Microorganisms in the Environment and Environmental Safety

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Microorganisms in the Environment and Environmental Safety



Floods, tsunamis, earthquakes, hurricanes, fires, and the use of chemical or biological forces are certainly not new to humankind. Some of these can be prevented; others cannot. The biblical story of Noah’s ark probably is a description of one major flood in that particular region of the world. Other natural disasters certainly have been described in various ways throughout the history of this planet. In addition to the natural disasters mentioned, humans have also faced attacks by microorganisms, causing major epidemics and pandemics over the centuries.

In the past, humankind has harnessed the destructive power of biology to be used as a weapon in conflict. For example, in ancient times armies would hurl dead or decomposing animals into a city under siege to spread disease. A Tartar attack on a city in 1346 involved catapulting corpses of plague victims into the city, causing the desired epidemic. In more modern times the Japanese army had a specific unit called Unit 731 during World War II that performed extensive experimentation with biological weapons on prisoners of war. These agents included the causative pathogens of anthrax, botulism, cholera, and the plague, to name but a few. In the most recent past, in October 2001, one month after the 9/11 attack, anthrax spores were sent through the mail, causing 22 infections. Five resulted in death. History is replete with examples of the use of biological agents as weapons, and this tool of warfare will certainly continue to be developed and used in various disputes and conflicts around the world.


Physical science evolved as humans built houses, dams, and other protective structures to help survive natural disasters. At the same time, life science moved forward with the help of philosophers such as Aristoteles (Aristotle), Plato, Socrates, and many others, who studied diverse subjects including biology in order to understand the functioning of the human body and life in general. However, it was not until the merging of physical and life sciences, with the invention of the microscope, that humans could “see” microorganisms and started to understand their power. The physical and biological sciences, combined, have since come a long way to help nations after natural disasters, and to help in the management of epidemics and pandemics.

Since the 9/11 attacks we have also come a long way in our study of potential weapons of terrorism, specifically bioterrorism. Once considered eradicated by the World Health Organization (WHO), the United States is now embarked on a program to produce the smallpox vaccine as it has been identified as a potential bioweapon that could have catastrophic effect if used deliberately against a population. There are numerous groups and agencies recently established or reorganized within the government to deal with a potential bioterrorism threat.


After successfully battling disease-causing microorganisms, new and reemerging ones are challenging today’s society. Advances in biotechnology do promise more effective prevention and treatment of infectious diseases. Ongoing climate changes and population movement will also play a role in the occurrence of natural disasters and emerging infectious diseases, respectively.

As new diseases emerge or are added to the list of potential bioweapons, the need for a coordinated and rapidly responding network to deal with the threat is becoming more obvious. The potential for the rapid spread of diseases, the shortage of facilities ready to handle a massive biological crisis, and the psychological impact of mass medical casualties among a civilian population all indicate the need for well-informed and prepared healthcare professionals and “first responders” to help face the increasing bioterrorism threat.

Normal Environmental Conditions

The study of microorganisms in the environment is referred to as environmental microbiology. A habitat is the physical location where organisms are found. Because of their adaptive capacity to change, microbes can be found in any niches of the environment. The habitats available to microbes include almost every place on earth, including glaciers, Antarctic ice, and hot springs. Depending on their metabolic cycles different microbes will take advantage of different environmental conditions. For example, if a population of aerobic microorganisms in the soil takes up all the oxygen, anaerobic microorganisms will flourish until oxygen is available again and aerobic organisms can emerge.

Microbial Ecology

The study of the interrelationships of microorganisms in their natural environments is referred to as microbial ecology. Terms used to describe the levels of microbial relationships in the environment are as follows (Figure 24.1):

• Populations are formed by individual organisms through growth and reproduction.

• Guilds are populations of microorganisms that perform linked metabolic activities.

• Communities are sets of guilds and are characteristically heterogeneous. On occasion, especially in extreme environments, a community can consist of a single population.

• Microhabitats are specific small niches in which populations and guilds within a community reside because of optimal conditions for survival.

• Habitats are physical locations where organisms are found and they consist of groups of microhabitats. Within habitats the microorganisms interact with larger organisms.

• Ecosystems consist of organisms, their abiotic environment, and the relationships between them.

• Biospheres are regions of the earth populated by living organisms.

