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[[File:Generalized biogeochemical cycle.jpg|thumb|upright=1.2| {{center|Generalized biogeochemical cycle{{hsp}}<ref name=Moses2012 />}}]]
[[File:Generalized biogeochemical cycle.jpg|thumb|upright=1.2| {{center|Generalized biogeochemical cycle{{hsp}}<ref name=Moses2012 />}}]]
能量在生态系统中定向流动，以阳光（或化能自养生物的无机分子）的形式进入，并在营养级之间的众多转移过程中以热量的形式离开。然而，组成生物体的物质是被保存和循环利用的。与有机分子相关的六种最常见元素——碳、氮、氢、氧、磷和硫——以各种化学形式存在，并可能长期存在于大气、陆地、水体或者地表以下。地质过程，如风化、侵蚀、排水和大陆板块的俯冲，都在这种物质循环中发挥作用。由于地质学和化学在对于该过程的研究中起主要作用，无机物在生物体及其环境之间的循环便被称为生物地球化学循环。<ref name=OpenStax>[https://cnx.org/contents/ZdFkREJc@7/Biogeochemical-Cycles Biogeochemical Cycles] {{Webarchive|url=https://web.archive.org/web/20210927040316/https://cnx.org/contents/ZdFkREJc@7/Biogeochemical-Cycles |date=2021-09-27 }}, ''OpenStax'', 9 May 2019. [[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>
能量在生态系统中定向流动，以阳光（或化能自养生物的无机分子）的形式进入，并在营养级之间的众多转移过程中以热量的形式离开。然而，组成生物体的物质是被保存和循环利用的。与有机分子相关的六种最常见元素——碳、氮、氢、氧、磷和硫——以各种化学形式存在，并可能长期存在于大气、陆地、水体或者地表以下。地质过程，如风化、侵蚀、排水和大陆板块的俯冲，都在这种物质循环中发挥作用。由于地质学和化学在对于该过程的研究中起主要作用，无机物在生物体及其环境之间的循环便被称为生物地球化学循环。<ref name=OpenStax>[https://cnx.org/contents/ZdFkREJc@7/Biogeochemical-Cycles Biogeochemical Cycles] , ''OpenStax'', 9 May 2019. [[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].</ref>
==箱模型==
==箱模型==
[[File:Simple box model.png|thumb|upright=1|right| {{center|'''Basic one-box model'''}}]]
[[File:Simple box model.png|thumb|upright=1|right| {{center|'''Basic one-box model'''}}]]
箱模型被广泛用于生物地球化学系统建模。<ref name=Sarmiento1984>{{cite journal| author = Sarmiento, J.L.|author2=Toggweiler, J.R.| year = 1984| title = A new model for the role of the oceans in determining atmospheric P CO 2| journal = Nature| volume = 308| pages = 621–24| doi = 10.1038/308621a0| issue=5960 |bibcode = 1984Natur.308..621S |s2cid=4312683}}</ref><ref name=Bianchi2007>[[Thomas S. Bianchi|Bianchi, Thomas]] (2007) [https://books.google.com/books?id=3no8DwAAQBAJ&printsec=frontcover&dq=%22Biogeochemistry+of+Estuaries%22&hl=en&newbks=1&newbks_redir=0&sa=X&ved=2ahUKEwixq4PYm_brAhXYILcAHUVzBf0QuwUwAHoECAIQBw#v=onepage&q=%22Biogeochemistry%20of%20Estuaries%22&f=false ''Biogeochemistry of Estuaries''] page 9, Oxford University Press. .</ref>箱模型是复杂系统的简化版本，将其简化为存放化学物质的箱（或储库），并由物质通量（流）进行连接。简单的箱模型含有少量属性不随时间变化的箱室，例如体积。这些箱室的行为被假定为是均匀混合的。这些模型经常被用于推导出解析公式以描述所涉及的化学物质的动力学和稳态丰度。
箱模型被广泛用于生物地球化学系统建模。<ref name=Sarmiento1984>{{cite journal| author = Sarmiento, J.L.|author2=Toggweiler, J.R.| year = 1984| title = A new model for the role of the oceans in determining atmospheric P CO 2| journal = Nature| volume = 308| pages = 621–24| doi = 10.1038/308621a0| issue=5960 |bibcode = 1984Natur.308..621S }}</ref><ref name=Bianchi2007>[[Thomas S. Bianchi|Bianchi, Thomas]] (2007) [https://books.google.com/books?id=3no8DwAAQBAJ&printsec=frontcover&dq=%22Biogeochemistry+of+Estuaries%22&hl=en&newbks=1&newbks_redir=0&sa=X&ved=2ahUKEwixq4PYm_brAhXYILcAHUVzBf0QuwUwAHoECAIQBw#v=onepage&q=%22Biogeochemistry%20of%20Estuaries%22&f=false ''Biogeochemistry of Estuaries''] page 9, Oxford University Press. .</ref>箱模型是复杂系统的简化版本，将其简化为存放化学物质的箱（或储库），并由物质通量（流）进行连接。简单的箱模型含有少量属性不随时间变化的箱室，例如体积。这些箱室的行为被假定为是均匀混合的。这些模型经常被用于推导出解析公式以描述所涉及的化学物质的动力学和稳态丰度。
当两个或多个储库相连通时，可以认为物质在储库之间循环，且循环流动具有可预测的模式。<ref name=Bianchi2007 />更复杂的多箱模型通常用数值方法求解。
当两个或多个储库相连通时，可以认为物质在储库之间循环，且循环流动具有可预测的模式。<ref name=Bianchi2007 />更复杂的多箱模型通常用数值方法求解。
[[File:Simplified budget of carbon flows in the ocean.png|thumb|upright=0.9|left| {{center|'''Simple three box model'''<br /> <small>simplified budget of ocean carbon flows{{hsp}}<ref name=Middelburg2019>Middelburg, J.J.(2019) ''Marine carbon biogeochemistry: a primer for earth system scientists'', page 5, Springer Nature. [[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></small>}}]]
[[File:Simplified budget of carbon flows in the ocean.png|thumb|upright=0.9|left| {{center|'''Simple three box model'''<br /> <small>simplified budget of ocean carbon flows{{hsp}}<ref name=Middelburg2019>Middelburg, J.J.(2019) ''Marine carbon biogeochemistry: a primer for earth system scientists'', page 5, Springer Nature. [[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].</ref></small>}}]]
[[File:Simplified diagram of the global carbon cycle.jpg|thumb|upright=2.2|right| {{center|'''More complex model with many interacting boxes'''<br /><small>export and burial rates of terrestrial organic carbon in the ocean{{hsp}}<ref name=Kandasamy2016 /></small>}}]]
[[File:Simplified diagram of the global carbon cycle.jpg|thumb|upright=2.2|right| {{center|'''More complex model with many interacting boxes'''<br /><small>export and burial rates of terrestrial organic carbon in the ocean{{hsp}}<ref name=Kandasamy2016 /></small>}}]]
