Halophiles, salt‐loving organisms that flourish in saline environments, are classified as slight, moderate or extreme, depending on their requirement for sodium chloride. While most marine organisms are slight halophiles, moderate and extreme halophiles are generally more specialised microbes inhabiting hypersaline environments found all over the world in arid, coastal and deep‐sea locations, underground salt mines and artificial salterns. Halophilic microorganisms include heterotrophic, phototrophic and methanogenic archaea, photosynthetic, lithotrophic and heterotrophic bacteria and photosynthetic and heterotrophic eukaryotes. Examples of extremely halophilic microorganisms include Halobacterium sp. NRC‐1, an archaeon; Aphanothece halophytica, a cyanobacterium; and Dunaliella salina, a green alga. Common multicellular halophilic eukaryotes include brine shrimp and brine fly larvae that serve as an important food source for birds. In order to balance the osmotic stress of hypersaline environments, halophilic microorganisms either accumulate organic compatible solutes internally, produce acidic proteins to increase solvation and improve function in high salinity, or use a combination of strategies.

Key Concepts

  • Halophiles are salt‐loving organisms that inhabit saline and hypersaline environments and include prokaryotic (archaeal and bacterial) and eukaryotic organisms.
  • Halophiles may be classified as slight, moderate or extreme, and as obligate halophiles or halotolerant.
  • Many halophiles accumulate compatible solutes in cells to balance the osmotic stress in their environment.
  • Some halophiles produce acidic proteins that function in high salinity by increasing solvation and prevent protein aggregation, precipitation and denaturation.
  • Halophiles and their biomolecules are useful for applications in biotechnology, medicine and industry.

Keywords: archaea; Artemia; biotechnology; Dunaliella; Halobacterium; hypersaline environments; microbial diversity; microbial mat; osmotic protection; salt resistance

Figure 1. Laguna Colorada, Bolivia. Dense growth of halophilic microorganisms in hypersaline environments leads to reddening of the brine. Feeding birds are visible. Photo Dr Daniel Guzmán.
Figure 2. Salt tolerance of halophilic organisms. Relative growth rate is plotted against both per cent salinity and NaCl concentration. The five microorganisms depicted are Synechococcus sp. PCC7002 (PR‐6), a slightly halotolerant cyanobacterium; Fabrea salina (Fs), a moderately halophilic protozoan; Dunaliella salina (Ds), a halophilic green algae; Aphanothece halophytica (Ah), an extremely halophilic cyanobacterium and Halobacterium sp. (H), an extremely halophilic archaeon. The salinity of seawater and the hatch range for brine shrimp are noted.
Figure 3. Structure of a hypersaline microbial mat. Adapted with permission from Caumette 1993 © Springer.
Figure 4. Common halophiles in hypersaline environments: (a) Aphanothece halophytica; (b) Dunaliella salina; (c) Halobacterium sp. NRC‐1; (d) brine shrimp and eggs. Scale bar: 30 µm for a–c, 10 mm for d. Photos Priya DasSarma (a–c) and Al Hartmann, Salt Lake Tribune (d).
Figure 5. Integrated view of the biology of the extremely halophilic archaeon Halobacterium sp. NRC‐1 derived from its genome sequence. Many informational and operational processes revealed from the genome sequence are shown. Transporters in the membrane are highlighted, including light‐driven proton and chloride pumps, bacteriorhodopsin (BR) and halorhodopsin (HR), and the sodium/proton antiporter (NhaC), potassium uniporter (TrkAH and KdpABC), dipeptide and amino acid transporters and anion transporters. Reproduced from Ng et al. 2000 © 2000 National Academy of Sciences, USA.
Figure 6. Extremely halophilic archaeal (a) and human (b) protein–DNA complexes. The models are for TBP–TFB transcription initiation complexes, showing the protein surface charges (red for acidic or negative and blue for basic or positive), surrounding the DNA double helix. The haloarchaeal proteins are acidic, whereas the human proteins are basic. Adapted from DasSarma et al. 2006 © S. DasSarma.
Figure 7. Structure of three common compatible solutes in halophiles. Zwitterionic forms of glycine betaine and ectoine, and the neutral glycerol are commonly found in halophilic microorganisms and help to balance the osmotic stress of the environment.


Abu Ghazleh S, Abed AM and Kempe S (2011) The dramatic drop of the dead sea: background, rates, impacts and solutions. In: Badescu V and Cathcart RB (eds) Macro‐engineering Seawater in Unique Environments, pp. 77–105. Heidelberg: Springer.

Anderson I, Scheuner C, Göker M, et al. (2011) Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes. PLoS One 6: e20237.