There is no natural habitat on earth that supports higher organisms and not microorganisms, but many microbial habitats do not support higher organisms. Regardless of their size, microorganisms are responsible for about half of all the biomass on earth. Biodiversity refers to the number of species living in a given ecosystem; biomass is the quantity of all organisms in an ecosystem. Microorganisms, in their great variety and numbers, represent tremendous metabolic diversity and act as the primary catalyst of many nutrient cycles in nature.

Thriving ecosystems are able to support great biodiversity, but many microbes live in harsh ecosystems where nutrients are limited. Therefore, in order to survive, these microbes must have special adaptation to a given environment. Environments may cycle between excess nutrient availability and depletion. To survive, some microorganisms form biofilms (see Chapter 6, Bacteria and Archaea) on surfaces where nutrients accumulate. Biodiversity is controlled by competition between the microbes, but usually an ecosystem is heterogenic. Microbes often use the waste products of other organisms for their own metabolic activities; in other cases the waste products of one type of microbe may make the environment more favorable for another. The formation of biofilms serves as a good example of this phenomenon.

Biodiversity ensures a healthy interaction between life forms on earth. This complex web of life is essential for the maintenance of sufficient food and freshwater. The United States Environmental Protection Agency (EPA) and other national and international organizations recognize the importance of biodiversity for human health and well-being. The EPA in partnership with other organizations implemented the biodiversity-human health project (http://epa.gov/ncer/biodiversity/index.html). One focus of the project is to better understand the relationship of emerging infectious diseases (see Chapter 18, Emerging Infectious Diseases), changing environments, and factors that manipulate biodiversity.

Biogeochemical Cycles and Microbes

A biogeochemical cycle is a circuit or pathway through which organic compounds or a chemical element is changed from one chemical state to another by moving through both biotic and abiotic compartments of an ecosystem (Box 24.1). The study of these chemical transformations is called biogeochemistry.

The Carbon Cycle

Carbon is the fourth most abundant element in the universe, and essential to life on earth. Carbon is the element that provides the backbone of all organic molecules (see Chapter 2, Chemistry of Life). All living organisms from microorganisms, to plants and animals, contain a large number of organic compounds and therefore a large amount of carbon. Thus the carbon cycle is considered to be the primary biogeochemical cycle.

For the carbon cycle to start, autotrophic organisms are necessary, either photoautotrophs or chemoautotrophs—organisms that use carbon dioxide as their primary source of carbon. Photoautotrophs are the primary organisms in the carbon cycle and include cyanobacteria, green and purple bacteria (sulfur and nonsulfur), algae, photosynthetic protozoa, and plants. All these organisms convert carbon dioxide (CO2) to organic molecules via carbon fixation during photosynthesis. Photoautotrophs require sunlight and for that reason are restricted to soil and water surfaces. Chemoautotrophs can also fix carbon dioxide into organic matter, but because they cannot use the energy of the sun, they need to metabolize compounds such as hydrogen sulfide for energy.

The next step in the carbon cycle involves the consumption of autotrophs by chemoheterotrophs such as animals and protozoans, which then catabolize the organic molecules for energy, resulting in the release of CO2. Some organic molecules produced by the autotrophs may be incorporated into the tissues of heterotrophs, where they remain until that organism dies. Dead organisms are decomposed with the help of microorganisms, metabolizing organic molecules and releasing CO2 in the process. The release of CO2 into the atmosphere starts the cycle over again (Figure 24.2).

The Nitrogen Cycle

Nitrogen gas is the most abundant gas in the earth’s atmosphere, representing about 79% of all the gases in air. Unfortunately, the nitrogen in the atmosphere is unusable by most organisms. Only about 0.03% of the earth’s nitrogen is fixed in the form of nitrates, nitrites, ammonium ion, and organic compounds. Nitrogen is necessary for all living organisms for the synthesis of proteins, nucleic acids, and other nitrogen-containing compounds. The nitrogen cycle consists of several steps as illustrated in Figure 24.3.

