Microbial Ecology and Microbiomes

Microbial Ecology and Microbiomes Fecal Microbiome Transfer: Medicine or Magic? ­ Irritable bowel syndromes (IBS), such as ulcerative colitis and Crohn’s disease, can be debilitating for patients. Symptoms include abdominal pain, fatigue, and severe and persistent diarrhea. Unfortunately, there is no medical cure for these conditions, and existing treatments to alleviate symptoms are expensive and are able to help only certain patients. Researchers are considering an alternative treatment based on the idea of “rebooting” the gut microbiome. A microbiome is the community of all microorganisms in a location, in this case, the human colon. The treatment, called fecal microbiome transfer (FMT), involves transferring a portion of the microbiome from a healthy person into the IBS patient—basically a transfer of feces. The procedure involves emptying the colon (as is done for a colonoscopy) and then introducing fecal microbiota via a tube about the size of a colonoscopy tube. FMT has helped some patients with a related disease caused by Clostridium difficile, but evidence for efficacy of FMT in treating irritable bowel syndrome is mixed; that is, some studies suggest that the procedure might be beneficial, whereas other studies show no positive effect. One FMT recipient experienced significant weight gain, and there is concern about transfer of pathogens, especially enteroviruses. A foundational principle in medicine and science is to base practices and procedures on evidence. Such evidence-based treatments and cures are determined by laboratory research, studies on animals, and numerous human clinical trials. Based on the results of research and human clinical trials, the United States Food and Drug Administration (FDA) approves medical treatments in the United States. FMT, although it has been the focus of multiple research studies, does not yet have data from supervised clinical trials and has not received FDA approval. Imagine you and your team have to make decisions concerning FMT. How would you initially answer these questions? Environmental Microbiology Environmental microbiology is the study of microorganisms as they occur in their natural habitats—the physical localities in which organisms are found. Because of their vast metabolic capacities, microbes flourish in every habitat on Earth, from Antarctic ice to boiling hot springs to bedrock. In the following sections, we will explore the roles microbes play in cycling chemical elements in soil and aquatic habitats. We will also consider the community of microbes in and on humans in hopes of developing new ways to diagnose, treat, or prevent disease. First, however, we turn our attention to the relationships among microbes in communities and between microbes and their habitats. Microbial Ecology LE A R N I N G O U TC O M E S 26.1 Define the terms used to describe microbial relationships within the environment. 26.2 Explain the influences of competition, antagonism, and cooperation on microbial survival. M26_BAUM7206_05_SE_C26.indd 802 1. Should FMT be used routinely to relieve the suffering of IBS patients, even though the procedure has not completed clinical trials and lacks FDA approval? 2. Should all procedures and drugs be held to the same standard of evidence? 3. What other information do you need to make an evidence-based decision? Go to the MasteringMicrobiology Study Area to solve the problem. Microorganisms use a variety of energy sources and grow under a variety of conditions. They adapt to changing conditions, compete with other organisms for scarce resources, and change their habitat in many ways. In some cases, their effects on the environment are undesirable from a human perspective, but in most cases they are beneficial and essential. The study of the interrelationships among microorganisms and the environment is called microbial ecology. Ecologists use the term biodiversity to refer to the number of species living within a given ecosystem, whereas the term biomass refers to the mass of all organisms in an ecosystem. By either measure, microorganisms are the most abundant of all living things: The number of species of microbes exceeds the number of larger organisms, and the biomass of microorganisms living throughout the biosphere—including places that are uninhabitable by plants, animals, or humans—is enormous. The first aspects of microbial ecology we will examine are the levels of microbial associations in the environment. Levels of Microbial Associations in the Environment A variety of terms are used to describe levels of microbial associations in the environment: 11/23/16 3:45 AM       Environmental Microbiology • All the members of a single species in a location is termed a population. • Populations of microorganisms performing metabolically related processes make up groups called guilds. For example, anaerobic fermenters in a habitat make up a guild. • A microbiome, or community, includes all of the microbes in one location, which includes sets of guilds. Microbiomes are typically quite heterogeneous. Only rarely—and usually only in extreme environments—does a microbiome consist of a single population. • Populations and guilds within a community typically reside in their own distinct microhabitats—specific small spaces where conditions are optimal for survival. • Groups of microhabitats form habitats in which microorganisms interact with larger organisms and the environment. Together, the organisms, the environment, and the relationships between the two constitute an ecosystem. • All of the ecosystems taken together constitute the bio­ sphere, that region of Earth inhabited by living organisms. To illustrate these concepts, consider two examples, a plot of soil and the human body (FIGURE 26.1). Soil is composed of tiny particles of rock and organic material, each of which forms a microhabitat for populations of microorganisms. Populations are distributed among the soil particles according to conditions necessary for their growth, including moisture, nutrients, and chemical properties such as pH. Populations of photosynthetic microbes, for example, live near the surface and form a photosynthetic guild, which provides nutrients to other guilds living deeper within the soil. A soil community is composed of all of these populations and guilds, whose activities are a major factor affecting soil quality. Your body is also an ecosystem with many habitats, such as the mouth or the large intestine. An example of a guild in the mouth is sucrose fermenters, which live within biofilms on the surface of teeth. Scientists can now routinely sample an ecosystem, such as soil or the human mouth, and determine the entire composition of all bacteria present in that sample by using next-generation DNA sequencing (NGS; see Chapter 8, Figure 8.10). Such modern methods have dramatically advanced our understanding of microbial ecology. The human intestine is the habitat with the greatest density and diversity of microbes, typically over 1000 species. Microbial guilds in the intestines have more metabolic functions than those of your own cells, contributing to digestion of food and producing nutrients such as vitamins. The microbiome of humans controls our health by affecting nutrition, digestion, immune system activation and inflammation, and possibly diabetes and obesity. Biosphere Soil ecosystem Soil habitats Heterogeneous microbial communities (all guilds together) Guilds of related populations (e.g., photosynthetic microorganisms at surface) Soil particle Populations of microbes microhabitats inhabit microhabitats (e.g., cyanobacteria, algae) Human body ecosystem Mouth habitats Anaerobic tooth crevice microhabitat ▲ FIGURE 26.1 Terms to describe levels of microbial association in the environment. Two environments are considered, soil and the human body. M26_BAUM7206_05_SE_C26.indd 803 11/23/16 3:45 AM ­ 26    Microbial Ecology and Microbiomes hapter       C The Role of Adaptation in Microbial Survival ­ What we might consider a lush ecosystem supports great biodiversity, but many microorganisms also live in what we consider harsh environments. The harsher the environment, the more specially adapted a microbe must be to survive. Some environments cycle between periods of excess and depletion, and the microbes that live in them must be capable of adapting to such constantly varying conditions. Extremophiles— microbes adapted to harsh temperatures, pH levels, or salt concentrations—are so adapted to extreme conditions that they cannot survive anywhere else. Microbial growth can be held in check by competition. The best-adapted microorganisms have traits that provide them advantages in nutrient uptake, reproduction, response to environmental changes, or some other factor. Antagonism, in which a microbe makes some product that actively inhibits the growth of another, may also occur. Although competition may limit microbial growth, rarely does a microorganism outcompete all other rivals; diversity is the norm, not the exception. Microbes often use the waste products of other microbes for their own metabolism, resulting in networks of cooperation. Moreover, one microbe’s metabolic activities sometimes make the environment more favorable for other microbes. Biofilms are examples