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Volume 69, Issue 8

sp. nov., isolated from cave soil Free

Abstract

A Gram-stain-positive, strictly aerobic, rod-shaped, motile, endospore-forming strain, SYSU K30001, was isolated from a soil sample collected from a cave in Xingyi county, Guizhou province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SYSU K30001 belonged to the genus , with the highest sequence similarity to the type strain of (98.1 %). Growth occurred at pH 6.0–9.0 (optimum, pH 7.0), at 28–55 °C (optimum, 28 °C) and in the presence of 0–3 % (w/v) NaCl (optimum in the absence of NaCl). Strain SYSU K30001 contained -2,6-diaminopimelic acid in the cell-wall peptidoglycan and MK-7 as the only isoprenoid quinone present. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid. The major fatty acids were iso-C, iso-C 10, anteiso-C and iso-C. The genome G+C content was 39.8 mol%. The average nucleotide identity values between SYSU K30001 and DSM 19096 were 72.1 % (ANIb) and 83.1 % (ANIm), which were below the cut-off level (95–96 %) for species delineation. Based on phenotypic, chemotaxonomic and molecular characterizations, strain SYSU K30001 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SYSU K30001 (=KCTC 33954=CGMCC 1.13871).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Bacillus antri , cave soil and genome analysis
© 2019 IUMS
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2019-08-01
2024-04-19
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References

  1. Cohn F. Untersuchungen über bakterien. Beitr Biol Pflanz Heft 1872; 1:127–224
     [Google Scholar]
  2. Zhang MY, Cheng J, Cai Y, Zhang TY, Wu YY 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]
  3. Jiang Z, Zhang DF, Khieu TN, Son CK, Zhang XM et al. Bacillus tianshenii sp. nov., isolated from a marine sediment sample. Int J Syst Evol Microbiol 2014; 64:1998–2002 [View Article][PubMed]
     [Google Scholar]
  4. Zhai L, Liao T, Xue Y, Ma Y. Bacillus daliensis sp. nov., an alkaliphilic, Gram-positive bacterium isolated from a soda lake. Int J Syst Evol Microbiol 2012; 62:949–953 [View Article][PubMed]
     [Google Scholar]
  5. Lim JM, Jeon CO, Lee SM, Lee JC, Xu LH et al. Bacillus salarius sp. nov., a halophilic, spore-forming bacterium isolated from a salt lake in China. Int J Syst Evol Microbiol 2006; 56:373–377 [View Article][PubMed]
     [Google Scholar]
  6. Wang QF, Li W, Liu YL, Cao HH, Li Z et al. Bacillus qingdaonensis sp. nov., a moderately haloalkaliphilic bacterium isolated from a crude sea-salt sample collected near Qingdao in eastern China. Int J Syst Evol Microbiol 2007; 57:1143–1147 [View Article][PubMed]
     [Google Scholar]
  7. Zhang L, Wu GL, Wang Y, Dai J, Fang CX. Bacillus deserti sp. nov., a novel bacterium isolated from the desert of Xinjiang, China. Antonie van Leeuwenhoek 2011; 99:221–229 [View Article][PubMed]
     [Google Scholar]
  8. Li QQ, Han MX, Fang BZ, Jiao JY, Liu L et al. Nocardia cavernae sp. nov., a novel actinobacterium isolated from a karst cave sample. Int J Syst Evol Microbiol 2017; 67:2998–3003 [View Article][PubMed]
     [Google Scholar]
  9. Fang BZ, Hua ZS, Han MX, Zhang ZT, Wang YH et al. Nonomuraea cavernae sp. nov., a novel actinobacterium isolated from a karst cave sample. Int J Syst Evol Microbiol 2017; 67:4692–4697 [View Article][PubMed]
     [Google Scholar]
  10. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia . Int J Syst Evol Microbiol 2007; 57:1424–1428 [View Article][PubMed]
     [Google Scholar]
  11. Yoon SH, Ha SM, 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]
  12. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
     [Google Scholar]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  14. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  15. 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]
  16. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
     [Google Scholar]
  17. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
     [Google Scholar]
  18. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  19. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article][PubMed]
     [Google Scholar]
  20. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703–704 [View Article][PubMed]
     [Google Scholar]
  21. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article][PubMed]
     [Google Scholar]
  22. Nguyen TM, Kim J. Bacillus polymachus sp. nov., with a broad range of antibacterial activity, isolated from forest topsoil samples by using a modified culture method. Int J Syst Evol Microbiol 2015; 65:704–709 [View Article][PubMed]
     [Google Scholar]
  23. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
     [Google Scholar]
  24. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
     [Google Scholar]
  25. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
     [Google Scholar]
  26. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded Ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
     [Google Scholar]
  27. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of cellulomonas, oerskovia and related taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
     [Google Scholar]
  28. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
  29. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: Microbial ID, Inc; 1990
     [Google Scholar]
  30. Ten LN, Baek SH, Im WT, Liu QM, Aslam Z et al. Bacillus panaciterrae sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2006; 56:2861–2866 [View Article][PubMed]
     [Google Scholar]
  31. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
     [Google Scholar]
  32. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article][PubMed]
     [Google Scholar]
  33. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self- Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607–2618
     [Google Scholar]
  34. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
     [Google Scholar]
  35. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al. Versatile and open software for comparing large genomes. Genome Biol 2004; 5:R12–2483 [View Article][PubMed]
     [Google Scholar]
  36. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article][PubMed]
     [Google Scholar]
  37. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  38. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
     [Google Scholar]
  39. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
     [Google Scholar]
  40. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
     [Google Scholar]
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Bacillus antri sp. nov., isolated from cave soil
Int J Syst Evol Microbiol 69, 2335 (2019); https://doi.org/10.1099/ijsem.0.003473
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