Methanogenesis Pathway Map

[Compounds and Reactions] [BBD Main Menu] This pathway is contributed by Dr.Larry Wackett and completed by Jian Ma, University of Minnesota. Methane is generated biologically by methanogenic bacteria, a major division of the Archaea kingdom, largely from acetate dissimilation and carbon dioxide reduction. The latter pathway, as shown below, contains novel coenzymes and biochemical reactions not previously observed in other organisms. Methanogenesis is part of the C1 Metabolic Cycle. The following is a text-format Methanogenesis pathway map. An organism which can initiate the pathway is given, but other organisms may also carry out later steps. Follow the links for more information on compounds or reactions. This map is also available in graphic (40k) format.
from the Carbon Dioxide <------ C1 Metabolic Cycle Methanobacterium thermoautotrophicum | | | formylmethanofuran | dehydrogenase | | v Formylmethanofuran | | | formylmethanofuran | formyltransferase | | v N5-Formyl-5,6,7,8-tetrahydromethanopterin | | | methenyl-H4MPT | cyclohydrolase | | v N5,N10-methenyltetrahydromethanopterin / \ / \ / \ | | F420 independent methylene-H4MPT | | methylene-H4MPT dehydrogenase | | dehydrogenase \ / \ / v v N5,N10-methylenetetrahydromethanopterin | | | methylene-H4MPT | reductase

| | v 5-Methyl-5,6,7,8-tetrahydromethanopterin | | | methyl-H4MPT | methyltransferase | | v Methyl-coenzyme M | | | methyl-coenzyme M | Methylreductase | | v Methane | | | | | | v to the C1 Metabolic Cycle

[Compounds and Reactions] [BBD Main Menu] Page Author(s): Jian Ma April 25, 2008 Contact Us
2010, University of Minnesota. All rights reserved. http://umbbd.msi.umn.edu/meth/meth_map.html

The microbial formation of methane, which is confined to anaerobic habitats where occurs the production of hydrogen, carbon dioxide, formic acid, methanol, methylamines, or acetate the major substrates used by methanogenic microbes (methanogens). In fresh-water or marine sediments, in the intestinal tracts of animals, or in habitats engineered by humans such as sewage sludge or biomass digesters, these substrates are the products of anaerobic bacterial

metabolism. Methanogens are terminal organisms in the anaerobic microbial food chainthe final product, methane, being poorly soluble, anaerobically inert, and not in equilibrium with the reaction which produces it. Two highly specialized digestive organs, the rumen and the cecum, have been evolved by herbivores to delay the passage of cellulose fibers so that microbial fermentation may be complete. In these organs, large quantities of methane are produced from hydrogen and carbon dioxide or formic acid by methanogens. From the rumen, an average cow may belch 26 gallons (100 liters) of methane per day. Methanogens are the only living organisms that produce methane as a way of life. The biochemistry of their metabolism is unique and definitively delineates the group. Two reductive biochemical strategies are employed: an eight-electron reduction of carbon dioxide to methane or a two-electron reduction of a methyl group to methane. All methogens form methane by reducing a methyl group. The major energy-yielding reactions used by methanogens utilize substrates such as hydrogen, formic acid, methanol, acetic acid, and methylamine. Dimethyl sulfide, carbon monoxide, and alcohols such as ethanol and propanol are substrates that are used less frequently. See Archaebacteria, Bacterial physiology and metabolism

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Methanogenesis
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methanogenesis
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(biochemistry) The biosynthesis of the hydrocarbon methane; common in certain bacteria. Also known as bacterial methanogenesis.

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Methanogenesis
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The microbial formation of methane, which is confined to anaerobic habitats where occurs the production of hydrogen, carbon dioxide, formic acid, methanol, methylamines, or acetate the major substrates used by methanogenic microbes (methanogens). In fresh-water or marine sediments, in the intestinal tracts of animals, or in habitats engineered by humans such as sewage sludge or biomass digesters, these substrates are the products of anaerobic bacterial metabolism. Methanogens are terminal organisms in the anaerobic microbial food chainthe final product, methane, being poorly soluble, anaerobically inert, and not in equilibrium with the reaction which produces it.