右上图显示了一个更复杂的模型，其中包含了许多相互作用的箱室。这里储库的质量代表碳储量，以Pg C为单位。碳交换通量以Pg C yr<sup>-1</sup>为单位，出现于大气和两个主要的碳汇，陆地和海洋之间。黑色的数字和箭头表示了1750年（工业革命之前）的碳库含量和交换通量的估计值。红色的箭头和对应的数字代表了2000-2009年人类活动导致的碳通量变化的年平均值。它们显示了1750年以来碳循环的变化情况。储库中的红色数字表示了自1750年至2011年，即工业革命开始以来人为碳的累积变化。<ref>{{cite journal |doi = 10.1063/1.1510279|title = Sinks for Anthropogenic Carbon|year = 2002|last1 = Sarmiento|first1 = Jorge L.|last2 = Gruber|first2 = Nicolas|journal = Physics Today|volume = 55|issue = 8|pages = 30–36|bibcode = 2002PhT....55h..30S}}</ref><ref>{{cite journal |doi = 10.13140/2.1.1081.8883|year = 2013|last1 = Chhabra|first1 = Abha|title = Carbon and Other Biogeochemical Cycles}}</ref><ref name=Kandasamy2016>{{cite journal |doi = 10.3389/fmars.2016.00259|title = Perspectives on the Terrestrial Organic Matter Transport and Burial along the Land-Deep Sea Continuum: Caveats in Our Understanding of Biogeochemical Processes and Future Needs|year = 2016|last1 = Kandasamy|first1 = Selvaraj|last2 = Nagender Nath|first2 = Bejugam|journal = Frontiers in Marine Science|volume = 3|s2cid = 30408500|doi-access = free}} [[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>
右上图显示了一个更复杂的模型，其中包含了许多相互作用的箱室。这里储库的质量代表碳储量，以Pg C为单位。碳交换通量以Pg C yr<sup>-1</sup>为单位，出现于大气和两个主要的碳汇，陆地和海洋之间。黑色的数字和箭头表示了1750年（工业革命之前）的碳库含量和交换通量的估计值。红色的箭头和对应的数字代表了2000-2009年人类活动导致的碳通量变化的年平均值。它们显示了1750年以来碳循环的变化情况。储库中的红色数字表示了自1750年至2011年，即工业革命开始以来人为碳的累积变化。<ref>{{cite journal |doi = 10.1063/1.1510279|title = Sinks for Anthropogenic Carbon|year = 2002|last1 = Sarmiento|first1 = Jorge L.|last2 = Gruber|first2 = Nicolas|journal = Physics Today|volume = 55|issue = 8|pages = 30–36|bibcode = 2002PhT....55h..30S}}</ref><ref>{{cite journal |doi = 10.13140/2.1.1081.8883|year = 2013|last1 = Chhabra|first1 = Abha|title = Carbon and Other Biogeochemical Cycles}}</ref><ref name=Kandasamy2016>{{cite journal |doi = 10.3389/fmars.2016.00259|title = Perspectives on the Terrestrial Organic Matter Transport and Burial along the Land-Deep Sea Continuum: Caveats in Our Understanding of Biogeochemical Processes and Future Needs|year = 2016|last1 = Kandasamy|first1 = Selvaraj|last2 = Nagender Nath|first2 = Bejugam|journal = Frontiers in Marine Science|volume = 3|doi-access = free}} [[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].</ref>
==隔室==
==隔室==
===生物圈===
===生物圈===
[[File:Role of marine organisms in biogeochemical cycling.jpg|thumb|upright=2.1| {{center|Role of marine organisms in biogeochemical cycling in the Southern Ocean{{hsp}}<ref name=Henley2020>{{cite journal |title = Changing Biogeochemistry of the Southern Ocean and Its Ecosystem Implications|year = 2020|doi = 10.3389/fmars.2020.00581|doi-access = free|last1 = Henley|first1 = Sian F.|last2 = Cavan|first2 = Emma L.|last3 = Fawcett|first3 = Sarah E.|last4 = Kerr|first4 = Rodrigo|last5 = Monteiro|first5 = Thiago|last6 = Sherrell|first6 = Robert M.|last7 = Bowie|first7 = Andrew R.|last8 = Boyd|first8 = Philip W.|last9 = Barnes|first9 = David K. A.|last10 = Schloss|first10 = Irene R.|last11 = Marshall|first11 = Tanya|last12 = Flynn|first12 = Raquel|last13 = Smith|first13 = Shantelle|journal = Frontiers in Marine Science|volume = 7}} [[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>}}]]
[[File:Role of marine organisms in biogeochemical cycling.jpg|thumb|upright=2.1| {{center|Role of marine organisms in biogeochemical cycling in the Southern Ocean{{hsp}}<ref name=Henley2020>{{cite journal |title = Changing Biogeochemistry of the Southern Ocean and Its Ecosystem Implications|year = 2020|doi = 10.3389/fmars.2020.00581|doi-access = free|last1 = Henley|first1 = Sian F.|last2 = Cavan|first2 = Emma L.|last3 = Fawcett|first3 = Sarah E.|last4 = Kerr|first4 = Rodrigo|last5 = Monteiro|first5 = Thiago|last6 = Sherrell|first6 = Robert M.|last7 = Bowie|first7 = Andrew R.|last8 = Boyd|first8 = Philip W.|last9 = Barnes|first9 = David K. A.|last10 = Schloss|first10 = Irene R.|last11 = Marshall|first11 = Tanya|last12 = Flynn|first12 = Raquel|last13 = Smith|first13 = Shantelle|journal = Frontiers in Marine Science|volume = 7}} [[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].</ref>}}]]
[[File:Oxygen Cycle.jpg|thumb| {{center|[[Oxygen cycle]]}}]]
[[File:Oxygen Cycle.jpg|thumb| {{center|[[Oxygen cycle]]}}]]
