorganisms also fulfill other vital roles in virtually all ecosystems, such as recycling other organisms’ dead remains and waste products through decomposition. Microbes have an important place in most higher-order multicellular organisms as symbionts, and they are also exploited by people in biotechnology, both in traditional food and beverage preparation, and in modern technologies based on genetic engineering. Pathogenic microbes are harmful, however, since they invade and grow within other organisms, causing diseases that kill humans, animals, and plants.
The Pathogenic Ecology of Microbes
Although many microorganisms are beneficial, many others are the cause of infectious diseases. The organisms involved include pathogenic bacteria, which cause diseases such as plague, tuberculosis, and anthrax. Biofilms —microbial communities that are very difficult to destroy—are considered responsible for diseases like bacterial infections in patients with cystic fibrosis, Legionnaires’ disease, and otitis media (middle ear infection). They produce dental plaque; colonize catheters, prostheses, transcutaneous, and orthopedic devices; and infect contact lenses, open wounds, and burned tissue.
Biofilms also produce foodborne diseases because they colonize the surfaces of food and food-processing equipment. Biofilms are a large threat because they are resistant to most of the methods used to control microbial growth. Moreover, the excessive use of antibiotics has resulted in a major global problem since resistant forms of bacteria have been selected over time. A very dangerous strain, methicillin-resistant Staphylococcus aureus (MRSA), has wreaked havoc recently.
In addition, protozoans are known to cause diseases such as malaria, sleeping sickness, and toxoplasmosis, while fungi can cause diseases such as ringworm, candidiasis, or histoplasmosis. Other diseases such as influenza, yellow fever, and AIDS are caused by viruses.
Food-borne diseases result from the consumption of contaminated food, pathogenic bacteria, viruses, or parasites that contaminate food. ” Hygiene ” is the avoidance of infection or food spoiling by eliminating microorganisms from the surroundings. As microorganisms (bacteria, in particular) are found virtually everywhere, the levels of harmful microorganisms can be reduced to acceptable levels with proper hygiene techniques. In some cases, however, it is required that an object or substance be completely sterile (i.e., devoid of all living entities and viruses). A good example of this is a hypodermic needle.
Key Points
• While most microbes are unicellular, some multicellular animals and plants are also microscopic and are therefore broadly defined as “microbes.”
• Microbes serve many functions in almost any ecosystem on Earth, including decomposition and nitrogen fixation.
• Many microbes are either pathogens or parasitic organisms, both of which can harm humans.
Key Terms
• symbiote: An organism in a partnership with another, such that each profits from the other.
• pathogenic: Able to cause a harmful disease.
• ecosystem: The interconnectedness of plants, animals, and microbes, not only with each other but also with their environment. | textbooks/bio/Microbiology/Microbiology_(Boundless)/01%3A_Introduction_to_Microbiology/1.01%3A_Introduction_to_Microbiology/1.1A%3A_Defining_Microbes.txt |
Learning Objectives
• Explain how Van Leeuwenhoek, Spallanzani, Pasteur, Cohn and Koch contributed to the field of microbiology
Pre-microbiology, the possibility that microorganisms existed was discussed for many centuries before their actual discovery in the 17th century. The existence of unseen microbiological life was postulated by Jainism, which is based on Mahavira’s teachings as early as 6th century BCE. In his first century book, On Agriculture, Roman scholar Marcus Terentius Varro was the first known to suggest the possibility of disease spreading by yet unseen organisms. In his book, he warns against locating a homestead near swamps because “there are bred certain minute creatures that cannot be seen by the eyes, which float in the air and enter the body through the mouth and nose and there cause serious diseases. ” In The Canon of Medicine (1020), Abū Alī ibn Sīnā (Avicenna) hypothesized that tuberculosis and other diseases might be contagious. In 1546, Girolamo Fracastoro proposed that epidemic diseases were caused by transferable seed-like entities that could transmit infection by direct or indirect contact, or even without contact over long distances. All these early claims about the existence of microorganisms were speculative and were not based on any data or science. Microorganisms were neither proven, observed, nor correctly and accurately described until the 17th century. The reason for this was that all these early studies lacked the microscope.
The Microscope and Discovery of Microorganisms
Antonie van Leeuwenhoek (1632–1723) was one of the first people to observe microorganisms, using a microscope of his own design, and made one of the most important contributions to biology. Robert Hooke was the first to use a microscope to observe living things. Hooke’s 1665 book, Micrographia, contained descriptions of plant cells. Before Van Leeuwenhoek’s discovery of microorganisms in 1675, it had been a mystery why grapes could be turned into wine, milk into cheese, or why food would spoil. Van Leeuwenhoek did not make the connection between these processes and microorganisms, but using a microscope, he did establish that there were forms of life that were not visible to the naked eye. Van Leeuwenhoek’s discovery, along with subsequent observations by Spallanzani and Pasteur, ended the long-held belief that life spontaneously appeared from non-living substances during the process of spoilage.
Lazzaro Spallanzani (1729–1799) found that boiling broth would sterilize it and kill any microorganisms in it. He also found that new microorganisms could settle only in a broth if the broth was exposed to the air.
Louis Pasteur (1822–1895) expanded upon Spallanzani’s findings by exposing boiled broths to the air in vessels that contained a filter to prevent all particles from passing through to the growth medium. He also did this in vessels with no filter at all, with air being admitted via a curved tube that prevented dust particles from coming in contact with the broth. By boiling the broth beforehand, Pasteur ensured that no microorganisms survived within the broths at the beginning of his experiment. Nothing grew in the broths in the course of Pasteur’s experiment. This meant that the living organisms that grew in such broths came from outside, as spores on dust, rather than spontaneously generated within the broth. Thus, Pasteur dealt the death blow to the theory of spontaneous generation and supported germ theory instead.
Ferdinand Julius Cohn (January 24, 1828 – June 25, 1898) was a German biologist. His classification of bacteria into four groups based on shape (sphericals, short rods, threads, and spirals) is still in use today. Among other things Cohn is remembered for being the first to show that Bacillus can change from a vegetative state to an endospore state when subjected to an environment deleterious to the vegetative state. His studies would lay the foundation for the classification of microbes and gave some of the first insights into the incredible complexity and diversity of microbial life.
In 1876, Robert Koch (1843–1910) established that microbes can cause disease. He found that the blood of cattle who were infected with anthrax always had large numbers of Bacillus anthracis. Koch found that he could transmit anthrax from one animal to another by taking a small sample of blood from the infected animal and injecting it into a healthy one, and this caused the healthy animal to become sick. He also found that he could grow the bacteria in a nutrient broth, then inject it into a healthy animal, and cause illness. Based on these experiments, he devised criteria for establishing a causal link between a microbe and a disease and these are now known as Koch’s postulates. Although these postulates cannot be applied in all cases, they do retain historical importance to the development of scientific thought and are still being used today.
Key Points
• Van Leeuwenhoek is largely credited with the discovery of microbes, while Hooke is credited as the first scientist to describe live processes under a microscope.
• Spallanzani and Pasteur performed several experiments to demonstrate that microbial life does not arise spontaneously.
• Cohn laid the groundwork for discovering and cataloging microbes, while Koch conclusively showed that microbes can cause diseases.