of microbial cooperation. The relationships among microorganisms and their environment constantly change; each microbe adapts to subtle changes in its environment. Most habitats support successions of microbial populations within a community. By studying how these successions occur, we learn much about the microbes’ effects on the environment. Bioremediation LE A R N I N G O UTC O M E 26.3 Describe the process of bioremediation. Each year, Americans produce more than 150 million tons of solid wastes, accumulated from household, industrial, medical, and agricultural sources; most of it ends up in landfills. A landfill is essentially a large, open pit into which wastes are dumped, compacted, and buried. Soil microbes anaerobically break down biodegradable wastes; methanogens, which are all Archaea, degrade organic molecules to methane. When a landfill is full, it is often covered with soil and revegetated. To prevent leaching of potentially hazardous materials into the soil and groundwater, a landfill pit is lined with clay or plastic, and sand and drainage pipes lining the bottom filter out small particulates and some microorganisms. Unfortunately, chemicals and hazardous compounds might still leak from landfills. Some of these substances are potentially carcinogenic (benzene), others are toxic (gasoline, lead), and still others are recalcitrant (resistant to decay, degradation, or reclamation by natural means). Bioremediation is the use of organisms, particularly microorganisms, to clean up toxic, hazardous, or recalcitrant compounds by degrading them to harmless compounds. Although microorganisms eventually degrade most naturally occurring organic compounds, synthetic compounds are not always easily removed from the environment. Petroleum, pesticides, munitions, herbicides, and industrial chemicals that accumulate in soil and water are degraded only slowly by naturally existing microbes. BENEFICIAL MICROBES Oil-Eating Microbes to the Rescue in the Gulf In April 2010, the worst oil spill in U.S. history occurred when an oil rig explosion led to the release of millions of gallons of oil into the Gulf of Mexico. Environmentalists, government officials, oil industry executives, and residents of the Gulf states immediately began efforts to minimize damage to the marine and wildlife habitats caused by this oil spill. By August, the cleanup crews had removed only about 2% of the oil from the Gulf. The huge oil slick, however, had seemingly disappeared. Where did all the oil go? Although some of the oil simply evaporated, scientists determined that a significant portion of it was devoured by oil-eating fungi and bacteria, such as Alcanivorax. M26_BAUM7206_05_SE_C26.indd 804 Alcanivorax is a bacterium that is native to the Gulf region and is named for its voracious appetite for alkanes, which are a major component of petroleum. Alcanivorax, along with other native species of oil-eating bacteria and fungi, metabolized much of the oil, converting it into carbon dioxide and water. Scientists were heartened to see that oil-eating microbes grew and reproduced faster in the warm waters of the Gulf of Mexico than they did in the cool waters off the Alaskan coast where the Exxon Valdez spill occurred in 1989. The long-term effects of the oil spill on the shores of the Gulf are not yet known, though the ecosystem has proved to be surprisingly resilient, thanks in part to the bioremediation efforts of oil-eating microbes. 11/23/16 3:45 AM       Environmental Microbiology The reason that one synthetic molecule is biodegradable while another is recalcitrant relates to chemical structure; sometimes a subtle variation—perhaps in a single atom or bond—can be enough to make a difference. Most recalcitrant molecules resist microbial degradation because the microbes lack enzymes capable of degrading them; after all, until very recently, synthetic compounds didn’t even exist. A widely known example of bioremediation is the microbial degradation of complex hydrocarbons released in an oil spill (see Beneficial Microbes: Oil-Eating Microbes to the Rescue in the Gulf). Cleanup crews can enhance bioremediation by applying nitrogen and phosphorus fertilizers to stimulate microbial growth. The Problem of Acid Mine Drainage LE A R N I N G O U TC O M E water is also unfit for human consumption or recreational use. The EPA requires that strip mines be reburied as soon as possible to halt the processes. Underground mining operations pose similar (but somewhat less severe) problems resulting from runoff from mine tailings, which are the low-grade ores remaining after the extraction of higher-grade ores. Typically, subsurface mines are backfilled as richer veins of minerals are depleted, thus limiting the exposure of iron sulfides to oxygen. Although acid mine drainage is generally devastating to the environment, some microbes—mostly archaea—actually flourish in acidic conditions. One unique archaeal species, found in mine drainage in California, is Ferroplasma acidarma­ nus (fe’rō-plaz-ma a-sid’ ar-mă-nŭs; FIGURE 26.3), which lives at a pH near zero and obtains its energy from oxidizing pyrite in mine sediments. Such an organism is just one example of the incredible diversity of microorganisms that colonize every habitat on Earth. 26.4 Discuss the problem of acid mine drainage. Acid mine drainage is a serious environmental problem resulting from the exposure of certain metal ores to oxygen and microbial action (FIGURE 26.2). Coal deposits are often found associated with reduced metal compounds such as pyrite (FeS2). Strip-mining for coal exposes pyrite to oxygen in the air, which oxidizes the iron, and bacteria such as Thiobacillus (thī-ō-băsil´ŭs) oxidize the sulfur. Rainwater then leaches the oxidized compounds from the soil to form sulfuric acid (H2SO4), which is carried into streams and rivers, reducing the pH enough (pH 2.5–4.5) to kill fish, plants, and other organisms. Such acidic ▲ FIGURE 26.2 The effects of acid mine drainage. Upon exposure to air, iron and sulfur in water leached from mine tailings are oxidized to Fe3+ . The activity of iron-sulfur bacteria can reduce the pH of the water to a level that kills plants and animals. M26_BAUM7206_05_SE_C26.indd 805 ▲ FIGURE 26.3 An acid-loving microbe. The filamentous archaeon Ferroplasma acidarmanus growing as long filaments in acid mine runoff (pH 3.6) in California. The ore from this mine is rich in iron. 11/23/16 3:45 AM 26    Microbial Ecology and Microbiomes ­ The Roles of Microorganisms in Biogeochemical Cycles 26.8 26.9 26.10 Six chemical elements make up most macromolecules—the building blocks of cells. These are hydrogen, oxygen, carbon, nitrogen, sulfur, and phosphorus. Most elements are tied up in chemical and physical forms unavailable to organisms. The release of many elements from rock, for example, requires years of degradation by rain, wind, and microbes, so these processes contribute little to the day-today availability of nutrients for living things. As a consequence, the actions of organisms in recycling elements are the major components of biogeochemical cycles—the processes by which organisms convert elements from one form to another, typically between oxidized and reduced forms. Microbes are the primary biological components of the biogeochemical cycles. The following sections examine the biogeochemical cycles for carbon, nitrogen, sulfur, phosphorus, and some trace metals. The Carbon Cycle Carbon is the fundamental element of all organic chemicals. The continual cycling of carbon in the form of organic molecules constitutes the majority of the carbon cycle (FIGURE 26.4). Carbon in rocks and sediments has a very low turnover rate (rate of conversion to other forms)—this form of carbon is incorporated into organic chemicals only slowly over long periods of time. The start of the carbon cycle is autotrophy. Photoautotrophic primary producers (cyanobacteria, green and purple sulfur bacteria, green and purple nonsulfur bacteria, algae, photosynthetic protozoa, and plants) convert CO2 to organic molecules—a process known as carbon fixation. Primary producers use the Calvin-Benson cycle to fix carbon (see Figure 5.26). The enzyme that fixes carbon dioxide, rubisco, is likely the most abundant enzyme on Earth. Photoautotrophs are restricted to the surfaces of soil and water systems because phototrophs require light. Chemoautotrophs can also fix carbon, but they acquire energy from H2S or other inorganic molecules; therefore, chemoautotrophs are found in a greater variety of habitats. However, they do not fix as much carbon as photoautotrophs and are not as important in the carbon cycle. Heterotrophs catabolize some organic molecules for energy in respiration, resulting in the release of CO2. Other organic molecules made by autotrophs are subsequently incorporated M26_BAUM7206_05_SE_C26.indd 806 Decomposition 26.6 26.7 carbon, nitrogen, sulfur, phosphorus, and trace metals. Explain the work of microorganisms in the carbon cycle. Contrast the actions of microbes involved in nitrogen fixation, nitrification, ammonification, denitrification, and anammox reactions. Describe the reduction and oxidation of sulfur by microbes. Define eutrophication, and explain in general how it arises. Explain the use of microbes in biomining. Methane