View source for Biology:Deep biosphere

{{short description|Life in the deep subsurface of the Earth}}
The '''deep biosphere''' is the part of the [[Biology:Biosphere|biosphere]] that resides below the first few meters of the surface. It extends down at least 5&nbsp;kilometers below the continental surface and 10.5&nbsp;kilometers below the sea surface, at temperatures that may reach beyond {{cvt|120|C|F}}<ref name=":1">{{Cite journal|last1=Heuer|first1=Verena B.|last2=Inagaki|first2=Fumio|last3=Morono|first3=Yuki|last4=Kubo|first4=Yusuke|last5=Spivack|first5=Arthur J.|last6=Viehweger|first6=Bernhard|last7=Treude|first7=Tina|last8=Beulig|first8=Felix|last9=Schubotz|first9=Florence|last10=Tonai|first10=Satoshi|last11=Bowden|first11=Stephen A.|date=2020-12-04|title=Temperature limits to deep subseafloor life in the Nankai Trough subduction zone|url=https://www.science.org/doi/10.1126/science.abd7934|journal=Science|language=en|volume=370|issue=6521|pages=1230–1234|doi=10.1126/science.abd7934|issn=0036-8075|pmid=33273103|bibcode=2020Sci...370.1230H |hdl=2164/15700|s2cid=227257205 |hdl-access=free}}</ref> which is comparable to [[Biology:Strain 121|the maximum temperature where a metabolically active organism has been found]]. It includes all three domains of life and the genetic diversity rivals that on the surface.

The first indications of deep life came from studies of oil fields in the 1920s, but it was not certain that the organisms were indigenous until methods were developed in the 1980s to prevent contamination from the surface. Samples are now collected in deep mines and [[Earth:Scientific drilling|scientific drilling]] programs in the ocean and on land. Deep observatories have been established for more extended studies.

Near the surface, living organisms consume organic matter and breathe oxygen. Lower down, these are not available, so they make use of "edibles" (electron donors) such as [[Chemistry:Hydrogen|hydrogen]] (released from rocks by various chemical processes), [[Chemistry:Methane|methane]] (CH<sub>4</sub>), reduced [[Chemistry:Sulfur|sulfur]] compounds, and [[Chemistry:Ammonium|ammonium]] (NH<sub>4</sub>). They "breathe" electron acceptors such as [[Chemistry:Nitrate|nitrate]]s and [[Chemistry:Nitrite|nitrite]]s, [[Chemistry:Manganese|manganese]] and [[Chemistry:Iron oxide|iron oxide]]s, oxidized sulfur compounds and [[Chemistry:Carbon dioxide|carbon dioxide]] (CO<sub>2</sub>). There is very little energy at greater depths, so metabolisms are up to a million times slower than at the surface. Cells may live for thousands of years before dividing and there is no known limit to their age.

The subsurface accounts for about 90% of the [[Biology:Biomass|biomass]] across two domains of life, [[Biology:Archaea|Archaea]] and [[Biology:Bacteria|Bacteria]], and 15% of the total for the biosphere. Eukarya are also found, including some multicellular life [[Biology:Fungus|fungi]], and animals ([[Biology:Nematode|nematode]]s, [[Biology:Flatworm|flatworm]]s, [[Biology:Rotifer|rotifer]]s, [[Biology:Annelid|annelid]]s, and [[Biology:Arthropod|arthropod]]s). Viruses are also present and infect the microbes.

== Definition ==
The deep biosphere is an ecosystem of organisms and their living space in the deep subsurface.<ref name=Hoehler>{{Cite journal|last1=Hoehler|first1=Tori M.|last2=Jorgensen|first2=Bo Barker|date=16 January 2013|title=Microbial life under extreme energy limitation|journal=Nature Reviews Microbiology|volume=11|issue=2|pages=83–94|doi=10.1038/nrmicro2939|pmid=23321532|bibcode=2013NatMb..11...83C |hdl=2060/20150018056|s2cid=461070|hdl-access=free}}</ref> For the seafloor, an operational definition of ''deep subsurface'' is the region that is not bioturbated by animals; this is generally about a meter or more below the surface.<ref name=MarineEncyclopedia>{{cite encyclopedia |first1=A. |last1=Schippers |title=Deep biosphere|editor-last1=Harff |editor-first1=J. |editor-last2=Meschede |editor-first2=M. |editor-last3=Petersen |editor-first3=S. |editor-last4=Thiede |editor-first4=J. |encyclopedia=Encyclopedia of Marine Geosciences |date=2015 |publisher=Springer |location=Dordrecht |isbn=978-94-007-6644-0}}</ref> On continents, it is below a few meters, not including soils.<ref name=Biomass>{{cite journal |last1=Bar-On |first1=Yinon M. |last2=Phillips |first2=Rob |last3=Milo |first3=Ron |title=The biomass distribution on Earth |journal=Proceedings of the National Academy of Sciences |date=19 June 2018 |volume=115 |issue=25 |pages=6506–6511 |doi=10.1073/pnas.1711842115|pmid=29784790 |pmc=6016768 |bibcode=2018PNAS..115.6506B |doi-access=free }}</ref> The organisms in this zone are sometimes referred to as ''intraterrestrials''.<ref name=NorthPond/><ref name=Judson>{{cite news |last1=Judson |first1=Olivia |title=Meet the Intraterrestrials |url=https://opinionator.blogs.nytimes.com/2008/06/10/meet-the-intraterrestrials/ |access-date=18 January 2019 |work=Opinionator |date=10 June 2008}}</ref>

== History ==
At the [[Organization:University of Chicago|University of Chicago]] in the 1920s, geologist Edson Bastin enlisted the help of microbiologist Frank Greer in an effort to explain why water extracted from oil fields contained [[Chemistry:Hydrogen sulfide|hydrogen sulfide]] and [[Chemistry:Bicarbonate|bicarbonate]]s. These chemicals are normally created by bacteria, but the water came from a depth where the heat and pressure were considered too great to support life. They were able to culture anaerobic [[Earth:Sulfate-reducing microorganisms|sulfate-reducing bacteria]] from the water, demonstrating that the chemicals had a bacterial origin.<ref>{{cite book |last1=Alley |first1=William M. |title=Regional Ground-Water Quality |date=1993 |publisher=John Wiley & Sons |isbn=9780471284536 |page=182}}</ref><ref name=Ward>{{cite book |last1=Ward |first1=Peter D. |last2=Brownlee |first2=Donald |title=Rare earth : why complex life is uncommon in the universe |date=2006 |publisher=Copernicus |isbn=9780387218489 |pages=7–12 |edition=Pbk.}}</ref><ref name=OnstottCh1>{{harvnb|Onstott|2016|loc=Chapter 1}}</ref>

Also in the 1920s, Charles Lipman, a microbiologist at the [[Organization:University of California, Berkeley|University of California, Berkeley]], noticed that bacteria that had been sealed in bottles for 40 years could be reanimated – a phenomenon now known as anhydrobiosis. He wondered whether the same was true of bacteria in coal seams. He sterilized samples of coal, wetted them, crushed them and then succeeded in culturing bacteria from the coal dust. One sterilization procedure, baking the coal at {{cvt|160|C|F}} for up to 50 hours, actually encouraged their growth. He published the results in 1931.<ref name=NorthPond>{{cite news |last1=Edwards |first1=Katrina |title=North Pond: Searching for Intraterrestrial Life |url=https://blogs.scientificamerican.com/expeditions/north-pond-searching-for-intraterrestrial-life/ |access-date=18 January 2019 |work=Scientific American Blog Network |date=2 September 2011 |language=en}}</ref><ref name=OnstottCh1/>

The first studies of subsurface life were conducted by Claude E. Zobell, the "father of marine microbiology",<ref name=LowLife/> in the late 1930s to the 1950s. Although the coring depth was limited, microbes were found wherever the sediments were sampled.<ref name=DeepDark>{{cite journal |last1=Edwards |first1=Katrina J. |last2=Becker |first2=Keir |last3=Colwell |first3=Frederick |title=The Deep, Dark Energy Biosphere: Intraterrestrial Life on Earth |journal=Annual Review of Earth and Planetary Sciences |date=30 May 2012 |volume=40 |issue=1 |pages=551–568 |doi=10.1146/annurev-earth-042711-105500|bibcode=2012AREPS..40..551E }}
</ref><ref name=Frederickson>{{cite journal |last1=Fredrickson |first1=James K. |last2=Onstott |first2=Tullis C. |title=Microbes Deep inside the Earth |journal=Scientific American |date=1996 |volume=275 |issue=4 |pages=68–73 |jstor=24993405|doi=10.1038/scientificamerican1096-68 |pmid=8797299 |bibcode=1996SciAm.275d..68F }}</ref> With increasing depth, [[Biology:Aerobic organism|aerobes]] gave way to [[Biology:Anaerobic organism|anaerobes]].<ref name=Colwell2013>{{cite journal |last1=Colwell |first1=F. S. |last2=D'Hondt |first2=S. |title=Nature and Extent of the Deep Biosphere |journal=Reviews in Mineralogy and Geochemistry |date=13 February 2013 |volume=75 |issue=1 |pages=547–574 |doi=10.2138/rmg.2013.75.17|bibcode=2013RvMG...75..547C }}</ref>

[[File:Alvin (DSV-2) sunk 1968.jpg|thumb|Photograph of the sunken ''Alvin'' taken in 1969]]
Most biologists dismissed the subsurface microbes as contamination, especially after the submersible ''Alvin'' sank in 1968 and the scientists escaped, leaving their lunches behind. When ''Alvin'' was recovered, the lunches showed no sign of microbial decay.<ref name=LowLife>{{cite journal|last1=Leigh Mascarelli|first1=Amanda|title=Low life|journal=Nature|date=11 June 2009|volume=459|issue=7248|pages=770–773|doi=10.1038/459770a|pmid=19516316|doi-access=free}}</ref> This reinforced a view of the deep sea (and by extension the subsurface) as a lifeless desert. The study of the deep biosphere, like many bacteria, was dormant for decades; an exception is a group of Soviet microbiologists who began to refer to themselves as [[Biology:Geomicrobiology|geomicrobiologists]].<ref name=OnstottCh1/>

Interest in subsurface life was renewed when the United States Department of Energy was looking for a safe way of burying nuclear waste, and Frank J. Wobber realized that microbes below the surface could either help by degrading the buried waste or hinder by breaching the sealed containers. He formed the Subsurface Science Program to study deep life. To address the problem of contamination, special equipment was designed to minimize contact between a core sample and the [[Engineering:Drilling fluid|drilling fluid]] that lubricates the [[Engineering:Drill bit|drill bit]]. In addition, tracers were added to the fluid to indicate whether it penetrated the core. In 1987, several [[Engineering:Borehole|borehole]]s were drilled near the Savannah River Site, and microorganisms were found to be plentiful and diverse at least 500 metres below the surface.<ref name=Frederickson/>

From 1983 until now, microbiologists analyze cell abundances in drill cores from the Ocean Drilling Program (now the [[Organization:International Ocean Discovery Program|International Ocean Discovery Program]]).<ref name="DeepDark" /> A group led by John Parkes of the [[Organization:University of Bristol|University of Bristol]] reported concentrations of 10<sup>4</sup> to 10<sup>8</sup> cells per gram of sediment down to depths of 500 metres (agricultural soils contain about 10<sup>9</sup> cells per gram).<ref name="OnstottCh6">{{harvnb|Onstott|2016|loc=Chapter 6}}</ref> This was initially met with skepticism and it took them four years to publish their results.<ref name="LowLife" /> In 1998, William Whitman and colleagues published a summary of twelve years of data in the ''Proceedings of the National Academy of Sciences''.<ref name=OnstottCh6/> They estimated that up to 95% of all [[Biology:Prokaryote|prokaryote]]s (archaea and bacteria) live in the deep subsurface, with 55% in the marine subsurface and 39% in the terrestrial subsurface.<ref name=DeepDark/> In 2002, Ocean Drilling Program Leg 201 was the first to be motivated by a search for deep life. Most of the previous exploration was on continental margins, so the goal was to drill in the open ocean for comparison.<ref>{{cite web |title=Leg 201: Controls on microbial communities in deeply buried sediments, eastern Equatorial Pacific and Peru Margin sites 1225–1231 |url=http://www-odp.tamu.edu/publications/leg_ndx/201ndex.htm |website=Ocean Drilling Program |access-date=20 July 2019}}</ref><ref name=NorthPond/> In 2016, International Ocean Discovery Program Leg 370 drilled into the marine sediment of the [[Earth:Nankai Trough|Nankai]] Accretionary Prism and observed 10<sup>2</sup> vegetative cells at 118&nbsp;°C.<ref name=":1" /><ref>{{Cite web|title=T-Limit of the Deep Biosphere off Muroto|url=https://www.jamstec.go.jp/chikyu/e/exp370/|access-date=2021-07-06|website=www.jamstec.go.jp}}</ref>