Antunes A, Ngugi DK and Stingl U (2011) Microbiology of the Red Sea (and other) deep‐sea anoxic brine lakes. Environmental Microbiology Reports 3: 4.

Bestvater T, Louis P and Galinski EA (2008) Heterologous ectoine production in Escherichia coli: by‐passing the metabolic bottle‐neck. Saline Systems 4: 12.

Bonete MJ, Martínez‐Espinosa RM, Pire C, Zafrilla B and Richardson DJ (2008) Nitrogen metabolism in haloarchaea. Saline Systems 4: 9.

Borin S, Brusetti L, Mapelli F, et al. (2009) Sulfur cycling and methanogenesis primarily drive microbial colonization of the highly sulfidic Urania deep hypersaline basin. Proceedings of the National Academy of Sciences of the United States of America 106: 9151–9156.

Bowers KJ, Mesbah NM and Wiegel J (2006) Biodiversity of poly‐extremophilic Bacteria: does combining the extremes of high salt, alkaline pH and elevated temperature approach a physico‐chemical boundary for life? Saline Systems 5: 9.

Busskamp V, Duebel J, Balya D, et al. (2010) Genetic reactivation of cone photoreceptors restores visual responses in retinitis pigmentosa. Science 329: 413–417.

Capes MD, DasSarma P and DasSarma S (2012) The core and unique proteins of haloarchaea. BMC Genomics 13: 39. DOI: 10.1186/1471-2164-13-39.

Caumette P (1993) Ecology and physiology of phototrophic bacteria and sulphate‐reducing bacteria in marine salterns. Experientia 49: 473–481.

Chen H and Jiang JG (2009) Osmotic responses of Dunaliella to the changes of salinity. Journal of Cellular Physiology 219: 251–258.

Crowley DJ, Boubriak I, Berquist BR, et al. (2006) ) The uvrA, uvrB and uvrC genes are required for repair of ultraviolet light induced DNA photoproducts in Halobacterium sp. NRC‐1. Saline Systems 2: 11.

DasSarma S (2004) Genome sequence of an extremely halophilic archaeon. In: Fraser C, Read T and Nelson KE (eds) Microbial Genomes, pp. 383–399. Totowa, NJ: C.M. Humana Press, Inc..

DasSarma S (2006) Extreme halophiles are models for astrobiology. Microbe 1: 120–127.

DasSarma S, Kennedy SP, Berquist BR, et al. (2001) Genomic perspective on the photobiology of Halobacterium species NRC‐1, a phototrophic, phototactic, and UV‐tolerant haloarchaeon. Photosynthesis Research 70: 3–17.

DasSarma S, Berquist BR, Coker JA, et al. (2006) Post‐genomics of the model haloarchaeon Halobacterium sp. NRC‐1. Saline Systems 2: 3.

DasSarma P, Coker JA, Huse V and DasSarma S (2010a) Halophiles, biotechnology. In: Flickinger MC (ed) Encyclopedia of Industrial Biotechnology, Bioprocess, Bioseparation, and Cell Technology, pp. 2769–2777. Hoboken, NJ: John Wiley & Sons Ltd.

DasSarma P, Klebahn G and Klebahn H (2010b) Translation of Henrich Klebahn's ‘Damaging agents of the klippfish – a contribution to the knowledge of the salt‐loving organisms’. Saline Systems 6: 7.

DasSarma S and DasSarma P (2015a) Gas vesicle nanoparticles for antigen display. Vaccines (Basel) 3: 686–702.

DasSarma S and DasSarma P (2015b) Halophiles and their enzymes: negativity put to good use. Current Opinion in Microbiology 25: 120–126.

DasSarma P, Laye VJ, Harvey J, et al. (2016a) Survival of halophilic Archaea in Earth's cold stratosphere. International Journal of Astrobiology. DOI: 10.1017/S1473550416000410.

DasSarma P, Tuel K, Nierenberg SD, et al. (2016b) Inquiry‐driven teaching & learning using the archaeal microorganism halobacterium NRC‐1. The American Biology Teacher 78: 7–13. DOI: 10.1525/abt.2016.78.1.7.

Dundas I (1998) Was the environment for primordial life hypersaline? Extremophiles 2: 375–377.

Eichler J (2013) Extreme sweetness: protein glycosylation in archaea. Nature Reviews Microbiology 11: 151–156. DOI: 10.1038/nrmicro2957.

Elshahed MS, Najar FZ, Roe BA, et al. (2004) Survey of archaeal diversity reveals an abundance of halophilic Archaea in a low‐salt, sulfide‐ and sulfur‐rich spring. Applied and Environmental Microbiology 70: 2230–2239.

