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Abstract

A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium, designated strain FJAT-27997, was isolated from the rhizosphere soil of a plant collected from Sichuan province in China. Growth was observed aerobically between 20  and 35 °C (optimum 30 °C), between 0 and 3.0 % (w/v) NaCl (optimum at 0 %) concentration and pH in the range 6.0–9.0 (optimum at pH 7.0). The cell-wall peptidoglycan contained -diaminopimelic acid and the major isoprenoid quinone was menaquinone MK-7. The main fatty acids were iso-C, anteiso-C, iso-C, C and C. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phylogenetic analyses based on 16S rRNA gene sequences showed that isolate FJAT-27997 was a member of the genus and was related most closely to DSM 1321 (97.95 % similarity), followed by GSS03 (97.9 %). The average nucleotide identity value between strain FJAT-27997 and the most closely related species, DSM 1321, was 71.60 % (JSpecies), less than the previously proposed cut-off value of 96 % for differentiating species within the genus. The DNA–DNA hybridization values between strain FJAT-27997 and its most closely related species were <70 %, again indicating they belong to different taxa. The main fatty acids were iso-C and anteiso-C. The novel strain could be differentiated from other known species on the basis of several phenotypic characters and fatty acid profiles. This taxononomic/genomic study revealed that strain FJAT-27997 represents a novel species, for which the name sp. nov. (type strain FJAT-27997=CCTCC AB 2015285=DSM 101776) is proposed.

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2016-07-01
2022-01-21
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References

