Haloarchaea

The extremely halophilic, aerobic members of Archaea are classified within the family Halobacteriaceae, order Halobacteriales in Class III. Halobacteria of the phylum Euryarchaeota (International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Halobacteriaceae). As of May 2016, the family Halobacteriaceae comprises 213 species in 50 genera.

Gupta et al.{{cite journal | vauthors = Gupta RS, Naushad S, Baker S | title = Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 65 | issue = Pt 3 | pages = 1050–1069 | date = March 2015 | pmid = 25428416 | doi = 10.1099/ijs.0.070136-0 | doi-access = free }}{{cite journal | vauthors = Gupta RS, Naushad S, Fabros R, Adeolu M | title = A phylogenomic reappraisal of family-level divisions within the class Halobacteria: proposal to divide the order Halobacteriales into the families Halobacteriaceae, Haloarculaceae fam. nov., and Halococcaceae fam. nov., and the order Haloferacales into the families, Haloferacaceae and Halorubraceae fam nov | journal = Antonie van Leeuwenhoek | volume = 109 | issue = 4 | pages = 565–587 | date = April 2016 | pmid = 26837779 | doi = 10.1007/s10482-016-0660-2 | s2cid = 10437481 }} divides the class of Halobacteria in three orders.

• Halobacteriales Grant and Larsen 1989
• Haladaptataceae Cui et al. 2023
• Haloarculaceae Gupta et al. 2016, 10 genera
• Halobacteriaceae Gibbons 1974, 24 genera
• Halococcaceae Gupta et al. 2016, 1 genus
• Natronoarchaeaceae Sorokin et al. 2023
• Haloferacales Gupta et al. 2015
• Haloferacaceae Gupta et al. 2015, 10 genera
• Halorubraceae Gupta et al. 2016, 9 genera
• Halorutilales Durán-Viseras et al. 2023
• Halorutilaceae Durán-Viseras et al. 2023
• Natrialbales Gupta et al. 2015
• Natrialbaceae Gupta et al. 2015, 18 genera

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN){{cite web|author=J.P. Euzéby |url=https://lpsn.dsmz.de/class/halobacteria |title=Halobacteria |accessdate=2021-11-17 |publisher=List of Prokaryotic names with Standing in Nomenclature (LPSN)}} and National Center for Biotechnology Information (NCBI).{{cite web |author = Sayers |display-authors=et al.| url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=183963&lvl=3&keep=1&srchmode=1&unlock |title=Halobacteria |accessdate=2022-06-05 |publisher=National Center for Biotechnology Information (NCBI) taxonomy database}}

Note: * polyphyletic Natronoarchaeaceae

: ** polyphyletic Haloferacaceae

Detailed phylogenetic and comparative analyses of genome sequences from members of the class Haloarchaea has led to division of this class into three orders, Halobacteriales, Haloferacales and Natrialbales, which can be reliably distinguished from each other as well as all other archaea/bacteria through molecular signatures known as conserved signature indels (CSIs). These studies have also identified 68 conserved signature proteins (CSPs) whose homologs are only found in the members of these three orders and 13 CSIs in different proteins that are uniquely present in the members of the class Haloarchaea. These CSIs are present in the following proteins: DNA topoisomerase VI, nucleotide sugar dehydrogenase, ribosomal protein L10e, RecJ-like exonuclease, ribosomal protein S15, adenylosuccinate synthase, phosphopyruvate hydratase, RNA-associated protein, threonine synthase, aspartate aminotransferase, precorrin-8x methylmutase, protoporphyrin IX magnesium chelatase and geranylgeranylglyceryl phosphate synthase-like protein.