Understanding of microbial life at depth was extended beyond the realm of oceanography to earth sciences (and even astrobiology) in 1992 when [[Biography:Thomas Gold|Thomas Gold]] published a paper in ''The Proceedings of the National Academy of Sciences'' that was titled "The Deep, Hot Biosphere",<ref>{{cite journal |last1=Gold |first1=Thomas |title=The Deep, Hot Biosphere |journal=Proc Natl Acad Sci |date=1992 |volume=89 |issue=13 |pages=6045–6049|doi=10.1073/pnas.89.13.6045 |pmid=1631089 |pmc=49434 |bibcode=1992PNAS...89.6045G |doi-access=free }}</ref> followed seven years later by his book, ''The Deep Hot Biosphere''.<ref>{{cite book |last1=Gold |first1=Thomas |title=The Deep Hot Biosphere |date=1999 |publisher=Springer-Verlag}}</ref> A 1993 article by journalist  William Broad, published in ''{{wipe|The New York Times}}'' and titled "Strange New Microbes Hint at a Vast Subterranean World,"<ref>{{cite news |last1=Broad |first1=William |title=Strange New Microbes Hint at a Vast Subterranean World |url=https://www.nytimes.com/1993/12/28/science/strange-new-microbes-hint-at-a-vast-subterranean-world.html |access-date=13 February 2021 |work=New York Times |date=28 December 1993}}</ref> carried Gold's thesis to public attention. The article began, "New forms of microbial life are being discovered in such abundance deep inside the Earth that some scientists are beginning to suspect that the planet has a hidden biosphere extending miles down whose total mass may rival or exceed that of all surface life. If a deep biosphere does exist, scientists say, its discovery will rewrite textbooks while shedding new light on the mystery of life's origins. Even skeptics say the thesis is intriguing enough to warrant new studies of the subterranean realm."

The 1993 article also features how Gold's thesis expands possibilities for [[Astronomy:Astrobiology|astrobiology]] research: "Dr. Thomas Gold, an astrophysicist at Cornell University known for bold theorizing, has speculated that subterranean life may dot the cosmos, secluded beneath the surfaces of planets and moons and energized by geological processes, with no need for the warming radiation of nearby stars. He wrote in ''The Proceedings of the National Academy of Sciences'' last year that the solar system might harbor at least 10 deep biospheres. 'Such life may be widely disseminated in the universe,' he said, 'since planetary type bodies with similar subsurface conditions may be common as solitary objects in space, as well as in other solar-type systems.'"

[[Biography:Freeman Dyson|Freeman Dyson]] wrote the foreword to Gold's 1999 book, where he concluded, "Gold's theories are always original, always important, usually controversial — and usually right. It is my belief, based on fifty years of observation of Gold as a friend and colleague, that the deep hot biosphere is all of the above: original, important, controversial — and right."<ref>{{cite book |last1=Gold |first1=Thomas |title=The Deep Hot Biosphere |date=1999 |publisher=Springer-Verlag |page=xi}}</ref>

Dyson also delivered a eulogy at Gold's memorial service in 2004, a segment of which pertaining to the deep hot biosphere theory is posted on youtube.<ref>{{cite web |title=Video: Freeman Dyson on Tommy Gold, hearing mechanism, and abiogenic oil |url=https://www.youtube.com/watch?v=lr42BP3wvOw |website=youtube |access-date=13 February 2021}}</ref>

Following Gold's death, scientific discoveries amplified and also shifted understanding of the deep biosphere. A term Gold coined in his 1999 book, however, carries forward<ref>{{cite web |last1=Wolfe |first1=David |title=Tales from the Underground |website=Amazon |url=https://www.amazon.com/product-reviews/0738201286/ref=dbs_a_def_rwt_hsch_vwpw_thcv_p1_i0}}</ref> and is a reminder of the worldview shift he advocated.<ref>{{cite journal |last1=Colman |first1=Daniel |title=The deep, hot biosphere: Twenty-five years of retrospection |journal=PNAS |date=3 July 2017 |volume=114 |issue=27 |pages=6895–6903 |doi=10.1073/pnas.1701266114 |pmid=28674200 |pmc=5502609 |bibcode=2017PNAS..114.6895C |doi-access=free }}</ref> The term is "surface chauvinism". Gold wrote, "In retrospect, it is not hard to understand why the scientific community has typically sought only ''surface'' life in the heavens. Scientists have been hindered by a sort of 'surface chauvinism.'".<ref>{{cite book |last1=Gold |first1=Thomas |title=The Deep Hot Biosphere |date=1999 |publisher=Springer-Verlag |location=New York |isbn=0387985468 |pages=8 & 81 |edition=first}}</ref>

== Scientific methods ==

The present understanding of subsurface biology was made possible by numerous advances in technology for sample collection, field analysis, molecular science, cultivation, imaging and computation.<ref name=Colwell2013/>

=== Sample collection ===
[[File:Chikyu mission.jpg|thumb|upright=1.6|Schematic of an expedition aboard the Japanese drilling ship [[Earth:Chikyū|D/V Chikyū]].<ref name=DCOdecadal/>]]
[[File:Sampling fluid from deep mine.jpg|thumb|Researcher sampling fluid from a deep mine.<ref name=DCOdecadal/>]]
The ocean floor is sampled by drilling boreholes and collecting cores. The methods must be adapted to different [[Earth:Lithology|types of rock]], and the cost of drilling limits the number of holes that can be drilled.<ref>{{cite book |last1=Kieft |first1=T. |last2=Phelps |first2=T. |last3=Fredrickson |first3=J. |chapter=66. Drilling, Coring, and Sampling Subsurface Environments |doi=10.1128/9781555815882.ch66
|editor-last1=Hurst |editor-first1=C. |editor-last2=Crawford |editor-first2=R. |editor-last3=Garland |editor-first3=J. |editor-last4=Lipson |editor-first4=D. |editor-last5=Mills |editor-first5=A. |editor-last6=Stetzenbach |editor-first6=L. |title=Manual of Environmental Microbiology |date=2007 |publisher=ASM Press |location=Washington, DC |edition=3rd |isbn=9781555815882}}</ref> Microbiologists have made use of scientific drilling programs: the Ocean Drilling Program (ODP), which used the JOIDES ''Resolution'' drilling platform, and the Integrated Ocean Drilling Program (IODP), which used the Japanese ship ''[[Earth:Chikyū|Chikyū]]''.<ref name=Colwell2013/>

Deep underground mines, for example South African gold mines and the Pyhäsalmi copper and zinc mine in {{wipe|Finland}}, have provided opportunities to sample the deep biosphere.<ref>{{Cite journal|last1=Gihring|first1=T. M.|last2=Moser|first2=D. P.|last3=Lin|first3=L.-H.|last4=Davidson|first4=M.|last5=Onstott|first5=T. C.|last6=Morgan|first6=L.|last7=Milleson|first7=M.|last8=Kieft|first8=T. L.|last9=Trimarco|first9=E.|date=1 September 2006|title=The Distribution of Microbial Taxa in the Subsurface Water of the Kalahari Shield, South Africa|journal=Geomicrobiology Journal|volume=23|issue=6|pages=415–430|doi=10.1080/01490450600875696|bibcode=2006GmbJ...23..415G |s2cid=84707436|issn=0149-0451}}</ref><ref>{{Cite journal|last1=Itävaara|first1=Merja|last2=Ahonen|first2=Lasse|last3=Numminen|first3=Mikko|last4=Sohlberg|first4=Elina|last5=Kietäväinen|first5=Riikka|last6=Miettinen|first6=Hanna|date=2015|title=Microbiome composition and geochemical characteristics of deep subsurface high-pressure environment, Pyhäsalmi mine Finland|journal=Frontiers in Microbiology|language=en|volume=6|page=1203|doi=10.3389/fmicb.2015.01203|pmid=26579109|pmc=4626562|issn=1664-302X|doi-access=free}}</ref> The deep subsurface has also been sampled at chosen or proposed nuclear waste repository sites (e.g. Yucca Mountain and the [[Physics:Waste Isolation Pilot Plant|Waste Isolation Pilot Plant]] in the United States, Äspö and surrounding areas in Sweden, Onkalo and surrounding areas in Finland, [[Physics:Mont Terri|Mont Terri]] in Switzerland).<ref name=Colwell2013/> Scientific drilling of continental deep subsurface has been promoted by the [[Organization:International Continental Scientific Drilling Program|International Continental Scientific Drilling Program]] (ICDP).<ref>{{cite journal |last1=Mangelsdorf |first1=Kai |last2=Kallmeyer |first2=Jens |title=Integration of Deep Biosphere Research into the International Continental Scientific Drilling Program |journal=Scientific Drilling |issue=10, September 2010 |date=10 September 2010 |volume=10 |pages=46–55 |doi=10.2204/iodp.sd.10.0.2010|doi-access=free }}</ref>

To allow continuous underground sampling, various kinds of observatories have been developed. On the ocean floor, the Circulation Obviation Retrofit Kit (CORK) seals a borehole to cut off the influx of seawater.<ref>{{cite web |title=CORKs |url=https://www.oceannetworks.ca/corks |website=Ocean Networks Canada |date=15 October 2012 |access-date=18 July 2019 |language=en}}</ref> An advanced version of CORK is able to seal off multiple sections of a drill hole using ''packers'', rubber tubes that inflate to seal the space between the drill string and the wall of the borehole.<ref>{{cite journal |last1=Becker |first1=Keir |last2=Davis |first2=Earl E. |title=A review of CORK designs and operations during the Ocean Drilling Program |journal=Proceedings of the Integrated Ocean Drilling Program |date=31 October 2005 |volume=301 |doi=10.2204/iodp.proc.301.104.2005 |series=Proceedings of the IODP |doi-access=free }}</ref><ref>{{cite web |title=Packers and Flowmeters Tool Sheet |url=http://www-odp.tamu.edu/publications/tnotes/tn31/packer/packer.htm |website=Overview of Ocean Drilling Program Engineering Tools and Hardware |publisher=Ocean Drilling Program |access-date=23 August 2019}}</ref> In sediments, the Simple Cabled Instrument for Measuring Parameters In-Situ (SCIMPI) is designed to remain and take measurements after a borehole has collapsed.<ref>{{cite journal |last1=Kulin |first1=Ian |last2=Riedel |first2=Michael |last3=Klaus |first3=Adam |title=Simple cabled instrument for measuring Parameters In situ (SCIMPI) and Hole 858G CORK replacement |journal=IODP Scientific Prospectus |date=2013 |volume=341S |doi=10.2204/iodp.sp.341S.2013|doi-access=free }}</ref>