微生物驱动了地球系统中大部分的生物地球化学循环。<ref>{{cite journal |title = The Microbial Engines That Drive Earth's Biogeochemical Cycles|year = 2008|doi = 10.1126/science.1153213|last1 = Falkowski|first1 = P. G.|last2 = Fenchel|first2 = T.|last3 = Delong|first3 = E. F.|journal = Science|volume = 320|issue = 5879|pages = 1034–1039|pmid = 18497287|bibcode = 2008Sci...320.1034F|s2cid = 2844984}}</ref><ref name=Zakem2020>{{cite journal |title = Redox-informed models of global biogeochemical cycles|year = 2020|doi = 10.1038/s41467-020-19454-w|last1 = Zakem|first1 = Emily J.|last2 = Polz|first2 = Martin F.|last3 = Follows|first3 = Michael J.|journal = Nature Communications|volume = 11|issue = 1|page = 5680|pmid = 33173062|pmc = 7656242|bibcode = 2020NatCo..11.5680Z}} [[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].</ref>
微生物驱动了地球系统中大部分的生物地球化学循环。<ref>{{cite journal |title = The Microbial Engines That Drive Earth's Biogeochemical Cycles|year = 2008|doi = 10.1126/science.1153213|last1 = Falkowski|first1 = P. G.|last2 = Fenchel|first2 = T.|last3 = Delong|first3 = E. F.|journal = Science|volume = 320|issue = 5879|pages = 1034–1039|pmid = 18497287|bibcode = 2008Sci...320.1034F}}</ref><ref name=Zakem2020>{{cite journal |title = Redox-informed models of global biogeochemical cycles|year = 2020|doi = 10.1038/s41467-020-19454-w|last1 = Zakem|first1 = Emily J.|last2 = Polz|first2 = Martin F.|last3 = Follows|first3 = Michael J.|journal = Nature Communications|volume = 11|issue = 1|page = 5680|pmid = 33173062|pmc = 7656242|bibcode = 2020NatCo..11.5680Z}} [[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].</ref>
===水圈===
===水圈===
海洋覆盖了地球表面的70%以上，并且具有很强的异质性。海洋生产区和沿海生态系统只占海洋表面积的一小部分，但对微生物群落（占海洋生物量的90%）<ref>{{cite journal |doi = 10.1007/s12526-011-0084-1|title = The Census of Marine Life—evolution of worldwide marine biodiversity research|year = 2011|last1 = Alexander|first1 = Vera|last2 = Miloslavich|first2 = Patricia|last3 = Yarincik|first3 = Kristen|journal = Marine Biodiversity|volume = 41|issue = 4|pages = 545–554|s2cid = 25888475}}</ref>所进行的全球生物地球化学循环有着巨大的影响。<ref name=Murillo2019 />近年来的工作主要集中在碳和常量营养元素（如氮、磷和硅酸盐）的循环上，对其它重要元素（如硫或微量元素）的研究较少，反映的相关的技术和后勤问题。这些海域以及构成其生态系统的分类群正日益受到人类活动的巨大压力，影响着海洋生物以及能量和营养物质的循环。<ref>Galton, D. (1884) [https://www.proquest.com/openview/792c496cb0a1bdf11778db87c126ff44/1?pq-origsite=gscholar&cbl=1816417 10th Meeting: report of the royal commission on metropolitan sewage] {{Webarchive|url=https://web.archive.org/web/20210924063154/https://www.proquest.com/openview/792c496cb0a1bdf11778db87c126ff44/1?pq-origsite=gscholar&cbl=1816417 |date=2021-09-24 }}. ''J. Soc. Arts'', '''33''': 290.</ref><ref>{{cite journal |doi = 10.2307/1294478|jstor = 1294478|last1 = Hasler|first1 = Arthur D.|title = Cultural Eutrophication is Reversible|journal = BioScience|year = 1969|volume = 19|issue = 5|pages = 425–431}}</ref><ref>{{cite journal |doi = 10.1002/2016GB005586|title = A reevaluation of the magnitude and impacts of anthropogenic atmospheric nitrogen inputs on the ocean|year = 2017|last1 = Jickells|first1 = T. D.|last2 = Buitenhuis|first2 = E.|last3 = Altieri|first3 = K.|last4 = Baker|first4 = A. R.|last5 = Capone|first5 = D.|last6 = Duce|first6 = R. A.|last7 = Dentener|first7 = F.|last8 = Fennel|first8 = K.|last9 = Kanakidou|first9 = M.|last10 = Laroche|first10 = J.|last11 = Lee|first11 = K.|last12 = Liss|first12 = P.|last13 = Middelburg|first13 = J. J.|last14 = Moore|first14 = J. K.|last15 = Okin|first15 = G.|last16 = Oschlies|first16 = A.|last17 = Sarin|first17 = M.|last18 = Seitzinger|first18 = S.|last19 = Sharples|first19 = J.|last20 = Singh|first20 = A.|last21 = Suntharalingam|first21 = P.|last22 = Uematsu|first22 = M.|last23 = Zamora|first23 = L. M.|journal = Global Biogeochemical Cycles|volume = 31|issue = 2|page = 289|bibcode = 2017GBioC..31..289J|hdl = 1874/348077}}</ref>一个关键的例子是人为富营养化的影响，农业生产的径流导致沿海生态系统的氮和磷富集，使生产力大大提高并造成藻类大量繁殖，水体和海床脱氧，温室气体排放增加，<ref name=Bouwman2005>{{cite journal |doi = 10.1029/2004GB002314|title = Exploring changes in river nitrogen export to the world's oceans|year = 2005|last1 = Bouwman|first1 = A. F.|last2 = Van Drecht|first2 = G.|last3 = Knoop|first3 = J. M.|last4 = Beusen|first4 = A. H. W.|last5 = Meinardi|first5 = C. R.|journal = Global Biogeochemical Cycles|volume = 19|issue = 1|bibcode = 2005GBioC..19.1002B}}</ref>直接影响了区域和全球的氮循环和碳循环。然而，有机物从大陆流入沿海生态系统只是全球变化对微生物群落造成的一系列胁迫之一。气候变化还导致了冰冻圈的变化，冰川和永久冻土融化加剧了海洋分层，而不同生物群落中氧化还原状态的变化正以前所未有的速度迅速重塑微生物组合。<ref>{{cite journal |doi = 10.1111/gcb.12754|title = Climate change and dead zones|year = 2015|last1 = Altieri|first1 = Andrew H.|last2 = Gedan|first2 = Keryn B.|journal = Global Change Biology|volume = 21|issue = 4|pages = 1395–1406|pmid = 25385668|bibcode = 2015GCBio..21.1395A}}</ref><ref name=Breitburg2018>{{cite journal |doi = 10.1126/science.aam7240|title = Declining oxygen in the global ocean and coastal waters|year = 2018|last1 = Breitburg|first1 = Denise|last2 = Levin|first2 = Lisa A.