The Domains Bacteria and Archaea - The Nature of Microorganisms - THE ORIGIN AND CLASSIFICATION OF LIFE - CONCEPTS IN BIOLOGY




21. The Nature of Microorganisms


21.2. The Domains Bacteria and Archaea

At one time, all prokaryotic organisms were lumped into one group of microorganisms called bacteria. Today, scientists recognize that there are two, very different kinds of prokaryotic organisms: the domains Bacteria and Archaea. The Bacteria and Archaea differ in several ways: Bacteria have a compound, called peptidoglycan, in their cell walls, which Archaea do not have. The chemical structure of the cell membranes of Archaea is different from that of all other kinds of organisms. When the DNA of Archaea is compared with that of other organisms, it is found that a large proportion of their genes are unique.

Today, most scientists still use the terms bacterium and bacteria. However, they are used in a restricted sense to refer to members of the domain Bacteria. The term archeon is frequently used to refer to members of the Domain Archaea.

The Domain Bacteria

The Bacteria are an extremely diverse group of organisms. Although only about 2,000 species of Bacteria have been named, most biologists feel that there are probably millions still to be identified (How Science Works 21.1). They occupy every conceivable habitat and have highly diverse metabolic abilities. They are typically spherical, rod-shaped, or spiralshaped. They are often identified by the characteristics of their metabolism or the chemistry of their cell walls. Many have a kind of flagellum, which rotates and allows for movement. Figure 21.1 shows the general structure of a bacterium. Some form resistant spores, which can withstand dry or other harsh conditions. Bacteria play several important ecological roles and interact with other organisms in many ways.

FIGURE 21.1. Bacteria Cell Structure

The plasma membrane regulates the movement of material between the cell and its environment. A rigid cell wall protects the cell and determines its shape. Some bacteria, usually pathogens, have a capsule to protect them from the host’s immune system. The genetic material consists of a loop of DNA.


Many kinds of bacteria are heterotrophs that are saprophytes. They break down organic matter to provide themselves with energy and raw materials for growth. Therefore, they function as decomposers in all ecosystems. Decomposers are a diverse group and use a wide variety of metabolic processes. Some are anaerobic and break down complex organic matter to simpler organic compounds. Others are aerobic and degrade organic matter to carbon dioxide and water. In nature, this decomposition process is important in the recycling of carbon, nitrogen, phosphorus, and many other elements.

The actions of decomposers have been harnessed for human purposes. Sewage treatment plants rely on bacteria and other organisms to degrade organic matter (figure 21.2) (How Science Works 21.2).


FIGURE 21.2. Decomposers in Sewage

A sewage treatment plant is designed to encourage the growth of bacteria and other microorganisms that break down organic matter. The tank in the foreground contains a mixture of sewage and microorganisms, which is being agitated to assure the optimal growth of microbes.

The food industry uses lactic acid fermentation by certain bacteria to produce cheeses, yogurt, sauerkraut, and many other foods. Alcohols, acetones, acids, and other chemicals are produced by bacterial cultures. Some bacteria can even metabolize oil and are used to clean up oil spills.

Unfortunately, decomposer bacteria do not distinguish between items that we want to decompose and those that we don’t want to decompose. Bacteria in food can cause milk to turn sour or vegetables and meat to spoil. Thus, it is often necessary to control the populations of some decomposer bacteria, so that foods and other valuable materials are not destroyed by rotting or spoiling.


How Many Microbes Are There?

Biologists have long suspected that there are large numbers of undiscovered species of microbes in the world. One of the major problems associated with identifying microbes is that they must be isolated and grown to be characterized. Unfortunately, it appears that most microbes cannot be grown in the lab and therefore cannot be studied in detail.

However, the technology of DNA sequencing has provided a better estimate of the number of kinds of microbes in our world. J. Craig Venter, one of the scientists who developed techniques for sequencing the human genome, has applied the DNA sequencing techniques to the ocean ecosystem. Water samples were collected from many parts of the ocean. The samples were filtered to collect the microbes. The DNA from these mixtures of organisms was then sequenced. The result was a "metagenome", a picture of the DNA of an ecosystem.

Once this composite of DNA was known, pieces of it could be compared to known genes and new, unique sequences could be identified. The result was the identification of 1.2 million new genes and a doubling of the number of kinds of proteins produced from those genes. Many new genes appear to be related to molecules responsible for trapping sunlight by autotrophic microbes. The identification of new genes and the proteins they produce implies that there are many new species in the ocean responsible for their production.