Fungi, bacteria Respiration Autotrophs (plants, algae, photoautotrophic bacteria, protozoa, chemoautotrophic bacteria) Combustion 26.5 Contrast the processes by which microorganisms cycle Fixation LE A R N I N G O U TC O M E S Atmospheric CO2 and CO2 dissolved in water Anaerobic oxidation hapter       C Consumption Animals Dead organisms Fossil fuels Plastics and other artificial products ▲ FIGURE 26.4 Simplified carbon cycle. The most mobile form of carbon in the cycle is CO2; this inorganic molecule is fixed by autotrophs, which incorporate its carbon into organic molecules. Processes that are performed solely by prokaryotes are represented by red lines–only prokaryotes produce methane and generate fossil fuels. Blue lines indicate processes carried out by both prokaryotes and eukaryotes. Only humans synthesize plastics and other artificial products from fossil fuels (green arrow). into the tissues of heterotrophs. There they remain until the organism dies, when decomposers catabolize the organic materials, releasing CO2—the reverse of autotrophy. Human and animal waste is also broken down by decomposers. The release of CO2 starts the cycle over again as primary producers fix CO2 once more into organic material. A rough balance exists between CO2 fixation and CO2 release. Many scientists are concerned by a growing imbalance in the carbon cycle due to an overabundance of CO2 in the atmosphere. The burning of fossil fuels and wood sends tons of CO2 into the atmosphere each year. Furthermore, in waterlogged soils, sewage treatment plants, landfills, and the digestive systems of ruminants, methanogens actively release methane gas (CH4), which can be photochemically transformed into CO (carbon monoxide) and CO2. Methane-oxidizing bacteria, working in conjunction with methanogens, can also directly convert methane to CO2. Worldwide, the rate of CO2 production exceeds the rate at which it is being incorporated into organic material. Carbon dioxide and methane are called “greenhouse gases” because their presence in the atmosphere prevents the escape of some infrared radiation into space, redirecting heat back to Earth, much as the glass panes of a greenhouse trap heat. Although this “greenhouse effect” is essential to life on Earth, it may result in climate change. The Nitrogen Cycle Nitrogen is an important nutritional element required by organisms as a component of proteins, nucleic acids, and other compounds. Most nitrogen in the environment is in the 11/23/16 3:45 AM       Environmental Microbiology ­ ­ N2 in atmosphere Nitrogen fixation NO2– Assimilation Organisms (proteins, nucleic acids, etc.) NO3– NH3 Ammonification Wastes, dead cells NO2– Deamination NH4+ Anammox reactions Denitrification Nitrification fix nitrogen only at night, when oxygen-producing photosynthesis does not occur, thereby separating nitrogen fixation from photosynthesis in time rather than in space. Nitrogen fixers may be free living or symbiotic. Among the free-living nitrogen fixers are aerobic species of Azotobacter (ā-zō-tō-bak’ter), anaerobic species of Bacillus and Clostridium, and deep-sea communities of archaea and bacteria. When they die, these microbes release fixed nitrogen into the soil or water, where it becomes available to other organisms, notably plants. None of the free-living genera are directly associated with the plants they fertilize. Symbiotic nitrogen fixers, in contrast, live in direct association with plants, forming root nodules on legumes (e.g., peas and peanuts; see Figure 11.20). The predominant genus of nitrogen-fixing, symbiotic bacteria is Rhizobium (rī-zō’bē-ŭm). In the symbiosis, the plants provide nutrients and an anaerobic environment in the nodules, while the bacteria provide usable nitrogen to the plant. Farmers do not have to apply nitrogen fertilizers to legume crops because nitrogen fixers provide enough. Bacteria and fungi in the soil decompose wastes and dead organisms, disassembling proteins into their constituent amino acids, which then undergo deamination (removal of their amino groups). Amino groups are converted to ammonia (NH3)—a process called ammonification. In dry or alkaline soils, NH3 escapes as a gas into the atmosphere, but in moist soils, NH3 is converted to ammonium ion (NH4+ ), which organisms absorb, or ammonium is oxidized. In nitrification, ammonium is oxidized to nitrate (NO3- ) via a two-step process requiring autotrophic archaea and bacteria. In the best-studied nitrification pathway, species of the bacteria Nitrosomonas (nī-trō-sō-mō’nas) convert NH4+ to nitrite (NO2- ), which is toxic to plants. Fortunately, Nitrosomonas spp. are usually found in association with species of the bacterium Nitrobacter (nī-trō-bak’ter) that rapidly convert nitrite to nitrate (NO3- ), which is soluble and can be used by plants. The soluble nature of nitrate, however, means that it is leached from the soil by water and accumulates in groundwater, lakes, and rivers. Certain microorganisms in waterlogged soils perform denitrification, in which NO3- is oxidized to N2 by anaerobic respiration. N2 gas escapes into the atmosphere. Many organisms can incorporate inorganic nitrogen compounds into organic compounds. An important aspect of the nitrogen cycle is anaerobic ammo­ nium oxidation, or anammox. Anammox prokaryotes oxidize 30% to 50% of the world’s ammonium into nitrogen gas using nitrite as an electron acceptor. ­ ­ atmosphere as dinitrogen gas (N2), which is unusable by most organisms. The majority of organisms acquire nitrogen as part of organic molecules or from soluble inorganic nitrogen compounds found in limited quantities in soil and water. These include nitrate, nitrite, and ammonia. Microbes cycle nitrogen atoms from dead organic materials and animal wastes to these soluble forms of nitrogen. They also cycle nitrogen between the biosphere and the atmosphere. FIGURE 26.5 summarizes the basic processes involved in the nitrogen cycle—nitrogen fixation, ammonification, nitrification, denitrification, and anammox reactions. Nitrogen fixation, a process whereby gaseous nitrogen (N2) is reduced to ammonia (NH3), is an energy-expensive process in which the extremely stable nitrogen-nitrogen triple bond is broken in a reaction catalyzed by the enzyme nitrogenase. A limited number of prokaryotes—but no eukaryotes—fix nitrogen. Nitrogenase functions only in the complete absence of oxygen, a condition that presents no problem for anaerobes. Aerobic nitrogen fixers, in contrast, must protect nitrogenase from oxygen. They can do this in a number of ways. For example, some aerobes use oxygen at such a high rate that it does not diffuse into the interior of the cell, where nitrogenase is sequestered. Some cyanobacteria form thick-walled, nonphotosynthetic cells called heterocysts to protect nitrogenase from oxygen in the environment as well as from the oxygen generated during photosynthesis (see Figure 11.14a). Other cyanobacteria The Sulfur Cycle Nitrification ▲ FIGURE 26.5 Simplified nitrogen cycle. Even though nitrogen gas (N2) is the most common form of nitrogen in the environment, most organisms cannot use it. To become available for their use, nitrogen from the atmosphere must be converted into ammonia (NH3), a process that is carried out by the very few species of nitrogen-fixing prokaryotes. Processes that are performed solely by prokaryotes are represented by red lines. Blue lines indicate processes carried out by both prokaryotes and eukaryotes. Nitrification is the multistep conversion of ammonia or ammonium to nitrate. M26_BAUM7206_05_SE_C26.indd 807 The sulfur cycle involves moving sulfur between several oxidation states (FIGURE 26.6). Bacteria decompose dead organisms, releasing sulfur-containing amino acids into the environment. Sulfur released from amino acids is converted to its most reduced form, hydrogen sulfide (H2S), by microorganisms via a process called sulfur dissimilation. H2S is oxidized to elemental sulfur (S0) and then to sulfate (SO42- ) under various conditions and by various organisms, including 11/23/16 3:45 AM ­ 26    Microbial Ecology and Microbiomes hapter       C Amino acids Proteins from dead organisms Animal proteins Dissimilation Plant, algal, and prokaryotic proteins Reduction H2S SO42– Oxidation Oxidation S0 ▲ FIGURE 26.6 Simplified sulfur cycle. The two main constituents of this cycle are hydrogen sulfide (H2S) and sulfate (SO42- ), the fully reduced and oxidized forms of sulfur, respectively. Processes that are performed solely by prokaryotes are represented by red lines. Blue lines indicate processes carried out by both prokaryotes and eukaryotes. ▲ FIGURE 26.7 Eutrophication. Such overgrowth of cyanobacteria and algae can occur when there is an excess of nutrients in water, as seen here in Dianchi Lake in Kunming, Yunnan province, Peoples Republic of China. nonphotosynthetic autotrophs such as Thiobacillus and Beggiatoa (bej’jē-a-tō’a) photoautotrophic green and purple sulfur bacteria. Sulfate is the most readily usable form of sulfur for plants and algae, which animals then eat. Anaerobic respiration by the bacterium Desulfovibrio (dē’sul-fō-vib’rē-ō) reduces SO42- back to H2S. Thus, the two major inorganic constituents of the sulfur cycle are H2S and SO42- . The Phosphorus Cycle Unlike nitrogen and