Editing Extremophile (section)

== Bioremediation ==
Extremophiles can also be useful players in the [[bioremediation]] of contaminated sites as some species are capable of biodegradation under conditions too extreme for classic bioremediation candidate species. Anthropogenic activity causes the release of pollutants that may potentially settle in extreme environments as is the case with tailings and sediment released from deep-sea mining activity.<ref>{{Cite journal |last1=Frid |first1=Christopher L. J. |last2=Caswell |first2=Bryony A. |date=2017-11-23 |title=Marine Pollution |journal=Oxford Scholarship Online |volume=1 |doi=10.1093/oso/9780198726289.001.0001 |isbn=9780198726289}}</ref> While most bacteria would be crushed by the pressure in these environments, piezophiles can tolerate these depths and can metabolize pollutants of concern if they possess bioremediation potential.{{citation needed|date=May 2023}}

=== Hydrocarbons ===
There are multiple potential destinations for hydrocarbons after an oil spill has settled and currents routinely deposit them in extreme environments. Methane bubbles resulting from the [[Deepwater Horizon oil spill]] were found 1.1 kilometers below water surface level and at concentrations as high as 183 ''μ''mol per kilogram.<ref>{{Cite journal |last1=Reddy |first1=C. M. |last2=Arey |first2=J. S. |last3=Seewald |first3=J. S. |last4=Sylva |first4=S. P. |last5=Lemkau |first5=K. L. |last6=Nelson |first6=R. K. |last7=Carmichael |first7=C. A. |last8=McIntyre |first8=C. P. |last9=Fenwick |first9=J. |last10=Ventura |first10=G. T. |last11=Van Mooy |first11=B. A. S. |author-link11=Benjamin Van Mooy |date=2011-07-18 |title=Composition and fate of gas and oil released to the water column during the Deepwater Horizon oil spill |journal=Proceedings of the National Academy of Sciences |volume=109 |issue=50 |pages=20229–34 |doi=10.1073/pnas.1101242108 |issn=0027-8424 |pmc=3528605 |pmid=21768331 |doi-access=free}}</ref>  The combination of low temperatures and high pressures in this environment result in low microbial activity. However, bacteria that are present including species of ''[[Pseudomonas]]'', ''[[Aeromonas]]'' and ''[[Vibrio]]'' were found to be capable of bioremediation, albeit at a tenth of the speed they would perform at sea level pressure.<ref>{{Cite journal |last1=Margesin |first1=R. |last2=Schinner |first2=F. |date=2001-09-01 |title=Biodegradation and bioremediation of hydrocarbons in extreme environments |journal=Applied Microbiology and Biotechnology |volume=56 |issue=5–6 |pages=650–63 |doi=10.1007/s002530100701 |issn=0175-7598 |pmid=11601610 |s2cid=13436065}}</ref> [[Polycyclic aromatic hydrocarbon]]s increase in solubility and bioavailability with increasing temperature.{{citation needed|date=April 2021}} Thermophilic ''[[Thermus]]'' and ''[[Bacillus]]'' species have demonstrated higher gene expression for the alkane mono-oxygenase ''[[alkB]]'' at temperatures exceeding {{Cvt|60|C}}.{{citation needed|date=April 2021}} The expression of this gene is a crucial precursor to the bioremediation process. Fungi that have been genetically modified with cold-adapted enzymes to tolerate differing pH levels and temperatures have been shown to be effective at remediating hydrocarbon contamination in freezing conditions in the Antarctic.<ref>{{Cite journal |last1=Duarte |first1=Alysson Wagner Fernandes |last2=dos Santos |first2=Juliana Aparecida |last3=Vianna |first3=Marina Vitti |last4=Vieira |first4=Juliana Maíra Freitas |last5=Mallagutti |first5=Vitor Hugo |last6=Inforsato |first6=Fabio José |last7=Wentzel |first7=Lia Costa Pinto |last8=Lario |first8=Luciana Daniela |last9=Rodrigues |first9=Andre |last10=Pagnocca |first10=Fernando Carlos |last11=Pessoa Junior |first11=Adalberto |date=2017-12-11 |title=Cold-adapted enzymes produced by fungi from terrestrial and marine Antarctic environments |journal=Critical Reviews in Biotechnology |volume=38 |issue=4 |pages=600–19 |doi=10.1080/07388551.2017.1379468 |issn=0738-8551 |pmid=29228814 |hdl-access=free |hdl=11449/175619 |s2cid=4201439}}</ref>