Bioremediation involves the use of naturally occurring microbes to break down unwanted or dangerous materials. In many ways we have been using bioremediation for centuries. Composting, sewage treatment plants, and the activities of soil bacteria to break down animal manure are common examples of how microbes break down unwanted organic matter. However, modern society has invented other kinds of pollution that are more resistant to the activities of microbes. Oil spills and the release of synthetic organic compounds such as polychlorinated biphenyls (PCBs), trichloroethylene (TCE), and many other persistent organic molecules have created a new kind of pollution that also can be treated with microbes.

Several types of activities are commonly involved when bioremediation is attempted. In order to find the microbes with the desired abilities, scientists screen many kinds. In some cases, genetic engineering techniques have been used to introduce genes into microbes that allow the microbes to survive in toxic situations. When bioremediation is to be attempted, several actions are commonly taken. Specific microbes with desirable properties may be added to break down the pollutant. Nutrients such as nitrogen or phosphorus may be added to stimulate the growth of microorganisms already present. In some cases, the concentration of the pollutant may be diluted so that the pollutant will not kill the microbes that will eventually metabolize it.

Bioremediation has been used to clean up oil spills, degrade pesticides, detoxify metallic contaminants, and in many other ways.

Commensal Bacteria

Many kinds of bacteria have commensal relationships with other organisms. They live on the surface or within other organisms and cause them no harm, but neither do they perform any valuable functions. Most organisms are lined and covered by populations of bacteria called normal flora (table 21.1). In fact, if an organism lacks bacteria, it is considered abnormal. The bacterium Escherichia coli (commonly called E. coli) is common in the intestinal tract of humans, other mammals, and birds. A large proportion of human feces is composed of E. coli and other bacteria. Many of the odors humans produce from the skin and gut are the result of commensal bacteria.

TABLE 21.1. Common Bacteria in or on Humans


Corynebacterium sp., Staphylococcus sp., Streptococcus sp., Escherichia coli, Mycobacterium sp.


Corynebacterium sp., Neisseria sp., Bacillus sp., Staphylococcus sp., Streptococcus sp.


Staphylococcus sp., Streptococcus sp., Corynebacterium sp., Bacillus sp.


Streptococcus sp., Staphylococcus sp., Lactobacillus sp., Corynebacterium sp., Fusobacterium sp., Vibrio sp., Haemophilus sp.


Corynebacterium sp., Staphylococcus sp., Streptococcus sp.

Intestinal tract

Lactobacillus sp., Escherichia coli, Bacillus sp., Clostridium sp., Pseudomonas sp., Bacteroides sp., Streptococcus sp.

Genital tract

Lactobacillus sp., Staphylococcus sp., Streptococcus sp., Clostridium sp., Peptostreptococcus sp., Escherichia coli

Photosynthetic Bacteria

Several kinds of Bacteria carry on a form of photosynthesis. A group called the cyanobacteria carries out a form of photosynthesis that is essentially the same as that in plants and algae. They use carbon dioxide and water as raw materials and release oxygen. In fact, the chloroplasts of eukaryotic organisms are assumed to be cyanobacteria that, in the past, formed an endosymbiotic relationship with other cells. Cyanobacteria are thought to be the first oxygenreleasing organisms; thus, their activities led to the presence of oxygen in the atmosphere and the subsequent evolution of aerobic respiration. Cyanobacteria are extremely common and are found in fresh and marine waters and soil and other moist environments. When conditions are favorable, asexual reproduction can result in what is called a bloom— a rapid increase in the population of microorganisms in a body of water (figure 21.3). Many cyanobacteria form filaments or other kinds of colonies, which produce large masses when a bloom occurs. Some species of cyanobacteria produce toxins. When blooms occur, the levels of toxins in the water may be high enough to poison humans and other animals.


FIGURE 21.3. Bloom of Cyanobacteria

Many kinds of cyanobacteria reproduce rapidly in nutrient-rich waters and produce masses of organisms known as a bloom.

Within the filaments of many cyanobacteria are specialized, larger cells capable of nitrogen fixation which converts atmospheric nitrogen, N2, to ammonia, NH3. This provides a form of nitrogen usable to other cells in the colony—an example of division of labor.