Two highly specialized digestive organs, the rumen and the cecum, have been evolved by herbivores to delay the passage of cellulose fibers so that microbial fermentation may be complete. In these organs, large quantities of methane are produced from hydrogen and carbon dioxide or formic acid by methanogens. From the rumen, an average cow may belch 26 gallons (100 liters) of methane per day. Methanogens are the only living organisms that produce methane as a way of life. The biochemistry of their metabolism is unique and definitively delineates the group. Two reductive biochemical strategies are employed: an eight-electron reduction of carbon dioxide to methane or a two-electron reduction of a methyl group to methane. All methanogens form methane by reducing a methyl group. The major energy-yielding reactions used by methanogens utilize substrates such as hydrogen, formic acid, methanol, acetic acid, and methylamine. Dimethyl sulfide, carbon monoxide, and alcohols such as ethanol and propanol are substrates that are used less frequently. See also Archaebacteria; Bacterial physiology and metabolism; Methane.
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Methanogenesis
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Methanogenesis or biomethanation is the formation of methane by microbes known as methanogens. Organisms capable of producing methane have been identified only from the domain Archaea, a group phylogenetically distinct from both eukaryotes and bacteria, although many live in close association with anaerobic bacteria. The production of methane is an important and widespread form of microbial metabolism. In most environments, it is the final step in the decomposition of biomass. Recently, some experiments have suggested that leaf tissues of living plants emit methane [1]. Other research has indicated that the plants are not actually generating methane; they are just absorbing methane from the soil and the emitting it through their leaf tissues [2]. There may still be some unknown mechanism by which plants produce methane, but that is by no means certain.
Contents [hide] 1 Biochemistry of methanogenesis 2 Importance in carbon cycle 3 In ruminants 4 In humans

5 Role in global warming 6 Methanogenesis and extraterrestrial life 7 See also 8 References

Biochemistry of methanogenesis
Methanogenesis in microbes is a form of anaerobic respiration[3]. Methanogens do not use oxygen to breathe; in fact, oxygen inhibits the growth of methanogens. The terminal electron acceptor in methanogenesis is not oxygen, but carbon. The carbon can occur in a small number of organic compounds, all with low molecular weights. The two best described pathways involve the use of carbon dioxide and acetic acid as terminal electron acceptors: CO2 + 4 H2 CH4 + 2H2O CH3COOH CH4 + CO2 However, methanogenesis has been shown to use carbon from other small organic compounds, such as formic acid (formate), methanol, methylamines, dimethyl sulfide, and methanethiol. The biochemistry of methanogenesis is relatively complex, involving the following coenzymes and cofactors: F430, coenzyme B, coenzyme M, methanofuran, and methanopterin.

Importance in carbon cycle

Methanogenesis is the final step in the decay of organic matter. During the decay process, electron acceptors (such as oxygen, ferric iron, sulfate, nitrate, and manganese) become depleted, while hydrogen (H2) and carbon dioxide accumulate. Light organics produced by fermentation also accumulate. During advanced stages of organic decay, all electron acceptors become depleted except carbon dioxide. Carbon dioxide is a product of most catabolic processes, so it is not depleted like other potential electron acceptors. Only methanogenesis and fermentation can occur in the absence of electron acceptors other than carbon. Fermentation only allows the breakdown of larger organic compounds, and produces small organic compounds. Methanogenesis effectively removes the semi-final products of decay: hydrogen, small organics, and carbon dioxide. Without methanogenesis, a great deal of carbon (in the form of fermentation products) would accumulate in anaerobic environments.

In ruminants
Methanogenesis occurs in the guts of humans and other animals, especially ruminants. In the rumen, anaerobic organisms, including methanogens, digest cellulose into forms usable by the animal. Without these microorganisms, animals such as cattle would not be able to consume grass. The useful products of methanogenesis are absorbed by the gut, but methane is released from the animal mainly by belching (eructation). The average cow emits around 250 liters of methane per day.[4]

In humans
Some humans produce flatus that contains methane. In one study of the faeces of nine adults, only five of the samples contained archaea capable of producing methane.[5] Similar results are found in samples of gas obtained from within the rectum.

