Most textbooks seems to restrict pathogens to the domains bacteria and eukarya. Are there any pathogenic archaeans?
To date, there isn't a single species that may be considered pathogenic to animals or plants. There are archeon who live in association with animals (in the case of human, they have been found in the gut microbiota aswell as certain skin surfaces) that are mainly methanogens. This could lead to think that archaons could produce "pathologic farting", but that condition has never been described.
In the case of ascidians and other marine invertebrates, some archeon have been found living in symbiosis, with the microbe aiding the animal by means of nitrogen fixation. One could think that, since they're able to live inside the organisms, they could behave as opportunistic pathogens, but none has been described.
Furthermore, it actually exists at least one known species who could be classified as parasitic, the nanoarchaeota Nanoarchaeum equitans, which has been described as a symbiont of some hyperthermophilic archaeon. Despite that description as symbiont, Nanoarchaeum cannot live by its own, while its companion does. Moreover, its genome contains the typical traits associated to parasitism, with great reduction in genome size and loss of many key pathways and cell functions, including methabolic pathways an even some key components of its transcriptional and translational machinery. Since there is no known function of the Nanoarchaeum itself, it should be considered as a parasite.
However, the lack of evidence may be biased, since few people has used metagenomic approach to look for archeon in clinical samples, and some rare cases may be found in the future.
Actually, there exist at least one reference to a negative effect of Nanoarchaeum towards its host. Jahn et al (2008) describes that single Ignicoccus cells wich had more than two Nanoarchaeum cells attached were unable to grow, while those with two or less could form a colony.
It's true that there isn't strong evidence to considere Nanoarchaeum as a parasite in the traditional sense, provided this is the only reference I have found to a negative (or positive) effect of this archeon. It's also true that even traditional symbiots such as micorhizic fungi can be harmful in certain conditions, and because of that, this lonely example wouldn't be representative. However, untill this reference there were the same evidence to consider this archaeon as a symbiot or as a parasite, and for unkown reasons the first hypothesis was assumed by default. This results sugest that Nanoarcheum is potentially harmful and, since there still isn't any evidence that demostrate that Nanoarchaeum has any benefit, I strongly believe the consideration of a putative parasite should be encouraged and used as the default hypothesis.
Some authors prefer to use the term "intimal association", and they define it as "a highly specialized system combining characteristics of symbiosis, commensalisms, and parasitism" wich tries to be something neutral beween the two hypothesis. However I find that expression unnecesary, confuse and with an strong lack of meaning; mainly because that kind of relationship can be described with classical ecologycal terms.
Are there any pathogenic archaeans? - Biology
PART V. THE ORIGIN AND CLASSIFICATION OF LIFE
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 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 SCIENCE WORKS 21.1
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.
HOW SCIENCE WORKS 21.2
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.
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.
Lactobacillus sp., Escherichia coli, Bacillus sp., Clostridium sp., Pseudomonas sp., Bacteroides sp., Streptococcus sp.
Lactobacillus sp., Staphylococcus sp., Streptococcus sp., Clostridium sp., Peptostreptococcus sp., Escherichia coli
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 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 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 10 43 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 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 (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
b. involved in the nitrogen cycle.
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?
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?
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Are there any pathogenic archaeans? - Biology
My goal with this entry is to use it as the basis for organizing as well as storing information that I will be using to generate an article for submission [drafted as of May 4] as well as a subsequent chapter. The article is due for submission at the end of May, 2013, and is an elaboration on this piece:
The chapter is due sometime during Fall of 2013. My hope is to use the research I do on this article to both create and beef up various entries in BaP.
Perhaps the most striking conundrum is the lack of any known archaeal pathogen for any animal or plant. No single reason has been described that can account for this observation. methanogens exist in the human gastrointestinal tract at concentrations of up to 10 10 per gram of stool sample, and they have been associated with colorectal and periodontal disease. However, other than an association with a disease state, no member of the Archaea has been shown (for example, by Koch's postulates) to be the primary cause of an animal or plant disease.
The first question to explore is just what is the known, in relatively broad terms, of the phenotypic and/or genotypic diversity of , which I consider as a series of BaP entries:
See also , (as member of Euryarchaeota ?), and .
Now that I've collected a reasonable (and Wikipedia approved!) sampling of archaeal genera, the next step should be to concentrate on identifying means by which organisms can each other (listed ):
Note that I would not feel comfortable including issues of indirect, i.e., exploitative competition on the above list. Presumably, that is, just about every species is capable of effecting exploitative competition of one form or another.