Packers are also used in the continental subsurface,<ref>{{Cite journal|last1=Purkamo|first1=Lotta|last2=Bomberg|first2=Malin|last3=Nyyssönen|first3=Mari|last4=Kukkonen|first4=Ilmo|last5=Ahonen|first5=Lasse|last6=Kietäväinen|first6=Riikka|last7=Itävaara|first7=Merja|date=2013|title=Dissecting the deep biosphere: retrieving authentic microbial communities from packer-isolated deep crystalline bedrock fracture zones|journal=FEMS Microbiology Ecology|language=en|volume=85|issue=2|pages=324–337|doi=10.1111/1574-6941.12126|pmid=23560597|issn=1574-6941|doi-access=free}}</ref> along with devices such as the flow-through {{Lang|la|in situ}} reactor (FTISR). Various methods are used to extract fluids from these sites, including passive gas samplers, U-tube systems and [[Physics:Osmosis|osmotic]] gas samplers.<ref name=Colwell2013/> In narrow (less than 50&nbsp;mm) holes, [[Chemistry:Polyamide|polyamide]] tubes with a back-pressure valve can be lowered to sample an entire column of fluid.<ref>{{cite journal |last1=Nurmi |first1=Pekka A. |last2=Kukkonen |first2=Ilmo T. |title=A new technique for sampling water and gas from deep drill holes |journal=Canadian Journal of Earth Sciences |date=1986 |volume=23 |issue=9 |pages=1540–1454|doi=10.1139/e86-138 |bibcode=1986CaJES..23.1450N }}</ref><ref>{{Cite journal |last1=Kietäväinen |first1=Riikka |last2=Ahonen |first2=Lasse |last3=Kukkonen|first3=Ilmo T.|last4=Hendriksson|first4=Nina|last5=Nyyssönen|first5=Mari|last6=Itävaara|first6=Merja|date=1 May 2013|title=Characterisation and isotopic evolution of saline waters of the Outokumpu Deep Drill Hole, Finland – Implications for water origin and deep terrestrial biosphere |journal=Applied Geochemistry |series=Special Issue Devoted to the 9th International Symposium on Applied Isotope Geochemistry (AIG9), Tarragona, Spain, September 2011 |volume=32 |pages=37–51|doi=10.1016/j.apgeochem.2012.10.013|bibcode=2013ApGC...32...37K |issn=0883-2927}}</ref>

=== Field analysis and manipulation ===
Some methods analyze microbes {{Lang|la|in situ}} rather than extract them. In [[Biology:Biogeophysics|biogeophysics]], the effects of microbes on properties of geological materials are remotely probed using electrical signals. Microbes can be tagged using a stable isotope such as [[Physics:Carbon-13|carbon-13]] and then re-injected in the ground to see where they go.<ref name=Colwell2013/> A "push-pull" method involves injection of a fluid into an aquifer and extraction of a mixture of injected fluid with the ground water; the latter can then be analyzed to determine what chemical reactions occurred.<ref>{{cite journal |last1=Haggerty |first1=R. |last2=Schroth |first2=M.H. |last3=Istok |first3=J.D. |title=Simplified Method of "Push-Pull" Test Data Analysis for Determining In Situ Reaction Rate Coefficients |journal=Ground Water |date=March 1998 |volume=36 |issue=2 |pages=314–324 |doi=10.1111/j.1745-6584.1998.tb01097.x|bibcode=1998GrWat..36..314H |s2cid=140663085 }}</ref>

=== Molecular methods and cultivation ===
Methods from modern molecular biology allow the extraction of nucleic acids, lipids and proteins from cells, [[Biology:DNA sequencing|DNA sequencing]], and the physical and chemical analysis of molecules using [[Physics:Mass spectrometry|mass spectrometry]] and [[Biology:Flow cytometry|flow cytometry]]. A lot can be learned about the microbial communities using these methods even when the individuals cannot be cultivated.<ref name=Colwell2013/> For example, at the Richmond Mine in California, scientists used [[Biology:Shotgun sequencing|shotgun sequencing]] to identify four new species of bacteria, three new species of archaea (known as the [[Biology:Archaeal Richmond Mine acidophilic nanoorganisms|Archaeal Richmond Mine acidophilic nanoorganisms]]), and 572 proteins unique to the bacteria.<ref>{{Cite press release |title=Proteomics brings researchers closer to understanding microbes that produce acid mine drainage |date=5 May 2005 |publisher=University of California Berkeley |url=https://www.berkeley.edu/news/media/releases/2005/05/05_banfield.shtml |last1=Sanders |first1=Robert |access-date=19 July 2019}}</ref><ref name="Orell">{{cite journal |last1=Orell |first1=Alvaro |last2=Fröls |first2=Sabrina |last3=Albers |first3=Sonja-Verena |date=8 September 2013 |title=Archaeal Biofilms: The Great Unexplored |journal=Annual Review of Microbiology |volume=67 |issue=1 |pages=337–354 |doi=10.1146/annurev-micro-092412-155616 |pmid=23808336}}</ref>

=== Geochemical methods ===
Deep microorganisms change the chemistry of their surroundings. They consume nutrients and product wastes from [[Biology:Metabolism|metabolism]]. Therefore we can estimate the activities of the deep microorganisms by measuring the chemical compositions in the subseafloor samples. Complementary techniques include measuring the [[Physics:Isotope|isotope]] compositions of the chemicals or the related [[Earth:Mineral|mineral]]s.<ref name=":0">{{Cite journal|title=Microbial Life Deep Under the Seafloor—A Story of Not Giving Up|journal=Frontiers for Young Minds|year=2020|language=en|doi=10.3389/frym.2020.00070|last1=Tsang|first1=Man-Yin|last2=Inagaki|first2=Fumio|volume=8|s2cid=218981468|doi-access=free}}</ref><ref>{{Cite journal |last1=Bowles |first1=Marshall W. |last2=Mogollón |first2=José M. |last3=Kasten |first3=Sabine |last4=Zabel |first4=Matthias |last5=Hinrichs |first5=Kai-Uwe |date=2014-05-23 |title=Global rates of marine sulfate reduction and implications for sub–sea-floor metabolic activities |url=http://dx.doi.org/10.1126/science.1249213 |journal=Science |volume=344 |issue=6186 |pages=889–891 |doi=10.1126/science.1249213 |pmid=24812207 |bibcode=2014Sci...344..889B |s2cid=25475098 |issn=0036-8075}}</ref><ref>{{Cite journal |last=Jørgensen |first=Bo Barker |date=April 1982 |title=Mineralization of organic matter in the sea bed—the role of sulphate reduction |url=http://www.nature.com/articles/296643a0 |journal=Nature |language=en |volume=296 |issue=5858 |pages=643–645 |doi=10.1038/296643a0 |bibcode=1982Natur.296..643J |s2cid=4308770 |issn=0028-0836}}</ref><ref>{{Citation |last1=Jørgensen |first1=Bo Barker |title=Sulfur Cycling and Methane Oxidation |url=http://dx.doi.org/10.1007/3-540-32144-6_8 |work=Marine Geochemistry |pages=271–309 |place=Berlin/Heidelberg |publisher=Springer-Verlag |isbn=3-540-32143-8 |access-date=2022-05-18 |last2=Kasten |first2=Sabine|year=2006 |doi=10.1007/3-540-32144-6_8 }}</ref>

== Conditions for life ==
For life to have metabolic activity, it must be able to take advantage of a [[Physics:Non-equilibrium thermodynamics|thermodynamic disequilibrium]] in the environment. This can occur when rocks from the mantle that are rich in the mineral [[Chemistry:Olivine|olivine]] are exposed to seawater and react with it to form serpentine minerals and [[Chemistry:Magnetite|magnetite]].<ref>{{cite web |title=The {{sic|T|he|nolink=y}} Lost City 2005 Expedition |url=https://oceanexplorer.noaa.gov/explorations/05lostcity/background/serp/serpentinization.html |website=Ocean Explorer |publisher=National Oceanic and Atmospheric Administration |access-date=11 November 2019}}</ref> Non-equilibrium conditions are also associated with [[Earth:Hydrothermal vent|hydrothermal vent]]s, volcanism, and geothermal activity. Other processes that might provide habitats for life include roll front development in ore bodies,{{refn|group=note|A roll front is a curved ore zone that precipitates out of a solution carrying dissolved ore.<ref>{{cite book |last1=Pohl |first1=Walter |title=Economic Geology : Principles and Practice. |date=2011 |publisher=Wiley |isbn=9781444394863 |page=89}}</ref>}} [[Earth:Subduction|subduction]], [[Chemistry:Methane clathrate|methane clathrate]] formation and decomposition, [[Earth:Permafrost|permafrost]] thawing, [[Physics:Infrared|infrared]] radiation and seismic activity. Humans also create new habitats for life, particularly through [[Engineering:Environmental remediation|remediation of contaminants]] in the subsurface.<ref name=DeepDark/>

=== Energy sources ===
Life requires enough energy to construct [[Chemistry:Adenosine triphosphate|adenosine triphosphate]] (ATP). Where there is sunlight, the main processes for capturing energy are [[Earth:Photosynthesis|photosynthesis]] (which harnesses the energy in sunlight by [[Earth:Carbon fixation|converting]] [[Chemistry:Carbon dioxide|carbon dioxide]] into organic molecules) and [[Biology:Cellular respiration|respiration]] (which consumes those molecules and releases carbon dioxide). Below the surface, the main source of energy is from chemical [[Chemistry:Redox|redox]] (reduction-oxidation) reactions. This requires [[Chemistry:Electron donor|electron donor]]s (compounds that can be oxidized) and [[Chemistry:Electron acceptor|electron acceptor]]s (compounds that can be reduced). An example of such a reaction is methane oxidation:
:CH<sub>4</sub> + O<sub>2</sub> → CO<sub>2</sub> + 2&nbsp;H<sub>2</sub>O
Here CH<sub>4</sub> is the donor and O<sub>2</sub> is the acceptor.<ref name=Orcutt2011>{{cite journal |last1=Orcutt |first1=B. N. |last2=Sylvan |first2=J. B. |last3=Knab |first3=N. J. |last4=Edwards |first4=K. J. |title=Microbial Ecology of the Dark Ocean above, at, and below the Seafloor |journal=Microbiology and Molecular Biology Reviews |date=6 June 2011 |volume=75 |issue=2 |pages=361–422 |doi=10.1128/MMBR.00039-10|pmid=21646433 |pmc=3122624 |doi-access=free }}</ref> Donors can be considered "edibles" and acceptors "breathables".<ref>{{cite journal |last1=Nealson |first1=Kenneth H. |title=Harnessing microbial appetites for remediation |journal=Nature Biotechnology |date=March 2003 |volume=21 |issue=3 |pages=243–244 |doi=10.1038/nbt0303-243|pmid=12610569 |s2cid=38153041 }}</ref>

The amount of energy that is released in a metabolic reaction depends on the redox potential of the chemicals involved. Electron donors have negative potentials. From highest to lowest redox potential, some common donors available in the subsurface are organic matter, hydrogen, methane, reduced sulfur compounds, reduced iron compounds and ammonium. From most negative to least, some acceptors are oxygen, [[Chemistry:Nitrate|nitrate]]s and [[Chemistry:Nitrite|nitrite]]s, manganese and iron oxides, oxidized sulfur compounds, and carbon dioxide.<ref name=Orcutt2011/>

