Alkalicoccus

Alkalicoccus is a genus of Gram-Positive rod-shaped bacteria in the family Bacillaceae from the order Bacillales.[1][2] The type species of this genus is Alkalicoccus saliphilus.[3]

Alkalicoccus
Scientific classification
Domain:
Bacteria
Phylum:
Bacillota
Class:
Bacilli
Order:
Bacillales
Family:
Bacillaceae
Genus:
Alkalicoccus Zhao et al. 2017, emend. Gupta et al. 2020
Species

Information based on LPSN 2021

Members of Alkalicoccus were previously species (except for the type species, Alkalicoccus saliphilus) belonging to Bacillus, a genus that has been recognized as displaying extensive polyphyly and phylogenetic heterogeneity due to the vague criteria[4] (such as the ability to form endospores in the presence of oxygen)[5] previously used to assign species to this clade. Multiple studies using comparative phylogenetic analyses have been published in an attempt to clarify the evolutionary relationships between Bacillus species, resulting in the establishment of numerous novel genera such as Alkalihalobacillus, Brevibacillus, Solibacillus, Alicyclobacillus, Virgibacillus and Evansella.[6][7][8][9][10][1] In addition, the genus Bacillus has been restricted to only include species closely related to Bacillus subtilis and Bacillus cereus.[6][1]

The name Alkalicoccus is derived from the prefix "-alkali" (from the Arabic article al, which translates to "the" and the Arabic noun galiy, referring to the ashes of saltwort) and the suffix "-coccus" (from the Latin coccus, referring to a sphere).[11] Together, Alkalicoccus translates to a coccus living in basic surroundings.

Biochemical characteristics and molecular signatures

Members of this genus are aerobic or facultatively anaerobic and found in mainly in saline lakes. Some members can produce endospores and are motile. Most species are moderately halophilic and alkali-tolerant and require NaCl (2–8%, w/v) for growth. Temperature range for growth is 8–45 °C, with optimum growth temperature generally in the range 30–37 °C.[1]`

Analyses of genome sequences from Alkalicoccus species identified nine conserved signature indels (CSIs) that are exclusive for this genus in the following proteins: bis(5'-nucleosyl)-tetraphosphatase PrpE, dihydroorotate dehydrogenase electron transfer subunit, DUF368 domain-containing protein, penicillin-binding protein, DNA polymerase/3'−5' exonuclease PolX, alpha-glucosidase, 1,4-alpha-glucan branching protein GlgB, SDR family oxidoreductase and tRNA1(Val) [adenine(37)-N6]-methyltransferase.[1] These molecular signatures provide a reliable method of identification and differentiation for Alkalicoccus species from other Bacillaceae genera and bacteria.

Taxonomy

Alkalicoccus, as of May 2021, contains a total of 6 species with validly published names.[3] This genus was identified as a monophyletic clade and phylogenetically unrelated to other Bacillus species in studies examining the taxonomic relationships within Bacillus.[1] This branching pattern is also observed in the Genome Taxonomy Database (GTDB).[12]

One non-validly published species, "Bacillus daqingensis", is also found to group with other members of Alkalicoccus in phylogenetic trees as well as share the same molecular markers in the form of conserved signature indels (CSIs).[1] However, its transfer was not officially proposed due to the lack of culture strain information. Further revision of this genus is required as additional genomes and novel species are discovered and assigned.