Key Terms
• classification: the act of forming into a class or classes; a distribution into groups, as classes, orders, families, etc., according to some common relations or attributes. | textbooks/bio/Microbiology/Microbiology_(Boundless)/01%3A_Introduction_to_Microbiology/1.01%3A_Introduction_to_Microbiology/1.1B%3A_History_of_Microbiology_-_Hooke_van_Leeuwenhoek_and_Cohn.txt |
Learning Objectives
• Explain the concept of spontaneous generation
Spontaneous generation is an obsolete body of thought on the ordinary formation of living organisms without descent from similar organisms. Typically, the idea was that certain forms such as fleas could arise from inanimate matter such as dust or that maggots could arise from dead flesh. A variant idea was that of equivocal generation, in which species such as tapeworms arose from unrelated living organisms, now understood to be their hosts.
Doctrines held that these processes were commonplace and regular. Such ideas were in contradiction to that of univocal generation: effectively exclusive reproduction from genetically related parent(s), generally of the same species. The doctrine of spontaneous generation was coherently synthesized by Aristotle, who compiled and expanded the work of prior natural philosophers and the various ancient explanations of the appearance of organisms; it held sway for two millennia.
Today spontaneous generation is generally accepted to have been decisively dispelled during the 19th century by the experiments of Louis Pasteur. He expanded upon the investigations of predecessors, such as Francesco Redi who, in the 17th century, had performed experiments based on the same principles.
Louis Pasteur’s 1859 experiment is widely seen as having settled the question. In summary, Pasteur boiled a meat broth in a flask that had a long neck that curved downward, like a goose. The idea was that the bend in the neck prevented falling particles from reaching the broth, while still allowing the free flow of air. The flask remained free of growth for an extended period. When the flask was turned so that particles could fall down the bends, the broth quickly became clouded. In detail, Pasteur exposed boiled broths to air in vessels that contained a filter to prevent all particles from passing through to the growth medium, and even in vessels with no filter at all, with air being admitted via a long tortuous tube that would not allow dust particles to pass. Nothing grew in the broths unless the flasks were broken open, showing that the living organisms that grew in such broths came from outside, as spores on dust, rather than spontaneously generated within the broth. This was one of the last and most important experiments disproving the theory of spontaneous generation.
Despite his experiment, objections from persons holding the traditional views persisted. Many of these residual objections were routed by the work of John Tyndall, succeeding the work of Pasteur. Ultimately, the ideas of spontaneous generation were displaced by advances in germ theory and cell theory. Disproof of the traditional ideas of spontaneous generation is no longer controversial among professional biologists. Objections and doubts have been dispelled by studies and documentation of the life cycles of various life forms. However, the principles of the very different matter of the original abiogenesis on this planet — of living from nonliving material — are still under investigation
Key Points
• Before the discovery of microbes, it was widely thought that life, as in the case of rotting food, arose from nothing. This idea was referred to as spontaneous generation.
• By sterilizing cultures and keeping them isolated from the open air, Pasteur found that contamination of the media only occurred upon exposure to the outside environment, showing that some element was needed to give rise to life. In other words, life does not arise spontaneously.
• Despite Pasteur’s work and the work of others, it still took a better understanding of germ theory and cell theory to finally displace the concept of spontaneous generation.
Key Terms
• abiogenesis: The origination of living organisms from lifeless matter; such genesis as does not involve the action of living parents; spontaneous generation.
• germ theory: The germ theory of disease, also called the pathogenic theory of medicine, is a theory that proposes that microorganisms are the cause of many diseases. Although highly controversial when first proposed, germ theory was validated in the late 19th century and is now a fundamental part of modern medicine and clinical microbiology, leading to such important innovations as antibiotics and hygienic practices. | textbooks/bio/Microbiology/Microbiology_(Boundless)/01%3A_Introduction_to_Microbiology/1.01%3A_Introduction_to_Microbiology/1.1C%3A_Pasteur_and_Spontaneous_Generation.txt |
Learning Objectives
• Explain Robert Koch’s postulates
Robert Koch was born in Clausthal in the Harz Mountains, then part of the Kingdom of Hanover, as the son of a mining official. He studied medicine at the University of Göttingen and graduated in 1866. He then served in the Franco-Prussian War and later became district medical officer in Wollstein (Wolsztyn), Prussian Poland. Working with very limited resources, he became one of the founders of bacteriology, the other major figure being Louis Pasteur.
After Casimir Davaine demonstrated the direct transmission of the anthrax bacillus between cows, Koch studied anthrax more closely. He invented methods to purify the bacillus from blood samples and grow pure cultures. He found that, while it could not survive outside a host for long, anthrax built persisting endospores that could last a long time. These endospores, embedded in soil, were the cause of unexplained “spontaneous” outbreaks of anthrax. Koch published his findings in 1876 and was rewarded with a job at the Imperial Health Office in Berlin in 1880. In 1881, he urged for the sterilization of surgical instruments using heat.
Probably as important as his work on tuberculosis, for which he was awarded a Nobel Prize in 1905, are Koch’s postulates. These postulates stated that to establish that an organism is the cause of a disease, it must be found in all cases of the disease examined. Additionally, it must be absent in healthy organisms prepared and maintained in a pure culture capable of producing the original infection, even after several generations in culture retrievable from an inoculated animal and cultured again. By using his methods, Koch’s pupils found the organisms responsible for diphtheria, typhoid, pneumonia, gonorrhoea, cerebrospinal meningitis, leprosy, bubonic plague, tetanus, and syphilis.
Perhaps the key method Koch developed was the ability to isolate pure cultures, explained in brief here. Pure cultures of multicellular organisms are often more easily isolated by simply picking out a single individual to initiate a culture. This is a useful technique for pure culture of fungi, multicellular algae, and small metazoa. Developing pure culture techniques is crucial to the observation of the specimen in question. The most common method to isolate individual microbes and produce a pure culture is to prepare a streak plate. The streak plate method is a way to physically separate the microbial population and is done by spreading the inoculate back and forth with an inoculating loop over the solid agar plate. Upon incubation, colonies will arise and single cells will have been isolated from the biomass.
Key Points
• Koch’s research and methods helped link the causal nature of microbes to certain diseases, such as anthrax.
• As developed by Koch, pure cultures allow the pure isolation of a microbe, which is vital in understanding how an individual microbe may contribute to a disease.
• According to Koch’s postulates, for an organism to be the cause of a disease, it must be found in all cases of the disease and must be absent from healthy organisms, as well as maintained in pure culture capable of producing the original infection.
Key Terms
• anthrax: An infectious bacterial disease of herbivores than can also occur in humans through contact with infected animals, tissue from infected animals, or high concentrations of anthrax spores.
• metazoa: All those multicellular animals, of the subkingdom Metazoa, that have differentiated tissue.
• tuberculosis: An infectious disease of humans and animals caused by a species of mycobacterium mainly infecting the lungs where it causes tubercles characterized by the expectoration of mucus and sputum, fever, weight loss, and chest pain, and transmitted through inhalation or ingestion of bacteria.
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Microorganisms make up a large part of the planet’s living material and play a major role in maintaining the Earth’s ecosystem.
Learning Objectives
• Define the differences between microbial organisms.