The following is a list of means by which bacteria (that is, domain Bacteria ) are known to be '' to other organisms (also in ):
I'm uncertain whether virulence factor should be included in the above list&hellip For more information that may be helpful in working on the above list, see http://www.mansfield.ohio-state.edu/
What sort of theory exists with regard to victim-exploiter interactions, that is, which addresses the question of why an exploiter may exploit? Presumably the answer to that question is for the most part straightforward, i.e., exploiters exploit in order to gain something from victims. Alternatively, one answer to that question likely may be found in the literature.
Here is a perhaps vague way of why archaea might not as readily display exotoxins and/or defenses against phagocytosis relative to bacteria. Let's assume that these factors exist as a means of evading not animal but instead predation by protozoa (need to see ) The first question to ask, then, what is the extent to which protozoa in fact exist within the environments in which archaea exist. The answer to that question must certainly be yes, but a well-qualified yes. That is, to what extent do protists exist within extremely hot, highly acidic, highly salty, or indeed anaerobic environments? The second question then should be whether those archaea that exist within environments within which predation by protozoa is likely in fact display metabolisms that would seem to be conducive to otherwise serving as pathogens particularly of animals, i.e., those organisms that have immune systems which possess phagocytic cells. Thus, do these archaeal species simultaneously employ that are available to them in animals and otherwise have had reason to evolve anti-phagocytosis mechanisms that nonetheless are independent of interactions with animals?
Is it possible that one reason that there is a seeming lack of archaeal pathogens is that there is a relative lack of predators of archaea in combination with a relatively lack of metabolic suitability of the remaining archaea to pathogenic life styles? Indeed, animals, as sponges, are basically just modified protists, so it's not unreasonable pathogenicity especially of animals to in a sense predate animals.
A perhaps related question is to what degree do archaea serve as animal saprophytes, that is, which in principle could transfer those tendencies, a la the , to developing mechanisms whereby otherwise living animal flesh is converted to dead and therefore more exploitable animal flesh?
- Many archaeons don't live in environments containing substantial numbers of exploitable .
The more basic question then is why did the archaeons not evolve down a road where they simultaneously developed metabolisms that were preadapted to exploiting multicellular organisms, within less extreme environments, in which anti-protist defenses may also have evolved. That is, where are the fast-growing, chemoheterotrophic, especially saprophytic, protist- evading archaea in this world? Basically, the above is a multi-factorial explanation for why they currently don't exist, but doesn't get to the issue of why these various impediments seem to exist. It also would be interesting to see whether phage-encoding of virulence factors might be worked into the narrative.
Are there any archaea that exist as endosymbionts? Is it telling that hypotheses of tend to posit, if they involve an archaeon, the intracellular acquisition of a member of domain Bacteria by an archaeon rather than the other way around. Alternatively, where do the archaea physically reside within those ?
What is the archaean composition of microbiomes and metagenomes?
Pretty much what I know of the viruses of domain Archaea can be found here:
Methanogenic Archaea have been reported in subgingival dental plaque as early as 1987 . To date, three genera have been successfully isolated from subgingival plaque: Methanobrevibacter [42,43], Methanosphaera (based on weak antigenic similarity) , and Methanosarcina (based on physiology and staining) . Additionally, 16S rRNA gene amplicon sequencing studies detected archaea related to Thermoplasmata [46,47] (which, in retrospect, probably belong to the seventh order of methanogens see gut methanogens section, above), as well as members of the Methanobacterium genus [48,49]. In general, it appears that the genetic diversity of archaea of the human subgingival dental plaques is low, much as is the case for the gut methanogens, and that Methanobrevibacter oralis is by far the most prevalent methanogen found in this environment. In a recent review, Nguyen-Hieu et al. pooled the data from several studies of methanogens in the oral cavity and concluded that M. oralis is significantly associated with periodontal disease both in terms of abundance comparisons between patients and controls and between diseases and healthy sites within the same patient . Furthermore, they concluded that indirect evidence supports the contribution of that methanogen to periodontal disease and that this contribution likely stems from syntrophic interactions with sulfate-reducing bacteria. Thus, a mixed infection may be required for a direct causal demonstration of the pathogenic contribution of M. oralis in an animal model of periodontal disease. Unlike many antibiotics that do not target archaea (because they do not have a peptidoglycan cell wall and have ribosomes that are more eukaryotic like ), metronidazole, which is commonly used to treat periodontitis, is highly effective against M. oralis  and, thus, suppression of M. oralis could contribute to its efficacy . Statins that inhibit the activity of 3-hydroxy-3-methylglutaryl coenzyme A reductases of eukaryotes and archaea lower blood cholesterol in humans, but they also effectively inhibit archaeal growth because they block the synthesis of their main membrane lipids . If indeed M. oralis is a "co-pathogen," it would be interesting to examine the effects of "archaea-specific" drugs such as statins on periodontal disease, for example, by examining the periodontal pockets of patients who have recently been prescribed statins before and after several months of statin use.