Nitrogen fixation is a process by which nitrogen gas (N2) is reduced to ammonia (NH3), a process catalyzed by the enzyme nitrogenase. Only a limited number of prokaryotes are capable of performing this process. Nitrogenase functions only in the complete absence of oxygen, which does not present a problem for anaerobic microbes. Aerobic nitrogen fixers must protect nitrogenase from oxygen, which is done in several ways. Some of these microbes use oxygen at such a high rate that it never enters the cell and therefore does not come in contact with the enzyme. Some cyanobacteria fix nitrogen only at night, when the oxygen-producing cycle of photosynthesis does not occur; other cyanobacteria form nonphotosynthetic cells referred to as heterocysts to protect the enzyme from oxygen in the atmosphere as well as from the oxygen produced during photosynthesis. Nitrogen fixers can be free-living or symbiotic.

Free-living, nitrogen-fixing bacteria include aerobic species of Azotobacter, aerobic cyanobacteria, and anaerobic species of Bacillus and Clostridium. They are found in particularly high concentrations in the rhizosphere, a region about 2 mm in diameter around the roots of plants. As these organisms die, they release the fixed nitrogen into the upper layers of the soil, where it then becomes available to plants and to the animals that graze on the plants.

Symbiotic nitrogen-fixing bacteria live in direct symbiosis with plants. The main organism in this category is Rhizobium, which is especially adapted to leguminous plant species, on which the organism forms root nodules. Nitrogen is fixed in the nodules, the plant provides an anaerobic environment and nutrients to the bacteria, and the bacteria then provides the plant with usable nitrogen. The nitrogen fixers provide enough nitrogen to the leguminous plants so that the farmer does not have to apply nitrogen fertilizers.

Lichens, which are a symbiotic (mutualistic) combination of a fungus and an algae or cyanobacteria, also play an important role in nitrogen fixation in the forest environment. If the symbiont is a nitrogen-fixing cyanobacterium, the fixed nitrogen will eventually enrich the forest soil.

Ammonification is the process by which amino groups are converted to ammonia. Almost all nitrogen in the soil is present in organic molecules of organisms. Bacteria and fungi decompose wastes and dead organisms and break down proteins into amino acids, which are then transported into the microbial cells. Next, in the process of deamination the amino groups of amino acids are removed and converted to ammonia. In dry or alkaline soil ammonia will escape as gas; however, in moist soil it is converted to ammonium ion, which can be absorbed by bacteria and plants and used for amino acid synthesis.

Nitrification involves oxidation of nitrogen in the ammonium ion to produce nitrate (NO3). This is a two-step process involving two genera of autotrophic nitrifying bacteria, which oxidize ammonia or nitrite (NO2) to obtain energy. The first step involves the oxidation of ammonia to nitrites, performed by Nitrosomonas spp. Nitrites are toxic to plants, but in the second stage Nitrobacter oxidize nitrites into nitrates, which are soluble and can be used by plants.

Denitrification is the process by which nitrate is reduced to nitrogen (N2) by anaerobic cellular respiration. The gas then escapes into the atmosphere. Denitrification takes place in waterlogged soils where little oxygen is available. Pseudomonas species seem to be the most prevalent group of bacteria involved in the denitrification of soil. This conversion of valuable nitrate into nitrogen gas represents a considerable economic loss in agriculture.

Anammox is the acronym for anaerobic ammonium oxidation and is a recent addition to knowledge of the nitrogen cycle. In this process, performed by anammox bacteria (previously thought to be denitrifying bacteria), nitrite and ammonium are directly converted to dinitrogen gas. This process accounts for up to 50% of the dinitrogen gas produced in the oceans. Ammonia is the major source of fixed nitrogen in the oceans and because the anammox bacteria remove ammonia efficiently from those bodies of water, these organisms limit oceanic primary productivity. On the positive side, the ability of anammox bacteria to convert ammonium and nitrite directly to dinitrogen gas provides a promising alternative to current methods of removal of nitrogen from wastewater (see Life Application: Anammox and Wastewater Treatment).

The Sulfur Cycle

Sulfur is the tenth most abundant element in the universe and is present in vitamins, proteins, and hormones. Sulfur is important for the appropriate functioning of proteins and enzymes in plants, as well as in animals that depend on plants for sulfur. Plants absorb sulfur when it is dissolved in water, and animals consume the plants for their sulfur needs. The majority of earth’s sulfur is stored underground in rocks and minerals, and as sulfate salts deep within the ocean sediments.

