1887

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.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001107
2016-07-01
2020-04-05
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/7/2678.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001107&mimeType=html&fmt=ahah

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 Sci2:117–134 [CrossRef][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 Microbiol57:2327–2332 [CrossRef][PubMed]
    [Google Scholar]
  3. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E.. 1977; Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol100:221–230 [CrossRef][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 Evol17:68–376[CrossRef]
    [Google Scholar]
  6. Felsenstein J.. 1985; Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution39:783–791 [CrossRef]
    [Google Scholar]
  7. Fitch W. M.. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool20:406–416[CrossRef]
    [Google Scholar]
  8. Fritze D.. 2004; Taxonomy of the genus bacillus and related genera: the aerobic endospore-forming bacteria. Phytopathology94:1245–1248 [CrossRef][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 Microbiol57:81–91 [CrossRef][PubMed]
    [Google Scholar]
  10. Gregersen T.. 1978; Rapid method for distinction of gram-negative from gram-positive bacteria. European Journal of Applied Microbiology and Biotechnology5:123–127 [CrossRef]
    [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 Metabolismvol. 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 Microbiol62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  14. Kämpfer P.. 1994; Limits and possibilities of total fatty acid analysis for classification and identification of bacillus species. Syst Appl Microbiol17:86–98[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 Leeuwenhoek106:357–363 [CrossRef][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 Leeuwenhoek105:501–510 [CrossRef][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 Leeuwenhoek106:1147–1155 [CrossRef][PubMed]
    [Google Scholar]
  19. Logan N. A., De Vos P.. 2009; Genus I. Bacillus . In Bergey's Manual of Systematic Bacteriologyvol. 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 Evolution11:789–797 [CrossRef]
    [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 Bioinformatics14:60 [CrossRef][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 Bacteriol47:87–95[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 Sci59:410–416[PubMed][CrossRef]
    [Google Scholar]
  25. Nielsen P., Fritze D., Priest F. G.. 1995; Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology141:1745–1761 [CrossRef]
    [Google Scholar]
  26. Priest F. G., Goodfellow M., Todd C.. 1988; A numerical classification of the genus Bacillus. J Gen Microbiol134:1847–1882 [CrossRef][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 Microbiol64:384–391 [CrossRef][PubMed]
    [Google Scholar]
  28. Saitou N., Nei M.. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol4:406–425[PubMed]
    [Google Scholar]
  29. Sasser M.. 1990; Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News2016
  30. Schleifer K. H.. 1985; Analysis of the chemical composition and primary structure of murein. Methods Microbiol18:123–156[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 Today33:152–155
    [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 Evol28:2731–2739 [CrossRef][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 Res25:4876–4882 [CrossRef][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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001107
Loading
/content/journal/ijsem/10.1099/ijsem.0.001107
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited this month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error