1887

Abstract

A Gram-staining-positive, non-spore-forming, rod-shaped, non-motile and aerobic bacterium, strain THG-e54, was isolated from soil of a flowerbed in Bucheon, South Korea. The taxonomic position of this bacterium was determined in an investigation based on a polyphasic approach. 16S rRNA gene sequence analysis revealed a clear affiliation of strain THG-e54 with the genus . Strain THG-e54 showed the closest phylogenetic relationship with DSM 20308 with a 16S rRNA gene sequence similarity of 98.6 %. The G+C content of the genomic DNA was 71.0 mol%. The major cellular fatty acids of strain THG-e54 were iso-C and iso-C, and the predominant menaquinone was menaquinone MK-8(H). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified amino-containing phosphoglycolipid, unidentified phospholipids, an unidentified aminolipid and an unidentified aminophospholipid. The cell-wall peptidoglycan type was -diaminopimelic acid and the cell-wall sugars were glucose and ribose. DNA–DNA hybridization experiments revealed a low level of DNA–DNA relatedness (less than 35.2 %) between strain THG-e54 and its five closest relatives. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain THG-e54 could be clearly distinguished from closely related recognized members of the genus . Therefore the results of this study indicated the existence of a novel species of the genus , for which we propose the name sp. nov., with strain THG-e54 ( = KACC 17589 = JCM 19342) as the type strain.

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2014-10-01
2019-11-18
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References

  1. Collins M. D., Dorsch M., Stackebrandt E.. ( 1989;). Transfer of Pimelobacter tumescens to Terrabacter gen. nov. as Terrabacter tumescens comb. nov. and of Pimelobacter jensenii to Nocardioides as Nocardioides jensenii comb. nov.. Int J Syst Bacteriol 39:, 1–6. [CrossRef]
    [Google Scholar]
  2. 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:, 224–229. [CrossRef]
    [Google Scholar]
  3. Felsenstein J.. ( 1985;). Confidence limit on phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  4. Fitch W. M.. ( 1971;). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20:, 406–416. [CrossRef]
    [Google Scholar]
  5. 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]
  6. 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:, 457–469. [CrossRef]
    [Google Scholar]
  7. Kim S. M., Park S. W., Park S. T., Kim Y. M.. ( 2011;). Terrabacter carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete. . Int J Syst Evol Microbiol 61:, 482–486. [CrossRef][PubMed]
    [Google Scholar]
  8. 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. [CrossRef][PubMed]
    [Google Scholar]
  9. Kimura M.. ( 1983;). The Neutral Theory of Molecular Evolution. Cambridge:: Cambridge University Press;. [CrossRef]
    [Google Scholar]
  10. Lee J.-E., Seo J. P., Lee D. W., Ko Y.-H., Lee S. D.. ( 2008;). Terrabacter lapilli sp. nov., an actinomycete isolated from stone. . Int J Syst Evol Microbiol 58:, 1084–1088. [CrossRef][PubMed]
    [Google Scholar]
  11. Liu Q.-M., Im W.-T., Lee M., Yang D.-C., Lee S.-T.. ( 2006;). Dyadobacter ginsengisoli sp. nov., isolated from soil of a ginseng field. . Int J Syst Evol Microbiol 56:, 1939–1944. [CrossRef][PubMed]
    [Google Scholar]
  12. 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. [CrossRef]
    [Google Scholar]
  13. Minnikin D. E., Alshamaony L., Goodfellow M.. ( 1975;). Differentiation of Mycobacterium, Nocardia, and related taxa by thin-layer chromatographic analysis of whole-organism methanolysates. . J Gen Microbiol 88:, 200–204. [CrossRef][PubMed]
    [Google Scholar]
  14. 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:, 104–117. [CrossRef]
    [Google Scholar]
  15. Montero-Barrientos M., Rivas R., Velázquez E., Monte E., Roig M. G.. ( 2005;). Terrabacter terrae sp. nov., a novel actinomycete isolated from soil in Spain. . Int J Syst Evol Microbiol 55:, 2491–2495. [CrossRef][PubMed]
    [Google Scholar]
  16. Moore D. D., Dowhan D.. ( 1995;). Preparation and analysis of DNA. . In Current Protocols in Molecular Biology, pp. 2–11. Edited by Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K... New York:: Wiley;.
    [Google Scholar]
  17. 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]
  18. Sasser M.. ( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc;.
  19. Schaeffer A. B., Fulton M. D.. ( 1933;). A simplified method of staining endospores. . Science 77:, 194. [CrossRef][PubMed]
    [Google Scholar]
  20. Schleifer K. H., Kandler O.. ( 1972;). Peptidoglycan types of bacterial cell walls and their taxonomic implications. . Bacteriol Rev 36:, 407–477.[PubMed]
    [Google Scholar]
  21. 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]
  22. Stackebrandt E.. ( 2012;). Genus XIII. Terrabacter Collins, Dorsch and Stackebrandt 1989, 4VP. . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 5, pp.788–790. Edited by Whitman W. B., Parte A., Goodfellow M., Kämpfer P., Busse H.-J., Trujillo M. E., Ludwig W., Suzuki K... New York:: Springer;.
    [Google Scholar]
  23. 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:, 846–849. [CrossRef]
    [Google Scholar]
  24. 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]
  25. Takahashi K., Nei M.. ( 2000;). Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. . Mol Biol Evol 17:, 1251–1258. [CrossRef][PubMed]
    [Google Scholar]
  26. 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. [CrossRef][PubMed]
    [Google Scholar]
  27. 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. [CrossRef][PubMed]
    [Google Scholar]
  28. 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:, 463–464. [CrossRef]
    [Google Scholar]
  29. 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]
  30. Weon H.-Y., Schumann P., Kroppenstedt R. M., Kim B.-Y., Song J., Kwon S.-W., Go S.-J., Stackebrandt E.. ( 2007;). Terrabacter aerolatus sp. nov., isolated from an air sample. . Int J Syst Evol Microbiol 57:, 2106–2109. [CrossRef][PubMed]
    [Google Scholar]
  31. Weon H.-Y., Son J.-A., Yoo S.-H., Kim B.-Y., Kwon S.-W., Schumann P., Kroppenstedt R., Stackebrandt E.. ( 2010;). Terrabacter aeriphilus sp. nov., isolated from an air sample. . Int J Syst Evol Microbiol 60:, 1130–1134. [CrossRef][PubMed]
    [Google Scholar]
  32. Yoon J.-H., Park S. Y., Kang S.-J., Jung Y.-T., Kim W. Y.. ( 2009;). Terrabacter terrigena sp. nov., isolated from soil. . Int J Syst Evol Microbiol 59:, 2798–2802. [CrossRef][PubMed]
    [Google Scholar]
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