Halobacteriaceae

Halobacteriaceae is a family in the order Halobacteriales and the domain Archaea.^[1] Halobacteriaceae represent a large part of halophilic Archaea, along with members in two other methanogenic families, Methanosarcinaceae and Methanocalculaceae.^[2] The family consists of many diverse genera that can survive extreme environmental niches.^[3] Most commonly, Halobacteriaceae are found in hypersaline lakes and can even tolerate sites polluted by heavy metals.^[4] They include neutrophiles, acidophiles (ex. Halarchaeum acidiphilum), alkaliphiles (ex. Natronobacterium), and there have even been psychrotolerant species discovered (ex. Hrr. lacusprofundi).^[3] Some members have been known to live aerobically, as well as anaerobically, and they come in many different morphologies.^[3] These diverse morphologies include rods in genus Halobacterium, cocci in Halococcus, flattened discs or cups in Haloferax, and other shapes ranging from flattened triangles in Haloarcula to squares in Haloquadratum, and Natronorubrum.^[5][6] Most species of Halobacteriaceae are best known for their high salt tolerance and red-pink pigmented members (due to bacterioruberin carotenoids^[5]), but there are also non-pigmented species and those that require moderate salt conditions.^[3][7] Some species of Halobacteriaceae have been shown to exhibit phosphorus solubilizing activities that contribute to phosphorus cycling in hypersaline environments.^[8] Techniques such as 16S rRNA analysis and DNA–DNA hybridization have been major contributors to taxonomic classification in Halobacteriaceae, partly due to the difficulty in culturing halophilic Archaea.^[7][3][2]

Halobacteriaceae
Scientific classification
Domain:	Archaea
Kingdom:	Euryarchaeota
Class:	Halobacteria
Order:	Halobacteriales
Family:	Halobacteriaceae Gibbons 1974
Genera
See text
Synonyms
"Haloarchaeaceae" (sic) DasSarma & DasSarma 2008

Overview

Halobacteriaceae are found in water saturated or nearly saturated with salt. They are also called halophiles, though this name is also used for other organisms which live in somewhat less concentrated salt water. They are common in most environments where large amounts of salt, moisture, and organic material are available. Large blooms appear reddish, from the pigment bacteriorhodopsin. This pigment is used to absorb light, which provides energy to create ATP. Halobacteria also possess a second pigment, halorhodopsin, which pumps in chloride ions 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 and halobacteria are incapable of fixing carbon from carbon dioxide.

Halobacteria can exist in salty environments because although they are aerobes, they have a separate and different way of creating energy through use of light energy. Parts of the membranes of halobacteria are purplish in color and contain retinal pigment. This allows them to create a proton gradient across the membrane of the cell which can be used to create ATP for their own use.

They have certain adaptations to live within their salty environments. For example, their cellular machinery is adapted to high salt concentrations by having charged amino acids on their surfaces, allowing the cell to keep its water molecules around these components. The osmotic pressure and these amino acids help to control the amount of salt within the cell. However, because of these adaptations, if the cell is placed in a wet, less salty environment, it is likely to immediately burst from the osmotic pressure.

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)^[9] and National Center for Biotechnology Information (NCBI).^[1]

16S rRNA based LTP_08_2023[10][11][12]

53 marker proteins based GTDB 08-RS214[13][14][15]

Halobacteriales Halobacteriaceae 2 * Halomarina Inoue et al. 2011 * Salinirubellus Hou et al. 2018 * "Halorarius" Sun et al. 2023 Salella Deshmukh & Oren 2023 Halosegnis Halocatena Verma et al. 2020 * Haloglomus Natronomonas Kamekura et al. 1997 * Halobacteriaceae 3 * Halosimplex Halorientalis Salinibaculum Han & Cui 2020 * Salinirussus Halovenus Makhdoumi-Kakhki et al. 2012 * Halapricum Halococcoides Halorhabdus Haloarculaceae Halomicrobium zhouii Halomicrobium mukohataei Halomicroarcula Haloarcula [incl. Halosiccatus; paraphyletic] Halobacteriaceae * Halanaeroarchaeum Sorokin et al. 2016 * Halodesulfurarchaeum Sorokin et al. 2017 * Salarchaeum Shimane et al. 2011 * Halobacterium Elazari-Volcani 1957 * Halocalculus Minegishi et al. 2015 * Halarchaeum Minegishi et al. 2010 * "Haladaptaceae" * Halorussus species-group 2 Halomicrococcus Chen et al 2020 * Halorussus halophilus Haladaptatus Savage et al. 2007 * Halorussus Cui et al. 2010 * Halostella Song et al. 2016 {QS-9-68-17} * Halalkalicoccus Xue et al. 2005 {"Halalkalicoccaceae"} * Halococcus {Halococcaceae} Halobacteriaceae 4 * Halorubellus Cui et al. 2014 * Haloarchaeobius Makhdoumi-Kakhki et al. 2012 * Natronoarchaeum Shimane et al. 2010 {"Natronoarchaeaceae"} * Salinarchaeum {"Salinarchaeaceae"} Natrialbaceae Salinirubrum corrig. Cui & Qiu 2014 * Haloferacaceae (incl. Halorubraceae)