|last3 = Oschlies|first3 = Andreas|last4 = Grégoire|first4 = Marilaure|last5 = Chavez|first5 = Francisco P.|last6 = Conley|first6 = Daniel J.|last7 = Garçon|first7 = Véronique|last8 = Gilbert|first8 = Denis|last9 = Gutiérrez|first9 = Dimitri|last10 = Isensee|first10 = Kirsten|last11 = Jacinto|first11 = Gil S.|last12 = Limburg|first12 = Karin E.|last13 = Montes|first13 = Ivonne|last14 = Naqvi|first14 = S. W. A.|last15 = Pitcher|first15 = Grant C.|last16 = Rabalais|first16 = Nancy N.|last17 = Roman|first17 = Michael R.|last18 = Rose|first18 = Kenneth A.|last19 = Seibel|first19 = Brad A.|last20 = Telszewski|first20 = Maciej|last21 = Yasuhara|first21 = Moriaki|last22 = Zhang|first22 = Jing|journal = Science|volume = 359|issue = 6371|pages = eaam7240|pmid = 29301986|bibcode = 2018Sci...359M7240B|s2cid = 206657115}}</ref><ref name=Cavicchioli2019>{{cite journal |doi = 10.1038/s41579-019-0222-5|title = Scientists' warning to humanity: Microorganisms and climate change|year = 2019|last1 = Cavicchioli|first1 = Ricardo|last2 = Ripple|first2 = William J.|last3 = Timmis|first3 = Kenneth N.|last4 = Azam|first4 = Farooq|last5 = Bakken|first5 = Lars R.|last6 = Baylis|first6 = Matthew|last7 = Behrenfeld|first7 = Michael J.|last8 = Boetius|first8 = Antje|last9 = Boyd|first9 = Philip W.|last10 = Classen|first10 = Aimée T.|last11 = Crowther|first11 = Thomas W.|last12 = Danovaro|first12 = Roberto|last13 = Foreman|first13 = Christine M.|last14 = Huisman|first14 = Jef|last15 = Hutchins|first15 = David A.|last16 = Jansson|first16 = Janet K.|last17 = Karl|first17 = David M.|last18 = Koskella|first18 = Britt|last19 = Mark Welch|first19 = David B.|last20 = Martiny|first20 = Jennifer B. H.|last21 = Moran|first21 = Mary Ann|last22 = Orphan|first22 = Victoria J.|last23 = Reay|first23 = David S.|last24 = Remais|first24 = Justin V.|last25 = Rich|first25 = Virginia I.|last26 = Singh|first26 = Brajesh K.|last27 = Stein|first27 = Lisa Y.|last28 = Stewart|first28 = Frank J.|last29 = Sullivan|first29 = Matthew B.|last30 = Van Oppen|first30 = Madeleine J. H.|journal = Nature Reviews Microbiology|volume = 17|issue = 9|pages = 569–586|pmid = 31213707|pmc = 7136171|display-authors = 1}}</ref><ref name=Hutchins2019>{{cite journal |doi = 10.1038/s41579-019-0178-5|title = Climate change microbiology — problems and perspectives|year = 2019|last1 = Hutchins|first1 = David A.|last2 = Jansson|first2 = Janet K.|last3 = Remais|first3 = Justin V.|last4 = Rich|first4 = Virginia I.|last5 = Singh|first5 = Brajesh K.|last6 = Trivedi|first6 = Pankaj|journal = Nature Reviews Microbiology|volume = 17|issue = 6|pages = 391–396|pmid = 31092905|s2cid = 155102440}}</ref><ref name=Murillo2019>{{cite journal |doi = 10.3389/fmars.2019.00657|doi-access = free|title = Editorial: Marine Microbiome and Biogeochemical Cycles in Marine Productive Areas|year = 2019|last1 = Murillo|first1 = Alejandro A.|last2 = Molina|first2 = Verónica|last3 = Salcedo-Castro|first3 = Julio|last4 = Harrod|first4 = Chris|journal = Frontiers in Marine Science|volume = 6}} [[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>
海洋覆盖了地球表面的70%以上，并且具有很强的异质性。海洋生产区和沿海生态系统只占海洋表面积的一小部分，但对微生物群落（占海洋生物量的90%）<ref>{{cite journal |doi = 10.1007/s12526-011-0084-1|title = The Census of Marine Life—evolution of worldwide marine biodiversity research|year = 2011|last1 = Alexander|first1 = Vera|last2 = Miloslavich|first2 = Patricia|last3 = Yarincik|first3 = Kristen|journal = Marine Biodiversity|volume = 41|issue = 4|pages = 545–554}}</ref>所进行的全球生物地球化学循环有着巨大的影响。<ref name=Murillo2019 />近年来的工作主要集中在碳和常量营养元素（如氮、磷和硅酸盐）的循环上，对其它重要元素（如硫或微量元素）的研究较少，反映的相关的技术和后勤问题。这些海域以及构成其生态系统的分类群正日益受到人类活动的巨大压力，影响着海洋生物以及能量和营养物质的循环。<ref>Galton, D. (1884) [https://www.proquest.com/openview/792c496cb0a1bdf11778db87c126ff44/1?pq-origsite=gscholar&cbl=1816417 10th Meeting: report of the royal commission on metropolitan sewage]. ''J. Soc. Arts'', '''33''': 290.</ref><ref>{{cite journal |doi = 10.2307/1294478|jstor = 1294478|last1 = Hasler|first1 = Arthur D.|title = Cultural Eutrophication is Reversible|journal = BioScience|year = 1969|volume = 19|issue = 5|pages = 425–431}}</ref><ref>{{cite journal |doi = 10.1002/2016GB005586|title = A reevaluation of the magnitude and impacts of anthropogenic atmospheric nitrogen inputs on the ocean|year = 2017|last1 = Jickells|first1 = T. D.|last2 = Buitenhuis|first2 = E.|last3 = Altieri|first3 = K.|last4 = Baker|first4 = A. R.|last5 = Capone|first5 = D.|last6 = Duce|first6 = R. A.|last7 = Dentener|first7 = F.|last8 = Fennel|first8 = K.|last9 = Kanakidou|first9 = M.|last10 = Laroche|first10 = J.|last11 = Lee|first11 = K.|last12 = Liss|first12 = P.