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{{biogeochemical cycle sidebar}}
 
A '''biogeochemical cycle''', or more generally a '''cycle of matter''',<ref>{{Cite web |title=CK12-Foundation |url=https://flexbooks.ck12.org/cbook/ck-12-college-human-biology-flexbook-2.0/section/24.7/primary/lesson/cycles-of-matter-chumbio/ |access-date=2022-03-21 |website=flexbooks.ck12.org}}</ref> refers tois the movement and transformation of chemical elements and compounds between living organisms, the atmosphere, and the Earth's crust. Major biogeochemical cycles include the [[carbon cycle]], the [[nitrogen cycle]] and the [[water cycle]]. In each cycle, the chemical element or molecule is transformed and cycled by living organisms and through various geological forms and reservoirs, including the atmosphere, the soil and the oceans. It can be thought of as the pathway by which a [[chemical substance]] [[Wiktionary:cycle|cycles]] (is turned over or moves through) the [[Biotic components|biotic compartment]] and the [[Abiotic|abiotic compartments]] of [[Earth]]. The biotic compartment is the [[biosphere]] and the abiotic compartments are the [[atmosphere]], [[lithosphere]] and [[hydrosphere]].
 
For example, in the carbon cycle, atmospheric [[carbon dioxide]] is absorbed by plants through [[photosynthesis]], which converts it into [[organic compound]]s that are used by organisms for energy and growth. [[Carbon]] is then released back into the atmosphere through [[Photorespiration|respiration]] and [[decomposition]]. Additionally, carbon is stored in [[fossil fuel]]s and is released into the atmosphere through human activities such as burning [[fossil fuels]]. In the nitrogen cycle, atmospheric [[nitrogen gas]] is converted by plants into usable forms such as [[ammonia]] and [[nitrate]]s through the process of [[nitrogen fixation]]. These compounds can be used by other organisms, and nitrogen is returned to the atmosphere through [[denitrification]] and other processes. In the water cycle, the [[Water#Properties|universal solvent]], water, evaporates from land and oceans to formsform clouds in the atmosphere, and then [[Precipitation|precipitates]] back to different parts of the planet. Precipitation can [[seep]] into the ground and become part of groundwater systems used by plants and other organisms, or can [[Surface runoff|runoff the surface]] to form lakes and rivers. Subterranean water can then seep into the ocean along with [[river discharge]]s, rich with [[dissolved organic matter|dissolved]] and [[particulate organic matter]] and other nutrients.
 
There are biogeochemical cycles for many other elements, such as for [[oxygen cycle|oxygen]], [[hydrogen cycle|hydrogen]], [[phosphorus cycle|phosphorus]], [[calcium cycle|calcium]], [[iron cycle|iron]], [[sulfur cycle|sulfur]], [[mercury cycle|mercury]] and [[selenium cycle|selenium]]. There are also cycles for molecules, such as [[water cycle|water]] and [[silica cycle|silica]]. In addition there are macroscopic cycles such as the [[rock cycle]], and human-induced cycles for synthetic compounds such as for [[polychlorinated biphenyl]]s (PCBs). In some cycles there are geological reservoirs where a substancesubstances can remain or be [[:Wiktionary:sequestered|sequestered]] for a long periodperiods of time.
 
Biogeochemical cycles involve the interaction of biological, geological, and chemical processes. Biological processes include the influence of [[microorganism]]s, which are critical drivers of biogeochemical cycling. TheyMicroorganisms have the ability to carry out wide ranges of [[metabolic process]]es essential for the cycling of nutrients and chemicals throughout global ecosystems. Without microorganisms, many of these processes would not occur, with significant impact on the functioning of land and ocean ecosystems and the planet's biogeochemical cycles as a whole. Changes to cycles can impact human health. The cycles are interconnected and play important roles regulating climate, supporting the growth of [[plant]]s, [[phytoplankton]] and other organisms, and maintaining the health of ecosystems generally. Changes to cycles can significantly impact human health. For example, humanHuman activities such as burning fossil fuels and using large amounts of fertilizer can disrupt cycles, contributing to climate change, pollution, and other environmental problems.
 
