Methanogenesis

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Methanogenesis or biomethanation is the formation of methane coupled to energy conservation by microbes known as methanogens. It is the fourth and final stage of anaerobic digestion. Organisms capable of producing methane for energy conservation 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 anoxic environments, it is the final step in the decomposition of biomass. Methanogenesis is responsible for significant amounts of natural gas accumulations, the remainder being thermogenic. [1] [2] [3]

Contents

Biochemistry

Cycle for methanogenesis, showing intermediates. Methanogenesis cycle.png
Cycle for methanogenesis, showing intermediates.

Methanogenesis in microbes is a form of anaerobic respiration. [4] Methanogens do not use oxygen to respire; in fact, oxygen inhibits the growth of methanogens. The terminal electron acceptor in methanogenesis is not oxygen, but carbon. The two best described pathways involve the use of acetic acid (acetoclastic) or inorganic carbon dioxide (hydrogenotrophic) as terminal electron acceptors:

CO2 + 4 H2 → CH4 + 2 H2O
CH3COOH → CH4 + CO2

During anaerobic respiration of carbohydrates, H2 and acetate are formed in a ratio of 2:1 or lower, so H2 contributes only c. 33% to methanogenesis, with acetate contributing the greater proportion. In some circumstances, for instance in the rumen, where acetate is largely absorbed into the bloodstream of the host, the contribution of H2 to methanogenesis is greater. [5]

However, depending on pH and temperature, methanogenesis has been shown to use carbon from other small organic compounds, such as formic acid (formate), methanol, methylamines, tetramethylammonium, dimethyl sulfide, and methanethiol. The catabolism of the methyl compounds is mediated by methyl transferases to give methyl coenzyme M. [4]

Proposed mechanism

The biochemistry of methanogenesis involves the following coenzymes and cofactors: F420, coenzyme B, coenzyme M, methanofuran, and methanopterin.

The mechanism for the conversion of CH
3–S bond into methane involves a ternary complex of the enzyme, with the substituents forming a structure α2β2γ2. Within the complex, methyl coenzyme M and coenzyme B fit into a channel terminated by the axial site on nickel of the cofactor F430. [6] One proposed mechanism invokes electron transfer from Ni(I) (to give Ni(II)), which initiates formation of CH
4. Coupling of the coenzyme M thiyl radical (RS.) with HS coenzyme B releases a proton and re-reduces Ni(II) by one-electron, regenerating Ni(I). [7]

Reverse methanogenesis

Some organisms can oxidize methane, functionally reversing the process of methanogenesis, also referred to as the anaerobic oxidation of methane (AOM). Organisms performing AOM have been found in multiple marine and freshwater environments including methane seeps, hydrothermal vents, coastal sediments and sulfate-methane transition zones. [8] These organisms may accomplish reverse methanogenesis using a nickel-containing protein similar to methyl-coenzyme M reductase used by methanogenic archaea. [9] Reverse methanogenesis occurs according to the reaction:

SO2−
4 + CH4 → HCO−
3 + HS− + H2O [10]

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, and nitrate) 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.

Natural occurrence

In ruminants

Testing Australian sheep for exhaled methane production (2001), CSIRO CSIRO ScienceImage 1898 Testing Sheep for Methane Production.jpg
Testing Australian sheep for exhaled methane production (2001), CSIRO

Enteric fermentation occurs in the gut of some animals, especially ruminants. In the rumen, anaerobic organisms, including methanogens, digest cellulose into forms nutritious to the animal. Without these microorganisms, animals such as cattle would not be able to consume grasses. 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. [11] In this way, ruminants contribute about 25% of anthropogenic methane emissions. One method of methane production control in ruminants is by feeding them 3-nitrooxypropanol. [12]

In humans

Some humans produce flatus that contains methane. In one study of the feces of nine adults, five of the samples contained archaea capable of producing methane. [13] Similar results are found in samples of gas obtained from within the rectum.