=== Metals ===
''[[Acidithiubacillus ferroxidans]]'' has been shown to be effective in remediating mercury in acidic soil due to its ''merA'' gene making it mercury resistant.<ref>{{Cite journal |last1=Takeuchi |first1=Fumiaki |last2=Iwahori |first2=Kenji |last3=Kamimura |first3=Kazuo |last4=Negishi |first4=Atsunori |last5=Maeda |first5=Terunobu |last6=Sugio |first6=Tsuyoshi |date=January 2001 |title=Volatilization of Mercury under Acidic Conditions from Mercury-polluted Soil by a Mercury-resistant Acidithiobacillus ferrooxidans SUG 2-2 |journal=Bioscience, Biotechnology, and Biochemistry |volume=65 |issue=9 |pages=1981–86 |doi=10.1271/bbb.65.1981 |issn=0916-8451 |pmid=11676009 |s2cid=2158906|doi-access=free }}</ref> Industrial effluent contain high levels of metals that can be detrimental to both human and ecosystem health.<ref>{{Cite journal |last=Nagajyoti |first=P.C. |date=2008 |title=Heavy metal toxicity: Industrial Effluent Effect on Groundnut (Arachis hypogaea L.) Seedlings |journal=Journal of Applied Sciences Research |volume=4 |issue=1 |pages=110–21}}</ref><ref>{{Cite journal |last=Fakayode |first=S.O. |date=2005 |title=Impact assessment of industrial effluent on water quality of the receiving Alaro River in Ibadan, Nigeria. |journal=African Journal of Environmental Assessment and Management |volume=10 |pages=1–13}}</ref> In extreme heat environments the extremophile ''[[Geobacillus thermodenitrificans]]'' has been shown to effectively manage the concentration of these metals within twelve hours of introduction.<ref>{{Cite journal |last1=Chatterjee |first1=S.K. |last2=Bhattacharjee |first2=I. |last3=Chandra |first3=G. |date=March 2010 |title=Biosorption of heavy metals from industrial waste water by Geobacillus thermodenitrificans |journal=Journal of Hazardous Materials |volume=175 |issue=1–3 |pages=117–25 |doi=10.1016/j.jhazmat.2009.09.136 |issn=0304-3894 |pmid=19864059}}</ref> Some acidophilic microorganisms are effective at metal remediation in acidic environments due to proteins found in their periplasm, not present in any mesophilic organisms, allowing them to protect themselves from high proton concentrations.<ref>{{Cite journal |last=Chi |first=A. |date=2007 |title=Periplasmic proteins of the extremophile Acidithiobacillus ferrooxidans: a high throughput proteomics analysis |journal=Molecular & Cellular Proteomics |volume=6 |issue=12 |pages=2239–51 |doi=10.1074/mcp.M700042-MCP200  |doi-access=free |pmc=4631397 |pmid=17911085}}</ref> [[Paddy field|Rice paddies]] are highly oxidative environments that can produce high levels of lead or cadmium. ''[[Deinococcus radiodurans]]'' are resistant to the harsh conditions of the environment and are therefore candidate species for limiting the extent of contamination of these metals.<ref>{{Cite journal |last1=Dai |first1=Shang |last2=Chen |first2=Qi |last3=Jiang |first3=Meng |last4=Wang |first4=Binqiang |last5=Xie |first5=Zhenming |last6=Yu |first6=Ning |last7=Zhou |first7=Yulong |last8=Li |first8=Shan |last9=Wang |first9=Liangyan |last10=Hua |first10=Yuejin |last11=Tian |first11=Bing |date=September 2021 |title=Colonized extremophile Deinococcus radiodurans alleviates toxicity of cadmium and lead by suppressing heavy metal accumulation and improving antioxidant system in rice |journal=Environmental Pollution |volume=284 |pages=117127 |doi=10.1016/j.envpol.2021.117127 |issn=0269-7491 |pmid=33892465|bibcode=2021EPoll.28417127D }}</ref>

