Editing Methanogenesis (section)

==Natural occurrence==

===In ruminants===
[[File:CSIRO ScienceImage 1898 Testing Sheep for Methane Production.jpg|thumb|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.<ref>[http://www.abc.net.au/ra/innovations/stories/s1159618.htm ''Radio Australia'': "Innovations – Methane In Agriculture."] 15 August 2004. Retrieved 28 August 2007.</ref> 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|3-nitrooxypropanol]].<ref>{{cite journal | last1 = Hristov | first1 = A. N. | display-authors = etal | year = 2015 | title = An inhibitor persistently decreased enteric methane emission from dairy cows with no negative effect on milk production | journal = Proc. Natl. Acad. Sci. U.S.A. | volume = 112 | issue = 34 | pages = 10663–10668 | doi = 10.1073/pnas.1504124112 | pmid = 26229078 | pmc = 4553761 | bibcode = 2015PNAS..11210663H | doi-access = free }}</ref>

===In humans===
Some humans produce [[flatulence|flatus]] that contains methane.  In one study of the [[feces]] of nine adults, five of the samples contained [[archaea]] capable of producing methane.<ref>{{cite journal| author=Miller TL|author2=Wolin MJ |author3=de Macario EC |author4=Macario AJ | title=Isolation of Methanobrevibacter smithii from human feces| journal=Appl Environ Microbiol| year=1982| volume=43| pages=227–32 |pmid=6798932 |pmc=241804 |url=| issue=1|doi=10.1128/aem.43.1.227-232.1982 |bibcode=1982ApEnM..43..227M }}</ref> 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.<ref>{{cite encyclopedia
  | title =Human Digestive System
  | encyclopedia =Encyclopædia Britannica
  | url =http://www.britannica.com/eb/article-45361/human-digestive-system#294193.hook
  | access-date = 2007-08-22 }}</ref>

===In plants===
Many experiments have suggested that [[leaf]] tissues of living plants emit methane.<ref>{{cite journal  |vauthors=Kepler F, etal | title = ''Methane emissions from terrestrial plants under aerobic conditions'' | journal = Nature | year = 2006 | volume = 439 | issue = 7073 | pmid = 16407949| pages = 187&ndash;191 | doi=  10.1038/nature04420 | bibcode=2006Natur.439..187K| s2cid = 2870347 }}</ref> A study done in 2006 estimated that global vegetation released between 60 and 240 million tonnes of methane yearly, corresponding to 40% of annual methane emissions.<ref>{{Cite journal |last=Schiermeier |first=Quirin |date=2006-01-01 |title=Methane finding baffles scientists |url=https://www.nature.com/articles/439128a?utm |journal=Nature |language=en |volume=439 |issue=7073 |pages=128–128 |doi=10.1038/439128a |issn=1476-4687}}</ref> In a follow up study done in 2009, plants grown in carbon-13 enriched environments were observed to not emit significant amounts of methane.<ref>{{Cite journal |last=Hopkin |first=Michael |date=2007-05-01 |title=Missing gas saps plant theory |url=https://www.nature.com/articles/447011a?utm |journal=Nature |language=en |volume=447 |issue=7140 |pages=11–11 |doi=10.1038/447011a |issn=1476-4687}}</ref> 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.<ref>{{Cite web | url=http://sciencenow.sciencemag.org/cgi/content/full/2009/114/1 | title=News| date=30 October 2014}}</ref> Such an instance can be seen in seasonally flooded parts of the Amazon Rainforest, where trees in said areas pumped 200 times the normal amount of methane out from each tree, accounting for around 40 million tonnes of methane emitted per year.<ref>{{Cite web |title=Scientists Zero in on Trees as a Surprisingly Large Source of Methane |url=https://e360.yale.edu/features/scientists-probe-the-surprising-role-of-trees-in-methane-emissions |access-date=2025-05-01 |website=Yale e360 |language=en-US}}</ref>