Even among humans whose flatus does contain methane, the amount is only 0% - 10% of the total amount of gas.[6]

Role in global warming

Methane in the Earth's atmosphere is an important greenhouse gas with a global warming potential 21 times greater than carbon dioxide (averaged over 100 years), and methanogenesis in livestock and the decay of organic material is thus a considerable contributor to global warming. It may not be a net contributor in the sense that it works on organic material which used up atmospheric carbon dioxide when it was created, but its overall effect is to convert the carbon dioxide into methane which is a much more potent greenhouse gas. Methanogenesis can also be beneficially exploited, to treat organic waste, to produce useful compounds, and the methane can be collected and used as biogas, a fuel. It is the primary pathway whereby most organic matter disposed of via landfill is broken down. [7]

Methanogenesis and extra-terrestrial life

The presence of atmospheric methane has a role in the scientific search for extra-terrestrial life[8]. The argument being that methane in the atmosphere will eventually dissipate, unless something is replenishing it. This can be detected (by using a spectrometer for example) then that means there is, or relatively recently was, life present. This was debated [9] when methane was discovered in the Martian atmosphere by M.J. Mumma of NASA's Goddard Flight Center, and verified by the Mars Express Orbiter (2004)[10] and in Titan's atmosphere by the Huygens probe (2005)[11]. It is also argued that atmospheric methane can come from volcanoes or other fissures in the planet's crust and that without an Isotopic signature it is difficult to say what exactly was the origin.[12][13]

Methanogens are microorganisms that produce methane as a metabolic byproduct in anoxic conditions. They are classified as archaea, a group quite distinct from bacteria. They are common in wetlands, where they are responsible for marsh gas, and in the guts of animals such as ruminants and humans, where they are responsible for the methane content of belching in ruminants and flatulence in humans.[1] In marine sediments biomethanation is generally confined to where sulfates are depleted, below the top layers.[2] Others are extremophiles, found in environments such as hot springs and submarine hydrothermal vents as well as in the "solid" rock of the Earth's crust, kilometers below the surface.
Contents [hide] 1 Physical description 2 Methanogens and (extreme) environments 3 Strains of methanogens

4 See also 5 References

Physical description
Methanogens are usually coccoid (spherical) or bacilli (rod shaped). There are over 50 described species of methanogens, which do not form a monophyletic group, although all methanogens belong to Archaea. Methanogens are also anaerobic. Although methanogens cannot function under aerobic conditions they can sustain oxygen stresses for a prolonged time.[3] Methanosarcina barkeri is exceptional in possessing a superoxide dismutase (SOD) enzyme, and may survive longer than the others.[4] Some methanogens, called hydrogenotrophic, use carbon dioxide (CO2) as a source of carbon, and hydrogen as a reducing agent. Some of the CO2 is reacted with the hydrogen to produce methane, which produces an electrochemical gradient across a 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 the Bacteria but not 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 and (extreme) environments

Although most marine biogenic methane is the result of carbon dioxide (CO2) reduction, a small amount is derived from acetate (CH3COO-).[5] Archaea that catabolize this for energy are referred to as acetotrophic or aceticlastic. Methylotrophic archaea utilize methylated compounds such as methylamines, methanol, and methanethiol as well. Methanogens play the 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, sulfate, and trivalent iron) have been depleted. In the deep rock they obtain their hydrogen from the thermal and radioactive breakdown of water. 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,[6] which account for a significant fraction of organic carbon in continental margin sediments and represent a key reservoir of a potent greenhouse gas.[7] 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 can reproduce at temperatures of 15 to 100 degrees Celsius. They are known to be the most common archaebacteria in deep subteranean habitats. Live microbes making methane were found in a glacial ice core sample retrieved from three kilometres under Greenland by researchers from the University of California, Berkeley.[8] Another study[9] 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.[10]

Some scientists have proposed that the presence of methane in the Martian atmosphere may be indicative of native methanogens on that planet.[11] 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.[12] Most methanogens are autotrophic producers, but those that oxidize CH3COO- are classed as Chemotroph instead.

Methanogenesis or biomethanation is the formation of methane by microbes known as methanogens. Organisms capable of producing methane have been identified only from the domain Archaea, a group phylogenetically distinct from both eukaryotes and bacteria, although many live in close association with anaerobic bacteria. The production of methane is an important and widespread form of microbial metabolism. In most environments, it is the final step in the decomposition of biomass. Recently, some experiments have suggested that leaf tissues of living plants emit methane [1]. Other research has indicated that the plants are not actually generating methane; they are just absorbing methane from the soil and the emitting it through their leaf tissues [2]. There may still be some unknown mechanism by which plants produce methane, but that is by no means certain.

