Editing Halophile

{{Not to be confused with|text=[[fandom]] of the [[Halo (franchise)|Halo]] video game franchise}}{{Short description|Organisms that live in high salt concentrations}}
A '''halophile''' (from the Greek word for 'salt-loving') is an [[extremophile]] that thrives in high [[salt]] concentrations. In chemical terms, halophile refers to a [[Lewis acids and bases|Lewis acidic]] species that has some ability to extract halides from other chemical species. 

While most halophiles are classified into the domain [[Archaea]], there are also [[bacteria]]l halophiles and some [[Eukaryote|eukaryotic]] species, such as the [[alga]] ''[[Dunaliella salina]]'' and [[fungus]] ''[[Wallemia ichthyophaga]]''. Some well-known species give off a red color from carotenoid compounds, notably [[bacteriorhodopsin]]. 

Halophiles can be found in water bodies with salt concentration more than five times greater than that of the ocean, such as the [[Great Salt Lake]] in Utah, [[Owens Lake]] in California, the [[Lake Urmia]] in Iran, the [[Dead Sea]], and in [[evaporation pond]]s. They are theorized to be a possible analogues for modeling extremophiles that might live in the salty subsurface water ocean of Jupiter's [[Europa (moon)|Europa]] and similar moons.<ref>{{cite journal |last1=Marion |first1=Giles M. |last2=Fritsen|first2=Christian H. |last3=Eicken |first3=Hajo |last4=Payne |first4=Meredith C. |date=2003-12-01 |title=The search for life on Europa: Limiting environmental factors, potential habitats, and Earth analogues |journal=Astrobiology |volume=3 |issue=4 |pages=785–811 |doi=10.1089/153110703322736105 |pmid=14987483 |bibcode=2003AsBio...3..785M |issn=1531-1074 |url=https://www.liebertpub.com/doi/abs/10.1089/153110703322736105|url-access=subscription }}</ref>

== Classification ==
Halophiles are categorized by the extent of their [[halotolerance]]: slight, moderate, or extreme. Slight halophiles prefer 0.3 to 0.8 [[Molar concentration|M]] (1.7 to 4.8%—seawater is 0.6 M or 3.5%), moderate halophiles 0.8 to 3.4 M (4.7 to 20%), and extreme halophiles 3.4 to 5.1 M (20 to 30%) salt content.<ref name=Ollivier>{{cite journal | vauthors = Ollivier B, Caumette P, Garcia JL, Mah RA | date = March 1994 | title = Anaerobic bacteria from hypersaline environments | journal = Microbiological Reviews | volume = 58 | issue = 1 | pages = 27–38 | doi = 10.1128/MMBR.58.1.27-38.1994 | pmid = 8177169 | pmc = 372951 }}</ref>  Halophiles require [[sodium chloride]] (salt) for growth, in contrast to halotolerant organisms, which do not require salt but can grow under saline conditions.

== Lifestyle ==
High salinity represents an extreme environment in which relatively few organisms have been able to adapt and survive. Most halophilic and all [[halotolerance|halotolerant]] organisms expend energy to exclude salt from their [[cytoplasm]] to avoid protein aggregation ('[[salting out]]'). To survive the high salinities, halophiles employ two differing strategies to prevent [[desiccation]] through [[osmosis|osmotic]] movement of water out of their cytoplasm. Both strategies work by increasing the internal [[osmolarity]] of the cell. The first strategy is employed by some archaea, the majority of halophilic bacteria, [[yeast]]s, [[algae]], and [[fungi]]; the organism accumulates [[organic compounds]] in the cytoplasm—[[osmoprotectant]]s which are known as compatible solutes. These can be either synthesised or accumulated from the environment.<ref name="Santos">{{cite journal | vauthors = Santos H, da Costa MS | year = 2002 | title = Compatible solutes of organisms that live in hot saline environments | journal = Environmental Microbiology | volume = 4 | issue = 9| pages = 501–509 | doi=10.1046/j.1462-2920.2002.00335.x| pmid = 12220406 | hdl = 10316/8134 | hdl-access = free }}</ref> The most common compatible solutes are [[pH|neutral]] or [[zwitterion]]ic, and include [[amino acid]]s, [[sugar]]s, [[polyol]]s, [[betaine]]s, and [[ectoine]]s, as well as derivatives of some of these compounds.

