1887

Abstract

A Gram-stain negative, strictly aerobic and non-motile bacterium, designated strain BN130233, was isolated from a soil sample collected from Gyeongsangbuk-do, Republic of Korea. Colonies were orange in colour, with wet and smooth surfaces. Phylogenetic analyses based on the 16S rRNA gene sequences resulted in strain BN130233 forming a cluster with members of the family Kämpfer 2011, while sharing the highest sequence identity of 91.2 % with JS16-4. Good growth was observed at 20–28 °C, pH 7.0 and in the absence of NaCl. The major fatty acids were summed feature 3 (C 6 and/or C 7), iso-C G, iso-C and iso-C 3-OH. The respiratory quinone was MK-7. Major polar lipids contained phosphatidylethanolamine, an unidentified phospholipid, three unidentified aminolipids and eight unidentified lipids. The genomic DNA G+C content was 40.6 mol%. Phenotypic and chemotaxonomic characteristics together with 16S rRNA gene sequence analyses showed that strain BN130233 was distinct from its close phylogenetic relatives in the family Kämpfer 2011. The strain is, therefore, proposed as a representative of a new genus and new species with the name . The type strain of is BN130233 (=CCTCC AB 2017051=KCTC 42642).

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2018-05-01
2024-12-03
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References

  1. Krieg NR, Ludwig W, Euzéby J, Whitman WB. Phylum XIV. Bacteroidetes phyl. nov. In Krieg JT, Staley DR, Brown DR, Hedlund BP, Paster BJ et al. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 4 New York, NY: Springer; 2010 pp. 25–469 [Crossref]
    [Google Scholar]
  2. Hahnke RL, Meier-Kolthoff JP, García-López M, Mukherjee S, Huntemann M et al. Genome-based taxonomic classification of Bacteroidetes . Front Microbiol 2016; 7:2003 [View Article][PubMed]
    [Google Scholar]
  3. 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 [View Article][PubMed]
    [Google Scholar]
  4. Sangkhobol V, Skerman VBD. Chitinophaga, a new genus of chitinolytic Myxobacteria. Int J Syst Evol Microbiol 1981; 31:285–293
    [Google Scholar]
  5. 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 [View Article][PubMed]
    [Google Scholar]
  6. Chaudhary DK, Kim J. Arvibacter flaviflagrans gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:4347–4354 [View Article][PubMed]
    [Google Scholar]
  7. Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT. Compostibacter hankyongensis gen. nov., sp. nov., isolated from compost. Int J Syst Evol Microbiol 2016; 66:3681–3687 [View Article][PubMed]
    [Google Scholar]
  8. 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 [View Article][PubMed]
    [Google Scholar]
  9. Zhang L, Chen XL, Hu Q, Chen K, Yan X et al. Haoranjiania flava gen. nov., sp. nov., a new member of the family Chitinophagaceae, isolated from activated sludge. Int J Syst Evol Microbiol 2016; 66:4686–4691 [View Article][PubMed]
    [Google Scholar]
  10. Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT. Panacibacter ginsenosidivorans gen. nov., sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2016; 66:4039–4045 [View Article][PubMed]
    [Google Scholar]
  11. 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 [View Article][PubMed]
    [Google Scholar]
  12. Siddiqi MZ, Im WT. Pseudobacter ginsenosidimutans gen. nov., sp. nov., isolated from ginseng cultivating soil. Int J Syst Evol Microbiol 2016; 66:3449–3455 [View Article][PubMed]
    [Google Scholar]
  13. 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 [View Article][PubMed]
    [Google Scholar]
  14. Hyeon JW, Lee HJ, Jeong SE, Cho GY, Jeon CO. Niveitalea solisilvae gen. nov., sp. nov., isolated from forest soil and emended description of the genus Flavihumibacter Zhang et al. 2010. Int J Syst Evol Microbiol 2017; 67:1374–1380 [View Article][PubMed]
    [Google Scholar]
  15. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia . Int J Syst Evol Microbiol 2007; 57:1424–1428 [View Article][PubMed]
    [Google Scholar]
  16. 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 [View Article][PubMed]
    [Google Scholar]
  17. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  18. 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 [View Article][PubMed]
    [Google Scholar]
  19. 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]
  20. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  21. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  23. 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 [View Article][PubMed]
    [Google Scholar]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  25. Kelly KL. Inter-Society Color Council–National Bureau of Standards Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
    [Google Scholar]
  26. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993[PubMed]
    [Google Scholar]
