1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 65, Issue Pt_12

sp. nov., isolated from the rhizosphere of rice ( L.) Free

Abstract

A Gram-stain-negative, coccobacilli-shaped bacterium, designated YC6724, was isolated from the rhizosphere of rice in Jinju, Korea. The taxonomy of strain YC6724 was studied using a polyphasic approach. Strain YC6724 grew optimally at 30 °C and pH 7.0–8.0. Comparative 16S rRNA gene sequence analyses showed that the strain was most closely related to 5N26 (98.4 % 16S rRNA gene sequence similarity), TH-G33 (97.3 %) and DS-48 (97.3 %). Sequence similarities with other species of the genus with validly published names were lower than 94.0 %. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain YC6724 formed a distinct phyletic lineage within the genus . Strain YC6724 had DNA–DNA relatedness values of 16.6 %, 44.0 % and 33.2 % with KACC 16376, KACC 12677 and KACC 11678, respectively. The predominant fatty acids of strain YC6724 were Cω7 and/or Cω6, C and C 2-OH. The polar lipid profile contained phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminolipid and two unknown lipids. The G+C content of the genomic DNA was 70.5 mol% and the major quinone was Q-10. Strain YC6724 contained spermidine as the major polyamine. On the basis of phenotypic, chemotaxonomic and molecular data, it is clear that strain YC6724 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is YC6724 ( = KCTC 22478 = NBRC 109439).

  • Published Online:
© 2015 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000656
2015-12-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/12/4839.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000656&mimeType=html&fmt=ahah

