Editing Methanogenesis (section)

==Biochemistry==
[[File:Methanogenesis cycle.png|thumb|320px|Cycle for methanogenesis, showing intermediates.]]

Methanogenesis in microbes is a form of [[anaerobic respiration]].<ref name=RT>{{cite journal|author=Thauer, R. K.|title=Biochemistry of Methanogenesis: a Tribute to Marjory Stephenson|journal=Microbiology|year=1998|volume=144|pages=2377–2406|doi=10.1099/00221287-144-9-2377|pmid=9782487|doi-access=free}}</ref> Methanogens do not use oxygen to respire; in fact, oxygen inhibits the growth of methanogens.  The terminal [[Oxidizing agent#Electron acceptor|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:
:CO<sub>2</sub> + 4 H<sub>2</sub> → [[Methane|CH<sub>4</sub>]] + 2 H<sub>2</sub>O

:CH<sub>3</sub>COOH → CH<sub>4</sub> + CO<sub>2</sub>

During anaerobic respiration of carbohydrates, H<sub>2</sub> and acetate are formed in a ratio of 2:1 or lower, so H<sub>2</sub> contributes only {{circa|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 H<sub>2</sub> to methanogenesis is greater.<ref>{{Cite journal|last=Conrad|first=Rolf|date=1999|title=Contribution of hydrogen to methane production and control of hydrogen concentrations in methanogenic soils and sediments|journal=FEMS Microbiology Ecology|volume=28|issue=3|pages=193–202|doi=10.1016/s0168-6496(98)00086-5|doi-access=free|bibcode=1999FEMME..28..193C }}</ref>

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.<ref name="RT" />

===Proposed mechanism===
The biochemistry of methanogenesis involves the following coenzymes and cofactors: [[Coenzyme F420|F420]], [[coenzyme B]], [[coenzyme M]], [[methanofuran]], and [[methanopterin]].

The mechanism for the conversion of {{chem|CH|3|–S}} bond into methane involves a ternary complex of the enzyme, with the substituents forming a structure α<sub>2</sub>β<sub>2</sub>γ<sub>2</sub>. Within the complex, methyl coenzyme M and coenzyme B fit into a channel terminated by the axial site on nickel of the [[cofactor F430]].<ref>{{cite journal |last1=Cedervall |first1=Peder |title=Structural Insight into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues |journal=Biochemistry |date=22 July 2010 |volume=49 |issue=35 |pages=7683–7693 |doi=10.1021/bi100458d |pmid=20707311 |pmc=3098740 }}</ref>  One proposed mechanism invokes electron transfer from Ni(I) (to give Ni(II)), which initiates formation of {{chem|CH|4}}.  Coupling of the coenzyme M [[thiyl radical]] (RS<sup>.</sup>) with HS coenzyme B releases a proton and re-reduces Ni(II) by one electron, regenerating Ni(I).<ref>{{cite journal  |vauthors=Finazzo C, Harmer J, Bauer C, etal |title=Coenzyme B induced coordination of coenzyme M via its thiol group to Ni(I) of F<sub>430</sub> in active methyl-coenzyme M reductase |journal=J. Am. Chem. Soc. |volume=125 |issue=17 |pages=4988–9 |date=April 2003 |pmid=12708843 |doi=10.1021/ja0344314 |bibcode=2003JAChS.125.4988F }}</ref>

===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.<ref>{{Cite journal|last1=Ruff|first1=S. Emil|last2=Biddle|first2=Jennifer F.|last3=Teske|first3=Andreas P.|last4=Knittel|first4=Katrin|last5=Boetius|first5=Antje|last6=Ramette|first6=Alban|date=2015-03-31|title=Global dispersion and local diversification of the methane seep microbiome|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=112|issue=13|pages=4015–4020|doi=10.1073/pnas.1421865112|issn=1091-6490|pmc=4386351|pmid=25775520|bibcode=2015PNAS..112.4015R|doi-access=free}}</ref> These organisms may accomplish '''reverse methanogenesis''' using a nickel-containing protein similar to [[Coenzyme-B sulfoethylthiotransferase|methyl-coenzyme M reductase]] used by methanogenic archaea.<ref>{{cite journal |doi=10.1155/2017/1654237 |title=Reverse Methanogenesis and Respiration in Methanotrophic Archaea |date=2017 |last1=Timmers |first1=Peer H. A. |last2=Welte |first2=Cornelia U. |last3=Koehorst |first3=Jasper J. |last4=Plugge |first4=Caroline M. |last5=Jetten |first5=Mike S. M. |last6=Stams |first6=Alfons J. M. |journal=Archaea |volume=2017 |pages=1–22 |doi-access=free |pmid=28154498 |pmc=5244752 |hdl=1822/47121 |hdl-access=free }}</ref> Reverse methanogenesis occurs according to the reaction:
: {{chem|SO|4|2−}} +  CH<sub>4</sub>   →   {{chem|HCO|3|−}}  + HS<sup>−</sup> + H<sub>2</sub>O<ref>{{cite journal  |vauthors=Krüger M, Meyerdierks A, Glöckner FO, etal |title=A conspicuous nickel protein in microbial mats that oxidize methane anaerobically |journal=Nature |volume=426 |issue=6968 |pages=878–81 |date=December 2003 |pmid=14685246 |doi=10.1038/nature02207 |bibcode = 2003Natur.426..878K |s2cid=4383740 }}</ref>

===Importance in carbon cycle===
Methanogenesis is the final step in the anaerobic decay of organic matter.  During the decay process, [[Oxidizing agent#Electron acceptor|electron acceptors]] (such as [[oxygen]], [[ferric]] [[iron]], [[sulfate]], and [[nitrate]]) become depleted, while [[hydrogen]] (H<sub>2</sub>) and [[carbon dioxide]] accumulate.  Light organics produced by [[fermentation (biochemistry)|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.