1887

Abstract

A novel bacterium, designated strain TAPY6, was isolated from a freshwater creek in Taiwan. The strain was Gram-stain-negative, strictly aerobic, motile-by-gliding, rod-shaped and formed translucent yellow colonies. Optimal growth occurred at 20–30 °C, pH 6 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TAPY6 belonged to the genus Flavobacterium and was most closely related to Flavobacterium succinicans LMG 10402 (97.3 % sequence similarity) and Flavobacterium glycines Gm-149 (96.3 %). Strain TAPY6 contained C15 : 0 and iso-C15 : 0 as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, five uncharacterized aminophospholipids, two uncharacterized phospholipids and one uncharacterized aminolipid. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6. The DNA G+C content of the genomic DNA was 39.8 mol%. Phenotypic characteristics of the novel strain also differed from those of the closest related species of the genus Flavobacterium . On the basis of the genotypic, chemotaxonomic and phenotypic data, strain TAPY6 represents a novel species in the genus Flavobacterium , for which the name Flavobacterium riviphilum sp. nov. is proposed. The type strain is TAPY6 (=BCRC 81007=LMG 29728=KCTC 52444).

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2018-10-15
2019-10-22
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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, 1st ed. Baltimore: Williams & Wilkins; 1923; pp.97–117
    [Google Scholar]
  2. 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 [CrossRef]
    [Google Scholar]
  3. 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 [CrossRef][PubMed]
    [Google Scholar]
  4. 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 [CrossRef][PubMed]
    [Google Scholar]
  5. Kuo I, Saw J, Kapan DD, Christensen S, Kaneshiro KY et al. Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai'i, and emended description of the genus Flavobacterium. Int J Syst Evol Microbiol 2013;63:3280–3286 [CrossRef][PubMed]
    [Google Scholar]
  6. Ludwig W, Euzéby J, Whitman WB. Taxonomic outlines of the phyla Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. In Whitman W. (editor) Bergey's Manual of Systematic Bacteriology, 2nd ed.vol. 4 Baltimore: Williams & Wilkins; 2011; pp.21–24
    [Google Scholar]
  7. Bernardet J-F, Bowman JP. The genus Flavobacterium. In Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E et al. (editors) The Prokaryotes: A Handbook on the Biology of Bacteria, 3rd ed.vol. 7 New York, NY: Springer; 2006; pp.481–531
    [Google Scholar]
  8. Bernardet J-F, 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]
  9. 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 [CrossRef][PubMed]
    [Google Scholar]
  10. Chen WM, Hsieh TY, Sheu SY. Mucilaginibacter amnicola sp. nov., isolated from a freshwater creek. Int J Syst Evol Microbiol 2018;68:394–401 [CrossRef][PubMed]
    [Google Scholar]
  11. Sheu SY, Hsieh TY, Kwon SW, Chen WM. Hymenobacter rivuli sp. nov., isolated from a freshwater creek. Int J Syst Evol Microbiol 2018;68:1220–1226 [CrossRef][PubMed]
    [Google Scholar]
  12. Chen WM, Su CL, Young CC, Sheu SY. Flavobacterium fluviatile sp. nov., isolated from a freshwater creek. Int J Syst Evol Microbiol 2018;68:1244–1250 [CrossRef][PubMed]
    [Google Scholar]
  13. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991;173:697–703 [CrossRef][PubMed]
    [Google Scholar]
  14. Anzai Y, Kudo Y, Oyaizu H. The phylogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. Int J Syst Bacteriol 1997;47:249–251 [CrossRef][PubMed]
    [Google Scholar]
  15. Chen WM, Laevens S, Lee TM, Coenye T, de Vos P et al. Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient. Int J Syst Evol Microbiol 2001;51:1729–1735 [CrossRef][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 [CrossRef][PubMed]
    [Google Scholar]
  17. 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]
  18. 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]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][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 [CrossRef][PubMed]
    [Google Scholar]
  21. Kluge AG, Farris JS. Quantitative Phyletics and the Evolution of Anurans. Syst Zool 1969;18:1–32 [CrossRef]
    [Google Scholar]
  22. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  23. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993;10:512–526 [CrossRef][PubMed]
    [Google Scholar]
  24. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983
    [Google Scholar]
  25. Nei M, Kumar S. Molecular Evolution and Phylogenetics New York: Oxford University Press; 2000
    [Google Scholar]
  26. Bernardet JF, Nakagawa Y, Holmes B. 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]