Of electron donors, organic matter has the most negative redox potential. It can consist of deposits from regions where sunlight is available or produced by local organisms. Fresh material is more easily utilized than aged. Terrestrial organic matter (mainly from plants) is typically harder to process than marine (phytoplankton). Some organisms break down organic compounds using [[Biology:Fermentation|fermentation]] and [[Chemistry:Hydrolysis|hydrolysis]], making it possible for others to convert it back to carbon dioxide. Hydrogen is a good energy source, but competition tends to make it scarce. It is particularly rich in hydrothermal fluids where it is produced by serpentinization. Multiple species can combine fermentation with [[Engineering:Methanogenesis|methanogenesis]] and iron oxidation with hydrogen consumption. Methane is mostly found in marine sediments, in gaseous form (dissolved or free) or in [[Chemistry:Methane clathrate|methane hydrates]]. About 20% comes from abiotic sources (breakdown of organic matter or serpentinization) and 80% from biotic sources (which reduce organic compounds such as carbon dioxide, carbon monoxide and [[Chemistry:Acetate|acetate]]). Over 90% of methane is oxidized by microbes before it reaches the surface; this activity is "one of the most important controls on greenhouse gas emissions and climate on Earth."<ref name=Orcutt2011/> Reduced sulfur compounds such as elemental sulfur, [[Chemistry:Hydrogen sulfide|hydrogen sulfide]] (H<sub>2</sub>S) and [[Chemistry:Pyrite|pyrite]] (FeS<sub>2</sub>) are found in [[Earth:Hydrothermal vent|hydrothermal vent]]s in basaltic crust, where they precipitate out when metal-rich fluids contact seawater. Reduced iron compounds in sediments are mainly deposited or produced by anaerobic reduction of [[Chemistry:Iron oxide|iron oxide]]s.<ref name=Orcutt2011/>

The electron acceptor with the highest redox potential is oxygen. Produced by photosynthesis, it is transported to the ocean floor. There, it is quickly taken up if there is a lot of organic material, and may only be present in the top few centimeters. In organic-poor sediments it can be found at greater depths, even to the oceanic crust. Nitrate can be produced by degradation of organic matter or nitrogen fixation.<ref name=Orcutt2011/> Oxygen and nitrate are derived from photosynthesis, so underground communities that utilize them are not truly independent of the surface.<ref>{{cite journal |last1=Jørgensen |first1=Bo Barker |last2=Boetius |first2=Antje |title=Feast and famine — microbial life in the deep-sea bed |journal=Nature Reviews Microbiology |date=October 2007 |volume=5 |issue=10 |pages=770–781 |doi=10.1038/nrmicro1745|pmid=17828281 |s2cid=22970703 }}</ref>

=== Nutrients ===
All life requires carbon, nitrogen, phosphorus and some trace elements such as nickel, [[Chemistry:Molybdenum|molybdenum]] and [[Chemistry:Vanadium|vanadium]]. Over 99.9% of Earth's carbon is stored in the crust and its overlying sediments, but the availability of this carbon can depend on the oxidation state of the environment. Organic carbon, nitrogen and phosphorus are primarily found in terrestrial sediments, which accumulate mainly in continental margins. Organic carbon is mainly produced at the surface of the oceans with [[Earth:Photosynthesis|photosynthesis]] or washed into oceans with terrestrial sediments. Only a small fraction is produced in the deep seas with [[Earth:Chemosynthesis|chemosynthesis]]. When organic carbon sinks from the surface of the ocean to the seafloor, most of the organic carbon is consumed by organisms in seawater. Only a small fraction of this sinking organic carbon can reach the seafloor and be available to the deep biosphere.<ref name=":0" /><ref>{{Cite journal |last1=Bender |first1=Michael L. |last2=Heggie |first2=David T. |date=May 1984 |title=Fate of organic carbon reaching the deep sea floor: a status report |url=https://linkinghub.elsevier.com/retrieve/pii/0016703784901893 |journal=Geochimica et Cosmochimica Acta |language=en |volume=48 |issue=5 |pages=977–986 |doi=10.1016/0016-7037(84)90189-3|bibcode=1984GeCoA..48..977B }}</ref> Deeper in the [[Earth:Marine sediment|marine sediment]]s, the organic content drops further.<ref name=":0" /> Phosphorus is taken up by [[Chemistry:Iron(III) oxide-hydroxide|iron oxyhydroxides]] when basalts and sulfide rocks are weathered, limiting its availability.<ref name=Schrenk/> The availability of nutrients are limiting the deep biosphere, determining where and what type of deep organisms can thrive.

=== Pressure ===
[[File:PUSH50.jpg|thumb|The PUSH50 device keeps deep-sea samples at high pressure.<ref name=DCOdecadal/>]]
On average, atmospheric pressure at sea level is about 101&nbsp;[[Pascal (unit)|kilopascals]] (kPa). In the ocean, the pressure increases at a rate of 10.5&nbsp;kPa per m of depth, so at a typical depth of the sea floor (3800&nbsp;m) the pressure is 38&nbsp;megapascals (MPa). At these depths, the boiling point of water is over 400&nbsp;°C. At the bottom of the Mariana Trench, the pressure is 110&nbsp;MPa. In the lithosphere, the pressure increases by 22.6&nbsp;kPa/m.<ref name=Schrenk/><ref name=Rothschild/> The deep biosphere withstands pressures much higher than the pressure at the surface of the Earth.<ref name=":0" />

An increased pressure compresses [[Chemistry:Lipid|lipid]]s, making membranes less fluid. In most chemical reactions, the products occupy more volume than the reactants, so the reactions are inhibited by pressure.<ref name=Rothschild/> Nevertheless, some studies claim that cells from the surface are still active at a pressure of 1&nbsp;gigapascal (GPa), about 10,000 times the standard atmospheric pressure. There are also [[Biology:Piezophile|piezophile]]s for which optimal growth occurs at pressures over 100&nbsp;MPa,<ref name=Schrenk/> and some do not grow in pressures less than 50&nbsp;MPa.<ref name=Rothschild/>

As of 2019, most sampling of organisms from the deep ocean and subsurface undergo decompression when they are removed to the surface. This can harm the cells in a variety of ways, and experiments at surface pressures produce an inaccurate picture of microbial activity in the deep biosphere.<ref>{{cite journal |last1=Cario |first1=Anaïs |last2=Oliver |first2=Gina C. |last3=Rogers |first3=Karyn L. |title=Exploring the Deep Marine Biosphere: Challenges, Innovations, and Opportunities |journal=Frontiers in Earth Science |date=4 September 2019 |volume=7 |page=225 |doi=10.3389/feart.2019.00225|bibcode=2019FrEaS...7..225C |doi-access=free }}</ref><ref>{{cite news |title=Deep-Sea Microbes Prefer High-Pressure Lifestyles |url=https://deepcarbon.net/deep-sea-microbes-prefer-high-pressure-lifestyles |date=23 July 2019 |access-date=15 November 2019 |work=Deep Carbon Observatory |language=en}}</ref><ref>{{cite journal |last1=Tamburini |first1=Christian |last2=Boutrif |first2=Mehdi |last3=Garel |first3=Marc |last4=Colwell |first4=Rita R. |last5=Deming |first5=Jody W. |title=Prokaryotic responses to hydrostatic pressure in the ocean - a review |journal=Environmental Microbiology |date=May 2013 |volume=15 |issue=5 |pages=1262–1274 |doi=10.1111/1462-2920.12084|pmid=23419081 |url=https://hal.archives-ouvertes.fr/hal-01988054/file/Tamburini_etal_EMI_draft.pdf |doi-access=free }}</ref> A Pressurized Underwater Sampler Handler (PUSH50) has been developed to maintain {{Lang|la|in situ}} pressure during sampling and afterwards in the laboratory.<ref>{{cite news |title=The PUSH for High-Pressure Microbiology |url=https://deepcarbon.net/index.php/push-high-pressure-microbiology |access-date=15 November 2019 |work=Deep Carbon Observatory |date=30 September 2019 |language=en}}</ref>

=== Temperature ===
High temperatures stress organisms, increasing the rates of processes that damage important molecules such as [[Biology:DNA|DNA]] and [[Chemistry:Amino acid|amino acid]]s. It also increases the energy requirements for repairing these molecules.<ref name=Heuer>{{cite journal |last1=Heuer |first1=Verena |last2=Lever |first2=Mark |last3=Morono |first3=Yuki |last4=Teske |first4=Andreas |title=The Limits of Life and the Biosphere in Earth's Interior |journal=Oceanography |date=1 March 2019 |volume=32 |issue=1 |pages=208–211 |doi=10.5670/oceanog.2019.147|doi-access=free }}</ref> However, cells can respond by changing the structure of these molecules to stabilize them.<ref name=Schrenk>{{cite journal |last1=Schrenk |first1=Matthew O. |last2=Huber |first2=Julie A. |last3=Edwards |first3=Katrina J. |title=Microbial Provinces in the Subseafloor |journal=Annual Review of Marine Science |date=January 2010 |volume=2 |issue=1 |pages=279–304 |doi=10.1146/annurev-marine-120308-081000|pmid=21141666 |bibcode=2010ARMS....2..279S }}</ref><ref name=Rothschild>{{cite book |last1=Rothschild |first1=Lynn J. |last2=Mancinelli |first2=Rocco L. |chapter=Life in extreme environments |journal=Nature |date=February 2001 |volume=409 |issue=6823 |pages=1092–1101 |doi=10.1038/35059215 |editor-last1=Yamagishi |editor-first1=Akihiko |editor-last2=Kakegawa |editor-first2=Takeshi |editor-last3=Usui |editor-first3=Tomhiro |title=Astrobiology : from the origins of life to the search for extraterrestrial intelligence |publisher=Springer |location=Singapore |pmid=11234023 |isbn=978-981-13-3639-3|s2cid=529873 |chapter-url=https://zenodo.org/record/1233097 }}</ref><ref>{{cite journal |last1=McKay |first1=C. P. |title=Requirements and limits for life in the context of exoplanets |journal=Proceedings of the National Academy of Sciences |date=9 June 2014 |volume=111 |issue=35 |pages=12628–12633 |doi=10.1073/pnas.1304212111|pmid=24927538 |pmc=4156692 |bibcode=2014PNAS..11112628M |doi-access=free }}</ref>

Microbes can survive at temperatures above 100&nbsp;°C if the pressure is high enough to keep the water from boiling. The highest temperature at which an organism has been cultured in a laboratory is 122&nbsp;°C,<ref name=Orcutt2011/><ref name=Schrenk/> under pressures of 20&nbsp;MPa and 40&nbsp;MPa.<ref>{{cite book |last1=Takai |first1=Ken |title=Astrobiology |chapter=Limits of Terrestrial Life and Biosphere |pages=323–344 |doi=10.1007/978-981-13-3639-3_20|year=2019 |isbn=978-981-13-3638-6 |s2cid=134158036 }}</ref> Theoretical estimates for the highest temperature that can sustain life are around 150&nbsp;°C.<ref name=Colman/> The 120&nbsp;°C isotherm can be less than 10 m deep at mid-ocean ridges and seamounts, but in other environments such as deep-sea trenches it can be kilometers deep.<ref name=Schrenk/> About 39% by volume of ocean sediments is at temperatures between 40&nbsp;°C and 120&nbsp;°C.<ref name=Colman/> Thermochronology data of Precambrian cratons suggest that habitable temperature conditions of the subsurface in these settings range back to about a billion years maximum.<ref>
Drake, H., Reiners, P.W. [https://www.pnas.org/content/118/45/e2109609118 Thermochronologic perspectives on the deep-time evolution of the deep biosphere]. Proceedings of the National Academy of Sciences Nov 2021, 118 (45) e2109609118; DOI:10.1073/pnas.2109609118
</ref>

