Biology:Halorubrum

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Short description: Genus of archaea

Halorubrum
Scientific classification
Domain:
Archaea
Kingdom:
Euryarchaeota
Phylum:
Euryarchaeota
Class:
Halobacteria
Order:
Haloferacales
Family:
Halorubraceae
Genus:
Halorubrum

McGenity and Grant 1996[1]
Type species
Halorubrum saccharovorum
(Tomlinson & Hochstein 1977) McGenity & Grant 1996
Species

See text

Synonyms
  • Halorubrobacterium Kamekura and Dyall-Smith 1996[1]

Halorubrum is a genus in the family Halorubraceae. Halorubrum species are usually halophilic and can be found in waters with high salt concentration such as the Dead Sea or Lake Zabuye.

Genetic exchange

A population of the haloarchaea Halorubrum in its natural high salt concentration environment exchanged genetic information frequently by recombination.[2] This population exhibited a degree of linkage equilibrium approaching that of a sexual population.

Taxonomy

In taxonomy, Halorubrum is a genus of the Halobacteriaceae.[3]

Species

Halorubrum ejinorense was first isolated from Lake Ejinor in Inner Mongolia, China.[4]

Halorubrum lacusprofundi was first isolated in the 1980s from Deep Lake, Antarctica.[5] Its genome, sequenced in 2008, consists of two chromosomes (one 2.74 Mb and the other 0.53 Mb) and one plasmid (0.43 Mb).[6] Its β-galactosidase enzyme has been extensively studied to understand how proteins function in low-temperature, high-saline environments.[7][8] One strain of H. lacusprofundi contains a plasmid for horizontal gene transfer, which takes place via a mechanism that uses vesicle-enclosed virus-like particles.[9]

Halorubrum sodomense was first identified in the Dead Sea in 1980. It requires a higher concentration of Mg2+ ions for growth than related halophiles.[10] Its cell surface membrane contains Archaerhodopsin-3 (AR3), a photoreceptor protein which harvests the energy from sunlight to establish a proton motive force that is used for ATP synthesis.[11][12] Mutants of AR3 are widely used as tools in optogenetics for neuroscience research.[13]

Halorubrum tibetense was first isolated from Lake Zabuye in Tibet, China.[14]

Halorubrum xinjiangense was first isolated from Xiao-Er-Kule Lake in Xinjiang, China.[15]

Proposed species

Several species and novel binomial names have been proposed, but not validly published. published.

  • Halorubrum africanae and Halorubrum constantinense were isolated in Algeria and proposed as new species in 2007[16] and 2005.[17]
  • Halorubrum alimentarium and Halorubrum koreense are the proposed names for the undescribed strains B43 and B6, appearing in a publication of 2008.[18]
  • Halorubrum halotolerans is the proposed name for an undescribed strain isolated from solar salterns in Baja California in 2009.[19]
  • Halorubrum hochstenium is the proposed name for the full genome of the undescribed strain ATCC 700873, supplied to databases in 2014.[20][21]
  • Halorubrum jeotgali was isolated from samples of traditional Korean seafood and proposed as new species in 2007.[22] Halorubrum cibarium was proposed in the same publication. It was proposed again under the name H. cibi and accepted in 2009.
  • Halorubrum kribbense and Halorubrum norisence' are proposed names of unisolated strains from the human gut microbiome, referenced in a publication in 2017.[23]
  • Halorubrum salipaludis was first published in 2021.[24]
  • "Halorubrum salsolis"
  • Halorubrum salsamenti was isolated from salt brine and proposed as new species in 2017.[25]
  • Halorubrum sfaxense was isolated in Tunisia and proposed as new species in 2017.[26]
  • Halorubrum tropicale was isolated in Puerto Rico and proposed as new species in 2016.[27]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[1] and National Center for Biotechnology Information (NCBI).[3]

16S rRNA based LTP_06_2022[28][29][30] 53 marker proteins based GTDB 08-RS214[31][32][33]
Halorubrum
 

H. gandharaense Kondô et al. 2015

 
 
 

H. luteum Hu et al. 2008

 
 
 