Even among humans whose flatus does contain methane, the amount is in the range of 10% or less of the total amount of gas. [14]

In plants

Many experiments have suggested that leaf tissues of living plants emit methane. [15] Other research has indicated that the plants are not actually generating methane; they are just absorbing methane from the soil and then emitting it through their leaf tissues. [16]

In soils

Methanogens are observed in anoxic soil environments, contributing to the degradation of organic matter. This organic matter may be placed by humans through landfill, buried as sediment on the bottom of lakes or oceans as sediments, and as residual organic matter from sediments that have formed into sedimentary rocks. [17]

In Earth's crust

Methanogens are a notable part of the microbial communities in continental and marine deep biosphere. [18] [19] [20]

Industry

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. [21] It is the primary pathway whereby most organic matter disposed of via landfill is broken down. [22] Some biogas plants use methanogenesis to combine the CO2 with hydrogen to create more methane. [23]

Role in global warming

Atmospheric methane is an important greenhouse gas with a global warming potential 25 times greater than carbon dioxide (averaged over 100 years), [24] 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.

Extra-terrestrial life

The presence of atmospheric methane has a role in the scientific search for extra-terrestrial life. The justification is that on an astronomical timescale, methane in the atmosphere of an Earth-like celestial body will quickly dissipate, and that its presence on such a planet or moon therefore indicates that something is replenishing it. If methane is detected (by using a spectrometer for example) this may indicate that life is, or recently was, present. This was debated [25] 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) [26] and in Titan's atmosphere by the Huygens probe (2005). [27] This debate was furthered with the discovery of 'transient', 'spikes of methane' on Mars by the Curiosity Rover. [28]

It is argued that atmospheric methane can come from volcanoes or other fissures in the planet's crust and that without an isotopic signature, the origin or source may be difficult to identify. [29] [30]

On 13 April 2017, NASA confirmed that the dive of the Cassini orbiter spacecraft on 28 October 2015 discovered an Enceladus plume which has all the ingredients for methanogenesis-based life forms to feed on. Previous results, published in March 2015, suggested hot water is interacting with rock beneath the sea of Enceladus; the new finding supported that conclusion, and add that the rock appears to be reacting chemically. From these observations scientists have determined that nearly 98 percent of the gas in the plume is water, about 1 percent is hydrogen, and the rest is a mixture of other molecules including carbon dioxide, methane and ammonia. [31]

See also

Related Research Articles

<span class="mw-page-title-main">Marsh gas</span> Gas produced naturally within marshes, swamps and bogs

Marsh gas, also known as swamp gas or bog gas, is a mixture primarily of methane and smaller amounts of hydrogen sulfide, carbon dioxide, and trace phosphine that is produced naturally within some geographical marshes, swamps, and bogs.

Anaerobic respiration is respiration using electron acceptors other than molecular oxygen (O2). Although oxygen is not the final electron acceptor, the process still uses a respiratory electron transport chain.

Methanogens are anaerobic archaea that produce methane as a byproduct of their energy metabolism, i.e., catabolism. Methane production, or methanogenesis, is the only biochemical pathway for ATP generation in methanogens. All known methanogens belong exclusively to the domain Archaea, although some bacteria, plants, and animal cells are also known to produce methane. However, the biochemical pathway for methane production in these organisms differs from that in methanogens and does not contribute to ATP formation. Methanogens belong to various phyla within the domain Archaea. Previous studies placed all known methanogens into the superphylum Euryarchaeota. However, recent phylogenomic data have led to their reclassification into several different phyla. Methanogens are common in various anoxic environments, such as marine and freshwater sediments, wetlands, the digestive tracts of animals, wastewater treatment plants, rice paddy soil, and landfills. While some methanogens are extremophiles, such as Methanopyrus kandleri, which grows between 84 and 110°C, or Methanonatronarchaeum thermophilum, which grows at a pH range of 8.2 to 10.2 and a Na+ concentration of 3 to 4.8 M, most of the isolates are mesophilic and grow around neutral pH.