|last13 = Middelburg|first13 = J. J.|last14 = Moore|first14 = J. K.|last15 = Okin|first15 = G.|last16 = Oschlies|first16 = A.|last17 = Sarin|first17 = M.|last18 = Seitzinger|first18 = S.|last19 = Sharples|first19 = J.|last20 = Singh|first20 = A.|last21 = Suntharalingam|first21 = P.|last22 = Uematsu|first22 = M.|last23 = Zamora|first23 = L. M.|journal = Global Biogeochemical Cycles|volume = 31|issue = 2|page = 289|bibcode = 2017GBioC..31..289J|hdl = 1874/348077}}</ref>一个关键的例子是人为富营养化的影响，农业生产的径流导致沿海生态系统的氮和磷富集，使生产力大大提高并造成藻类大量繁殖，水体和海床脱氧，温室气体排放增加，<ref name=Bouwman2005>{{cite journal |doi = 10.1029/2004GB002314|title = Exploring changes in river nitrogen export to the world's oceans|year = 2005|last1 = Bouwman|first1 = A. F.|last2 = Van Drecht|first2 = G.|last3 = Knoop|first3 = J. M.|last4 = Beusen|first4 = A. H. W.|last5 = Meinardi|first5 = C. R.|journal = Global Biogeochemical Cycles|volume = 19|issue = 1|bibcode = 2005GBioC..19.1002B}}</ref>直接影响了区域和全球的氮循环和碳循环。然而，有机物从大陆流入沿海生态系统只是全球变化对微生物群落造成的一系列胁迫之一。气候变化还导致了冰冻圈的变化，冰川和永久冻土融化加剧了海洋分层，而不同生物群落中氧化还原状态的变化正以前所未有的速度迅速重塑微生物组合。<ref>{{cite journal |doi = 10.1111/gcb.12754|title = Climate change and dead zones|year = 2015|last1 = Altieri|first1 = Andrew H.|last2 = Gedan|first2 = Keryn B.|journal = Global Change Biology|volume = 21|issue = 4|pages = 1395–1406|pmid = 25385668|bibcode = 2015GCBio..21.1395A}}</ref><ref name=Breitburg2018>{{cite journal |doi = 10.1126/science.aam7240|title = Declining oxygen in the global ocean and coastal waters|year = 2018|last1 = Breitburg|first1 = Denise|last2 = Levin|first2 = Lisa A.|last3 = Oschlies|first3 = Andreas|last4 = Grégoire|first4 = Marilaure|last5 = Chavez|first5 = Francisco P.|last6 = Conley|first6 = Daniel J.|last7 = Garçon|first7 = Véronique|last8 = Gilbert|first8 = Denis|last9 = Gutiérrez|first9 = Dimitri|last10 = Isensee|first10 = Kirsten|last11 = Jacinto|first11 = Gil S.|last12 = Limburg|first12 = Karin E.|last13 = Montes|first13 = Ivonne|last14 = Naqvi|first14 = S. W. A.|last15 = Pitcher|first15 = Grant C.|last16 = Rabalais|first16 = Nancy N.|last17 = Roman|first17 = Michael R.|last18 = Rose|first18 = Kenneth A.|last19 = Seibel|first19 = Brad A.|last20 = Telszewski|first20 = Maciej|last21 = Yasuhara|first21 = Moriaki|last22 = Zhang|first22 = Jing|journal = Science|volume = 359|issue = 6371|pages = eaam7240|pmid = 29301986|bibcode = 2018Sci...359M7240B}}</ref><ref name=Cavicchioli2019>{{cite journal |doi = 10.1038/s41579-019-0222-5|title = Scientists' warning to humanity: Microorganisms and climate change|year = 2019|last1 = Cavicchioli|first1 = Ricardo|last2 = Ripple|first2 = William J.|last3 = Timmis|first3 = Kenneth N.|last4 = Azam|first4 = Farooq|last5 = Bakken|first5 = Lars R.|last6 = Baylis|first6 = Matthew|last7 = Behrenfeld|first7 = Michael J.|last8 = Boetius|first8 = Antje|last9 = Boyd|first9 = Philip W.|last10 = Classen|first10 = Aimée T.|last11 = Crowther|first11 = Thomas W.|last12 = Danovaro|first12 = Roberto|last13 = Foreman|first13 = Christine M.|last14 = Huisman|first14 = Jef|last15 = Hutchins|first15 = David A.|last16 = Jansson|first16 = Janet K.|last17 = Karl|first17 = David M.|last18 = Koskella|first18 = Britt|last19 = Mark Welch|first19 = David B.|last20 = Martiny|first20 = Jennifer B. H.|last21 = Moran|first21 = Mary Ann|last22 = Orphan|first22 = Victoria J.|last23 = Reay|first23 = David S.|last24 = Remais|first24 = Justin V.|last25 = Rich|first25 = Virginia I.|last26 = Singh|first26 = Brajesh K.|last27 = Stein|first27 = Lisa Y.|last28 = Stewart|first28 = Frank J.|last29 = Sullivan|first29 = Matthew B.|last30 = Van Oppen|first30 = Madeleine J. H.|journal = Nature Reviews Microbiology|volume = 17|issue = 9|pages = 569–586|pmid = 31213707|pmc = 7136171|display-authors = 1}}</ref><ref name=Hutchins2019>{{cite journal |doi = 10.1038/s41579-019-0178-5|title = Climate change microbiology — problems and perspectives|year = 2019|last1 = Hutchins|first1 = David A.|last2 = Jansson|first2 = Janet K.|last3 = Remais|first3 = Justin V.|last4 = Rich|first4 = Virginia I.|last5 = Singh|first5 = Brajesh K.|last6 = Trivedi|first6 = Pankaj|journal = Nature Reviews Microbiology|volume = 17|issue = 6|pages = 391–396|pmid = 31092905}}</ref><ref name=Murillo2019>{{cite journal |doi = 10.3389/fmars.2019.00657|doi-access = free|title = Editorial: Marine Microbiome and Biogeochemical Cycles in Marine Productive Areas|year = 2019|last1 = Murillo|first1 = Alejandro A.|last2 = Molina|first2 = Verónica|last3 = Salcedo-Castro|first3 = Julio|last4 = Harrod|first4 = Chris|journal = Frontiers in Marine Science|volume = 6}} [[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].</ref>