sulfur, phosphorus undergoes little change in oxidation state in the environment. Phosphorus usually exists in the environment, though often in a metabolically limited amount. Organisms typically use phosphorus in phosphate ion (PO43- ). The phosphorus cycle involves the movement of phosphorus from insoluble to soluble forms available for uptake by organisms and the conversion of phosphorus from organic to inorganic forms by pH-dependent processes. No gaseous form exists to be lost to the atmosphere, but dissolved phosphates do accumulate in water, particularly the oceans, and organic forms of phosphorus are deposited in surface soils following the decomposition of dead animals and plants. Too much phosphorus can be a problem in a habitat; for example, agricultural fertilizers rich in phosphate are easily leached from fields by rain. The resulting runoff into rivers and lakes can result in eutrophication (yū-trō’fi-kā’shŭn)— the overgrowth of microorganisms (particularly algae and cyanobacteria) in nutrient-rich waters (FIGURE 26.7). Such overgrowth, called a bloom, depletes oxygen from the water, killing aerobic organisms, such as fish. Anaerobic organisms then take over the water system, leading to an increased production of H2S and the release of foul odors. When excess M26_BAUM7206_05_SE_C26.indd 808 phosphate (and nitrogen) are removed, such a water system recovers over time. The Cycling of Metals Metal ions, including Fe2+ , Zn2+ , Cu2+ , Cd2+ , and Mg2+ , are important microbial nutrients. Though they are needed only in trace amounts, they can nonetheless be limiting factors in the growth of organisms. Many metals—including the most important trace metal, iron—are present in the natural environment in the form of poorly soluble molecules in rocks, soils, and sediments and are generally unavailable for uptake by organisms. The cycling of metal ions involves primarily a transition from an insoluble to a soluble form, allowing them to be used by organisms and to move through the environment. In the ecosystem of the human body, iron is sequestered so as to not be available for invading pathogens to use; this constitutes part of innate immunity (see Chapter 15). Generally, oxidized metal ions (those having fewer electrons) dissolve more readily than reduced ions of the same metal. Miners have successfully used biomining—a process in which microbes (typically archaea) oxidize copper, gold, uranium, or other metals so that the oxidized metallic ions dissolve in water. The miners can then extract the mineral-laden water and reduce the ions, which causes the metals to come out of solution where the miner can collect them. Biogeochemical cycles are sustained by microorganisms, most of which live in soil. Next we examine aspects of soil microbes and their habitats. 11/23/16 3:45 AM       Environmental Microbiology Soil Microbiology LE A R N I N G O U TC O M E 26.11 Identify five factors affecting microbial abundance in soils. 26.12 Describe three human and plant diseases caused by soil microbes. Soil microbiology examines the roles played by organisms living in soil. They rarely cause human disease, though plant pathogens are prevalent in soils and are agriculturally and economically important. The Nature of Soils Soil arises both from the weathering of rocks and through the actions of microorganisms, which produce wastes and organic materials needed to support more complex life forms, such as plants. Soil is composed of two major layers (FIGURE 26.8): topsoil, which is rich in humus (organic chemicals); and subsoil, which is composed primarily of inorganic materials. Soil overlies bedrock, which contains little organic material. Most microorganisms are found in topsoil, where the richness of the organic deposits sustain a large biomass. Topsoil itself, however, is highly heterogeneous, and therefore different kinds and amounts of microbes are found in various soils around the world. Factors Affecting Microbial Abundance in Soils Several environmental factors influence the density and the composition of the microbiome within a soil, including the amount of water, availability of oxygen and other electron acceptors, acidity, temperature, and the availability of nutrients. Moisture and oxygen content are closely linked in soils. Moisture is essential for microbial survival; microbes exhibit Topsoil Subsoil Organics, nutrients Numbers of microorganisms Decrease with depth Decrease with depth but still present in bedrock Bedrock ▲ FIGURE 26.8 The soil layers and the distributions of nutrients and microorganisms within them. Although topsoils in general are richer in nutrients and microbes than are subsoils, the nutrient and microbial content of topsoils is highly variable. M26_BAUM7206_05_SE_C26.indd 809 lower metabolic activity, are present in lower numbers, and are less diverse in dry soils than in moist soils. Because oxygen dissolves poorly in water, moist soils have a lower oxygen content than drier soils. When soil is waterlogged, anaerobes predominate, even at the surface. Weather patterns also affect oxygen content, as the presence or absence of rainwater determines moisture and thus dissolved oxygen. The pH of a soil determines in part whether it favors bacteria or fungi. Highly acidic and highly basic soils favor fungi over bacteria, though fungi typically prefer acidic conditions. Bacteria dominate when soil pH is closer to 7. Most soil organisms are mesophiles and prefer temperatures between 20°C and 50°C. Thus, most soil microbes live quite well in areas where winters and summers are not too extreme. Psychrophiles grow only in consistently cold environments and cannot survive in soils that experience spring thawing; the opposite is true for thermophiles, which cannot survive where winters are harsh. Nutrient availability also affects microbial diversity in soil habitats. Most soil microbes are heterotrophic, utilizing organic matter in the soil. The biomass of a microbial community is determined more by the amount of organic material than by the kind of organic material: any soil that has a relatively constant input of organic material can support a wider array of microorganisms than soil that is more barren. Microbial Populations in Soils Because of the variety of soils, microbial populations differ tremendously from soil to soil and even within the same soil over the course of a season. Bacteria are numerous, and diverse inhabitants of soil and are found in all soil layers. Archaea are present in soils, but the inability to culture many of them has limited our ability to study them. The fungi are also a nearly ubiquitous group of soil microorganisms. Free-living and symbiotic fungi are found only in topsoil, where they can form gigantic mycelia that cover acres. Many viruses, mostly bacteriophages, are found within soils. Some algae and protozoa also live in soils. Soil algae live on or near the surface because, as photoautotrophs, they require light. Protozoa are mobile and move through the soil, grazing on other microbes. For the most part, protozoa require oxygen and remain in the topsoil. Neither algae nor protozoa can withstand dramatic environmental changes or the introduction of pollutants. Wherever present, microbes perform a variety of necessary functions. They cycle nitrogen, sulfur, phosphorus, and other elements, converting them into usable forms. Microbes degrade dead organisms and their wastes, and some can clean up industrial pollutants. Further, microbes produce an incredible variety of compounds that have potential human uses. Researchers search natural populations of microbes to discover species that produce valuable chemicals or have useful biological functions. The capability of modern scientists to directly extract DNA from soil, skipping the need to culture soil microorganisms, 11/23/16 3:45 AM 26    Microbial Ecology and Microbiomes ­ hapter       C allows dramatic advances in our understanding of the structure and function of soil microbiomes. TABLE 26.1 Selected Soilborne Diseases of Humans and Plants Soilborne Diseases of Humans and Plants Microorganism Although the majority of soil microorganisms are harmless, there are exceptions. Soilborne infections of humans generally result from either direct contact with, ingestion of, or inhalation of microorganisms deposited in soil in animal or human feces or urine. In some cases, the microbes live and replicate in the soil, but in most cases soil is simply a vehicle for moving the pathogen from one host to another. The majority of soilborne disease agents are fungal or bacterial. Few soil protozoa or viruses cause disease. Soil pathogens include the bacterium Bacillus anthracis (an-thrā’sis), the causative agent of anthrax, which produces endospores shed from the skins of infected livestock. Endospores may remain dormant in soil for decades or centuries. Disturbing the soil can lead to infection if endospores enter cuts or abrasions on the skin (cutaneous anthrax) or are inhaled into the lungs (inhalation anthrax). Histoplasma capsulatum (his-tō-plaz’mă kap-soo-lā’tŭm) is a fungus that causes histoplasmosis—a serious respiratory tract infection. Histoplasma grows in soil and is also deposited there as spores in the droppings of infected birds and bats. The spores can be inhaled by humans