Before 1977, all life on Earth was classified into two groups: single-celled microorganisms and complex cellular life such as fungi, plants, and animals. A seminal discovery in 1977 rewrote the tree of life and introduced a whole new domain of organisms known as the archaea – mysterious microbes that are genetically distinct from bacteria. Fast forward to the 21st century, and again new discoveries about archaea are leading scientists to reshape the tree of life and rewrite the evolutionary history of complex organisms. Dr. Dipti Nayak introduces the fascinating organisms known as archaea and explains how they are helping scientists answer the question Where do we come from?.
Where are archaea found?
Archaea were originally only found in extreme environments which is where they are most commonly studied. They are now known to live in many environments that we would consider hospitable such as lakes, soil, wetlands, and oceans.
Many archaea are extremophiles i.e lovers of extreme conditions. Different groups thrive in different extreme conditions such as hot springs, salt lakes or highly acidic environments.
Archaea that live in extremely salty conditions are known as extreme halophiles – lovers of salt. Extreme halophiles are found in places such as the Dead Sea, the Great Salt Lake and Lake Assal which have salt concentrations much higher than ocean water.
Other organisms die in extremely salty conditions. High concentrations of salt draw the water out of cells and cause them to die of dehydration. Extreme halophiles have evolved adaptations to prevent their cells from losing too much water.
Archaea that are found in extremely hot environments are known as extreme thermophiles. Most organisms die in extremely hot conditions because the heat damages the shape and structure of the DNA and proteins found in their cells. Extreme thermophiles struggle to grow and survive in moderate temperatures but are known to live in environments hotter than 100 ℃.
Acidophiles are organisms that love highly acidic conditions such as our stomachs and sulfuric pools. Acidophiles have various methods for protecting themselves from the highly acidic conditions. Structural changes to the cellular membranes can prevent acid entering their cell. Channels in the membrane of their cell can be used to pump hydrogen ions out of the cell to maintain the pH inside the cell.
Phages: The source of many pathogen-associated genes
One of the changes that occurs in a benign bacterial strain that enables it to become a pathogen is the acquisition of novel genetic material via horizontal gene transfer 27 . Mobile genetic elements, including phages, play a key role in this gene transfer process and in generating bacterial genomic diversity 28 . Many genes that enable Bacteria to become pathogenic are clustered in or adjacent to such elements. In fact, a study of 631 genomes recently showed that virulence factors, as well as pathogen-associated genes, are disproportionately associated with genomic islands (an inclusive grouping of larger mobile genetic elements, including phages), with high statistical significance 8 , 29 . Most genomic islands are derived from phages 8 , 30-32 . Since such studies tend to under-predict the occurrence of genomic islands and phages, the association of virulence genes with genomic islands and phages is likely to be even higher 8 , 30 . There are many individual studies of pathogens that support this observation and the related role of phages in virulence, for example the integration of phages has been shown to help Staphylococcus aureus adapt to its human host during infection 33 . It is logical that virulence factors would be associated with phages and related mobile elements such as genomic islands 8 . Otherwise, such virulence factors would simply become extinct if the bacterium they were contained in became too virulent and killed its host. Virulence factors are better able to survive through their association with the more flexible phage gene pool, through which genes can transfer in and out of bacterial genomes.
Extensive lists of genes in Bacteria, which are associated with virulence and are derived from phages, have been compiled 34 , 35 . From our analysis, the great majority of these virulence genes are from phages belonging to the families myoviridae (phages with long contractile tails) and syphoviridae (phages with long non-contractile tails), plus a few others including inoviruses and podoviruses. However, this could reflect a bias in the available phage genome data, as the vast majority of sequenced phages are siphoviruses and myoviruses 35 . Members of these phage families infect both Gram-positive and Gram-negative Bacteria 35 and so comparing these phages with archaeal viruses is, perhaps, most relevant.
