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Biogeochemical cycle
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==Deep cycles== {{further|Deep carbon cycle}} The terrestrial subsurface is the largest reservoir of carbon on earth, containing 14–135 [[Orders of magnitude (mass)|Pg]] of carbon<ref>{{cite journal |doi = 10.1111/1574-6941.12196|title = Weighing the deep continental biosphere|year = 2014|last1 = McMahon|first1 = Sean|last2 = Parnell|first2 = John|journal = FEMS Microbiology Ecology|volume = 87|issue = 1|pages = 113–120|pmid = 23991863| s2cid=9491320 |doi-access = free| bibcode=2014FEMME..87..113M }}</ref> and 2–19% of all biomass.<ref>{{cite journal |doi = 10.1073/pnas.1203849109|title = Global distribution of microbial abundance and biomass in subseafloor sediment|year = 2012|last1 = Kallmeyer|first1 = J.|last2 = Pockalny|first2 = R.|last3 = Adhikari|first3 = R. R.|last4 = Smith|first4 = D. C.|last5 = d'Hondt|first5 = S.|journal = Proceedings of the National Academy of Sciences|volume = 109|issue = 40|pages = 16213–16216|pmid = 22927371|pmc = 3479597|doi-access = free}}</ref> Microorganisms drive organic and inorganic compound transformations in this environment and thereby control biogeochemical cycles. Current knowledge of the microbial ecology of the subsurface is primarily based on [[16S ribosomal RNA]] (rRNA) gene sequences. Recent estimates show that <8% of 16S rRNA sequences in public databases derive from subsurface organisms<ref>{{cite journal |doi = 10.1128/mBio.00201-16|title = Status of the Archaeal and Bacterial Census: An Update|year = 2016|last1 = Schloss|first1 = Patrick D.|last2 = Girard|first2 = Rene A.|last3 = Martin|first3 = Thomas|last4 = Edwards|first4 = Joshua|last5 = Thrash|first5 = J. Cameron|journal = mBio|volume = 7|issue = 3|pmid = 27190214|pmc = 4895100}}</ref> and only a small fraction of those are represented by genomes or isolates. Thus, there is remarkably little reliable information about microbial metabolism in the subsurface. Further, little is known about how organisms in subsurface ecosystems are metabolically interconnected. Some cultivation-based studies of [[syntrophic]] [[microbial consortia|consortia]]<ref>{{cite journal |doi = 10.1093/femsre/fuw019|title = Decoding molecular interactions in microbial communities|year = 2016|last1 = Abreu|first1 = Nicole A.|last2 = Taga|first2 = Michiko E.|journal = FEMS Microbiology Reviews|volume = 40|issue = 5|pages = 648–663|pmid = 27417261|pmc = 5007284}}</ref><ref>{{cite journal |doi = 10.1186/s13040-015-0054-4|title = Interaction networks for identifying coupled molecular processes in microbial communities|year = 2015|last1 = Bosse|first1 = Magnus|last2 = Heuwieser|first2 = Alexander|last3 = Heinzel|first3 = Andreas|last4 = Nancucheo|first4 = Ivan|last5 = Melo Barbosa Dall'Agnol|first5 = Hivana|last6 = Lukas|first6 = Arno|last7 = Tzotzos|first7 = George|last8 = Mayer|first8 = Bernd|journal = BioData Mining|volume = 8|page = 21|pmid = 26180552|pmc = 4502522 | doi-access=free }}</ref><ref>{{cite journal |doi = 10.1111/j.1574-6941.2011.01237.x|title = Genetic characterization of denitrifier communities with contrasting intrinsic functional traits|year = 2012|last1 = Braker|first1 = Gesche|last2 = Dörsch|first2 = Peter|last3 = Bakken|first3 = Lars R.|journal = FEMS Microbiology Ecology|volume = 79|issue = 2|pages = 542–554|pmid = 22092293|doi-access = free| bibcode=2012FEMME..79..542B }}</ref> and small-scale metagenomic analyses of natural communities<ref name=Hug2015>{{cite journal|doi = 10.1111/1462-2920.12930|title = Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages|year = 2016|last1 = Hug|first1 = Laura A.|last2 = Thomas|first2 = Brian C.|last3 = Sharon|first3 = Itai|last4 = Brown|first4 = Christopher T.|last5 = Sharma|first5 = Ritin|last6 = Hettich|first6 = Robert L.|last7 = Wilkins|first7 = Michael J.|last8 = Williams|first8 = Kenneth H.|last9 = Singh|first9 = Andrea|last10 = Banfield|first10 = Jillian F.|journal = Environmental Microbiology|volume = 18|issue = 1|pages = 159–173|pmid = 26033198| bibcode=2016EnvMi..18..159H | s2cid=43160538 |url = https://escholarship.org/uc/item/2f1480x2|access-date = 2021-09-27|archive-date = 2021-09-27|archive-url = https://web.archive.org/web/20210927050621/https://escholarship.org/uc/item/2f1480x2|url-status = live}}</ref><ref>{{cite journal |doi = 10.1073/pnas.1010732107|title = Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea|year = 2010|last1 = McCarren|first1 = J.