when contaminated soil is disturbed. Hantavirus (han’tā-vī-rŭs) pulmonary syndrome is a life-threatening viral respiratory disease acquired via the inhalation of soil contaminated by mouse droppings and urine containing Hantavirus (see Emerging Disease Case Study on p. 438). Hantavirus has been found throughout North America. Soil contains many more plant pathogens than human pathogens. Microbial plant infections are generally characterized by one or more of the following signs: necrosis (rot), cankers/lesions, wilt (droopiness), blight (loss of foliage), galls (tumors), growth aberrations (too much or too little), or bleaching (loss of chlorophyll). Bacteria, fungi, and viruses all cause diseases in plants and spread either as airborne spores, through roots or wounds, or by insects. TABLE 26.1 lists selected bacterial, fungal, and viral soilborne diseases of humans and plants. Bacteria Aquatic Microbiology LE A R N I N G O U TC O M E 26.13 Compare the characteristics and microbial populations of freshwater and marine ecosystems. Aquatic microbiologists study microorganisms living in freshwater and marine environments. Compared to soil habitats, water ecosystems support fewer microbes overall because nutrients are diluted. Many organisms that live in aquatic systems exist in biofilms attached to surfaces. Biofilms allow M26_BAUM7206_05_SE_C26.indd 810 Host Disease Bacillus anthracis Humans Anthrax Clostridium tetani Humans Tetanus Agrobacterium tumefaciens Plants Crown gall disease Ralstonia solanacearum Plants Potato wilt Streptomyces scabies Plants Potato scab Histoplasma capsulatum Humans Histoplasmosis Blastomyces dermatitidis Humans Blastomycosis Coccidioides immitis Humans Coccidioidomycosis Polymyxa spp. Plants Root rot in cereals Fusarium oxysporum Plants Root rot in many plants Phytophthora cinnamomi Plants Potato blight; root rot in many plants Hantavirus Humans Hantavirus pulmonary syndrome Tobamovirus tobacco mosaic virus Plants Necrotic spots in various plants Furovirus soil-borne wheat mosaic virus Plants Mosaic disease in winter wheat and barley Fungi Viruses aquatic organisms to concentrate enough nutrients to sustain growth; without forming biofilms, they likely would starve. Types of Aquatic Habitats Aquatic habitats are divided primarily into freshwater and marine systems. Freshwater systems, which are characterized by low salt content (about 0.05%), include groundwater, water from deep wells and springs, and surface water in the form of lakes, streams, rivers, shallow wells, and springs. Marine environments, characterized by a salt content of about 3.5%, encompass the open ocean and coastal waters, such as bays, estuaries, and lagoons. Natural aquatic systems can be greatly affected by the release of so-called domestic water, which is water resulting from the treatment of sewage and industrial waste. Domestic water released into the environment affects water chemistry and the microorganisms living in the water. Changing levels of chemicals cause increases or decreases in microbial numbers. Furthermore, faulty treatment of sewage leads to contamination of natural water systems with pathogenic microorganisms. Freshwater Ecosystems Microorganisms become distributed vertically within lake systems according to oxygen availability, light intensity, and temperature. Surface waters are high in 11/23/16 3:45 AM       Environmental Microbiology Littoral zone Nutrients and light Numbers of microorganisms Temperature Decrease with depth Limnetic zone Decrease with depth Pressure Decreases with depth Profundal zone –1637 m (–5371 ft) Benthic zone (a) Lake Baikal, Russia Abyssal zone Increases with depth –11,521 m (–37,797 ft) (b) Mariana Trench, Pacific Ocean ▲ FIGURE 26.9 Vertical zonation in deep bodies of water. (a) Lake Baikal, Russia, the world’s deepest freshwater lake, and (b) the Mariana Trench in the Pacific Ocean, the deepest place in the ocean. Both deep lakes and oceans can be divided into zones that vary with respect to light penetration, concentration of nutrients, temperature, and pressure—and thus the types and abundance of microorganisms. Why would a bacterium from the bottom of Lake Baikal die in the Mariana Trench? Figure 26.9 A bacterium from the bottom of Lake Baikal could not survive the even greater pressure and the salinity of the seawater deep in the Mariana Trench. oxygen, well lighted, and warmer than deeper waters. In large lakes, wave action continually mixes nutrients, oxygen, and organisms, which allows efficient utilization of resources. In stagnant waters, oxygen is readily depleted, resulting in more anaerobic metabolism and poorer water quality. Scientists observe four zones in deep lakes (FIGURE 26.9a): The littoral zone (li’ter-al) is the area along the shoreline where nutrients enter the lake. The littoral zone is shallow, and light penetrates it; most microbes live here. The limnetic zone (lim-net’ik) is the upper layer of water away from the shore. Photoautotrophs reside here and in the littoral zone. The profundal zone (prō-fun’dal) is the deeper water beneath the limnetic zone. It has a lesser oxygen content and more diffuse light than the previous two zones. Some photosynthetic organisms, such as purple and green sulfur bacteria, perform anaerobic photosynthesis here. Beneath this is the benthic zone (ben’thik), which encompasses deeper lake water and M26_BAUM7206_05_SE_C26.indd 811 sediments. Anaerobic bacteria in the sediments produce H2S, which is used by organisms nearer the surface. In contrast to lakes, streams and rivers are more uniform because organisms and nutrients are swept along and mixed. Biofilms are particularly important in moving waterways, and the majority of organisms live toward the edges, where surfaces are available, currents are less severe, and organic materials enter the water. Marine Ecosystems Marine ecosystems are typically nutrient poor, dark, cold, and subject to great pressure. Photoautotrophic prokaryotes, diatoms, dinoflagellates, and algae are found near the surface. Most marine waters are extreme environments inhabited only by highly specialized microorganisms. All microbes in marine systems must be salt tolerant and possess highly efficient nutrient-uptake mechanisms to compensate for the scarcity of nutrients. 11/23/16 3:45 AM 26    Microbial Ecology and Microbiomes ­ hapter       C As with freshwater lake systems, scientists delineate zones in the oceans (FIGURE 26.9b). The majority of marine microorganisms are found in the littoral zone, where nutrient levels are high and light is available for photosynthesis. The benthic zone makes up the majority of the marine environment. Oceans have a fifth zone—the abyssal zone (a-bis’sal), which encompasses deep ocean trenches. Even though the benthic and abyssal zones have sparse nutrients, they still support microbial growth, particularly around hydrothermal vents located in the abyssal zone. Such vents spew superheated, nutrient-rich water, providing nutrients and an energy source for thermophilic chemoautotrophic anaerobes, which in turn support a variety of invertebrate and vertebrate animals. Specialized Novel Aquatic Ecosystems In addition to the two broad categories of water systems just described, many distinctive aquatic ecosystems also exist, including salt lakes, iron springs, and sulfur springs. Each of these systems is inhabited by specialized microorganisms that are highly adapted to the conditions. The Great Salt Lake in Utah, for example, has a salt concentration of 5% to 7%, depending on its level, and contains the extreme halophile Halobacterium salinarium (hā’lō-bak-tēr’ē-ŭmsal-ē-nar’ē-ŭm), an archaeon that thrives in highly saline water. TELL ME WHY A blogger stated that germs (microorganisms) are dangerous and should be avoided in all cases. Why is this idea wrong? Biological Warfare and Bioterrorism ­ The properties of microorganisms that allow scientists to manipulate organisms to make advancements in medicine, food production, and industry also enable humans to fashion microbes into biological weapons, which can be directed at people, livestock, or crops. Bioterrorism, the use of microbes or their toxins to terrorize human populations, is a topic of major concern in today’s world. A topic of growing concern is agroterrorism—the bioterrorist use of microbes to destroy a food supply. International treaties and laws of the United States, Great Britain, and other countries prohibit the use of biological weapons. Assessing Microorganisms as Potential Agents of Warfare or Terror LE A R N I N G O U TC O M E 26.14 Identify the criteria used to assess microorganisms for potential use as biological weapons or agents of bioterrorism. Many microorganisms cause disease, but not all disease-causing organisms have potential as biological weapons. Governments M26_BAUM7206_05_SE_C26.indd 812 establish criteria for evaluating the potential of microorganisms to be “weaponized.” Establishing such criteria helps focus research and defense efforts where they are needed most and facilitates efforts to develop better response and deterrence capabilities. Criteria for Assessing Biological Threats to Humans In the United States, the assessment of a potential biological threat to humans is based on the following four criteria: • Public