The record-setting thermophile, ''[[Biology:Methanopyrus|Methanopyrus kandlerii]]'', was isolated from a hydrothermal vent.<ref name=Colman/> Hydrothermal vents provide abundant energy and nutrients. Several groups of Archaea and Bacteria thrive in the shallow seafloor at temperatures between 80&nbsp;°C and 105&nbsp;°C. As the environment becomes more energy-limited, such as being deeper, bacteria can survive but their number decreases. Although microorganisms have been detected at temperatures up to 118&nbsp;°C in cored sediments,<ref name=":1" /><ref>{{cite journal |last1=Biddle |first1=Jennifer F. |last2=Sylvan |first2=Jason B. |last3=Brazelton |first3=William J. |last4=Tully |first4=Benjamin J. |last5=Edwards |first5=Katrina J. |last6=Moyer |first6=Craig L. |last7=Hedelberg |first7=John F. |last8=Nelson |first8=William C. |title=Prospects for the study of evolution in the deep biosphere |journal=Frontiers in Microbiology |date=2012 |volume=2 |page=285 |doi=10.3389/fmicb.2011.00285|pmid=22319515 |pmc=3265032 |doi-access=free }}</ref> attempts to isolate the organisms have failed. There can also be depth intervals with less cells than the deeper part of the location.<ref name=":1" /> Reasons for such 'low- or no-cell intervals' are still unknown but may be related to the underground flow of hot fluid.<ref>{{Cite journal|last1=Tsang|first1=Man-Yin|last2=Bowden|first2=Stephen A.|last3=Wang|first3=Zhibin|last4=Mohammed|first4=Abdalla|last5=Tonai|first5=Satoshi|last6=Muirhead|first6=David|last7=Yang|first7=Kiho|last8=Yamamoto|first8=Yuzuru|last9=Kamiya|first9=Nana|last10=Okutsu|first10=Natsumi|last11=Hirose|first11=Takehiro|last12=Kars|first12=Myriam|last13=Schubotz|first13=Florence|last14=Ljiri|first14=Akira|last15=Yamada|first15=Yasuhiro|last16=Kubo|first16=Yusuke|last17=Morono|first17=Yuki|last18=Inagaki|first18=Fumio|last19=Heuer|first19=Verena B.|last20=Hinrichs|first20=Kai-Uwe|date=2020-02-01|title=Hot fluids, burial metamorphism and thermal histories in the underthrust sediments at IODP 370 site C0023, Nankai Accretionary Complex|url=https://www.sciencedirect.com/science/article/pii/S0264817219305161|journal=Marine and Petroleum Geology|language=en|volume=112|pages=104080|doi=10.1016/j.marpetgeo.2019.104080|bibcode=2020MarPG.11204080T |issn=0264-8172|hdl=2164/13157|s2cid=207994536 |hdl-access=free}}</ref> In deep oil reservoirs, no microbial activity has been seen hotter than 80&nbsp;°C.<ref name=Heuer/>

=== Living with energy limitation ===
In most of the subsurface, organisms live in conditions of extreme energy and nutrient limitation.<ref name=":0" /> This is far from the conditions in which cells are cultured in labs. A lab culture goes through a series of predictable phases. After a short lag phase, there is a period of exponential growth in which the population can double in as little as 20 minutes. A death phase follows in which almost all the cells die off. The remainder enter an extended stationary phase in which they can last for years without further input of substrate. However, each live cell has 100 to 1000 dead cells to feed on, so they still have abundant nutrients compared to the subsurface.<ref name=Hoehler/>

In the subsurface, cells catabolize (break down molecules for energy or building materials) 10,000 to one million times slower than at the surface. Biomass may take centuries or millennia to [[Biology:Cell cycle|turn over]]. There is no known limit to the age that cells could reach. The viruses that are present could kill cells and there may be grazing by eukaryotes, but there is no evidence of that.<ref name=Hoehler/>

It is difficult to establish clear limits on the energy needed to keep cells alive but not growing.<ref name=":0" /> They need energy to perform certain basic functions like [[Biology:Osmoregulation|the maintenance of osmotic pressure]] and maintenance of macromolecules such as [[Biology:Enzyme|enzyme]]s and [[Biology:RNA|RNA]] (e.g., [[Biology:Proofreading|proofreading]] and synthesis). However, laboratory estimates of the energy needed are several orders of magnitude greater than the energy supply that appears to sustain life underground.<ref name=Hoehler/>

It was thought, at first, that most underground cells are [[Biology:Dormancy|dormant]]. However, some extra energy is required to come out of dormancy. This is not a good strategy in an environment where the energy sources are stable over millions of years but decreasing slowly. The available evidence suggests that most cells in the subsurface are active and viable.<ref name=Hoehler/>

A low-energy environment favors cells with minimal self-regulation, because there are no changes in the environment that they need to respond to. There could be low-energy specialists. However, there is unlikely to be strong [[Biology:Evolutionary pressure|evolutionary pressure]] for such organisms to evolve because of the low turnover and because the environment is a dead end.<ref name=Hoehler/>

== Diversity ==
The [[Biology:Biomass|biomass]] in the deep subsurface is about 15% of the total for the biosphere.<ref name=Biomass/> Life from all three domains ([[Biology:Archaea|Archaea]], [[Biology:Bacteria|Bacteria]], and Eukarya) have been found in the deep subsurface;<ref name=DCOtonnes/> indeed, the deep subsurface accounts for about 90% of all the biomass in Archaea and Bacteria.<ref name=Biomass/> The genetic diversity is at least as great as that on the surface.<ref name=DCOtonnes/> Also aerobic microbes are present; methane-feeding bacteria will break down nitrites into nitrogen and oxygen, and then use the oxygen to split methane for energy. Some of the oxygen produced this way will leak out of the cells and into the surrounding environment, where it will benefit other oxygen-dependent microorganisms.<ref>[https://www.quantamagazine.org/underground-cells-make-dark-oxygen-without-light-20230717/ Underground Cells Make ‘Dark Oxygen’ Without Light | Quanta Magazine]</ref>

In the ocean, plankton species are distributed globally and are constantly being deposited almost everywhere. Quite different communities are found even in the top of ocean floor, and species diversity decreases with depth.<ref name=Petro/> However, there are still some taxa that are widespread in the subsurface.<ref name=Parkes>{{cite journal |last1=Parkes |first1=R. John |last2=Cragg |first2=Barry |last3=Roussel |first3=Erwan |last4=Webster |first4=Gordon |last5=Weightman |first5=Andrew |last6=Sass |first6=Henrik |title=A review of prokaryotic populations and processes in sub-seafloor sediments, including biosphere:geosphere interactions |journal=Marine Geology |date=June 2014 |volume=352 |pages=409–425 |doi=10.1016/j.margeo.2014.02.009|bibcode=2014MGeol.352..409P |doi-access=free }}</ref> In [[Earth:Marine sediment|marine sediment]]s, the main [[Biology:Bacterial phyla|bacterial phyla]] are "''Candidatus'' Atribacteria" (formerly OP9<ref>{{cite journal |last1=Hug |first1=Laura A. |last2=Baker |first2=Brett J. |last3=Anantharaman |first3=Karthik |last4=Brown |first4=Christopher T. |last5=Probst |first5=Alexander J. |last6=Castelle |first6=Cindy J. |last7=Butterfield |first7=Cristina N. |last8=Hernsdorf |first8=Alex W. |last9=Amano |first9=Yuki |last10=Ise |first10=Kotaro |last11=Suzuki |first11=Yohey |last12=Dudek |first12=Natasha |last13=Relman |first13=David A. |last14=Finstad |first14=Kari M. |last15=Amundson |first15=Ronald |last16=Thomas |first16=Brian C. |last17=Banfield |first17=Jillian F. |title=A new view of the tree of life |journal=Nature Microbiology |date=11 April 2016 |volume=1 |issue=5 |page=16048 |doi=10.1038/NMICROBIOL.2016.48|pmid=27572647 |doi-access=free }}</ref> and JS1<ref>{{cite journal |last1=Lee |first1=Yung Mi |last2=Hwang |first2=Kyuin |last3=Lee |first3=Jae Il |last4=Kim |first4=Mincheol |last5=Hwang |first5=Chung Yeon |last6=Noh |first6=Hyun-Ju |last7=Choi |first7=Hakkyum |last8=Lee |first8=Hong Kum |last9=Chun |first9=Jongsik |last10=Hong |first10=Soon Gyu |last11=Shin |first11=Seung Chul |title=Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments |journal=Frontiers in Microbiology |date=29 November 2018 |volume=9 |page=2909 |doi=10.3389/fmicb.2018.02909|pmid=30555444 |pmc=6281690 |doi-access=free }}</ref>),<ref name=Orsi/> [[Biology:Pseudomonadota|Pseudomonadota]], [[Biology:Chloroflexota|Chloroflexota]], and [[Biology:Planctomycetota|Planctomycetota]].<ref name=Parkes/> Members of Archaea were first identified using [[Biology:Metagenomics|metagenomic analysis]]; some of them have since been cultured and they have acquired new names. The Deep Sea Archaeal Group (DSAG) became the Marine Benthic Group B (MBG-B) and is now a proposed phylum "Lokiarchaeota".<ref name=Petro>{{cite journal |last1=Petro |first1=C |last2=Starnawski |first2=P |last3=Schramm |first3=A |last4=Kjeldsen |first4=KU |title=Microbial community assembly in marine sediments |journal=Aquatic Microbial Ecology |date=12 June 2017 |volume=79 |issue=3 |pages=177–195 |doi=10.3354/ame01826|doi-access=free }}</ref> Along with the former Ancient Archaeal Group (AAG) and Marine Hydrothermal Vent Group (MHVG), "Lokiarchaeota" is part of a candidate superphylum, [[Biology:Asgard (archaea)|Asgard]].<ref>{{cite journal |last1=MacLeod |first1=Fraser |last2=S. Kindler |first2=Gareth |last3=Lun Wong |first3=Hon |last4=Chen |first4=Ray |last5=P. Burns |first5=Brendan |title=Asgard archaea: Diversity, function, and evolutionary implications in a range of microbiomes |journal=AIMS Microbiology |date=2019 |volume=5 |issue=1 |pages=48–61 |doi=10.3934/microbiol.2019.1.48|pmid=31384702 |pmc=6646929 |doi-access=free }}</ref> Other phyla are "Bathyarchaeota" (formerly the Miscellaneous Chrenarchaeotal Group), ''[[Biology:Nitrososphaerota|Nitrososphaerota]]'' (formerly Thaumarchaeota or Marine Group I),<ref name=Petro/> and [[Biology:Euryarchaeota|Euryarchaeota]] (including "[[Biology:Hadesarchaea|Hadesarchaea]]", Archaeoglobales and [[Biology:Thermococcales|Thermococcales]]).<ref name=Colman>{{cite journal |last1=Colman |first1=Daniel R. |last2=Poudel |first2=Saroj |last3=Stamps |first3=Blake W. |last4=Boyd |first4=Eric S. |last5=Spear |first5=John R. |title=The deep, hot biosphere: Twenty-five years of retrospection |journal=Proceedings of the National Academy of Sciences |date=3 July 2017 |volume=114 |issue=27 |pages=6895–6903 |doi=10.1073/pnas.1701266114|pmid=28674200 |pmc=5502609 |bibcode=2017PNAS..114.6895C |doi-access=free }}</ref> A related clade, anaerobic methanotrophic archaea (ANME), is also represented.<ref name=Orell/> Other bacterial phyla include [[Biology:Thermotogota|Thermotogota]].<ref name=Colman/>

In the continental subsurface, the main bacterial groups are Pseudomonadota and [[Biology:Bacillota|Bacillota]] while the Archaea are mainly [[Biology:Methanomicrobia|Methanomicrobia]] and Nitrososphaerota.<ref name=Magnabosco>{{cite journal |last1=Magnabosco |first1=C. |last2=Lin |first2=L.-H. |last3=Dong |first3=H. |last4=Bomberg |first4=M. |last5=Ghiorse |first5=W. |last6=Stan-Lotter |first6=H. |last7=Pedersen |first7=K. |last8=Kieft |first8=T. L. |last9=van Heerden |first9=E. |last10=Onstott |first10=T. C. |title=The biomass and biodiversity of the continental subsurface |journal=Nature Geoscience |date=24 September 2018 |volume=11 |issue=10 |pages=707–717 |doi=10.1038/s41561-018-0221-6|bibcode=2018NatGe..11..707M |s2cid=133768246 }}</ref> Other phyla include "Bathyarchaeota" and "Aigarchaeota", while bacterial phyla include [[Biology:Aquificota|Aquificota]] and [[Biology:Nitrospirota|Nitrospirota]].<ref name=Colman/>

