1887

Abstract

A novel aerobic bacterium, designated strain RR11, was isolated from peat soil and was characterized by using a polyphasic taxonomic approach and identified in order to determine its taxonomic position. Strain RR11 is a Gram-negative, non-sporulating, motile, short-rod-shaped bacterium. 16S rRNA gene sequence analysis identified this strain as a member of the genus of the class . The highest degrees of gene sequence similarity were found with Ppe8 (98.0 %), E25 (97.3 %), FeGI01 (97.1 %), MTI-641 (97.1 %) and SA41 (97.1 %). Strain RR11 had the following chemotaxonomic characteristics: the major ubiquinone was Q-8, the DNA G+C content was 60.8 mol%, the major fatty acids were C, C cyclo ω8 and C cyclo and the polar lipid profile contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unknown aminophospholipid. Based on its morphological, physiological and chemotaxonomic characteristics, together with 16S rRNA gene sequence comparison results, strain RR11 represents a novel species, for which the name sp. nov. is proposed. The type strain is strain RR11 ( = KEMC 7302-065 = JCM 18070).

Funding
This study was supported by the:
  • Korea Ministry of Environment
  • GAIA Project (Award 173-092-012)
  • Korea National Environmental Microorganisms Bank (Award 2010-0007473)
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2014-04-01
2024-04-19
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References

