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Abstract

A Gram-stain-positive, facultatively anaerobic, rod-shaped, endospore-forming, oxidase-positive, and catalase-negative strain designated as BRMEA1 was isolated from the surface-sterilized roots. Growth of strain BRMEA1 was found to occur at pH 6.0–8.0 (optimum, pH 7.0), 15–50 °C (optimum, 25–30 °C) and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BRMEA1 formed a lineage within the genus (family ) and showed the highest sequence similarity to DSM 15600 (98.3 %) and KCTC 13885 (98.2 %), and less than 98.2 % 16S rRNA gene sequence similarity to the other members of the genus . Whole-genome analysis of strain BRMEA1 comprised a circular chromosome (5 632 809 bp in size) with 38.5 mol% G+C content. Digital DNA–DNA hybridization analyses revealed that strain BRMEA1 showed 20.5 and 22.0% genomic DNA relatedness with the closest species DSM 15600 and KCTC 13885, respectively. The whole-genome sequence of strain BRMEA1 showed the presence of 11 specific conserved signature indels for the genus . The major cellular fatty acids (>10 %) of strain BRMEA1 were found to be iso-C and anteiso-C, while the major polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Polyphasic analysis results revealed that BRMEA1 represents a novel species of the genus , with the proposed name sp. nov. The type strain is BRMEA1 (=KCTC 43208=CCTCC AB 2020071).

Funding
This study was supported by the:
  • Korea Research Institute of Bioscience and Biotechnology (Award KGM5282021)
    • Principle Award Recipient: ChaYoung Kim
  • National Research Foundation of Korea (Award RBM0142011)
    • Principle Award Recipient: JiyoungLee
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2021-02-23
2021-10-20
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References

  1. Patel S, Gupta RS. 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. Int J Syst Evol Microbiol 2020; 70:406–438 [View Article][PubMed]
    [Google Scholar]
  2. Adeolu M, Alnajar S, Naushad S, S Gupta R. Genome-based phylogeny and taxonomy of the 'Enterobacteriales': proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int J Syst Evol Microbiol 2016; 66:5575–5599 [View Article][PubMed]
    [Google Scholar]
  3. Dobritsa AP, Samadpour M. Reclassification of Burkholderia insecticola as Caballeronia insecticola comb. nov. and reliability of conserved signature indels as molecular synapomorphies. Int J Syst Evol Microbiol 2019; 69:2057–2063 [View Article][PubMed]
    [Google Scholar]
  4. Jiang L, Wang D, Kim J-S, Lee JH, Kim D-H et al. Reclassification of genus Izhakiella into the family Erwiniaceae based on phylogenetic and genomic analyses. Int J Syst Evol Microbiol 2020; 70:3541–3546 [View Article][PubMed]
    [Google Scholar]
  5. Naushad HS, Lee B, Gupta RS. Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria . Int J Syst Evol Microbiol 2014; 64:366–383 [View Article][PubMed]
    [Google Scholar]
  6. Nagel M, Andereesen JR. Bacillus niacini sp. nov., a nicotinate-metabolizing mesophile isolated from soil. Int J Syst Bacteriol 1991; 41:134–139 [View Article]
    [Google Scholar]
  7. Logan NA, Lebbe L, Hoste B, Goris J, Forsyth G et al. Aerobic endospore-forming bacteria from geothermal environments in northern Victoria Land, Antarctica, and Candlemas Island, South Sandwich archipelago, with the proposal of Bacillus fumarioli sp. nov. Int J Syst Evol Microbiol 2000; 50 Pt 5:1741–1753 [View Article][PubMed]
    [Google Scholar]
  8. Heyrman J, Vanparys B, Logan NA, Balcaen A, Rodríguez-Díaz M et al. Bacillus novalis sp. nov., Bacillus vireti sp. nov., Bacillus soli sp. nov., Bacillus bataviensis sp. nov. and Bacillus drentensis sp. nov., from the Drentse a grasslands. Int J Syst Evol Microbiol 2004; 54:47–57 [View Article]
    [Google Scholar]
  9. Han L, Yang G, Zhou X, Yang D, Hu P et al. Bacillus thermocopriae sp. nov., isolated from a compost. Int J Syst Evol Microbiol 2013; 63:3024–3029 [View Article][PubMed]
    [Google Scholar]
  10. Liu B, Liu G-H, Hu G-H, Chen M-C. Bacillus mesonae sp. nov., isolated from the root of Mesona chinensis . Int J Syst Evol Microbiol 2014; 64:3346–3352 [View Article][PubMed]
    [Google Scholar]
  11. Kämpfer P, Busse H-J, Glaeser SP, Kloepper JW, Hu C-H et al. Bacillus cucumis sp. nov. isolated from the rhizosphere of cucumber (Cucumis sativus). Int J Syst Evol Microbiol 2016; 66:1039–1044 [View Article][PubMed]
    [Google Scholar]
  12. Zhang M-Y, Cheng J, Cai Y, Zhang T-Y, Wu Y-Y et al. Bacillus notoginsengisoli sp. nov., a novel bacterium isolated from the rhizosphere of Panax notoginseng . Int J Syst Evol Microbiol 2017; 67:2581–2585 [View Article][PubMed]
    [Google Scholar]
  13. Bittar F, Bibi F, Ramasamy D, Lagier J-C, Azhar EI et al. Non contiguous-finished genome sequence and description of Bacillus jeddahensis sp. nov. Stand Genomic Sci 2015; 10:47 [View Article][PubMed]
    [Google Scholar]
  14. Jiang L, Lim CJ, Kim S-G, Jeong JC, Kim CY et al. Saccharibacillus brassicae sp. nov., an endophytic bacterium isolated from kimchi cabbage (Brassica rapa subsp. pekinensis) seeds. J Microbiol 2020; 58:24–29 [View Article][PubMed]
    [Google Scholar]
  15. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: 4.19; John Wiley and Sons; 1991 pp 115–175
    [Google Scholar]
  16. 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][PubMed]
    [Google Scholar]
  17. 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][PubMed]
    [Google Scholar]
  18. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  19. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. Ncbi prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article][PubMed]
    [Google Scholar]
  20. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  21. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
    [Google Scholar]
  22. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I, SI N et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article][PubMed]
    [Google Scholar]
  23. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
    [Google Scholar]
  24. Hwang SH, Hwang WM, Kang K, Ahn T-Y. Gramella fulva sp. nov., isolated from a dry surface of tidal flat. J Microbiol 2019; 57:23–29 [View Article][PubMed]
    [Google Scholar]
  25. Lee SA, Kim Y, Sang M-K, Song J, Kwon S-W et al. Chryseolinea soli sp. nov., isolated from soil. J Microbiol 2019; 57:122–126 [View Article][PubMed]
    [Google Scholar]
  26. Lee Y, Jeon CO. Cohnella algarum sp. nov., isolated from a freshwater green alga Paulinella chromatophora . Int J Syst Evol Microbiol 2017; 67:4767–4772 [View Article][PubMed]
    [Google Scholar]
  27. Sasser M. Bacterial identification by gas chromatographic analysis of fatty acids methyl esters (GC-FAME) 19713, MIDI Technical Note #101 2006. MIDI Inc, 125 Sandy Drive Newark, DE;
    [Google Scholar]
  28. 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]
  29. Collins MD, Shah HN, Minnikin DE. A note on the separation of natural mixtures of bacterial menaquinones using reverse phase thin-layer chromatography. J Appl Bacteriol 1980; 48:277–282 [View Article][PubMed]
    [Google Scholar]
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