The eukarya in the deep biosphere include some multicellular life. In 2009 a species of [[Biology:Nematode|nematode]], ''[[Biology:Halicephalobus mephisto|Halicephalobus mephisto]]'', was discovered in rock fissures more than a kilometer down a South African gold mine. Nicknamed the "devil worm",<ref>{{cite news |last1=Mosher |first1=Dave |title=New "Devil Worm" Is Deepest-Living Animal |url=https://news.nationalgeographic.com/news/2011/06/110601-deepest-worm-earth-devil-science-animals-life/ |archive-url=https://web.archive.org/web/20110604125906/http://news.nationalgeographic.com/news/2011/06/110601-deepest-worm-earth-devil-science-animals-life |url-status=dead |archive-date=4 June 2011 |access-date=2 July 2019 |work=National Geographic News |date=2 June 2011}}</ref> it may have been forced down along with pore water by earthquakes.<ref>{{Cite press release |title=Deep life not limited to microbes: Earthquakes move surface animals to the deep |date=4 March 2019 |publisher=Deep Carbon Observatory |url=https://deepcarbon.net/deep-life-not-limited-microbes-earthquakes-move-surface-animals-deep |language=en |access-date=14 July 2019}}</ref> Other multicellular organisms have since been found, including [[Biology:Fungus|fungi]], [[Biology:Platyhelminthes|Platyhelminthes]] (flatworms), [[Biology:Rotifera|Rotifera]], [[Biology:Annelida|Annelida]] (ringed worms) and [[Biology:Arthropoda|Arthropoda]].<ref>{{Cite journal|last1=Itävaara|first1=Merja|last2=Vikman|first2=Minna|last3=Salavirta|first3=Heikki|last4=Nyyssönen|first4=Mari|last5=Miettinen|first5=Hanna|last6=Bomberg|first6=Malin|last7=Sohlberg|first7=Elina|date=2015|title=Revealing the unexplored fungal communities in deep groundwater of crystalline bedrock fracture zones in Olkiluoto, Finland|journal=Frontiers in Microbiology|language=en|volume=6|page=573|doi=10.3389/fmicb.2015.00573|pmid=26106376|pmc=4460562|issn=1664-302X|doi-access=free}}</ref><ref>{{Cite journal|last1=Bomberg|first1=Malin|last2=Itävaara|first2=Merja|last3=Kukkonen|first3=Ilmo|last4=Sohlberg|first4=Elina|last5=Miettinen|first5=Hanna|last6=Kietäväinen|first6=Riikka|last7=Purkamo|first7=Lotta|date=1 August 2018|title=Diversity and functionality of archaeal, bacterial and fungal communities in deep Archaean bedrock groundwater|url=https://academic.oup.com/femsec/article/94/8/fiy116/5035813|journal=FEMS Microbiology Ecology|language=en|volume=94|issue=8|doi=10.1093/femsec/fiy116|pmid=29893836|issn=0168-6496|doi-access=free}}</ref><ref>{{Cite web|url=https://www.sciencedaily.com/releases/2017/07/170704093956.htm|title=Fungi are key players of the deep biosphere|website=ScienceDaily|language=en|access-date=22 August 2019}}</ref><ref>{{cite journal |last1=Borgonie |first1=G. |last2=Linage-Alvarez |first2=B. |last3=Ojo |first3=A. O. |last4=Mundle |first4=S.O.C. |last5=Freese |first5=L B. |last6=Van Rooyen |first6=C. |last7=Kuloyo |first7=O. |last8=Albertyn |first8=J. |last9=Pohl |first9=C. |last10=Cason |first10=E. D. |last11=Vermeulen |first11=J. |last12=Pienaar |first12=C. |last13=Litthauer |first13=D. |last14=Van Niekerk |first14=H. |last15=Van Eeden |first15=J. |last16=Lollar |first16=B. Sherwood. |last17=Onstott |first17=T. C. |last18=Van Heerden |first18=E. |title=Eukaryotic opportunists dominate the deep-subsurface biosphere in South Africa |journal=Nature Communications |date=24 November 2015 |volume=6 |issue=1 |pages=8952 |doi=10.1038/ncomms9952|pmid=26597082 |pmc=4673884 |bibcode=2015NatCo...6.8952B }}</ref><ref>{{cite news |last1=Ravindran |first1=Sandeep |title=Inner Earth Is Teeming With Exotic Forms of Life |url=https://www.smithsonianmag.com/science-nature/inner-earth-teeming-exotic-forms-life-180958243/ |access-date=14 July 2019 |work=Smithsonian |date=29 February 2016 |language=en}}</ref><ref>{{cite journal |last1=Ivarsson |first1=M. |last2=Bengtson |first2=S. |last3=Neubeck |first3=A. |title=The igneous oceanic crust – Earth's largest fungal habitat? |journal=Fungal Ecology |date=April 2016 |volume=20 |pages=249–255 |doi=10.1016/j.funeco.2016.01.009|doi-access=free }}</ref><ref name="Drake 1–10">{{Cite journal|last1=Drake|first1=Henrik|last2=Ivarsson|first2=Magnus|last3=Heim|first3=Christine|last4=Snoeyenbos-West|first4=Oona|last5=Bengtson|first5=Stefan|last6=Belivanova|first6=Veneta|last7=Whitehouse|first7=Martin|date=2021-02-18|title=Fossilized anaerobic and possibly methanogenesis-fueling fungi identified deep within the Siljan impact structure, Sweden|journal=Communications Earth & Environment|language=en|volume=2|issue=1|page=34 |doi=10.1038/s43247-021-00107-9|bibcode=2021ComEE...2...34D |issn=2662-4435|doi-access=free}}</ref> However, their range may be limited because [[Chemistry:Sterol|sterol]]s, needed to construct membranes in eukarya, are not easily made in anaerobic conditions.<ref name=Colwell2013/>

Viruses are also present in large numbers and infect a diverse range of microbes in the deep biosphere. They may contribute significantly to cell turnover and transfer of genetic information between cells.<ref name=Colwell2013/>

== Habitats ==
[[File:Subsurface life environments.jpg|thumb|upright=2|Environments in which subsurface life has been found.<ref name=DCOdecadal/>]]
Life has been found at depths of 5&nbsp;km in continents and 10.5&nbsp;km below the ocean surface.<ref name=DCOtonnes>{{Cite press release |title=Life in deep Earth totals 15 to 23 billion tonnes of carbon—hundreds of times more than humans |date=10 December 2018 |publisher=Deep Carbon Observatory |url=https://deepcarbon.net/life-deep-earth-totals-15-23-billion-tonnes-carbon |last1=Collins |first1=Terry |last2=Pratt |first2=Katie |access-date=14 July 2019 |archive-date=30 December 2018 |archive-url=https://web.archive.org/web/20181230091455/https://deepcarbon.net/life-deep-earth-totals-15-23-billion-tonnes-carbon |url-status=dead }}</ref> In 1992, [[Biography:Thomas Gold|Thomas Gold]] calculated that if the estimated pore space of the terrestrial land mass down to 5&nbsp;km depth was filled with water, and if 1% of this volume were microbial biomass, it would be enough living matter to cover Earth's land surface with a 1.5 m thick layer.<ref>{{Cite journal|last=Gold|first=T.|date=1 July 1992|title=The deep, hot biosphere |journal=Proceedings of the National Academy of Sciences|language=en|volume=89|issue=13|pages=6045–6049|doi=10.1073/pnas.89.13.6045|issn=0027-8424|pmid=1631089|pmc=49434|bibcode=1992PNAS...89.6045G |doi-access=free }}</ref> The estimated volume of the deep biosphere is 2–2.3 billion cubic kilometers, about twice the volume of the oceans.<ref name=BBCnews>{{cite news |last1=Amos |first1=Jonathan |title=The vast scale of life beneath our feet |url=https://www.bbc.com/news/science-environment-46502570 |access-date=14 July 2019 |work=BBC News |date=10 December 2018}}</ref>

=== Ocean floor ===
The main types of habitat below the seafloor are sediments and [[Earth:Igneous rock|igneous rock]]. The latter may be partially altered and coexist with its alteration products such as sulfides and carbonates. In rock, chemicals are mainly carried through an [[Earth:Aquifer|aquifer]] system that cycles all of the ocean's water every 200,000 years. In sediments below the top few centimeters, chemicals mainly spread by the much slower process of [[Physics:Diffusion|diffusion]].<ref name=Schrenk/>

==== Sediments ====
Nearly all of the seafloor is covered by marine sediments. They can vary in thickness from centimeters near ocean ridges to over 10 kilometers in deep [[Earth:Oceanic trench|trenches]]. In the mid-ocean, [[Chemistry:Coccolith|coccolith]]s and shells settling down from the surface form [[Earth:Pelagic sediment#Oozes|oozes]], while near shore sediment is carried from the continents by rivers. Minerals from hydrothermal vents and wind-blown particles also contribute.<ref name=Orcutt2011/> As organic matter is deposited and buried, the more easily utilized compounds are depleted by microbial oxidation, leaving the more recalcitrant compounds. Thus, the energy available for life declines. In the top few meters, metabolic rates decline by 2 to 3 orders of magnitude, and throughout the sediment column cell numbers decline with depth.<ref name=Petro/>

Sediments form layers with different conditions for life. In the top 5–10 centimeters, animals burrow, reworking the sediment and extending the sediment-water interface. The water carries oxygen, fresh organic matter and dissolved [[Biology:Metabolite|metabolite]]s, resulting in a heterogenous environment with abundant nutrients. Below the burrowed layer is a layer dominated by sulfate reduction. Below that, the anaerobic reduction of methane is facilitated by sulfate in the [[Earth:Sulfate-methane transition zone|sulfate-methane transition zone]] (SMTZ). Once the sulfates are depleted, [[Engineering:Methanogenesis|methane formation]] takes over.<ref name=Petro/> The depth of the chemical zones depends on the rate that organic matter is deposited. Where it is rapid, oxygen is taken up rapidly as organic matter is consumed; where slow, oxygen can persist much deeper because of the lack of nutrients to oxidize.<ref name=Petro/>

Ocean sediment habitats can be divided into [[Earth:Subduction|subduction]] zones, [[Earth:Abyssal plain|abyssal plain]]s, and [[Earth:Passive margin|passive margin]]s. At a subduction zone, where one plate is diving under another, a thick wedge of sediment tends to form. At first the sediment has 50 to 60 percent [[Earth:Porosity|porosity]]; as it is compressed, fluids are expelled to form [[Earth:Cold seep|cold seep]]s or [[Physics:Clathrate hydrate|gas hydrates]].

