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Abstract

An aerobic, Gram-staining-positive, endospore-forming bacterium, isolated from the rhizosphere of roots of maize (), was taxonomically studied. On the basis of 16S rRNA gene sequence similarity comparisons, strain JJ-125 clustered together with species of the genus and showed the highest similarities with (98.7 %). The 16S rRNA gene sequence similarities to the sequences of the type strains of other species of the genus were <98.4 %. The genome sequence of JJ-125 was 4 516 360 bp long and had a DNA G+C content of 37.3 %. A DNA–DNA hybridization with the type strain of DSM 23010 resulted in values of 42.3 and 43.9 % (reciprocal). The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between the JJ-125 genome assembly and those of the other type strains of species of the genus were <75%, <80 % and <21 %, respectively. Chemotaxonomic features supported the grouping of the strain with the genus e.g. the major fatty acids included iso-C iso-C ω10 and iso-C, the polar lipid profile contained the major components diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, the only quinone was menaquinone MK-7 and the characteristic diamino acid was -diaminopimelic acid. Physiological and biochemical test results were also different from those of the most closely related species. As a consequence, JJ-125 represents a novel species of the genus , for which we propose the name sp. nov., with JJ-125 (= CIP 111883 = LMG 32156 = CCM 9046) as the type strain.

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2022-10-11
2024-11-05
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References

  1. Gupta RS, Patel S, Saini N, Chen S. 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. Int J Syst Evol Microbiol 2020; 70:5753–5798 [View Article]
    [Google Scholar]
  2. Sultanpuram VR, Mothe T, Chintalapati S, Chintalapati VR. Bacillus catenulatus sp. nov., an alkalitolerant bacterium isolated from a soda lake. Arch Microbiol 2017; 199:1391–1397 [View Article]
    [Google Scholar]
  3. Spanka R, Fritze D. Bacillus cohnii sp. nov., a new, obligately alkaliphilic, oval-spore-forming Bacillus species with ornithine and aspartic acid instead of diaminopimelic acid in the cell wall. Int J Syst Bacteriol 1993; 43:150–156 [View Article]
    [Google Scholar]
  4. Nielsen P, Fritze D, Priest FG. Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 1995; 141:1745–1761 [View Article]
    [Google Scholar]
  5. Bae P, Zhang S, Chen Y, Ping W, Pang H et al. Sutcliffiella deserti sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2022; 72005259:
    [Google Scholar]
  6. Chen Y-G, Hu S-P, Tang S-K, He J-W, Xiao J-Q et al. Bacillus zhanjiangensis sp. nov., isolated from an oyster in South China Sea. Antonie Van Leeuwenhoek 2011; 99:473–480 [View Article]
    [Google Scholar]
  7. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics London: Wiley; 1990 pp 115–175
    [Google Scholar]
  8. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 1977; 74:5463–5467 [View Article]
    [Google Scholar]
  9. Coloqhoun JA. Discovery of deep-sea actinomycetes. PhD dissertation Canterbury, UK: Research school of biosciences, university of Kent; 1997
    [Google Scholar]
  10. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
    [Google Scholar]
  11. Brosius J, Palmer ML, Kennedy PJ, Noller HF. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A 1978; 75:4801–4805 [View Article]
    [Google Scholar]
  12. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article]
    [Google Scholar]
  13. Ludwig W, Viver T, Westram R, Francisco Gago J, Bustos-Caparros E et al. Release LTP_12_2020, featuring a new ARB alignment and improved 16S rRNA tree for prokaryotic type strains. Syst Appl Microbiol 2021; 44:126218 [View Article] [PubMed]
    [Google Scholar]
  14. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241–250 [View Article]
    [Google Scholar]
  15. Ludwig W, Strunk O, Westram R, Richter L, Meier H et al. ARB: a software environment for sequence data. Nucleic Acids Res 2004; 32:1363–1371 [View Article]
    [Google Scholar]
  16. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688–2690 [View Article] [PubMed]
    [Google Scholar]
  17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  18. Cherif-Silini H, Thissera B, Bouket AC, Saadaoui N, Silini A et al. Durum wheat stress tolerance induced by endophyte Pantoea agglomerans with genes contributing to plant functions and secondary metabolite arsenal. Int J Mol Sci 2019; 20:3989 [View Article]
    [Google Scholar]
  19. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
    [Google Scholar]
  20. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
    [Google Scholar]
  21. Katoh K, Standley DM. A simple method to control over-alignment in the MAFFT multiple sequence alignment program. Bioinformatics 2016; 32:1933–1942 [View Article]
    [Google Scholar]
  22. Criscuolo A, Gribaldo S. BMGE (block mapping and gathering with entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol 2010; 10:210 [View Article]
    [Google Scholar]
  23. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020; 37:1530–1534 [View Article]
    [Google Scholar]
  24. Ziemke F, Höfle MG, Lalucat J, Rosselló-Mora R. Reclassification of Shewanella putrefaciens Owen’s genomic group II as Shewanella baltica sp. nov. Int J Syst Bacteriol 1998; 48 Pt 1:179–186 [View Article]
    [Google Scholar]
  25. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for general and molecular bacteriology Washington, DC: American society for microbiology; 1994
    [Google Scholar]
  26. Kämpfer P, Steiof M, Dott W. Microbiological characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol 1991; 21:227–251 [View Article]
    [Google Scholar]
  27. Kämpfer P. Evaluation of the titertek-enterobac-automated system (TTE-AS) for identification of members of the family Enterobacteriaceae. Zentralbl Bakteriol 1990; 273:164–172 [View Article]
    [Google Scholar]
  28. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. eds In Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  29. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1990; 42:989–1005 [View Article]
    [Google Scholar]
  30. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  31. Wiertz R, Schulz SC, Müller U, Kämpfer P, Lipski A. Corynebacterium frankenforstense sp. nov. and Corynebacterium lactis sp. nov., isolated from raw cow milk. Int J Syst Evol Microbiol 2013; 63:4495–4501 [View Article]
    [Google Scholar]
  32. Schumann P. Peptidoglycan structure. In Rainey F, Oren A. eds In Taxonomy of Prokaryotes, Methods in Microbiology vol 38 London: Academic Press; 2011 pp 101–129
    [Google Scholar]
  33. Jiang Z, Zhang D-F, Khieu T-N, Son CK, Zhang X-M et al. Bacillus tianshenii sp. nov., isolated from a marine sediment sample. Int J Syst Evol Microbiol 2014; 64:1998–2002 [View Article]
    [Google Scholar]
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