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Brief Summary

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The halobacteriaceae are the most extreme of the world’s halophilic (Greek: salt-loving) organisms: in environments above 20% salinity, halobacteria abound in numbers above all other organisms.Although this family has the term “bacteria” in its name and its members are prokaryotic, as are bacteria, the halobacteria are organisms belonging to the domain Archaea, an evolutionary lineage recognized in the 1990s as fundamentally and basally distinct from other two domains of life, Bacteria and Eukaryota (Woese et al. 1990).Relationships among and nomenclature involving the three domains remain highly controversial, for e.g. see Cavalier-Smith 2002.

Halobacteria were first isolated about 100 years ago but like other Archaea they were not recognized as separate from bacterial prokaryotes until the late 1970s (Oren 2012 and references within).Scientists sometimes use the “unofficial” term ‘haloarchaea’ to designate the halophilic Archaea as distinct from bacteria, since the nomenclature term holobacteria is a confusing holdover from the time when all prokaryotic organisms were classified together in kingdom Monera (Oren 2012).

Molecular and chemical (especially lipid analysis) methods have brought significant advances in distinguishing species of Archaea, and the number of recognized species in the Halobacteriaceae has grown dramatically in the last 30 years (for example, see Ghai et al. 2011); in 2011 there were 36 recognized genera and 129 species (Arahal 2011; Oren 2012) and the "List of Prokaryotic Names with Standing (LPNS)" on clearinghouse site bacterio.net reports a currently accepted 40 genera and 144 species (Parte 2013). The rapid discovery of species is facilitating a new understanding of the diversity within this family.

Species of Halobacteria have been found to inhabit diverse extreme conditions: alkaline, acidic, warm- and cold temperatures, and show a range of different morphologies: rods, coccoid (spherical), flat, square; some can change shape with environmental conditions.There is a non-pigmented aerobic species (Natrialba asiatica; see below for more on halobacteria pigmentation) and a non-pigmented species with an anaerobic life style (Halorhabdus tiamatea).Unlike bacterial and eukaryotic halophiles, halobacteria don’t just survive in high salt concentrations, instead most require high salt solutions for growth and stability and many grow best in 3-4M solutions (Gutierrez et al. 2002).However, as it turns out, not all halobacteria thrive at saturated salt concentrations, some appear to have lower salt requirements (Oren 2012).

Most halobacteriaceans are tinted red or purple from carotinoid pigments bound up in bacteriorhodopsin proteins, which they use in low-nutrient enviornments for capturing energy from sunlight in a manner similar to photosynthesis.Lake Owens in California, the Great Salt Lake in Utah, Lake Eyre in Australia, and the upper Volga region of the Caspian Sea are just a few of the thousands of salt lakes with salinities >30% where halobacteria populations exist in enormous numbers (106-107 cells/ml), and are visible by their pink hue (Dyall-Smith 2013).Archaea are the only organisms to make bacteriorhodopsins (although the proteins have been cloned and expressed in E. coli) and the scientific community has become increasingly interested in these proteins for medical and technological uses, for example computer screens (NASA news 1998); a range of uses is reviewed in Trivedi et al. 2011.

Complete genome sequences of members of the family Halobacteriaceae are becoming available rapidly. The first, Halobacterium NRC-1 (a strain of Hbt. salinarum), was published in 2000 and at least fourteen more have been sequenced subsequently (Oren 2012).These are available in the HaloWeb database http://halo4.umbi.umd.edu (DasSarma et al. 2010).

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Halobacteriaceae

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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]

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 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 atacamensisLizama 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 rarusCui 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 zhouiiYang & 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. ^ a b 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. ^ a b c d e 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. ^ a b 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. ^ a b 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.
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Wikipedia authors and editors
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wikipedia EN

Halobacteriaceae: Brief Summary

provided by wikipedia EN

In taxonomy, the Halobacteriaceae are a family of the Halobacteriales in the domain Archaea. Halobacteriaceae represent a large part of halophilic Archaea, along with members in two other methanogenic families, Methanosarcinaceae and Methanocalculaceae. The family consists of many diverse genera that can survive extreme environmental niches. Most commonly, Halobacteriaceae are found in hypersaline lakes and can even tolerate sites polluted by heavy metals. They include neutrophiles, acidophiles (ex. Halarchaeum acidiphilum), alkaliphiles (ex. Natronobacterium), and there have even been psychrotolerant species discovered (ex. Hrr. lacusprofundi). Some members have been known to live aerobically, as well as anaerobically, and they come in many different morphologies. 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. Most species of Halobacteriaceae are best known for their high salt tolerance and red-pink pigmented members(due to bacterioruberin carotenoids), but there are also non-pigmented species and those that require moderate salt conditions. Some species of Halobacteriaceae have been shown to exhibit phosphorus solubilizing activities that contribute to phosphorus cycling in hypersaline environments. 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.

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