Some bacteria are known to also use [[Rare-earth element|rare earth elements]] on their biological processes. For example, ''[[Methylacidiphilum fumariolicum]]'', ''[[Methylorubrum extorquens]],'' and ''[[Methylobacterium radiotolerans]]'' are known to be able to use [[Lanthanide#Biological effects|lanthanides]] as cofactors to increase their [[methanol dehydrogenase]] activity.<ref>{{Cite journal |last1=Phi |first1=Manh Tri |last2=Singer |first2=Helena |last3=Zäh |first3=Felix |last4=Haisch |first4=Christoph |last5=Schneider |first5=Sabine |last6=Op den Camp |first6=Huub J. M. |last7=Daumann |first7=Lena J. |date=2024-03-01 |title=Assessing Lanthanide-Dependent Methanol Dehydrogenase Activity: The Assay Matters |url=https://pubmed.ncbi.nlm.nih.gov/38269599/ |journal=ChemBioChem |volume=25 |issue=5 |pages=e202300811 |doi=10.1002/cbic.202300811 |issn=1439-7633 |pmid=38269599}}</ref><ref>{{Citation |last1=Good |first1=Nathan M. |date=2021-01-01 |volume=650 |pages=97–118 |editor-last=Cotruvo |editor-first=Joseph A. |url=https://www.sciencedirect.com/science/article/pii/S0076687921000719 |access-date=2024-04-10  |publisher=Academic Press |last2=Martinez-Gomez |first2=N. Cecilia|title=Rare-Earth Element Biochemistry: Methanol Dehydrogenases and Lanthanide Biology |chapter=Expression, purification and testing of lanthanide-dependent enzymes in Methylorubrum extorquens AM1 |series=Methods in Enzymology |doi=10.1016/bs.mie.2021.02.001 |pmid=33867027 |isbn=978-0-12-823856-1 |url-access=subscription }}</ref>{{citation needed|date=May 2023}}

=== Acid mine drainage ===
[[File:Acid mine drainage comparison.jpg|thumb|Before (left) and after (right) a cleanup project of the [[Little Conemaugh River]]<ref>{{Cite web |last=US EPA |first=REG 03 |date=2016-09-09 |title=Actions Eliminate Long-Time, Major Acid Mine Discharge |url=https://www.epa.gov/pa/actions-eliminate-long-time-major-acid-mine-discharge |access-date=2024-04-13 |website=www.epa.gov |language=en}}</ref>]]
[[Acid mine drainage]] is a major environmental concern associated with many metal mines. This is due to the fact that this highly acidic water can mix with groundwater, streams, and lakes. The drainage turns the pH in these water sources from a more neutral pH to a pH lower than 4. This is close to the acidity levels of battery acid or stomach acid. Exposure to the polluted water can greatly affect the health of plants, humans, and animals. However, a productive method of remediation is to introduce the extremophile, [[Thiobacillus ferrooxidans|''Thiobacillus'' ''ferrooxidans'']]. This extremophile is useful for its bioleaching property. It helps to break down minerals in the waste water created by the mine. By breaking down the minerals ''Thiobacillus ferrooxidans'' start to help neutralize the acidity of the waste water. This is a way to reduce the environmental impact and help remediate the damage caused by the acid mine drainage leaks.<ref>{{Cite web |last=US EPA |first=OW |date=2015-09-15 |title=Abandoned Mine Drainage |url=https://www.epa.gov/nps/abandoned-mine-drainage |access-date=2024-04-13 |website=www.epa.gov |language=en}}</ref><ref>{{Cite web |title=Acid Mine Drainage |url=https://earthworks.org/issues/acid-mine-drainage/ |access-date=2024-04-13 |website=Earthworks |language=en-US}}</ref><ref>{{Cite journal |last1=Valdés |first1=Jorge |last2=Pedroso |first2=Inti |last3=Quatrini |first3=Raquel |last4=Dodson |first4=Robert J |last5=Tettelin |first5=Herve |last6=Blake |first6=Robert |last7=Eisen |first7=Jonathan A |last8=Holmes |first8=David S |date=December 2008 |title=Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications |journal=BMC Genomics |language=en |volume=9 |issue=1 |page=597 |doi=10.1186/1471-2164-9-597 |doi-access=free |issn=1471-2164 |pmc=2621215 |pmid=19077236}}</ref>

=== Oil-based, hazardous pollutants in Arctic regions ===
[[Psychrophile|Psychrophilic]] microbes metabolize hydrocarbons which assists in the remediation of hazardous, oil-based pollutants in the Arctic and Antarctic regions. These specific microbes are used in this region due to their ability to perform their functions at extremely cold temperatures.<ref>{{Cite journal |last1=Chaudhary |first1=Dhiraj Kumar |last2=Kim |first2=Dong-Uk |last3=Kim |first3=Dockyu |last4=Kim |first4=Jaisoo |date=2019-03-11 |title=Flavobacterium petrolei sp. nov., a novel psychrophilic, diesel-degrading bacterium isolated from oil-contaminated Arctic soil|journal=Scientific Reports |language=en |volume=9 |issue=1 |pages=4134 |doi=10.1038/s41598-019-40667-7 |pmid=30858439 |bibcode=2019NatSR...9.4134C |issn=2045-2322|pmc=6411956 }}</ref><ref>{{Cite journal |last=Wackett |first=Lawrence P. |date=May 2012 |title=Bioremediation of oil spills: An annotated selection of World Wide Web sites relevant to the topics in Microbial Biotechnology |journal=Microbial Biotechnology |language=en |volume=5 |issue=3 |pages=450–451 |doi=10.1111/j.1751-7915.2011.00330.x |issn=1751-7915 |pmc=3821688}}</ref>