==Overview==
[[File:Generalized biogeochemical cycle.jpg|thumb|upright=1.2| {{center|Generalized biogeochemical cycle{{hsp}}<ref name=Moses2012 />}}]]
[[File:The Nitrogen Cycle (1).png|thumb|upright=1.2| {{center|Simplified version of the nitrogen cycle}}]]
 
Energy flows directionally through ecosystems, entering as sunlight (or inorganic molecules for [[chemoautotroph]]s) and leaving as heat during the many transfers between [[trophic level]]s. However, the matter that makes up living organisms is conserved and recycled. The six most common elements associated with organic molecules — carbon, nitrogen, hydrogen, oxygen, phosphorus, and sulfur — take a variety of chemical forms and may exist for long periods in the atmosphere, on land, in water, or beneath the Earth's surface. Geologic processes, such as [[weathering]], [[erosion]], [[water drainage]], and the [[subduction]] of the [[continental plate]]s, all play a role in this recycling of materials. Because [[geology]] and [[chemistry]] have major roles in the study of this process, the recycling of inorganic matter between living organisms and their environment is called a biogeochemical cycle.<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>
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The major parts of the biosphere are connected by the flow of chemical elements and compounds in biogeochemical cycles. In many of these cycles, the [[biota (ecology)|biota]] plays an important role. Matter from the Earth's interior is released by volcanoes. The atmosphere exchanges some compounds and elements rapidly with the biota and oceans. Exchanges of materials between rocks, soils, and the oceans are generally slower by comparison.<ref name=Moses2012>Moses, M. (2012) [http://editors.eol.org/eoearth/wiki/biogeochemical_cycles Biogeochemical cycles] {{Webarchive|url=https://web.archive.org/web/20211122221017/https://editors.eol.org/eoearth/wiki/Biogeochemical_cycles |date=2021-11-22 }}. ''[[Encyclopedia of Earth]]''.</ref>
 
The flow of energy in an ecosystem is an ''open system''; the sunSun constantly gives the planet energy in the form of light while it is eventually used and lost in the form of heat throughout the [[trophic level]]s of a food web. Carbon is used to make carbohydrates, fats, and proteins, the major sources of [[food energy]]. These compounds are oxidized to release carbon dioxide, which can be captured by plants to make organic compounds. The [[chemical reaction]] is powered by the light energy of the sunsunshine.
 
Sunlight is required to combine carbon with hydrogen and oxygen into an energy source, but ecosystems in the [[deep sea]], where no sunlight can penetrate, obtain energy from sulfur. [[Hydrogen sulfide]] near [[hydrothermal vent]]s can be utilized by organisms such as the [[giant tube worm]]. In the [[sulfur cycle]], sulfur can be forever recycled as a source of energy. Energy can be released through the [[oxidation]] and [[redox|reduction]] of sulfur compounds (e.g., oxidizing elemental sulfur to [[sulfite]] and then to [[sulfate]]).
 
<gallery mode="packed" style="float:left;" heights="170px">
File:BIOGEOCHEMICAL CYCLING OF ELEMENTS.svg| {{center|Examples of major biogeochemical processes}}
File:WhalePump.jpg|The oceanic [[whale pump]] showing how whales cycle nutrients through the ocean [[water column]]
File:Global carbon cycle.webp|The implications of shifts in the [[global carbon cycle]] due to human activity are concerning scientists.<ref>Avelar, S., van der Voort, T.S. and Eglinton, T.I. (2017) "Relevance of carbon stocks of marine sediments for national greenhouse gas inventories of maritime nations". ''Carbon balance and management'', '''12'''(1): 10.{{doi|10.1186/s13021-017-0077-x}}. [[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>
</gallery>
 
Although the Earth constantly receives energy from the sunSun, its chemical composition is essentially fixed, as the additional matter is only occasionally added by meteorites. Because this chemical composition is not replenished like energy, all processes that depend on these chemicals must be recycled. These cycles include both the living biosphere and the nonliving [[lithosphere]], [[atmosphere]], and [[hydrosphere]].▼
{{clear}}
 
▲Although the Earth constantly receives energy from the sun, its chemical composition is essentially fixed, as the additional matter is only occasionally added by meteorites. Because this chemical composition is not replenished like energy, all processes that depend on these chemicals must be recycled. These cycles include both the living biosphere and the nonliving [[lithosphere]], [[atmosphere]], and [[hydrosphere]].
 