Archaea have unique properties separating them from the other two domains of life, Bacteria and Eukaryota. The Archaea are further divided into multiple recognized phyla. Classification is difficult because the majority have not been isolated in the laboratory and have only been detected by analysis of their nucleic acids in samples from their environment. Archaea and bacteria are generally similar in size and shape, although a few archaea have very strange shapes. Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes. Archaea use more energy sources than eukaryotes: these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea use sunlight as an energy source, and other species of archaea fix carbon however, unlike plants and cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding unlike bacteria and eukaryotes, no known species forms spores. Archaea were initially viewed as extremophiles living in harsh environments, such as hot springs and salt lakes, but they have since been found in a broad range of habitats, including soils, oceans, and marshlands. They are also part of the human microbiota, found in the colon, oral cavity, and skin. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. Archaea are a major part of Earth’s life and may play roles in both the carbon cycle and the nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, but they are often mutualists or commensals. One example is the methanogens that inhabit human and ruminant guts, where their vast numbers aid digestion. Methanogens are also used in biogas production and sewage treatment, and biotechnology exploits enzymes from extremophile archaea that can endure high temperatures and organic solvents.
Making the Case Against Archaea
Thirty years ago, a University of Illinois microbiologist named Carl Woese famously declared that some microbes are so different from the rest that they should be classified as a third branch of life. They are archaea, sharing the stage with bacteria and with eukarya, the branch that includes plants, animals, fungi and microscopic protists. Their toughness soon became legendary.
They cropped up in places that would kill most things: from geysers and oil wells to salt lakes and polar seas. Then some were found inside animals, including us, and suddenly scientists were seeing them everywhere: in the soil, the water, anywhere the rest of life can exist and even where it can’t. That’s when the chin-scratching began. Many bacteria and eukarya are well known pathogens – if you can name the infection, one of them is probably responsible. Yet archaea seemed innocent. Maybe they are, which prompts speculation that they could hold a genetic key to curing disease. Or maybe they have been causing disease all along right under our noses.
“There is no inherent reason why archaea should not be involved in diseases. There is no fundamental biological or ecological barrier,” said Torsten Thomas, a microbiologist at the University of New South Wales in Sydney, Australia. “It has been talked about in the scientific community for many years but nobody has really studied the reasons for the existence or nonexistence of pathogenic archaea.”
Thomas thinks that should change. Archaea, he argues, may be responsible for some diseases with no known causes, such as Crohn’s disease, arthritis, lupus and gingivitis, to name some of the better known on his list. Many of his peers disagree, but if Thomas is right, then science is at a loss now to defend us against those diseases. There are no anti-archaeal drugs in development, and these microbes are daunting potential foes because they are poorly understood, hard to study and easily foil common techniques developed to ferret out conventional microbial culprits of disease.
So far, the case against archaea is circumstantial, but they have no obvious alibi: archaea live inside us and other animals in guts and orifices – the same places where many diseases take their toll.
Some scientists have begun peering into those places, this time with an eye out for archaea. In one study, microbiologists at Stanford University teamed up with peridontologists – experts on gum disease – at the University of California, San Francisco to plot the kinds of archaea found in the mouth.
“What became apparent fairly quickly was that somebody either had archaea or they didn’t,” said Paul Lepp, now at Minot State University in North Dakota. “And if they had it, you found it in peridontitis sites.”
The more archaea the researchers found, the worse the gum disease. But the evidence wasn’t exactly a smoking gun, since the archaea were present in only about one-third of diseased gums, and shared the space with many other kinds of microbes. They published their results in April 2004 in the journal Proceedings of the National Academy of Sciences.
A similar study by scientists in Brazil and Germany found archaea in five out of 20 gum disease samples. They also linked archaea with infectious disease without implicating them explicitly as the cause, according to a paper published in April 2006 in the Journal of Clinical Microbiology. And sights were not just on gum disease. That same year, Japanese researchers examined plaque from 13 coronary arteries and found evidence of archaea in all of them. They published their results in the journal Clinics, concluding that they may be the first to discover disease-causing archaea inside human organs. Lepp warned, however, that their methods may have been flawed in part because they lacked proper experimental controls.
Stanford’s David Relman, who headed the American gum disease study, has forged a reputation as an archaea disease hunter. But unlike Torsten Thomas at New South Wales, he does not suspect they could be a direct cause.
“I think that the archaea can contribute to pathology and to disease, but I don’t think they do so alone or in a direct manner,” Relman said. Instead, he believes, “They allow other organisms to flourish to a much greater degree than they would otherwise. But it’s a consortium, a group effect. It’s not an effect they are able to carry out on their own.”
