Halobacteriaceae

In taxonomy, the Halobacteriaceae are a family of the Halobacteriales in 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
Phylum:	Euryarchaeota
Class:	Halobacteria Grant et al. 2002
Order:	Halobacteriales Grant and Larsen 1989
Family:	Halobacteriaceae Gibbons 1974
Genera
Haladaptatus Savage et al. 2007 emend. Roh et al. 2010 Halalkalicoccus Xue et al. 2005 Halarchaeum Minegishi et al. 2010 Haloalcalophilium ♠ Lizama et al. 2000 Haloarcula Torreblanca et al. 1986 emend. Oren et al. 2009 Halobacterium Elazari-Volcani 1957 emend. Oren et al. 2009 Halobaculum Oren et al. 1995 Halobellus Cui et al. 2011 Halobiforma Hezayen et al. 2002 emend. Oren et al. 2009 Halococcus Schoop 1935 emend. Oren et al. 2009 Haloferax Torreblanca et al. 1986 emend. Oren et al. 2009 Halogeometricum Montalvo-Rodríguez et al. 1998 emend. Cui et al. 2010 Halogranum Cui et al. 2010 emend. Cui et al. 2011 Halolamina Cui et al. 2011 Halomarina Inoue et al. 2011 Halomicrobium Oren et al. 2002 Halonotius Burns et al. 2010 Halopelagius Cui et al. 2010 Halopiger Gutiérrez et al. 2007 Haloplanus Bardavid et al. 2007 emend. Cui et al. 2010 Haloquadratum Burns et al. 2007 Halorhabdus Wainø et al. 2000 emend. Antunes et al. 2008 Halorientalis Cui et al. 2011 Halorubrum McGenity and Grant 1996 emend. Oren et al. 2009 Halorussus ♠ Cui et al. 2010 Halosarcina Savage et al. 2008 emend. Cui et al. 2010 Halosimplex Vreeland et al. 2003 Halostagnicola Castillo et al. 2006 Haloterrigena Ventosa et al. 1999 emend. Oren et al. 2009 Halovivax Castillo et al. 2006 Natrialba Kamekura and Dyall-Smith 1996 emend. Oren et al. 2009 Natrinema McGenity et al. 1998 emend. Xin et al. 2000 Natronoarchaeum Shimane et al. 2010 Natronobacterium Tindall et al. 1984 Natronococcus Tindall et al. 1984 Natronolimnobius Itoh et al. 2005 Natronomonas Kamekura et al. 1997 emend. Burns et al. 2010 Natronorubrum Xu et al. 1999 emend. Oren et al. 2009 Salarchaeum Shimane et al. 2011

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; however, 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)[10] and the phylogeny is based on 16S rRNA-based LTP release 106 by 'The All-Species Living Tree' Project.[11]

?Haloalcalophilium atacamensis ♠ Lizama et al. 2000     ?Halobaculum gomorrense Oren et al. 1995     ?Halobellus clavatus Cui et al. 2011     ?Halolamina pelagica Cui et al. 2011     ?Halorientalis regularis Cui et al. 2011     ?Halorussus rarus ♠ Cui et al. 2010     ?Salarchaeum japonicum Shimane et al. 2011     Halomarina oriensis Inoue et al. 2011       Natronomonas Kamekura et al. 1997 emend. Burns et al. 2010         ?Halomicrobium zhouii ♣ Yang & Cui 2011         Halomicrobium mukohataei [type sp.] (Ihara et al. 1997) Oren et al. 2002     Halorhabdus Wainø et al. 2000 emend. Antunes et al. 2008         Halarchaeum acidiphilum Minegishi et al. 2010     Halobacterium Elazari-Volcani 1957 emend. Oren et al. 2009           Halosimplex carlsbadense Vreeland et al. 2003       Halomicrobium katesii Kharroub et al. 2008     Haloarcula Torreblanca et al. 1986 emend. Oren et al. 2009               Haladaptatus Savage et al. 2007 emend. Roh et al. 2010         Haloquadratum walsbyi Burns et al. 2007       Halopelagius inordinatus Cui et al. 2010       Halosarcina limi Cui et al. 2010       Halosarcina pallida Savage et al. 2008 [type sp.]     Halogeometricum Montalvo-Rodríguez et al. 1998 emend. Cui et al. 2010               Haloferax Torreblanca et al. 1986 emend. Oren et al. 2009       Halogranum Cui et al. 2010 emend. Cui et al. 2011         Halonotius pteroides Burns et al. 2010     Haloplanus Bardavid et al. 2007 emend. Cui et al. 2010       Halorubrum McGenity and Grant 1996 emend. Oren et al. 2009                   Halalkalicoccus Xue et al. 2005     Halococcus Schoop 1935 emend. Oren et al. 2009         Natronoarchaeum mannanilyticum Shimane et al. 2010       Halovivax Castillo et al. 2006       Halopiger Gutiérrez et al. 2007         Halobiforma Hezayen et al. 2002 emend. Oren et al. 2009       Natronobacterium Tindall et al. 1984     Natronococcus Tindall et al. 1984           Haloterrigena species-group 1 [incl. Halorubrum trapanicum, Natrinema & Natronorubrum sediminis]       Haloterrigena species-group 2       Natronolimnobius Itoh et al. 2005       Natronorubrum Xu et al. 1999 emend. Oren et al. 2009     Natrialba [incl. Halostagnicola]

Notes:
♠ Strains found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LPSN)
♣ International Journal of Systematic Bacteriology or International Journal of Systematic and Evolutionary Microbiology (IJSB/IJSEM) published species that are in press.

References

1. See the NCBI webpage on Halobacteriaceae. Data extracted from the "NCBI taxonomy resources". National Center for Biotechnology Information. Retrieved 2007-03-19.
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.
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). Archived from the original on 2013-01-27. Retrieved 2011-11-17.
10. Sayers; et al. "Halobacteriaceae". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2011-06-05.
11. 'The All-Species Living Tree' Project."16S rRNA-based LTP release 106 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2011-11-17.

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: 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. .

Scientific databases

• PubMed references for Halobacteriaceae
• PubMed Central references for Halobacteriaceae
• Google Scholar references for Halobacteriaceae

External links

• NCBI taxonomy page for Halobacteriaceae
• Search Tree of Life taxonomy pages for Halobacteriaceae
• Search Species2000 page for Halobacteriaceae
• MicrobeWiki page for Halobacteriaceae
• LPSN page for Halobacteriaceae
• Correct names of taxa within the family Halobacteriaceae