Biogeochemical cycles can be contrasted with [[geochemical cycle]]s. The latter deals only with [[Earth's crust|crustal]] and subcrustal reservoirs even though some process from both overlap.
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{{main|Hydrosphere}}
{{see also|Marine biogeochemical cycles}}
[[File:90 mile beach.jpg|thumb|upright=1.6| {{center|[[Beach]] scene simultaneously showing the atmosphere (air), hydrosphere (ocean) and lithosphere (ground)]]
[[File:Role of marine organisms in biogeochemical cycling.jpg|thumb|upright=1.6| {{center|Some roles 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|hdl = 11336/128446|hdl-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>}}]]▼
}}]]
▲[[File:Role of marine organisms in biogeochemical cycling.jpg|thumb|upright=1.6| {{center|Some roles 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>}}]]
 
The global ocean covers more than 70% of the Earth's surface and is remarkably heterogeneous. Marine productive areas, and [[coastal ecosystem]]s comprise a minor fraction of the ocean in terms of surface area, yet have an enormous impact on global biogeochemical cycles carried out by [[microbial communities]], which represent 90% of the ocean's biomass.<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|doi-access = free| bibcode=2011MarBd..41..545A }}</ref> Work in recent years has largely focused on cycling of carbon and macronutrients such as nitrogen, phosphorus, and silicate: other important elements such as sulfur or trace elements have been less studied, reflecting associated technical and logistical issues.<ref name=Murillo2019 /> Increasingly, these marine areas, and the taxa that form their ecosystems, are subject to significant anthropogenic pressure, impacting marine life and recycling of energy and nutrients.<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| s2cid=5158406 |hdl-access = free}}</ref> A key example is that of [[cultural eutrophication]], where [[agricultural runoff]] leads to nitrogen and phosphorus enrichment of coastal ecosystems, greatly increasing productivity resulting in [[algal bloom]]s, [[Ocean deoxygenation|deoxygenation]] of the water column and seabed, and increased greenhouse gas emissions,<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| s2cid=131163837 |doi-access = free}}</ref> with direct local and global impacts on [[nitrogen cycle|nitrogen]] and [[carbon cycle]]s. However, the runoff of [[organic matter]] from the mainland to [[coastal ecosystem]]s is just one of a series of pressing threats stressing microbial communities due to global change. Climate change has also resulted in changes in the [[cryosphere]], as glaciers and permafrost melt, resulting in intensified [[Ocean stratification|marine stratification]], while shifts of the [[redox|redox-state]] in different biomes are rapidly reshaping [[microbial assemblage]]s at an unprecedented rate.<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| s2cid=24002134 }}</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|doi-access = free}}</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>
 
Global change is, therefore, affecting key processes including [[Marine primary production|primary productivity]], CO<sub>2</sub> and N<sub>2</sub> fixation, organic matter respiration/[[remineralization]], and the sinking and burial deposition of fixed CO<sub>2</sub>.<ref name=Hutchins2019 /> In addition to this, oceans are experiencing an [[Ocean acidification|acidification process]], with a change of ~0.1 [[pH]] units between the pre-industrial period and today, affecting [[carbonate]]/[[bicarbonate]] [[Buffering agent|buffer]] chemistry. In turn, acidification has been reported to impact [[planktonic]] communities, principally through effects on calcifying taxa.<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|doi-access = free}}</ref> There is also evidence for shifts in the production of key intermediary volatile products, some of which have marked greenhouse effects (e.g., N<sub>2</sub>O and CH<sub>4</sub>, reviewed by Breitburg in 2018,<ref name=Breitburg2018 /> due to the increase in global temperature, ocean stratification and deoxygenation, driving as much as 25 to 50% of nitrogen loss from the ocean to the atmosphere in the so-called [[oxygen minimum zone]]s{{hsp}}<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> or [[Anoxic waters|anoxic]] marine zones,<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> driven by microbial processes. Other products, that are typically toxic for the marine [[nekton]], including reduced sulfur species such as H<sub>2</sub>S, have a negative impact for marine resources like fisheries and coastal aquaculture. While global change has accelerated, there has been a parallel increase in awareness of the complexity of marine ecosystems, and especially the fundamental role of microbes as drivers of ecosystem functioning.<ref name=Cavicchioli2019 /><ref name=Murillo2019 />
 