Key Points
• Microorganisms are divided into seven types: bacteria, archaea, protozoa, algae, fungi, viruses, and multicellular animal parasites ( helminths ).
• Each type has a characteristic cellular composition, morphology, mean of locomotion, and reproduction.
• Microorganisms are beneficial in producing oxygen, decomposing organic material, providing nutrients for plants, and maintaining human health, but some can be pathogenic and cause diseases in plants and humans.
Key Terms
• Gram stain: A method of differentiating bacterial species into two large groups (Gram-positive and Gram-negative).
• peptidoglycan: A polymer of glycan and peptides found in bacterial cell walls.
Microorganisms or microbes are microscopic organisms that exist as unicellular, multicellular, or cell clusters. Microorganims are widespread in nature and are beneficial to life, but some can cause serious harm. They can be divided into six major types: bacteria, archaea, fungi, protozoa, algae, and viruses.
Bacteria
Bacteria are unicellular organisms. The cells are described as prokaryotic because they lack a nucleus. They exist in four major shapes: bacillus (rod shape), coccus (spherical shape), spirilla (spiral shape), and vibrio (curved shape). Most bacteria have a peptidoglycan cell wall; they divide by binary fission; and they may possess flagella for motility. The difference in their cell wall structure is a major feature used in classifying these organisms.
According to the way their cell wall structure stains, bacteria can be classified as either Gram-positive or Gram-negative when using the Gram staining. Bacteria can be further divided based on their response to gaseous oxygen into the following groups: aerobic (living in the presence of oxygen), anaerobic (living without oxygen), and facultative anaerobes (can live in both environments).
According to the way they obtain energy, bacteria are classified as heterotrophs or autotrophs. Autotrophs make their own food by using the energy of sunlight or chemical reactions, in which case they are called chemoautotrophs. Heterotrophs obtain their energy by consuming other organisms. Bacteria that use decaying life forms as a source of energy are called saprophytes.
Archaea
Archaea or Archaebacteria differ from true bacteria in their cell wall structure and lack peptidoglycans. They are prokaryotic cells with avidity to extreme environmental conditions. Based on their habitat, all Archaeans can be divided into the following groups: methanogens (methane-producing organisms), halophiles (archaeans that live in salty environments), thermophiles (archaeans that live at extremely hot temperatures), and psychrophiles (cold-temperature Archaeans). Archaeans use different energy sources like hydrogen gas, carbon dioxide, and sulphur. Some of them use sunlight to make energy, but not the same way plants do. They absorb sunlight using their membrane pigment, bacteriorhodopsin. This reacts with light, leading to the formation of the energy molecule adenosine triphosphate (ATP).
Fungi
Fungi (mushroom, molds, and yeasts) are eukaryotic cells (with a true nucleus). Most fungi are multicellular and their cell wall is composed of chitin. They obtain nutrients by absorbing organic material from their environment (decomposers), through symbiotic relationships with plants (symbionts), or harmful relationships with a host (parasites). They form characteristic filamentous tubes called hyphae that help absorb material. The collection of hyphae is called mycelium. Fungi reproduce by releasing spores.
Protozoa
Protozoa are unicellular aerobic eukaryotes. They have a nucleus, complex organelles, and obtain nourishment by absorption or ingestion through specialized structures. They make up the largest group of organisms in the world in terms of numbers, biomass, and diversity. Their cell walls are made up of cellulose. Protozoa have been traditionally divided based on their mode of locomotion: flagellates produce their own food and use their whip-like structure to propel forward, ciliates have tiny hair that beat to produce movement, amoeboids have false feet or pseudopodia used for feeding and locomotion, and sporozoans are non-motile. They also have different means of nutrition, which groups them as autotrophs or heterotrophs.
Algae
Algae, also called cyanobacteria or blue-green algae, are unicellular or multicellular eukaryotes that obtain nourishment by photosynthesis. They live in water, damp soil, and rocks and produce oxygen and carbohydrates used by other organisms. It is believed that cyanobacteria are the origins of green land plants.
Viruses
Viruses are noncellular entities that consist of a nucleic acid core (DNA or RNA) surrounded by a protein coat. Although viruses are classified as microorganisms, they are not considered living organisms. Viruses cannot reproduce outside a host cell and cannot metabolize on their own. Viruses often infest prokaryotic and eukaryotic cells causing diseases.
Multicellular Animal Parasites
A group of eukaryotic organisms consisting of the flatworms and roundworms, which are collectively referred to as the helminths. Although they are not microorganisms by definition, since they are large enough to be easily seen with the naked eye, they live a part of their life cycle in microscopic form. Since the parasitic helminths are of clinical importance, they are often discussed along with the other groups of microbes.
1.2B: Classification of Microorganisms
Microorganisms are classified into taxonomic categories to facilitate research and communication.
Learning Objectives
• Assess how early life changed the earth
Key Points
• The classification system is constantly changing with the advancement of technology.
• The most recent classification system includes five kingdoms that are further split into phylum, class, order, family, genus, and species.
• Microorganisms are assigned a scientific name using binomial nomenclature.
Key Terms
• DNA fingerprinting: A method of isolating and mapping sequences of a cell’s DNA to identify it.
Life on Earth is famous for its diversity. Throughout the world we can find many millions of different forms of life. Biologic classification helps identify each form according to common properties (similarities) using a set of rules and an estimate as to how closely related it is to a common ancestor (evolutionary relationship) in a way to create an order. By learning to recognize certain patterns and classify them into specific groups, biologists are better able to understand the relationships that exist among a variety of living forms that inhabit the planet.
The first, largest, and most inclusive group under which organisms are classified is called a domain and has three subgroups: bacteria, archae, and eukarya. This first group defines whether an organism is a prokaryote or a eukaryote. The domain was proposed by the microbiologist and physicist Carl Woese in 1978 and is based on identifying similarities in ribosomal RNA sequences of microorganisms.
The second largest group is called a kingdom. Five major kingdoms have been described and include prokaryota (e.g. archae and bacteria), protoctista (e.g. protozoa and algae), fungi, plantae, and animalia. A kingdom is further split into phylum or division, class, order, family, genus, and species, which is the smallest group.
The science of classifying organisms is called taxonomy and the groups making up the classification hierarchy are called taxa. Taxonomy consists of classifying new organisms or reclassifying existing ones. Microorganisms are scientifically recognized using a binomial nomenclature using two words that refer to the genus and the species. The names assigned to microorganisms are in Latin. The first letter of the genus name is always capitalized. Classification of microorganisms has been largely aided by studies of fossils and recently by DNA sequencing. Methods of classifications are constantly changing. The most widely employed methods for classifying microbes are morphological characteristics, differential staining, biochemical testing, DNA fingerprinting or DNA base composition, polymerase chain reaction, and DNA chips. | textbooks/bio/Microbiology/Microbiology_(Boundless)/01%3A_Introduction_to_Microbiology/1.02%3A_Microbes_and_the_World/1.2.01%3A_1.2A_Types_of_Microorganisms.txt |
Life on Earth is thought to have originated from the oldest single-cell archaea and bacteria.
Learning Objectives
• Assess the characteristics of pre-life earth and which adaptations allowed early microbial life to flourish.
Key Points
• The proposed mechanisms for the origin of life on Earth include endosymbiosis and panspermia. Both are debatable theories.