  1. Aizawa T., Ve N. B., Nakajima M., Sunairi M. ( 2010 ). Burkholderia heleia sp. nov., a nitrogen-fixing bacterium isolated from an aquatic plant, Eleocharis dulcis, that grows in highly acidic swamps in actual acid sulfate soil areas of Vietnam. . Int J Syst Evol Microbiol 60, 11521157. [View Article] [PubMed]
    [Google Scholar]
  2. Aizawa T., Vijarnsorn P., Nakajima M., Sunairi M. ( 2011 ). Burkholderia bannensis sp. nov., an acid-neutralizing bacterium isolated from torpedo grass (Panicum repens) growing in highly acidic swamps. . Int J Syst Evol Microbiol 61, 16451650. [View Article] [PubMed]
    [Google Scholar]
  3. Brämer C. O., Vandamme P., da Silva L. F., Gomez J. G., Steinbüchel A. ( 2001 ). Burkholderia sacchari sp. nov., a polyhydroxyalkanoate-accumulating bacterium isolated from soil of a sugar-cane plantation in Brazil. . Int J Syst Evol Microbiol 51, 17091713. [View Article] [PubMed]
    [Google Scholar]
  4. Brown A. E. ( 2008 ). Benson’s Microbiological Applications: Laboratory Manual in General Microbiology, , 10th edn.. New York:: McGraw-Hill;.
    [Google Scholar]
  5. Caballero-Mellado J., Martínez-Aguilar L., Paredes-Valdez G., Santos P. E. ( 2004 ). Burkholderia unamae sp. nov., an N2-fixing rhizospheric and endophytic species. . Int J Syst Evol Microbiol 54, 11651172. [View Article] [PubMed]
    [Google Scholar]
  6. Cappuccino J. G., Sherman N. ( 2010 ). In Microbiology: a Laboratory Manual, , 9th edn., pp. 6974, 161–164. San Francisco:: Benjamin Cummings;.
    [Google Scholar]
  7. Chen W. M., James E. K., Coenye T., Chou J. H., Barrios E., de Faria S. M., Elliott G. N., Sheu S. Y., Sprent J. I., Vandamme P. ( 2006 ). Burkholderia mimosarum sp. nov., isolated from root nodules of Mimosa spp. from Taiwan and South America. . Int J Syst Evol Microbiol 56, 18471851. [View Article] [PubMed]
    [Google Scholar]
  8. Chen W. M., de Faria S. M., James E. K., Elliott G. N., Lin K. Y., Chou J. H., Sheu S. Y., Cnockaert M., Sprent J. I., Vandamme P. ( 2007 ). Burkholderia nodosa sp. nov., isolated from root nodules of the woody Brazilian legumes Mimosa bimucronata and Mimosa scabrella . . Int J Syst Evol Microbiol 57, 10551059. [View Article] [PubMed]
    [Google Scholar]
  9. Coenye T., Vandamme P. ( 2003 ). Diversity and significance of Burkholderia species occupying diverse ecological niches. . Environ Microbiol 5, 719729. [View Article] [PubMed]
    [Google Scholar]
  10. Doetsch R. N. ( 1981 ). Determinative methods of light microscopy. . In Manual of Methods for General Bacteriology, pp. 2133. Edited by Gerhardt P., Murray R. G. E., Costilow R. N., Nester E. W., Wood W. A., Krieg N. R., Phillips G. H. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  11. Ezaki T., Hashimoto Y., Yabuuchi E. ( 1989 ). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. . Int J Syst Bacteriol 39, 224229. [View Article]
    [Google Scholar]
  12. Felsenstein J. ( 1985 ). Confidence limit on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  13. Fitch W. M. ( 1971 ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [View Article]
    [Google Scholar]
  14. Frank J. A., Reich C. I., Sharma S., Weisbaum J. S., Wilson B. A., Olsen G. J. ( 2008 ). Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. . Appl Environ Microbiol 74, 24612470. [View Article] [PubMed]
    [Google Scholar]
  15. 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, 9598.
    [Google Scholar]
  16. Hiraishi A., Ueda Y., Ishihara J., Mori T. ( 1996 ). Comparative lipoquinone analysis of influent sewage and activated sludge by high performance liquid chromatography and photodiode array detection. . J Gen Appl Microbiol 42, 457469. [View Article]
    [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, 716721. [View Article] [PubMed]
    [Google Scholar]
  18. Kimura M. ( 1983 ). The Neutral Theory of Molecular Evolution. Cambridge:: Cambridge University Press;. [View Article]
    [Google Scholar]
  19. Komagata K., Suzuki K. ( 1987 ). Lipid and cell-wall analysis in bacterial systematics. . Methods Microbiol 19, 161207.
    [Google Scholar]
  20. Kuykendall L. D., Roy M. A., O’Neill J. J., Devine T. E. ( 1988 ). Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . . Int J Syst Bacteriol 38, 358361. [View Article]
    [Google Scholar]
  21. Marmur J. ( 1961 ). A procedure for the isolation of deoxyribonucleic acid from microorganisms. . J Mol Biol 3, 208218. [View Article]
    [Google Scholar]
  22. 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, 159167. [View Article]
    [Google Scholar]
  23. Minnikin D. E., Patel P. V., Alshamaony L., Goodfellow M. ( 1977 ). Polar lipid composition in the classification of Nocardia and related bacteria. . Int J Syst Bacteriol 27, 104117. [View Article]
    [Google Scholar]
  24. 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, 233241. [View Article]
    [Google Scholar]
  25. Otsuka Y., Muramatsu Y., Nakagawa Y., Matsuda M., Nakamura M., Murata H. ( 2011 ). Burkholderia oxyphila sp. nov., a bacterium isolated from acidic forest soil that catabolizes (+)-catechin and its putative aromatic derivatives. . Int J Syst Evol Microbiol 61, 249254. [View Article] [PubMed]
    [Google Scholar]
  26. Perin L., Martínez-Aguilar L., Paredes-Valdez G., Baldani J. I., Estrada-de Los Santos P., Reis V. M., Caballero-Mellado J. ( 2006 ). Burkholderia silvatlantica sp. nov., a diazotrophic bacterium associated with sugar cane and maize. . Int J Syst Evol Microbiol 56, 19311937. [View Article] [PubMed]
    [Google Scholar]
  27. Reis V. M., Estrada-de los Santos P., Tenorio-Salgado S., Vogel J., Stoffels M., Guyon S., Mavingui P., Baldani V. L., Schmid M. & other authors ( 2004 ). Burkholderia tropica sp. nov., a novel nitrogen-fixing, plant-associated bacterium. . Int J Syst Evol Microbiol 54, 21552162. [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, 406425.[PubMed]
    [Google Scholar]
  29. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc;.
    [Google Scholar]
  30. Sheu S. Y., Chou J. H., Bontemps C., Elliott G. N., Gross E., dos Reis F. B. Jr, Melkonian R., Moulin L., James E. K. & other authors ( 2013 ). Burkholderia diazotrophica sp. nov., isolated from root nodules of Mimosa spp.. Int J Syst Evol Microbiol 63, 435441. [View Article] [PubMed]
    [Google Scholar]
  31. Stackebrandt E., Goebel B. M. ( 1994 ). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. . Int J Syst Bacteriol 44, 846849. [View Article]
    [Google Scholar]
  32. Tamaoka J., Komagata K. ( 1984 ). Determination of DNA base composition by reversed phase high-performance liquid chromatography. . FEMS Microbiol Lett 25, 125128. [View Article]
    [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, 27312739. [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, 48764882. [View Article] [PubMed]
    [Google Scholar]
  35. Valverde A., Delvasto P., Peix A., Velázquez E., Santa-Regina I., Ballester A., Rodríguez-Barrueco C., García-Balboa C., Igual J. M. ( 2006 ). Burkholderia ferrariae sp. nov., isolated from an iron ore in Brazil. . Int J Syst Evol Microbiol 56, 24212425. [View Article] [PubMed]
    [Google Scholar]
  36. 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. & other authors ( 1987 ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37, 463464. [View Article]
    [Google Scholar]
  37. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. ( 1991 ). 16S ribosomal DNA amplification for phylogenetic study. . J Bacteriol 173, 697703.[PubMed]
    [Google Scholar]
  38. Yabuuchi E., Kosako Y., Oyaizu H., Yano I., Hotta H., Hashimoto Y., Ezaki T., Arakawa M. ( 1992 ). Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov.. Microbiol Immunol 36, 12511275. [View Article] [PubMed]
    [Google Scholar]
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