The sulfur cycle is similar to the nitrogen cycle, except that sulfur originates from natural sedimentary deposits. The sulfur cycle includes both atmospheric and terrestrial processes (Figure 24.4). The terrestrial process begins with the weathering of rocks, resulting in the release of stored sulfur. Subsequently, the sulfur comes in contact with air and is then converted into sulfate (SO4). Plants and microorganisms will take up the sulfate and convert it into organic forms. Animals will consume the organic forms via food they consume, thereby moving the sulfur through the food chain. As organisms die, bacteria decompose them, releasing sulfur-containing amino acids into the environment. The sulfur released from the amino acids is converted by microorganisms to its most reduced form, hydrogen sulfide (H2S). This process is called sulfur dissimulation. H2S is then oxidized to elemental sulfur and then to sulfate by various microorganisms under various conditions. These organisms include nonphotosynthetic autotrophs such as Thiobacillus and Beggiatoa and photoautotrophic green and purple sulfur bacteria. The cycle starts again with the uptake of sulfate by plants and algae that animals eat. Anaerobic respiration by the bacterium Desulfovibrio reduces sulfate back to H2S.

Sulfur can also be found in the atmosphere. A variety of natural sources emit sulfur directly into the atmosphere, including volcanic eruptions, bacterial processes, decaying organisms, and the evaporation of water. When sulfur dioxide enters the atmosphere it will react with oxygen to produce sulfur trioxide gas, or it can react with other chemicals in the atmosphere to produce sulfur salts. Furthermore, sulfur dioxide can react with water to produce sulfuric acid. All these particles will eventually settle back onto the earth, or react with rain and fall back to earth as acid deposition. The particles will then be absorbed by plants, and the sulfur cycle will start over again.

The Phosphorus Cycle

Phosphorus is an essential nutrient for plants, animals, and microorganisms. It is part of nucleic acids (DNA, RNA, ATP, and ADP) and of the plasma membranes (phospholipids). Phosphorus can be found in water, soil, and sediments. Unlike nitrogen and sulfur, phosphorus cannot be found in the atmosphere in the gaseous state. Phosphorus exists in the form of phosphate ion and undergoes little change in its oxidation state. The phosphorus cycle (Figure 24.5) involves changes of phosphorus from insoluble to soluble forms that are available for uptake by organisms, and from organic to inorganic forms by pH-dependent processes. Because no gaseous form of phosphorus exists it has the tendency to accumulate in the seas and other bodies of water.

Excess phosphorus can present a problem in a habitat. Agricultural fertilizers rich in phosphate and nitrogen are easily leached from the fields by rain. The resulting runoff into rivers and lakes can cause eutrophication, the overgrowth of microorganisms in nutrient-rich waters. The organisms involved include mainly algae and cyanobacteria. Such overgrowth, referred to as a bloom, depletes oxygen from the water, resulting in the death of aerobic organisms such as fish. Anaerobic organisms then take over, leading to increased production of H2S and resulting in the release of foul odors.

Soil Microbiology

Soil composition such as organic matter, soil structure, nutrient content, nutrient cycling, nutrient availability, and water-holding capacity are influenced by, or dependent on, billions of organisms, microscopic ones as well as fairly large insects and earthworms. All these organisms together form a pulsating, living community in soil. Soil microorganisms can be classified into major groups such as microarthropods, nematodes, protozoa, fungi, algae, and bacteria. The most numerous organisms in the soil are bacteria—each gram of typical soil contains millions of bacteria. The population of bacteria is largest in the top few centimeters of soil and declines rapidly with depth. Organic matter is metabolized by microbes in the soil, and via the biogeochemical cycles, elements are oxidized and reduced (see Chapter 2, Chemistry of Life, for oxidation/reduction reactions) by microorganisms to meet their metabolic needs.

A healthy soil high in humus content provides a rich culture medium for an array for microorganisms. Several environmental factors influence the density and composition of microbes in the soil. These factors include the amount of moisture/water, oxygen content, pH, temperature, and availability of nutrients:

• Moisture is essential for the survival of microorganisms. In dry soil microbes will exhibit lower metabolic activity, they will be less diverse, and lower numbers will be present than in moist soil.

