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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 69, Issue 6

Bacillus urbisdiaboli sp. nov., isolated from soil sampled in Xinjiang Free

Abstract

A rod-shaped, endospore-forming, facultative anaerobic bacterium, designated FJAT-45385, was isolated from soil collected from Devil City in the Xinjiang Autonomous Region in China. Growth was observed at 20–40 °C (optimum, 30 °C), pH 7.0–11.0 (pH 9.0) and in 0–10.0 % NaCl (4 %), respectively. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the isoprenoid quinone was MK-7. The main fatty acids were anteiso-C15 : 0 (37.4 %), iso-C15 : 0 (15.1 %) and C16 : 0 (12.6 %). The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain FJAT-45385 to the genus Bacillus , and showed the highest sequence similarity to Bacillus wakoensis DSM 2521 (96.0 %). The average nucleotide identity and in silico DNA–DNA hybridization values between strain FJAT-45385 and its closest related species were 67.8 and 35.5 %, respectively, which were much lower than the thresholds commonly used to define species (96 and 70 %, respectively) indicating that it belong to a different taxon. The DNA G+C content was 38.1 mol%. The phenotypic characters and taxono-genomics study revealed that strain FJAT-45385 represents a novel Bacillus species, for which the name Bacillus urbisdiaboli sp. nov. is proposed. The type strain is FJAT-45385 (=DSM 104651=CCTCC AB 2016263).

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Keyword(s): Bacillus urbisdiaboli sp. nov. , devil city , soil , taxono-genomics and Xinjiang China
© 2019 IUMS
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2019-03-26
2024-04-19
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References

