1887

Abstract

A Gram-stain-negative, non-motile, light-pink-pigmented, aerobic, rod-shaped bacterium, designated V5RD, was isolated from soil of Damxung county in the Qinghai-Tibetan Plateau. Strain V5RD grew luxuriously at 10 °C, at pH 9.0 and in the presence of 1 % NaCl (w/v). Phylogenetic analysis of 16S rRNA gene sequences placed strain V5RD in the genus and found that it was most closely related to DSM 19624 (97.3 %), JCM 16721 (96.84 %), DSM 19486 (96.28 %), JCM 13399 (96.22 %), KCTC 12559 (95.92 %) and DSM 19626 (95.85 %). The G+C content of the genomic DNA of the type strain V5RD was 37.40 mol%. DNA–DNA relatedness for the type strain V5RD with respect to its closest phylogenetic relative, DSM 19624, was 62.5±1.7 %. The polar lipid profile of the strain consisted of phosphatidylethanolamine, one unidentified aminolipid, one unidentified glycolipid and two unidentified polar lipids. Menaquinone MK-7 was the predominant respiratory quinone, and summed feature 3 (comprising C 7 and/or C 6), iso-C and iso-C 3-OH were the major fatty acids. With respect to phenotypic characteristics, biochemical properties and phylogenetic inference, strain V5RD represents a novel species of the genus , for which the name sp. nov is proposed. The type strain is V5RD (=CGMCC 1.15644=DSM 103236).

Keyword(s): Nobel species , Soil and Tibetan Plateau
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2016-11-01
2022-01-21
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References

  1. Altenburger P., Kämpfer P., Makristathis A., Lubitz W., Busse H.-J. 1996; Classification of bacteria isolated from a medieval wall painting. J Biotechnol 47:39–52 [View Article]
    [Google Scholar]
  2. Baik K. S., Park Y.-D., Kim M. S., Park S. C., Moon E. Y., Rhee M. S., Choi J. H., Seong C. N. 2007; Pedobacter koreensis sp. nov., isolated from fresh water. Int J Syst Evol Microbiol 57:2079–2083 [View Article]
    [Google Scholar]
  3. De Ley J., Cattoir H., Reynaerts A. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142[PubMed] [CrossRef]
    [Google Scholar]
  4. Derichs J., Kampfer P., Lipski A. 2014; Pedobacter nutrimenti sp. nov., isolated from chilled food. Int J Syst Evol Microbiol 64:1310–1316 [View Article]
    [Google Scholar]
  5. Du J., Singh H., Ngo H. T., Won K. H., Kim K. Y., Yi T. H. 2015; Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov., isolated from an ancient tree trunk, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 65:1241–1246 [View Article][PubMed]
    [Google Scholar]
  6. Embley T. M. 1991; The linear PCR reaction: a simple and robust method for sequencing amplified rRNA genes. Lett Appl Microbiol 13:171–174 [View Article][PubMed]
    [Google Scholar]
  7. Farfán M., Montes M. J., Marqués A. M. 2014; Reclassification of Sphingobacterium antarcticum Shivaji et al. 1992 as Pedobacter antarcticus comb. nov. and Pedobacter piscium (Takeuchi and Yokota 1993) Steyn et al. 1998 as a later heterotypic synonym of Pedobacter antarcticus. Int J Syst Evol Microbiol 64:863–868 [View Article][PubMed]
    [Google Scholar]
  8. 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 [View Article]
    [Google Scholar]
  9. 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 MIicrobiol 59:1720–1726 [View Article]
    [Google Scholar]
  10. Gu Z., Liu Y., Shen L., Liu X., Xiao N., Jiao N., Liu H., Zhou Y., Zhang S. 2015; Hafnia psychrotolerans sp. nov., isolated from lake water. Int J Syst Evol Microbiol 65:971–974 [View Article]
    [Google Scholar]
  11. Hiraishi A., Ueda Y., Ishihara J. 1998; Quinone profiling of bacterial communities in natural and synthetic sewage activated sludge for enhanced phosphate removal. Applied Environ Microbiol 64:992–998
    [Google Scholar]
  12. Huss V. A. R., Festl H., Schleifer K. H. 1983; Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192 [View Article]
    [Google Scholar]
  13. 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 MicrobioI 56:1831–1836 [View Article]
    [Google Scholar]
  14. Jung Y. T., Lee S. Y., Choi W. C., Oh T. K., Yoon J. H. 2012; Pedobacter boryungensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 62:13–17 [View Article]
    [Google Scholar]
  15. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. 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]
    [Google Scholar]
  16. Kim D. U., Kim Y. J., Shin D. H., Weon H. Y., Kwon S. W., Seong C. N., Ka J. O. 2013; Pedobacter namyangjuensis sp. nov. isolated from soil and reclassification of Nubsella zeaxanthinifaciens Asker et al. 2008 as Pedobacter zeaxanthinifaciens comb. nov. J Microbiol 51:25–30 [View Article][PubMed]
    [Google Scholar]
  17. Kook M., Park Y., Yi T. H. 2014; Pedobacter jejuensis sp. nov., isolated from soil of a pine grove, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 64:1789–1794 [View Article]
    [Google Scholar]
  18. 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 [View Article]
    [Google Scholar]
  19. Lee H.-G., Kim S.-G., Im W.-T., Oh H.-M., Lee S.-T. 2009; Pedobacter composti sp. nov., isolated from compost. Int J Syst Evol Microbiol 59:345–349 [View Article]
    [Google Scholar]
  20. Marmur J. 1961; A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Bio 3:208–218 [CrossRef]
    [Google Scholar]
  21. Qiu X., Qu Z., Jiang F., Ren L., Chang X., Kan W., Fang C., Peng F. 2014; Pedobacter huanghensis sp. nov. and Pedobacter glacialis sp. nov., isolated from Arctic glacier foreland. Int J Syst Evol Microbiol 64:2431–2436 [View Article]
    [Google Scholar]
  22. Roh S. W., Quan Z., Nam Y. D., Chang H. W., Kim K. H., Kim M. K., Im W. T., Jin L., Kim S. H. et al. 2008; Pedobacter agri sp. nov., from soil. Int J Syst Evol Microbiol 58:1640–1643 [View Article]
    [Google Scholar]
  23. Romano I., Lama L., Nicolaus B., Poli A., Gambacorta A., Giordano A. 2006; Halomonas alkaliphila sp. nov., a novel halotolerant alkaliphilic bacterium isolated from a salt pool in Campania (Italy). J Gen Appl Microbiol 52:339–348 [View Article]
    [Google Scholar]
  24. Smitbert 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]
  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 [View Article]
    [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 [View Article]
    [Google Scholar]
  27. Tindall B. J. 1990; Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202 [View Article]
    [Google Scholar]
  28. 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]
    [Google Scholar]
  29. 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. et al. 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]
  30. Yang J. E., Son H. M., Lee J. M., Shin H. S., Park S. Y., Lee D. G., Kook M., Yi T. H. 2013; Pedobacter ginsenosidimutans sp. nov., with ginsenoside-converting activity. Int J Syst Evol Microbiol 63:4396–4401 [View Article]
    [Google Scholar]
  31. 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 [View Article]
    [Google Scholar]
  32. 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 [View Article]
    [Google Scholar]
  33. 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 [View Article]
    [Google Scholar]
  34. Zhu L., Si M., Li C., Xin K., Chen C., Shi X., Huang R., Zhao L., Shen X., Zhang L. 2015; Sphingomonas gei sp. nov., isolated from roots of Geum aleppicum. Int J Syst Evol Microbiol 65:1160–1166 [View Article]
    [Google Scholar]
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