The second, more radical adaptation involves selectively absorbing [[potassium]] (K<sup>+</sup>) ions into the cytoplasm. This adaptation is restricted to the extremely halophilic archaeal family ''[[Halobacteriaceae]]'', the moderately halophilic bacterial order ''[[Halanaerobiales]]'', and the extremely halophilic bacterium ''[[Salinibacter ruber]]''. The presence of this adaptation in three distinct evolutionary lineages suggests [[convergent evolution]] of this strategy, it being unlikely to be an ancient characteristic retained in only scattered groups or passed on through massive lateral gene transfer.<ref name=Santos/> The primary reason for this is the entire intracellular machinery (enzymes, structural proteins, etc.) must be adapted to high salt levels, whereas in the compatible solute adaptation, little or no adjustment is required to intracellular macromolecules; in fact, the compatible solutes often act as more general stress protectants, as well as just osmoprotectants.<ref name=Santos/>

Of particular note are the extreme halophiles or [[haloarchaea]] (often known as [[halobacteria]]), a group of archaea, which require at least a 2 M salt concentration and are usually found in saturated solutions (about 36% [[Mass concentration (chemistry)#Usage in biology|w/v]] salts). These are the primary inhabitants of salt lakes, inland seas, and evaporating ponds of seawater, such as the deep [[saltern]]s, where they tint the water column and sediments bright colors. These species most likely perish if they are exposed to anything other than a very high-concentration, salt-conditioned environment. These prokaryotes require salt for growth. The high concentration of sodium chloride in their environment limits the availability of oxygen for respiration. Their cellular machinery is adapted to high salt concentrations by having charged [[amino acid]]s on their surfaces, allowing the retention of water molecules around these components. They are [[heterotroph]]s that normally respire by aerobic means. Most halophiles are unable to survive outside their high-salt native environments. Many halophiles are so fragile that when they are placed in distilled water, they immediately [[cytolysis|lyse]] from the change in osmotic conditions.

Halophiles use a variety of energy sources and can be aerobic or anaerobic; anaerobic halophiles include phototrophic, fermentative, sulfate-reducing, homoacetogenic, and methanogenic species.<ref name=Ollivier/><ref>{{cite journal | vauthors = Oren A | date = January 2002 | title = Diversity of halophilic microorganisms: environments, phylogeny, physiology, and applications | journal = Journal of Industrial Microbiology & Biotechnology | volume = 28 | issue = 1 | pages = 56–63 | pmid = 11938472 | doi = 10.1038/sj/jim/7000176 | s2cid = 24223243 }}</ref>

The Haloarchaea, and particularly the family Halobacteriaceae, are members of the domain ''[[Archaea]]'', and comprise the majority of the prokaryotic population in [[hypersaline lake|hypersaline environments]].<ref name="Oren">{{cite journal |last1=Oren |first1=Aharon |year=2002 |title=Molecular ecology of extremely halophilic Archaea and Bacteria |journal=FEMS Microbiology Ecology |volume=39 |issue=1 |pages=1–7 |issn=0168-6496 |doi=10.1111/j.1574-6941.2002.tb00900.x |pmid=19709178 |doi-access=free}}</ref> Currently, 15 recognised genera are in the family.<ref>{{cite journal | vauthors = Gutierrez MC, Kamekura M, Holmes ML, Dyall-Smith ML, Ventosa A | date = December 2002 | title = Taxonomic characterization of Haloferax sp. (" H. alicantei") strain Aa 2.2: description of Haloferax lucentensis sp. nov | journal = Extremophiles | volume = 6 | issue = 6 | pages = 479–83 | pmid = 12486456 | doi = 10.1007/s00792-002-0282-7 | s2cid = 24337996 }}</ref> The domain [[Bacteria]] (mainly ''[[Salinibacter ruber]]'') can comprise up to 25% of the prokaryotic community, but is more commonly a much lower percentage of the overall population.<ref>{{cite journal | vauthors = Antón J, Rosselló-Mora R, Rodríguez-Valera F, Amann R | date = July 2000 | title = Extremely halophilic bacteria in crystallizer ponds from solar salterns | journal = Applied and Environmental Microbiology | volume = 66 | issue = 7 | pages = 3052–3057 | pmid = 10877805 | pmc = 92110 | doi = 10.1128/aem.66.7.3052-3057.2000 }}</ref> At times, the alga ''[[Dunaliella salina]]'' can also proliferate in this environment.<ref>{{cite journal | vauthors =Casamayor EO, Massana R, Benlloch S, Øvreås L, Díez B, Goddard VJ, Gasol JM, Joint I, Rodríguez-Valera F, Pedrós-Alió C | year = 2002 | title = Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern | journal = Environmental Microbiology | volume = 4 | issue = 6 | pages = 338–348 | doi=10.1046/j.1462-2920.2002.00297.x | pmid = 12071979 }}</ref>