Filker S, Kaiser M, Rosselló‐Móra R, et al. (2014) “Candidatus Haloectosymbiotes riaformosensis” (Halobacteriaceae), an archaeal ectosymbiont of the hypersaline ciliate Platynematum salinarum. Systematic and Applied Microbiology 37: 244–251.

Fish SA, Shepherd TJ, McGenity TJ and Grant WD (2002) Recovery of 16S ribosomal RNA gene fragments from ancient halite. Nature 417: 432–436. Erratum in: Nature (2002) 420: 202.

Flassig RJ, Fachet M, Höffner K, Barton PI and Sundmacher K (2016) Dynamic flux balance modeling to increase the production of high‐value compounds in green microalgae. Biotechnology for Biofuels 9: 165. DOI: 10.1186/s13068-016-0556-4.

Fourcans A, de Oteyza TG, Wieland A, et al. (2004) Characterization of functional bacterial groups in a hypersaline microbial mat community (Salins‐de‐Giraud, Camargue, France). FEMS Microbiology Ecology 51: 55–70.

Gonzalez NA, Vázquez A, Ortiz Zuazaga HG, et al. (2009) Genome‐wide expression profiling of the osmoadaptation response of Debaryomyces hansenii. Yeast 26: 111–124.

Han J, Hou J, Liu H, et al. (2010) Wide distribution among halophilic archaea of a novel polyhydroxyalkanoate synthase subtype with homology to bacterial type III synthases. Applied and Environmental Microbiology 26: 7811–7819.

Han J, Wu LP, Hou J, Zhao D and Xiang H (2015) Biosynthesis, characterization, and hemostasis potential of tailor‐made poly(3‐hydroxybutyrate‐co‐3‐hydroxyvalerate) produced by Haloferax mediterranei. Biomacromolecules 16: 578–588.

Harding T, Brown MW, Simpson AGB and Roger AJ (2016) Osmoadaptative strategy and its molecular signature in obligately halophilic heterotrophic protists. Genome Biology and Evolution 8: 2241–2258. DOI: 10.1093/gbe/evw152.

Horneck G, Klaus DM and Mancinelli RL (2010) Space microbiology. Microbiology and Molecular Biology Reviews 74: 121–156.

Karan R, Capes MD and DasSarma S (2012) Function and biotechnology of extremophilic enzymes in low water activity. Aquatic Biosystems 8: 4.

Karan R, DasSarma P, Balcer‐Kubiczek E, et al. (2013) Bioengineering radioresistance by overproduction of RPA, a mammalian‐type single‐stranded DNA‐binding protein, in a halophilic archaeon. Applied Microbiology and Biotechnology 98: 1737–1747.

Khomyakova M, Bükmez Ö, Thomas LK, Erb TJ and Berg IA (2011) A methylaspartate cycle in haloarchaea. Science 331: 334–337.

King GM (2015) Carbon monoxide as a metabolic energy source for extremely halophilic microbes: implications for microbial activity in Mars regolith. Proceedings of the National Academy of Sciences of the United States of America 112: 4465–4470.

Lamers PP, van de Laak CCW, Kaasenbrood PS, et al. (2010) Carotenoid and fatty acid metabolism in light‐stressed Dunaliella salina. Biotechnology and Bioengineering 106: 638–648.

Lanyi JK (2004) Bacteriorhodopsin. Annual Review of Physiology 66: 665–688.

Larson R, Eilers J, Kreuz K, et al. (2016) Recent desiccation‐related ecosystem changes at Lake Abert, Oregon: a terminal alkaline salt lake. Western North American Naturalist 76: 389–404.

Lenassi M, Vaupotič T, Gunde‐Cimerman N and Plemenitaš A (2007) The MAP kinase HwHog1 from the halophilic black yeast Hortaea werneckii: coping with stresses in solar salterns. Saline Systems 3: 3.

Madern D, Ebel C and Zaccai G (2000) Halophilic adaptation of enzymes. Extremophiles 4: 91–98.

McIsaac RS, Bedbrook CN and Arnold FH (2015) Recent advances in engineering microbial rhodopsins for optogenetics. Current Opinion in Structural Biology 33: 8–15. DOI: 10.1016/j.sbi.2015.05.001.

Narasingarao P, Podell S, Ugalde JA, et al. (2012) De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. The ISME Journal 6: 81–93. DOI: 10.1038/ismej.2011.78.

Ng WV, Kennedy SP, Mahairas GG, et al. (2000) Genome sequence of Halobacterium species NRC‐1. Proceedings of the National Academy of Sciences of the United States of America 97: 12176–12181.

Ollivier B, Caumette P, Garcia JL and Mah RA (1994) Anaerobic bacteria from hypersaline environments. Microbiology Reviews 58: 27–38.