H. vacuolatum (Mwatha & Grant 1993) Kamekura et al. 1997

 
 
 
 
 

H. alkaliphilum Feng et al. 2005

 
 

H. tibetense Fan et al. 2004

 
 
 
 

H. aquaticum Gutierrez et al. 2011

 
 
 

H. halodurans Corral et al. 2016

 
 
 
 

H. cibi Roh & Bae 2009

 
 

H. glutamatedens Xu et al. 2019

 
 
 
 

H. aethiopicum Gibtan et al. 2018

 
 

H. rubrum Qiu et al. 2014

 
 
 
 
 
 
 
 
 

H. orientale Castillo et al. 2006

 
 

H. trueperi Chen et al. 2017

 
 
 
 
 
 

H. lacusprofundi (Franzmann et al. 1989) McGenity & Grant 1996

 
 

H. salsamenti Chen et al. 2019

 
 
 
 

H. kocurii Gutierrez et al. 2008

 
 
 

H. aidingense Cui et al. 2006

 
 
 

H. yunnanense Chen et al. 2015

 
 
 

H. depositum Chen et al. 2019

 
 

H. rutilum Yin et al. 2016

 
 
 
 
 
 
 
 
 

H. halophilum Yim et al. 2014

 
 

H. lipolyticum Cui et al. 2006

 
 
 
 
 

H. amylolyticum Sun et al. 2019

 
 
 

H. persicum Corral et al. 2015

 
 

H. saccharovorum (Tomlinson & Hochstein 1977) McGenity & Grant 1996

 
 
 
 
 
 

H. pallidum Chen et al. 2016

 
 
 

H. laminariae Han & Cui 2015

 
 

H. salinum Zhang & Cui 2014

 
 
 
 
 

H. distributum (Zvyagintseva & Tarasov 1989) Oren & Ventosa 1996

 
 
 
 

H. ejinorense Castillo et al. 2007

 
 

H. tebenquichense Lizama et al. 2002

 
 
 
 

H. sodomense (Oren 1983) McGenity & Grant 1996

 
 
 

H. californiense Pesenti et al. 2008

 
 
 

H. ezzemoulense Kharroub et al. 2006

 
 
 

H. coriense (Kamekura & Dyall-Smith 1996) Oren & Ventosa 1996

 
 
 

H. trapanicum (Petter 1931) McGenity & Grant 1996

 
 
 

H. salinarum Han et al. 2022

 
 

H. xinjiangense Feng et al. 2004

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Halorubrum
 

H. vacuolatum

 
 
 
 

H. alkaliphilum

 
 
 

H. aquaticum

 
 
 

H. cibi

 
 
 

H. rubrum

 
 
 

H. aethiopicum

 
 

H. halodurans

 
 
 
 
 
 
 
 
 
 

"H. hochstenium"

 
 

H. tebenquichense

 
 
 
 

H. trapanicum

 
 
 

H. sodomense

 
 
 

H. distributum

 
 
 

H. xinjiangense

 
 
 

H. salinarum

 
 
 

H. californiense

 
 
 

H. coriense

 
 

H. ezzemoulense

 
 
 
 
 
 
 
 
 
 
 
 

H. laminariae

 
 

H. salinum

 
 
 
 
 

H. aidingense

 
 
 

H. depositum

 
 

H. rutilum

 
 
 
 
 

H. lacusprofundi

 
 
 
 

H. kocurii

 
 

H. lipolyticum

 
 
 
 
 

H. persicum

 
 

H. saccharovorum

 
 
 
 

"H. salipaludis" Gong et al. 2021

 
 
 

H. halophilum

 
 
 

H. amylolyticum

 
 

H. salsamenti

 
 
 
 
 
 
 
 
 
 
 
 