因此，全球变化正在影响着关键过程，包括净初级生产力，CO<sub>2</sub>和N<sub>2</sub>固定，有机物呼吸/再矿化以及固定CO<sub>2</sub>的沉积和埋藏。<ref name=Hutchins2019 />除此之外，海洋正在经历酸化过程，从前工业化时期到如今pH值变化了约0.1个单位，影响了碳酸盐和碳酸氢盐缓冲的化学过程。反过来，酸化主要通过对钙化类群的影响从而影响浮游生物群落。<ref>{{cite journal |doi = 10.1242/jeb.115584|title = Biochemical adaptation to ocean acidification|year = 2015|last1 = Stillman|first1 = Jonathon H.|last2 = Paganini|first2 = Adam W.|journal = Journal of Experimental Biology|volume = 218|issue = 12|pages = 1946–1955|pmid = 26085671}}</ref>还有证据表明，关键的中间挥发性产物的生产过程发生了变化，其中一些产物具有明显的温室效应（例如N<sub>2</sub>O和CH<sup>4</sup>，Breitburg在2018年的综述中所言。<ref name=Breitburg2018 />由于全球温度升高，海洋分层和脱氧，在所谓的最低含氧区<ref>{{cite journal |doi = 10.1038/s41579-018-0087-z|title = Microbial niches in marine oxygen minimum zones|year = 2018|last1 = Bertagnolli|first1 = Anthony D.|last2 = Stewart|first2 = Frank J.|journal = Nature Reviews Microbiology|volume = 16|issue = 12|pages = 723–729|pmid = 30250271}}</ref>或缺氧海洋区<ref>{{cite journal |doi = 10.1073/pnas.1205009109|title = Microbial oceanography of anoxic oxygen minimum zones|year = 2012|last1 = Ulloa|first1 = O.|last2 = Canfield|first2 = D. E.|last3 = Delong|first3 = E. F.|last4 = Letelier|first4 = R. M.|last5 = Stewart|first5 = F. J.|journal = Proceedings of the National Academy of Sciences|volume = 109|issue = 40|pages = 15996–16003|pmid = 22967509|pmc = 3479542|bibcode = 2012PNAS..10915996U|doi-access = free}}</ref> 由于微生物的驱动导致大洋中25%-50%的氮损失到大气中）。其它对海洋自游生物有毒的产物，包括诸如H<sub>2</sub>S等硫的还原产物，对渔业和沿海水产养殖等海洋资源有负面影响。虽然全球变化加速，但人们对海洋生态系统复杂性的认识也在同步提高，尤其是微生物作为生态系统功能驱动因素的基本作用。<ref name=Cavicchioli2019 /><ref name=Murillo2019 />
因此，全球变化正在影响着关键过程，包括净初级生产力，CO<sub>2</sub>和N<sub>2</sub>固定，有机物呼吸/再矿化以及固定CO<sub>2</sub>的沉积和埋藏。<ref name=Hutchins2019 />除此之外，海洋正在经历酸化过程，从前工业化时期到如今pH值变化了约0.1个单位，影响了碳酸盐和碳酸氢盐缓冲的化学过程。反过来，酸化主要通过对钙化类群的影响从而影响浮游生物群落。<ref>{{cite journal |doi = 10.1242/jeb.115584|title = Biochemical adaptation to ocean acidification|year = 2015|last1 = Stillman|first1 = Jonathon H.|last2 = Paganini|first2 = Adam W.|journal = Journal of Experimental Biology|volume = 218|issue = 12|pages = 1946–1955|pmid = 26085671|s2cid = 13071345}}</ref>还有证据表明，关键的中间挥发性产物的生产过程发生了变化，其中一些产物具有明显的温室效应（例如N<sub>2</sub>O和CH<sup>4</sup>，Breitburg在2018年的综述中所言。<ref name=Breitburg2018 />由于全球温度升高，海洋分层和脱氧，在所谓的最低含氧区<ref>{{cite journal |doi = 10.1038/s41579-018-0087-z|title = Microbial niches in marine oxygen minimum zones|year = 2018|last1 = Bertagnolli|first1 = Anthony D.|last2 = Stewart|first2 = Frank J.|journal = Nature Reviews Microbiology|volume = 16|issue = 12|pages = 723–729|pmid = 30250271|s2cid = 52811177}}</ref>或缺氧海洋区<ref>{{cite journal |doi = 10.1073/pnas.1205009109|title = Microbial oceanography of anoxic oxygen minimum zones|year = 2012|last1 = Ulloa|first1 = O.|last2 = Canfield|first2 = D. E.|last3 = Delong|first3 = E. F.|last4 = Letelier|first4 = R. M.|last5 = Stewart|first5 = F. J.|journal = Proceedings of the National Academy of Sciences|volume = 109|issue = 40|pages = 15996–16003|pmid = 22967509|pmc = 3479542|bibcode = 2012PNAS..10915996U|s2cid = 6630698|doi-access = free}}</ref> 由于微生物的驱动导致大洋中25%-50%的氮损失到大气中）。其它对海洋自游生物有毒的产物，包括诸如H<sub>2</sub>S等硫的还原产物，对渔业和沿海水产养殖等海洋资源有负面影响。虽然全球变化加速，但人们对海洋生态系统复杂性的认识也在同步提高，尤其是微生物作为生态系统功能驱动因素的基本作用。<ref name=Cavicchioli2019 /><ref name=Murillo2019 />
快速的碳循环案例如左下图所示。这一循环包括环境和生物圈中生命体之间相对短期的地球化学过程。它包括碳在大气以及陆地和海洋生态系统、泥土和海底沉积物之间的运移。快速循环包括涉及光合作用的年周期和涉及植被生长和分解的年代周期。快速碳循环对人类活动的响应将决定气候变化许多更直接的影响。<ref name=Bush2020 /><ref>{{cite journal |doi = 10.1073/pnas.022055499|title = Atmospheric carbon dioxide levels for the last 500 million years|year = 2002|last1 = Rothman|first1 = D. H.|journal = Proceedings of the National Academy of Sciences|volume = 99|issue = 7|pages = 4167–4171|pmid = 11904360|pmc = 123620|bibcode = 2002PNAS...99.4167R|doi-access = free}}</ref><ref name=Carpinteri2019>{{cite journal |doi = 10.3390/sci1010017|title = Correlation between the Fluctuations in Worldwide Seismicity and Atmospheric Carbon Pollution|year = 2019|last1 = Carpinteri|first1 = Alberto|last2 = Niccolini|first2 = Gianni|journal = Sci|volume = 1|page = 17|doi-access = free}} [[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><ref>{{Cite journal|last=Rothman|first=Daniel|date=January 2015|title=Earth's carbon cycle: A mathematical perspective|url=https://www.ams.org/bull/2015-52-01/S0273-0979-2014-01471-5/|journal=Bulletin of the American Mathematical Society|language=en|volume=52|issue=1|pages=47–64|doi=10.1090/S0273-0979-2014-01471-5|issn=0273-0979|hdl=1721.1/97900|hdl-access=free|access-date=2021-09-27|archive-date=2021-11-22|archive-url=https://web.archive.org/web/20211122221018/https://www.ams.org/journals/bull/2015-52-01/S0273-0979-2014-01471-5/|url-status=live}}</ref>