===Lithosphere===
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== Reservoirs ==
The chemicals are sometimes held for long periods of time in one place. This place is called a ''reservoir'', which, for example, includes such things as [[coal]] deposits that are storing [[carbon]] for a long period of time.<ref name="carbon">{{cite web|last1=Baedke|first1=Steve J.|last2=Fichter|first2=Lynn S.|title=Biogeochemical Cycles: Carbon Cycle|url=http://csmgeo.csm.jmu.edu/geollab/idls/carboncycle.htm|website=SupplimentalSupplemental Lecture Notes for Geol 398|publisher=James Madison University|access-date=20 November 2017|archive-date=1 December 2017|archive-url=https://web.archive.org/web/20171201043948/http://csmgeo.csm.jmu.edu/geollab/idls/carboncycle.htm|url-status=live}}</ref> When chemicals are held for only short periods of time, they are being held in ''exchange pools''. Examples of exchange pools include plants and animals.<ref name="carbon" />
 
Plants and animals utilize carbon to produce carbohydrates, fats, and proteins, which can then be used to build their internal structures or to obtain energy. Plants and animals temporarily use carbon in their systems and then release it back into the air or surrounding medium. Generally, reservoirs are abiotic factors whereas exchange pools are biotic factors. Carbon is held for a relatively short time in plants and animals in comparison to coal deposits. The amount of time that a chemical is held in one place is called its [[residence time]] or [[turnover time]] (also called the renewal time or exit age).<ref name="carbon" />
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==Box models==
{{see also|Climate box models}}
[[File:Simple box model.png|thumb|upright=1|right| {{center|'''Basic one-box model'''}}]]
 
Box models are widely used to model biogeochemical systems.<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&q=%22Biogeochemistry+of+Estuaries%22 ''Biogeochemistry of Estuaries''] {{Webarchive|url=https://web.archive.org/web/20210925012739/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 |date=2021-09-25 }} page 9, Oxford University Press. {{ISBN|9780195160826}}.</ref> Box models are simplified versions of complex systems, reducing them to boxes (or storage [[Thermodynamics#Instrumentation|reservoir]]s) for chemical materials, linked by material [[flux]]es (flows). Simple box models have a small number of boxes with properties, such as volume, that do not change with time. The boxes are assumed to behave as if they were mixed homogeneously.<ref name=Bianchi2007 /> These models are often used to derive analytical formulas describing the dynamics and steady-state abundance of the chemical species involved.
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The diagram at the right shows a basic one-box model. The reservoir contains the amount of material ''M'' under consideration, as defined by chemical, physical or biological properties. The source ''Q'' is the flux of material into the reservoir, and the sink ''S'' is the flux of material out of the reservoir. The budget is the check and balance of the sources and sinks affecting material turnover in a reservoir. The reservoir is in a [[steady state]] if ''Q'' = ''S'', that is, if the sources balance the sinks and there is no change over time.<ref name=Bianchi2007 />
 
The residence or turnover time is the average time material spends resident in the reservoir. If the reservoir is in a steady state, this is the same as the time it takes to fill or drain the reservoir. Thus, if τ is the turnover time, then τ = ''M''/''S''.<ref name=Bianchi2007 /> The equation describing the rate of change of content in a reservoir is
 
:: <math> \frac{dM}{dt} = Q - S = Q - \frac{M}{\tau}.</math>
 
When two or more reservoirs are connected, the material can be regarded as cycling between the reservoirs, and there can be predictable patterns to the cyclic flow.<ref name=Bianchi2007 /> More complex [[multi-compartment model|multibox models]] are usually solved using numerical techniques.
 