Abyssal plains are the region between [[Earth:Continental margin|continental margin]]s and mid-ocean ridges, usually at depths below 4 kilometers. The ocean surface is very poor in nutrients such as nitrate, phosphate and iron, limiting the growth of [[Earth:Phytoplankton|phytoplankton]]; this results in low sedimentation rates.<ref name=Orsi>{{cite journal |last1=Orsi |first1=William D. |title=Ecology and evolution of seafloor and subseafloor microbial communities |journal=Nature Reviews Microbiology |date=2 July 2018 |volume=16 |issue=11 |pages=671–683 |doi=10.1038/s41579-018-0046-8|pmid=29967420 |s2cid=49559285 }}</ref> The sediment tends to be very poor in nutrients, so not all the oxygen is consumed; oxygen has been found all the way down to [[Earth:Basement (geology)|the underlying rock]]. In such environments, cells are mostly either [[Biology:Obligate aerobe|strictly aerobic]] or [[Biology:Facultative anaerobic organism|facultative anaerobic]] (using oxygen where available but able to switch to other electron acceptors in its absence<ref>{{cite book |last1=Hentges |first1=D. J. |chapter=17. Anaerobes: General Characteristics|editor-last1=Baron |editor-first1=S. |title=Medical Microbiology |date=1996 |publisher=University of Texas Medical Branch at Galveston |pmid=21413255 |isbn=9780963117212 |edition=4th |chapter-url=https://www.ncbi.nlm.nih.gov/books/NBK7638/ |access-date=19 November 2019}}</ref>) and they are [[Biology:Heterotroph|heterotroph]]ic (not primary producers). They include Pseudomonadota, Chloroflexota, Marine Group II archaea and [[Earth:Lithoautotroph|lithoautotroph]]s in the Nitrososphaerota phylum. Fungi are diverse, including members of the [[Biology:Ascomycota|Ascomycota]] and [[Biology:Basidiomycota|Basidiomycota]] phyla as well as yeasts<ref name=Orsi/>

Passive margins (continental shelves and slopes) are under relatively shallow water. Upwelling brings nutrient-rich water to the surface, stimulating abundant growth of phytoplankton, which then settles to the bottom (a phenomenon known as the [[Biology:Biological pump|biological pump]]).<ref name=Orsi/> Thus, there is a lot of organic material in the sediments, and all the oxygen is used up in its consumption. They have very stable temperature and pressure profiles.<ref name=Schrenk/> The population of microbes is orders of magnitude greater than in the abyssal plains. It includes [[Biology:Obligate anaerobe|strict anaerobes]] including members of the Chloroflexi phylum, "''Ca.'' Atribacteria", [[Earth:Sulfate-reducing microorganisms|sulfate-reducing bacteria]], and fermenters, [[Biology:Methanogen|methanogen]]s and [[Biology:Methanotroph|methanotroph]]s in the Archaea. Fungi are less diverse than in abyssal plains, mainly including Ascomycota and yeasts. Viruses in the ''[[Biology:Inoviridae|Inoviridae]]'', ''[[Biology:Siphoviridae|Siphoviridae]]'', and ''[[Biology:Lipothrixviridae|Lipothrixviridae]]'' families have been identified.<ref name=Orsi/>

==== Rocks ====
[[File:Sumatra-subduction.jpg|thumb|upright=1.5|Schematic of the Sumatra Trench and the associated island arcs and back-arc regions]]
Ocean crust forms at [[Earth:Mid-ocean ridge|mid-ocean ridge]]s and is removed by subduction. The top half kilometer or so is a series of basaltic flows, and only this layer has enough porosity and permeability to allow fluid flow. Less suitable for life are the layers of sheeted dikes and gabbros underneath.<ref name=Schrenk/>

Mid-ocean ridges are a hot, rapidly changing environment with a steep vertical temperature gradient, so life can only exist in the top few meters. High-temperature interactions between water and rock reduce sulfates, producing abundant sulfides that serve as energy sources; they also strip the rock of metals that can be sources of energy or toxic. Along with degassing from magma, water interactions also produce a lot of methane and hydrogen. No drilling has yet been accomplished, so information on microbes comes from samples of hydrothermal fluids coming out of vents.<ref name=Schrenk/>

About 5 kilometers off the ridge axis, when the crust is about 1 million years old, ridge flanks begin. Characterized by [[Earth:Hydrothermal circulation|hydrothermal circulation]], they extend to about 80 million years in age. This circulation is driven by latent heat from the cooling of crust, which heats seawater and drives it up through more permeable rock. Energy sources come from alteration of the rock, some of which is mediated by living organisms. In the younger crust, there is a lot of iron and sulfur cycling. Sediment cover slows the cooling and reduces the flow of water. There is little evidence of microbe activity in older (more than 10 million year old) crust.<ref name=Schrenk/>

Near subduction zones, volcanoes can form in [[Earth:Island arc|island arc]]s and [[Earth:Back-arc region|back-arc]] regions. The subducting plate releases volatiles and solutes to these volcanoes, resulting in acidic fluids with higher concentrations of gases and metals than in the mid-ocean ridge. It also releases water that can mix with mantle material to form serpentinite. When [[Earth:Hotspot (geology)|hotspot]] volcanoes occur in the middle of oceanic plates, they create permeable and porous basalts with higher concentrations of gas than at mid-ocean ridges. Hydrothermal fluids are cooler and have a lower sulfide content. Iron-oxidizing bacteria create extensive deposits of iron oxides.<ref name=Schrenk/>

==== Porewater ====
Microorganisms live in the cracks, holes and empty space inside sediments and rocks. Such empty space provides water and dissolved nutrients to the microorganisms. Note that as the depth increases, there are less nutrients in the porewater as nutrients are continuously consumed by microorganisms. As the depth increases, the sediment is more [[Earth:Compaction (geology)|compact]] and there is less space between [[Earth:Mineral|mineral]] grains. As a result, there is less porewater per volume. The environment gets drier and drier when sediments are transitioned into rocks. At this stage, water can also be a limiting factor to the deep biosphere.<ref name=":0" />

==== Continents ====
Continents have a complex history and a great variety of rocks, sediments and soils; the climate on the surface, temperature profiles and hydrology also vary. Most of the information on subsurface life comes from a small number of sampling sites that are mainly in North America. With the exception of ice cores, densities of cells decline steeply with depth, decreasing by several orders of magnitude. In the top one or two meters of soils, organisms depend on oxygen and are [[Biology:Heterotroph|heterotroph]]s, depending on the breakdown of organic carbon for their nutrition, and their decline in density parallels that of the organic material. Below that, there is no correlation, although both cell density and organic content declines by a further five [[Order of magnitude|orders of magnitude]] or so (by contrast, there is a correlation in ocean sediments). Increasing depth, temperature and salinity do correlate with declining cell numbers, although the rates depend strongly on type of crust and rate of [[Earth:Groundwater recharge|groundwater recharge]].<ref name=Magnabosco/>

Microbes have been found in sedimentary rocks down to about 3 kilometers, the deepest sampled. There is a lot of diversity, although the deepest tend to be [[Chemistry:Iron(III)|iron(III)]]- or sulfate-reducing bacteria that use fermentation and can thrive in high temperature and salinity. Even more salt-tolerant [[Biology:Halophile|halophile]]s have been found in deep salt deposits, and such deposits are found all over the world.<ref name=Pedersen>{{cite journal |last1=Pedersen |first1=K |title=Exploration of deep intraterrestrial microbial life: current perspectives |journal=FEMS Microbiology Letters |date=April 2000 |volume=185 |issue=1 |pages=9–16 |doi=10.1111/j.1574-6968.2000.tb09033.x|pmid=10731600 |doi-access=free }}</ref>  In 2019 microbial organisms were discovered living 2,400 meters below the surface, breathing sulfur and eating rocks such as pyrite as their regular food source.<ref>{{cite journal |last1=Lollar |first1=Garnet S. |last2=Warr |first2=Oliver |last3=Telling |first3=Jon |last4=Osburn |first4=Magdalena R. |last5=Lollar |first5=Barbara Sherwood |title='Follow the Water': Hydrogeochemical Constraints on Microbial Investigations 2.4 km Below Surface at the Kidd Creek Deep Fluid and Deep Life Observatory |journal=Geomicrobiology Journal |date=18 July 2019 |volume=36 |issue=10 |pages=859–872 |doi=10.1080/01490451.2019.1641770|bibcode=2019GmbJ...36..859L |s2cid=199636268 }}</ref><ref>{{cite news |title=World's Oldest Groundwater Supports Life Through Water-Rock Chemistry |url=https://deepcarbon.net/worlds-oldest-groundwater-supports-life-through-water-rock-chemistry |access-date=15 November 2019 |work=Deep Carbon Observatory |date=29 July 2019 |language=en |archive-date=10 September 2019 |archive-url=https://web.archive.org/web/20190910013319/https://deepcarbon.net/worlds-oldest-groundwater-supports-life-through-water-rock-chemistry |url-status=dead }}</ref><ref>{{cite news |last1=Powell |first1=Corey S. |title=Strange life forms found deep in a mine point to vast 'underground Galapagos' |url=https://www.nbcnews.com/mach/science/strange-life-forms-found-deep-mine-point-vast-underground-galapagos-ncna1050906 |access-date=15 November 2019 |work=NBC News |date=7 September 2019 |language=en}}</ref> The discovery occurred in the oldest known water on Earth.<ref>{{cite news |last1=Romuld |first1=Maggie |title=Oldest Water on Earth Found Deep Within the Canadian Shield |url=http://thescienceexplorer.com/nature/oldest-water-earth-found-deep-within-canadian-shield |access-date=15 November 2019 |work=The Science Explorer |date=14 December 2016 |language=en}}</ref> A study of biosignatures in vein mineral samples from more than 30 deep mines in the Fennoscandian Shield proves that signatures of ancient life are omnipresent across the shield.<ref>{{Cite journal|last1=Drake|first1=Henrik|last2=Roberts|first2=Nick M. W.|last3=Reinhardt|first3=Manuel|last4=Whitehouse|first4=Martin|last5=Ivarsson|first5=Magnus|last6=Karlsson|first6=Andreas|last7=Kooijman|first7=Ellen|last8=Kielman-Schmitt|first8=Melanie|date=2021-06-03|title=Biosignatures of ancient microbial life are present across the igneous crust of the Fennoscandian shield|journal=Communications Earth & Environment|language=en|volume=2|issue=1|pages=1–13|doi=10.1038/s43247-021-00170-2|issn=2662-4435|doi-access=free}}</ref>

Humans have accessed deep aquifers in igneous rocks for a variety of purposes including groundwater extraction, mining, and storage of hazardous wastes. Most or all of these aquifers host microbes. At all the sites that have been tested, hydrogen, methane and carbon dioxide have been found.<ref name=Pedersen/> Hydrogen-based communities of prokaryotes have also been found in hot springs and hydrothermal systems. A variety of mechanisms have been proposed for the production of hydrogen, some of which would be independent of photosynthesis.<ref name="Parkes"/>

== Ecology ==
[[File:Candidatus Desulforudis audaxviator.jpg|thumb|The purplish rod-shaped cells, a few microns long, are "''Candidatus'' Desulforudis audaxviator".<ref name=DCOdecadal>{{cite book |last1=Deep Carbon Observatory |title=Deep Carbon Observatory: A Decade of Discovery |doi=10.17863/CAM.44064 |date=2019 |location=Washington, DC |url=https://deepcarbon.net/deep-carbon-observatory-decade-discovery |access-date=13 December 2019}}</ref>]]
One species of bacteria, "[[Biology:Candidatus Desulforudis audaxviator|''Candidatus'' Desulforudis audaxviator]]", is the first known to comprise a complete ecosystem by itself.<ref name=LowLife/> It was found 2.8&nbsp;kilometers below the surface in a gold mine near [[Place:Johannesburg|Johannesburg]], South Africa. In [[Earth:Alkalinity|alkaline]] water at a temperature of about 60&nbsp;°C, with no access to oxygen, it gets energy by reducing sulfate, its nitrogen from ammonia molecules and ammonium ions, and its carbon from carbon dioxide or formate.<ref>{{cite journal |last1=Starr |first1=Laura |title=One is the loneliest number for mine-dwelling bacterium |journal=Nature |date=9 October 2008 |doi=10.1038/news.2008.1160|doi-access=free }}</ref><ref>{{cite news |last1=DOE/Lawrence Berkeley National Laboratory |title=Journey Toward The Center Of The Earth: One-of-a-kind Microorganism Lives All Alone |url=https://www.sciencedaily.com/releases/2008/10/081009143708.htm |access-date=21 November 2019 |work=ScienceDaily |date=10 October 2008 |language=en}}</ref> Stable isotope records of (secondary) fracture-lining minerals of the continental igneous rock-hosted deep biosphere point to long-term occurrence of methanogenesis, methanotrophy and sulfate reduction.<ref>{{Cite journal|last1=Drake|first1=Henrik|last2=Åström|first2=Mats E.|last3=Heim|first3=Christine|last4=Broman|first4=Curt|last5=Åström|first5=Jan|last6=Whitehouse|first6=Martin|last7=Ivarsson|first7=Magnus|last8=Siljeström|first8=Sandra|last9=Sjövall|first9=Peter|date=2015-05-07|title=Extreme 13 C depletion of carbonates formed during oxidation of biogenic methane in fractured granite|journal=Nature Communications|language=en|volume=6|issue=1|pages=7020|doi=10.1038/ncomms8020|pmid=25948095 |issn=2041-1723|pmc=4432592|bibcode=2015NatCo...6.7020D }}</ref> Morphological and spatiotemporal relations point to potential syntrophic relation of these prokaryotic metabolisms with fungi.<ref name="Drake 1–10"/><ref>{{Cite journal|last1=Drake|first1=Henrik|last2=Ivarsson|first2=Magnus|last3=Bengtson|first3=Stefan|last4=Heim|first4=Christine|last5=Siljeström|first5=Sandra|last6=Whitehouse|first6=Martin J.|last7=Broman|first7=Curt|last8=Belivanova|first8=Veneta|last9=Åström|first9=Mats E.|date=2017-07-04|title=Anaerobic consortia of fungi and sulfate reducing bacteria in deep granite fractures|journal=Nature Communications|language=en|volume=8|issue=1|pages=55|doi=10.1038/s41467-017-00094-6|pmid=28676652 |issn=2041-1723|pmc=5496868|bibcode=2017NatCo...8...55D }}</ref>

