1887

Abstract

A Gram-stain-negative and strictly aerobic bacterial strain, designated 6-4, was isolated from forest soil in Jeju island, South Korea. Cells showing oxidase-positive and catalase-negative reactions were thin and long non-motile rods. Growth of strain 6-4 was observed at 20–35 °C (optimum, 30 °C) and pH 6.0–9.0 (optimum, pH 7.0). Strain 6-4 contained iso-C, anteiso-C, iso-C G and iso-C 3-OH as the major fatty acids and menaquinone-7 (MK-7) as the sole isoprenoid quinone. Phosphatidylethanolamine was the major polar lipid and five unidentified aminolipids, one unidentified aminophospholipid and one unidentified lipid were also detected as minor polar lipids. The G+C content of the genomic DNA was 45.8 mol%. Strain 6-4 was most closely related to 3-3 with a low 16S rRNA gene sequence similarity (94.2 %) and phylogenetic analysis indicated that the strain formed a distinct phylogenetic lineage from members of the genus and other closely related genera. On the basis of phylogenetic inference and phenotypic, chemotaxonomic and molecular properties, strain 6-4 represents a novel species of a new genus of the family , for which the name gen. nov., sp. nov. is proposed. The type strain of is 6-4 (=KACC 18808=JCM 31525). An emended description of the genus is also proposed.