References
  1. Gupta, Radhey S.; Patel, Sudip; Saini, Navneet; Chen, Shu (2020-11-01). "Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species". International Journal of Systematic and Evolutionary Microbiology. 70 (11): 5753–5798. doi:10.1099/ijsem.0.004475. ISSN 1466-5026. PMID 33112222.
  2. Brenner, Don J.; Krieg, Noel R.; Staley, James T.; Garrity, George M.; Boone, David R.; De Vos, Paul; Goodfellow, Michael; Rainey, Fred A.; Schleifer, Karl-Heinz, eds. (2005). Bergey's Manual® of Systematic Bacteriology. doi:10.1007/0-387-28022-7. ISBN 978-0-387-24144-9.
  3. "Genus: Alkalicoccus". lpsn.dsmz.de. Retrieved 2021-05-30.
  4. Ash, Carol; Farrow, J.A.E.; Wallbanks, Sally; Collins, M.D. (2008-06-28). "Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences". Letters in Applied Microbiology. 13 (4): 202–206. doi:10.1111/j.1472-765x.1991.tb00608.x. ISSN 0266-8254. S2CID 82988953.
  5. Logan, N. A.; Berge, O.; Bishop, A. H.; Busse, H.-J.; De Vos, P.; Fritze, D.; Heyndrickx, M.; Kampfer, P.; Rabinovitch, L.; Salkinoja-Salonen, M. S.; Seldin, L. (2009-06-30). "Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria". International Journal of Systematic and Evolutionary Microbiology. 59 (8): 2114–2121. doi:10.1099/ijs.0.013649-0. ISSN 1466-5026. PMID 19567583.
  6. Patel, Sudip; Gupta, Radhey S. (2020-01-01). "A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov". International Journal of Systematic and Evolutionary Microbiology. 70 (1): 406–438. doi:10.1099/ijsem.0.003775. ISSN 1466-5026. PMID 31617837.
  7. SHIDA, O.; TAKAGI, H.; KADOWAKI, K.; KOMAGATA, K. (1996-10-01). "Proposal for Two New Genera, Brevibacillus gen. nov. and Aneurinibacillus gen. nov". International Journal of Systematic Bacteriology. 46 (4): 939–946. doi:10.1099/00207713-46-4-939. ISSN 0020-7713. PMID 8863420.
  8. Wisotzkey, J. D.; Jurtshuk, P.; Fox, G. E.; Deinhard, G.; Poralla, K. (1992-04-01). "Comparative Sequence Analyses on the 16S rRNA (rDNA) of Bacillus acidocaldarius, Bacillus acidoterrestris, and Bacillus cycloheptanicus and Proposal for Creation of a New Genus, Alicyclobacillus gen. nov". International Journal of Systematic Bacteriology. 42 (2): 263–269. doi:10.1099/00207713-42-2-263. ISSN 0020-7713. PMID 1374624.
  9. Mual, Poonam; Singh, Nitin Kumar; Verma, Ashish; Schumann, Peter; Krishnamurthi, Srinivasan; Dastager, Syed; Mayilraj, Shanmugam (2016-05-01). "Reclassification of Bacillus isronensis Shivaji et al. 2009 as Solibacillus isronensis comb. nov. and emended description of genus Solibacillus Krishnamurthi et al. 2009". International Journal of Systematic and Evolutionary Microbiology. 66 (5): 2113–2120. doi:10.1099/ijsem.0.000982. ISSN 1466-5026. PMID 26907585.
  10. Heyndrickx, M.; Lebbe, L.; Kersters, K.; Hoste, B.; De Wachter, R.; De Vos, P.; Forsyth, G.; Logan, N. A. (1999-07-01). "Proposal of Virgibacillus proomii sp. nov. and emended description of Virgibacillus pantothenticus (Proom and Knight 1950) Heyndrickx et al. 1998". International Journal of Systematic and Evolutionary Microbiology. 49 (3): 1083–1090. doi:10.1099/00207713-49-3-1083. ISSN 1466-5026. PMID 10425765.
  11. Zhao, Baisuo; Lu, Weidong; Zhang, Shanshan; Liu, Kang; Yan, Yanchun; Li, Jun (2017-05-01). "Reclassification of Bacillus saliphilus as Alkalicoccus saliphilus gen. nov., comb. nov., and description of Alkalicoccus halolimnae sp. nov., a moderately halophilic bacterium isolated from a salt lake". International Journal of Systematic and Evolutionary Microbiology. 67 (5): 1557–1563. doi:10.1099/ijsem.0.001759. ISSN 1466-5026. PMID 28032538.
  12. "GTDB - Tree". gtdb.ecogenomic.org. Retrieved 2021-05-28.
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