References

  1. ↑ 1.0 1.1 1.2 J.P. Euzéby. "Halorubrum". List of Prokaryotic names with Standing in Nomenclature (LPSN). https://lpsn.dsmz.de/genus/halorubrum. Retrieved 2023-10-10. 
  2. ↑ "Frequent recombination in a saltern population of Halorubrum". Science 306 (5703): 1928–9. December 2004. doi:10.1126/science.1103289. PMID 15591201. Bibcode: 2004Sci...306.1928P. 
  3. ↑ 3.0 3.1 Sayers. "Halorubrum". National Center for Biotechnology Information (NCBI) taxonomy database. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=56688&lvl=3&keep=1&srchmode=1&unlock. Retrieved 2023-10-10. 
  4. ↑ "Halorubrum Ejinorense Sp. Nov., Isolated From Lake Ejinor, Inner Mongolia, China". International Journal of Systematic and Evolutionary Microbiology 57 (11): 2538–2542. 2007. doi:10.1099/ijs.0.65241-0. PMID 17978215. 
  5. ↑ "Halobacterium lacusprofundii sp. nov., a halophilic bacterium isolated from Deep Lake, Antarctica". Systematic and Applied Microbiology 11 (1): 20–27. 1988. doi:10.1016/S0723-2020(88)80044-4. 
  6. ↑ "Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34". Standards in Genomic Sciences 11 (1): 70. 2008. doi:10.1186/s40793-016-0194-2. PMID 27617060. 
  7. ↑ "Cloning, Overexpression, Purification, and Characterization of a Polyextremophilic β-galactosidase From the Antarctic Haloarchaeon Halorubrum lacusprofundi". BMC Biotechnol. 13: 10.1186/1472-6750-13-3. 2013. doi:10.1186/1472-6750-13-3. PMID 23320757. 
  8. ↑ "Key amino acid residues conferring enhanced enzyme activity at cold temperatures in an Antarctic polyextremophilic β-galactosidase". PNAS 114 (47): 12530–35. 2017. doi:10.1073/pnas.1711542114. PMID 29109294. Bibcode: 2017PNAS..11412530L. 
  9. ↑ "A plasmid from an Antarctic haloarchaeon uses specialized membrane vesicles to disseminate and infect plasmid-free cells". Nature Microbiology 2 (10): 1446–1455. 9 September 2017. doi:10.1038/s41564-017-0009-2. PMID 28827601. 
  10. ↑ "Halobacterium sodomense sp. nov. a Dead Sea Halobacterium with an extremely high magnesium requirement". International Journal of Systematic Bacteriology 33 (2): 381–386. 1983. doi:10.1099/00207713-33-2-381. 
  11. ↑ "Evolution of the archaeal rhodopsins: evolution rate changes by gene duplication and functional differentiation". Journal of Molecular Biology 285 (1): 163–74. January 1999. doi:10.1006/jmbi.1998.2286. PMID 9878396. 
  12. ↑ "Structures of the archaerhodopsin 3 transporter reveal that disordering of internal water networks underpins receptor sensitization". Nature Communications 12 (1): 629. 2021. doi:10.1038/s41467-020-20596-0. PMID 33504778. Bibcode: 2021NatCo..12..629B. 
  13. ↑ "Archaerhodopsin variants with enhanced voltage-sensitive fluorescence in mammalian and Caenorhabditis elegans neurons". Nature Communications 5: 4894. 2014. doi:10.1038/ncomms5894. PMID 25222271. Bibcode: 2014NatCo...5.4894F. 
  14. ↑ "Halorubrum tibetense sp. nov., a novel haloalkaliphilic archaeon from Lake Zabuye in Tibet, China". International Journal of Systematic and Evolutionary Microbiology 54 (4): 1213–1216. 2004. doi:10.1099/ijs.0.03032-0. PMID 15280294. 
  15. ↑ "Halorubrum xinjiangense sp. nov., a novel halophile isolated from saline lakes in China". International Journal of Systematic and Evolutionary Microbiology 54 (5): 1789–1791. 2004. doi:10.1099/ijs.0.63209-0. PMID 15388744. 
  16. ↑ NCBI Taxonomy browser (Halorubrum africanae), https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=435915, retrieved 2022-07-14 
  17. ↑ NCBI Taxonomy browser (Halorubrum constantinense), https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=340066, retrieved 2022-07-14 
  18. ↑ Nam Young-Do; Chang Ho-Won; Kim Kyoung-Ho; Roh Seong Woon; Kim Min-Soo; Jung Mi-Ja; Lee Si-Woo; Kim Jong-Yeol et al. (2008). "Bacterial, archaeal, and eukaryal diversity in the intestines of Korean people". Journal of Microbiology 46 (5): 491–501. doi:10.1007/s12275-008-0199-7. PMID 18974948. 
  19. ↑ "Characterization of halophiles isolated from solar salterns in Baja California, Mexico". Extremophiles 13 (4): 643–656. 2009. doi:10.1007/s00792-009-0247-1. PMID 19418017. 
  20. ↑ NCBI Taxonomy browser (Halorubrum hochstenium ATCC 700873), https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1227481, retrieved 2022-07-14 
  21. ↑ Page: "Halorubrum hochstenium 1-13-28" in Integrated Microbial Genomes&Microbioms, https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2554235503, retrieved 2022-07-14 
  22. ↑ NCBI Taxonomy browser (Halorubrum cibarium), https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=413814, retrieved 2022-07-14 
  23. ↑ Nkamga, Vanessa Demonfort; Henrissat, Bernard; Drancourt, Michel (2017). "Archaea: Essential inhabitants of the human digestive microbiota". Human Microbiome Journal 3: 1–8. doi:10.1016/j.humic.2016.11.005. 
  24. ↑ Page: "Species: Halorubrum salipaludis" in "LPSN - List of Prokaryotic names with Standing in Nomenclature". Deutsche Sammlung von Mikroorganismen und Zellkulturen. https://lpsn.dsmz.de/species/halorubrum-salipaludis. 
  25. ↑ NCBI Taxonomy browser (Halorubrum salsamenti), https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2583990, retrieved 2022-07-14 
  26. ↑ NCBI Taxonomy browser (Halorubrum sfaxense), https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=725131, retrieved 2022-07-14 
  27. ↑ NCBI Taxonomy browser (Halorubrum tropicale), https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1765655, retrieved 2022-07-14 
  28. ↑ "The LTP". https://imedea.uib-csic.es/mmg/ltp/#LTP. 
  29. ↑ "LTP_all tree in newick format". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_all_06_2022.ntree. 
  30. ↑ "LTP_06_2022 Release Notes". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_06_2022_release_notes.pdf. 
  31. ↑ "GTDB release 08-RS214". https://gtdb.ecogenomic.org/about#4%7C. 
  32. ↑ "ar53_r214.sp_label". https://data.gtdb.ecogenomic.org/releases/release214/214.0/auxillary_files/ar53_r214.sp_labels.tree. 
  33. ↑ "Taxon History". https://gtdb.ecogenomic.org/taxon_history/. 