Two kinds of Bacteria, known as purple and green bacteria, carry on different forms of photosynthesis that do not release oxygen. Many of these organisms release sulfur as a result of their photosynthesis.

Mutualistic Bacteria

Mutualistic relationships occur between bacteria and other organisms. Some intestinal bacteria benefit humans by producing antibiotics, which inhibit the development of disease- causing bacteria. They also compete with disease-causing bacteria for nutrients, thereby helping keep them in check. They aid digestion by releasing various nutrients. They produce and release vitamin K. Mutualistic bacteria establish this symbiotic relationship when humans ingest them along with food or drink. When people travel, they consume local bacteria with their food and drink and may have problems establishing a new symbiotic relationship with these foreign bacteria. Both the host and the symbionts must adjust to their new environment, which can result in a very uncomfortable situation for both. Some people develop traveler’s diarrhea as a result.

There are many other examples of mutualistic relationships between bacteria and other organisms. Many kinds of plants have nitrogen-fixing bacteria in their roots in a symbiotic relationship. Some fish and other aquatic animals have bioluminescent bacteria in their bodies, allowing them to produce light. Many kinds of lichens contain cyanobacteria as symbionts with their fungal cells.

Bacteria and Mineral Cycles

Many different bacteria are involved in the nitrogen cycle. In addition to symbiotic nitrogen-fixing bacteria, free-living nitrogen-fixing bacteria in the soil convert N2 to NH3. Other bacteria convert ammonia to nitrite and nitrate. These bacteria are chemoautotrophs that use inorganic chemical reactions involving nitrogen to provide themselves with energy. All of these bacteria are extremely important ecologically, because they are ultimately the source of nitrogen for plant growth. Finally, some bacteria convert nitrite to atmospheric nitrogen.

In addition to nitrogen; iron, sulfur, manganese, and many other inorganic materials are cycled by chemoautotrophic bacteria with specialized metabolic abilities. Some of these are important ecologically, because they produce acid mine drainage or convert metallic mercury to methylmercury, which can enter animals and cause health problems.

Disease-Causing Bacteria

Disease-causing bacteria are heterotrophs that use the organic matter of living cells as food. Bacteria and other kinds of organisms that are capable of causing harm to their host are called pathogens. Only a small minority of bacteria fall into this category; however, because historically they have been responsible for huge numbers of deaths and continue to be a serious problem, they have been studied intensively and many pathogens are well understood.

Pathogenic bacteria can cause disease in several ways. Many are normally harmless commensals but cause disease when their populations increase to excessively high numbers. For example, Streptococcus pneumoniae can grow in the throats of healthy people without any pathogenic effects. But if a person’s resistance is lowered, as after a bout with viral flu, Streptococcus pneumoniae can invade the lungs and reproduce rapidly, causing pneumonia. The relationship changes from commensalistic to parasitic.

Other bacteria invade the healthy tissue of their host and cause disease by altering the tissue’s normal physiology. Bacteria living in the host release a variety of enzymes that cause the destruction of tissue. The disease ends when the pathogens are killed by the body’s defenses or an outside agent, such as an antibiotic. Examples are the infectious diseases strep throat, syphilis, anthrax, pneumonia, tuberculosis, and leprosy.

Many other illnesses are caused by toxins or poisons produced by bacteria. Some of these bacteria release toxins that may be consumed with food or drink. In this case, disease can be caused even though the pathogens never enter the host. For example, botulism is a deadly disease caused by bacterial toxins in food or drink. Other bacterial diseases are the result of toxins released from bacteria growing inside the host tissue; tetanus and diphtheria are examples. In general, toxins cause tissue damage, fever, and aches and pains.

Bacterial pathogens are also important factors in certain plant diseases. Bacteria cause many types of plant blights, wilts, and soft rots. Apples and other fruit trees are susceptible to fire blight, a disease that lowers the fruit yield because it kills the tree’s branches. Citrus canker, a disease of citrus fruits that causes cancerlike growths on stems and lesions on leaves and fruit, can generate widespread damage. Federal and state governments have spent billions of dollars controlling this disease (figure 21.4).


FIGURE 21.4. A Bacterial Plant Disease

Citrus canker is a disease of citrus trees caused by the bacterium Xanthomonas axonopodis. This photograph shows the typical lesions on the fruit and leaves of an orange tree.