  1. Logan NA, De Vos P. et al. Genus I. bacillus. In De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB. (editors) Bergey's Manual of Systematic Bacteriology vol. 3 New York: Springer; 2009 pp. 21–128
     [Google Scholar]
  2. Ash C, Farrow JAE, Wallbanks S, Collins MD. Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences. Lett Appl Microbiol 1991; 13:202–206 [View Article]
     [Google Scholar]
  3. Nielsen P. Comparative 16S rDNA sequence analysis of some alkaliphilic bacilli and the establishment of a sixth rRNA group within the genus Bacillus . FEMS Microbiol Lett 1994; 117:61–65 [View Article]
     [Google Scholar]
  4. Zhang YG, Zhou XK, Guo JW, Xiao M, Wang HF et al. Bacillus tamaricis sp. nov., an alkaliphilic bacterium isolated from a Tamarix cone soil. Int J Syst Evol Microbiol 2018; 68:558–563 [View Article][PubMed]
     [Google Scholar]
  5. Liu B, Liu GH, Wang XY, Wang JP, Zhu YJ et al. Bacillus populi sp. nov. isolated from Populus euphratica rhizosphere soil of the Taklamakan desert. Int J Syst Evol Microbiol 2018; 68:155–159 [View Article][PubMed]
     [Google Scholar]
  6. Wang HF, Li QL, Zhang YG, Xiao M, Zhou XK et al. Bacillus capparidis sp. nov., an endophytic bacterium isolated from roots of Capparis spinosa L. Int J Syst Evol Microbiol 2017; 67:282–287 [View Article][PubMed]
     [Google Scholar]
  7. Zhang S, Li Z, Yan Y, Zhang C, Li J et al. Bacillus urumqiensis sp. nov., a moderately haloalkaliphilic bacterium isolated from a salt lake. Int J Syst Evol Microbiol 2016; 66:2305–2312 [View Article][PubMed]
     [Google Scholar]
  8. Liu B, Liu GH, Cetin S, Schumann P, Pan ZZ et al. Bacillus gobiensis sp. nov., isolated from a soil sample. Int J Syst Evol Microbiol 2016; 66:379–384 [View Article][PubMed]
     [Google Scholar]
  9. Liu B, Liu GH, Sengonca C, Schumann P, Ge CB et al. Bacillus solani sp. nov., isolated from rhizosphere soil of a potato field. Int J Syst Evol Microbiol 2015; 65:4066–4071 [View Article][PubMed]
     [Google Scholar]
  10. Zhang WY, Hu J, Zhang XQ, Zhu XF, Wu M. Bacillus salitolerans sp. nov., a novel bacterium isolated from a salt mine in Xinjiang province, China. Antonie van Leeuwenhoek 2015; 108:443–451 [View Article][PubMed]
     [Google Scholar]
  11. Lei Z, Qiu P, Ye R, Tian J, Liu Y et al. Bacillus shacheensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil. J Gen Appl Microbiol 2014; 60:101–105 [View Article][PubMed]
     [Google Scholar]
  12. 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]
  13. Zhang L, Wang Y, Dai J, Tang Y, Yang Q et al. Bacillus korlensis sp. nov., a moderately halotolerant bacterium isolated from a sand soil sample in China. Int J Syst Evol Microbiol 2009; 59:1787–1792 [View Article][PubMed]
     [Google Scholar]
  14. Ramasamy D, Mishra AK, Lagier JC, Padhmanabhan R, Rossi M et al. A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol 2014; 64:384–391 [View Article][PubMed]
     [Google Scholar]
  15. Gregersen T. Rapid method for distinction of gram-negative from gram-positive bacteria. Eur J Appl Microbiol Biotechnol 1978; 5:123–127 [View Article]
     [Google Scholar]
  16. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 607–654
     [Google Scholar]
  17. Murray RGE, Doetsch RN, Robinow CF. Determinative and cytological light microscopy. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington: American Society for Microbiology; 1994 pp. 21–41
     [Google Scholar]
  18. Chen YG, Cui XL, Pukall R, Li HM, Yang YL et al. Salinicoccus kunmingensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, south-west China. Int J Syst Evol Microbiol 2007; 57:2327–2332 [View Article][PubMed]
     [Google Scholar]
  19. Liu B, Liu GH, Hu GP, Sengonca C, Cetin S et al. Bacillus bingmayongensis sp. nov., isolated from the pit soil of Emperor Qin's Terra-cotta warriors in China. Antonie van Leeuwenhoek 2014; 105:501–510 [View Article][PubMed]
     [Google Scholar]
  20. 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]
  21. 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]
  22. 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]
  23. Rzhetsky A, Nei M. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 1992; 9:945–967
     [Google Scholar]
  24. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  25. 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]
  26. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. (editor) Mammalian Protein Metabolism vol. 3 New York: Academic Press; 1969 pp. 21–132
     [Google Scholar]
  27. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  28. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article][PubMed]
     [Google Scholar]
  29. 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]
  30. Liu B, Gp H, Tang WQ. Characteristic of average nucleotide identity (ANI) based on the whole genomes from Bacillus species in Bacillus-like genus. Fujian J Agri Sci 2013; 28:833–843
     [Google Scholar]
  31. Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article][PubMed]
     [Google Scholar]
  32. 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]
  33. 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]
  34. 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]
  35. Groth I, Schumann P, Weiss N, Martin K, Rainey FA. Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol 1996; 46:234–239 [View Article][PubMed]
     [Google Scholar]
  36. Schleifer KH. Analysis of the chemical composition and primary structure of murein. Methods Microbiol 1985; 18:123–156
     [Google Scholar]
  37. 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]
  38. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News 1990; 20:16
     [Google Scholar]
  39. Kämpfer P. Limits and possibilities of total fatty acid analysis for classification and identification of Bacillus species. Syst Appl Microbiol 1994; 17:86–98 [View Article]
     [Google Scholar]
  40. Nogi Y, Takami H, Horikoshi K. Characterization of alkaliphilic Bacillus strains used in industry: proposal of five novel species. Int J Syst Evol Microbiol 2005; 55:2309–2315 [View Article][PubMed]
     [Google Scholar]
  41. Yumoto I, Yamaga S, Sogabe Y, Nodasaka Y, Matsuyama H et al. Bacillus krulwichiae sp. nov., a halotolerant obligate alkaliphile that utilizes benzoate and m-hydroxybenzoate. Int J Syst Evol Microbiol 2003; 53:1531–1536 [View Article][PubMed]
     [Google Scholar]
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Bacillus urbisdiaboli sp. nov., isolated from soil sampled in Xinjiang
Int J Syst Evol Microbiol 69, 1591 (2019); https://doi.org/10.1099/ijsem.0.003363
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