health impact. This criterion relates to the ability of hospitals and clinics to deal effectively with numerous casualties. The more casualties, the more difficult it is for hospitals and clinics to effectively respond to the needs of all patients. If an agent causes numerous serious cases, emergency response systems could be overwhelmed and even cease to function. If an agent is highly lethal, proper disposal of bodies might become difficult, which would contribute to the spread of disease. • Delivery potential. This criterion evaluates how easily an agent can be introduced into a population. The more people that can be infected at one time, the more devastating a primary attack. If an introduced agent spreads on its own through a population, secondary and tertiary waves of illness will augment the number of casualties. Also assessed as part of delivery potential are ease of mass production (the easier an agent is to produce in quantity, the greater its potential threat), availability (the more prevalent it is in the environment, the easier it is to obtain and weaponize), and environmental stability (the longer it remains infective once released, the greater the threat). • Public perception. This criterion evaluates the effect of public fear on the ability of response personnel to control a disease outbreak following an attack. Agents with high mortality, few treatment options, and no vaccine instill greater fear into a populace, making quarantine (isolating infected and sick patients from the rest of the population) difficult to enforce. The resulting chaos could dramatically decrease the ability of response personnel to control disease transmission and treat patients. • Public health preparedness. This criterion assesses existing response measures and attempts to identify improvements needed in the health care infrastructure to prepare for a biological attack. Diagnosis and recognition involve proper surveillance and training medical personnel to ascertain whether an attack has occurred. Once an attack has been confirmed, predetermined responses are required to reduce confusion and allow rapid control of the situation. Public health preparedness also involves funding for research and development of new vaccines, treatments, and diagnostic capabilities. When assessing a threat, government authorities assign each potential bioterrorist agent a score for each of the criteria. Agents with the highest total scores are considered the most serious threats. 11/23/16 3:45 AM       Biological Warfare and Bioterrorism The criteria used to evaluate biological threats to livestock and poultry include agricultural impact, delivery potential, and analysis to determine if the outbreak is the result of terrorism or is a naturally occurring event. Infectious agents prove the most devastating for agricultural livestock kept in large herds or flocks. Many animal pathogens exist naturally in soil or are already endemic in livestock and poultry, so they can be easily obtained and readily grown in large quantities. The highly infectious nature of some agents means that by the time a disease is recognized, much of a herd is infected already, so all must be destroyed to control an outbreak. Further, some pathogens can persist in the soil even after the animals are destroyed. Many animal diseases are spread either by contact or by inhalation, thus making attack easier for a terrorist. Though highly contagious among animals, most are not infectious to humans, making them “safe” for terrorists to handle. Criteria for Assessing Biological Threats to Agricultural Crops Plant diseases are generally not as contagious as animal or human diseases. Threats to crops are evaluated on predicted extent of crop loss, delivery and dissemination potential, and containment potential. Plant pathogens that either cause severe crop loss or produce toxins are considered the greatest threats. Such agents already exist in the environment and can be readily obtained; however, plant pathogens are not as easily mass-produced as animal agents. Plant pathogens that can be spread systematically through fields by natural means, such as through contaminated soil or by insects, could remain in the environment even after destruction of the target crop. Successive plantings in contaminated fields could result in continued crop loss for as long as the agent persists. Because the causes of many plant diseases are not easily diagnosed, such a pathogen could be widely disseminated before response measures are instituted. Economic losses would be staggering, particularly given that embargos on affected crops would likely remain in place for years after an attack. Known Microbial Threats In the following sections, we briefly discuss some of the microorganisms currently considered threats as agents of bioterrorism. Note that as threat assessments become more refined and technology advances, the list of known bioterrorist agents is likely to change. Human Pathogens The National Institute of Allergy and Infectious Diseases (NIAID) categorizes biological agents that could be used against humans into three categories (TABLE 26.2 on p. 814). Category A agents are those with the greatest potentials as weapons. Cat­ egory B agents have some potential as weapons but for various M26_BAUM7206_05_SE_C26.indd 813 reasons are not as dangerous as category A agents (most lack the potential to cause mass casualties). Category C agents are potential threats; not enough is currently known about them to determine their true potential as weapons. Agents in all three categories are known as biological select agents or more simply as select agents. Biomedical research with select agents is carefully regulated. Research that could be misapplied to bioterrorism is called dual use research of concern (DURC). Government agencies have additional special oversight over DURC. Smallpox currently tops the list of bioterrorist threats. Fortunately, it is difficult for would-be terrorists to acquire viral samples for propagation; it also takes a high degree of skill, in addition to specific containment facilities, to work with smallpox virus. An effective vaccine is available, and the vaccine is effective when administered soon after infection. Animal Pathogens Biological agents against animals are also divided into categories, with category A agents being the most dangerous. Whereas many potential agents are spread via inhalation, others are spread by insect vectors, making them less likely to be used as weapons. Some agents infect wild animal populations in addition to livestock, potentially amplifying any outbreak that might occur. Foot-and-mouth disease virus, the most dangerous of potential agroterrorism agents, affects all wild and domestic cloven-hoofed animals. The virus is spread by aerosols and by direct or indirect contact. Humans can transport it from herd to herd on their person, on farm equipment, or through the movement of animals between auctions and farms. Any appearance of foot-and-mouth disease on a farm requires destruction of entire herds, complete disinfection of all areas occupied by the herd, and disposal of all animals by burning or burial. A vaccine exists but not in sufficient quantities to protect all animals. Plant Pathogens Many plant pathogens exist, but the categorization of plant pathogens as terrorist agents lags behind similar efforts for humans and animals. Most potential agents are fungi whose dissemination could easily result in contamination of soils, which would be difficult to neutralize. Attacks against grains, corn, rice, and potatoes are considered the most dangerous because they would have significant negative effects on national economies and food supplies. All of the agents are naturally present, so detecting the difference between a natural outbreak and an intentional attack would be difficult. Defense Against Bioterrorism No defense can completely prevent a carefully planned biological attack against any group or nation. However, much can be done to limit the effect of an attack. The key is coupling surveillance—the active diagnosis and tracking of human, animal, and plant diseases—with effective response protocols. Because category A human biological agents are not common, the appearance of more than a few scattered cases is ­ Criteria for Assessing Biological Threats to Livestock and Poultry 11/23/16 3:45 AM 26    Microbial Ecology and Microbiomes ­ hapter       C TABLE 26.2 National Institute of Allergy and Infectious Diseases (NIAID) Microbial Bioterrorist Threats to Humans Disease Agent Natural Source Category A Threats: Highest Priority Smallpox Variola (Orthopoxvirus) None Anthrax Bacillus anthracis (bacterium) Soil Plague Yersinia pestis (bacterium) Small rodents Botulism Clostridium botulinum toxin (bacterial) Soil Tularemia Francisella tularensis (bacterium) Wild animals Viral hemorrhagic fevers Filoviruses and arenaviruses Unknown in most cases Coxiella burnetii (bacterium) Sheep, goats, cattle Category B Threats: Moderate Q fever (fever + flulike syndrome) Brucellosis (severe flulike syndrome) Brucella spp. (bacteria) Livestock Glanders (pulmonary syndrome) Burkholderia mallei (bacterium) Horses Melioidosis (severe pulmonary syndrome) Burkholderia pseudomallei (bacterium) Horses, livestock, rodents, soil