Probably all species of organisms have bacterial pathogens. Plants and animals get sick and die all the time. However, scientists are not likely to spend time and money studying these diseases unless the organisms have economic value to us. Therefore, scientists know much about bacterial diseases in humans, domesticated animals, and crop plants but know very little about the diseases of jellyfish, squid, or most plants.

Control of Bacterial Populations

The diseases and many kinds of environmental problems caused by bacteria are actually population control problems. Small numbers of bacteria cause little harm. However, when the population increases, their negative effects are multiplied. Despite large investments of time and money, scientists have found it difficult to control bacterial populations. Three factors operate in favor of the bacteria: their reproductive rate, their ability to form resistant stages, and their ability to mutate and produce strains that resist antibiotics and other control agents.

Under ideal conditions, some bacteria can grow and divide every 20 minutes. If one bacterial cell and all its offspring were to reproduce at this ideal rate, in 48 hours there would be 2.2 x 1043 cells. In reality, bacteria cannot achieve such incredibly large populations, because they would eventually run out of food and be unable to dispose of their wastes. However, many of the methods used to control pathogenic bacteria are those that control their numbers by interfering with their ability to reproduce. Many antibiotics interfere with a certain aspect of bacterial physiology so that the bacteria are killed or become unable to divide and reproduce. This allows the host’s immune system to gain control and destroy the disease-causing organism. Without the antibiotic, the immune system may be overwhelmed and the person may die.

Although antibiotics can save lives, they don’t always work because bacteria mutate and produce individuals that are resistant to the effects of an antibiotic. Because bacteria reproduce so rapidly, a few antibiotic-resistant cells in a bacterial population can increase to dangerous levels in a very short time. This requires the use of stronger doses or new types of antibiotics to bring the bacteria under control. Furthermore, these resistant strains can be transferred from one host to another, making it difficult to control the spread of disease. For example, sulfa drugs and penicillin, once widely used to fight infections, are now ineffective against many strains of pathogenic bacteria. Methicillin has been a valuable antibiotic for many years. However, some strains of Staphylococcus aureus, a common skin bacterium, have become resistant to methicillin. As a result, common skin infections that should be controlled easily have become life- threatening. These strains have become known as methicillin-resistant Staphylococcus aureus (MRSA). As with methicillin, when any new antibiotic is developed, natural selection encourages the development of resistant bacterial strains. Therefore, humans are constantly waging battles against new strains of resistant bacteria.

In addition to antibiotics, various kinds of antiseptics are used to control the numbers of pathogenic bacteria. Antiseptics are chemicals able to kill or inhibit the growth of microbes. They can be used on objects or surfaces that have colonies of potentially harmful bacteria. Certain antiseptics are used on the skin or other tissues of people who are receiving injections or undergoing surgery. Reducing the numbers of bacteria lessens the likelihood that the microbes on the skin will be carried into the body, causing disease. We all are constantly in contact with pathogenic bacteria; however, as long as their numbers are controlled, they do not become a problem.

Another factor that enables some bacteria to survive a hostile environment is their ability to form endospores. An endospore is a unique bacterial structure with a low metabolic rate that can withstand hostile environmental conditions and germinate later, when there are favorable conditions to form a new, actively growing cell (figure 21.5). Endospores thought to be Bacillus sphaericus and estimated to be 25 million to 40 million years old have been isolated from the intestinal tract of a bee fossilized in amber. When placed in an optimum growth environment, they have germinated and grown into numerous colonies.

FIGURE 21.5. Bacterial Endospore

(a) The body at the top end of the cell is an endospore. It contains the bacterial DNA, as well as a concentration of cytoplasmic material surrounded and protected by a thick wall. (b) The photo shows a Bacillus bacterium that has formed endospores in some cells.

Some spore-forming bacteria are important disease-causing organisms. People who preserve food by canning often boil the food in the canning jars to kill the bacteria, but not all are killed by boiling, because some form endospores. The endo- spores of Clostridium botulinum, the bacterium that causes botulism, can withstand boiling and remain for years in the endospore state. However, endospores do not germinate and produce botulism toxin if the pH of the canned goods is in the acid range; in that case, the food remains preserved and edible. If conditions become favorable for Clostridium endospores to germinate, they become actively growing cells and produce toxin. Using a pressure cooker and heating the food to temperatures higher than 121°C for 15 to 20 minutes destroys both the botulism toxin and the endospores.