• In these two theories, bacteria and extremophile archaea are thought to have initiated an oxygenated atmosphere creating new forms of life.
• Evolutionary processes over billions of years gave rise to the biodiversity of life on Earth.
Key Terms
• endosymbiosis: A condition of living within the body or cells of another organism.
• panspermia: The hypothesis that microorganisms may transmit life from outer space to habitable bodies; or the process of such transmission.
Scientific evidence suggests that life began on Earth some 3.5 billion years ago. Since then, life has evolved into a wide variety of forms, which biologists have classified into a hierarchy of taxa. Some of the oldest cells on Earth are single-cell organisms called archaea and bacteria. Fossil records indicate that mounds of bacteria once covered young Earth. Some began making their own food using carbon dioxide in the atmosphere and energy they harvested from the sun. This process (called photosynthesis) produced enough oxygen to change Earth’s atmosphere.
Soon afterward, new oxygen-breathing life forms came onto the scene. With a population of increasingly diverse bacterial life, the stage was set for more life to form. There is compelling evidence that mitochondria and chloroplasts were once primitive bacterial cells. This evidence is described in the endosymbiotic theory. Symbiosis occurs when two different species benefit from living and working together. When one organism actually lives inside the other it’s called endosymbiosis. The endosymbiotic theory describes how a large host cell and ingested bacteria could easily become dependent on one another for survival, resulting in a permanent relationship.
Over millions of years of evolution, mitochondria and chloroplasts have become more specialized and today they cannot live outside the cell. Mitochondria and chloroplasts have striking similarities to bacteria cells. They have their own DNA, which is separate from the DNA found in the nucleus of the cell. And both organelles use their DNA to produce many proteins and enzymes required for their function. A double membrane surrounding both mitochondria and chloroplasts is further evidence that each was ingested by a primitive host. The two organelles also reproduce like bacteria, replicating their own DNA and directing their own division.
Mitochondrial DNA (mtDNA) has a unique pattern of inheritance. It is passed down directly from mother to child, and it accumulates changes much more slowly than other types of DNA. Because of its unique characteristics, mtDNA has provided important clues about evolutionary history. For example, differences in mtDNA are examined to estimate how closely related one species is to another.
Conditions on Earth 4 billion years ago were very different than they are today. The atmosphere lacked oxygen, and an ozone layer did not yet protect Earth from harmful radiation. Heavy rains, lightning, and volcanic activity were common. Yet the earliest cells originated in this extreme environment. Extremophiles archaea still thrive in extreme habitats. Astrobiologists are now using archaea to study the origins of life on Earth and other planets. Because archaea inhabit places previously considered incompatible with life, they may provide clues that will improve our ability to detect extraterrestrial life. Interestingly, current research suggests archaea may be capable of space travel by meteorite. Such an event termed panspermia could have seeded life on Earth or elsewhere.
The presence of archaea and bacteria changed Earth dramatically. They helped establish a stable atmosphere and produced oxygen in such quantities that eventually life forms could evolve that needed oxygen. The new atmospheric conditions calmed the weather so that the extremes were less severe. Life had created the conditions for new life to be formed. This process is one of the great wonders of nature.
1.2D: Environmental Diversity of Microbes
Learning Objectives
• Summarize how microbial diversity contributes to microbial occupation of diverse geographical niches.
The microbial world encompasses most of the phylogenetic diversity on Earth, as all Bacteria, all Archaea, and most lineages of the Eukarya are microorganisms. Microbes live in every kind of habitat (terrestrial, aquatic, atmospheric, or living host) and their presence invariably affects the environment in which they grow. Their diversity enables them to thrive in extremely cold or extremely hot environments. Their diversity also makes them tolerant of many other conditions, such as limited water availability, high salt content, and low oxygen levels.
Not every microbe can survive in all habitats, though. Each type of microbe has evolved to live within a narrow range of conditions. Although the vast majority of microbial diversity remains undetermined, it is globally understood that the effects of microorganisms on their environment can be beneficial. The beneficial effects of microbes derive from their metabolic activities in the environment, their associations with plants and animals, and from their use in food production and biotechnological processes.
In turn, the environment and the recent temperature anomalies play a crucial role in driving changes to the microbial communities. For instance, the assemblage of microbes that exists on the surface of seawater is thought to have undergone tremendous change with respect to composition, abundance, diversity, and virulence as a result of climate-driving sea surface warming.
For microbiologists, it is critical to study microbial adaptation to different environments and their function in those environments to understand global microbial diversity, ecology, and evolution. They rely on specific physical and chemical factors such as measuring temperature, pH, and salinity within a certain geography to formulate a comparison among microbial communities and the environment different species can tolerate. Researchers collect samples from geographical areas with different environmental conditions and between seasons to determine how dispersal patterns shape microbial communities and understand why organisms live where they do. As such, microbial communities from coastal and open oceans, polar regions, rivers, lakes, soils, atmosphere, and the human body can be tested. These samplings create a starting point to understand how the abundance and composition of microbial communities correlate with climatic perturbations, interact to effect ecosystem processes, and influence human health. Interfering with natural microbial biomass disrupts the balance of nature and the ecosystem and leads to loss of biodiversity.
Key Points
• Different microbial species thrive under different environmental conditions.
• Microbial communities occupy aquatic and terrestrial habitats and constitute the majority of biodiversity on Earth.
• Microbial diversities sustain the ecosystem in which they grow.
Key Terms
• biodiversity: The diversity (number and variety of species) of plant and animal life within a region.
• biomass: The total mass of all living things within a specific area or habitat.
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The information gained by microbiologists can be applied to many medicinal and commercial endeavors.
Learning Objectives
• Explain applied microbiology
Key Points
• Using knowledge gained by microbiologists studying microbes, several fields of applied microbiology have formed.
• While food and medicinal applications are a big portion of applied microbiology, the study of microbes has lead to entire commercial industries which affect almost all aspects of human life.
• There are a myriad of practical applications that microbiology contributes to, including several parts of food production and medicinal applications.
Key Terms
• rhizosphere: The soil region subject to the influence of plant roots and their associated microorganisms.
• biotechnology: The use of living organisms (especially microorganisms) in industrial, agricultural, medical, and other technological applications.
• pathogenic: Able to cause harmful disease.
Microbiology is the study of microbes, which affect almost every aspect of life on the earth. In addition, there are huge commercial and medicinal benefits in understanding microbes. The application of this understanding is known as applied microbiology. There are many different types of applied microbiology which can be briefly defined as follows:
Medical Microbiology
Medical microbiology is the study of the pathogenic microbes and the role of microbes in human illness. This includes the study of microbial pathogenesis and epidemiology and is related to the study of disease pathology and immunology.
Pharmaceutical Microbiology
The study of microorganisms that are related to the production of antibiotics, enzymes, vitamins, vaccines, and other pharmaceutical products. Pharmaceutical microbiology also studies the causes of pharmaceutical contamination and spoil.
Industrial Microbiology
The exploitation of microbes for use in industrial processes. Examples include industrial fermentation and waste-water treatment. Closely linked to the biotechnology industry. This field also includes brewing, an important application of microbiology.
Microbial Biotechnology
The manipulation of microorganisms at the genetic and molecular level to generate useful products.
