1887

Abstract

Two novel strains, J116-2 and J116-1, were isolated from forest soil and were taxonomically characterized by a polyphasic approach. Both strains were yellow-coloured, Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacteria. The strains were non-sporulating, catalase-positive and oxidase-negative. Strains J116-2 and J116-1 were able to grow at 20–32 °C, pH 6.0–8.5, and 0–0.5 % (w/v) NaCl concentration. Based on 16S rRNA gene sequence analyses, strains J116-2 and J116-1 formed a distinct lineage within the family of the phylum and were closely related to genera (89.86–89.30 % sequence similarity), (89.20–89.06 %), (89.06 %) and (89.01–88.77 %). The pairwise sequence similarity between strains J116-2 and J116-1 was found to be 99.86 %. Flexirubin-type pigments were absent in both strains. The only respiratory quinone was menaquinone-7 (MK-7); the major polar lipid was phosphatidylethanolamine; the predominant polyamine was homospermidine; and the major fatty acids were Ciso, Ciso G and Ciso 3-OH. The genomic DNA G+C content values of strains J116-2 and J116-1 were 51.1 and 50.9 mol%, respectively. On the basis of phenotypic, genotypic and phylogenetic analysis, strain J116-2 represents a novel species of a new genus in the family , for which the name gen. nov., sp. nov. is proposed. The type strain of is J116-2 (=KEMB 9005–550=KACC 19168=NBRC 112827).

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2018-02-01
2019-12-15
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References

  1. Kämpfer P, Lodders N, Falsen E. Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov. Int J Syst Evol Microbiol 2011;61:518–523 [CrossRef][PubMed]
    [Google Scholar]
  2. Chaudhary DK, Kim J. Arvibacter flaviflagrans gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016;66:4347–4354 [CrossRef][PubMed]
    [Google Scholar]
  3. Kim MK, Kim TS, Joung Y, Han JH, Kim SB. Taibaiella soli sp. nov., isolated from pine forest soil. Int J Syst Evol Microbiol 2016;66:3230–3234 [CrossRef][PubMed]
    [Google Scholar]
  4. Son HM, Kook M, Kim JH, Yi TH. Taibaiella koreensis sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2014;64:1018–1023 [CrossRef][PubMed]
    [Google Scholar]
  5. Singh H, Du J, Won K, Yang JE, Akter S et al. Taibaiella yonginensis sp. nov., a bacterium isolated from soil of Yongin city. Antonie van Leeuwenhoek 2015;108:517–524 [CrossRef][PubMed]
    [Google Scholar]
  6. Zhang L, Wang Y, Wei L, Wang Y, Shen X et al. Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus. Int J Syst Evol Microbiol 2013;63:3769–3776 [CrossRef][PubMed]
    [Google Scholar]
  7. Tan X, Zhang RG, Meng TY, Liang HZ, Lv J. Taibaiella chishuiensis sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 2014;64:1795–1801 [CrossRef][PubMed]
    [Google Scholar]
  8. Lee HJ, Jeong SE, Cho MS, Kim S, Lee SS et al. Flavihumibacter solisilvae sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2014;64:2897–2901 [CrossRef][PubMed]
    [Google Scholar]
  9. Sangkhobol V, Skerman VBD. Chitinophaga, a new genus of chitinolytic myxobacteria. Int J Syst Bacteriol 1981;31:285–293 [CrossRef]
    [Google Scholar]
  10. Kämpfer P, Young CC, Sridhar KR, Arun AB, Lai WA et al. Transfer of [Flexibacter] sancti, [Flexibacter] filiformis, [Flexibacter] japonensis and [Cytophaga] arvensicola to the genus Chitinophaga and description of Chitinophaga skermanii sp. nov. Int J Syst Evol Microbiol 2006;56:2223–2228 [CrossRef][PubMed]
    [Google Scholar]
  11. Lee HG, An DS, Im WT, Liu QM, Na JR et al. Chitinophaga ginsengisegetis sp. nov. and Chitinophaga ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 2007;57:1396–1401 [CrossRef][PubMed]
    [Google Scholar]
  12. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961;3:208–IN1 [CrossRef]
    [Google Scholar]
  13. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008;74:2461–2470 [CrossRef][PubMed]
    [Google Scholar]
  14. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017;67:1613–1617 [CrossRef][PubMed]
    [Google Scholar]
  15. 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]
  16. Hall TA. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999;41:95–98
    [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. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  20. 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 [CrossRef][PubMed]
    [Google Scholar]
  21. 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]
  22. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  23. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008;31:241–250 [CrossRef][PubMed]
    [Google Scholar]
  24. Doetsch RN. Determinative methods of light microscopy. In Gerhardt P. (editor) Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology; 1981; pp.21–33
    [Google Scholar]
  25. Breznak JA, Costilow RN. Physicochemical factors in growth. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007; pp.309–329
    [Google Scholar]
  26. Hemraj V, Diksha S, Avneet G. A review on commonly used biochemical test for bacteria. Innovare J Life Sci 2013;1:1–7
    [Google Scholar]
  27. Reichenbach H. The order Cytophagales. In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH et al. (editors) The Prokaryotes, 2nd ed.vol. 4 New York: Springer; 1992; pp.3631–3675[Crossref]
    [Google Scholar]
  28. 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]
  29. Komagata K, Suzuki K. Lipids and cell wall analysis in bacterial systematics. Methods Microbiol 1987;19:161–203[Crossref]
    [Google Scholar]
  30. 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]
  31. 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]
  32. Busse H-J, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 1997;47:698–708 [CrossRef]
    [Google Scholar]
  33. Pedrol N, Tiburcio AF. Polyamine determination by TLC and HPLC. In Reigosa Roger MJ. (editor) Handbook of Plant Ecophysiology Techniques Netherlands: Springer; 2001; pp.335–363
    [Google Scholar]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  35. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989;39:159–167 [CrossRef]
    [Google Scholar]
  36. Ezaki T, Hashimoto Y, Yabuuchi E. 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 1989;39:224–229 [CrossRef]
    [Google Scholar]
  37. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. 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]
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