Viral encephalitis Alphaviruses Rodents, birds Epidemic typhus Rickettsia prowazekii (bacterium) Humans Toxins (especially of Clostridium perfringens and Staphylococcus) Various bacteria Various Psittacosis (pneumonia like syndrome) Chlamydophila psittaci (bacterium) Birds Food safety threats (including Salmonella spp., Escherichia coli O157:H7, Shigella) Various bacteria and viruses Soil or animals Water safety threats (e.g., Vibrio cholerae, Cryptosporidium parvum) Various bacteria and viruses Water Henipavirus Nipah virus Bats Category C Threats: Low Risk Nipah and Hendra viruses (encephalitis) H. Hendra virus Hantavirus pulmonary syndrome Hantavirus Rodents, soil Tick-borne encephalitis viruses Flavivirus species Ticks Yellow fever Flavivirus yellow fever virus Monkeys, Aedes mosquito Tuberculosis Mycobacterium tuberculosis Humans Influenza Influenzavirus Pigs, birds, humans Coronavirus respiratory syndromes Severe acute respiratory syndrome (SARS) virus; Bats, badgers, civets Middle East respiratory syndrome (MERS) virus Camels, bats Rabies Lyssavirus rabies virus Non-rodent mammals Chikungunya Alphavirus chikungunya virus Aedes mosquito Variant Creutzfeldt-Jacob disease prion PrP Humans, bovines Coccidioidomycosis Coccidioides species Soil highly suggestive that an attack of some kind has occurred. This is one reason why the diseases of category A are reportable; that is, they must be reported to state departments of health whenever they occur. Active monitoring of reportable diseases allows epidemiologists to quickly determine when unusual outbreaks are occurring. Once an unexpected pattern is seen, diagnostic confirmation can be obtained and, if an attack is deemed to have occurred, appropriate responses implemented (FIGURE 26.10). Such responses may entail forced quarantine, distribution of antimicrobial drugs, or mass vaccination. Agroterrorism has become more of a concern with the realization that very little security protects the nation’s agricultural M26_BAUM7206_05_SE_C26.indd 814 enterprises. Livestock and poultry are routinely moved around the country without being tested for disease and without being quarantined prior to introduction into new herds or flocks. Infected animals could therefore spread disease as they pass from facility to facility. Compounding the problem is the fact that farms, ranches, auction houses, livestock shows, and irrigation facilities are all open to the public and impose few security measures to prevent purposeful infection of animals. It has been suggested that a step in defending against agroterrorism would be to restrict public access to such facilities. Additionally, effective screening of imported animals and plants would help prevent the introduction of foreign pathogens into the United 11/23/16 3:45 AM       Biological Warfare and Bioterrorism level, BSL-4, is for agents that are often fatal and untreatable, such as Ebola and Nipah viruses. Workers wear sealed suits and do not breathe the air in the lab (see Disease in Depth: Ebola on pp. 652–653). Roles of Recombinant Genetic Technology in Bioterrorism conducting an investigation at the time of the delivery of anthrax-containing mail in Washington, D.C., in October 2001. States. Further, better diagnostic techniques, vaccines, and treatments need to be developed for animal pathogens. Scientific research is critical to our efforts to be prepared for bioterrorist attacks. Since the Eisenhower administration, only defensive research has been legal in the United States. Scientists who research pathogens, including select agents, work at four biosafety levels: Investigations with microbes that do not commonly cause disease in humans occurs in BSL-1 labs, which include many university student labs. BSL-2 is suitable for organisms that pose moderate hazards, including HIV, MRSA, and Shigella. For agents that spread easily, often via inhalation, and cause serious disease, labs are at BSL-3. Pathogens requiring BSL-3 include Mycobacterium tuberculosis, West Nile virus, and Francisella tularensis. BSL-3 rooms have negative airflow, which draws air into the room, and all exiting air is sterilized by HEPA filtration. The maximum containment A New Treatment? The next week, Penelope and Dr. Kasper meet with the coordinators of the clinical study. Their approach is to examine Penelope’s lung microbiome and compare it to microbiomes of healthy patients. The proposed treatment is to try to reestablish a healthy lung microbiome in an effort to decrease the frequency and intensity of Penelope’s lung infections. The coordinators point out that the treatment won’t cure Penelope of cystic fibrosis, but it might reduce the infections that are leading to tissue damage. If successful, the approach will decrease the likelihood that Penelope will need a lung transplant. After further discussion with Dr. Kasper and consideration, Penelope decides to enroll in the clinical trial. Although it will take M26_BAUM7206_05_SE_C26.indd 815 TELL ME WHY Compare human, animal, and plant pathogens that could be used as biological agents in terms of environmental survivability. Why are animal and plant pathogens more common in environmental reservoirs than are human pathogens? t im e to dete r m in e w h et h e r t h e n ew approach is effective, Penelope is hopeful that the microbiome-based treatment will lead to fewer and less severe infections and an improved quality of life. 1. What do you think about the possibility of microbiome-based treatment of diseases like cystic fibrosis? Does this type of approach offer hope for patients? Why or why not? 2. What do you envision as some of the challenges to microbiome-based treatment of diseases? ­ ▲ FIGURE 26.10 One aspect of the response to a bioterrorist attack. Shown here are biohazard-suited personnel Recombinant genetic technology could be used to create new biological threats or modify existing ones so that, for example, vaccines against them no longer work. Traits of various agents could be combined to create novel agents for which no immunity exists in the population. In addition to allowing the manipulation of existing threat agents, the techniques of recombinant DNA technology enable agents to be synthesized from scratch. Researchers were able to generate infectious poliovirus particles in the lab, based on genetic sequences that were published on the Internet. However, poliovirus is a relatively simple virus. There is no guarantee that such a process would work for more complex agents such as smallpox, but there is concern that terrorists could make deadly microbes. The techniques of recombinant genetic technology may also be used to thwart bioterrorism. Scientists can identify unique genetic sequences—“fingerprints,” or signatures—of recombinants, which may aid in tracking biological agents and determining their source. Genetic techniques may also help in developing vaccines and treatments, and recombinant DNA technology could be used to create pathogen-resistant crops. 11/23/16 3:45 AM ­ 26    Microbial Ecology and Microbiomes hapter       C ­ Bioterrorism in the Mail? CHAPTER SUMMARY Environmental Microbiology (pp. 802–812) 1. Microorganisms live in microhabitats within larger habitats, or physical localities, in the environment. Organisms and habitats together form ecosystems. Single cells give rise to populations, populations performing similar functions form guilds, and many guilds together form a microbiome, or community of organisms living in a habitat. The study of the interactions of microorganisms among themselves and with their environment is microbial ecology, which is a part of environmental microbiology along with studies of microbial habitats. 2. All the ecosystems on Earth form the biosphere. Biodiversity describes the number of species living in a given ecosystem, whereas biomass refers to the quantity of all these species. 3. Microbes compete for the scarce resources that characterize the majority of habitats. Some microbes actively oppose the growth of other microbes (antagonism), but many microbes cooperate, forming complex biofilms. 4. Bioremediation is the use of microorganisms to metabolize toxins in the environment to reclaim soils and waterways. Industrial products are either biodegradable or recalcitrant (resistant to degradation by natural means). Recombinant DNA technology enables scientists to create microbes to degrade some recalcitrant chemicals. M26_BAUM7206_05_SE_C26.indd 816 5. Acid mine drainage is an environmental problem in places where ores contain iron. Microbial action on leached iron in water from mines results in the production of acid and ferric iron deposits that acidify water, which is destructive to most plant and animal life. 6. Biogeochemical cycling involves the movement of elements and nutrients from unusable forms to usable forms by the activities of microorganisms. These processes involve production of new biomass, consumption of existing biomass, and decomposition of dead biomass for reuse in the cycle. The four major biogeochemical cycles are the carbon, nitrogen, sulfur, and phosphorus cycles. The cycling of trace metals is also important. 7. In the carbon cycle, CO2 is fixed by photoautotrophs and chemoautotrophs into organic molecules, which are used by other organisms. Organic carbon is converted back to CO2 in aerobic respiration, by decomposition, and by combustion. 