His hypothesis hinges on the archaea’s diet. Those found in humans and other animals are methanogens – they consume hydrogen made by bacteria and excrete methane gas. (Not all archaea produce methane, but they are the only creatures that can – it’s one of the differences that sets them apart from the other two domains of life.) Thriving on the waste of other microbes, they clean house, which may allow disease-causing bacteria to multiply.
Archaea have a so-called grandfather, Ralph Wolfe, who is skeptical they could cause disease. Wolfe, a microbiologist at the University of Illinois, earned his nickname studying archaea for decades, since before they were given their own taxonomic domain. He worked alongside Carl Woese as the concept of three domains of life gained momentum. Archaea, Wolfe believes, are too primitive and biologically isolated to cause disease in animals, though he does not discount the idea of the consortium effect.
“I would say it’s a dead end, but in science you can never tell,” he said. He does agree with Thomas on one point, though: studying archaea is tough, and was harder still when he started his work without the benefit of the technology available today.
The old technique, he said, was to swab an abscess, for example, and breed the extracted microbes on agar – a seaweed gelatin that nourishes them. Outside of the body in oxygen-rich open air, only those bacteria that survive in oxygen multiplied. The methanogens and other anaerobes vulnerable to oxygen, if there were any, were smothered.
“So,” Wolfe conceded, “unless a laboratory takes a lot of caution to separate anaerobes from the sample then they could be missing something.”
Thomas insists that archaea need to be studied further before they can be eliminated as suspects in causing unsolved diseases. Even if they are ultimately proven harmless, he says, that finding could be important if it turns out that archaea have a gene that suppresses toxicity – a gene that might be useful someday in stifling the power bacteria have to inflict damage.
“I think that if we don’t find any pathogenic archaea it would be very interesting to find out why they aren’t,” Thomas says. “Obviously that’s the best target to attack in bacteria. If we find something that bacteria do have and archaea don’t have, we need to attack that.”
Methanogens are coccoid (spherical shaped) or bacilli (rod shaped). There are over 50 described species of methanogens, which do not form a monophyletic group, although all known methanogens belong to Archaea. They are mostly anaerobic organisms that cannot function under aerobic conditions, but recently a species (Candidatus Methanothrix paradoxum) has been identified that can function in anoxic microsites within aerobic environments. They are very sensitive to the presence of oxygen even at trace level. Usually, they cannot sustain oxygen stress for a prolonged time. However, Methanosarcina barkeri is exceptional in possessing a superoxide dismutase (SOD) enzyme, and may survive longer than the others in the presence of O2.   Some methanogens, called hydrogenotrophic, use carbon dioxide (CO2) as a source of carbon, and hydrogen as a reducing agent.
The reduction of carbon dioxide into methane in the presence of hydrogen can be expressed as follows:
Some of the CO2 reacts with the hydrogen to produce methane, which creates an electrochemical gradient across the cell membrane, used to generate ATP through chemiosmosis. In contrast, plants and algae use water as their reducing agent.
Methanogens lack peptidoglycan, a polymer that is found in the cell walls of Bacteria but not in those of Archaea. Some methanogens have a cell wall that is composed of pseudopeptidoglycan. Other methanogens do not, but have at least one paracrystalline array (S-layer) made up of proteins that fit together like a jigsaw puzzle. 
Methanogens play a vital ecological role in anaerobic environments of removing excess hydrogen and fermentation products that have been produced by other forms of anaerobic respiration. Methanogens typically thrive in environments in which all electron acceptors other than CO2 (such as oxygen, nitrate, ferric iron (Fe(III)), and sulfate) have been depleted. In deep basaltic rocks near the mid ocean ridges, they can obtain their hydrogen from the serpentinisation reaction of olivine as observed in the hydrothermal field of Lost City.
The thermal breakdown of water and water radiolysis are other possible sources of hydrogen.
Methanogens are key agents of remineralization of organic carbon in continental margin sediments and other aquatic sediments with high rates of sedimentation and high sediment organic matter. Under the correct conditions of pressure and temperature, biogenic methane can accumulate in massive deposits of methane clathrates,  which account for a significant fraction of organic carbon in continental margin sediments and represent a key reservoir of a potent greenhouse gas. 
Methanogens have been found in several extreme environments on Earth – buried under kilometres of ice in Greenland and living in hot, dry desert soil. They are known to be the most common archaebacteria in deep subterranean habitats. Live microbes making methane were found in a glacial ice core sample retrieved from about three kilometres under Greenland by researchers from the University of California, Berkeley. They also found a constant metabolism able to repair macromolecular damage, at temperatures of 145 to –40 °C. 
