Halorubrum

Halorubrum
Scientific classification
Domain:	Archaea
Kingdom:	Methanobacteriati
Phylum:	Halobacteriota
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
HalorubrobacteriumKamekura 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_10_2024 [28] [29] [30]

53 marker proteins based GTDB 09-RS220 [31] [32] [33]

Halorubrum H. vacuolatum (Mwatha & Grant 1993) Kamekura et al. 1997 H. gandharaenseKondô et al. 2015 H. luteum Hu et al. 2008 H. alkaliphilum Feng et al. 2005 H. tibetense Fan et al. 2004 H. glutamatedensXu et al. 2019 H. aquaticumGutierrez et al. 2011 H. aethiopicumGibtan et al. 2018 H. rubrumQiu et al. 2014 H. cibiRoh & Bae 2009 H. haloduransCorral et al. 2016 H. distributum (Zvyagintseva & Tarasov 1989) Oren & Ventosa 1996 H. ejinorense Castillo et al. 2007 H. tebenquichense Lizama et al. 2002 "H. hochsteinianum" Vreeland et al. 2023 H. salinarumHan et al. 2022 H. xinjiangense Feng et al. 2004 H. coriense (Kamekura & Dyall-Smith 1996) Oren & Ventosa 1996 H. ezzemoulense Kharroub et al. 2006 H. sodomense (Oren 1983) McGenity & Grant 1996 H. californiense Pesenti et al. 2008 H. trapanicum (Petter 1931) McGenity & Grant 1996 H. amylolyticumSun et al. 2019 H. persicumCorral et al. 2015 H. saccharovorum (Tomlinson & Hochstein 1977) McGenity & Grant 1996 H. pallidumChen et al. 2016 H. laminariaeHan & Cui 2015 H. salinumZhang & Cui 2014 H. lipolyticum Cui et al. 2006 H. kocurii Gutierrez et al. 2008 H. lacusprofundi (Franzmann et al. 1989) McGenity & Grant 1996 H. salsamentiChen et al. 2019 H. halophilumYim et al. 2014 H. orientale Castillo et al. 2006 H. trueperiChen et al. 2017 H. aidingense Cui et al. 2006 H. yunnanenseChen et al. 2015 H. depositumChen et al. 2019 H. rutilumYin et al. 2016

Halorubrum H. vacuolatum H. alkaliphilum H. aquaticum H. cibi H. rubrum H. aethiopicum H. halodurans H. xinjiangense H. salinarum "H. tropicale" Sanchez-Nieves et al. 2016 H. coriense H. ezzemoulense H. californiense H. distributum "H. ruber" Hwang et al. 2022 H. sodomense H. trapanicum "H. hochsteinianum" H. tebenquichense H. laminariae H. salinum H. aidingense H. depositum H. rutilum H. yunnanense H. lacusprofundi H. kocurii H. lipolyticum H. persicum H. saccharovorum "H. salipaludis" Gong et al. 2021 H. halophilum H. amylolyticum H. salsamenti

