Halorubrum

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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
  • 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.

Contents

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.

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. laminariae

H. salinum

H. aidingense

H. depositum

H. rutilum

H. yunnanense

H. lacusprofundi

H. persicum

H. saccharovorum

"H. salipaludis" Gong et al. 2021

H. halophilum

H. amylolyticum

H. salsamenti

Related Research Articles

A halophile is an extremophile that thrives in high salt concentrations. In chemical terms, halophile refers to a Lewis acidic species that has some ability to extract halides from other chemical species.

<i>Halobacterium</i> Genus of archaea

Halobacterium is a genus in the family Halobacteriaceae.

Halobacteriaceae is a family in the order Halobacteriales and 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, alkaliphiles, and there have even been psychrotolerant species discovered. 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, 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.

<i>Haloarcula</i> Genus of archaea

Haloarcula is a genus of extreme halophilic Archaea in the class of Halobactaria.

<i>Haloferax</i> Genus of archaea

Haloferax is a genus of halobacteria in the order Haloferacaceae.

Halopiger is a genus of archaeans in the family Natrialbaceae that have high tolerance to salinity.

In taxonomy, Haloplanus is a genus of the Halobacteriaceae.

Haloterrigena is a genus of the Natrialbaceae.

In taxonomy, Halovivax is a genus of the Natrialbaceae. Some species of Halovivax are halophiles and have been found in Iran's Aran-Bidgol hypersaline lake.

In taxonomy, Natrialba is a genus of the Natrialbaceae. The genus consists of many diverse species that can survive extreme environmental niches, especially they are capable to live in the waters saturated or nearly saturated with salt (halophiles). 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.

Natrinema is a genus of the Natrialbaceae.

In taxonomy, Natronococcus is a genus of the Natrialbaceae.

Natronomonas is a genus of the Halobacteriaceae.

Natronorubrum is a genus in the family Halobacteriaceae.

<span class="mw-page-title-main">Shiladitya DasSarma</span>

Shiladitya DasSarma is a molecular biologist well-known for contributions to the biology of halophilic and extremophilic microorganisms. He is a Professor in the University of Maryland Baltimore. He earned a PhD degree in biochemistry from the Massachusetts Institute of Technology and a BS degree in chemistry from Indiana University Bloomington. Prior to taking a faculty position, he conducted research at the Massachusetts General Hospital, Harvard Medical School, and Pasteur Institute, Paris.

<i>Halorubrum lacusprofundi</i> Species of archaeon

Halorubrum lacusprofundi is a rod-shaped, halophilic Archaeon in the family of Halorubraceae. It was first isolated from Deep Lake in Antarctica in the 1980s.

<span class="mw-page-title-main">Archaerhodopsin</span> Family of archaea

Archaerhodopsin proteins are a family of retinal-containing photoreceptors found in the archaea genera Halobacterium and Halorubrum. Like the homologous bacteriorhodopsin (bR) protein, archaerhodopsins harvest energy from sunlight to pump H+ ions out of the cell, establishing a proton motive force that is used for ATP synthesis. They have some structural similarities to the mammalian G protein-coupled receptor protein rhodopsin, but are not true homologs.

Halorubraceae is a family of halophilic, chemoorganotrophic or heterotrophic archaea within the order Haloferacales. The type genus of this family is Halorubrum. Its biochemical characteristics are the same as the order Haloferacales.

Halorubrum californiense is a halophilic Archaeon in the family of Halorubraceae. It was isolated from saline environments solar saltern in Newark, California.

Halorubrum kocurii is a halophilic archaean belonging to the genus Halorubrum. This genus contains a total of thirty-seven different species, all of which thrive in high-salinity environments. Archaea belonging to this genus are typically found in hypersaline environments due to their halophilic nature, specifically in solar salterns. Halorubrum kocurii is a rod-shaped, Gram-negative archaeon. Different from its closest relatives, Halorubrum kocurii is non-motile and contains no flagella or cilia. This archaeon thrives at high pH levels, high salt concentrations, and moderate temperatures. It has a number of close relatives, including Halorubrum aidingense, Halorubrum lacusprofundi, and more.

References

  1. 1 2 3 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. 1 2 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. 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.

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