1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 64, Issue Pt_9

sp. nov., isolated from rice soil and emended description of the genus Free

Abstract

A bacterial strain, designated RHs22, was isolated from a soil sample cultivated with rice in the Suwon region of South Korea. The cells were aerobic, Gram-stain-negative, non-spore-forming, non-flagellated rods or occasionally filaments. The strain grew at 10–37 °C (optimum, 28–30 °C), at pH 5.0–10.0 (optimum, 7.0) and in the presence of 0–1 % (w/v) NaCl (optimum, 0 %). Phylogenetically, the strain was closely related to members of the genus , as its 16S rRNA gene sequence had similarity of 90.3–92.1 % with respect to those of members of the genus , showing the highest sequence similarity with DSM 21099. Strain RHs22 revealed relatively low sequence similarities of less than 90 % with all the other species with validly published names. It contained MK-7 as the predominant menaquinone and summed feature 3 (Cω6 and/or Cω7), Cω5, iso-C and iso-C 3-OH as the main fatty acids. The polar lipids of strain RHs22 were phosphatidylethanolamine, one unknown aminolipid, two unknown aminophospholipids, one unknown phospholipid and five unknown lipids. The DNA G+C content was 57.0 mol%. Phylogenetic, phenotypic and chemotaxonomic data obtained in this study indicate that strain RHs22 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is RHs22 ( = KACC 17324 = DSM 28354). An emended description of the genus is also proposed.

  • Published Online:
Funding
This study was supported by the:
  • National Academy of Agricultural Science, Rural Development Administration, Republic of Korea (Award Project no. PJ008666)
© 2014 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.062901-0
2014-09-01
2024-04-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/9/3230.html?itemId=/content/journal/ijsem/10.1099/ijs.0.062901-0&mimeType=html&fmt=ahah

References

  1. Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. (editors) ( 1987 ). Current Protocols in Molecular Biology. New York:: Greene/Wiley Interscience;.
     [Google Scholar]
  2. Baik K. S., Kim M. S., Park S. C., Lee D. W., Lee S. D., Ka J.-O., Choi S. K., Seong C. N. ( 2007 ). Spirosoma rigui sp. nov., isolated from fresh water. . Int J Syst Evol Microbiol 57, 2870–2873. [View Article] [PubMed]
    [Google Scholar]
  3. 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]
  4. Collins M. D., Goodfellow M., Minnikin D. E. ( 1980 ). Fatty acid, isoprenoid quinone and polar lipid composition in the classification of Curtobacterium and related taxa. . J Gen Microbiol 118, 29–37.[PubMed]
    [Google Scholar]
  5. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368–376. [View Article] [PubMed]
    [Google Scholar]
  6. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783–791. [View Article] [PubMed]
    [Google Scholar]
  7. Finster K. W., Herbert R. A., Lomstein B. A. ( 2009 ). Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov., isolated from a high Arctic permafrost soil, and emended description of the genus Spirosoma . . Int J Syst Evol Microbiol 59, 839–844. [View Article] [PubMed]
    [Google Scholar]
  8. 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]
  9. Fries J., Pfeiffer S., Kuffner M., Sessitsch A. ( 2013 ). Spirosoma endophyticum sp. nov., isolated from Zn- and Cd-accumulating Salix caprea . . Int J Syst Evol Microbiol 63, 4586–4590. [View Article] [PubMed]
    [Google Scholar]
  10. Gonzalez J. M., Saiz-Jimenez C. ( 2002 ). A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. . Environ Microbiol 4, 770–773. [View Article] [PubMed]
    [Google Scholar]
  11. 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]
  12. Kimura M. ( 1980 ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16, 111–120. [View Article] [PubMed]
    [Google Scholar]
  13. Larkin J. M., Borrall R. ( 1984 ). Family 1. Spirosomaceae Larkin and Borrall 1978 595AL . . In Bergey’s Manual of Systematic Bacteriology, vol. 1, pp. 125–132. Edited by Krieg N. R., Holt J. G. . Baltimore, MD:: Williams & Wilkins;.
     [Google Scholar]
  14. 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]
  15. Pruesse E., Peplies J., Glöckner F. O. ( 2012 ). sina: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. . Bioinformatics 28, 1823–1829. [View Article] [PubMed]
    [Google Scholar]
  16. 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]
  17. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. Newark, DE:: Microbial ID;.
     [Google Scholar]
  18. 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]
  19. Ten L. N., Xu J.-L., Jin F.-X., Im W.-T., Oh H.-M., Lee S.-T. ( 2009 ). Spirosoma panaciterrae sp. nov., isolated from soil. . Int J Syst Evol Microbiol 59, 331–335. [View Article] [PubMed]
    [Google Scholar]
  20. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. ( 1991 ). 16S ribosomal DNA amplification for phylogenetic study. . J Bacteriol 173, 697–703.[PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.062901-0
Loading
Spirosoma oryzae sp. nov., isolated from rice soil and emended description of the genus Spirosoma
Int J Syst Evol Microbiol 64, 3230 (2014); https://doi.org/10.1099/ijs.0.062901-0
/content/journal/ijsem/10.1099/ijs.0.062901-0
/content/journal/ijsem/10.1099/ijs.0.062901-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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