Contents
[hide] 1 Biochemistry of methanogenesis 2 Importance in carbon cycle 3 In ruminants 4 In humans 5 Role in global warming 6 Methanogenesis and extraterrestrial life 7 See also 8 References

[edit] Biochemistry of methanogenesis

Methanogenesis in microbes is a form of anaerobic respiration[3]. Methanogens do not use oxygen to breathe; in fact, oxygen inhibits the growth of methanogens. The terminal electron acceptor in methanogenesis is not oxygen, but carbon. The carbon can occur in a small number of organic compounds, all with low molecular weights. The two best described pathways involve the use of carbon dioxide and acetic acid as terminal electron acceptors:

CO2 + 4 H2 CH4 + 2H2O CH3COOH CH4 + CO2 However, methanogenesis has been shown to use carbon from other small organic compounds, such as formic acid (formate), methanol, methylamines, dimethyl sulfide, and methanethiol. The biochemistry of methanogenesis is relatively complex, involving the following coenzymes and cofactors: F430, coenzyme B, coenzyme M, methanofuran, and methanopterin.

[edit] Importance in carbon cycle

Methanogenesis is the final step in the decay of organic matter. During the decay process, electron acceptors (such as oxygen, ferric iron, sulfate, nitrate, and manganese) become depleted, while hydrogen (H2) and carbon dioxide accumulate. Light organics produced by fermentation also accumulate. During advanced stages of organic decay, all electron acceptors become depleted except carbon dioxide. Carbon dioxide is a product of most catabolic processes, so it is not depleted like other potential electron acceptors. Only methanogenesis and fermentation can occur in the absence of electron acceptors other than carbon. Fermentation only allows the breakdown of larger organic compounds, and produces small organic compounds. Methanogenesis effectively removes the semi-final products of decay: hydrogen, small organics, and carbon dioxide. Without methanogenesis, a great deal of carbon (in the form of fermentation products) would accumulate in anaerobic environments.

[edit] In ruminants
Methanogenesis occurs in the guts of humans and other animals, especially ruminants. In the rumen, anaerobic organisms, including methanogens, digest cellulose into forms usable by the animal. Without these microorganisms, animals such as cattle would not be able to consume grass. The useful products of methanogenesis are absorbed by the gut, but methane is released from the animal mainly by belching (eructation). The average cow emits around 250 liters of methane per day.[4]

[edit] In humans
Some humans produce flatus that contains methane. In one study of the faeces of nine adults, only five of the samples contained archaea capable of producing methane.[5] Similar results are found in samples of gas obtained from within the rectum. Even among humans whose flatus does contain methane, the amount is only 0% - 10% of the total amount of gas.[6]

[edit] Role in global warming

Methane in the Earth's atmosphere is an important greenhouse gas with a global warming potential 21 times greater than carbon dioxide (averaged over 100 years), and methanogenesis in livestock and the decay of organic material is thus a considerable contributor to global warming. It may not be a net contributor in the sense that it works on organic material which used up atmospheric carbon dioxide when it was created, but its overall effect is to convert the carbon dioxide into methane which is a much more potent greenhouse gas.

Methanogenesis can also be beneficially exploited, to treat organic waste, to produce useful compounds, and the methane can be collected and used as biogas, a fuel. It is the primary pathway whereby most organic matter disposed of via landfill is broken down. [7]

[edit] Methanogenesis and extra-terrestrial life

The presence of atmospheric methane has a role in the scientific search for extra-terrestrial life[8]. The argument being that methane in the atmosphere will eventually dissipate, unless something is replenishing it. This can be detected (by using a spectrometer for example) then that means there is, or relatively recently was, life present. This was debated [9] when methane was discovered in the Martian atmosphere by M.J. Mumma of NASA's Goddard Flight Center, and verified by the Mars Express Orbiter (2004)[10] and in Titan's atmosphere by the Huygens probe (2005)[11]. It is also argued that atmospheric methane can come from volcanoes or other fissures in the planet's crust and that without an Isotopic signature it is difficult to say what exactly was the origin.[12][13]