  1. Auch A. F., von Jan M., Klenk H. P., Göker M. 2010; Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134 [View Article][PubMed]
    [Google Scholar]
  2. Chen Y. G., Cui X. L., Pukall R., Li H. M., Yang Y. L., Xu L. H., Wen M. L., Peng Q., Jiang C. L. 2007; Salinicoccus kunmingensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, south-west China. Int J Syst Evol Microbiol 57:2327–2332 [View Article][PubMed]
    [Google Scholar]
  3. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. 1977; Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230 [View Article][PubMed]
    [Google Scholar]
  4. Euzéby J. P. List of Prokaryotic Names with Standing in Nomenclature 2015 http://www.bacterio.cict.fr/
  5. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:68–376 [CrossRef]
    [Google Scholar]
  6. Felsenstein J. 1985; Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  7. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 [CrossRef]
    [Google Scholar]
  8. Fritze D. 2004; Taxonomy of the genus bacillus and related genera: the aerobic endospore-forming bacteria. Phytopathology 94:1245–1248 [View Article][PubMed]
    [Google Scholar]
  9. Goris J., Konstantinidis K. T., Klappenbach J. A., Coenye T., Vandamme P., Tiedje J. M. 2007; DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91 [View Article][PubMed]
    [Google Scholar]
  10. Gregersen T. 1978; Rapid method for distinction of gram-negative from gram-positive bacteria. European Journal of Applied Microbiology and Biotechnology 5:123–127 [View Article]
    [Google Scholar]
  11. Groth I., Schumann P., Weiss N., Martin K., Rainey F. A. 1996; Agrococcus jenensis gen nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Evol Microbiol 46:234–239
    [Google Scholar]
  12. Jukes T. H., Cantor C. R. 1969; Evolution of protein molecules. In Mammalian Protein Metabolism vol. 3 pp. 21–132 Edited by Munro H. N. New York: Academic Press; [CrossRef]
    [Google Scholar]
  13. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721 [View Article][PubMed]
    [Google Scholar]
  14. Kämpfer P. 1994; Limits and possibilities of total fatty acid analysis for classification and identification of bacillus species. Syst Appl Microbiol 17:86–98 [CrossRef]
    [Google Scholar]
  15. Li J. B., Yang G., Wu M., Zhao Y., Zhou S. 2014; Bacillus huizhouensis sp. nov., isolated from a paddy field soil. Antonie Van Leeuwenhoek 106:357–363 [View Article][PubMed]
    [Google Scholar]
  16. Liu B., Hu G. P., Tang W. Q. 2013; Characteristic of average nucleotide identity (ANI) based on the whole genomes from Bacillus species in Bacillus-like genus. Fujian J Agri. Sci. 28:833–843
    [Google Scholar]
  17. Liu B., Liu G. H., Hu G. P., Sengonca C., Cetin S., Lin N. Q., Tang J. Y., Tang W. Q., Lin Y. Z. 2014; Bacillus bingmayongensis sp. nov., isolated from the pit soil of Emperor Qin's Terra-cotta warriors in China. Antonie Van Leeuwenhoek 105:501–510 [View Article][PubMed]
    [Google Scholar]
  18. Liu B., Liu G. H., Sengonca C., Schumann P., Wang M. K., Tang J. Y., Chen M. C., Cetin S. 2014; Bacillus cihuensis sp. nov., isolated from rhizosphere soil of a plant in the Cihu area of Taiwan. Antonie Van Leeuwenhoek 106:1147–1155 [View Article][PubMed]
    [Google Scholar]
  19. Logan N. A., De Vos P. 2009; Genus I. Bacillus . In Bergey's Manual of Systematic Bacteriology vol. 3 pp. 21–128 Edited by De Vos P. , Garrity G. , Jones D. , Krieg N. R., Ludwig W. , Rainey F. A. , Schleifer K. H. , Whitman W. B. . New York: Springer;
    [Google Scholar]
  20. Maughan H., Van der Auwera G. 2011; Bacillus taxonomy in the genomic era finds phenotypes to be essential though often misleading. Infection, Genetics and Evolution 11:789–797 [View Article]
    [Google Scholar]
  21. Meier-Kotloff J. P., Auch A. F., Klenk H. P., Göker M. 2013; Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60 [View Article][PubMed]
    [Google Scholar]
  22. Minnikin D. E., Collins M. D., Goodfellow M. 1979; Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 47:87–95 [CrossRef]
    [Google Scholar]
  23. Murray R. G. E., Doetsch R. N., Robinow C. F. 1994; Determinative and cytological light microscopy. In Methods for General and Molecular Bacteriology pp. 21–41 Edited by Gerhardt P. , Murray R. G. E. , Wood W. A. , Krieg N. R. . Washington: American Society for Microbiology;
    [Google Scholar]
  24. Nicholson W. L. 2002; Roles of Bacillus endospores in the environment. Cell Mol Life Sci 59:410–416[PubMed] [CrossRef]
    [Google Scholar]
  25. Nielsen P., Fritze D., Priest F. G. 1995; Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 141:1745–1761 [View Article]
    [Google Scholar]
  26. Priest F. G., Goodfellow M., Todd C. 1988; A numerical classification of the genus Bacillus. J Gen Microbiol 134:1847–1882 [View Article][PubMed]
    [Google Scholar]
  27. Ramasamy D., Mishra A. K., Lagier J. C., Padhmanabhan R., Rossi M., Sentausa E., Raoult D., Fournier P. E. 2014; A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol 64:384–391 [View Article][PubMed]
    [Google Scholar]
  28. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425[PubMed]
    [Google Scholar]
  29. Sasser M. 1990; Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News 2016
  30. Schleifer K. H. 1985; Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18:123–156 [CrossRef]
    [Google Scholar]
  31. Smibert R. M., Krieg N. R. 1994; Phenotypic characterization. In Methods for General and Molecular Bacteriology pp. 607–654 Edited by Gerhardt P. , Murray R. G. E. , Wood W. A. , Krieg N. R. . Washington, DC: American Society for Microbiology;
    [Google Scholar]
  32. Stackebrandt E., Ebers J. 2006; Taxonomic parameters revisited: tarnished gold standards. Microbial Today 33:152–155
    [Google Scholar]
  33. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. 2011; mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739 [View Article][PubMed]
    [Google Scholar]
  34. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  35. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. et al. 1987; International Committee on Systematic Bacteriology . Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [CrossRef]
    [Google Scholar]
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