• Oxygen dissolves poorly in water; therefore, moist soils are lower in oxygen content than dry soils. Waterlogged soil will result in a decline in microbial diversity and anaerobic organisms will dominate. The presence or absence of rainwater determines moisture, and thus dissolved oxygen.

• The pH of soil influences the type of organisms that predominate. It will influence whether the soil is rich in bacteria or rich in fungi. In highly acidic or highly basic soils fungi will predominate, whereas bacteria prefer soil with a pH of about 7.

• The temperature of soil determines the types of microbe that can flourish. Most soil organisms are mesophiles and grow well in areas where winters and summers are not too extreme. Psychrophiles grow only in cold environments and cannot survive in areas that experience spring thawing. Thermophiles, on the other hand, grow only in warm environments where winters are not harsh.

• Nutrient availability also affects the microbial abundance and diversity of soil. The majority of soil microbes are heterotrophic and utilize the organic matter present in the soil. It is the amount of organic material rather than the kind of organic material that determines the abundance of microorganisms in a microbial community. A continuous influx of organic material (i.e., agricultural land) will support a wider assortment of microorganisms than soil with low amounts of organic material.

Microbial Populations in Soil

The microbial populations in soil vary depending on the type of soil. Bacteria are the most abundant and diverse soil inhabitants; they are found in all layers and often form biofilms, especially around plant roots. Bacteria are highly adaptable to changing environments, and therefore are plentiful in most soils. Fungi are next in numbers. Both free-living and symbiotic fungi are present only in topsoil, where they can form large mycelia (mats of fibrous hyphae) that potentially cover several acres. Algae and protozoa are also present in soil but in smaller numbers than bacteria and fungi. Soil algae are photoautotrophs and therefore exist on or near the soil surface. Protozoans are mobile and move around the soil feeding on other microbes, especially bacteria. Although viruses are present within microorganisms, they generally are not found free.

Examples of Soil-borne Diseases

Microorganism Disease
Bacillus anthracis Anthrax
Clostridium tetani Tetanus
Hantavirus Hantavirus pulmonary syndrome
Histoplasma capsulatum Histoplasmosis
Blastomyces dermatitidis Blastomycosis
Sporothrix schenckii Sporotrichosis

Aquatic Microbiology

Water occupies nearly three-fourths of the earth’s surface. Aquatic microbiology deals with the study of microorganisms and their activities in freshwater and marine environments, including lakes, ponds, streams, rivers, estuaries, and oceans. Many microorganisms that live in aquatic systems form biofilms attached to surfaces. Biofilms allow these microbes to concentrate enough nutrients to survive and sustain growth. Basically, aquatic habitats are divided into freshwater and marine systems. Natural aquatic systems are affected by the release of domestic water, a result of sewage treatment plants and industrial waste. The amount and quality of domestic water released into the environment greatly affects the chemistry and microbial content of the aquasystem. Large numbers of microorganisms in a body of water indicate a high level of nutrients, often a result of contaminated inflows from sewage systems or from biodegradable industrial organic wastes. Ocean estuaries often have a higher nutrient level than other shoreline waters, and therefore have larger microbial populations.

Freshwater Ecosystems

About 3% of the world’s water is freshwater, 99% of which is either frozen in glaciers and pack ice, or is buried in aquifers. The remainder of the freshwater is found in lakes, ponds, rivers, and streams. Microorganisms are dispersed vertically within lake and pond systems, according to the availability of oxygen, light intensity, and temperature. Surface waters are higher in oxygen and light intensity, and warmer than deeper waters. In contrast to stagnant waters where oxygen is readily depleted, in larger lakes the wave action continuously mixes nutrients, oxygen, and organisms, resulting in efficient use of its resources. In stagnant waters, because of the depletion of oxygen, anaerobic organism will dominate and a lesser water quality will be the result. Four distinct vertical zones can be observed in lakes and ponds (Figure 24.6): a littoral zone, a limnetic zone, a profundal zone, and a benthic zone:

• The littoral zone (Figure 24.7) is the area along the shoreline with considerable rooted vegetation and good light source. This is the zone where nutrients enter the lake or pond, providing an abundance of food and promoting a high diversity of animals and bacteria in the biotope.

• The limnetic zone is the well-lit, upper layer of water away from the shore. This area is occupied by phytoplankton consisting of algae and cyanobacteria, and zooplankton, small crustaceans, and fish. Areas of the limnetic zone with sufficient oxygen supply also contain Pseudomonas spp., Cytophaga, Caulobacter, and Hyphomicrobium.