A comparatively wide range of taxa has been isolated from saltern crystalliser ponds, including members of these genera: ''Haloferax, Halogeometricum, Halococcus, Haloterrigena, Halorubrum, Haloarcula'', and ''Halobacterium''.<ref name=Oren /> However, the viable counts in these cultivation studies have been small when compared to total counts, and the numerical significance of these isolates has been unclear. Only recently has it become possible to determine the identities and relative abundances of organisms in natural populations, typically using [[Polymerase chain reaction|PCR]]-based strategies that target 16[[Svedberg|S]] small subunit ribosomal ribonucleic acid (16S rRNA) genes.<ref>{{Cite journal |last=Ali |first=Ahmed Mohamed |last2=Abdel-Rahman |first2=Tahany M.A. |last3=Farahat |first3=Mohamed G. |date=2024-03-28 |title=Bioprospecting of Culturable Halophilic Bacteria Isolated from Mediterranean Solar Saltern for Extracellular Halotolerant Enzymes |url=http://www.mbl.or.kr/journal/view.html?doi=10.48022/mbl.2401.01010 |journal=Microbiology and Biotechnology Letters |language=en |volume=52 |issue=1 |pages=76–87 |doi=10.48022/mbl.2401.01010 |issn=1598-642X}}</ref> While comparatively few studies of this type have been performed, results from these suggest that some of the most readily isolated and studied genera may not in fact be significant in the ''in situ'' community. This is seen in cases such as the genus ''[[Haloarcula]]'', which is estimated to make up less than 0.1% of the'' in situ'' community,<ref name="pmid11207773">{{cite journal | vauthors = Antón J, Llobet-Brossa E, Rodríguez-Valera F, Amann R | date = December 1999 | title = Fluorescence in situ hybridization analysis of the prokaryotic community inhabiting crystallizer ponds | journal = Environmental Microbiology | volume = 1 | issue = 6 | pages = 517–23 | pmid = 11207773 | doi = 10.1046/j.1462-2920.1999.00065.x }}</ref> but commonly appears in isolation studies.