===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.<ref>{{cite journal|author1=Le Mer, J.|author2=Roger, P.|title=Production, oxidation, Emission and Consumption of Methane by Soils: A Review|journal=European Journal of Soil Biology|year=2001|volume=37|issue=1 |pages=25–50|doi=10.1016/S1164-5563(01)01067-6|bibcode=2001EJSB...37...25L |s2cid=62815957 }}</ref> Methanogenesis is not strictly limited to anoxic ecosystems such as peats and bogs; damp mineral soils can also contain high methane levels between the microscopic spaces of decaying organic matter.<ref>{{Cite web |date=2025-02-02 |title=Emission of methane from plants - PMC |url=https://web.archive.org/web/20250202173345/https://pmc.ncbi.nlm.nih.gov/articles/PMC2660970/ |access-date=2025-05-01 |website=web.archive.org}}</ref> As a result, the process of methanogenesis is common in rice fields and wetlands as these areas are flooded fields and are a natural methane sink.<ref>{{Cite journal |last=Aliyev |first=Z. H. |date=2020-12-07 |title=Review on Methanogenesis and its Role |url=https://irispublishers.com/wjass/fulltext/review-on-methanogenesis-and-its-role.ID.000632.php |journal=World Journal of Agriculture and Soil Science |language=English |volume=6 |issue=2 |pages=1–7}}</ref> The production of methane in flooded soils like these requires microbes that prefer low oxygen levels. Aerating methanogenic soils increases levels of sulfates and nitrates, nutrients that reduce the production of methane.<ref>{{Cite web |date=2025-02-25 |title=Methane Production in Soil Environments—Anaerobic Biogeochemistry and Microbial Life between Flooding and Desiccation |url=https://web.archive.org/web/20250225063228/https://www.mdpi.com/2076-2607/8/6/881 |access-date=2025-05-01 |website=web.archive.org}}</ref> For methanogenesis to continue, nitrate and sulfate levels will need to decrease. In a separate study conducted in remote arctic soils, higher amounts of methanogens had a direct correlation with increased potential methane production.<ref>{{Cite journal |last=Wagner |first=Robert |last2=Zona |first2=Donatella |last3=Oechel |first3=Walter |last4=Lipson |first4=David |date=2017 |title=Microbial community structure and soil pH correspond to methane production in Arctic Alaska soils |url=https://enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.13854?utm= |journal=Environmental Microbiology |language=en |volume=19 |issue=8 |pages=3398–3410 |doi=10.1111/1462-2920.13854 |issn=1462-2920|url-access=subscription }}</ref>

=== In Earth's crust ===
Methanogens are a notable part of the microbial communities in continental and marine [[deep biosphere]].<ref>{{Cite journal|last=Kotelnikova|first=Svetlana|date=October 2002|title=Microbial production and oxidation of methane in deep subsurface|journal=Earth-Science Reviews|language=en|volume=58|issue=3–4|pages=367–395|doi=10.1016/S0012-8252(01)00082-4|bibcode=2002ESRv...58..367K}}</ref><ref>{{Cite journal|last1=Purkamo|first1=Lotta|last2=Bomberg|first2=Malin|last3=Kietäväinen|first3=Riikka|last4=Salavirta|first4=Heikki|last5=Nyyssönen|first5=Mari|last6=Nuppunen-Puputti|first6=Maija|last7=Ahonen|first7=Lasse|last8=Kukkonen|first8=Ilmo|last9=Itävaara|first9=Merja|date=2016-05-30|title=Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids|journal=Biogeosciences|language=en|volume=13|issue=10|pages=3091–3108|doi=10.5194/bg-13-3091-2016|issn=1726-4189|bibcode=2016BGeo...13.3091P|doi-access=free|hdl=10023/10226|hdl-access=free}}</ref><ref>{{Cite journal|last1=Newberry|first1=Carole J.|last2=Webster|first2=Gordon|last3=Cragg|first3=Barry A.|last4=Parkes|first4=R. John|last5=Weightman|first5=Andrew J.|last6=Fry|first6=John C.|date=2004|title=Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190|journal=Environmental Microbiology|language=en|volume=6|issue=3|pages=274–287|doi=10.1111/j.1462-2920.2004.00568.x|pmid=14871211|bibcode=2004EnvMi...6..274N |s2cid=15644142 |issn=1462-2920|url=http://orca.cf.ac.uk/7547/1/Newberry_et_al_EM_2004.pdf}}</ref>

