Biology:Caldibacillus

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Short description: Genus of bacteria


Caldibacillus
Scientific classification
Domain:
Bacteria
Phylum:
Bacillota
Class:
Bacilli
Order:
Bacillales
Family:
Bacillaceae
Genus:
Caldibacillus

Coorevits et al. 2012
Type species
Caldibacillus debilis
(Banat et al. 2004) Coorevits et al. 2012
Species[1]
  • C. debilis
  • C. hisashii
  • C. kokeshiiformis
  • C. lycopersici
  • C. pasinlerensis
  • C. thermolactis

Caldibacillus is a facultative anaerobe genus of bacteria that stains Gram-positive (except for Caldibacillus debilis) from the family of Bacillaceae.[2][3][4] The type species of this genus is Caldibacillus debilis.[1]

Members of Caldibacillus were previously species (except for the type species, Caldibacillus debilis) belonging to Bacillus, a genus that has been recognized as displaying extensive polyphyly and phylogenetic heterogeneity due to the vague criteria[5] (such as the ability to form endospores in the presence of oxygen)[6] 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.[7][8][9][10][11][12] In addition, the genus Bacillus has been restricted to only include species closely related to Bacillus subtilis and Bacillus cereus. [7][12]

The name Caldibacillus is derived from the prefix "-caldi" (from the Latin adjective caldus which translates to "warm, hot") and the suffix "-bacillus" (from the Latin noun bacillus, referring to a small staff or rod).[1] Together, Caldibacillus translates to a warm bacillus, referring to the organism's thermophily.

Biochemical Characteristics and Molecular Signatures

Members of this genus are aerobic or facultatively anaerobic and found in mainly in saline lakes. All members can produce endospores and some are motile. Temperature range for growth is 25–70 °C. For some species optimum growth temperature is in the range 30–37 °C, while a few other species such as C. debilis and C. thermoamylovorans are obligate thermophiles with optimum growth temperatures of 65 and 50°C, respectively.[12]

Genomic analyses identified eight conserved signature indels (CSIs) that are exclusively present in this genus in the following proteins: DHH family phosphoesterase, tRNA uridine-5- carboxymethylaminomethyl(34) synthesis enzyme MnmG, O-succinylbenzoate-CoA ligase, tetratricopeptide repeat protein, d-alanyl-d-alanine carboxypeptidase, ribonuclease Z, late competence protein ComER, and DNA polymerase III subunit delta.[12] These CSIs provide a reliable molecular method of differentiating Caldibacillus species from other Bacillaceae genera and bacteria.

Taxonomy

Caldibacillus, as of May 2021, contains a total of 6 species with validly published names.[1] This genus was identified as a monophyletic clade and phylogenetically unrelated to other Bacillus species in studies examining the taxonomic relationships within Bacillus.[12] This branching pattern is also observed in the Genome Taxonomy Database (GTDB).[13]

Two non-validly published species, "Bacillus andreaoultii" and "Bacillus kwashiorkori", is also found to group with other members of Caldibacillus in phylogenetic trees as well as share the same molecular markers in the form of conserved signature indels (CSIs).[12] 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.

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)[14]

16S rRNA based LTP_01_2022[15][16][17] 120 marker proteins based GTDB 07-RS207[18][19][20]
 
 
 

C. hisashii

 
 

Bacillus thermoamylovorans

 
 
 
 

C. pasinlerensis

 
 
 

C. kokeshiiformis

 
 

C. thermolactis

 
 
 
 
 
Bacillus species-group
 

"Bacillus kwashiorkori" Seck et al. 2018

 
 
 

"Bacillus andreraoultii" Traore et al. 2015

 
 

Bacillus thermoamylovorans Combet-Blanc et al. 1995

 
 
 
Caldibacillus
 

C. hisashii (Nishida et al. 2015) Gupta et al. 2020

 
 
 

C. pasinlerensis (Baltaci et al. 2020) Gupta et al. 2020

 
 
 

C. kokeshiiformis (Poudel et al. 2014) Gupta et al. 2020

 
 

C. thermolactis (Coorevits et al. 2011) Gupta et al. 2020

 
 
 
 
 

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 J.P. Euzéby. "Caldibacillus". List of Prokaryotic names with Standing in Nomenclature (LPSN). https://lpsn.dsmz.de/genus/Caldibacillus. 
  2. ↑ Parker, Charles Thomas; Garrity, George M (2012). Parker, Charles Thomas; Garrity, George M. eds. "Nomenclature Abstract for Caldibacillus Coorevits et al. 2012" (in en). The NamesforLife Abstracts. doi:10.1601/nm.23151. 
  3. ↑ (in en) Caldibacillus. https://www.uniprot.org/taxonomy/1276290. 
  4. ↑ Wushke, S; Spicer, V; Zhang, XL; Fristensky, B; Krokhin, OV; Levin, DB; Cicek, N; Sparling, R (July 2017). "Understanding aerobic/anaerobic metabolism in Caldibacillus debilis through a comparison with model organisms.". Systematic and Applied Microbiology 40 (5): 245–253. doi:10.1016/j.syapm.2017.03.004. PMID 28527624. 
  5. ↑ 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. http://dx.doi.org/10.1111/j.1472-765x.1991.tb00608.x. 
  6. ↑ Logan, N. A.; Berge, O.; Bishop, A. H.; Busse, H.-J.; De Vos, P.; Fritze, D.; Heyndrickx, M.; Kampfer, P. et al. (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. http://dx.doi.org/10.1099/ijs.0.013649-0. 
  7. ↑ 7.0 7.1 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." (in en). International Journal of Systematic and Evolutionary Microbiology 70 (1): 406–438. doi:10.1099/ijsem.0.003775. ISSN 1466-5026. PMID 31617837. 
  8. ↑ 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. 
  9. ↑ 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. http://dx.doi.org/10.1099/00207713-42-2-263. 
  10. ↑ 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. 
  11. ↑ 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. 
  12. ↑ 12.0 12.1 12.2 12.3 12.4 12.5 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" (in en). International Journal of Systematic and Evolutionary Microbiology 70 (11): 5753–5798. doi:10.1099/ijsem.0.004475. ISSN 1466-5026. PMID 33112222. https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.004475. 
  13. ↑ "GTDB - Tree". https://gtdb.ecogenomic.org/tree?r=d__Bacteria. 
  14. ↑ Sayers. "Caldibacillus". National Center for Biotechnology Information (NCBI) taxonomy database. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=1276290&lvl=3&lin=f&keep=1&srchmode=1&unlock. 
  15. ↑ "The LTP". https://imedea.uib-csic.es/mmg/ltp/#LTP. 
  16. ↑ "LTP_all tree in newick format". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/Tree_LTP_all_01_2022.ntree. 
  17. ↑ "LTP_01_2022 Release Notes". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_01_2022_release_notes.pdf. 
  18. ↑ "GTDB release 07-RS207". https://gtdb.ecogenomic.org/about#4%7C. 
  19. ↑ "bac120_r207.sp_labels". https://data.gtdb.ecogenomic.org/releases/release207/207.0/auxillary_files/bac120_r207.sp_labels.tree. 
  20. ↑ "Taxon History". https://gtdb.ecogenomic.org/taxon_history/. 

Further reading

Wikidata ☰ Q26219532 entry

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