[[File:Simplified budget of carbon flows in the ocean.png|thumb|upright=0.9|left| {{center|'''Simple three box model'''<br. /> <small>simplifiedSimplified 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. {{ISBN|9783030108229}}. {{doi|10.1007/978-3-030-10822-9}}. [[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 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>}}]]▼
 
{{Quote box
|title = Measurement units
|quote = Global biogeochemical box models usually measure:
|quote = Global biogeochemical box models usually measure:<br />{{space|12}}— ''reservoir masses'' in petagrams (Pg)<br />{{space|12}}— ''flow fluxes'' in petagrams per year (Pg yr<sup>−1</sup>)<br />&nbsp;________________________________________________<br />&nbsp;<small>one [[petagram]] {{=}} 10<sup>15</sup> grams = one [[gigatonne]] {{=}} one [[billion]] (10<sup>9</sup>) [[tonne]]s</small>
* ''reservoir masses'' in [[petagram]]s (Pg)
* ''flow fluxes'' in petagrams per year {{nobr|(Pg yr<sup>−1</sup>)}}
|source =
|align = right
|width = 360px30em
}}
 
The diagram on the left above shows a simplified budget of ocean carbon flows. It is composed of three simple interconnected box models, one for the [[euphotic zone]], one for the [[Aphotic zone|ocean interior]] or dark ocean, and one for [[ocean sediment]]s. In the euphotic zone, net [[phytoplankton production]] is about 50 Pg C each year. About 10 Pg is exported to the ocean interior while the other 40 Pg is respired. Organic carbon degradation occurs as [[Particulate organic carbon|particles]] ([[marine snow]]) settle through the ocean interior. Only 2 Pg eventually arrives at the seafloor, while the other 8 Pg is respired in the dark ocean. In sediments, the time scale available for degradation increases by orders of magnitude with the result that 90% of the organic carbon delivered is degraded and only 0.2 Pg C yr<sup>−1</sup> is eventually buried and transferred from the biosphere to the geosphere.<ref name=Middelburg2019 />▼
{{clear left}}
 
▲[[File:Simplified diagram of the global carbon cycle.jpg|thumb|upright=2.2|right| {{center|'''More complex model with many interacting boxes'''<br. /><small>exportExport and burial rates of terrestrial organic carbon in the ocean{{hsp}}<ref name=Kandasamy2016 /></small>}}]]
▲The diagram on the left above shows a simplified budget of ocean carbon flows. It is composed of three simple interconnected box models, one for the [[euphotic zone]], one for the [[Aphotic zone|ocean interior]] or dark ocean, and one for [[ocean sediment]]s. In the euphotic zone, net [[phytoplankton production]] is about 50 Pg C each year. About 10 Pg is exported to the ocean interior while the other 40 Pg is respired. Organic carbon degradation occurs as [[Particulate organic carbon|particles]] ([[marine snow]]) settle through the ocean interior. Only 2 Pg eventually arrives at the seafloor, while the other 8 Pg is respired in the dark ocean. In sediments, the time scale available for degradation increases by orders of magnitude with the result that 90% of the organic carbon delivered is degraded and only 0.2 Pg C yr<sup>−1</sup> is eventually buried and transferred from the biosphere to the geosphere.<ref name=Middelburg2019 />
 
The diagram on the right above shows a more complex model with many interacting boxes. Reservoir masses here represents ''carbon stocks'', measured in Pg C. Carbon exchange fluxes, measured in Pg C yr<sup>−1</sup>, occur between the atmosphere and its two major sinks, the land and the ocean. The black numbers and arrows indicate the reservoir mass and exchange fluxes estimated for the year 1750, just before the [[Industrial Revolution]]. The red arrows (and associated numbers) indicate the annual flux changes due to anthropogenic activities, averaged over the 2000–2009 time period. They represent how the carbon cycle has changed since 1750. Red numbers in the reservoirs represent the cumulative changes in anthropogenic carbon since the start of the Industrial Period, 1750–2011.<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| s2cid=128553441 |doi-access = free}}</ref><ref>{{cite journal |doi = 10.13140/2.1.1081.8883|year = 2013|last1 = Chhabra|first1 = Abha|title = Carbon and Other Biogeochemical Cycles |journal=Intergovernmental Panel on Climate Change}}</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>
 
