1887

Abstract

A yellow-pigmented and strictly aerobic bacterial strain, designated FJY8, was isolated from the soil of Goyang, South Korea. The cells of FJY8 were Gram-reaction-negative, non-motile rods. Colonies were circular, convex and transparent. Strain FJY8 grew optimally at 30 °C, with 0 % (w/v) NaCl and at pH 8. Phylogenetic analysis of the 16S rRNA gene sequence of FJY8 revealed a clear affiliation of this bacterium to the family , and it was related to members of the genus , with KCTC 22558 being its closest relative (98.7 % sequence similarity). The DNA G+C content was 68.0±0.4 mol%. Diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids, and an unidentified phospholipid and two unidentified aminophospholipids were also detected as the minor polar lipids. The major fatty acids were iso-C, summed feature 9 (iso-Cω9 and/or C 10-methyl) and iso-C. Only ubiquinone-8 (Q-8) was detected as the isoprenoid quinone. DNA–DNA hybridization values of strain FJY8 with RCML-52 and 9NM-14 were 55.8±2.0 and 45.2±4.8 %, respectively. On the basis of DNA–DNA hybridization, phylogenetic distinctiveness, and some physiological and biochemical tests, strain FJY8 (=KCTC 42810=JCM 31019) represents a novel species of the genus , for which the name sp. nov. is proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001722
2017-04-01
2020-09-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/4/951.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001722&mimeType=html&fmt=ahah

References

  1. Christensen P, Cook FD. Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Evol Microbiol 1978;28:367–393 [CrossRef]
    [Google Scholar]
  2. Miess H, van Trappen S, Cleenwerck I, de Vos P, Gross H. Reclassification of Pseudomonas sp. PB-6250T as Lysobacter firmicutimachus sp. nov. Int J Syst Evol Microbiol 2016;66:4162–4166 [CrossRef][PubMed]
    [Google Scholar]
  3. Xie B, Li T, Lin X, Wang CJ, Chen YJ et al. Lysobacter erysipheiresistens sp. nov., an antagonist of powdery mildew, isolated from tobacco-cultivated soil. Int J Syst Evol Microbiol 2016;66:4016–4021 [CrossRef][PubMed]
    [Google Scholar]
  4. Siddiqi MZ, Im WT. Lysobacter hankyongensis sp. nov., isolated from activated sludge and Lysobacter sediminicola sp. nov., isolated from freshwater sediment. Int J Syst Evol Microbiol 2016;66:212–218 [CrossRef][PubMed]
    [Google Scholar]
  5. Singh H, Won K, du J, Yang JE, Akter S et al. Lysobacter agri sp. nov., a bacterium isolated from soil. Antonie van Leeuwenhoek 2015;108:553–561 [CrossRef][PubMed]
    [Google Scholar]
  6. Oh KH, Kang SJ, Jung YT, Oh TK, Yoon JH. Lysobacter dokdonensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2011;61:1089–1093 [CrossRef][PubMed]
    [Google Scholar]
  7. Srinivasan S, Kim MK, Sathiyaraj G, Kim HB, Kim YJ et al. Lysobacter soli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2010;60:1543–1547 [CrossRef][PubMed]
    [Google Scholar]
  8. Wang Y, Dai J, Zhang L, Luo X, Li Y et al. Lysobacter ximonensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009;59:786–789 [CrossRef][PubMed]
    [Google Scholar]
  9. Weon HY, Kim BY, Kim MK, Yoo SH, Kwon SW et al. Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea. Int J Syst Evol Microbiol 2007;57:548–551 [CrossRef][PubMed]
    [Google Scholar]
  10. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991;173:697–703 [CrossRef][PubMed]
    [Google Scholar]
  11. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389–3402[PubMed][CrossRef]
    [Google Scholar]
  12. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  13. Larkin MA, Blackshields G, Brown NP, Chenna R, Mcgettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007;23:2947–2948 [CrossRef][PubMed]
    [Google Scholar]
  14. Hall T. BioEdit. Biological sequence alignment editor for Win 95/98/NT/2K/XP Carlsbad, CA: Ibis Therapeutics; 1997
    [Google Scholar]
  15. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28:2731–2739 [CrossRef][PubMed]
    [Google Scholar]
  16. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25:4876–4882 [CrossRef][PubMed]
    [Google Scholar]
  17. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425[PubMed]
    [Google Scholar]
  18. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16:111–120 [CrossRef][PubMed]
    [Google Scholar]
  19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef]
    [Google Scholar]
  20. Fitch WM. Toward defining the course of evolution: minimum change for a specified tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  21. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982;44:992–993[PubMed]
    [Google Scholar]
  22. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984;2:233–241 [CrossRef]
    [Google Scholar]
  23. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987;19:161–205[CrossRef]
    [Google Scholar]
  24. Kuykendall LD, Roy MA, O'Neill JJ, Devine TE. Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Evol Microbiol 1988;38:358–361 [CrossRef]
    [Google Scholar]
  25. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996;42:457–469 [CrossRef]
    [Google Scholar]
  26. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981;45:316–354[PubMed]
    [Google Scholar]
  27. Zhang L, Bai J, Wang Y, Wu GL, Dai J et al. Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2011;61:2259–2265 [CrossRef][PubMed]
    [Google Scholar]
  28. Liu M, Liu Y, Wang Y, Luo X, Dai J et al. Lysobacter xinjiangensis sp. nov., a moderately thermotolerant and alkalitolerant bacterium isolated from a gamma-irradiated sand soil sample. Int J Syst Evol Microbiol 2011;61:433–437 [CrossRef][PubMed]
    [Google Scholar]
  29. Ausubel FM, Brent R, Kingston R. E, Moore D. D, Seidman J. et al. (editors) Short Protocols in Molecular Biology: A Compendium of Methods from Current Protocols in Molecular Biology, 3rd ed. New York: Wiley; 1995
    [Google Scholar]
  30. de Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970;12:133–142 [CrossRef][PubMed]
    [Google Scholar]
  31. Gillis M, Ley JD, Cleene MD. The determination of molecular weight of bacterial genome DNA from renaturation rates. Eur J Biochem 1970;12:143–153 [CrossRef]
    [Google Scholar]
  32. Loveland-Curtze J, Miteva VI, Brenchley JE, Vanya IM, Jean EB. Evaluation of a new fluorimetric DNA–DNA hybridization method. Can J Microbiol 2011;57:250–255 [CrossRef][PubMed]
    [Google Scholar]
  33. Gonzalez JM, Saiz-Jimenez C. A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 2002;4:770–773[PubMed][CrossRef]
    [Google Scholar]
  34. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA–DNA reassociation and 16s rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994;44:846–849 [CrossRef]
    [Google Scholar]
  35. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987;37:463–464[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001722
Loading
/content/journal/ijsem/10.1099/ijsem.0.001722
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited this month Most Cited RSS feed

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