Other ecosystems have multiple interdependent species. They can be divided into [[Biology:Autotroph|autotroph]]s, which derive energy from non-living sources, and [[Biology:Heterotroph|heterotroph]]s, which feed on autotrophs or their remains. Some organisms engage in [[Biology:Syntrophy|syntrophy]], where one organism lives off the byproducts of another's metabolic activity. At the surface, most autotrophs use photosynthesis, but where there is no light, chemoautotrophs make use of chemical energy.<ref>{{cite book |last1=Chapman |first1=J. L. |last2=Reiss |first2=Michael J. |title=Ecology : principles and applications |date=1999 |publisher=Cambridge University Press |isbn=9780521588027 |pages=8, 120–121 |edition=2nd}}</ref>

In [[Earth:Marine sediment|marine sediment]]s where oxygen is available, a major group of chemoautotrophs is ammonia-oxidizing Nitrososphaerota. It supports 19% of the heterotrophic production. In some environments such as abyssal Pacific Ocean sediments, the supply of ammonia dwindles with depth; but in other environments ammonia actually increases because heterotrophic bacteria, living on organic material, remineralize the ammonia. This interdependence of the heterotrophic bacteria and Nitrososphaerota is an example of syntrophy. However, some Nitrososphaerota are [[Biology:Mixotroph|mixotroph]]ic, able to use both organic matter and carbon dioxide for carbon.<ref name=Orsi/>

In anoxic sediments, hydrogen is an important "edible". Members of the Chloroflexi draw energy from it to produce [[Chemistry:Acetate|acetate]] by reducing carbon dioxide or organic matter (a process known as acetogenesis). Metal-reducing and sugar-fermenting Bacteroidetes produce [[Chemistry:Propionate|propionate]], among other compounds, and this is fermented by "''Ca.'' Atribacteria" to produce hydrogen. In upper sediments, sulfate-reducing bacteria take up most of the hydrogen, while in lower sediments the sulfate is depleted and methanogens dominate. In the sulfate-methane transition zone (SMTZ), anaerobic methanotrophic (ANME) archaea form consortia with sulfate-reducing bacteria.<ref name=Orsi/><ref name=Petro/>

== See also ==
{{div col}}
*{{slink|Deep Carbon Observatory|Deep Life}}
*[[Biology:Endolith|Endolith]]
*[[Earth:Extremophile|Extremophile]]
*[[Biology:Lithophile|Lithophile]]
*[[Biology:Oligotroph|Oligotroph]]
*[[Biology:Rare biosphere|Rare biosphere]]
*[[Biology:Subsurface lithoautotrophic microbial ecosystem|Subsurface lithoautotrophic microbial ecosystem]]
{{div col end}}

== Notes ==
{{Reflist|group=note}}

== References ==
{{Reflist}}

== Further reading ==
{{Refbegin}}
*{{cite news |last1=Abe |first1=Shige |title=Life without the Sun |url=https://astrobiology.nasa.gov/news/life-without-the-sun/ |access-date=16 July 2019 |work=Astrobiology at NASA |date=10 October 2008 |language=en-EN}}
*{{cite press release |title=Amino Acid Metabolism Fuels Fracking Communities |url=https://deepcarbon.net/index.php/amino-acid-metabolism-fuels-fracking-communities |access-date=3 September 2019 |work=Deep Carbon Observatory |date=13 August 2018 |language=en}}
*{{cite journal |last1=Biddle |first1=Jennifer F. |title=Prospects for the study of evolution in the deep biosphere |journal=Frontiers in Microbiology |date=2012 |volume=2 |page=285 |doi=10.3389/fmicb.2011.00285|pmid=22319515 |pmc=3265032 |doi-access=free }}
*{{cite book |last1=Bomberg |first1=Malin |last2=Ahonen |first2=Lasse |title=Geomicrobes: life in terrestrial deep subsurface |date=2017 |publisher=Frontiers Media SA |isbn=9782889451791}}
*{{cite journal |last1=Bradley |first1=James A. |last2=Amend |first2=Jan P. |last3=LaRowe |first3=Douglas E. |title=Survival of the fewest: Microbial dormancy and maintenance in marine sediments through deep time |journal=Geobiology |date=January 2019 |volume=17 |issue=1 |pages=43–59 |doi=10.1111/gbi.12313|pmid=30248245 |pmc=6585783 |bibcode=2019Gbio...17...43B }}
*{{cite news |last1=Brahic |first1=Catherine |title=The 19 superbugs that rule Earth's hidden depths |url=https://www.newscientist.com/article/dn24727-the-19-superbugs-that-rule-earths-hidden-depths/ |access-date=3 September 2019 |work=NewScientist |date=9 December 2013}}
*{{Cite AV media |url=https://www.youtube.com/watch?v=LZzxM8bX2Mc |title=North Pond: The Search for Intraterrestrials |access-date=10 July 2019 |last1=Brown (Director) |first1=Michael |last2=Santell (Story) |first2=Ad Lucien |type=Video |publisher=Center for Dark Energy Biosphere Investigations |date=3 December 2013}} ([https://www.imdb.com/title/tt3385652/ IMDb])
*{{cite journal |last1=D'Hondt |first1=S. |title=Metabolic Activity of Subsurface Life in Deep-Sea Sediments |journal=Science |date=15 March 2002 |volume=295 |issue=5562 |pages=2067–2070 |doi=10.1126/science.1064878|pmid=11896277 |bibcode=2002Sci...295.2067D |s2cid=26979705 }}
*{{cite news |last1=Frazer |first1=Jennifer |title=Inside Earth, Microbes Approach Immortality |url=https://blogs.scientificamerican.com/artful-amoeba/inside-earth-microbes-approach-immortality/ |access-date=5 July 2019 |work=Scientific American Blog Network |date=23 January 2019 |language=en}}
*{{cite news |last1=Ghose |first1=Tia |title=What lies beneath: Tiny organisms thrive below Earth's surface |url=https://www.livescience.com/42213-insights-census-deep-life.html |access-date=16 July 2019 |work=Live Science |date=29 December 2013}}
*{{cite journal |last1=Gould |first1=Stephen Jay |title=Planet of the Bacteria |url=http://www.stephenjaygould.org/library/gould_bacteria.html |access-date=10 July 2019 |journal=Washington Post Horizon |volume=119 |page=344 |date=13 November 1996}}
*{{cite news |last1=Hignett |first1=Katherine |title=Have scientists been looking for life on Mars in the wrong place? |url=https://www.newsweek.com/mars-subsurface-origin-life-crust-751069 |access-date=18 January 2019 |work=Newsweek |date=18 December 2017 |language=en}}
*{{cite journal |last1=Hinrichs |first1=K.-U. |last2=Inagaki |first2=F. |title=Downsizing the Deep Biosphere |journal=Science |date=11 October 2012 |volume=338 |issue=6104 |pages=204–205 |doi=10.1126/science.1229296|pmid=23066067 |bibcode=2012Sci...338..204H |s2cid=29231881 }}
*{{cite book |last1=Kallmeyer |first1=Jens |last2=Wagner |first2=Dirk |title=Microbial life of the deep biosphere |date=2014 |publisher=Walter De Gruyter |isbn=9783110370676}}
*{{cite news |last1=Leitch |first1=Carmen |title=The 'Deep Biosphere' of the Earth Teems with Life |url=https://www.labroots.com/trending/microbiology/13490/deep-biosphere-earth-teems-life |access-date=18 January 2019 |work=LabRoots |date=10 December 2018}}
*{{cite journal |last1=Lever |first1=Mark A. |last2=Rogers |first2=Karyn L. |last3=Lloyd |first3=Karen G. |last4=Overmann |first4=Jörg |last5=Schink |first5=Bernhard |last6=Thauer |first6=Rudolf K. |last7=Hoehler |first7=Tori M. |last8=Jørgensen |first8=Bo Barker |last9=Giudici-Orticoni |first9=Marie-Therese |title=Life under extreme energy limitation: a synthesis of laboratory- and field-based investigations |journal=FEMS Microbiology Reviews |date=September 2015 |volume=39 |issue=5 |pages=688–728 |doi=10.1093/femsre/fuv020|pmid=25994609 |doi-access=free }}
*{{cite journal |last1=Nealson |first1=Kenneth H. |title=Harnessing microbial appetites for remediation |journal=Nature Biotechnology |date=March 2003 |volume=21 |issue=3 |pages=243–244 |doi=10.1038/nbt0303-243|pmid=12610569 |s2cid=38153041 }}
*{{Cite encyclopedia |encyclopedia=Encyclopedia of Astrobiology |publisher=Springer Berlin Heidelberg |location=Berlin, Heidelberg |last=Onstott |first=Tullis C. |title=Deep Subsurface Microbiology |date=2014 |pages=1–4 |language=en |doi=10.1007/978-3-642-27833-4_573-3 |isbn=9783642278334}}
*{{cite book |last1=Onstott |first1=Tullis C. |title=Deep Life |date=2016 |publisher=Princeton University Press |isbn=9781400884247 }}
*{{cite journal |last1=Teske |first1=Andreas |last2=Sørensen |first2=Ketil B |title=Uncultured archaea in deep marine subsurface sediments: have we caught them all? |journal=The ISME Journal |date=8 November 2007 |volume=2 |issue=1 |pages=3–18 |doi=10.1038/ismej.2007.90|pmid=18180743 |doi-access=free |hdl=10379/14139 |hdl-access=free }}
*{{cite journal |last1=Trembath-Reichert |first1=Elizabeth |last2=Morono |first2=Yuki |last3=Ijiri |first3=Akira |last4=Hoshino |first4=Tatsuhiko |last5=Dawson |first5=Katherine S. |last6=Inagaki |first6=Fumio |last7=Orphan |first7=Victoria J. |title=Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds |journal=Proceedings of the National Academy of Sciences |date=31 October 2017 |volume=114 |issue=44 |pages=E9206–E9215 |doi=10.1073/pnas.1707525114|pmid=29078310 |pmc=5676895 |bibcode=2017PNAS..114E9206T |doi-access=free }}
*{{cite news |last1=Watts |first1=Jonathan |title=Scientists identify vast underground ecosystem containing billions of micro-organisms |url=https://www.theguardian.com/science/2018/dec/10/tread-softly-because-you-tread-on-23bn-tonnes-of-micro-organisms |access-date=18 January 2019 |work=The Guardian |date=10 December 2018}}
{{Refend}}

== External links ==
*[https://deepcarbon.net/index.php/tag/census-deep-life Census of Deep Life]
*[https://www.darkenergybiosphere.org Center for Dark Energy Biosphere Investigations]
*[http://portal.gplates.org/portal/biosphere/ Deep Biosphere map on 3D globe] (GPlates Portal)

[[Category:Biological systems]]
[[Category:Geomicrobiology]]

{{Sourceattribution|Deep biosphere}}