sp. nov., isolated from fallow farmland soil Free

Abstract

A novel bacterial strain, designated THG-PC7, was isolated from fallow farmland soil in Yongin, South Korea. Cells of strain THG-PC7 were Gram-stain-negative, dark yellow, aerobic, rod-shaped and had gliding motility. Strain THG-PC7 grew optimally at 25–35 °C, at pH 7 and in the absence of NaCl. Comparative 16S rRNA gene sequence analysis identified strain THG-PC7 as belonging to the genus , exhibiting highest sequence similarity with KCTC 22336 (98.7 %) followed by KACC 11588 (95.7 %). In DNA–DNA hybridization tests, DNA relatedness between strain THG-PC7 and its closest phylogenetic neighbour was below 25 %. The DNA G+C content of the novel isolate was determined to be 62.5 mol%. Flexirubin-type pigments were found to be present. The major cellular fatty acids were determined to be iso-C, iso-C, anteiso-C and iso-Cω9. The major respiratory quinone was identified as ubiquonone-8 (Q8). The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospolipid. On the basis of results from DNA–DNA hybridization and the polyphasic data, strain THG-PC7 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is THG-PC7( = KACC 18276 = CCTCC AB 2014319).

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2015-09-01
2024-03-29
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References

  1. Christensen W.B. ( 1946;). Urea decomposition as a means of differentiating proteus and paracolon cultures from each other and from Salmonella and Shigella types. J Bacteriol 52 461466 [PubMed].
    [Google Scholar]
  2. Christensen P., Cook F.D. ( 1978;). Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol 28 367393 [View Article].
    [Google Scholar]
  3. Collins M.D. ( 1985;). Isoprenoid quinone analyses in bacterial classification and identification. . In Chemical Methods in Bacterial Systematics, pp. 267287. Edited by Goodfellow M., Minnikin D. E. London: Academic Press;.
    [Google Scholar]
  4. 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]
  5. Fautz E., Reichenbach H. ( 1980;). A simple test for flexirubin-type pigments. FEMS Microbiol Ecol 8 8791 [View Article].
    [Google Scholar]
  6. Felsenstein J. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 368376 [View Article] [PubMed] .
    [Google Scholar]
  7. 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]
  8. Gillis M., De Ley J., De Cleene M. ( 1970;). The determination of molecular weight of bacterial genome DNA from renaturation rates. Eur J Biochem 12 143153 [View Article] [PubMed] .
    [Google Scholar]
  9. Gomori G. ( 1955;). Preparation of buffers for use in enzyme studies. . In Methods in Enzymology, pp. 138146. Edited by Colowick S. P., Kaplan N. O. New York: Academic Press; [View Article].
    [Google Scholar]
  10. 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]
  11. 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]
  12. Kimura M. ( 1983). The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; [View Article].
    [Google Scholar]
  13. Lee J.W., Im W.T., Kim M.K., Yang D.C. ( 2006;). Lysobacter koreensis sp. nov., isolated from a ginseng field. Int J Syst Evol Microbiol 56 231235 [View Article] [PubMed] .
    [Google Scholar]
  14. Liu M., Liu Y., Wang Y., Luo X., Dai J., Fang C. ( 2011;). Lysobacter xinjiangensis sp. nov., a moderately thermotolerant and alkalitolerant bacterium isolated from a gamma-irradiated sand soil sample. Int J Syst Evol Microbiol 61 433437 [View Article] [PubMed] .
    [Google Scholar]
  15. Luo G., Shi Z., Wang G. ( 2012;). Lysobacter arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from iron-mined soil. Int J Syst Evol Microbiol 62 16591665 [View Article] [PubMed] .
    [Google Scholar]
  16. McConaughy B.L., Laird C.D., McCarthy B.J. ( 1969;). Nucleic acid reassociation in formamide. Biochemistry 8 32893295 [View Article] [PubMed] .
    [Google Scholar]
  17. 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]
  18. Minnikin D.E., O'Donnel A.G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J.H. ( 1984;). An intergrated procedure for the extraction of bacterial isoprenoid quinines and polar lipids. J Microbiol Methods 2 233241 [View Article].