Food Microbiology and Dairy Microbiology
The study of microorganisms causing food spoilage and food-borne illness. Microorganisms can produce foods, for example by fermentation.
Agricultural Microbiology
The study of agriculturally relevant microorganisms. This field can be further classified into the following subfields:
• Plant microbiology and plant pathology – The study of the interactions between microorganisms and plants and plant pathogens.
• Soil microbiology – The study of those microorganisms that are found in soil.
• Veterinary microbiology – The study of the role in microbes in veterinary medicine or animal taxonomy.
• Environmental microbiology – The study of the function and diversity of microbes in their natural environments. This involves the characterization of key bacterial habitats such as the rhizosphere and phyllosphere, soil and groundwater ecosystems, open oceans or extreme environments (extremophiles). This field includes other branches of microbiology such as: microbial ecology (microbially-mediated nutrient cycling), geomicrobiology, (microbial diversity), water microbiology (the study of those microorganisms that are found in water), aeromicrobiology (the study of airborne microorganisms) and epidemiology (the study of the incidence, spread, and control of disease).
This is by no means an exhaustive list of the different types of applied microbiology, but gives an indication of the expansive variety of the field and some of the benefits these studies entail.
1.3A: Basic Microbiology
Microbiology is the study of microscopic organisms and how they interact with humans and the environment.
Learning Objectives
• Evaluate the science of basic microbiology; understand the fundamental aspects of microbiology.
Key Points
• Microbiology focuses on organisms that are very small using various tools, which is a process done by microbiologists.
• As microbes are essential for human life and as microbes can cause human diseases, microbiology is therefore very important.
• The numbers of individual microbes and the number of microbes in and on the earth is staggering in proportions.
Key Terms
• quantitation: The process of quantitating.
• immunology: The branch of medicine that studies the body’s immune system.
• culturable: Able to be cultured (grown in a suitable environment).
Microbiology is the study of microscopic organisms (microbes), which are defined as any living organism that is either a single cell (unicellular), a cell cluster, or has no cells at all (acellular). This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses and prions, though not strictly classed as living organisms, are also studied.
Microbiology typically includes the study of the immune system, or immunology. Generally, immune systems interact with pathogenic microbes; these two disciplines often intersect which is why many colleges offer a paired degree such as “Microbiology and Immunology. ”
Microbiology is a broad term which includes virology, mycology, parasitology, bacteriology, immunology, and other branches. A microbiologist is a specialist in microbiology and these related topics. Microbiological procedures usually must be aseptic and use a variety of tools such as light microscopes with a combination of stains and dyes. As microbes are absolutely required for most facets of human life (including the air we breathe and the food we eat) and are potential causes of many human diseases, microbiology is paramount for human society.
Research in the microbiology field is expanding, and in the coming years, we should see the demand for microbiologists in the workforce increase. It is estimated that only about one percent of the microorganisms present in a given environmental sample are culturable and the number of bacterial cells and species on Earth is still not possible to be determined. Recent estimates indicate that this number might be extremely high at five to the power of thirty. Although microbes were directly observed over three hundred years ago, the precise determination, quantitation, and description of its functions is far from complete, given the overwhelming diversity detected by genetic and culture-independent means. | textbooks/bio/Microbiology/Microbiology_(Boundless)/01%3A_Introduction_to_Microbiology/1.03%3A_The_Science_of_Microbiology/1.3.01%3A_1.3B_Applied_Microbiology.txt |
Understanding microbes gives us the ability to fight pathogens using immunization, antiseptics, and antibiotics.
Learning Objectives
• Compare immunization, antiseptics and antibiotics, and how they are used to combat human pathogens
Key Points
• Immunization is the fortification of our own immune system, priming it against potential future infections by specific microbes.
• Antiseptics are broadly defined as substances we can use on our body or surfaces around us to slow or kill microbes that could potentially harm us.
• Antibiotics, like antiseptics, can slow or kill microbes. However, unlike antiseptics, antibiotics can circulate in the human blood system and be used to fight microbial infections.
Key Terms
• anaphylactic shock: A severe and rapid systemic allergic reaction to an allergen, constricting the trachea and preventing breathing.
• immunogen: any substance that elicits a immune response; an antigen
Surprisingly, most microbes are not harmful to humans. In fact, they are all around us and even a part of us. However, some microbes are human pathogens; to combat these, we use immunization, antiseptics, and antibiotics.
Immunization is the process by which an individual’s immune system becomes fortified against an agent (known as the immunogen ).
When the immune system is exposed to molecules that are foreign to the body, it will orchestrate an immune response. It will also develop the ability to respond quickly to subsequent encounters with the same substance, a phenomenon known as immunological memory. Therefore, by exposing a person to an immunogen in a controlled way, the body can learn to protect itself: this is called active immunization.
Vaccines against microorganisms that cause diseases can prepare the body’s immune system, thus helping it fight or prevent an infection. The most important elements of the immune system that are improved by immunization are the T cells, the B cells, and the antibodies B cells produce. Memory B cells and memory T cells are responsible for the swift response to a second encounter with a foreign molecule. Through the use of immunizations, some infections and diseases have been almost completely eradicated throughout the United States and the world. For example, polio was eliminated in the U.S. in 1979. Active immunization and vaccination has been named one of the “Ten Great Public Health Achievements in the 20th Century. ”
By contrast, in passive immunization, pre-synthesized elements of the immune system are transferred to a human body so it does not need to produce these elements itself. Currently, antibodies can be used for passive immunization. This method of immunization starts to work very quickly; however, it is short-lasting because the antibodies are naturally broken down and will disappear altogether if there are no B cells to produce more of them. Passive immunization occurs physiologically, when antibodies are transferred from mother to fetus during pregnancy, to protect the fetus before and shortly after birth. The antibodies can be produced in animals, called ” serum therapy,” although there is a high chance of anaphylactic shock because of immunity against animal serum itself. Thus, humanized antibodies produced in vitro by cell culture are used instead if available.
In early inquiries before there was an understanding of microbes, much emphasis was given to the prevention of putrefaction. Procedures were carried out to determine the amount of agent that needed to be added to a given solution in order to prevent the development of pus and putrefaction. However, due to a lack of understanding of germ theory, this method was inaccurate. Today, an antiseptic is judged by its effect on pure cultures of a defined microbe or on their vegetative and spore forms.
Antiseptics are antimicrobial substances that are applied to living tissue to reduce the possibility of infection, sepsis, or putrefaction. Their earliest known systematic use was in the ancient practice of embalming the dead. Antiseptics are generally distinguished from antibiotics by the latter’s ability to be transported through the lymphatic system to destroy bacteria within the body, and from disinfectants, which destroy microorganisms found on non-living objects. Some antiseptics are true germicides, capable of destroying microbes (bacteriocidal), while others are bacteriostatic and only prevent or inhibit bacterial growth. Microbicides that destroy virus particles are called viricides or antivirals.
An antibacterial is a compound or substance that kills or slows down the growth of bacteria. The term is often used synonymously with the term antibiotic; today, however, with increased knowledge of the causative agents of various infectious diseases, the term “antibiotic” has come to denote a broader range of antimicrobial compounds, including anti-fungal and other compounds.
