1887

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Volume 64, Issue Pt_8

sp. nov., a moderately halophilic bacterium isolated from rice husks Free

Abstract

A Gram-stain-positive, aerobic, endospore-forming, moderately halophilic rod, designated strain R1, was isolated from rice husks and subjected to a taxonomic study using a polyphasic approach. Strain R1 produced spherical or ellipsoidal endospores at a subterminal position in swollen sporangia, and was catalase- and oxidase-positive. The isolate grew optimally at 37 °C and pH 6.0–7.0, and could grow in the presence of up to 9 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R1 belongs to the genus . The closest relatives of strain R1 were NCIB 3610, TF-12, and TF-11, with 16S rRNA gene sequence similarities of 96.0 %, 98.4 %, and 98.7 %, respectively. DNA–DNA relatedness values between the isolate and the reference strains were ≤42±3 %. The predominant menaquinones were MK-5 (50 %) and MK-7 (50 %). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethanolamine. The major cellular fatty acids were iso-C (48.6 %) and anteiso-C (20.6 %), and the cell-wall diamino acid was -diaminopimelic acid. On the basis of 16S rRNA gene sequence analyses and chemotaxonomic and phenotypic characteristics, it is concluded that strain R1 represents a novel species of the genus , for which we propose the name sp. nov. The type strain is R1 ( = KACC 17217 = KCCM 90231 = JCM 19602).

  • Published Online:
Funding
This study was supported by the:
  • Yonsei University Research Fund of 2012 and 2013
  • Postdoctoral Fellowship Program of National Institute of Animal Science, Rural Development Administration, Republic of Korea
© 2014 IUMS
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2014-08-01
2024-12-05
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References