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2017-05-01
2020-01-23
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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. Sangkhobol V, Skerman VBD. Chitinophaga, a new genus of chitinolytic myxobacteria. Int J Syst Bacteriol 1981;31:285–293[CrossRef]
    [Google Scholar]
  3. Qu JH, Yuan HL. Sediminibacterium salmoneum gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from sediment of a eutrophic reservoir. Int J Syst Evol Microbiol 2008;58:2191–2194 [CrossRef][PubMed]
    [Google Scholar]
  4. Qu JH, Yuan HL, Yang JS, Li HF, Chen N. Lacibacter cauensis gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from sediment of a eutrophic lake. Int J Syst Evol Microbiol 2009;59:1153–1157 [CrossRef][PubMed]
    [Google Scholar]
  5. Zhang NN, Qu JH, Yuan HL, Sun YM, Yang JS. Flavihumibacter petaseus gen. nov., sp. nov., isolated from soil of a subtropical rainforest. Int J Syst Evol Microbiol 2010;60:1609–1612 [CrossRef][PubMed]
    [Google Scholar]
  6. Yoon MH, Im WT. Flavisolibacter ginsengiterrae gen. nov., sp. nov. and Flavisolibacter ginsengisoli sp. nov., isolated from ginseng cultivating soil. Int J Syst Evol Microbiol 2007;57:1834–1839 [CrossRef][PubMed]
    [Google Scholar]
  7. Kim BY, Weon HY, Yoo SH, Hong SB, Kwon SW et al. Niabella aurantiaca gen. nov., sp. nov., isolated from a greenhouse soil in Korea. Int J Syst Evol Microbiol 2007;57:538–541 [CrossRef][PubMed]
    [Google Scholar]
  8. Weon HY, Kim BY, Yoo SH, Lee SY, Kwon SW et al. Niastella koreensis gen. nov., sp. nov. and Niastella yeongjuensis sp. nov., novel members of the phylum Bacteroidetes, isolated from soil cultivated with Korean ginseng. Int J Syst Evol Microbiol 2006;56:1777–1782 [CrossRef][PubMed]
    [Google Scholar]
  9. An DS, Lee HG, Im WT, Liu QM, Lee ST. Segetibacter koreensis gen. nov., sp. nov., a novel member of the phylum Bacteroidetes, isolated from the soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 2007;57:1828–1833 [CrossRef][PubMed]
    [Google Scholar]
  10. Zhang K, Tang Y, Zhang L, Dai J, Wang Y et al. Parasegetibacter luojiensis gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from a forest soil. Int J Syst Evol Microbiol 2009;59:3058–3062 [CrossRef][PubMed]
    [Google Scholar]
  11. Xie CH, Yokota A. Reclassification of [Flavobacterium] ferrugineum as Terrimonas ferruginea gen. nov., comb. nov., and description of Terrimonas lutea sp. nov., isolated from soil. Int J Syst Evol Microbiol 2006;56:1117–1121 [CrossRef][PubMed]
    [Google Scholar]
  12. Lim JH, Baek SH, Lee ST. Ferruginibacter alkalilentus gen. nov., sp. nov. and Ferruginibacter lapsinanis sp. nov., novel members of the family 'Chitinophagaceae' in the phylum Bacteroidetes, isolated from freshwater sediment. Int J Syst Evol Microbiol 2009;59:2394–2399 [CrossRef][PubMed]
    [Google Scholar]
  13. Shiratori H, Tagami Y, Morishita T, Kamihara Y, Beppu T et al. Filimonas lacunae gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from fresh water. Int J Syst Evol Microbiol 2009;59:1137–1142 [CrossRef][PubMed]
    [Google Scholar]
  14. Eder W, Peplies J, Wanner G, Frühling A, Verbarg S. Hydrobacter penzbergensis gen. nov., sp. nov., isolated from purified water. Int J Syst Evol Microbiol 2015;65:920–926 [CrossRef][PubMed]
    [Google Scholar]
  15. Kang JY, Chun J, Seo JW, Kim CH, Jahng KY. Flaviaesturariibacter amylovorans gen. nov., sp. nov., a starch-hydrolysing bacterium, isolated from estuarine water. Int J Syst Evol Microbiol 2015;65:2209–2214 [CrossRef][PubMed]
    [Google Scholar]
  16. Kang H, Kim H, Joung Y, Joh K. Parasediminibacterium paludis gen. nov., sp. nov., isolated from wetland. Int J Syst Evol Microbiol 2016;66:326–331 [CrossRef][PubMed]
    [Google Scholar]
  17. Madhaiyan M, Poonguzhali S, Senthilkumar M, Pragatheswari D, Lee JS et al. Arachidicoccus rhizosphaerae gen. nov., sp. nov., a plant-growth-promoting bacterium in the family Chitinophagaceae isolated from rhizosphere soil. Int J Syst Evol Microbiol 2015;65:578–586 [CrossRef][PubMed]
    [Google Scholar]
  18. 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]
  19. Kim SJ, Cho H, Ahn JH, Weon HY, Seok SJ et al. Pseudoflavitalea rhizosphaerae gen. nov., sp. nov., isolated from rhizosphere of tomato, and proposal to reclassify Flavitalea soli as Pseudoflavitalea soli comb. nov. Int J Syst Evol Microbiol 2016;66:4167–4171 [CrossRef][PubMed]
    [Google Scholar]
  20. Lv YY, Wang J, Chen MH, You J, Qiu LH. Dinghuibacter silviterrae gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016;66:1785–1791 [CrossRef][PubMed]
    [Google Scholar]
  21. Siddiqi MZ, Im WT. Pseudobacter ginsenosidimutans gen. nov., sp. nov., isolated from ginseng cultivating soil. Int J Syst Evol Microbiol 2016;66:3449–3455 [CrossRef][PubMed]
    [Google Scholar]
  22. Siddiqi MZ, Shafi SM, Choi KD, Im WT. Panacibacter ginsenosidivorans gen. nov., sp. nov., isolated from soil of ginseng cultivating field. Int J Syst Evol Microbiol 2016;66:4039–4045 [CrossRef]
    [Google Scholar]
  23. Kim JM, Le NT, Chung BS, Park JH, Bae JW et al. Influence of soil components on the biodegradation of benzene, toluene, ethylbenzene, and o-, m-, and p-xylenes by the newly isolated bacterium Pseudoxanthomonas spadix BD-a59. Appl Environ Microbiol 2008;74:7313–7320 [CrossRef][PubMed]
    [Google Scholar]
  24. 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]
  25. Nawrocki EP, Eddy SR. Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput Biol 2007;3:e56 [CrossRef][PubMed]
    [Google Scholar]
  26. Felsenstein J. PHYLIP (Phylogeny Inference Package), Version 3.6a Seattle: Department of Genetics, University of Washington, Seattle, WA, USA; 2002
    [Google Scholar]
  27. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014;30:1312–1313 [CrossRef][PubMed]
    [Google Scholar]
  28. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007;73:5261–5267 [CrossRef][PubMed]
    [Google Scholar]
  29. Chang HW, Nam YD, Jung MY, Kim KH, Roh SW et al. Statistical superiority of genome-probing microarrays as genomic DNA-DNA hybridization in revealing the bacterial phylogenetic relationship compared to conventional methods. J Microbiol Methods 2008;75:523–530 [CrossRef][PubMed]
    [Google Scholar]
  30. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014;12:635–645 [CrossRef][PubMed]
    [Google Scholar]
  31. Li X, Zhang D, Chen F, Ma J, Dong Y et al. Klebsiella singaporensis sp. nov., a novel isomaltulose-producing bacterium. Int J Syst Evol Microbiol 2004;54:2131–2139 [CrossRef][PubMed]
    [Google Scholar]
  32. Gomori G. Preparation of buffers for use in enzyme studies. In Colowick SP, Kaplan NO. (editors) Methods in Enzymology New York: Academic Press; 1955; pp.138–146
    [Google Scholar]
  33. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982;44:992–993[PubMed]
    [Google Scholar]
  34. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P. (editor) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
  35. 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 [CrossRef][PubMed]
    [Google Scholar]
  36. Lányi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1987;19:1–67[CrossRef]
    [Google Scholar]
  37. Han Y, Zhang F, Wang Q, Zheng S, Guo W et al. Flavihumibacter stibioxidans sp. nov., an antimony-oxidizing bacterium isolated from antimony mine soil. Int J Syst Evol Microbiol 2016;66:4676–4680 [CrossRef][PubMed]
    [Google Scholar]
  38. 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]
  39. 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]
  40. Komagata K, Suzuki K. 4 Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988;19:161–208[CrossRef]
    [Google Scholar]
  41. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  42. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977;27:104–117 [CrossRef]
    [Google Scholar]
  43. 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]
  44. Baik KS, Kim MS, Lee JH, Lee SS, Im WT et al. Flavisolibacter rigui sp. nov., isolated from freshwater of an artificial reservoir and emended description of the genus Flavisolibacter. Int J Syst Evol Microbiol 2014;64:4038–4042 [CrossRef][PubMed]
    [Google Scholar]
  45. Kim YJ, Nguyen NL, Weon HY, Yang DC. Sediminibacterium ginsengisoli sp. nov., isolated from soil of a ginseng field, and emended descriptions of the genus Sediminibacterium and of Sediminibacterium salmoneum. Int J Syst Evol Microbiol 2013;63:905–912 [CrossRef][PubMed]
    [Google Scholar]
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