Caldibacillus

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

• List of bacterial orders
• List of bacteria genera

References

1. J.P. Euzéby. "Caldibacillus". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2022-09-09.
2. Parker, Charles Thomas; Garrity, George M (2012). Parker, Charles Thomas; Garrity, George M (eds.). "Nomenclature Abstract for Caldibacillus Coorevits et al. 2012". The NamesforLife Abstracts. doi:10.1601/nm.23151.
3. "Caldibacillus". Www.uniprot.org.
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. Bibcode:2017SyApM..40..245W. 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. S2CID   82988953.
6. 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.
7. 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.
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.
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. 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.
13. "GTDB - Tree". gtdb.ecogenomic.org. Retrieved 2021-05-28.
14. Sayers; et al. "Caldibacillus". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2022-09-09.
15. "The LTP" . Retrieved 23 February 2022.
16. "LTP_all tree in newick format". Archived from the original on 4 September 2022. Retrieved 23 February 2022.
17. "LTP_01_2022 Release Notes" (PDF). Retrieved 23 February 2022.
18. "GTDB release 07-RS207". Genome Taxonomy Database . Retrieved 20 June 2022.
19. "bac120_r207.sp_labels". Genome Taxonomy Database . Retrieved 20 June 2022.
20. "Taxon History". Genome Taxonomy Database . Retrieved 20 June 2022.

Further reading

• Wushke, Scott; Levin, David B.; Cicek, Nazim; Sparling, Richard; Parales, R. E. (15 August 2015). "Facultative Anaerobe Caldibacillus debilis GB1: Characterization and Use in a Designed Aerotolerant, Cellulose-Degrading Coculture with Clostridium thermocellum". Applied and Environmental Microbiology. 81 (16): 5567–5573. Bibcode:2015ApEnM..81.5567W. doi:10.1128/AEM.00735-15. PMC   4510191 . PMID   26048931.