== Genomic and proteomic signature ==

The comparative genomic and proteomic analysis showed distinct molecular signatures exist for the environmental adaptation of halophiles. At the protein level, the halophilic species are characterized by low hydrophobicity, an overrepresentation of acidic residues, underrepresentation of Cys, lower propensities for helix formation, and higher propensities for coil structure. The core of these proteins is less hydrophobic, such as [[DHFR]], that was found to have narrower β-strands.<ref>{{cite journal | vauthors = Kastritis PL, Papandreou NC, Hamodrakas SJ | date = October 2007 | title = Haloadaptation: Insights from comparative modeling studies of halophilic archaeal DHFRs | journal = International Journal of Biological Macromolecules | volume = 41 | issue = 4 | pages = 447–453 | pmid = 17675150 | doi = 10.1016/j.ijbiomac.2007.06.005 }}</ref>
In one study, the net charges (at pH 7.4) of the ribosomal proteins (r-proteins) that comprise the ''S10-spc'' cluster were observed to have an inverse relationship with the halophilicity/halotolerance levels in both bacteria and archaea.<ref>{{cite journal | vauthors = Tirumalai MR, Anane-Bediakoh D, Rajesh S, Fox GE| date = December 2021 | title = Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance | journal = Microbiol Spectr| volume = 9 | issue = 3 | page = e0178221 | pmid = 34908470 | pmc = 8672879 | doi = 10.1128/spectrum.01782-21 }}</ref> At the DNA level, the halophiles exhibit distinct dinucleotide and codon usage.<ref>{{cite journal | vauthors = Paul S, Bag SK, Das S, Harvill ET, Dutta C | date = April 2008 | title = Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes | journal = Genome Biology | volume = 9 | issue = 4 | page = R70 | pmid = 18397532 | pmc = 2643941 | doi = 10.1186/gb-2008-9-4-r70 | doi-access = free }}</ref>

== Examples ==
''[[Halobacteriaceae]]'' is a family that includes a large part of halophilic archaea.<ref name="oren2">{{cite journal |last1=Oren |first1=Aharon |date=September 2014 |title=Taxonomy of halophilic Archaea: Current status and future challenges |journal=Extremophiles |volume=18 |issue=5 |pages=825–834 |doi=10.1007/s00792-014-0654-9 |pmid=25102811 |s2cid=5395569}}</ref> The genus ''[[Halobacterium]]'' under it has a high tolerance for elevated levels of salinity. Some species of halobacteria have acidic proteins that resist the denaturing effects of salts. ''[[Halococcus]]'' is another genus of the family Halobacteriaceae.

Some [[hypersaline lake]]s are habitat to numerous families of halophiles. For example, the [[Makgadikgadi Pans]] in [[Botswana]] form a vast, seasonal, high-salinity water body that manifests halophilic species within the [[diatom]] genus ''[[Nitzschia]]'' in the family [[Bacillariaceae]], as well as species within the genus ''[[Lovenula]]'' in the family [[Diaptomidae]].<ref>{{cite web |author=Hogan, C. Michael |date=5 December 2008 |title= Makgadikgadi – ancient settlement in Botswana |website=The Megalithic Portal |editor=Burnham, A. |url=http://www.megalithic.co.uk/article.php?sid=22373&mode=&order=0}} — website hosts a collection of fossil and archeological find-site profiles.</ref> Owens Lake in California also contains a large population of the halophilic bacterium ''Halobacterium halobium''.

''[[Wallemia ichthyophaga]]'' is a [[Basidiomycota|basidiomycetous]] [[fungus]], which requires at least 1.5 M [[sodium chloride]] for ''in vitro'' growth, and it thrives even in media saturated with salt.<ref>{{cite journal | vauthors = Zalar P, Sybren de Hoog G, Schroers HJ, Frank JM, Gunde-Cimerman N | date = May 2005 | title = Taxonomy and phylogeny of the xerophilic genus Wallemia (Wallemiomycetes and Wallemiales, ''cl. et ord. nov''.) | journal = Antonie van Leeuwenhoek | volume = 87 | issue = 4 | pages = 311–28 | pmid = 15928984 | doi = 10.1007/s10482-004-6783-x | s2cid = 4821447 }}</ref> Obligate requirement for salt is an exception in fungi. Even species that can tolerate salt concentrations close to saturation (for example ''[[Hortaea werneckii]]'') in almost all cases grow well in standard microbiological media without the addition of salt.<ref>{{cite journal | vauthors = Gostincar C, Grube M, de Hoog S, Zalar P, Gunde-Cimerman N | date = January 2010 | title = Extremotolerance in fungi: evolution on the edge | journal = FEMS Microbiology Ecology | volume = 71 | issue = 1 | pages = 2–11 | pmid = 19878320 | doi = 10.1111/j.1574-6941.2009.00794.x | doi-access = free }}</ref>

The fermentation of salty foods (such as [[soy sauce]], [[douchi|Chinese fermented beans]], [[salted cod]], salted [[Anchovies as food|anchovies]], [[sauerkraut]], etc.) often involves halophiles as either essential ingredients or accidental contaminants. One example is ''[[Chromohalobacter beijerinckii]]'', found in salted beans preserved in brine and in salted [[herring]]. ''[[Tetragenococcus halophilus]]'' is found in salted anchovies and soy sauce.