8. In the nitrogen cycle, nitrogen gas in the atmosphere is converted to ammonia via a process called nitrogen fixation. Ammonia may be converted to nitrate via a two-step process called nitrification. Organisms also use ammonia and nitrate to make nitrogenous compounds. Such compounds in wastes and dead cells are converted back to ammonia via ammonification. Nitrate can be converted to nitrogen gas by denitrification. Anammox prokaryotes oxidize ammonium anaerobically into nitrogen. 11/23/16 3:45 AM       Questions for Review 9. In the sulfur cycle, sulfur moves between several inorganic oxidation states (primarily H2S, SO42-, and S0) and proteins. 10. The phosphorus cycle involves the conversion of PO43- among organic and inorganic forms. 11. Eutrophication—the overgrowth of microorganisms in aquatic systems—can result from the presence of excess nitrogen and phosphorus, which act as fertilizers. The overgrowth of microbes depletes the oxygen in the water, resulting in the death of fish and other animals. ­ ­ 12. Biomining is a process that uses microorganisms (usually archaea) to oxidize metals in rocks to make a soluble ion. Mineral-laden water is collected and subjected to a reducing regimen, and the metal ions solidify. 13. Soil microbiology is the study of the roles of microbes in the ground. Soils are fairly diverse and differ greatly in nutrients, water content, pH, oxygen content, and temperature. Microbes inhabit topsoil in high numbers and are less abundant in deeper rock and sediments. 14. Pathogenic microorganisms found in soil can be acquired through contact, but often disease follows the consumption of contaminated soil in food or water. 15. Some human diseases caused by soil microbes are anthrax (bacterial), histoplasmosis (fungal), and Hantavirus pulmonary syndrome. Soil diseases of plants include rots, blights, and galls. 16. Aquatic habitats include freshwater and marine water systems. Scientists recognize four zones in freshwater based on temperature, light, and nutrient levels: the nutrient-rich littoral zone along the shore, the sunlit limnetic zone at and near the surface, the profundal zone just below the limnetic zone, and the benthic zone on the bottom, which is devoid of light and nutrients. Marine environments have the same four zones plus an abyssal zone (below the benthic zone), which is virtually devoid of life except around hydrothermal vents. 17. Microorganisms living in aquatic environments typically form biofilms to better accumulate nutrients that are limiting in most nonpolluted water systems. Biological Warfare and Bioterrorism (pp. 812–816) 1. Of the relatively few microorganisms that can cause disease in humans, animals, and plants, some might be used to purposely infect individuals and are thus potential agents of biological warfare and bioterrorism. It is illegal to deploy such weapons. Agroterrorism is the deliberate infection of livestock or crops. 2. The degree to which an organism is considered a biological threat depends on several criteria concerning public health impact, dissemination or delivery potential, public perception, and public health preparedness. 3. The National Institute of Allergy and Infectious Diseases (NIAID) categorizes human pathogens by threat level. Category A agents have the greatest potential to be used for bioterrorism, and category C refers to agents whose threat potential needs further study. 4. Defense against bioterrorism begins with surveillance—the reporting and monitoring required for effective response to biological attacks. To limit the impact of any attack that may occur, diagnoses must be reliable, and efficient control measures must be in place. 5. Recombinant genetic technology could potentially lead to the development of novel agents or the modification of existing agents to make them more difficult to control in the event of an attack. Such technology could also lead to potential vaccines, cures, or pathogen-resistant crops. QUESTIONS FOR REVIEW Answers to the Questions for Review (except Short Answer questions) begin on p. A-1. Multiple Choice .               5. In the carbon cycle, microbes convert . a. CO2 into organic material for consumption b. CO2 into inorganic material for storage c. fossil fuels into usable organic compounds d. oxygen into water as a by-product of photosynthesis 2. When examining the microbiome of the human intestine, you would expect to find how many bacterial species present? a. one c. hundreds b. three d. thousands 4. Most chemical elements exist in the environment as a. usable forms in soil and rock b. usable forms in water c. unusable forms in soil and rock d. unusable forms in water M26_BAUM7206_05_SE_C26.indd 817               c. NH4+ or NH3 to NO3d. NO3- to N2 7. In aquatic environments, most microbial life is found in the . a. littoral zone c. profundal zone b. limnetic zone d. benthic zone                             3. In the environment, nutrients are generally . a. limiting c. stable b. present in excess d. artificially induced 6. Nitrification converts . a. organic nitrogen to NH3 b. NH3 to NH4+                             1. A microbiome is composed of a. single, pure populations b. all organisms in a locale c. all microbes in a location d. only the bacteria are considered . 8. Which of the following diseases is not caused by NIAID category A biological weapons agents? a. smallpox c. Q fever b. plague d. tularemia 11/23/16 3:45 AM ­ 26    Microbial Ecology and Microbiomes 1. Label the general phases in the carbon cycle. Atmospheric CO2 and CO2 dissolved in water a. ______________               10. Anammox reactions are . a. anaerobic and part of nitrogen cycling b. anaerobic and part of carbon cycling c. aerobic and part of sulfur cycling d. aerobic and part of metal ion oxidation VISUALIZE IT! Modified True/False c. ______________ Autotrophs (plants, algae, photosynthetic bacteria, protozoa, chemoautotrophic bacteria) e. ___________ Methane Indicate whether each of the following statements is true or false. Rewrite the underlined word to make a false statement true. 1.                           Biofilms of microorganisms form in aquatic environments only. Fungi, bacteria 2.                           Cooperation is common among microorganisms living in microhabitats. d. __________ f. ___________ 9. Of the following characteristics, which would contribute most to making a microorganism an effective biological warfare agent? a. is readily available in the environment b. can be spread by contact after original dissemination c. cannot be treated well outside a hospital d. is easily identified by symptoms b. ___________ hapter       C Animals Dead organisms Fossil fuels 3.                           Aquatic microorganisms are more prevalent near the surface than at the bottom of waterways. Plastics and other artificial products 4.                           Abyssal organisms are found near shores of oceans. 5.                           Plants and bacteria start the carbon cycle with consumption. 2. Label the processes of the nitrogen cycle. Fill in the Blanks a. ____________________                    in the environment. 5. Carbon fixation is the conversion of compounds. Organisms (proteins, nucleic acids, etc.) in the environment.               4. Phosphorus exists primarily as                    3. Nitrogen exists primarily as into organic NO2– NH3 c. ____________________ Wastes, dead cells NO3– NO2– Deamination e. ____________________                    ,                    2. Biogeochemical cycling involves three primary steps: , and .                    b. ____________________ N2 in atmosphere                                       1. Leaching of compounds from mine tailings often results in the oxidation of two elements: and . NH4+ d. ____________________ M26_BAUM7206_05_SE_C26.indd 818 11/23/16 3:45 AM       Questions for Review CRITICAL THINKING 1. Explain why influenzaviruses could be potentially devastating biological weapons. 4. How has the technology of next-generation DNA sequencing advanced the field of microbial ecology so significantly? 2. Microbes are found mostly in topsoil, but some are found miles deep in bedrock. Nutritionally, how do deeply buried microbes survive? 5. Given the fact that microbes are present in almost every niche on Earth, why is it not surprising that bacterial genomes contain a vast diversity of genes, as you learned in Chapter 7? 3. What effect might explain the fact that the intestinal microbiome of humans is typically stable over time, despite constant intake of new microbes in food? CONCEPT MAPPING Using the following terms, fill in the following concept map that describes microbial ecology and biogeochemical cycles. Carbon cycle Guilds Metabolic activity Nitrogen cycle Phosphorus cycle Pollution Primary producers Sulfur cycle Microbiome contains many 1 2 have related can function in 3 Bioremediation reside in part of Microhabitats Biogeochemical cycling reduces includes includes includes includes 4 5 6 7 one process is includes participants include excess leads to Carbon fixation Anammox reactions Thiobacillus & Beggiatoa Eutrophication carried out by 8 M26_BAUM7206_05_SE_C26.indd 819 3/6/18 4:33 PM