1887

Abstract

Two strains of bacteria designated CB-3 and CB-31 were isolated from Kyonggi University forest soil. Cells were aerobic, Gram-stain-negative, oxidase-positive, non-motile, non-spore-forming, rod-shaped and yellow-pigmented. They were able to grow at 15–42 °C, pH 5.5–9.5 and with 0–1.5 % (w/v) NaCl concentration. Flexirubin-type pigments were absent. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains CB-3 and CB-31 formed a lineage within the family of the phylum that was distinct from various species of the genus , including UCM-46 (99.58 % sequence similarity), GH29-5 (98.12 %), UCM-R36 (97.57 %), UCM-R15 (96.8 %) and R2A-7 (96.31 %). Both strains contained MK-6 as the sole quinone. The major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were iso-C, iso-C 3-OH, iso-C 3-OH, summed feature 9 (iso-Cω9 and/or C 10-methyl) and iso-C G. The DNA G+C content of the strains was 35.8–36.7 mol%. DNA–DNA relatedness between strain CB-3 and the most closely related members of the genus ranged from 32 % to 59 %. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished strains CB-3 and CB-31 from their closest phylogenetic neighbours. Thus, strains CB-3 and CB-31 represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is CB-3 (=KEMB 9005-535=KACC 19112=NBRC 112704).

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2017-08-01
2024-11-05
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References

