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Abstract

A yellow-pigmented, oxidase-positive, catalase-negative, Gram-stain-negative, rod-shaped, aerobic and non-motile bacterial strain designated K3R-10 was isolated from a freshwater source. The strain grew over a temperature range from 4 to 35 °C (optimum, 30 °C), pH range pH 6–8 (optimum, pH 7) and in the presence of 0–0.5 % NaCl (optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain K3R-10 belonged to the genus and shared close similarities with LMG 10402 (97.0 %), LMG 26729 (96.4 %), IFO 15030 (96.4 %) and 412R-09 (96.3 %), but formed a distinct phylogenetic line of its own in the phylogenetic trees. The polar lipids consisted of phosphatidylethanolamine, an unidentified aminolipid and three unidentified phospholipids. The DNA G+C content was 35.4 mol%, MK-6 was the major isoprenoid quinone, and homospermidine was the predominant polyamine. The predominant cellular fatty acids were iso-C 3-OH, iso-C, a summed feature comprising Cω7 and/or Cω6 and iso-C G. The absence of aminophospholipid, acid production from carbohydrates, DNA G+C content and colony morphology differentiated strain K3R-10 from related species of the genus . Thus, on the basis of phenotypic, chemotaxonomic and phylogenetic features, strain K3R-10 evidently represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain is K3R-10 (=JCM 31220=KCTC 52563).

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2017-07-01
2024-04-19
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References

  1. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM et al. Genus II. Flavobacterium gen. nov. In Bergey’s Manual of Determinative Bacteriology Baltimore: Williams & Wilkins; 1923 pp. 97–117
    [Google Scholar]
  2. Bernardet JF, Bowman JP. Genus I. Flavobacterium Bergey, et al. 1923. In Whitman W. (editor) Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 4 Baltimore: Williams & Wilkins; 2011 pp. 112–154
    [Google Scholar]
  3. Bernardet J-F, Segers P, Vancanneyt M, Berthe F, Kersters K et al. Cutting a gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (Basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 1996; 46:128–148 [View Article]
    [Google Scholar]
  4. McBride MJ, Xie G, Martens EC, Lapidus A, Henrissat B et al. Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Appl Environ Microbiol 2009; 75:6864–6875 [View Article][PubMed]
    [Google Scholar]
  5. Jit S, Dadhwal M, Prakash O, Lal R. Flavobacterium lindanitolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil. Int J Syst Evol Microbiol 2008; 58:1665–1669 [View Article][PubMed]
    [Google Scholar]
  6. Fu Y, Tang X, Lai Q, Zhang C, Zhong H et al. Flavobacterium beibuense sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2011; 61:205–209 [View Article][PubMed]
    [Google Scholar]
  7. Sang MK, Kim KD. The volatile-producing Flavobacterium johnsoniae strain GSE09 shows biocontrol activity against Phytophthora capsici in pepper. J Appl Microbiol 2012; 113:383–398 [View Article][PubMed]
    [Google Scholar]
  8. Kolton M, Sela N, Elad Y, Cytryn E. Comparative genomic analysis indicates that niche adaptation of terrestrial F lavobacteria is strongly linked to plant glycan metabolism. PLoS One 2013; 8:e76704 [View Article][PubMed]
    [Google Scholar]
  9. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  10. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article][PubMed]
    [Google Scholar]
  11. Delong EF. Archaea in coastal marine environments. Proc Natl Acad Sci USA 1992; 89:5685–5689 [View Article][PubMed]
    [Google Scholar]
  12. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 2017 in press
    [Google Scholar]
  13. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  14. 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]
  15. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  16. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
    [Google Scholar]
  17. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
    [Google Scholar]
  18. Han SJ, Yoo YJ, Kang HS. Characterization of a bifunctional cellulase and its structural gene. The cell gene of Bacillus sp. D04 has exo- and endoglucanase activity. J Biol Chem 1995; 270:26012–26019 [View Article][PubMed]
    [Google Scholar]
  19. Barrow G, Feltham RKA. Cowan and Steel's Manual for the Identification of Medical Bacteria, 3rd ed. Cambridge: Cambridge University Press; 1993 [CrossRef]
    [Google Scholar]
  20. Dong K, Chen F, Du Y, Wang G. Flavobacterium enshiense sp. nov., isolated from soil, and emended descriptions of the genus Flavobacterium and Flavobacterium cauense, Flavobacterium saliperosum and Flavobacterium suncheonense . Int J Syst Evol Microbiol 2013; 63:886–892 [View Article][PubMed]
    [Google Scholar]
  21. 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 [View Article]
    [Google Scholar]
  22. Collins MD. Isoprenoid quinone analysis in classification and identification. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp. 267–287
    [Google Scholar]
  23. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207 [CrossRef]
    [Google Scholar]
  24. 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 [View Article][PubMed]
    [Google Scholar]
  25. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 1988; 11:1–8 [View Article]
    [Google Scholar]
  26. Feng H, Zeng Y, Huang Y. Flavobacterium palustre sp. nov., isolated from soil of xixi wetland in Zhejiang Province, China. Int J Syst Evol Microbiol 2015; 65:1003–1007 [CrossRef]
    [Google Scholar]
  27. Liu Y, Jin JH, Zhou YG, Liu HC, Liu ZP. Flavobacterium caeni sp. nov., isolated from a sequencing batch reactor for the treatment of malachite green effluents. Int J Syst Evol Microbiol 2010; 60:417–421 [View Article][PubMed]
    [Google Scholar]
  28. Kim JH, Kim KY, Cha CJ. Flavobacterium chungangense sp. nov., isolated from a freshwater lake. Int J Syst Evol Microbiol 2009; 59:1754–1758 [View Article][PubMed]
    [Google Scholar]
  29. Anderson RL, Ordal EJ. Cytophaga succinicans sp. n., a factaltatively anaerobic, aquatic myxobacterium. J Bacteriol 1961; 81:130–138[PubMed]
    [Google Scholar]
  30. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  31. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. (editor) Mammalian Protein Metabolism New York: Academic Press; 1969 pp. 21–132 [CrossRef]
    [Google Scholar]
  32. 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 [View Article][PubMed]
    [Google Scholar]
  33. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983 [CrossRef]
    [Google Scholar]
  34. Wakabayashi H, Huh GJ, Kimura N. Flavobacterium branchiophila sp. nov., a causative agent of bacterial gill disease of freshwater fishes. Int J Syst Bacteriol 1989; 39:213–216 [View Article]
    [Google Scholar]
  35. Zamora L, Vela AI, Sánchez-Porro C, Palacios MA, Moore ER et al. Flavobacterium tructae sp. nov. and Flavobacterium piscis sp. nov., isolated from farmed rainbow trout (Oncorhynchus mykiss). Int J Syst Evol Microbiol 2014; 64:392–399 [View Article][PubMed]
    [Google Scholar]
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