=== In Marine Environments ===
Approximately one third of [[methanogen]]s which have been described arise from marine origins, a majority being from the clade ''[[Euryarchaeota]]''.<ref name=":0">{{Cite journal |last=Ferry |first=James G. |last2=Lessner |first2=Daniel J. |date=March 2008 |title=Methanogenesis in Marine Sediments |url=https://nyaspubs.onlinelibrary.wiley.com/doi/10.1196/annals.1419.007 |journal=Annals of the New York Academy of Sciences |language=en |volume=1125 |issue=1 |pages=147–157 |doi=10.1196/annals.1419.007 |issn=0077-8923|url-access=subscription }}</ref> In the marine environment, methanogenic microorganisms compete for resources with [[Sulfate-reducing microorganism|sulfate-reducers]].<ref name=":0" /> As a result of this, sulfate-depleted areas of high organic matter loading and sediments are areas of methanogen predominance.<ref name=":0" /> The anaerobic nature of sediments allow for methanogenic activity and flourishing of methanogenic communities, making marine sediments an important habitat for methane generating microbial communities. A major compound which methanogens consume to generate methane is [[acetate]], which composes two thirds of global methane production.<ref name=":0" /> Another compound which contributes to marine sediment methanogenesis is [[carbon monoxide]], which is oxidized into [[carbon dioxide]], before undergoing a series of reactions to produce energy as [[methane]] is released from the microbe.<ref name=":0" /> This compound is considered non-competitive with sulfate-reducers, allowing for free use by methanogens. In examination of the microorganism ''M. acetivorans'', methane synthesis pathways retain similarities with freshwater taxa, however proteins distinct to the marine sediment microbes are found which operate on the methanogenic pathway.<ref name=":0" /> The estimated annual release of methane from the ocean into the atmosphere is approximately 0.7-14x10<sup>9</sup> kg CH<sub>4</sub> per year.<ref name=":0" /> Despite the requirement of anoxic conditions for main methanogenic processes, supersaturation of methane in surface ocean waters creates the “marine methane paradox”, which leads to the release of methane into the atmosphere from the ocean.<ref name=":0" /><ref name=":1">{{Cite journal |last=Repeta |first=Daniel J. |last2=Ferrón |first2=Sara |last3=Sosa |first3=Oscar A. |last4=Johnson |first4=Carl G. |last5=Repeta |first5=Lucas D. |last6=Acker |first6=Marianne |last7=DeLong |first7=Edward F. |last8=Karl |first8=David M. |date=December 2016 |title=Marine methane paradox explained by bacterial degradation of dissolved organic matter |url=https://www.nature.com/articles/ngeo2837 |journal=Nature Geoscience |language=en |volume=9 |issue=12 |pages=884–887 |doi=10.1038/ngeo2837 |issn=1752-0894|url-access=subscription }}</ref><ref name=":2">{{Cite journal |last=Metcalf |first=William W. |last2=Griffin |first2=Benjamin M. |last3=Cicchillo |first3=Robert M. |last4=Gao |first4=Jiangtao |last5=Janga |first5=Sarath Chandra |last6=Cooke |first6=Heather A. |last7=Circello |first7=Benjamin T. |last8=Evans |first8=Bradley S. |last9=Martens-Habbena |first9=Willm |last10=Stahl |first10=David A. |last11=van der Donk |first11=Wilfred A. |date=2012-08-31 |title=Synthesis of Methylphosphonic Acid by Marine Microbes: A Source for Methane in the Aerobic Ocean |url=https://www.science.org/doi/10.1126/science.1219875 |journal=Science |language=en |volume=337 |issue=6098 |pages=1104–1107 |doi=10.1126/science.1219875 |issn=0036-8075 |pmc=3466329 |pmid=22936780}}</ref><ref name=":3">{{Cite journal |last=Carini |first=Paul |last2=White |first2=Angelicque E. |last3=Campbell |first3=Emily O. |last4=Giovannoni |first4=Stephen J. |date=2014-07-07 |title=Methane production by phosphate-starved SAR11 chemoheterotrophic marine bacteria |url=https://www.nature.com/articles/ncomms5346 |journal=Nature Communications |language=en |volume=5 |issue=1 |doi=10.1038/ncomms5346 |issn=2041-1723}}</ref>

Recent studies seek to explain this paradox by examining the possibility of methane synthesis in the surface ocean despite oxic conditions. Oxic sources of methane were discovered in microbial communities starved of phosphorus in surface oceans,<ref name=":2" /> where the [[catabolism]] of the compound [[Methylphosphonic acid|methyl-phosphonic acid]] (Mpn) has been found to co-produce methane in oxic ocean waters, providing a potential explanation to the paradox.<ref name=":1" /><ref name=":2" /><ref name=":3" /> ''[[Nitrosopumilus maritimus|N. maritimus]]'', a widespread archaeon in the ocean, was found to contain pathways for the synthesis of methyl-phosphonic acid within these oxic ocean waters.<ref name=":2" /> The production of this compound from surrounding materials allows for methanogenesis via breakdown by surrounding bacteria and microbes. Furthermore, the prevalence of Mpn synthesis is consistent with abundance of Mpn reducing taxa such as ''[[Candidatus Pelagibacter communis|Pelagibacter]]'',<ref name=":2" /> The linkage between the producers of Mpn and the degraders of the compound lead to the production of methane. In microbes which reduce methyl-phosphonic acids, C-P lyase proteins have been found to be crucial to this reduction process <ref name=":1" /><ref name=":2" /><sup>[4]</sup>, which acts as a source of phosphorus for the microbes as well as releasing methane. Mutants which disrupted Mpn degradation pathways were found to also show degradation of methanogenesis, confirming the link between the breakdown of methyl-phosphonic acid compounds and the production of methane within oxic ocean environments. Upregulation of transport and [[hydrolysis]] of [[phosphonate]] compounds within bacteria was found to occur in phosphate limitation,<ref name=":2" /> further illustrating the use of these compounds for necessary metabolic activity. The presence of this Mpn synthesis-degradation within the oxic conditions of the surface ocean explain the supersaturation of methane which caused the “marine methane paradox”, providing evidence for methanogenesis outside of the anoxic conditions which are necessary for the usual methanogenic pathways.