The word “antibiotic” was first used in 1942 by Selman Waksman and his collaborators to describe any substance produced by a microorganism that is antagonistic to the growth of other microorganisms in high dilution. This definition excluded substances that kill bacteria but are not produced by microorganisms (such as gastric juices and hydrogen peroxide). It also excluded synthetic antibacterial compounds, such as the sulfonamides. Many antibacterial compounds are relatively small molecules with a molecular weight of less than 2000 amu. With advances in medicinal chemistry, most of today’s antibacterials are semisynthetic modifications of various natural compounds. | textbooks/bio/Microbiology/Microbiology_(Boundless)/01%3A_Introduction_to_Microbiology/1.03%3A_The_Science_of_Microbiology/1.3C%3A_Immunization_Antiseptics_and_Antibiotics.txt |
Learning Objectives
• Discuss the fundamental aspects of microbiology
Modern microbiolgy began with the discovery of microbes, and the scope and scale of the field continues to expand today. While there is some debate, modern microbiology is accepted by most to begin with observations by the Dutch draper and haberdasher, Antonie van Leeuwenhoek, who lived for most of his life in Delft, Holland. In 1676, van Leeuwenhoek observed bacteria and other microorganisms, using a single-lens microscope of his own design. While van Leeuwenhoek is often cited as the first to observe microbes, Robert Hooke made the first recorded microscopic observation, of the fruiting bodies of molds, in 1665.
It has been suggested that a Jesuit priest called Athanasius Kircher was the first to observe microorganisms. One of his books contains a chapter in Latin, which reads in translation – “Concerning the wonderful structure of things in nature, investigated by Microscope.” Here, he wrote “who would believe that vinegar and milk abound with an innumerable multitude of worms. ” He noted that putrid material is full of innumerable creeping animalcule. These observations antedate Robert Hooke’s Micrographia by nearly 20 years and were published some 29 years before van Leeuwenhoek saw protozoa.
The field of bacteriology (later a subdiscipline of microbiology) was founded in the 19th century by Ferdinand Cohn, a botanist whose studies on algae and photosynthetic bacteria led him to describe several bacteria including Bacillus and Beggiatoa. Cohn was also the first to formulate a scheme for the taxonomic classification of bacteria and discover spores. Louis Pasteur and Robert Koch were contemporaries of Cohn’s and are often considered to be the father of microbiology and medical microbiology, respectively. Pasteur is most famous for his series of experiments designed to disprove the then widely held theory of spontaneous generation, thereby solidifying microbiology’s identity as a biological science. Pasteur also designed methods for food preservation (pasteurization) and vaccines against several diseases such as anthrax, fowl cholera, and rabies.
Koch is best known for his contributions to the germ theory of disease, proving that specific diseases were caused by specific pathogenic microorganisms. He developed a series of criteria that have become known as the Koch’s postulates. Koch was one of the first scientists to focus on the isolation of bacteria in pure culture resulting in his description of several novel bacteria including Mycobacterium tuberculosis, the causative agent of tuberculosis. While Pasteur and Koch are often considered the founders of microbiology, their work did not accurately reflect the true diversity of the microbial world because of their exclusive focus on microorganisms having direct medical relevance.
It was not until the late 19th century and the work of Martinus Beijerinck and Sergei Winogradsky, the founders of general microbiology (an older term encompassing aspects of microbial physiology, diversity, and ecology), that the true breadth of microbiology was revealed. Beijerinck made two major contributions to microbiology: the discovery of viruses and the development of enrichment culture techniques. While his work on the tobacco mosaic virus (TMV) established the basic principles of virology, it was his development of enrichment culturing that had the most immediate impact on microbiology by allowing for the cultivation of a wide range of microbes with wildly different physiologies. Winogradsky was the first to develop the concept of chemoautotrophy and to thereby reveal the essential role microorganisms played in geochemical processes. Specifically, he was responsible for the first isolation and description of both nitrifying and nitrogen-fixing bacteria.
Key Points
• There is some debate as to who was exactly first, but Antonie van Leeuwenhoek, Athanasius Kircher, and Robert Hooke were the first people to view microbes using some of the first self-built microscopes.
• Ferdinand Cohn, Louis Pasteur, and Robert Koch were pioneers in bacteriology, the discovery and understanding of the subset of microbes that are bacteria. This had a direct and immediate impact on food storage and disease causality.
• Martinus Beijerinck and Sergei Winogradsky are credited with the discovery of general microbiology, which laid the ground work for our understanding of microbial physiology, diversity, and ecology.
Key Terms
• chemoautotrophy: When a simple organism, such as a protozoan, derives its energy from chemical processes rather than photosynthesis.
• pasteurization: heat-treatment of a perishable food to destroy heat-sensitive vegetative cells followed by immediate cooling to limit growth of the surviving cells and germination of spores
• rabies: a viral disease that causes acute encephalitis in warm-blooded animals and people, characterised by abnormal behaviour such as excitement, aggressiveness, and dementia, followed by paralysis and death
• animalcule: An older term for a minute or microscopic animal or protozoan.
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• US Navy 100916-N-2729A-104 Capt.nStephen Pachuta self-administers the nasal spray flu immunization FluMist during an immunization clinic at U.S.nNa. Provided by: Wikimedia. Located at: commons.wikimedia.org/wiki/File:US_Navy_100916-N-2729A-104_Capt._Stephen_Pachuta_self-administers_the_nasal_spray_flu_immunization_FluMist_during_an_immunization_clinic_at_U.S._Na.jpg. License: Public Domain: No Known Copyright
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• Athanasius%20Kircher%20Portrait. Provided by: Wikimedia. Located at: commons.wikimedia.org/wiki/Fi...r_Portrait.jpg. License: Public Domain: No Known Copyright | textbooks/bio/Microbiology/Microbiology_(Boundless)/01%3A_Introduction_to_Microbiology/1.03%3A_The_Science_of_Microbiology/1.3D%3A_Modern_Microbiology.txt |
Atoms are made up of particles called protons, neutrons, and electrons, which are responsible for the mass and charge of atoms.
Learning Objectives
• Discuss the electronic and structural properties of an atom
Key Points
• An atom is composed of two regions: the nucleus, which is in the center of the atom and contains protons and neutrons, and the outer region of the atom, which holds its electrons in orbit around the nucleus.
• Protons and neutrons have approximately the same mass, about 1.67 × 10-24 grams, which scientists define as one atomic mass unit (amu) or one Dalton.
• Each electron has a negative charge (-1) equal to the positive charge of a proton (+1).
• Neutrons are uncharged particles found within the nucleus.
Key Terms
• atom: The smallest possible amount of matter which still retains its identity as a chemical element, consisting of a nucleus surrounded by electrons.
• proton: Positively charged subatomic particle forming part of the nucleus of an atom and determining the atomic number of an element. It weighs 1 amu.
• neutron: A subatomic particle forming part of the nucleus of an atom. It has no charge. It is equal in mass to a proton or it weighs 1 amu.
An atom is the smallest unit of matter that retains all of the chemical properties of an element. Atoms combine to form molecules, which then interact to form solids, gases, or liquids. For example, water is composed of hydrogen and oxygen atoms that have combined to form water molecules. Many biological processes are devoted to breaking down molecules into their component atoms so they can be reassembled into a more useful molecule.