快速的碳循环案例如左下图所示。这一循环包括环境和生物圈中生命体之间相对短期的地球化学过程。它包括碳在大气以及陆地和海洋生态系统、泥土和海底沉积物之间的运移。快速循环包括涉及光合作用的年周期和涉及植被生长和分解的年代周期。快速碳循环对人类活动的响应将决定气候变化许多更直接的影响。<ref name=Bush2020 /><ref>{{cite journal |doi = 10.1073/pnas.022055499|title = Atmospheric carbon dioxide levels for the last 500 million years|year = 2002|last1 = Rothman|first1 = D. H.|journal = Proceedings of the National Academy of Sciences|volume = 99|issue = 7|pages = 4167–4171|pmid = 11904360|pmc = 123620|bibcode = 2002PNAS...99.4167R|doi-access = free}}</ref><ref name=Carpinteri2019>{{cite journal |doi = 10.3390/sci1010017|title = Correlation between the Fluctuations in Worldwide Seismicity and Atmospheric Carbon Pollution|year = 2019|last1 = Carpinteri|first1 = Alberto|last2 = Niccolini|first2 = Gianni|journal = Sci|volume = 1|page = 17|doi-access = free}} [[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] .</ref><ref>{{Cite journal|last=Rothman|first=Daniel|date=January 2015|title=Earth's carbon cycle: A mathematical perspective|url=https://www.ams.org/bull/2015-52-01/S0273-0979-2014-01471-5/|journal=Bulletin of the American Mathematical Society|language=en|volume=52|issue=1|pages=47–64|doi=10.1090/S0273-0979-2014-01471-5|issn=0273-0979|hdl=1721.1/97900|hdl-access=free|access-date=2021-09-27|archive-date=2021-11-22|archive-url=https://web.archive.org/web/20211122221018/https://www.ams.org/journals/bull/2015-52-01/S0273-0979-2014-01471-5/|url-status=live}}</ref>
[[File:Carbon cycle.jpg|thumb|upright=1.8|left| 快速循环贯穿生物圈，包括陆地、大气和海洋之间的交换。黄色数字表示每年的自然碳通量，以十亿吨（gigatons）为单位。红色数字表示人类的贡献，白色数字表示被储存的碳。<ref name="nasacc">{{cite web|last1=Riebeek|first1=Holli|title=The Carbon Cycle|url=http://earthobservatory.nasa.gov/Features/CarbonCycle/?src=eoa-features|website=Earth Observatory|publisher=NASA|access-date=5 April 2018|date=16 June 2011|archive-url=https://web.archive.org/web/20160305010126/http://earthobservatory.nasa.gov/Features/CarbonCycle/?src=eoa-features|archive-date=5 March 2016|url-status=live|df=dmy-all}}</ref>]]
[[File:Carbon cycle.jpg|thumb|upright=1.8|left| 快速循环贯穿生物圈，包括陆地、大气和海洋之间的交换。黄色数字表示每年的自然碳通量，以十亿吨（gigatons）为单位。红色数字表示人类的贡献，白色数字表示被储存的碳。<ref name="nasacc">{{cite web|last1=Riebeek|first1=Holli|title=The Carbon Cycle|url=http://earthobservatory.nasa.gov/Features/CarbonCycle/?src=eoa-features|website=Earth Observatory|publisher=NASA|access-date=5 April 2018|date=16 June 2011|archive-url=https://web.archive.org/web/20160305010126/http://earthobservatory.nasa.gov/Features/CarbonCycle/?src=eoa-features|archive-date=5 March 2016|url-status=live|df=dmy-all}}</ref>]]
慢速循环如右上图所示，它涉及到岩石循环中的中长期地球化学过程。海洋和大气之间的交换可能需要几个世纪，而岩石的风化可能需要数百万年。海洋中的碳沉积在海底，在那里形成沉积岩并潜入地幔。造山运动使得这种地质碳回到地表。在地表，岩石被风化，碳通过脱气作用返回大气，通过河流返回海洋。其它的地质碳通过含钙离子热液的排放回到海洋。在一年中，有一千万至一亿吨的碳在这个缓慢的循环中移动。这包括火山将地质碳以二氧化碳的形式直接返还大气。然而，这还不足燃烧化石燃料排放到大气中的二氧化碳的百分之一。<ref name=Libes2015 /><ref name="Bush2020">{{cite book|doi = 10.1007/978-3-030-15424-0_3|url = https://books.google.com/books?id=h_60DwAAQBAJ&q=%22Climate+Change+and+Renewable+Energy%22+%22The+Carbon+Cycle%22chapter+%3D+The+Carbon+Cycle&pg=PA109|title = Climate Change and Renewable Energy|year = 2020|last1 = Bush|first1 = Martin J.|pages = 109–141|isbn = 978-3-030-15423-3|s2cid = 210305910|access-date = 2021-09-27|archive-date = 2021-09-27|archive-url = https://web.archive.org/web/20210927001642/https://books.google.com/books?id=h_60DwAAQBAJ&q=%22Climate+Change+and+Renewable+Energy%22+%22The+Carbon+Cycle%22chapter+%3D+The+Carbon+Cycle&pg=PA109|url-status = live}}</ref>
慢速循环如右上图所示，它涉及到岩石循环中的中长期地球化学过程。海洋和大气之间的交换可能需要几个世纪，而岩石的风化可能需要数百万年。海洋中的碳沉积在海底，在那里形成沉积岩并潜入地幔。造山运动使得这种地质碳回到地表。在地表，岩石被风化，碳通过脱气作用返回大气，通过河流返回海洋。其它的地质碳通过含钙离子热液的排放回到海洋。在一年中，有一千万至一亿吨的碳在这个缓慢的循环中移动。这包括火山将地质碳以二氧化碳的形式直接返还大气。然而，这还不足燃烧化石燃料排放到大气中的二氧化碳的百分之一。<ref name=Libes2015 /><ref name="Bush2020">{{cite book|doi = 10.1007/978-3-030-15424-0_3|url = https://books.google.com/books?id=h_60DwAAQBAJ&q=%22Climate+Change+and+Renewable+Energy%22+%22The+Carbon+Cycle%22chapter+%3D+The+Carbon+Cycle&pg=PA109|title = Climate Change and Renewable Energy|year = 2020|last1 = Bush|first1 = Martin J.|pages = 109–141|isbn = 978-3-030-15423-3|access-date = 2021-09-27|archive-date = 2021-09-27|archive-url = https://web.archive.org/web/20210927001642/https://books.google.com/books?id=h_60DwAAQBAJ&q=%22Climate+Change+and+Renewable+Energy%22+%22The+Carbon+Cycle%22chapter+%3D+The+Carbon+Cycle&pg=PA109|url-status = live}}</ref>
==深层循环==
==深层循环==