<span class="mw-page-title-main">Sulfate-reducing microorganism</span> Microorganisms that "breathe" sulfates

Sulfate-reducing microorganisms (SRM) or sulfate-reducing prokaryotes (SRP) are a group composed of sulfate-reducing bacteria (SRB) and sulfate-reducing archaea (SRA), both of which can perform anaerobic respiration utilizing sulfate (SO2−
4) as terminal electron acceptor, reducing it to hydrogen sulfide (H2S). Therefore, these sulfidogenic microorganisms "breathe" sulfate rather than molecular oxygen (O2), which is the terminal electron acceptor reduced to water (H2O) in aerobic respiration.

An acetogen is a microorganism that generates acetate (CH3COO−) as an end product of anaerobic respiration or fermentation. However, this term is usually employed in a narrower sense only to those bacteria and archaea that perform anaerobic respiration and carbon fixation simultaneously through the reductive acetyl coenzyme A (acetyl-CoA) pathway (also known as the Wood-Ljungdahl pathway). These genuine acetogens are also known as "homoacetogens" and they can produce acetyl-CoA (and from that, in most cases, acetate as the end product) from two molecules of carbon dioxide (CO2) and four molecules of molecular hydrogen (H2). This process is known as acetogenesis, and is different from acetate fermentation, although both occur in the absence of molecular oxygen (O2) and produce acetate. Although previously thought that only bacteria are acetogens, some archaea can be considered to be acetogens.

<span class="mw-page-title-main">Hydrogen cycle</span> Hydrogen exchange between the living and non-living world

The hydrogen cycle consists of hydrogen exchanges between biotic (living) and abiotic (non-living) sources and sinks of hydrogen-containing compounds.

<i>Methanosarcina</i> Genus of archaea

Methanosarcina is a genus of euryarchaeote archaea that produce methane. These single-celled organisms are known as anaerobic methanogens that produce methane using all three metabolic pathways for methanogenesis. They live in diverse environments where they can remain safe from the effects of oxygen, whether on the earth's surface, in groundwater, in deep sea vents, and in animal digestive tracts. Methanosarcina grow in colonies.

Microbial metabolism is the means by which a microbe obtains the energy and nutrients it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics. The specific metabolic properties of a microbe are the major factors in determining that microbe's ecological niche, and often allow for that microbe to be useful in industrial processes or responsible for biogeochemical cycles.

In biology, syntrophy, syntrophism, or cross-feeding is the cooperative interaction between at least two microbial species to degrade a single substrate. This type of biological interaction typically involves the transfer of one or more metabolic intermediates between two or more metabolically diverse microbial species living in close proximity to each other. Thus, syntrophy can be considered an obligatory interdependency and a mutualistic metabolism between different microbial species, wherein the growth of one partner depends on the nutrients, growth factors, or substrates provided by the other(s).

<span class="mw-page-title-main">Wood–Ljungdahl pathway</span> A set of biochemical reactions used by some bacteria

The Wood–Ljungdahl pathway is a set of biochemical reactions used by some bacteria. It is also known as the reductive acetyl-coenzyme A (acetyl-CoA) pathway. This pathway enables these organisms to use hydrogen as an electron donor, and carbon dioxide as an electron acceptor and as a building block for biosynthesis.

<i>Methanobacterium</i> Genus of archaea

Methanobacterium is a genus of the Methanobacteria class in the Archaea kingdom, which produce methane as a metabolic byproduct. Despite the name, this genus belongs not to the bacterial domain but the archaeal domain. Methanobacterium are nonmotile and live without oxygen, which is toxic to them, and they only inhabit anoxic environments.

Anaerobic oxidation of methane (AOM) is a methane-consuming microbial process occurring in anoxic marine and freshwater sediments. AOM is known to occur among mesophiles, but also in psychrophiles, thermophiles, halophiles, acidophiles, and alkophiles. During AOM, methane is oxidized with different terminal electron acceptors such as sulfate, nitrate, nitrite and metals, either alone or in syntrophy with a partner organism.