Atomic Particles
Atoms consist of three basic particles: protons, electrons, and neutrons. The nucleus (center) of the atom contains the protons (positively charged) and the neutrons (no charge). The outermost regions of the atom are called electron shells and contain the electrons (negatively charged). Atoms have different properties based on the arrangement and number of their basic particles.
The hydrogen atom (H) contains only one proton, one electron, and no neutrons. This can be determined using the atomic number and the mass number of the element (see the concept on atomic numbers and mass numbers).
Atomic Mass
Protons and neutrons have approximately the same mass, about 1.67 × 10-24 grams. Scientists define this amount of mass as one atomic mass unit (amu) or one Dalton. Although similar in mass, protons are positively charged, while neutrons have no charge. Therefore, the number of neutrons in an atom contributes significantly to its mass, but not to its charge.
Electrons are much smaller in mass than protons, weighing only 9.11 × 10-28grams, or about 1/1800 of an atomic mass unit. Therefore, they do not contribute much to an element’s overall atomic mass. When considering atomic mass, it is customary to ignore the mass of any electrons and calculate the atom’s mass based on the number of protons and neutrons alone.
Electrons contribute greatly to the atom’s charge, as each electron has a negative charge equal to the positive charge of a proton. Scientists define these charges as “+1” and “-1. ” In an uncharged, neutral atom, the number of electrons orbiting the nucleus is equal to the number of protons inside the nucleus. In these atoms, the positive and negative charges cancel each other out, leading to an atom with no net charge.
Exploring Electron Properties: Compare the behavior of electrons to that of other charged particles to discover properties of electrons such as charge and mass.
Volume of Atoms
Accounting for the sizes of protons, neutrons, and electrons, most of the volume of an atom—greater than 99 percent—is, in fact, empty space. Despite all this empty space, solid objects do not just pass through one another. The electrons that surround all atoms are negatively charged and cause atoms to repel one another, preventing atoms from occupying the same space. These intermolecular forces prevent you from falling through an object like your chair.
Interactive: Build an Atom: Build an atom out of protons, neutrons, and electrons, and see how the element, charge, and mass change. Then play a game to test your ideas! | textbooks/bio/Microbiology/Microbiology_(Boundless)/02%3A_Chemistry/2.01%3A_Atomic_Structure/2.1.01%3A_Overview_of__Atomic_Structure.txt |
Electron orbitals are three-dimensional representations of the space in which an electron is likely to be found.
Learning Objectives
• Distinguish between electron orbitals in the Bohr model versus the quantum mechanical orbitals
Key Points
• The Bohr model of the atom does not accurately reflect how electrons are spatially distributed around the nucleus as they do not circle the nucleus like the earth orbits the sun.
• The electron orbitals are the result of mathematical equations from quantum mechanics known as wave functions and can predict within a certain level of probability where an electron might be at any given time.
• The number and type of orbitals increases with increasing atomic number, filling in various electron shells.
• The area where an electron is most likely to be found is called its orbital.
Key Terms
• electron shell: The collective states of all electrons in an atom having the same principal quantum number (visualized as an orbit in which the electrons move).
• orbital: A specification of the energy and probability density of an electron at any point in an atom or molecule.
Although useful to explain the reactivity and chemical bonding of certain elements, the Bohr model of the atom does not accurately reflect how electrons are spatially distributed surrounding the nucleus. They do not circle the nucleus like the earth orbits the sun, but are rather found in electron orbitals. These relatively complex shapes result from the fact that electrons behave not just like particles, but also like waves. Mathematical equations from quantum mechanics known as wave functions can predict within a certain level of probability where an electron might be at any given time. The area where an electron is most likely to be found is called its orbital.
First Electron Shell
The closest orbital to the nucleus, called the 1s orbital, can hold up to two electrons. This orbital is equivalent to the innermost electron shell of the Bohr model of the atom. It is called the 1s orbital because it is spherical around the nucleus. The 1s orbital is always filled before any other orbital. Hydrogen has one electron; therefore, it has only one spot within the 1s orbital occupied. This is designated as 1s1, where the superscripted 1 refers to the one electron within the 1s orbital. Helium has two electrons; therefore, it can completely fill the 1s orbital with its two electrons. This is designated as 1s2, referring to the two electrons of helium in the 1s orbital. On the periodic table, hydrogen and helium are the only two elements in the first row (period); this is because they are the sole elements to have electrons only in their first shell, the 1s orbital.
Second Electron Shell
The second electron shell may contain eight electrons. This shell contains another spherical s orbital and three “dumbbell” shaped p orbitals, each of which can hold two electrons. After the 1s orbital is filled, the second electron shell is filled, first filling its 2s orbital and then its three p orbitals. When filling the p orbitals, each takes a single electron; once each p orbital has an electron, a second may be added. Lithium (Li) contains three electrons that occupy the first and second shells. Two electrons fill the 1s orbital, and the third electron then fills the 2s orbital. Its electron configuration is 1s22s1. Neon (Ne), on the other hand, has a total of ten electrons: two are in its innermost 1s orbital, and eight fill its second shell (two each in the 2s and three p orbitals). Thus, it is an inert gas and energetically stable: it rarely forms a chemical bond with other atoms.
Third Electron Shell
Larger elements have additional orbitals, making up the third electron shell. Subshells d and f have more complex shapes and contain five and seven orbitals, respectively. Principal shell 3n has s, p, and d subshells and can hold 18 electrons. Principal shell 4n has s, p, d, and f orbitals and can hold 32 electrons. Moving away from the nucleus, the number of electrons and orbitals found in the energy levels increases. Progressing from one atom to the next in the periodic table, the electron structure can be worked out by fitting an extra electron into the next available orbital. While the concepts of electron shells and orbitals are closely related, orbitals provide a more accurate depiction of the electron configuration of an atom because the orbital model specifies the different shapes and special orientations of all the places that electrons may occupy.
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Ionic bonds are attractions between oppositely charged atoms or groups of atoms where electrons are donated and accepted.
Learning Objectives
• Predict whether a given element will more likely form a cation or an anion
Key Points
• Ions form from elements when they gain or lose an electron causing the number of protons to be unequal to the number of electrons, resulting in a net charge.
• If there are more electrons than protons (from an element gaining one or more electrons), the ion is negatively charged and called an anion.
• If there are more protons than electrons (via loss of electrons), the ion is positively charged and is called a cation.
• Ionic bonds result from the interaction between a positively charged cation and a negatively charged anion.
Key Terms
• ion: An atom, or group of atoms, bearing an electrical charge, such as the sodium and chlorine atoms in a salt solution.
• ionic bond: A strong chemical bond caused by the electrostatic attraction between two oppositely charged ions.
Ions and Ionic Bonds
Some atoms are more stable when they gain or lose an electron (or possibly two) and form ions. This results in a full outermost electron shell and makes them energetically more stable. Now, because the number of electrons does not equal the number of protons, each ion has a net charge. Cations are positive ions that are formed by losing electrons (as the number of protons is now greater than the number of electrons). Negative ions are formed by gaining electrons and are called anions (wherein there are more electrons than protons in a molecule ). Anions are designated by their elemental name being altered to end in “-ide”. For example, the anion of chlorine is called chloride, and the anion of sulfur is called sulfide.