陆地地下是地球上最大的碳储库，含有14-135Pg的碳和总生物量<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}}</ref>的2-19%。<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>微生物在这种环境下驱动有机和无机化合物的转化，从而控制生物地球化学循环。目前对于地下微生物生态学的了解主要是基于16S核糖体RNA（rRNA）基因序列。最近的估计显示，公共数据库中小于8%的16S rRNA序列来自于地下生物，<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>且其中仅一小部分由基因组或分离物表示。因此，关于地下微生物代谢的可靠信息非常少。此外，关于地下生态系统中的生物体是如何在新陈代谢上互相关联的，我们知之甚少。一些基于栽培的同养群落研究<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}}</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}}</ref>和对自然群落的小规模宏基因组学分析表明，<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|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>生物体通过代谢传递相联系：一个生物的氧化还原产物转移到另一生物。然而，还没有一个复杂的环境被彻底剖析，以解决支撑它们的代谢相互作用网络。这限制了生物地球化学模型捕捉碳和其他养分循环关键方面的能力。<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}}</ref>新的方法，如基因组解析宏基因组学，可以在无需实验室分离的情况下为生物体提供一套全面的草图甚至是完整的基因组，<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}}</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>这种方法或许是理解生物地球化学过程的关键。<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>
陆地地下是地球上最大的碳储库，含有14-135Pg的碳和总生物量<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}}</ref>的2-19%。<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>微生物在这种环境下驱动有机和无机化合物的转化，从而控制生物地球化学循环。目前对于地下微生物生态学的了解主要是基于16S核糖体RNA（rRNA）基因序列。最近的估计显示，公共数据库中小于8%的16S rRNA序列来自于地下生物，<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>且其中仅一小部分由基因组或分离物表示。因此，关于地下微生物代谢的可靠信息非常少。此外，关于地下生态系统中的生物体是如何在新陈代谢上互相关联的，我们知之甚少。一些基于栽培的同养群落研究<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}}</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}}</ref>和对自然群落的小规模宏基因组学分析表明，<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|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>生物体通过代谢传递相联系：一个生物的氧化还原产物转移到另一生物。然而，还没有一个复杂的环境被彻底剖析，以解决支撑它们的代谢相互作用网络。这限制了生物地球化学模型捕捉碳和其他养分循环关键方面的能力。<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}}</ref>新的方法，如基因组解析宏基因组学，可以在无需实验室分离的情况下为生物体提供一套全面的草图甚至是完整的基因组，<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}}</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}}</ref>这种方法或许是理解生物地球化学过程的关键。<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] .</ref>
==一些案例==
==一些案例==
<gallery mode=packed style=float:left; heights=155px>
<gallery mode=packed style=float:left; heights=155px>
File:Plagiomnium affine laminazellen.jpeg|叶绿体在植物细胞和其他真核生物体中进行[[光合作用]]。
File:Plagiomnium affine laminazellen.jpeg|叶绿体在植物细胞和其他真核生物体中进行[[光合作用]]。
File:Organic carbon cycle including the flow of kerogen.png|油母质循环<ref>{{cite journal |doi = 10.1038/nature14400|title = Global carbon export from the terrestrial biosphere controlled by erosion|year = 2015|last1 = Galy|first1 = Valier|last2 = Peucker-Ehrenbrink|first2 = Bernhard|last3 = Eglinton|first3 = Timothy|journal = Nature|volume = 521|issue = 7551|pages = 204–207|pmid = 25971513|bibcode = 2015Natur.521..204G|s2cid = 205243485}}</ref><ref>{{cite journal |doi = 10.1016/S0146-6380(97)00056-9|title = Comparative organic geochemistries of soils and marine sediments|year = 1997|last1 = Hedges|first1 = J.I|last2 = Oades|first2 = J.M|journal = Organic Geochemistry|volume = 27|issue = 7–8|pages = 319–361}}</ref>
File:Organic carbon cycle including the flow of kerogen.png|油母质循环<ref>{{cite journal |doi = 10.1038/nature14400|title = Global carbon export from the terrestrial biosphere controlled by erosion|year = 2015|last1 = Galy|first1 = Valier|last2 = Peucker-Ehrenbrink|first2 = Bernhard|last3 = Eglinton|first3 = Timothy|journal = Nature|volume = 521|issue = 7551|pages = 204–207|pmid = 25971513|bibcode = 2015Natur.521..204G}}</ref><ref>{{cite journal |doi = 10.1016/S0146-6380(97)00056-9|title = Comparative organic geochemistries of soils and marine sediments|year = 1997|last1 = Hedges|first1 = J.I|last2 = Oades|first2 = J.M|journal = Organic Geochemistry|volume = 27|issue = 7–8|pages = 319–361}}</ref>
File:Coal anthracite.jpg|煤炭是碳的一个储库
File:Coal anthracite.jpg|煤炭是碳的一个储库
</gallery>
</gallery>
==历史==
==历史==
[[File:1934-V I Vernadsky.jpg|thumb|upright=0.9| {{center|[[Vladimir Vernadsky]] 1934<br />father of biogeochemistry{{hsp}}<ref name=Bianchi2021>{{cite journal |doi = 10.1007/s10533-020-00708-0|title = The evolution of biogeochemistry: Revisited|year = 2021|last1 = Bianchi|first1 = Thomas S.|journal = Biogeochemistry|volume = 154|issue = 2|pages = 141–181|s2cid = 227165026}} [[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>}}]]
[[File:1934-V I Vernadsky.jpg|thumb|upright=0.9| {{center|[[Vladimir Vernadsky]] 1934<br />father of biogeochemistry{{hsp}}<ref name=Bianchi2021>{{cite journal |doi = 10.1007/s10533-020-00708-0|title = The evolution of biogeochemistry: Revisited|year = 2021|last1 = Bianchi|first1 = Thomas S.|journal = Biogeochemistry|volume = 154|issue = 2|pages = 141–181}} [[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].</ref>}}]]