  1. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM et al. Bergey’s Manual of Determinative Bacteriology Baltimore: Williams & Wilkins; 1923
    [Google Scholar]
  2. Frankland GC, Frankland PF. Ueber einige typische microorganismen im Wasser und Im Boden. Z. Hyg. Infektionskrankh 1889; 6:373–400
    [Google Scholar]
  3. Weeks OB. Flavobacterium aquatile (Frankland and Frankland) Bergey et al., type species of the genus Flavobacterium. J Bacteriol 1955; 69:649–658[PubMed]
    [Google Scholar]
  4. Ludwig W, Klenk HP. Overview: a phylogenetic backbone and taxonomic framework for prokaryotic systematic. In Boone DR, Castenholz RW, Garrity GM. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 1 New York: Springer; 2001 pp. 49–65 [CrossRef]
    [Google Scholar]
  5. Bernardet JF, Bowman JP. The genus Flavobacterium. In Whitman WB, Parte AC. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 4 New York, Dordrecht, Heidelberg, London: Springer; 2010 pp. 112–155
    [Google Scholar]
  6. 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 Pt 3:1055–1063 [View Article][PubMed]
    [Google Scholar]
  7. Mccammon SA, Innes BH, Bowman JP, Franzmann PD, Dobson SJ et al. Flavobacterium hibernum sp. nov., a lactose-utilizing bacterium from a freshwater antarctic lake. Int J Syst Bacteriol 1998; 48:1405–1412 [View Article][PubMed]
    [Google Scholar]
  8. Humphry DR, George A, Black GW, Cummings SP. Flavobacterium frigidarium sp. nov., an aerobic, psychrophilic, xylanolytic and laminarinolytic bacterium from Antarctica. Int J Syst Evol Microbiol 2001; 51:1235–1243 [View Article][PubMed]
    [Google Scholar]
  9. van Trappen S, Mergaert J, Swings J. Flavobacterium gelidilacus sp. nov., isolated from microbial mats in antarctic lakes. Int J Syst Evol Microbiol 2003; 53:1241–1245 [View Article][PubMed]
    [Google Scholar]
  10. van Trappen S, Vandecandelaere I, Mergaert J, Swings J. Flavobacterium degerlachei sp. nov., Flavobacterium frigoris sp. nov. and Flavobacterium micromati sp. nov., novel psychrophilic bacteria isolated from microbial mats in antarctic lakes. Int J Syst Evol Microbiol 2004; 54:85–92 [View Article][PubMed]
    [Google Scholar]
  11. van Trappen S, Vandecandelaere I, Mergaert J, Swings J. Flavobacterium fryxellicola sp. nov. and Flavobacterium psychrolimnae sp. nov., novel psychrophilic bacteria isolated from microbial mats in antarctic lakes. Int J Syst Evol Microbiol 2005; 55:769–772 [View Article][PubMed]
    [Google Scholar]
  12. Yi H, Oh HM, Lee JH, Kim SJ, Chun J. Flavobacterium antarcticum sp. nov., a novel psychrotolerant bacterium isolated from the antarctic. Int J Syst Evol Microbiol 2005; 55:637–641 [View Article][PubMed]
    [Google Scholar]
  13. Nogi Y, Soda K, Oikawa T. Flavobacterium frigidimaris sp. nov., isolated from antarctic seawater. Syst Appl Microbiol 2005; 28:310–315 [View Article][PubMed]
    [Google Scholar]
  14. Yi H, Chun J. Flavobacterium weaverense sp. nov. and Flavobacterium segetis sp. nov., novel psychrophiles isolated from the antarctic. Int J Syst Evol Microbiol 2006; 56:1239–1244 [View Article][PubMed]
    [Google Scholar]
  15. Li DD, Liu C, Zhang YQ, Wang XJ, Wang N et al. Flavobacterium arcticum sp. nov., isolated from Arctic seawater. Int J Syst Evol Microbiol 2017; 67: [View Article][PubMed]
    [Google Scholar]
  16. Lata P, Lal D, Lal R. Flavobacterium ummariense sp. nov., isolated from hexachlorocyclohexane-contaminated soil, and emended description of Flavobacterium ceti Vela et al. 2007. Int J Syst Evol Microbiol 2012; 62:2674–2679 [View Article][PubMed]
    [Google Scholar]
  17. 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]
  18. Ao L, Zeng XC, Nie Y, Mu Y, Zhou L et al. Flavobacterium arsenatis sp. nov., a novel arsenic-resistant bacterium from high-arsenic sediment. Int J Syst Evol Microbiol 2014; 64:3369–3374 [View Article][PubMed]
    [Google Scholar]
  19. Yoon HS, Aslam Z, Song GC, Kim SW, Jeon CO et al. Flavobacterium sasangense sp. nov., isolated from a wastewater stream polluted with heavy metals. Int J Syst Evol Microbiol 2009; 59:1162–1166 [View Article][PubMed]
    [Google Scholar]
  20. 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]
  21. Duchaud E, Boussaha M, Loux V, Bernardet JF, Michel C et al. Complete genome sequence of the fish pathogen Flavobacterium psychrophilum. Nat Biotechnol 2007; 25:763–769 [View Article][PubMed]
    [Google Scholar]
  22. Starliper CE. Bacterial coldwater disease of fishes caused by Flavobacterium psychrophilum. J Adv Res 2011; 2:97–108 [View Article]
    [Google Scholar]
  23. Loch TP, Faisal M. Flavobacterium spartansii sp. nov., a pathogen of fishes, and emended descriptions of Flavobacterium aquidurense and Flavobacterium araucananum. Int J Syst Evol Microbiol 2014; 64:406–412 [View Article][PubMed]
    [Google Scholar]
  24. 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]
  25. 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]
  26. Kang JY, Chun J, Jahng KY. Flavobacterium aciduliphilum sp. nov., isolated from freshwater, and emended description of the genus Flavobacterium. Int J Syst Evol Microbiol 2013; 63:1633–1638 [View Article][PubMed]
    [Google Scholar]
  27. Kirchman DL. The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol 2002; 39:91–100 [View Article][PubMed]
    [Google Scholar]
  28. Wang ZW, Liu YH, Dai X, Wang BJ, Jiang CY et al. Flavobacterium saliperosum sp. nov., isolated from freshwater lake sediment. Int J Syst Evol Microbiol 2006; 56:439–442 [View Article][PubMed]
    [Google Scholar]
  29. Qu JH, Yuan HL, Li HF, Deng CP, Jh Q, Hf L. Flavobacterium cauense sp. nov., isolated from sediment of a eutrophic lake. Int J Syst Evol Microbiol 2009; 59:2666–2669 [View Article][PubMed]
    [Google Scholar]
  30. 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]
  31. Nguyen TM, Kim J. Flavobacterium fulvum sp. nov., Flavobacterium pedocola sp. nov. and Flavobacterium humicola sp. nov., three new members of the family Flavobacteriaceae, isolated from soil. Int J Syst Evol Microbiol 2016; 66:3108–3118 [View Article][PubMed]
    [Google Scholar]
  32. Dahal RH, Kim J. Pedobacter humicola sp. nov., a member of the genus Pedobacter isolated from soil. Int J Syst Evol Microbiol 2016; 66:2205–2211 [View Article][PubMed]
    [Google Scholar]
  33. 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 [View Article][PubMed]
    [Google Scholar]
  34. 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: [View Article][PubMed]
    [Google Scholar]
  35. 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]
  36. 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]
  37. 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]
  38. 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]
  39. 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]
  40. 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]
  41. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  42. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  43. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936; 31:575–580[PubMed]
    [Google Scholar]
  44. Doetsch RN. Determinative methods of light microscopy. In Gerhardt P. (editor) Manual of Methods for General Bacteriology Washington, DC, USA: American Society for Microbiology; 1981 pp. 21–33
    [Google Scholar]
  45. 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]
  46. 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, D. C: American Society for Microbiology; 2007 pp. 309–329
    [Google Scholar]
  47. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC, USA: American Society for Microbiology; 1994 pp. 607–654
    [Google Scholar]
  48. Dahal RH, Kim J. Microvirga soli sp. nov., an alphaproteobacterium isolated from soil. Int J Syst Evol Microbiol 2017; 67:127–132 [View Article][PubMed]
    [Google Scholar]
  49. 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]
  50. Macfaddin JF. Bacterial Tests for Identification of Medical Bacteria, 2nd ed. Baltimore, MD: Williams and Wilkins; 1980 pp. 162–218
    [Google Scholar]
  51. Mormak DA, Casida LE. Study of Bacillus subtilis endospores in soil by use of a modified endospore stain. Appl Environ Microbiol 1985; 49:1356–1360[PubMed]
    [Google Scholar]
  52. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Newark, DE: MIDI Inc; 1990 MIDI Technical Note 101
    [Google Scholar]
  53. 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]
  54. Card GL. Metabolism of phosphatidylglycerol, phosphatidylethanolamine, and cardiolipin of Bacillus stearothermophilus. J Bacteriol 1973; 114:1125–1137[PubMed]
    [Google Scholar]
  55. 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]
  56. Komagata K, Suzuki K. Lipids and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–203 [CrossRef]
    [Google Scholar]
  57. Wilson K. et al. Preparation of genomic DNA from bacteria. In Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K. (editors) Current Protocols in Molecular Biology New York: John Wiley and Sons, Inc; 1997 pp. 2.4.1–2.4.2
    [Google Scholar]
  58. 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]
  59. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric DNA–DNA hybridization in microdilution wells as an alternative to member filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Evol Microbiol 1989; 39:224–229
    [Google Scholar]
  60. 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 [View Article]
    [Google Scholar]
  61. Kim BY, Weon HY, Cousin S, Yoo SH, Kwon SW et al. Flavobacterium daejeonense sp. nov. and Flavobacterium suncheonense sp. nov., isolated from greenhouse soils in Korea. Int J Syst Evol Microbiol 2006; 56:1645–1649 [View Article][PubMed]
    [Google Scholar]
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