Further reading

Scientific journals

  • "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. 2000. doi:10.1099/00207713-50-3-1405. PMID 10843089. 
  • "A proposal for the transfer of Halorubrobacterium distributum and Halorubrobacterium coriense to the genus Halorubrum as Halorubrum distributum comb. nov. and Halorubrum coriense comb. nov., respectively". Int. J. Syst. Bacteriol. 46 (4): 1180. 1996. doi:10.1099/00207713-46-4-1180. 
  • "Transfer of Halobacterium saccharovorum, Halobacterium sodomense, Halobacterium trapanicum NRC 34021 and Halobacterium lacusprofundi to the genus Halorubrum gen. nov., as Halorubrum saccharovorum comb. nov., Halorubrumsodomense comb. nov., Halorubrum trapanicum comb. nov., and Halorubrum lacusprofundi comb.nov". Syst. Appl. Microbiol. 18 (2): 237–243. 1995. doi:10.1016/s0723-2020(11)80394-2. 
  • "Taxonomy of the family Halobacteriaceae and the description of two new genera Halorubrobacterium and Natrialba". J. Gen. Appl. Microbiol. 41 (4): 333–350. 1995. doi:10.2323/jgam.41.333. 
  • "Population and genomic analysis of the genus Halorubrum". Frontiers in Microbiology 5 (Article No.: 140): 140. 11 April 2014. doi:10.3389/fmicb.2014.00140. PMID 24782836. 

Scientific books

Scientific databases

External links

Wikidata ☰ Q5643444 entry



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