Anthrax is an acute infectious disease caused by the spore-forming bacterium Bacillus anthracis. Anthrax spores can live in the soil as spores for long periods and cause disease when they are inhaled, are swallowed, or invade the skin. Because anthrax spores can survive dry conditions, they were used to contaminate mail as an agent of bioterrorism.

Contaminated food and water are common ways that people encounter bacteria that cause them harm. These disease episodes are commonly referred to as food poisoning or stomach flu (Outlooks 21.1).


Food Poisoning/Foodborne Illness/Stomach Flu

Many people talk about a disease experience they call stomach flu but it is not caused by the influenza virus. The disease usually involves nausea, vomiting, and diarrhea. It may also involve headache, fever, and abdominal cramping. The Centers for Disease Control and Prevention estimates that food poisoning causes about 75 million cases of illness in the United States each year. The U.S. population is about 310 million, so we all have about a 1 in 4 chance of having this uncomfortable experience each year.

Food poisoning is not caused by the virus that causes influenza and should more properly be called gastroenteritis. In addition, it is not a single disease but is caused by a variety of organisms and mechanisms. The typical way of contracting the disease is through food or water contaminated with viruses, bacteria, or protozoa that, when ingested, multiply and cause the symptoms—hence the name food poisoning. Furthermore, these diseases are usually contagious because those who are sick pass the organism in their feces and can transmit it to those around them if those infected do not practice good hygiene.

Norovirus is responsible for about 50% of cases in United States and generally is contracted as a result of focally contaminated food. Rotavirus is the most common cause of severe diarrhea in infants and young children. Nearly every child in the world has been infected with rotavirus at least once, but they develop partial immunity following infection and subsequent infections tend to be mild. Many kinds of bacteria are involved in cases of food poisoning: Salmonella, Escherichia coli, Shigella, and Staphylococcus are examples.

An additional cause that leads to similar symptoms involves changes in the kinds and numbers of bacteria normally found in your intestine. Your gut is an ecosystem in which there are many different kinds of Bacteria, Archaea, and protozoa. Each has specific metabolic requirements and produces specific kinds of metabolic waste products. Some of these products may be gases. If you change the kind of food you eat, or if the water you drink has different kinds of minerals in it, some of your intestinal microbes may experience population increases that lead to symptoms similar to those of food poisoning.

Treatment usually does not involve medication. One simply waits until the illness runs its course. The most serious health concern is dehydration from vomiting and diarrhea. Consequently, providing liquids is important and, in severe cases, intravenous fluids may be required.

The Domain Archaea

The Archaea are distinct from the Bacteria. They differ from Bacteria in the nature of their cell walls, cell membranes, DNA, and other details of structure and physiology. In addition to the spherical, rod-shaped, and spiral-shaped forms found in the Bacteria, some Archaea are lobed, platelike, or irregular in shape. Like the Bacteria, the Archaea are extremely diverse and extremely common. Only a couple hundred species have been described, but DNA sampling of the ocean and soil suggests that there is a huge number of undescribed species. Some species are found in extreme habitats—high temperature, high acid, high salt—and are referred as extremophiles (lovers of extremes).Others are very common in the ocean, freshwater, soil, and the digestive tract of animals where they play a variety of ecological roles. To date only one archeon has been identified as a parasite and it is a parasite on other Archaea.

Extreme Halophiles

Extreme halophiles (salt lovers) are Archaea that can live only in extremely salty environments—such as the Great Salt Lake in Utah and the Dead Sea, located between Israel and Jordan. They require a solution of at least 8% salt and grow best in solutions that are about 20% salt. The Atlantic Ocean is about 3.5% salt. The Dead Sea is about 15% salt. They also live in artificial salt ponds used to evaporate seawater to produce salt. Because they contain the reddish pigment carotene, they color these salt ponds pinkish or red.

Most of these organisms are aerobic heterotrophs. They use organic matter from their environment as a source of food. Some have been found growing on food products, such as salted fish, causing spoilage. However, some of them are also photosynthetic autotrophs that have a carotene-containing pigment, called bacteriorhodopsin, which absorbs sunlight and allows the cells to make ATP.


The thermophiles (heat lovers) are a diverse group of the Archaea that live in extremely hot environments, such as the hot springs found in Yellowstone National Park and hydrothermal vents on the ocean floor (figure 21.6). All require high environmental temperatures—typically, above 50°C (122°F)—and some grow well at temperatures above 100°C (212°F). They are diverse metabolically; some are aerobic whereas others are anaerobic. Some can reduce sulfur or sulfur-containing compounds by attaching hydrogen to sulfur (S + 2H H2S). Thus, they release hydrogen sulfide gas (H2S). Some live in extremely acidic conditions, with a pH of 1-2 or even less.