''Artemia'' is a ubiquitous genus of small halophilic crustaceans living in salt lakes (such as Great Salt Lake) and solar salterns that can exist in water approaching the precipitation point of NaCl (340 g/L)<ref>{{cite journal | vauthors = Gajardo GM, Beardmore JA | year = 2012 | title = The brine shrimp artemia: adapted to critical life conditions | language = en | journal = Frontiers in Physiology | volume = 3 | pages = 185 | pmid = 22737126 | pmc = 3381296 | doi = 10.3389/fphys.2012.00185 | doi-access = free }}</ref><ref>{{cite journal | vauthors = de Vos S, Van Stappen G, Vuylsteke M, Rombauts S, Bossier P |year=2018 |title=Identification of salt stress response genes using the Artemia transcriptome |journal = Aquaculture |volume = 500 |pages = 305–314 |doi=10.1016/j.aquaculture.2018.09.067 |s2cid = 92842322}}</ref> and can withstand strong osmotic shocks due to its mitigating strategies for fluctuating salinity levels, such as its unique larval salt gland and osmoregulatory capacity.

== See also ==
* [[Arid Forest Research Institute]]
* [[Biosalinity]]
* [[Halotolerance]]

== References ==
{{reflist|25em}}

== Further reading ==
{{refbegin|25em}}
* {{cite journal | vauthors = Weinisch L, Kühner S, Roth R, Grimm M, Roth T, Netz DJ, Pierik AJ, Filker S | display-authors = 6 | title = Identification of osmoadaptive strategies in the halophile, heterotrophic ciliate Schmidingerothrix salinarum | journal = PLOS Biology | volume = 16 | issue = 1 | pages = e2003892 | date = January 2018 | pmid = 29357351 | pmc = 5794333 | doi = 10.1371/journal.pbio.2003892 | veditors = Sourjik V | doi-access = free }}
* {{cite journal | vauthors = Yin J, Fu XZ, Wu Q, Chen JC, Chen GQ | title = Development of an enhanced chromosomal expression system based on porin synthesis operon for halophile Halomonas sp | journal = Applied Microbiology and Biotechnology | volume = 98 | issue = 21 | pages = 8987–97 | date = November 2014 | pmid = 25070598 | doi = 10.1007/s00253-014-5959-1 | s2cid = 1773197 }}
* {{cite journal | vauthors = Zaretsky M, Roine E, Eichler J | title = Halorubrum sp. PV6 | journal = Frontiers in Microbiology | volume = 9 | pages = 2133 | date = 2018-09-07 | pmid = 30245679 | pmc = 6137143 | doi = 10.3389/fmicb.2018.02133 | doi-access = free }}
* {{cite journal | vauthors = Batista-García RA, Balcázar-López E, Miranda-Miranda E, Sánchez-Reyes A, Cuervo-Soto L, Aceves-Zamudio D, Atriztán-Hernández K, Morales-Herrera C, Rodríguez-Hernández R, Folch-Mallol J | display-authors = 6 | title = Characterization of lignocellulolytic activities from a moderate halophile strain of Aspergillus caesiellus isolated from a sugarcane bagasse fermentation | journal = PLOS ONE | volume = 9 | issue = 8 | pages = e105893 | date = 2014-08-27 | pmid = 25162614 | pmc = 4146556 | doi = 10.1371/journal.pone.0105893 | veditors = Mormile MR | bibcode = 2014PLoSO...9j5893B | doi-access = free }}
* {{cite journal | vauthors = Chua MJ, Campen RL, Wahl L, Grzymski JJ, Mikucki JA | title = Genomic and physiological characterization and description of Marinobacter gelidimuriae sp. nov., a psychrophilic, moderate halophile from Blood Falls, an antarctic subglacial brine | journal = FEMS Microbiology Ecology | volume = 94 | issue = 3 | date = March 2018 | pmid = 29444218 | doi = 10.1093/femsec/fiy021 | doi-access = free }}