Image:San Francisco Bay Salt Ponds.jpg, near Fremont, California]]

Haloarchaea require salt concentrations in excess of 2 mol/L (or about 10%, three times the ocean salinity which is around 35g/L salt – 3.5%) in the water to grow, and optimal growth usually occurs at much higher concentrations, typically 20–30% (3.4 - 5.2 mol/L of NaCl). {{cite journal | vauthors = Li J, Gao Y, Dong H, Sheng GP | title = Haloarchaea, excellent candidates for removing pollutants from hypersaline wastewater | journal = Trends in Biotechnology | volume = 40 | issue = 2 | pages = 226–239 | date = February 2022 | pmid = 34284891 | doi = 10.1016/j.tibtech.2021.06.006 | s2cid = 236158869 }} However, Haloarchaea can grow up to saturation (about 37% salts).{{cite journal | vauthors = Yadav AN, Sharma D, Gulati S, Singh S, Dey R, Pal KK, Kaushik R, Saxena AK | display-authors = 6 | title = Haloarchaea Endowed with Phosphorus Solubilization Attribute Implicated in Phosphorus Cycle | journal = Scientific Reports | volume = 5 | pages = 12293 | date = July 2015 | pmid = 26216440 | pmc = 4516986 | doi = 10.1038/srep12293 | bibcode = 2015NatSR...512293Y }} Optimal growth also occurs when pH is neutral or basic and at 45°C temperature. Some haloarchaea can grow even when temperatures exceed 50°C.

Haloarchaea are found mainly in hypersaline lakes and solar salterns. Their high densities in the water often lead to pink or red colourations of the water (the cells possessing high levels of carotenoid pigments, presumably for UV protection).{{Cite journal |title=Extreme Microbes | vauthors = DasSarma S |journal=American Scientist |date=2007 |volume=95 |issue=3 | pages=224–231 |issn=0003-0996 | doi=10.1511/2007.65.1024}} The pigmentation will become enhanced when oxygen levels are low due to an increase in a red pigmented ATP. Some of them live in underground rock salt deposits, including one from middle-late Eocene (38-41 million years ago).{{cite journal | vauthors = Jaakkola ST, Zerulla K, Guo Q, Liu Y, Ma H, Yang C, Bamford DH, Chen X, Soppa J, Oksanen HM | display-authors = 6 | title = Halophilic archaea cultivated from surface sterilized middle-late eocene rock salt are polyploid | journal = PLOS ONE | volume = 9 | issue = 10 | pages = e110533 | date = 2014 | pmid = 25338080 | pmc = 4206341 | doi = 10.1371/journal.pone.0110533 | doi-access = free | bibcode = 2014PLoSO...9k0533J }} Some even older ones from more than 250 million years ago have been reported.{{cite journal | vauthors = Vreeland RH, Rosenzweig WD, Lowenstein T, Satterfield C, Ventosa A | title = Fatty acid and DNA analyses of Permian bacteria isolated from ancient salt crystals reveal differences with their modern relatives | journal = Extremophiles | volume = 10 | issue = 1 | pages = 71–78 | date = February 2006 | pmid = 16133658 | doi = 10.1007/s00792-005-0474-z | s2cid = 25102006 }} Haloarchaea are also used to treat water high in salinity. This is due to its ability to withstand high nutrient levels and the heavy metals that may be present.