{{clear}}
 
==Fast and slow cycles==
There are fast and slow biogeochemical cycles. Fast cycle operate in the [[biosphere]] and slow cycles operate in [[rock (geology)|rocks]]. Fast or biological cycles can complete within years, moving substances from atmosphere to biosphere, then back to the atmosphere. Slow or geological cycles can take millions of years to complete, moving substances through the Earth's [[Earth's crust|crust]] between rocks, soil, ocean and atmosphere.<ref name=Libes2015>Libes, Susan M. (2015). [https://books.google.com/books?id=5tC9CgAAQBAJ&dq=%22blue+planet%22+libes&pg=PA89 Blue planet: The role of the oceans in nutrient cycling, maintain the atmosphere system, and modulating climate change] {{Webarchive|url=https://web.archive.org/web/20210120070507/https://books.google.com/books?hl=en&lr=&id=5tC9CgAAQBAJ&oi=fnd&pg=PA89&dq=%22blue+planet%22+libes&ots=oesDSXq1NZ&sig=B7HrLG0Y6iE9p_AqfDfSVktQGN4#v=onepage&q=%22blue%20planet%22%20libes&f=false |date=2021-01-20 }} In: ''Routledge Handbook of Ocean Resources and Management'', Routledge, pages 89–107. {{isbn|9781136294822}}.</ref>▼
 
[[File:Carbon cycle.jpg|thumb|upright=1.8|left5| The fast cycle operates through the biosphere, including exchanges between land, atmosphere, and oceans. The yellow numbers are natural fluxes of carbon in billions of tons (gigatons) per year. Red are human contributions and white are stored carbon.<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>]]▼
As an example, the fast carbon cycle is illustrated in the diagram below on the left. This cycle involves relatively short-term [[biogeochemical]] processes between the environment and living organisms in the biosphere. It includes movements of carbon between the atmosphere and terrestrial and marine ecosystems, as well as soils and [[seafloor sediments]]. The fast cycle includes annual cycles involving photosynthesis and decadal cycles involving vegetative growth and decomposition. The reactions of the fast carbon cycle to human activities will determine many of the more immediate impacts of climate change.<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>▼
 
[[File:Rock cycle nps.PNG|thumb|upright=21.255|right| {{center|The slow cycle operates through rocks, including volcanic and tectonic activity}}]]▼
▲[[File:Carbon cycle.jpg|thumb|upright=1.8|left| The fast cycle operates through the biosphere, including exchanges between land, atmosphere, and oceans. The yellow numbers are natural fluxes of carbon in billions of tons (gigatons) per year. Red are human contributions and white are stored carbon.<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>]]
 
▲There are fast and slow biogeochemical cycles. Fast cycle operate in the [[biosphere]] and slow cycles operate in [[rock (geology)|rocks]]. Fast or biological cycles can complete within years, moving substances from atmosphere to biosphere, then back to the atmosphere. Slow or geological cycles can take millions of years to complete, moving substances through the Earth's [[Earth's crust|crust]] between rocks, soil, ocean and atmosphere.<ref name=Libes2015>Libes, Susan M. (2015). [https://books.google.com/books?id=5tC9CgAAQBAJ&dq=%22blue+planet%22+libes&pg=PA89 Blue planet: The role of the oceans in nutrient cycling, maintain the atmosphere system, and modulating climate change] {{Webarchive|url=https://web.archive.org/web/20210120070507/https://books.google.com/books?hl=en&lr=&id=5tC9CgAAQBAJ&oi=fnd&pg=PA89&dq=%22blue+planet%22+libes&ots=oesDSXq1NZ&sig=B7HrLG0Y6iE9p_AqfDfSVktQGN4#v=onepage&q=%22blue%20planet%22%20libes&f=false |date=2021-01-20 }} In: ''Routledge Handbook of Ocean Resources and Management'', Routledge, pages 89–107. {{isbn|9781136294822}}.</ref>
▲[[File:Rock cycle nps.PNG|thumb|upright=2.25|right| {{center|The slow cycle operates through rocks, including volcanic and tectonic activity}}]]
 