Another study  has also discovered methanogens in a harsh environment on Earth. Researchers studied dozens of soil and vapour samples from five different desert environments in Utah, Idaho and California in the United States, and in Canada and Chile. Of these, five soil samples and three vapour samples from the vicinity of the Mars Desert Research Station in Utah were found to have signs of viable methanogens. 
Some scientists have proposed that the presence of methane in the Martian atmosphere may be indicative of native methanogens on that planet.  In June 2019, NASA’s Curiosity rover detected methane, commonly generated by underground microbes such as methanogens, which signals possibility of life on Mars. 
Closely related to the methanogens are the anaerobic methane oxidizers, which utilize methane as a substrate in conjunction with the reduction of sulfate and nitrate.  Most methanogens are autotrophic producers, but those that oxidize CH3COO − are classed as chemotroph instead.
Comparative proteomic analysis has led to the identification of 31 signature proteins which are specific for methanogens (also known as Methanoarchaeota). Most of these proteins are related to methanogenesis, and they could serve as potential molecular markers for methanogens. Additionally, 10 proteins found in all methanogens which are shared by Archaeoglobus, suggest that these two groups are related. In phylogenetic trees, methanogens are not monophyletic and they are generally split into three clades. Hence, the unique shared presence of large numbers of proteins by all methanogens could be due to lateral gene transfers.  Additionally, more recent novel proteins associated with sulfide trafficking have been linked to methanogen archaea.  More proteomic analysis is needed to further differentiate specific genera within the methanogen class and reveal novel pathways for methanogenic metabolism.
Modern DNA or RNA sequencing approaches has elucidated several genomic markers specific to several groups of methanogens. One such finding isolated nine methanogens from genus Methanoculleus and found that there were at least 2 trehalose synthases genes that were found in all nine genomes.  Thus far, the gene has been observed only in this genus, therefore it can be used as a marker to identify the archaea Methanoculleus. As sequencing techniques progress and databases become populated with an abundance of genomic data, a greater number of strains and traits can be identified, but many genera have remained understudied. For example, halophilic methanogens are potentially important microbes for carbon cycling in coastal wetland ecosystems but seem to be greatly understudied. One recent publication isolated a novel strain from genus Methanohalophilus which resides in sulfide-rich seawater. Interestingly, they have isolated several portions of this strain's genome that are different than other isolated strains of this genus (Methanohalophilus mahii, Methanohalophilus halophilus, Methanohalophilus portucalensis, Methanohalophilus euhalbius). Some differences include a highly conserved genome, sulfur and glycogen metabolisms and viral resistance.  Genomic markers consistent with the microbes environment have been observed in many other cases. One such study found that methane producing archaea found in hydraulic fracturing zones had genomes which varied with vertical depth. Subsurface and surface genomes varied along with the constraints found in individual depth zones, though fine-scale diversity was also found in this study.  It is important to recognize that genomic markers pointing at environmentally relevant factors are often non-exclusive. A survey of Methanogenic Thermoplasmata has found these organisms in human and animal intestinal tracts. This novel species was also found in other methanogenic environments such as wetland soils, though the group isolated in the wetlands did tend to have a larger number of genes encoding for anti-oxidation enzymes that were not present in the same group isolated in the human and animal intestinal tract.  A common issue with identifying and discovering novel species of methanogens is that sometimes the genomic differences can be quite small, yet the research group decides they are different enough to separate into individual species. One study took a group of Methanocellales and ran a comparative genomic study. The three strains were originally considered identical, but a detailed approach to genomic isolation showed differences among their previously considered identical genomes. Differences were seen in gene copy number and there was also metabolic diversity associated with the genomic information. 
Genomic signatures not only allow one to mark unique methanogens and genes relevant to environmental conditions it has also led to a better understanding of the evolution of these archaea. Some methanogens must actively mitigate against oxic environments. Functional genes involved with the production of antioxidants have been found in methanogens, and some specific groups tend to have an enrichment of this genomic feature. Methanogens containing a genome with enriched antioxidant properties may provide evidence that this genomic addition may have occurred during the Great Oxygenation Event.  In another study, three strains from the lineage Thermoplasmatales isolated from animal gastro-intestinal tracts revealed evolutionary differences. The eukaryotic-like histone gene which is present in most methanogen genomes was not present, eluding to evidence that an ancestral branch was lost within Thermoplasmatales and related lineages.  Furthermore, the group Methanomassiliicoccus has a genome which appears to have lost many common genes coding for the first several steps of methanogenesis. These genes appear to have been replaced by genes coding for a novel methylated methogenic pathway. This pathway has been reported in several types of environments, pointing to non-environment specific evolution, and may point to an ancestral deviation. 