Haloarchaea can grow at water activity (a_w) close to 0.75, even though a_w lower than 0.90 is inhibitory to most microbes.{{cite journal | vauthors = Stevenson A, Cray JA, Williams JP, Santos R, Sahay R, Neuenkirchen N, McClure CD, Grant IR, Houghton JD, Quinn JP, Timson DJ, Patil SV, Singhal RS, Antón J, Dijksterhuis J, Hocking AD, Lievens B, Rangel DE, Voytek MA, Gunde-Cimerman N, Oren A, Timmis KN, McGenity TJ, Hallsworth JE | display-authors = 6 | title = Is there a common water-activity limit for the three domains of life? | journal = The ISME Journal | volume = 9 | issue = 6 | pages = 1333–1351 | date = June 2015 | pmid = 25500507 | pmc = 4438321 | doi = 10.1038/ismej.2014.219 }} The high solute concentration causes osmotic stress on microbes, which can cause cell lysis, unfolding of proteins, and inactivation of enzymes.{{cite journal| vauthors = Cheftel JC |title=Review : High-pressure, microbial inactivation and food preservation|journal=Food Science and Technology International|volume=1|issue=2–3|pages=75–90|language=en|doi=10.1177/108201329500100203|date=1 August 1995|s2cid=85703396}} Haloarchaea combat this by retaining compatible solutes such as potassium chloride (KCl) in their intracellular space to allow them to balance osmotic pressure.{{cite book| vauthors = da Costa MS, Santos H, Galinski EA |title=Biotechnology of Extremophiles|volume=61|publisher=Springer, Berlin, Heidelberg |pages=117–153 |doi=10.1007/bfb0102291|date=1998|series=Advances in Biochemical Engineering/Biotechnology|pmid=9670799|isbn=978-3-540-63817-9}} Retaining these salts is referred to as the “salt-in” method where the cell accumulates a high internal concentration of potassium.{{cite journal | vauthors = Williams TJ, Allen M, Tschitschko B, Cavicchioli R | title = Glycerol metabolism of haloarchaea | journal = Environmental Microbiology | volume = 19 | issue = 3 | pages = 864–877 | date = March 2017 | pmid = 27768817 | doi = 10.1111/1462-2920.13580 | doi-access = free | hdl = 1959.4/unsworks_49888 | hdl-access = free }} Because of the elevated potassium levels, haloarchaea have specialized proteins that have a highly negative surface charge to tolerate high potassium concentrations.{{cite journal | vauthors = Soppa J, Baumann A, Brenneis M, Dambeck M, Hering O, Lange C | title = Genomics and functional genomics with haloarchaea | journal = Archives of Microbiology | volume = 190 | issue = 3 | pages = 197–215 | date = September 2008 | pmid = 18493745 | doi = 10.1007/s00203-008-0376-4 | s2cid = 21222667 }}

Haloarchaea have adapted to use glycerol as a carbon and energy source in catabolic processes, which is often present in high salt environments due to Dunaliella species that produce glycerol in large quantities.

Bacteriorhodopsin is used to absorb light, which provides energy to transport protons (H⁺) across the cellular membrane. The concentration gradient generated from this process can then be used to synthesize ATP. Many haloarchaea also possess related pigments, including halorhodopsin, which pump chloride ions in the cell in response to photons, creating a voltage gradient and assisting in the production of energy from light. The process is unrelated to other forms of photosynthesis involving electron transport, however, and haloarchaea are incapable of fixing carbon from carbon dioxide.{{cite journal | vauthors = Bryant DA, Frigaard NU | title = Prokaryotic photosynthesis and phototrophy illuminated | journal = Trends in Microbiology | volume = 14 | issue = 11 | pages = 488–496 | date = November 2006 | pmid = 16997562 | doi = 10.1016/j.tim.2006.09.001 }} Early evolution of retinal proteins has been proposed in the purple Earth hypothesis.

Haloarchaea are often considered pleomorphic, or able to take on a range of shapes—even within a single species. This makes identification by microscopic means difficult, and it is now more common to use gene sequencing techniques for identification instead.

One of the more unusually shaped Haloarchaea is the "Square Haloarchaeon of Walsby", classified in 2004 using a very low nutrition solution to allow growth along with a high salt concentration. Haloquadratum is square in shape and extremely thin (like a postage stamp). This shape is probably only permitted by the high osmolarity of the water, permitting cell shapes that would be difficult, if not impossible, under other conditions.

Haloarchaea have been proposed as a kind of life that could live on Mars; since the Martian atmosphere has a pressure below the triple point of water, freshwater species would have no habitat on the Martian surface. The presence of high salt concentrations in water lowers its freezing point, in theory allowing for halophiles to exist in saltwater on Mars.{{cite journal | vauthors = DasSarma S | title = Extreme halophiles are models for astrobiology. | journal = Microbe-American Society for Microbiology | date = 2006 | volume = 1 | issue = 3 | pages = 120 |url= http://www.asm.org/ASM/files/ccLibraryFiles/Filename/000000002127/znw00306000120.pdf |archive-url = https://web.archive.org/web/20070202065749/http://www.asm.org/ASM/files/ccLibraryFiles/Filename/000000002127/znw00306000120.pdf |archive-date = 2007-02-02 }} Recently, haloarchaea were sent 36 km (about 22 miles) up into Earth's atmosphere, within a balloon. The two types that were sent up were able to survive the freezing temperatures and high radiation levels, supporting the hypothesis that halophiles could survive on Mars.{{cite journal | vauthors = DasSarma P, DasSarma S | title = Survival of microbes in Earth's stratosphere | journal = Current Opinion in Microbiology | volume = 43 | pages = 24–30 | date = June 2018 | pmid = 29156444 | doi = 10.1016/j.mib.2017.11.002 | series = Environmental Microbiology * The New Microscopy | s2cid = 19041112 }}