  1. Ahmed A. E., Adam F. ( 2007 ). Indium incorporated silica from rice husk and its catalytic activity. . Microporous Mesoporous Mater 103, 284–295. [View Article]
    [Google Scholar]
  2. Arahal D. R., Márquez M. C., Volcani B. E., Schleifer K. H., Ventosa A. ( 1999 ). Bacillus marismortui sp. nov., a new moderately halophilic species from the Dead Sea. . Int J Syst Bacteriol 49, 521–530. [View Article] [PubMed]
    [Google Scholar]
  3. Ash C., Farrow J. A. E., Wallbanks S., Collins M. D. ( 1991 ). Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences. . Lett Appl Microbiol 13, 202–206. [View Article]
    [Google Scholar]
  4. Bae S. S., Lee J. H., Kim S. J. ( 2005 ). Bacillus alveayuensis sp. nov., a thermophilic bacterium isolated from deep-sea sediments of the Ayu Trough. . Int J Syst Evol Microbiol 55, 1211–1215. [View Article] [PubMed]
    [Google Scholar]
  5. Breznak J. A., Costilow R. N. ( 1994 ). Physicochemical factors in growth. . In Methods for General and Molecular Bacteriology, pp. 137–154. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
     [Google Scholar]
  6. Cohn F. ( 1872 ). Untersuchungen über Bakterien. . Beitrage zur Biologie der Pflanzen 1, 127–224 (in German).
     [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. [View Article]
    [Google Scholar]
  8. Hall T. A. ( 1999 ). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. . Nucleic Acids Symp Ser 41, 95–98.
     [Google Scholar]
  9. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. & other authors ( 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]
  10. Lane D. J., Pace B., Olsen G. J., Stahl D. A., Sogin M. L., Pace N. R. ( 1985 ). Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. . Proc Natl Acad Sci U S A 82, 6955–6959. [View Article] [PubMed]
    [Google Scholar]
  11. Lee Y. J., Kim B. K., Lee B. H., Jo K. I., Lee N. K., Chung C. H., Lee Y. C., Lee J. W. ( 2008 ). Purification and characterization of cellulase produced by Bacillus amyoliquefaciens DL-3 utilizing rice hull. . Bioresour Technol 99, 378–386. [View Article] [PubMed]
    [Google Scholar]
  12. Lim J. M., Jeon C. O., Kim C. J. ( 2006 ). Bacillus taeanensis sp. nov., a halophilic Gram-positive bacterium from a solar saltern in Korea. . Int J Syst Evol Microbiol 56, 2903–2908. [View Article] [PubMed]
    [Google Scholar]
  13. Logan N. A., Berkeley R. C. W. ( 1984 ). Identification of Bacillus strains using the API system. . J Gen Microbiol 130, 1871–1882.[PubMed]
    [Google Scholar]
  14. Logan N. A., De Vos P. ( 2009 ). Genus Bacillus Cohn 1872. . In Bergey's Manual of Systematic Bacteriology, , 2nd edn., vol. 3, pp. 21–128. Edited by De Vos P., Garrity G. M., Jones D., Krieg N. R., Ludwig W., Rainey F. R., Schleifer K. H., Whitman W. B. . New York:: Springer;.
     [Google Scholar]
  15. Logan N. A., Popovitch T. J., Hoffmaster A. ( 2007 ). Bacillus and related genera. . In Manual of Clinical Microbiology, , 9th edn., vol. 1, pp. 445–460. Edited by Murray P. R., Baron E. J., Jorgensen J. H., Pfaller M. A., Yolken R. H. . Washington, DC:: American Society for Microbiology;.
     [Google Scholar]
  16. Miller L. T. ( 1982 ). Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. . J Clin Microbiol 16, 584–586.[PubMed]
    [Google Scholar]
  17. Minnikin D. E., O’Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H. ( 1984 ). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods 2, 233–241. [View Article]
    [Google Scholar]
  18. Morisaki N., Phae C. G., Nakasaki K., Shoda M., Kubota H. ( 1989 ). Nitrogen transformation during thermophilic composting. . J Ferment Bioeng 67, 57–61. [View Article]
    [Google Scholar]
  19. Nakagawa Y., Yamasato K. ( 1993 ). Phylogenetic diversity of the genus Cytophaga revealed by 16S rRNA sequencing and menaquinone analysis. . J Gen Microbiol 139, 1155–1161. [View Article] [PubMed]
    [Google Scholar]
  20. 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]
  21. Schleifer K. H., Kandler O. ( 1972 ). Peptidoglycan types of bacterial cell walls and their taxonomic implications. . Bacteriol Rev 36, 407–477.[PubMed]
    [Google Scholar]
  22. Smibert R. M., Krieg N. R. ( 1981 ). General characterization. . In Manual of Methods for General Bacteriology, pp. 409–443. Edited by Gerhardt P., Murray R. G. E., Costilow R. N., Nester E. W., Wood W. A., Krieg N. R., Phillips G. B. . Washington, DC:: American Society for Microbiology;.
     [Google Scholar]
  23. Staneck J. L., Roberts G. D. ( 1974 ). Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. . Appl Microbiol 28, 226–231.[PubMed]
    [Google Scholar]
  24. Takaku H., Kodaira S., Kimoto A., Nashimoto M., Takagi M. ( 2006 ). Microbial communities in the garbage composting with rice hull as an amendment revealed by culture-dependent and -independent approaches. . J Biosci Bioeng 101, 42–50. [View Article] [PubMed]
    [Google Scholar]
  25. 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]
  26. 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]
  27. Ventosa A., Garcia M. T., Kamekura M., Onishi H., Ruiz-Berraquero F. ( 1989 ). Bacillus halophilus sp. nov., a moderately halophilic Bacillus species. . Syst Appl Microbiol 12, 162–166. [View Article]
    [Google Scholar]
  28. Xue Y., Ventosa A., Wang X., Ren P., Zhou P., Ma Y. ( 2008 ). Bacillus aidingensis sp. nov., a moderately halophilic bacterium isolated from Ai-Ding salt lake in China. . Int J Syst Evol Microbiol 58, 2828–2832. [View Article] [PubMed]
    [Google Scholar]
  29. Yoon J. H., Kim I. G., Kang K. H., Oh T. K., Park Y. H. ( 2003 ). Bacillus marisflavi sp. nov. and Bacillus aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea. . Int J Syst Evol Microbiol 53, 1297–1303. [View Article] [PubMed]
    [Google Scholar]
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Bacillusoryzaecorticis sp. nov., a moderately halophilic bacterium isolated from rice husks
Int J Syst Evol Microbiol 64, 2786 (2014); https://doi.org/10.1099/ijs.0.058768-0
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