Methane production Edit
Methanogens are known to produce methane from substrates such as H2/CO2, acetate, formate, methanol and methylamines in a process called methanogenesis.  Different methanogenic reactions are catalyzed by unique sets of enzymes and coenzymes. While reaction mechanism and energetics vary between one reaction and another, all of these reactions contribute to net positive energy production by creating ion concentration gradients that are used to drive ATP synthesis.  The overall reaction for H2/CO2 methanogenesis is:
Well-studied organisms that produce methane via H2/CO2 methanogenesis include Methanosarcina barkeri, Methanobacterium thermoautotrophicum, and Methanobacterium wolfei.    These organisms are typically found in anaerobic environments. 
In the earliest stage of H2/CO2 methanogenesis, CO2 binds to methanofuran (MF) and is reduced to formyl-MF. This endergonic reductive process (∆G˚’= +16 kJ/mol) is dependent on the availability of H2 and is catalyzed by the enzyme formyl-MF dehydrogenase. 
The formyl constituent of formyl-MF is then transferred to the coenzyme tetrahydromethanopterin (H4MPT) and is catalyzed by a soluble enzyme known as formyl transferase. This results in the formation of formyl-H4MPT. 
Formyl-H4MPT is subsequently reduced to methenyl-H4MPT. Methenyl-H4MPT then undergoes a one-step hydrolysis followed by a two-step reduction to methyl-H4MPT. The two-step reversible reduction is assisted by coenzyme F420 whose hydride acceptor spontaneously oxidizes.  Once oxidized, F420’s electron supply is replenished by accepting electrons from H2. This step is catalyzed by methylene H4MPT dehydrogenase. 
Next, the methyl group of methyl-M4MPT is transferred to coenzyme M via a methyltransferase-catalyzed reaction.  
The final step of H2/CO2 methanogenic involves methyl-coenzyme M reductase and two coenzymes: N-7 mercaptoheptanoylthreonine phosphate (HS-HTP) and coenzyme F430. HS-HTP donates electrons to methyl-coenzyme M allowing the formation of methane and mixed disulfide of HS-CoM.  F430, on the other hand, serves as a prosthetic group to the reductase. H2 donates electrons to the mixed disulfide of HS-CoM and regenerates coenzyme M. 
Wastewater treatment Edit
Methanogens are widely used in anaerobic digestors to treat wastewater as well as aqueous organic pollutants. Industries have selected methanogens for their ability to perform biomethanation during wastewater decomposition thereby rendering the process sustainable and cost-effective. 
Bio-decomposition in the anaerobic digester involves a four-staged cooperative action performed by different microorganisms.  The first stage is the hydrolysis of insoluble polymerized organic matter by anaerobes such as Streptococcus and Enterobacterium.  In the second stage, acidogens break down dissolved organic pollutants in wastewater to fatty acids. In the third stage, acetogens convert fatty acids to acetates. In the final stage, methanogens metabolize acetates to gaseous methane. The byproduct methane leaves the aqueous layer and serves as an energy source to power wastewater-processing within the digestor, thus generating a self-sustaining mechanism. 
Methanogens also effectively decrease the concentration of organic matter in wastewater run-off.  For instance, agricultural wastewater, highly rich in organic material, has been a major cause of aquatic ecosystem degradation. The chemical imbalances can lead to severe ramifications such as eutrophication. Through anaerobic digestion, the purification of wastewater can prevent unexpected blooms in water systems as well as trap methanogenesis within digesters. This allocates biomethane for energy production and prevents a potent greenhouse gas, methane, from being released into the atmosphere.
The organic components of wastewater vary vastly. Chemical structures of the organic matter select for specific methanogens to perform anaerobic digestion. An example is the members of Methanosaeta genus dominate the digestion of palm oil mill effluent (POME) and brewery waste.  Modernizing wastewater treatment systems to incorporate higher diversity of microorganisms to decrease organic content in treatment is under active research in the field of microbiological and chemical engineering.  Current new generations of Staged Multi-Phase Anaerobic reactors and Upflow Sludge Bed reactor systems are designed to have innovated features to counter high loading wastewater input, extreme temperature conditions, and possible inhibitory compounds. 