Halobacteriales "Haladaptaceae" * Halorussus * Haladaptatus * Halobacteriaceae * Halanaeroarchaeum * Halodesulfurarchaeum * Salarchaeum * Halocalculus * Halarchaeum * Halobacterium * Salinarchaeum {"Salinarchaeaceae"} Halostella {QS-9-68-17} * Natronoarchaeum {"Natronoarchaeaceae"} * Natrialbaceae Halococcus {Halococcaceae} Haloarculaceae Halocatena * Halomarina * Haloglomus Halosegnis Natronomonas* Halorientalis Halapricum Halococcoides Halorhabdus Halosimplex Salinirussus Salinibaculum * Halovenus * Halomicrobium [incl. Halosiccatus] Halomicroarcula Haloarcula Halalkalicoccus {"Halalkalicoccaceae"} * Haloferacaceae (incl. Halorubraceae)

Note 1: * paraphyletic Halobacteriaceae
Note 2: Unassigned Halobacteriaceae

• "Actinoarchaeum" Tang et al. 2023
• "Haloalcalophilium" Lizama et al. 2000a
• "Halorarius" Sun et al. 2023

See also

• List of Archaea genera

References

1. Sayers; et al. "Halobacteriaceae". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2023-08-15.
2. Oren, Aharon (September 2014). "Taxonomy of halophilic Archaea: current status and future challenges". Extremophiles. 18 (5): 825–834. doi:10.1007/s00792-014-0654-9. PMID 25102811. S2CID 5395569.
3. Oren, Aharon (February 1, 2012). "Taxonomy of the family Halobacteriaceae: a paradigm for changing concepts in prokaryote systematics". International Journal of Systematic and Evolutionary Microbiology. 62 (2): 263–271. doi:10.1099/ijs.0.038653-0. PMID 22155757.
4. Naik, Sanika; Furtado, Irene (2017). Marine Pollution and Microbial Remediation. Singapore: Springer Nature. pp. 143–152. ISBN 978-981-10-1044-6.
5. Oren, Aharon; Arahal, David; Ventosa, Antonio (2009). "Emended descriptions of genera of the family Halobacteriaceae". International Journal of Systematic and Evolutionary Microbiology. 59 (3): 637–642. doi:10.1099/ijs.0.008904-0. PMID 19244452.
6. Tully, Benjamin; Emerson, Joanne; Andrade, Karen; Brocks, Jochen; Allen, Eric; Banfield, Jillian; Heidelberg, Karla (September 16, 2014). "De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape". Archaea. 2015: 875784. doi:10.1155/2015/875784. PMC 4330952. PMID 25709557.
7. Ventosa, A.; Marquez, M.; Sanchez-Porro, C.; Haba, R. (2012). Advances in understanding the biology of halophilic microorganisms ([Updated ed.]. ed.). Dordrecht: Springer, Dordrecht. doi:10.1007/978-94-007-5539-0_3. ISBN 978-94-007-5538-3.
8. Yadav, Ajar Nath; Sharma, Divya; Gulati, Sneha; Singh, Surender; Dey, Rinku; Pal, Kamal Krishna; Kaushik, Rajeev; Saxena, Anil Kumar (28 July 2015). "Haloarchaea Endowed with Phosphorus Solubilization Attribute Implicated in Phosphorus Cycle". Scientific Reports. 5 (1): 12293. Bibcode:2015NatSR...512293Y. doi:10.1038/srep12293. PMC 4516986. PMID 26216440.
9. J.P. Euzéby. "Halobacteriaceae". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2023-08-15.
10. "The LTP". Retrieved 20 November 2023.
11. "LTP_all tree in newick format". Retrieved 20 November 2023.
12. "LTP_08_2023 Release Notes" (PDF). Retrieved 20 November 2023.
13. "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
14. "ar53_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
15. "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.

Further reading

Scientific journals

• Wright, A-DG (2006). "Phylogenetic relationships within the order Halobacteriales inferred from 16S rRNA gene sequences". Int. J. Syst. Evol. Microbiol. 56 (Pt 6): 1223–1227. doi:10.1099/ijs.0.63776-0. PMID 16738095.
• Judicial, Commission of the International Committee on Systematics of Prokaryotes (2005). "The nomenclatural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79". Int. J. Syst. Evol. Microbiol. 55 (Pt 1): 517–518. doi:10.1099/ijs.0.63548-0. PMID 15653928.
• Euzeby JP, Tindall BJ (2001). "Nomenclatural type of orders: corrections necessary according to Rules 15 and 21a of the Bacteriological Code (1990 Revision), and designation of appropriate nomenclatural types of classes and subclasses. Request for an Opinion". Int. J. Syst. Evol. Microbiol. 51 (Pt 2): 725–727. doi:10.1099/00207713-51-2-725. PMID 11321122.
• Oren A, Ventosa A (2000). "International Committee on Systematic Bacteriology Subcommittee on the taxonomy of Halobacteriaceae. Minutes of the meetings, 16 August 1999, Sydney, Australia". Int. J. Syst. Evol. Microbiol. 50 (3): 1405–1407. doi:10.1099/00207713-50-3-1405. PMID 10843089.

Scientific books

• Grant WD, Larsen H (1989). "Group III. Extremely halophilic archaeobacteria. Order Halobacteriales ord. nov.". In JT Staley, MP Bryant, N Pfennig, JG Holt (eds.). Bergey's Manual of Systematic Bacteriology, Volume 3 (1st ed.). Baltimore: The Williams & Wilkins Co. p. 169.
• Gibbons, NE (1974). "Family V. Halobacteriaceae fam. nov.". In RE Buchanan and NE Gibbons (ed.). Bergey's Manual of Determinative Bacteriology (8th ed.). Baltimore: The Williams & Wilkins Co.
• Blum P, ed. (2008). Archaea: New Models for Prokaryotic Biology. Caister Academic Press. ISBN 978-1-904455-27-1. .

External links

• Correct names of taxa within the family Halobacteriaceae