• The profundal zone is the deeper water located below the limnetic zone. It is characterized by limited light penetration (diffuse light), lower oxygen content, and lower temperature. The organisms of this zone depend on import of organic matter drifting down from the littoral and limnetic zones. This zone is inhabited mainly by primary consumers that are either attached to or crawl along the sediments at the bottom of the lake. These bottom-dwelling organisms are referred to as benthos. Purple and green sulfur bacteria can also be found in this zone.

• The benthic zone consists of the sediments at the bottom of a lake; it includes the sediment surface as well as some subsurface layers. This layer also contains benthos, which generally live in close relationship with the substrate bottom. These life forms can tolerate cool temperatures and low oxygen levels. Bacteria found in this zone include Desulfovibrio, methane-producing bacteria, and Clostridium species.

Contrary to the vertical stratification of lakes and ponds, rivers and streams lack this stratification because the organisms and nutrients are continuously swept along and mixed. Many organisms live toward the edges, where currents are low and organic material enters the water. Furthermore, biofilms can readily be found on rocks of rivers and streams.

Marine Ecosystems

Marine (saltwater) ecosystems are part of the largest aquatic system on earth, covering more than 70% of the earth’s surface. Marine ecosystems host many different species ranging from planktonic organisms that comprise the base of the marine food web, to fish, and large marine mammals. These ecosystems have some unique qualities, specifically the presence of dissolved compounds, particularly salts. As in freshwater systems the oceans can also be divided into layers, but they do have a fifth zone, the abyssal zone, which encompasses the deep ocean trenches (Figure 24.8). The majority of marine microorganisms are present in the littoral zone, where light is readily available and nutrient levels are high. The upper 200 m of ocean contains an unseen population of microbes that supports oceanic life. These are photosynthetic organisms called the marine phytoplankton. The many kinds of different bacteria among the phytoplankton are a food source for protozoa, which in turn are prey for the multicellular organisms among the zooplankton. The zooplankton is a source of food for the fish. The carbon dioxide and mineral nutrients released as by-products of the metabolic activities of bacteria, protozoa, and zooplankton are recycled into the photosynthetic phytoplankton.

The benthic abyssal zones have sparse nutrients, but they still support microbial growth, especially around hydrothermal vents. These vents release superheated, nutrient-rich water, providing nutrients and energy for thermophilic chemoautotrophic anaerobes. These organisms in turn support a variety of invertebrate and vertebrate animals.

Natural Disasters

Natural disasters are the consequence of natural hazards, including such naturally occurring phenomena as earthquakes, volcanic eruptions, landslides, hurricanes, tsunamis, floods, and drought. Natural disasters result in a serious breakdown in sustainability of economic and social progress, and also provide a major challenge to public health. The type of medical care required during and after a natural disaster is determined by variables such as the cycle of nature, the type of the disaster, the population, and endemic disease.

During the past two decades, natural disasters have been increasing in frequency, complexity, scope, and destructive capacity. Earthquakes, hurricanes, tornadoes, tsunamis, floods, landslides, volcanic eruptions, and wildfires have killed millions of people, and adversely affected the life of many more due to enormous economic damage. Poor and developing countries show the greatest losses due to the lack of infrastructure, disease prevention, and disaster preparedness and prevention.


A flood is an overflowing of water onto land that is normally dry. When the volume of water within a body of water, such as a river or lake, surpasses the total capacity of the body, water will flow out of its perimeters, causing a flood. The flood of the Yellow River in 1931 is generally considered to be the deadliest natural disaster ever recorded, certainly in the twentieth century, discounting pandemic diseases such as the influenza pandemic of 1918. The estimated number of people killed in this flood is between 1 and 2 million. Flooding in more recent times is illustrated in Table 24.1.

TABLE 24.1

Lethal Flooding in the Years 2000 to 2008

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Year Location Event Estimated Death Toll
2008 United States Midwest flooding 17
2007 China Mountain torrents, mud-rock flows, landslide 1029
2007 Sudan, Nigeria, Burkina Faso, Ghana, Kenya, and other African countries African Nations Flood 353
2007 Indonesia