This movement of electrons from one element to another is referred to as electron transfer. As illustrated, sodium (Na) only has one electron in its outer electron shell. It takes less energy for sodium to donate that one electron than it does to accept seven more electrons to fill the outer shell. When sodium loses an electron, it will have 11 protons, 11 neutrons, and only 10 electrons. This leaves it with an overall charge of +1 since there are now more protons than electrons. It is now referred to as a sodium ion. Chlorine (Cl) in its lowest energy state (called the ground state) has seven electrons in its outer shell. Again, it is more energy efficient for chlorine to gain one electron than to lose seven. Therefore, it tends to gain an electron to create an ion with 17 protons, 17 neutrons, and 18 electrons. This gives it a net charge of -1 since there are now more electrons than protons. It is now referred to as a chloride ion. In this example, sodium will donate its one electron to empty its shell, and chlorine will accept that electron to fill its shell. Both ions now satisfy the octet rule and have complete outer shells. These transactions can normally only take place simultaneously; in order for a sodium atom to lose an electron, it must be in the presence of a suitable recipient like a chlorine atom.
Ionic bonds are formed between ions with opposite charges. For instance, positively charged sodium ions and negatively charged chloride ions bond together to form sodium chloride, or table salt, a crystalline molecule with zero net charge. The attractive force holding the two atoms together is called the electromagnetic force and is responsible for the attraction between oppositely charged ions.
Certain salts are referred to in physiology as electrolytes (including sodium, potassium, and calcium). Electrolytes are ions necessary for nerve impulse conduction, muscle contractions, and water balance. Many sports drinks and dietary supplements provide these ions to replace those lost from the body via sweating during exercise. | textbooks/bio/Microbiology/Microbiology_(Boundless)/02%3A_Chemistry/2.02%3A_Chemical_Bonds/2.2.01%3A_Ions_and_Ionic_Bonds.txt |
Covalent bonds result from a sharing of electrons between two atoms and hold most biomolecules together.
Learning Objectives
• Compare the relative strength of different types of bonding interactions
Key Points
• A polar covalent bond arises when two atoms of different electronegativity share two electrons unequally.
• A non-polar covalent bond is one in which the electrons are shared equally between two atoms.
• Hydrogen bonds and Van Der Waals are responsible for the folding of proteins, the binding of ligands to proteins, and many other processes between molecules.
Key Terms
• hydrogen bond: A weak bond in which a hydrogen atom in one molecule is attracted to an electronegative atom (usually nitrogen or oxygen) in the same or different molecule.
• covalent bond: A type of chemical bond where two atoms are connected to each other by the sharing of two or more electrons.
• dipole: Any object (such as a magnet, polar molecule or antenna), that is oppositely charged at two points (or poles).
Covalent Bonds and Other Bonds and Interactions
The octet rule can be satisfied by the sharing of electrons between atoms to form covalent bonds. These bonds are stronger and much more common than are ionic bonds in the molecules of living organisms. Covalent bonds are commonly found in carbon-based organic molecules, such as DNA and proteins. Covalent bonds are also found in inorganic molecules such as H2O, CO2, and O2. One, two, or three pairs of electrons may be shared between two atoms, making single, double, and triple bonds, respectively. The more covalent bonds between two atoms, the stronger their connection. Thus, triple bonds are the strongest.
The strength of different levels of covalent bonding is one of the main reasons living organisms have a difficult time in acquiring nitrogen for use in constructing nitrogenous molecules, even though molecular nitrogen, N2, is the most abundant gas in the atmosphere. Molecular nitrogen consists of two nitrogen atoms triple bonded to each other. The resulting strong triple bond makes it difficult for living systems to break apart this nitrogen in order to use it as constituents of biomolecules, such as proteins, DNA, and RNA.
The formation of water molecules is an example of covalent bonding. The hydrogen and oxygen atoms that combine to form water molecules are bound together by covalent bonds. The electron from the hydrogen splits its time between the incomplete outer shell of the hydrogen atom and the incomplete outer shell of the oxygen atom. In return, the oxygen atom shares one of its electrons with the hydrogen atom, creating a two-electron single covalent bond. To completely fill the outer shell of oxygen, which has six electrons in its outer shell, two electrons (one from each hydrogen atom) are needed. Each hydrogen atom needs only a single electron to fill its outer shell, hence the well-known formula H2O. The electrons that are shared between the two elements fill the outer shell of each, making both elements more stable.
Polar Covalent Bonds
There are two types of covalent bonds: polar and nonpolar. In a polar covalent bond, the electrons are unequally shared by the atoms because they are more attracted to one nucleus than the other. The relative attraction of an atom to an electron is known as its electronegativity: atoms that are more attracted to an electron are considered to be more electronegative. Because of the unequal distribution of electrons between the atoms of different elements, a slightly positive (δ+) or slightly negative (δ-) charge develops. This partial charge is known as a dipole; this is an important property of water and accounts for many of its characteristics. The dipole in water occurs because oxygen has a higher electronegativity than hydrogen, which means that the shared electrons spend more time in the vicinity of the oxygen nucleus than they do near the nucleus of the hydrogen atoms.
Nonpolar Covalent Bonds
Nonpolar covalent bonds form between two atoms of the same element or between different elements that share electrons equally. For example, molecular oxygen (O2) is nonpolar because the electrons will be equally distributed between the two oxygen atoms. The four bonds of methane are also considered to be nonpolar because the electronegativies of carbon and hydrogen are nearly identical.
Hydrogen Bonds and Van Der Waals Interactions
Not all bonds are ionic or covalent; weaker bonds can also form between molecules. Two types of weak bonds that frequently occur are hydrogen bonds and van der Waals interactions. Without these two types of bonds, life as we know it would not exist.
Hydrogen bonds provide many of the critical, life-sustaining properties of water and also stabilize the structures of proteins and DNA, the building block of cells. When polar covalent bonds containing hydrogen are formed, the hydrogen atom in that bond has a slightly positive charge (δ+) because the shared electrons are pulled more strongly toward the other element and away from the hydrogen atom. Because the hydrogen has a slightly positive charge, it’s attracted to neighboring negative charges. The weak interaction between the δ+ charge of a hydrogen atom from one molecule and the δ- charge of a more electronegative atom is called a hydrogen bond. Individual hydrogen bonds are weak and easily broken; however, they occur in very large numbers in water and in organic polymers, and the additive force can be very strong. For example, hydrogen bonds are responsible for zipping together the DNA double helix.
Like hydrogen bonds, van der Waals interactions are weak interactions between molecules. Van der Waals attractions can occur between any two or more molecules and are dependent on slight fluctuations of the electron densities, which can lead to slight temporary dipoles around a molecule. For these attractions to happen, the molecules need to be very close to one another. These bonds, along with hydrogen bonds, help form the three-dimensional structures of the proteins in our cells that are required for their proper function.
Interactions between different types of molecules: In this interactive, you can explore how different types of molecules interact with each other based on their bonds. | textbooks/bio/Microbiology/Microbiology_(Boundless)/02%3A_Chemistry/2.02%3A_Chemical_Bonds/2.2.02%3A_Colvalent_Bonds_and_Other_Bonds_and_Interaction.txt |
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