1887

Abstract

A Gram-reaction-negative, strictly aerobic, non-motile, non-spore-forming and rod-shaped bacterial strain, designated THG-45, was isolated from soil of a ginseng field of Pocheon province in the Republic of Korea and its taxonomic position was investigated by a polyphasic approach. Growth occurred at 4–30 °C, at pH 5.5–9.0 and with 0–2 % (w/v) NaCl on nutrient agar. On the basis of 16S rRNA gene sequence similarity, strain THG-45 was shown to belong to the genus and was related to G-1 (98.8 %), NWER-II11 (97.9 %), PB92 (97.9 %), DS-57 (97.5 %), 15-52 (97.4 %), DS-27 (97.0 %) and 15-51 (97.0 %), but DNA relatedness between strain THG-45 and these strains was below 36 %. The G+C content of the genomic DNA was 39 mol%. The only isoprenoid quinone detected in strain THG-45 was menaquinone-7 (MK-7). The predominant fatty acids were iso-C, summed feature 3 (comprising Cω6 and/or Cω7) and iso-C 3-OH, and the major polar lipids were phosphatidylethanolamine and an unidentified aminophosphoglycolipid. Phenotypic data and phylogenetic inference supported the affiliation of strain THG-45 to the genus , and a number of biochemical tests differentiated strain THG-45 from the recognized species of the genus . Therefore, the novel isolate represents a novel species, for which the name sp. nov. is proposed, with THG-45 as the type strain ( = KACC 14530 = JCM 16721).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.051102-0
2013-12-01
2019-10-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/12/4396.html?itemId=/content/journal/ijsem/10.1099/ijs.0.051102-0&mimeType=html&fmt=ahah

References

  1. Bernardet J.-F., Nakagawa Y., Holmes B..Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes ( 2002;). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. . Int J Syst Evol Microbiol 52:, 1049–1070. [CrossRef][PubMed]
    [Google Scholar]
  2. Buck J. D.. ( 1982;). Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. . Appl Environ Microbiol 44:, 992–993.[PubMed]
    [Google Scholar]
  3. 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]
  4. Felsenstein J.. ( 1985;). Confidence limit on phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  5. 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]
  6. Gallego V., García M. T., Ventosa A.. ( 2006;). Pedobacter aquatilis sp. nov., isolated from drinking water, and emended description of the genus Pedobacter. . Int J Syst Evol Microbiol 56:, 1853–1858. [CrossRef][PubMed]
    [Google Scholar]
  7. Gordon N. S., Valenzuela A., Adams S. M., Ramsey P. W., Pollock J. L., Holben W. E., Gannon J. E.. ( 2009;). Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil. . Int J Syst Evol Microbiol 59:, 1720–1726. [CrossRef][PubMed]
    [Google Scholar]
  8. Hall T. A.. ( 1999;). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. . Nucl Acids Symp Ser 41:, 95–98.
    [Google Scholar]
  9. 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]
  10. Hoang V. A., Kim Y. J., Nguyen N. L., Min J. W., Yang D. C.. ( 2013;). Pedobacter ginsengiterrae sp. nov., isolated from soil of a ginseng field. . Int J Syst Evol Microbiol 63:, 1273–1279. [CrossRef][PubMed]
    [Google Scholar]
  11. Hwang C. Y., Choi D. H., Cho B. C.. ( 2006;). Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter. . Int J Syst Evol Microbiol 56:, 1831–1836. [CrossRef][PubMed]
    [Google Scholar]
  12. 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]
  13. Kimura M.. ( 1983;). The Neutral Theory of Molecular Evolution. Cambridge:: Cambridge University Press;. [CrossRef]
    [Google Scholar]
  14. Kumar S., Nei M., Dudley J., Tamura K.. ( 2008;). mega: a biologist-centric software for evolutionary analysis of DNA and protein sequences. . Brief Bioinform 9:, 299–306. [CrossRef][PubMed]
    [Google Scholar]
  15. Kwon S. W., Kim B. Y., Lee K. H., Jang K. Y., Seok S. J., Kwon J. S., Kim W. G., Weon H. Y.. ( 2007;). Pedobacter suwonensis sp. nov., isolated from the rhizosphere of Chinese cabbage (Brassica campestris). . Int J Syst Evol Microbiol 57:, 480–484. [CrossRef][PubMed]
    [Google Scholar]
  16. Kwon S. W., Son J. A., Kim S. J., Kim Y. S., Park I. C., Bok J. I., Weon H. Y.. ( 2011;). Pedobacter rhizosphaerae sp. nov. and Pedobacter soli sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris). . Int J Syst Evol Microbiol 61:, 2874–2879. [CrossRef][PubMed]
    [Google Scholar]
  17. Margesin R., Shivaji S.. ( 2011;). Genus II. Pedobacter Steyn et al. 1998. . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 4, pp. 339–347. Edited by Krieg N. R., Ludwig W., Whitman W. B., Hedlund B. P., Paster B. J., Staley J. T., Ward N., Brown D., Parte A... New York:: Springer;.
    [Google Scholar]
  18. 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]
  19. 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]
  20. Moore D. D., Dowhan D.. ( 1995;). Preparation and analysis of DNA. . In Current Protocols in Molecular Biology, pp. 2–11. Edited by Ausubel F. W., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K... New York:: Wiley;.
    [Google Scholar]
  21. Roh S. W., Quan Z. X., Nam Y. D., Chang H. W., Kim K. H., Kim M. K., Im W. T., Jin L., Kim S. H.. & other authors ( 2008;). Pedobacter agri sp. nov., from soil. . Int J Syst Evol Microbiol 58:, 1640–1643. [CrossRef][PubMed]
    [Google Scholar]
  22. 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]
  23. Sasser M.. ( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE:: MIDI Inc.;
    [Google Scholar]
  24. 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]
  25. Steyn P. L., Segers P., Vancanneyt M., Sandra P., Kersters K., Joubert J. J.. ( 1998;). Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov.. Int J Syst Bacteriol 48:, 165–177. [CrossRef][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. [CrossRef][PubMed]
    [Google Scholar]
  27. Vanparys B., Heylen K., Lebbe L., De Vos P.. ( 2005;). Pedobacter caeni sp. nov., a novel species isolated from a nitrifying inoculum. . Int J Syst Evol Microbiol 55:, 1315–1318. [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. Yoon J. H., Lee M. H., Kang S. J., Park S. Y., Oh T. K.. ( 2006;). Pedobacter sandarakinus sp. nov., isolated from soil. . Int J Syst Evol Microbiol 56:, 1273–1277. [CrossRef][PubMed]
    [Google Scholar]
  31. Yoon J. H., Kang S. J., Oh T. K.. ( 2007;). Pedobacter terrae sp. nov., isolated from soil. . Int J Syst Evol Microbiol 57:, 2462–2466. [CrossRef][PubMed]
    [Google Scholar]
  32. Zhou Z., Jiang F., Wang S., Peng F., Dai J., Li W., Fang C.. ( 2012;). Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter, Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus. . Int J Syst Evol Microbiol 62:, 1963–1969. [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.051102-0
Loading
/content/journal/ijsem/10.1099/ijs.0.051102-0
Loading

Data & Media loading...

Supplements

Supplementary material 

PDF

Most Cited This Month

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