=== Radioactive materials ===
{{see also|Uranium#Biotic and abiotic}}

Any bacteria capable of inhabiting radioactive mediums can be classified as an extremophile. Radioresistant organisms are therefore critical in the bioremediation of radionuclides. Uranium is particularly challenging to contain when released into an environment and very harmful to both human and ecosystem health.<ref>{{Citation |title=Toxicological Profile for Uranium |date=2002-01-12 |work=ATSDR's Toxicological Profiles |publisher=CRC Press |doi=10.1201/9781420061888_ch157 |doi-broken-date=11 November 2024 |isbn=978-1-4200-6188-8 |hdl=2027/mdp.39015032949136 |hdl-access=free}}</ref><ref>{{Cite journal |last=Heising-Goodman |first=Carolyn |date=March 1981 |title=Nuclear Power and Its Environmental Effects |journal=Nuclear Technology |volume=52 |issue=3 |pages=445 |doi=10.13182/nt81-a32724 |bibcode=1981NucTe..52..445H |issn=0029-5450}}</ref> The NANOBINDERS project is equipping bacteria that can survive in uranium rich environments with gene sequences that enable proteins to bind to uranium in mining effluent, making it more convenient to collect and dispose of.<ref>{{Cite journal |last=Marques |first=Catarina R. |date=2018-06-01 |title=Extremophilic Microfactories: Applications in Metal and Radionuclide Bioremediation |journal=Frontiers in Microbiology |volume=9 |page=1191 |doi=10.3389/fmicb.2018.01191 |issn=1664-302X |pmc=5992296 |pmid=29910794 |doi-access=free}}</ref> Some examples are ''[[Shewanella putrefaciens]]'', ''[[Geobacter metallireducens]]'' and some strains of ''[[Burkholderia fungorum]].''{{citation needed|date=May 2023}}

[[Radiotrophic fungi]], which use radiation as an energy source, have been found inside and around the [[Chernobyl Nuclear Power Plant]].<ref name="sciencenews_20070526">{{Cite magazine |url=http://www.sciencenews.org/articles/20070526/fob5.asp |archiveurl=https://web.archive.org/web/20080424001002/http://www.sciencenews.org/articles/20070526/fob5.asp |archivedate=2008-04-24 |magazine=Science News |title=Dark Power: Pigment seems to put radiation to good use |date=May 26, 2007 |volume=171 |number=21 |page=325 |first=Davide |last=Castelvecchi}}</ref>

Radioresistance has also been observed in certain species of macroscopic lifeforms. The lethal dose required to kill up to 50% of a tortoise population is 40,000 [[roentgens]], compared to only 800 roentgens needed to kill 50% of a human population.<ref>{{Cite web|url=https://www.upi.com/Science_News/2002/05/06/Tortoise-blood-fights-radiation-sickness/36041020716491/|title=Tortoise blood fights radiation sickness - UPI.com|website=UPI}}</ref> In experiments exposing [[lepidopteran]] [[insects]] to [[gamma radiation]], significant DNA damage was detected only at 20&nbsp;[[gray (unit)|Gy]] and higher doses, in contrast with human cells that showed similar damage at only 2&nbsp;Gy.<ref>{{Cite journal |last1=Chandna |first1=S. |last2=Dwarakanath |first2=B. S. |last3=Seth |first3=R. K. |last4=Khaitan |first4=D. |last5=Adhikari |first5=J. S. |last6=Jain |first6=V. |year=2004 |title=Radiation responses of Sf9, a highly radioresistant lepidopteran insect cell line |url=https://pubmed.ncbi.nlm.nih.gov/15204707/ |journal=International Journal of Radiation Biology |volume=80 |issue=4 |pages=301–315 |doi=10.1080/09553000410001679794 |pmid=15204707 |s2cid=24978637}}</ref>