Certain types of haloarchaea that produce carotenoids could potentially serve as a source of carotenoids for medical use.{{cite journal | vauthors = Giani M, Miralles-Robledillo JM, Peiró G, Pire C, Martínez-Espinosa RM | title = Deciphering Pathways for Carotenogenesis in Haloarchaea | journal = Molecules | volume = 25 | issue = 5 | pages = 1197 | date = March 2020 | pmid = 32155882 | pmc = 7179442 | doi = 10.3390/molecules25051197 | doi-access = free }} Haloarchaea have been proposed to help meet the high demand of carotenoids by pharmaceutical companies due to how easily it can be grown in a lab.{{cite book | vauthors = Rodrigo-Baños M, Montero Z, Torregrosa-Crespo J, Garbayo I, Vílchez C, Martínez-Espinosa RM | title = Carotenoids: Biosynthetic and Biofunctional Approaches | chapter = Haloarchaea: A Promising Biosource for Carotenoid Production | series = Advances in Experimental Medicine and Biology | volume = 1261 | pages = 165–174 | date = 2021 | pmid = 33783738 | doi = 10.1007/978-981-15-7360-6_13 | publisher = Springer | isbn = 978-981-15-7360-6 | s2cid = 232419066 | place = Singapore | veditors = Misawa N }} Genes in Haloarchaea can also be manipulated in order to produce various strands of carotenoids, further helping meet pharmaceutical companies' needs.

Haloarchaea are also present within the human gut, mostly predominant in the gut of people who live in Korea. Haloarchaea are most abundant in Koreans' guts rather than methanogens due to their saltier diets. This also shows that the archaeome in the human gut can vary drastically depending on region and what is eaten.{{cite journal | vauthors = Kim JY, Whon TW, Lim MY, Kim YB, Kim N, Kwon MS, Kim J, Lee SH, Choi HJ, Nam IH, Chung WH, Kim JH, Bae JW, Roh SW, Nam YD | display-authors = 6 | title = The human gut archaeome: identification of diverse haloarchaea in Korean subjects | journal = Microbiome | volume = 8 | issue = 1 | pages = 114 | date = August 2020 | pmid = 32753050 | pmc = 7409454 | doi = 10.1186/s40168-020-00894-x | doi-access = free }}

Certain types of haloarchaea have been proposed as sources of biodegradable plastics, which could help decrease plastic pollution. Haloarchaea are able to produce polyhydroxyalkanote (PHA), polyhydroxybutyrate (PHB), and polyhydroxyvalerate (PHV) when exposed to certain conditions. For large-scale production of these bioplastics, haloarchaea are favored due to the low cost, fast growth, and lack of need to sterilize area due to the salty environment they prefer. They are also a cleaner option for bioplastics due to them not needing chemicals for cell lysis and the higher recyclability of the process.{{cite journal | vauthors = Simó-Cabrera L, García-Chumillas S, Hagagy N, Saddiq A, Tag H, Selim S, AbdElgawad H, Arribas Agüero A, Monzó Sánchez F, Cánovas V, Pire C, Martínez-Espinosa RM | display-authors = 6 | title = Haloarchaea as Cell Factories to Produce Bioplastics | journal = Marine Drugs | volume = 19 | issue = 3 | pages = 159 | date = March 2021 | pmid = 33803653 | pmc = 8003077 | doi = 10.3390/md19030159 | doi-access = free }}