    [Google Scholar]
  19. Moore D.D., Dowhan D. ( 1995;). Preparation and analysis of DNA. . In Current Protocols in Molecular Biology, pp. 211. 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]
  20. Park J.H., Kim R., Aslam Z., Jeon C.O., Chung Y.R. ( 2008;). Lysobacter capsici sp. nov., with antimicrobial activity, isolated from the rhizosphere of pepper, and emended description of the genus Lysobacter . Int J Syst Evol Microbiol 58 387392 [View Article] [PubMed] .
    [Google Scholar]
  21. Romanenko L.A., Uchino M., Tanaka N., Frolova G.M., Mikhailov V.V. ( 2008;). Lysobacter spongiicola sp. nov., isolated from a deep-sea sponge. Int J Syst Evol Microbiol 58 370374 [View Article] [PubMed] .
    [Google Scholar]
  22. Saitou N., Nei M. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 406425 [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. Skerman V.B.D. ( 1967). A Guide to the Identification of the Genera of Bacteria, 2nd edn. Baltimore: Williams and Wilkins;.
    [Google Scholar]
  25. Srinivasan S., Kim M.K., Sathiyaraj G., Kim H.B., Kim Y.J., Yang D.C. ( 2010;). Lysobacter soli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 60 15431547 [View Article] [PubMed] .
    [Google Scholar]
  26. Stabili L., Gravili C., Tredici S.M., Piraino S., Talà A., Boero F., Alifano P. ( 2008;). Epibiotic Vibrio luminous bacteria isolated from some hydrozoa and bryozoa species. Microb Ecol 56 625636 [View Article] [PubMed] .
    [Google Scholar]
  27. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. ( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30 27252729 [View Article] [PubMed] .
    [Google Scholar]
  28. Ten L.N., Jung H.M., Im W.T., Yoo S.A., Oh H.M., Lee S.T. ( 2009;). Lysobacter panaciterrae sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 59 958963 [View Article] [PubMed] .
    [Google Scholar]
  29. 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]
  30. Wang Y., Dai J., Zhang L., Luo X., Li Y., Chen G., Tang Y., Meng Y., Fang C. ( 2009;). Lysobacter ximonensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 59 786789 [View Article] [PubMed] .
    [Google Scholar]
  31. Wang G.L., Wang L., Chen H.H., Shen B., Li S.P., Jiang J.D. ( 2011;). Lysobacter ruishenii sp. nov., a chlorothalonil-degrading bacterium isolated from a long-term chlorothalonil-contaminated soil. Int J Syst Evol Microbiol 61 674679 [View Article] [PubMed] .
    [Google Scholar]
  32. 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]
  33. Wei D.Q., Yu T.T., Yao J.C., Zhou E.M., Song Z.Q., Yin Y.R., Ming H., Tang S.K., Li W.J. ( 2012;). Lysobacter thermophilus sp. nov., isolated from a geothermal soil sample in Tengchong, south-west China. Antonie van Leeuwenhoek 102 643651 [View Article] [PubMed] .
    [Google Scholar]
  34. 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]
  35. Weon H.Y., Kim B.Y., Baek Y.K., Yoo S.H., Kwon S.W., Stackebrandt E., Go S.J. ( 2006;). Two novel species, Lysobacter daejeonensis sp. nov. and Lysobacter yangpyeongensis sp. nov., isolated from Korean greenhouse soils. Int J Syst Evol Microbiol 56 947951 [View Article] [PubMed] .
    [Google Scholar]
  36. Weon H.Y., Kim B.Y., Kim M.K., Yoo S.H., Kwon S.W., Go S.J., Stackebrandt E. ( 2007;). Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea. Int J Syst Evol Microbiol 57 548551 [View Article] [PubMed] .
    [Google Scholar]
  37. Yang S.Z., Feng G.D., Zhu H.H., Wang Y.H. ( 2015;). Lysobacter mobilis sp. nov., isolated from abandoned lead-zinc ore. Int J Syst Evol Microbiol. 65 833837 [View Article] [PubMed] .
    [Google Scholar]
  38. Yu T.-T., Zhou E.-M., Yin Y.-R., Yao J.-C., Ming H., Dong L., Li S., Nie G.-X., Li W.-J. ( 2013;). Vulcaniibacterium tengchongense gen. nov., sp. nov. isolated from a geothermally heated soil sample, and reclassification of Lysobacter thermophilus Wei et al. 2012 as Vulcaniibacterium thermophilum comb. nov. Antonie van Leeuwenhoek 104 369376 [View Article] [PubMed] .
    [Google Scholar]
  39. Zhang L., Bai J., Wang Y., Wu G.L., Dai J., Fang C.X. ( 2011;). Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 61 22592265 [View Article] [PubMed] .
    [Google Scholar]
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