References

  1. Aslam Z., Yasir M., Yoon H. S., Jeon C. O., Chung Y. R. ( 2013;). Diversity of the bacterial community in the rice rhizosphere managed under conventional and no-tillage practices. J Microbiol 51 747–756 [View Article] [PubMed].
     [Google Scholar]
  2. Ausubel F. W., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. ( 1995). Current Protocols in Molecular Biology., New York: Wiley;.
     [Google Scholar]
  3. Baik K. S., Park S. C., Choe H. N., Kim S. N., Moon J. H., Seong C. N. ( 2012;). Roseomonas riguiloci sp. nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 62 3024–3029 [View Article] [PubMed].
     [Google Scholar]
  4. Busse H.-J., Auling G. ( 1988;). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 11 1–8 [View Article].
     [Google Scholar]
  5. Busse H.-J., Bunka S., Hensel A., Lubitz W. ( 1997;). Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 47 698–708 [View Article].
     [Google Scholar]
  6. Chen Q., Sun L. N., Zhang X. X., He J., Kwon S. W., Zhang J., Li S. P., Gu J. G. ( 2014;). Roseomonas rhizosphaerae sp. nov., a triazophos-degrading bacterium isolated from soil. Int J Syst Evol Microbiol 64 1127–1133 [View Article] [PubMed].
     [Google Scholar]
  7. Dé I., Rolston K. V., Han X. Y. ( 2004;). Clinical significance of Roseomonas species isolated from catheter and blood samples: analysis of 36 cases in patients with cancer. Clin Infect Dis 38 1579–1584 [View Article] [PubMed].
     [Google Scholar]
  8. Dittmer J. C., Lester R. L. ( 1964;). A simple, specific spray for the detection of phospholipids on thin-layer chromatograms. J Lipid Res 5 126–127 [PubMed].
     [Google Scholar]
  9. Felsenstein J. ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 783–791 [View Article].
     [Google Scholar]
  10. 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]
  11. Gallego V., Sánchez-Porro C., García M. T., Ventosa A. ( 2006;). Roseomonas aquatica sp. nov., isolated from drinking water. Int J Syst Evol Microbiol 56 2291–2295 [View Article] [PubMed].
     [Google Scholar]
  12. Gomori G. ( 1955;). Preparation of buffers for use in enzyme studies. Methods Enzymol 1 138–146 [View Article].
     [Google Scholar]
  13. Helsel L. O., Hollis D. G., Steigerwalt A. G., Levett P. N. ( 2006;). Reclassification of Roseomonas fauriae Rihs et al. 1998 as a later heterotypic synonym of Azospirillum brasilense Tarrand et al. 1979. Int J Syst Evol Microbiol 56 2753–2755 [View Article] [PubMed].
     [Google Scholar]
  14. Jacin H., Mishkin A. R. ( 1965;). Separation of carbohydrates on borate impregnated silica gel G plates. J Chromatogr A 18 170–173 [View Article] [PubMed].
     [Google Scholar]
  15. Jiang C. Y., Dai X., Wang B. J., Zhou Y. G., Liu S. J. ( 2006;). Roseomonas lacus sp. nov., isolated from freshwater lake sediment. Int J Syst Evol Microbiol 56 25–28 [View Article] [PubMed].
     [Google Scholar]
  16. Kim D. U., Ka J. O. ( 2014;). Roseomonas soli sp. nov., isolated from an agricultural soil cultivated with Chinese cabbage (Brassica campestris). Int J Syst Evol Microbiol 64 1024–1029 [View Article] [PubMed].
     [Google Scholar]
  17. 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]
  18. Kim S. J., Weon H. Y., Ahn J. H., Hong S. B., Seok S. J., Whang K. S., Kwon S. W. ( 2013;). Roseomonas aerophila sp. nov., isolated from air. Int J Syst Evol Microbiol 63 2334–2337 [View Article] [PubMed].
     [Google Scholar]
  19. 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]
  20. Komagata K., Suzuki K. ( 1987;). Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19 161–207 [View Article].
     [Google Scholar]
  21. Lane D. J. ( 1991;). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by Stackebrandt E., Goodfellow M. Chichester: Wiley;.
     [Google Scholar]
  22. Lányi B. ( 1987;). Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19 1–67 [View Article].
     [Google Scholar]
  23. Lopes A., Espirito Santo C., Grass G., Chung A. P., Morais P. V. ( 2011;). Roseomonas pecuniae sp. nov., isolated from the surface of a copper-alloy coin. Int J Syst Evol Microbiol 61 610–615 [View Article] [PubMed].
     [Google Scholar]
  24. McLean T. W., Rouster-Stevens K., Woods C. R., Shetty A. K. ( 2006;). Catheter-related bacteremia due to Roseomonas species in pediatric hematology/oncology patients. Pediatr Blood Cancer 46 514–516 [View Article] [PubMed].
     [Google Scholar]
  25. Mesbah M., Premachandran U., Whitman W. B. ( 1989;). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39 159–167 [View Article].
     [Google Scholar]
  26. 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]
  27. Nawrocki E. P., Eddy S. R. ( 2007;). Query-dependent banding (QDB) for faster RNA similarity searches. PLOS Comput Biol 3 e56 [View Article] [PubMed].
     [Google Scholar]
  28. Park M. S., Park Y. J., Jung J. Y., Lee S. H., Park W., Lee K., Jeon C. O. ( 2011;). Pusillimonas harenae sp. nov., isolated from a sandy beach, and emended description of the genus Pusillimonas . Int J Syst Evol Microbiol 61 2901–2906 [View Article] [PubMed].
     [Google Scholar]
  29. Rihs J. D., Brenner D. J., Weaver R. E., Steigerwalt A. G., Hollis D. G., Yu V. L. ( 1993;). Roseomonas, a new genus associated with bacteria and other human infections. J Clin Microbiol 31 3275–3283 [PubMed].
     [Google Scholar]
  30. Ross H. N. M., Grant W. D., Harris J. E. ( 1985;). Lipids in archaebacterial taxonomy. . In Chemical Methods in Bacterial Systematics, pp. 289–300. Edited by Goodfellow M., Minnikin D. E. London: Academic Press;.
     [Google Scholar]
  31. Rosselló-Mora R., Amann R. ( 2001;). The species concept for prokaryotes. FEMS Microbiol Rev 25 39–67 [View Article] [PubMed].
     [Google Scholar]
  32. 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]
  33. Sánchez-Porro C., Gallego V., Busse H. J., Kämpfer P., Ventosa A. ( 2009;). Transfer of Teichococcus ludipueritiae and Muricoccus roseus to the genus Roseomonas, as Roseomonas ludipueritiae comb. nov. and Roseomonas rosea comb. nov., respectively, and emended description of the genus Roseomonas . Int J Syst Evol Microbiol 59 1193–1198 [View Article] [PubMed].
     [Google Scholar]
  34. Sfanos K., Harmody D., Dang P., Ledger A., Pomponi S., McCarthy P., Lopez J. ( 2005;). A molecular systematic survey of cultured microbial associates of deep-water marine invertebrates. Syst Appl Microbiol 28 242–264 [View Article] [PubMed].
     [Google Scholar]
  35. 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]
  36. Struthers M., Wong J., Janda J. M. ( 1996;). An initial appraisal of the clinical significance of Roseomonas species associated with human infections. Clin Infect Dis 23 729–733 [View Article] [PubMed].
     [Google Scholar]
  37. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. ( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30 2725–2729 [View Article] [PubMed].
     [Google Scholar]
  38. 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]
  39. Venkata Ramana V., Sasikala Ch., Takaichi S., Ramana ChV. ( 2010;). Roseomonas aestuarii sp. nov., a bacteriochlorophyll-a containing alphaproteobacterium isolated from an estuarine habitat of India. Syst Appl Microbiol 33 198–203 [View Article] [PubMed].
     [Google Scholar]
  40. Yoon J. H., Kang S. J., Oh H. W., Oh T. K. ( 2007;). Roseomonas terrae sp. nov. Int J Syst Evol Microbiol 57 2485–2488 [View Article] [PubMed].
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000656
Loading
Roseomonas oryzicola sp. nov., isolated from the rhizosphere of rice (Oryza sativa L.)
Int J Syst Evol Microbiol 65, 4839 (2015); https://doi.org/10.1099/ijsem.0.000656
/content/journal/ijsem/10.1099/ijsem.0.000656
/content/journal/ijsem/10.1099/ijsem.0.000656
Loading

Data & Media loading...

Supplements

Supplementary Data

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