Biology's big brainteaser
If you hang around the bar at a sufficiently obscure science conference you might overhear talk of one of modern biology's most intriguing puzzles. The conundrum concerns a fifth of all life on the planet, and answering it could help us to treat diseases that have evaded medicine for thousands of years.
At the very least it could point us towards a new generation of drugs. Yet perhaps the biggest puzzle is why modern science has largely ignored it. Have you even heard of the archaea? A growing number of microbiologists have, and they are beginning to turn the study of this third branch of life from bar room chat to scientific reality.
It all started back in 1990. The microbiologist Carl Woese at the University of Illinois found that life could be divided into three distinct groups, each of which had branched from a common, primitive ancestor billions of years ago. He assigned organisms to each category depending, among other things, on what their cells looked like and how their internal machinery worked. Bacteria are one such category. The other two are eukaryotes and archaea. Humans belong to the former, along with animals, plants and fungi. The latter, the archaea, lie somewhere between us and bacteria. Like bacteria, they are tiny, single-celled organisms. Their genetic machinery, however, is much closer to ours.
The greatest outstanding mystery of archaea became apparent when people looked at the organisms known to cause disease in humans and animals. Plenty of bacteria are known culprits and there are numerous disease-causing eukaryotes, mostly fungi. But archaea seemed to be entirely harmless. "What's puzzling is that we have these three kinds of life, but only two bear organisms that cause disease," says Rick Cavicchioli, a molecular biologist at the University of New South Wales. "What is it about these archaea that means they don't cause disease?"
The answer could have huge significance. If there is a fundamental reason why archaea cannot or do not cause disease, then this could be the key to "switching off" pathogenic microbes that make people ill, says Cavicchioli. But there's a problem. What if archaea aren't as benign as we might think? Perhaps they are causing disease, and have been for millennia, but we just haven't realised.
The prospect is looking ever more likely. Archaea are estimated to make up a fifth of all life, meaning they outnumber animals. And they live in all the right places to cause disease. As well as being found in extreme environments on Earth, from hot undersea vents to Antarctica, archaea have been found in the intestines, the mouth and in slimy films of mucous elsewhere in the body. A gram of human faeces can hold 10bn of them. "On the evidence we've got so far, we should be finding more than 30 types of archaea that cause disease," says Cavicchioli.
Peter Westerman, an expert in archaea at the Technical University of Denmark is hunting archaea that may be responsible for unexplained diseases. "It's surprising how many illnesses are caused by unknown pathogens," he says. Archaea might be playing a part in some of those. Westerman's team is painstakingly looking at samples of diseased tissue to look for tell-tale signs of archaea.
Other researchers say they are already starting to see links between disease and archaea, but that the results are often surprising. Paul Lepp, a microbiologist at Stanford University, California, has been looking at whether archaea play a role in gum disease. The study is not finished, but Lepp says first results show archaea are far more prevalent in the mouths of people with severe gum disease than those with healthy gums. They may simply grow better on diseased tissue, but it's a lead worth following.
Working out the real culprit of a disease is often complicated because a whole community of different bacteria and other organisms can be found thriving on diseased tissue. Lepp suspects that, as members of a wider community, archaea might sometimes play a more subtle role in progressing a disease. Most of the archaea found in humans and other animals convert hydrogen around them into methane, earning them the name "methanogens". This could be invaluable for a community of disease-causing bacteria. "Bacteria often produce hydrogen, but when it gets to a high enough level it becomes toxic so it kills them off," says Lepp. With archaea around, the toxic hydrogen will be converted into methane. "That means the pathogens could grow to a much larger population than otherwise, making them much more of a problem," says Lepp.
Lepp's colleague at Stanford, Paul Eckburg, is also hunting for pathogenic archaea. His focus is on inflammatory bowel conditions, one being Crohn's disease. Again, his work is in its early stages, but his findings are proving unusual. "In the data we've got so far, it looks like patients with Crohn's disease do not have archaea in their intestines while those without the disease do have them," he says. "In this case, it may be that archaea actually have a protective role."
Unravelling what role, if any, archaea play in disease is becoming a priority for teams of microbiologists around the world. Most believe it's a matter of time before they are confirmed, at least, as contributing to the progress of certain illnesses. "It's very important we get to the bottom of this, because if archaea are causing diseases we may have a problem," says Westerman. The antibiotics we have now have all been designed with bacteria in mind, and a new generation of drugs would be needed to tackle archaea. "It's all a bit scary," he says.