* {{cite journal | vauthors = González-Martínez S, Galindo-Sánchez C, López-Landavery E, Paniagua-Chávez C, Portillo-López A | title = Aspergillus loretoensis, a single isolate from marine sediment of Loreto Bay, Baja California Sur, México resulting as a new obligate halophile species | journal = Extremophiles | volume = 23 | issue = 5 | pages = 557–568 | date = September 2019 | pmid = 31227903 | doi = 10.1007/s00792-019-01107-6 | s2cid = 195246075 }}
* {{cite journal | vauthors = Laye VJ, DasSarma S | title = An Antarctic Extreme Halophile and Its Polyextremophilic Enzyme: Effects of Perchlorate Salts | journal = Astrobiology | volume = 18 | issue = 4 | pages = 412–418 | date = April 2018 | pmid = 29189043 | pmc = 5910040 | doi = 10.1089/ast.2017.1766 | bibcode = 2018AsBio..18..412L }}
* {{cite journal | vauthors = Ongagna-Yhombi SY, McDonald ND, Boyd EF | title = Deciphering the role of multiple betaine-carnitine-choline transporters in the Halophile Vibrio parahaemolyticus | journal = Applied and Environmental Microbiology | volume = 81 | issue = 1 | pages = 351–63 | date = January 2015 | pmid = 25344241 | pmc = 4272712 | doi = 10.1128/AEM.02402-14 | veditors = Pettinari MJ }}
* {{cite journal | vauthors = Solovchenko AE, Selivanova EA, Chekanov KA, Sidorov RA, Nemtseva NV, Lobakova ES | title = Induction of Secondary Carotenogenesis in New Halophile Microalgae from the Genus Dunaliella (Chlorophyceae) | journal = Biochemistry. Biokhimiia | volume = 80 | issue = 11 | pages = 1508–13 | date = November 2015 | pmid = 26615443 | doi = 10.1134/S0006297915110139 | s2cid = 9259513 }}
* {{cite journal | vauthors = Strillinger E, Grötzinger SW, Allers T, Eppinger J, Weuster-Botz D | title = Production of halophilic proteins using Haloferax volcanii H1895 in a stirred-tank bioreactor | journal = Applied Microbiology and Biotechnology | volume = 100 | issue = 3 | pages = 1183–1195 | date = February 2016 | pmid = 26428236 | doi = 10.1007/s00253-015-7007-1 | hdl = 10754/579494 | s2cid = 15001309 | hdl-access = free }}
* {{cite journal | vauthors = Tao P, Li H, Yu Y, Gu J, Liu Y | title = Ectoine and 5-hydroxyectoine accumulation in the halophile Virgibacillus halodenitrificans PDB-F2 in response to salt stress | journal = Applied Microbiology and Biotechnology | volume = 100 | issue = 15 | pages = 6779–6789 | date = August 2016 | pmid = 27106915 | doi = 10.1007/s00253-016-7549-x | s2cid = 14058059 }}
* {{cite journal | vauthors = Van-Thuoc D, Huu-Phong T, Minh-Khuong D, Hatti-Kaul R | title = Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) production by a moderate halophile Yangia sp. ND199 using glycerol as a carbon source | journal = Applied Biochemistry and Biotechnology | volume = 175 | issue = 6 | pages = 3120–32 | date = March 2015 | pmid = 25600362 | doi = 10.1007/s12010-015-1479-4 | s2cid = 30712412 }}
{{refend}}

== External links ==
* [http://www.haloarchaea.com HaloArchaea.com]
* [http://textbookofbacteriology.net/procaryotes.html Important Groups of Prokaryotes] - Kenneth Todar
* [https://web.archive.org/web/20070827013216/http://library.thinkquest.org/C003763/index.php?page=origin07 Astrobiology: extremophiles- life in extreme environments]

{{Extremophile}}
{{Salt topics}}

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[[Category:Halophiles|*]]