▲As an example, the fast carbon cycle is illustrated in the diagram below on the left. This cycle involves relatively short-term [[biogeochemical]] processes between the environment and living organisms in the biosphere. It includes movements of carbon between the atmosphere and terrestrial and marine ecosystems, as well as soils and [[seafloor sediments]]. The fast cycle includes annual cycles involving photosynthesis and decadal cycles involving vegetative growth and decomposition. The reactions of the fast carbon cycle to human activities will determine many of the more immediate impacts of climate change.<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>
{{clear}}
 
The slow cycle is illustrated in the diagram above on the right. It involves medium to long-term [[geochemical]] processes belonging to the [[rock cycle]]. The exchange between the ocean and atmosphere can take centuries, and the [[weathering]] of rocks can take millions of years. Carbon in the ocean precipitates to the ocean floor where it can form [[sedimentary rock]] and be [[subducted]] into the [[earthEarth's mantle]]. [[Mountain building]] processes result in the return of this geologic carbon to the Earth's surface. There the rocks are weathered and carbon is returned to the atmosphere by [[degassing]] and to the ocean by rivers. Other geologic carbon returns to the ocean through the [[Hydrothermal circulation|hydrothermal emission]] of calcium ions. In a given year between 10 and 100 million tonnes of carbon moves around this slow cycle. This includes volcanoes returning geologic carbon directly to the atmosphere in the form of carbon dioxide. However, this is less than one percent of the carbon dioxide put into the atmosphere by burning fossil fuels.<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>
 
==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{{hsp}}<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{{hsp}}<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]]{{hsp}}<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{{hsp}}<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{{hsp}}<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>
 
==Some examples==
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File:Phosphorus cycle.png|alt=Diagram of the phosphorus cycle|[[Phosphorus cycle]]
File:Sulfur Cycle (Ciclo do Enxofre).png|alt=Diagram of the sulfur cycle|[[Sulfur cycle]]
File:RockcycleCycle of rocks 1.jpgpng|alt=Diagram of the rock cycle|[[Rock cycle]]
File:Water cycle.png|alt=Diagram of the water cycle|[[Water cycle]]
</gallery>
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<gallery mode="packed" style="float:left;" heights="155px">
File:Plagiomnium affine laminazellen.jpeg|[[Chloroplasts]] conduct [[photosynthesis]] in [[plant cell]]s and other [[eukaryote|eukaryotic]] organisms.
File:Organic carbon cycle including the flow of kerogen.png|[[Kerogen]] cycle{{hsp}}<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| bibcode=1997OrGeo..27..319H }}</ref>
File:Coal anthracite.jpg|Coal is a reservoir of carbon
</gallery>
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Biogeochemical cycles always involve active equilibrium states: a balance in the cycling of the element between compartments. However, overall balance may involve compartments distributed on a global scale.
 
As biogeochemical cycles describe the movements of substances on the entire globe, the study of these is inherently multidisciplinary. The carbon cycle may be related to research in [[ecology]] and [[atmospheric sciences]].<ref>{{cite book|last1=McGuire|firstfirst1=1A. D.|last2=Lukina|first2=N. V.|chapter=Biogeochemical cycles|editor-last1=Groisman|editor-first1=P.|editor-last2=Bartalev|editor-first2=S. A.|editor-last3=NEESPI Science Plan Development Team|title=Northern Eurasia earth science partnership initiative (NEESPI), Science plan overview|date=2007|pages=215&ndash;234|series=Global Planetary Change|volume=56|chapter-url=http://neespi.org/science/NEESPI_SP_chapters/SP_Chapter_3.2.pdf|access-date=20 November 2017|archive-date=5 March 2016|archive-url=https://web.archive.org/web/20160305025005/http://neespi.org/science/NEESPI_SP_chapters/SP_Chapter_3.2.pdf|url-status=live}}</ref> Biochemical dynamics would also be related to the fields of [[geology]] and [[pedology]].<ref>{{cite web|title=Distributed Active Archive Center for Biogeochemical Dynamics|url=http://daac.ornl.gov/|website=daac.ornl.gov|publisher=Oak Ridge National Laboratory|access-date=20 November 2017|archive-date=11 February 2011|archive-url=https://web.archive.org/web/20110211040758/http://daac.ornl.gov/|url-status=live}}</ref>
 
{{clear}}
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