<span class="mw-page-title-main">Coenzyme-B sulfoethylthiotransferase</span> Class of enzymes

In enzymology, coenzyme-B sulfoethylthiotransferase, also known as methyl-coenzyme M reductase (MCR) or most systematically as 2-(methylthio)ethanesulfonate:N-(7-thioheptanoyl)-3-O-phosphothreonine S-(2-sulfoethyl)thiotransferase is an enzyme that catalyzes the final step in the formation of methane. It does so by combining the hydrogen donor coenzyme B and the methyl donor coenzyme M. Via this enzyme, most of the natural gas on earth was produced. Ruminants produce methane because their rumens contain methanogenic prokaryotes (Archaea) that encode and express the set of genes of this enzymatic complex.

<span class="mw-page-title-main">Methane</span> Hydrocarbon compound (CH₄) in natural gas; simplest alkane

Methane is a chemical compound with the chemical formula CH4. It is a group-14 hydride, the simplest alkane, and the main constituent of natural gas. The abundance of methane on Earth makes it an economically attractive fuel, although capturing and storing it is difficult because it is a gas at standard temperature and pressure. In the Earth's atmosphere methane is transparent to visible light but absorbs infrared radiation, acting as a greenhouse gas. Methane is an organic compound, and among the simplest of organic compounds. Methane is also a hydrocarbon.

<i>Methanococcus maripaludis</i> Species of archaeon

Methanococcus maripaludis is a species of methanogenic archaea found in marine environments, predominantly salt marshes. M. maripaludis is a non-pathogenic, gram-negative, weakly motile, non-spore-forming, and strictly anaerobic mesophile. It is classified as a chemolithoautotroph. This archaeon has a pleomorphic coccoid-rod shape of 1.2 by 1.6 μm, in average size, and has many unique metabolic processes that aid in survival. M. maripaludis also has a sequenced genome consisting of around 1.7 Mbp with over 1,700 identified protein-coding genes. In ideal conditions, M. maripaludis grows quickly and can double every two hours.

Hydrogenotrophs are organisms that are able to metabolize molecular hydrogen as a source of energy.

Biological methanation (also: biological hydrogen methanation (BHM) or microbiological methanation) is a conversion process to generate methane by means of highly specialized microorganisms (Archaea) within a technical system. This process can be applied in a power-to-gas system to produce biomethane and is appreciated as an important storage technology for variable renewable energy in the context of energy transition. This technology was successfully implemented at a first power-to-gas plant of that kind in the year 2015.

The sulfate-methane transition zone (SMTZ) is a zone in oceans, lakes, and rivers typically found below the sediment surface in which sulfate and methane coexist. The formation of a SMTZ is driven by the diffusion of sulfate down the sediment column and the diffusion of methane up the sediments. At the SMTZ, their diffusion profiles meet and sulfate and methane react with one another, which allows the SMTZ to harbor a unique microbial community whose main form of metabolism is anaerobic oxidation of methane (AOM). The presence of AOM marks the transition from dissimilatory sulfate reduction to methanogenesis as the main metabolism utilized by organisms.

<span class="mw-page-title-main">Hydrothermal vent microbial communities</span> Undersea unicellular organisms

The hydrothermal vent microbial community includes all unicellular organisms that live and reproduce in a chemically distinct area around hydrothermal vents. These include organisms in the microbial mat, free floating cells, or bacteria in an endosymbiotic relationship with animals. Chemolithoautotrophic bacteria derive nutrients and energy from the geological activity at Hydrothermal vents to fix carbon into organic forms. Viruses are also a part of the hydrothermal vent microbial community and their influence on the microbial ecology in these ecosystems is a burgeoning field of research.

<span class="mw-page-title-main">Hydroxyarchaeol</span> Chemical compound

Hydroxyarchaeol is a core lipid unique to archaea, similar to archaeol, with a hydroxide functional group at the carbon-3 position of one of its ether side chains. It is found exclusively in certain taxa of methanogenic archaea, and is a common biomarker for methanogenesis and methane-oxidation. Isotopic analysis of hydroxyarchaeol can be informative about the environment and substrates for methanogenesis.

References

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