FIGURE 21.6. Hydrothermal Vents

Extremely hot, mineral-rich water enters the ocean from hydrothermal vents on the ocean floor. Many kinds of specialized Archaea live in these places, where they use sulfur as a source of energy. These archeons are, in turn, eaten by other organisms that live in the vicinity.

Acidophiles and Alkaliphiles

Some Archaea live at extreme pHs. One acidophile is known to live at a pH of 0. Another acidophile has been identified as important in the acid drainage from abandoned mines where they oxidize iron. Alkalophiles live in lakes with basic pHs of 9-11 and maintain a near normal internal pH by pumping hydrogen ions from their environment into their cells.


Methanogens are members of the Archaea that are strict anaerobes (do not live where there is oxygen) and release methane as a waste product of cellular metabolism. Most are chemo- synthetic autotrophs that produce methane by transferring hydrogen to carbon dioxide (4H2 + CO2 CH4 + 2H2O). Others are heterotrophic decomposers that break down simple organic molecules, such as acetate, to produce methane (CH3COOH CO2 + CH4). They live in a variety of environments where oxygen is absent. Many live in mud at the bottom of lakes and swamps, and some live in the intestinal tracts of animals, including humans, where they generate methane gas. The digestive system of cattle and some other organisms involves a complex mixture of microorganisms. Some are Bacteria that break down cellulose to simpler molecules, such as acetate, and release hydrogen. Others are methane- producing Archaea that convert the breakdown products of the Bacteria to methane (Outlooks 21.2). Methanogens are also present in certain kinds of waste treatment systems used to manage animal and human waste. Anaerobic digesters containing methanogens can be used to produce methane from human or animal waste. Methanogens are also common in flooded rice paddies. The two most common sources of methane released to the atmosphere are rice paddies and the digestive tracts of animals.

Methane is a greenhouse gas tied to the problem of global warming, so scientists have tried to characterize the role of Archaea as producers of methane. However, because they are involved as components of important agricultural activities (rice growing and cattle raising), it is not likely that this source of methane will be controlled.


Although at one time it was thought that the Archaea were all extremophiles, that impression is changing. It is becoming clear that archeons are common in most environments where there is moisture, not just in extreme environments. A major problem with characterizing the roles played by Archaea is that they are difficult to isolate and grow in captivity. However, when environments such as the ocean and soil are sampled for DNA, large amounts of Archaea DNA are found. They appear to be extremely common in the ocean, in freshwater, and in the soil, where they perform a variety of functions (Outlooks 21.3). Many are heterotrophs that degrade organic material and thus are decomposers. Some of these decomposers are aerobic whereas others are anaerobic heterotrophs. Other Archaea are chemoautotrophs that use inorganic chemical reactions to make organic matter. In addition, it appears that there are many archeons that are photoautotrophs that use light to produce organic molecules. In the ocean it appears that these two kinds of autotrophs are important contributors to the base of the marine food web. Because of their small size, they are referred to as picoplankton. These autotrophic archeons are eaten by bacteria, protozoa, and other organisms. In the ocean it is becoming clear that some of chemoautotrophic Archaea are involved in several steps in the nitrogen cycle. Since Archaea are also common in the soil, it is likely that they are also involved in the terrestrial part of the nitrogen cycle as well.


The Microbial Ecology of a Cow

Ruminants are animals, such as cattle, deer, bison, sheep, and goats, that have a special design to their digestive system. These animals have a large, pouchlike portion of the gut, called a rumen, connected to the esophagus. Ruminants eat plant materials that are often dry and consist of large amounts of cellulose from the plants' cell walls. They do not have enzymes (cellulases) that allow them to break down the cellulose. The rumen is essentially a fermentation chamber for a variety of anaerobic microorganisms, including fungi, members of the domains Bacteria and Archaea, and ciliates and other protozoa from the kingdom Protista.

Cows and other ruminants chew their cud. This is a process in which the animal eat grasses and other plant materials, which go into the rumen. Later, they regurgitate the food and chew it again, which further reduces the size of the food particles and thoroughly mixes the food with liquids containing the mixture of microorganisms.