  27. Powers EM. Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 1995;61:3756–3758[PubMed]
    [Google Scholar]
  28. Reichenbach H. The order Cytophagales. In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH et al. (editors) The Prokaryotes, a Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, 2nd ed. New York, NY: Springer; 1992; pp.3631–3675
    [Google Scholar]
  29. Schmidt K, Connor A, Britton G. Analysis of pigments: carotenoids and related polyenes. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994; pp.403–461
    [Google Scholar]
  30. 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]
  31. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparativesystematic. 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.330–393
    [Google Scholar]
  32. Wen CM, Tseng CS, Cheng CY, Li YK. Purification, characterization and cloning of a chitinase from Bacillus sp. NCTU2. Biotechnol Appl Biochem 2002;35:213–219 [CrossRef][PubMed]
    [Google Scholar]
  33. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000;50:1861–1868 [CrossRef][PubMed]
    [Google Scholar]
  34. Chang SC, Wang JT, Vandamme P, Hwang JH, Chang PS et al. Chitinimonas taiwanensis gen. nov., sp. nov., a novel chitinolytic bacterium isolated from a freshwater pond for shrimp culture. Syst Appl Microbiol 2004;27:43–49 [CrossRef][PubMed]
    [Google Scholar]
  35. Palleroni NJ, Palleroni AV. Alcaligenes latus, a New Species of Hydrogen-Utilizing Bacteria. Int J Syst Bacteriol 1978;28:416–424 [CrossRef]
    [Google Scholar]
  36. Nokhal T-H, Schlegel HG. Taxonomic Study of Paracoccus denitrificans. Int J Syst Bacteriol 1983;33:26–37 [CrossRef]
    [Google Scholar]
  37. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [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. Dittmer JC, Lester RL. A simple, specific spray for the detection of phospholipids on thin-layer chromatograms. J Lipid Res 1964;5:126–127[PubMed]
    [Google Scholar]
  40. Lee S, Weon HY, Han K, Ahn TY. Flavobacterium dankookense sp. nov., isolated from a freshwater reservoir, and emended descriptions of Flavobacterium cheonanense, F. chungnamense, F. koreense and F. aquatile. Int J Syst Evol Microbiol 2012;62:2378–2382 [CrossRef][PubMed]
    [Google Scholar]
  41. 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 [CrossRef][PubMed]
    [Google Scholar]
  42. Fujii D, Nagai F, Watanabe Y, Shirasawa Y. Flavobacterium longum sp. nov. and Flavobacterium urocaniciphilum sp. nov., isolated from a wastewater treatment plant, and emended descriptions of Flavobacterium caeni and Flavobacterium terrigena. Int J Syst Evol Microbiol 2014;64:1488–1494 [CrossRef][PubMed]
    [Google Scholar]
  43. Kim YJ, Kim SR, Nguyen NL, Yang DC. Flavobacterium ginsengisoli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2013;63:4289–4293 [CrossRef][PubMed]
    [Google Scholar]
  44. Sheu SY, Lin YS, Chen WM. Flavobacterium squillarum sp. nov., isolated from a freshwater shrimp culture pond, and emended descriptions of Flavobacterium haoranii, Flavobacterium cauense, Flavobacterium terrae and Flavobacterium aquatile. Int J Syst Evol Microbiol 2013;63:2239–2247 [CrossRef][PubMed]
    [Google Scholar]
  45. Chen WM, Chen YL, Sheu SY. Flavobacterium brevivitae sp. nov., isolated from river water. Int J Syst Evol Microbiol 2016;66:1705–1712 [CrossRef][PubMed]
    [Google Scholar]
  46. Sheu SY, Chen YL, Chen WM. Flavobacterium verecundum sp. nov., isolated from a freshwater river. Int J Syst Evol Microbiol 2016;66:3337–3344 [CrossRef][PubMed]
    [Google Scholar]
  47. Chen WM, Huang WC, Young CC, Sheu SY. Flavobacterium tilapiae sp. nov., isolated from a freshwater pond, and emended descriptions of Flavobacterium defluvii and Flavobacterium johnsoniae. Int J Syst Evol Microbiol 2013;63:827–834 [CrossRef][PubMed]
    [Google Scholar]
  48. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the proteobacteria. Syst Appl Microbiol 1988;11:1–8 [CrossRef]
    [Google Scholar]
  49. 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]
  50. Kämpfer P, Rosselló-Mora R, Hermansson M, Persson F, Huber B et al. Undibacterium pigrum gen. nov., sp. nov., isolated from drinking water. Int J Syst Evol Microbiol 2007;57:1510–1515 [CrossRef][PubMed]
    [Google Scholar]
  51. Collins MD. Isoprenoid quinones. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994; pp.265–309
    [Google Scholar]
  52. 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]
  53. Madhaiyan M, Poonguzhali S, Lee JS, Lee KC, Sundaram S. Flavobacterium glycines sp. nov., a facultative methylotroph isolated from the rhizosphere of soybean. Int J Syst Evol Microbiol 2010;60:2187–2192 [CrossRef][PubMed]
    [Google Scholar]
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