  27. Skerman VBD. A Guide to the Identification of the Genera of Bacteria, 2nd ed. Baltimore: Williams & Wilkins; 1967
    [Google Scholar]
  28. Mccammon SA, Bowman JP. Taxonomy of Antarctic Flavobacterium species: description of Flavobacterium gillisiae sp. nov., Flavobacterium tegetincola sp. nov., and Flavobacterium xanthum sp. nov., nom. rev. and reclassification of [Flavobacterium] salegens as Salegentibacter salegens gen. nov., comb. nov. Int J Syst Evol Microbiol 2000; 50:1055–1063 [View Article][PubMed]
    [Google Scholar]
  29. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article][PubMed]
    [Google Scholar]
  30. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
    [Google Scholar]
  31. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL . In Williams ST, Sharpe ME, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology vol. 4 Baltimore: Williams & Wilkins; 1989 pp. 2452–2492
    [Google Scholar]
  32. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article][PubMed]
    [Google Scholar]
  33. Groth I, Rodríguez C, Schütze B, Schmitz P, Leistner E et al. Five novel Kitasatospora species from soil: Kitasatospora arboriphila sp. nov., K. gansuensis sp. nov., K. nipponensis sp. nov., K. paranensis sp. nov. and K. terrestris sp. nov. Int J Syst Evol Microbiol 2004; 54:2121–2129 [View Article][PubMed]
    [Google Scholar]
  34. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:16
    [Google Scholar]
  35. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
    [Google Scholar]
  36. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54:31–36[PubMed] [Crossref]
    [Google Scholar]
  37. 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]
  38. Embley TM, Wait R. Structural lipids of eubacteria. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994 pp. 121–161
    [Google Scholar]
  39. 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 [View Article]
    [Google Scholar]
  40. Proença DN, Nobre MF, Morais PV. Chitinophaga costaii sp. nov., an endophyte of Pinus pinaster, and emended description of Chitinophaga niabensis . Int J Syst Evol Microbiol 2014; 64:1237–1243 [View Article][PubMed]
    [Google Scholar]
  41. 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 [View Article][PubMed]
    [Google Scholar]
  42. Albert RA, Waas NE, Pavlons SC, Pearson JL, Roecker J et al. Filimonas aurantiibacter sp. nov., an orange-pigmented bacterium isolated from lake water and emended description of the genus Filimonas . Int J Syst Evol Microbiol 2016; 66:4027–4032 [View Article][PubMed]
    [Google Scholar]
  43. Kim WH, Lee S, Ahn TY. Flavihumibacter cheonanensis sp. nov., isolated from sediment of a shallow stream. Int J Syst Evol Microbiol 2014; 64:3235–3239 [View Article][PubMed]
    [Google Scholar]
  44. 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 [View Article][PubMed]
    [Google Scholar]
  45. 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 [View Article][PubMed]
    [Google Scholar]
  46. 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 [View Article][PubMed]
    [Google Scholar]
  47. Jin D, Wang P, Bai Z, Jin B, Yu Z et al. Terrimonas pekingensis sp. nov., isolated from bulking sludge, and emended descriptions of the genus Terrimonas, Terrimonas ferruginea, Terrimonas lutea and Terrimonas aquatica . Int J Syst Evol Microbiol 2013; 63:1658–1664 [View Article][PubMed]
    [Google Scholar]
  48. Kim SJ, Park JH, Lim JM, Ahn JH, Anandham R et al. Parafilimonas terrae gen. nov., sp. nov., isolated from greenhouse soil. Int J Syst Evol Microbiol 2014; 64:3040–3045 [View Article][PubMed]
    [Google Scholar]
  49. Albuquerque L, Rainey FA, Nobre MF, da Costa MS. Hydrotalea sandarakina sp. nov., isolated from a hot spring runoff, and emended descriptions of the genus Hydrotalea and the species Hydrotalea flava . Int J Syst Evol Microbiol 2012; 62:1603–1608 [View Article][PubMed]
    [Google Scholar]
  50. 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 [View Article][PubMed]
    [Google Scholar]
  51. Dai J, Jiang F, Wang Y, Yu B, Qi H et al. Niabella tibetensis sp. nov., isolated from soil, and emended description of the genus Niabella . Int J Syst Evol Microbiol 2011; 61:1201–1205 [View Article][PubMed]
    [Google Scholar]
  52. 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 [View Article][PubMed]
    [Google Scholar]
  53. 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 [View Article][PubMed]
    [Google Scholar]
  54. 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 [View Article][PubMed]
    [Google Scholar]
  55. Chung EJ, Park TS, Jeon CO, Chung YR. Chitinophaga oryziterrae sp. nov., isolated from the rhizosphere soil of rice (Oryza sativa L.). Int J Syst Evol Microbiol 2012; 62:3030–3035 [View Article][PubMed]
    [Google Scholar]
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