Some of the microorganisms (certain bacteria, fungi, and protozoa) in the rumen produce enzymes that can break down cellulose to short-chain fatty acids. These fatty acids are absorbed into the cow's bloodstream and are used by its cells to provide energy. But the story does not end there. Methanogens (certain Archaea) are common in the gut of ruminants. They metabolize some of the fatty acids to methane. A cow typically releases 200 to 500 liters of methane gas per day. Methane production by ruminants and termites that have a similar gut metabolism contributes significantly to the level of methane in the atmosphere. Because methane is a greenhouse gas, cows and their archeon companions are a factor in global warming.

Agricultural researchers look at methane production by cows as an opportunity to increase the food efficiency of cattle. If the researchers could prevent the methanogens from using some of the fatty acids to make methane, there would be more for the cows to turn into meat or milk. They have experimented with substances that inhibit the growth of methanogens.

The digestive system of ruminants encourages the growth of microorganisms that assist in the breakdown of cellulose.


The Marine Microbial Food Web

The analysis of terrestrial ecosystems typically involves the categorization of organisms into functional groups based on their metabolic abilities and their position in food chains. Plants are identified as producers, animals as consumers, and fungi and bacteria as decomposers. Scientists have long known that microorganisms were important in marine food webs but have been hampered in their study by the nature of the organisms involved.

There are significant problems in studying microbes. Their small size makes it difficult to identify organisms. A new term, picoplankton, is used to describe aquatic organisms that are in a size range between 0.2 and 2 pm. In addition, once organisms are detected it is often difficult or impossible to grow microbes to study their metabolic abilities and determine how they contribute to food webs.

However, by using new techniques for identifying organisms and indirect methods to get an idea of their metabolic abilities, it is becoming clear that the ocean is dominated by a microbial food web. As with all ecosystems, the base consists of autotrophs that use a source of energy to manufacture organic matter. The majority of photosynthesis in the ocean is the result of cyanobacteria and the eukaryotic dinoflagellates and diatoms. The photosynthetic cyanobacteria are the most common bacteria in the ocean. The Archaea also appear to be important as autotrophs, although many are chemoautotrophs that use inorganic chemical reactions to provide themselves with energy. They are extremely common, particularly in deep ocean waters where sunlight does not penetrate.

Once we get beyond the producer level in the ocean, various kinds of microbes are first in line to consume the cells of autotrophs. Flagellates, ciliates, fungi, and bacteria consume other organisms. Finally, we arrive at the animals that are filterfeeding animals, such as sponges, corals, and crustaceans that sift a mixture of organisms from water. These become food for larger animals such as crabs, snails, fish, and squid.

There is an important subplot to this microbial food web picture. Much of the organic matter never reaches animals at higher trophic levels. It is trapped in a microbial loop that involves many kinds of microbes that simply recycle organic matter. It is thought that bacteria alone process more than half of all the carbon involved in metabolism in the oceans. Dissolved organic carbon is an important part of the microbial food web. Autotrophic microbes produce organic molecules from inorganic molecules. Dissolved organic carbon enters the water as a result of leakage and waste products from microbes (both autotrophs and heterotrophs) and the death and decay of organisms. It is becoming clear that viruses have an important role to play in this process. Studies that sample the DNA in the ocean identify a large virus component. Many scientists estimate that there are millions of viruses per milliliter of seawater. Viruses infect and kill their hosts: Bacteria, Archaea, and eukaryotic microbes. The disintegration of their host cells releases organic matter into the water, which, in turn, becomes food for saprophytic microbes.

These studies are significant to understanding the basis for ecologic interactions in the ocean. These interactions can impact fisheries biology and human health when there are huge increases in the population of certain toxic marine microbes that restrict the use of fish for food and cause the closure of beaches to prevent illness.


3. List three ways that Bacteria and Archaea differ.

4. Give an example of a member of the Bacteria that is

a. photosynthetic.

b. involved in the nitrogen cycle.

c. mutualistic.

d. commensal.

5. Give two examples of how humans use Bacteria as decomposers.

6. What is meant by the term bloom?

7. What is a pathogen? Give two examples.

8. Define the term saprophyte.

9. What is a bacterial endospore?

10. What are methanogens?

11. Describe how members of the Archaea are involved in the nitrogen cycle.

12. Describe three roles played by Archaea in the ocean.

13. What is a thermophile? A halophile?