Ongagna‐Yhombi SY, McDonald ND and Boyd EF (2015) Deciphering the role of multiple betaine choline carnitine transporters in the halophile Vibrio parahaemolyticus. Applied and Environmental Microbiology 81: 351–363.

Oren A (2010) Industrial and environmental applications of halophilic microorganisms. Environmental Technology 31: 825–834.

Oxley APA, Lanfranconi MP, Würdemann D, et al. (2010) Halophilic archaea in the human intestinal mucosa. Environmental Microbiology 12: 2398–2410.

Pade N and Hagemann M (2015) Salt acclimation of cyanobacteria and their application in biotechnology. Life 5: 25–49.

Patel S (2016) Salicornia: evaluating the halophytic extremophile as a food and a pharmaceutical candidate. 3 Biotech 6: 104. DOI: 10.1007/s13205-016-0418-6.

Pfeifer F (2015) Haloarchaea and the formation of gas vesicles. Life (Basel) 5: 385–402.

Podell S, Emerson JB, Jones CM, et al. (2014) Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME Journal 8: 979–990. DOI: 10.1038/ismej.2013.221.

Roberts MF (2005) Organic compatible solutes of halotolerant and halophilic microorganisms. Saline Systems 1: 5.

Šajna N, Kaligarič M and Ivajnšič D (2013) Reproduction biology of an alien invasive plant: a case of drought‐tolerant Aster squamatus on the Northern Adriatic Seacoast, Slovenia. In: Managing Protected Areas in Central and Eastern Europe Under Climate Change, pp. 279–288 Volume 58 of the series Advances in Global Change Research, Springer, Netherlands.

Sato T and Atomi H (2011) Novel metabolic pathways in Archaea. Current Opinion in Microbiology 14: 307–314.

Sorokin DY, Tourova TP, Abbas B, Suhacheva MV and Muyzer G (2012) Desulfonatronovibrio halophilus sp. nov., a novel moderately halophilic sulfate‐reducing bacterium from hypersaline chloride‐sulfate lakes in Central Asia. Extremophiles 16: 411–417. DOI: 10.1007/s00792-012-0440-5.

Steitz TA (2010) From the structure and function of the ribosome to new antibiotics. Angewandte Chemie International Edition (Nobel Lecture) 49: 4381–4398.

Suresh AV and Lin CK (1992) Tilapia culture in saline waters: a review. Aquaculture 106: 201–226.

Ventosa A, Márquez MC, Garabito MJ and Arahal DR (1998) Moderately halophilic gram‐positive bacterial diversity in hypersaline environments. Extremophiles 2: 297–304.

Ventura Y, Eshel A, Pasternak D and Sagi M (2014) The development of halophyte‐based agriculture: past and present. Annals of Botany 115: 529–540. DOI: 10.1093/aob/mcu173.

Wagner NL, Greco JA, Ranaghan MJ and Birge RR (2013) Directed evolution of bacteriorhodopsin for applications in bioelectronics. Journal of the Royal Society Interface 10: 20130197. DOI: 10.1098/rsif.2013.0197.

Wurtsbaugh WA, Miller C and Null S et al. (2016) Impacts of water development on Great Salt Lake and the Wasatch Front. Watershed Sciences Faculty Publications Paper 875. http://digitalcommons.usu.edu/wats_facpub/875

Yin J, Chen JC, Wu Q and Chen GQ (2015) Halophiles, coming stars for industrial biotechnology. Biotechnology Advances 33: 1433–1442. DOI: 10.1016/j.biotechadv.2014.10.008.

Zhao R, Cao Y, Xu H, et al. (2011) Analysis of expressed sequence tags from the green alga Dunaliella salina (Chlorophyta). Journal of Phycology 47: 1454–1460.

Further Reading

DasSarma S, Fleischmann EM, Robb FT, et al. (eds) (1995) Archaea, A Laboratory Manual – Halophiles. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

Gunde‐Cimerman N, Oren A and Plemenitaš A (eds) (2005) Adaptation to Life at High Salt Concentrations in Archaea, Bacteria, and Eukarya. Dordrecht, Netherlands: Springer.

Javor B (1989) Hypersaline Environments, Microbiology and Biogeochemistry. Berlin: Springer‐Verlag.

Maheshwari DK and Saraf M (eds) (2015) Halophiles‐Biodiversity and Sustainable Exploitation. Cham Heidelberg New York Dordrecht London: Springer.

Vreeland RH and Hochstein LI (eds) (1993) The Biology of Halophilic Bacteria. Boca Raton, FL: CRC Press, Inc.

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DasSarma, Shiladitya, and DasSarma, Priya(May 2017) Halophiles. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000394.pub4]