Certain types of haloarchaea have also been found to have denitrifying characteristics. If haloarchaea are complete denitrifiers, they could aid salt marshes and other salty environments by buffering these areas of nitrate and nitrite. This could help animal diversity and decrease pollution in these waterways. However, when tested in the lab, haloarchaea have been found to be partial denitrifiers. This means that if haloarchaea are used to treat areas that are high in nitrite and nitrate, they could contribute to nitrogen contaminates and cause an increase in ozone depletion, furthering climate change.{{cite journal | vauthors = Torregrosa-Crespo J, Bergaust L, Pire C, Martínez-Espinosa RM | title = Denitrifying haloarchaea: sources and sinks of nitrogenous gases | journal = FEMS Microbiology Letters | volume = 365 | issue = 3 | date = February 2018 | pmid = 29237000 | doi = 10.1093/femsle/fnx270 | doi-access = free | hdl = 10045/73332 | hdl-access = free }} The only type of haloarchaea that has been found to reduce atmospheric nitrogen pollution is Haloferax mediterranei.{{cite journal | vauthors = Torregrosa-Crespo J, Pire C, Martínez-Espinosa RM, Bergaust L | title = Denitrifying haloarchaea within the genus Haloferax display divergent respiratory phenotypes, with implications for their release of nitrogenous gases | journal = Environmental Microbiology | volume = 21 | issue = 1 | pages = 427–436 | date = January 2019 | pmid = 30421557 | doi = 10.1111/1462-2920.14474 | hdl = 10045/83647 | s2cid = 53292259 | hdl-access = free }} This shows that haloarchaea may be contributing to nitrogen pollution and are not a suitable solution for reducing nitrate and nitrite within high-salinity areas.   

• Life on Mars
• Purple Earth hypothesis
• List of Archaea genera

{{Reflist}}

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• {{cite journal | vauthors = Soppa J | title = From genomes to function: haloarchaea as model organisms | journal = Microbiology | volume = 152 | issue = Pt 3 | pages = 585–590 | date = March 2006 | pmid = 16514139 | doi = 10.1099/mic.0.28504-0 | doi-access = free }}
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• {{cite journal | vauthors = Woese CR, Kandler O, Wheelis ML | title = Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 87 | issue = 12 | pages = 4576–4579 | date = June 1990 | pmid = 2112744 | pmc = 54159 | doi = 10.1073/pnas.87.12.4576 | doi-access = free | bibcode = 1990PNAS...87.4576W }}
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{{refend}}

{{refbegin}}

• {{cite book | vauthors = Grant WD, Kamekura M, McGenity TJ, Ventosa A | date = 2001 | chapter = Class III. Halobacteria class. nov. | title = Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the deeply branching and phototrophic Bacteria | edition = 2nd | editor1 = DR Boone | editor2 = RW Castenholz | pages = [https://archive.org/details/bergeysmanualofs00boon/page/169 169] | publisher = Springer Verlag | location = New York | isbn = 978-0-387-98771-2 | chapter-url-access = registration | chapter-url = https://archive.org/details/bergeysmanualofs00boon/page/169 }}
• {{cite book | vauthors = Garrity GM, Holt JG | date = 2001 | chapter = Phylum AII. Euryarchaeota phy. nov. | title = Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the deeply branching and phototrophic Bacteria | edition = 2nd | editor1 = DR Boone | editor2 = RW Castenholz | pages = [https://archive.org/details/bergeysmanualofs00boon/page/169 169] | publisher = Springer Verlag | location = New York | isbn = 978-0-387-98771-2 | chapter-url-access = registration | chapter-url = https://archive.org/details/bergeysmanualofs00boon/page/169 }}

{{refend}}

• [https://web.archive.org/web/20141014204338/http://halo.umbi.umd.edu/~haloed/ An educational website on haloarchaea]
• [http://www.haloarchaea.com HaloArchaea.com]
• [http://www.microbiol.unimelb.edu.au/people/dyallsmith/index.html Mike Dyall-Smith's Homepage]

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Category:Halophiles

Category:Euryarchaeota

Category:Archaea classes