References

1. J.P. Euzéby. "Halorubrum". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2023-10-10.
2. Papke RT, Koenig JE, Rodríguez-Valera F, Doolittle WF (December 2004). "Frequent recombination in a saltern population of Halorubrum". Science. 306 (5703): 1928–9. Bibcode:2004Sci...306.1928P. doi:10.1126/science.1103289. PMID   15591201. S2CID   21595153.
3. Sayers; et al. "Halorubrum". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2023-10-10.
4. Castillo AM, Gutiérrez MC, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A (2007). "Halorubrum Ejinorense Sp. Nov., Isolated From Lake Ejinor, Inner Mongolia, China". International Journal of Systematic and Evolutionary Microbiology. 57 (11): 2538–2542. doi: 10.1099/ijs.0.65241-0 . PMID   17978215.
5. Franzmann PD, Stacklebrandt E, Sanderson K, Volkman JK, Camberon DE, Stevenson PL, McMeekin TA, Burton HR (1988). "Halobacterium lacusprofundii sp. nov., a halophilic bacterium isolated from Deep Lake, Antarctica". Systematic and Applied Microbiology. 11 (1): 20–27. doi:10.1016/S0723-2020(88)80044-4.
6. Anderson IJ, DasSarma P, Lucas S, Copeland A, Lapidus A, Del Rio T, Tice H, Dalin E, Bruce DC, Goodwin L, Pitluck S, Sims D, Brettin TS, Detter JC, Han CS, Larimer F, Hauser L, Land M, Ivanova N, Richardson P, Cavicchioli R, DasSarma S, Woese CR, Kyrpides (2008). "Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34". Standards in Genomic Sciences. 11 (1): 70. doi: 10.1186/s40793-016-0194-2 . PMC   5018182 . PMID   27617060.
7. Karan R, Capes MD, DasSarma P, DasSarma S (2013). "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. doi: 10.1186/1472-6750-13-3 . PMC   3556326 . PMID   23320757.
8. Laye VJ, Karan R, Kim JM, Pecher WT, DasSarma P, DasSarma S (2017). "Key amino acid residues conferring enhanced enzyme activity at cold temperatures in an Antarctic polyextremophilic β-galactosidase". PNAS. 114 (47): 12530–35. Bibcode:2017PNAS..11412530L. doi: 10.1073/pnas.1711542114 . PMC   5703305 . PMID   29109294.
9. Erdmann S, Tschitschko B, Zhong L, Raftery MJ, Cavicchioli R (9 September 2017). "A plasmid from an Antarctic haloarchaeon uses specialized membrane vesicles to disseminate and infect plasmid-free cells". Nature Microbiology. 2 (10): 1446–1455. doi:10.1038/s41564-017-0009-2. hdl: 1959.4/unsworks_49908 . PMID   28827601. S2CID   38729395.
10. Oren A (1983). "Halobacterium sodomense sp. nov. a Dead Sea Halobacterium with an extremely high magnesium requirement". International Journal of Systematic Bacteriology. 33 (2): 381–386. doi: 10.1099/00207713-33-2-381 .
11. Ihara K, Umemura T, Katagiri I, Kitajima-Ihara T, Sugiyama Y, Kimura Y, Mukohata Y (January 1999). "Evolution of the archaeal rhodopsins: evolution rate changes by gene duplication and functional differentiation". Journal of Molecular Biology. 285 (1): 163–74. doi:10.1006/jmbi.1998.2286. PMID   9878396.
12. Bada Juarez JF, Judge PJ, Adam S, Axford D, Vinals J, Birch J, Kwan TO, Hoi KK, Yen HY, Vial A, Milhiet PE, Robinson CV, Schapiro I, Moraes I, Watts A (2021). "Structures of the archaerhodopsin 3 transporter reveal that disordering of internal water networks underpins receptor sensitization". Nature Communications. 12 (1): 629. Bibcode:2021NatCo..12..629B. doi:10.1038/s41467-020-20596-0. PMC   7840839 . PMID   33504778.
13. Flytzanis NC, Bedbrook CN, Chiu H, Engqvist MK, Xiao C, Chan KY, Sternberg PW, Arnold FH, Gradinaru V (2014). "Archaerhodopsin variants with enhanced voltage-sensitive fluorescence in mammalian and Caenorhabditis elegans neurons". Nature Communications. 5: 4894. Bibcode:2014NatCo...5.4894F. doi:10.1038/ncomms5894. PMC   4166526 . PMID   25222271.
14. Fan H, Xue Y, Ma Y, Ventosa A, Grant WD (2004). "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. doi: 10.1099/ijs.0.03032-0 . PMID   15280294.
15. Feng J, Zhou PJ, Liu SJ (2004). "Halorubrum xinjiangense sp. nov., a novel halophile isolated from saline lakes in China". International Journal of Systematic and Evolutionary Microbiology. 54 (5): 1789–1791. doi: 10.1099/ijs.0.63209-0 . PMID   15388744.
16. NCBI Taxonomy browser (Halorubrum africanae) , retrieved 2022-07-14
17. NCBI Taxonomy browser (Halorubrum constantinense) , 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; Yoon Jung-Hoon; Bae Jin-Woo (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. S2CID   24070213.
19. Sabet S, Diallo L, Hays L, Jung W, Dillon JG (2009). "Characterization of halophiles isolated from solar salterns in Baja California, Mexico". Extremophiles. 13 (4): 643–656. doi:10.1007/s00792-009-0247-1. PMID   19418017. S2CID   1040194.
20. NCBI Taxonomy browser (Halorubrum hochstenium ATCC 700873) , retrieved 2022-07-14
21. Page: "Halorubrum hochstenium 1-13-28" in Integrated Microbial Genomes&Microbioms , retrieved 2022-07-14
22. NCBI Taxonomy browser (Halorubrum cibarium) , 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 . Retrieved 2022-07-14.
25. NCBI Taxonomy browser (Halorubrum salsamenti) , retrieved 2022-07-14
26. NCBI Taxonomy browser (Halorubrum sfaxense) , retrieved 2022-07-14
27. NCBI Taxonomy browser (Halorubrum tropicale) , retrieved 2022-07-14
28. "The LTP" . Retrieved 10 December 2024.
29. "LTP_all tree in newick format" . Retrieved 10 December 2024.
30. "LTP_10_2024 Release Notes" (PDF). Retrieved 10 December 2024.
31. "GTDB release 09-RS220". Genome Taxonomy Database . Retrieved 10 May 2024.
32. "ar53_r220.sp_label". Genome Taxonomy Database . Retrieved 10 May 2024.
33. "Taxon History". Genome Taxonomy Database . Retrieved 10 May 2024.

Further reading

Scientific journals

• 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.
• Oren A, Ventosa A (1996). "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. doi: 10.1099/00207713-46-4-1180 .
• McGenity TJ, Grant WD (1995). "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. doi:10.1016/s0723-2020(11)80394-2.
• Kamekura M, Dyall-Smith ML (1995). "Taxonomy of the family Halobacteriaceae and the description of two new genera Halorubrobacterium and Natrialba". J. Gen. Appl. Microbiol. 41 (4): 333–350. doi: 10.2323/jgam.41.333 .
• Papke T, Fullmer M, Soucy S, Swithers K, Makkay A, Wheeler R, Ventosa A, Gogarten P (11 April 2014). "Population and genomic analysis of the genus Halorubrum". Frontiers in Microbiology. 5 (Article No.: 140): 140. doi: 10.3389/fmicb.2014.00140 . PMC   3990103 . PMID   24782836.

Scientific books

• Gibbons, NE (1974). "Family V. Halobacteriaceae fam. nov.". In RE Buchanan; NE Gibbons (eds.). Bergey's Manual of Determinative Bacteriology (8th ed.). Baltimore: The Williams & Wilkins Co. ISBN   0-683-01117-0.

External links

• Halorubrum at BacDive - the Bacterial Diversity Metadatabase