|last2 = Becker|first2 = J. W.|last3 = Repeta|first3 = D. J.|last4 = Shi|first4 = Y.|last5 = Young|first5 = C. R.|last6 = Malmstrom|first6 = R. R.|last7 = Chisholm|first7 = S. W.|last8 = Delong|first8 = E. F.|journal = Proceedings of the National Academy of Sciences|volume = 107|issue = 38|pages = 16420–16427|pmid = 20807744|pmc = 2944720|doi-access = free}}</ref><ref>{{cite journal |doi = 10.1073/pnas.1506034112|title = Networks of energetic and metabolic interactions define dynamics in microbial communities|year = 2015|last1 = Embree|first1 = Mallory|last2 = Liu|first2 = Joanne K.|last3 = Al-Bassam|first3 = Mahmoud M.|last4 = Zengler|first4 = Karsten|journal = Proceedings of the National Academy of Sciences|volume = 112|issue = 50|pages = 15450–15455|pmid = 26621749|pmc = 4687543|bibcode = 2015PNAS..11215450E|doi-access = free}}</ref> suggest that organisms are linked via metabolic handoffs: the transfer of redox reaction products of one organism to another. However, no complex environments have been dissected completely enough to resolve the metabolic interaction networks that underpin them. This restricts the ability of biogeochemical models to capture key aspects of the carbon and other nutrient cycles.<ref>{{cite journal |doi = 10.1016/j.tim.2016.04.006|title = Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes|year = 2016|last1 = Long|first1 = Philip E.|last2 = Williams|first2 = Kenneth H.|last3 = Hubbard|first3 = Susan S.|last4 = Banfield|first4 = Jillian F.|journal = Trends in Microbiology|volume = 24|issue = 8|pages = 600–610|pmid = 27156744| s2cid=3983278 |doi-access = free}}</ref> New approaches such as genome-resolved metagenomics, an approach that can yield a comprehensive set of draft and even complete genomes for organisms without the requirement for laboratory isolation<ref name=Hug2015 /><ref>{{cite journal |doi = 10.7717/peerj.1319|title = Anvi'o: An advanced analysis and visualization platform for 'omics data|year = 2015|last1 = Eren|first1 = A. Murat|last2 = Esen|first2 = Özcan C.|last3 = Quince|first3 = Christopher|last4 = Vineis|first4 = Joseph H.|last5 = Morrison|first5 = Hilary G.|last6 = Sogin|first6 = Mitchell L.|last7 = Delmont|first7 = Tom O.|journal = PeerJ|volume = 3|pages = e1319|pmid = 26500826|pmc = 4614810 | doi-access=free }}</ref><ref>{{cite journal |doi = 10.1038/nmeth.3103|title = Binning metagenomic contigs by coverage and composition|year = 2014|last1 = Alneberg|first1 = Johannes|last2 = Bjarnason|first2 = Brynjar Smári|last3 = De Bruijn|first3 = Ino|last4 = Schirmer|first4 = Melanie|last5 = Quick|first5 = Joshua|last6 = Ijaz|first6 = Umer Z.|last7 = Lahti|first7 = Leo|last8 = Loman|first8 = Nicholas J.|last9 = Andersson|first9 = Anders F.|last10 = Quince|first10 = Christopher|journal = Nature Methods|volume = 11|issue = 11|pages = 1144–1146|pmid = 25218180|s2cid = 24696869}}</ref> have the potential to provide this critical level of understanding of biogeochemical processes.<ref name=Anantharaman2016>{{cite journal |doi = 10.1038/ncomms13219|title = Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system|year = 2016|last1 = Anantharaman|first1 = Karthik|last2 = Brown|first2 = Christopher T.|last3 = Hug|first3 = Laura A.|last4 = Sharon|first4 = Itai|last5 = Castelle|first5 = Cindy J.|last6 = Probst|first6 = Alexander J.|last7 = Thomas|first7 = Brian C.|last8 = Singh|first8 = Andrea|last9 = Wilkins|first9 = Michael J.|last10 = Karaoz|first10 = Ulas|last11 = Brodie|first11 = Eoin L.|last12 = Williams|first12 = Kenneth H.|last13 = Hubbard|first13 = Susan S.|last14 = Banfield|first14 = Jillian F.|journal = Nature Communications|volume = 7|page = 13219|pmid = 27774985|pmc = 5079060|bibcode = 2016NatCo...713219A}} [[File:CC-BY icon.svg|50px]] Material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License] {{Webarchive|url=https://web.archive.org/web/20171016050101/https://creativecommons.org/licenses/by/4.0/ |date=2017-10-16 }}.</ref>
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