1887

Abstract

A bacterial strain, designated TTM-43, was isolated from a water sample taken from the Caohu River in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain TTM-43 were Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and surrounded by a thick capsule. The strain formed bright-yellow colonies. Growth occurred at 15–30 °C (optimum, 20 °C), at pH 5–9 (optimum, pH 6) and with 0–0.3 % NaCl (optimum growth in the absence of added NaCl). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TTM-43 belonged to the genus and was most closely related to R2A1-13, with 97.8 % sequence similarity. Strain TTM-43 contained iso-C (24.9 %), iso-C G (12.6 %), summed feature 9 (iso-Cω9 and/or 10-methyl C; 12.2 %), iso-C 3-OH (10.9 %), iso-C 3-OH (7.3 %) and iso-C (6.7 %) as the predominant fatty acids. The major isoprenoid quinone was MK-6. The polar lipid profile consisted of phosphatidylethanolamine and several uncharacterized aminophospholipids and phospholipids. The major polyamine was homospermidine. The genomic DNA G+C content of strain TTM-43 was 31 mol%. DNA–DNA relatedness of strain TTM-43 with respect to type strains of recognized species of the genus was less than 70 %. On the basis of phylogenetic inference and phenotypic data, strain TTM-43 should be assigned to a novel species, for which the name sp. nov. is presented. The type strain is TTM-43 ( = BCRC 80913 = KCTC 42744 = LMG 29004).

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2016-04-01
2020-08-05
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References

  1. Adachi M., Fukami K., Kondo R., Nishijima T.. 2002; Identification of marine algicidal Flavobacterium sp. 5N-3 using multiple probes and whole-cell hybridization. Fish Sci68:713–720 [CrossRef]
    [Google Scholar]
  2. Anzai Y., Kudo Y., Oyaizu H.. 1997; The phylogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. Int J Syst Bacteriol47:249–251 [CrossRef][PubMed]
    [Google Scholar]
  3. Bergey D. H., Harrison F. C., Breed R. S., Hammer B. W., Huntoon F. M.. editors 1923; Bergey's Manual of Determinative Bacteriology Baltimore: Williams & Wilkins;
    [Google Scholar]
  4. Bernardet J.-F., Bowman J. P.. 2006; The genus Flavobacterium . In The Prokaryotes, 3rd edn.vol. 7 pp481531Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K. H., Stackebrandt E.. New York: Springer; [CrossRef]
    [Google Scholar]
  5. Bernardet J.-F., Bowman J. P.. 2010; Genus I. Flavobacterium Bergey et al. 1923. In Bergey's Manual of Systematic Bacteriology, 2nd edn.vol. 4 pp112–154Edited by Krieg N. R., Ludwig W., Whitman W., Hedlund B. P., Paster B. J., Staley J. T., Ward N., Brown D., Parte A.. New York: Springer;
    [Google Scholar]
  6. Bernardet J.-F., Grimont P. A. D.. 1989; Deoxyribonucleic acid relatedness and phenotypic characterization of Flexibacter columnuris sp. nov., nom. rev., Flexibacter psychrophilus sp. nov., nom. rev., and Flexibacter maritimus Wakabayashi, Hikida, and Masumura 1986. Int J Syst Bacteriol39:346–354 [CrossRef]
    [Google Scholar]
  7. Bernardet J.-F., Segers P., Vancanneyt M., Berthe F., Kersters K., Vandamme P.. 1996; 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 Bacteriol46:128–148 [CrossRef]
    [Google Scholar]
  8. Bernardet J.-F., Nakagawa Y., Holmes B., Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes. 2002; Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol52:1049–1070[PubMed]
    [Google Scholar]
  9. Bodour A. A., Guerrero-Barajas C., Jiorle B. V., Malcomson M. E., Paull A. K., Somogyi A., Trinh L. N., Bates R. B., Maier R. M.. 2004; Structure and characterization of flavolipids, a novel class of biosurfactants produced by Flavobacterium sp. strain MTN11. Appl Environ Microbiol70:114–120 [CrossRef][PubMed]
    [Google Scholar]
  10. Bowman J. P.. 2000; 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 Microbiol50:1861–1868 [CrossRef][PubMed]
    [Google Scholar]
  11. Breznak J. A., Costilow R. N.. 2007; Physicochemical factors in growth. In Methods for General and Molecular Bacteriology, 3rd edn. pp309–329Edited by Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R.. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  12. Busse H.-J., Auling G.. 1988; Polyamine pattern as chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol11:1–8 [CrossRef]
    [Google Scholar]
  13. Busse H.-J., Bunka S., Hensel A., Lubitz W.. 1997; Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol47:698–708 [CrossRef]
    [Google Scholar]
  14. Chen W. M., Laevens S., Lee T. M., Coenye T., De Vos P., Mergeay M., Vandamme P.. 2001; Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient. Int J Syst Evol Microbiol51:1729–1735 [CrossRef][PubMed]
    [Google Scholar]
  15. Chen W. M., Huang W. C., Young C. C., Sheu S. Y.. 2013; Flavobacterium tilapiae sp. nov., isolated from a freshwater pond, and emended descriptions of Flavobacterium defluvii and Flavobacterium johnsoniae . Int J Syst Evol Microbiol63:827–834 [CrossRef][PubMed]
    [Google Scholar]
  16. Cole J. R., Wang Q., Cardenas E., Fish J., Chai B., Farris R. J., Kulam-Syed-Mohideen A. S., McGarrell D. M., Marsh T., other authors. 2009; The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res37:D141–D145 [CrossRef][PubMed]
    [Google Scholar]
  17. Collins M. D.. 1994; Isoprenoid quinones. In Chemical Methods in Prokaryotic Systematics pp265–309Edited by Goodfellow M., O'Donnell A. G.. Chichester: Wiley;
    [Google Scholar]
  18. Dong K., Liu H., Zhang J., Zhou Y., Xin Y.. 2012; Flavobacterium xueshanense sp. nov. and Flavobacterium urumqiense sp. nov., two psychrophilic bacteria isolated from glacier ice. Int J Syst Evol Microbiol62:1151–1157 [CrossRef][PubMed]
    [Google Scholar]
  19. Dong K., Chen F., Du Y., Wang G.. 2013; 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 Microbiol63:886–892 [CrossRef][PubMed]
    [Google Scholar]
  20. Embley T. M., Wait R.. 1994; Structural lipids of eubacteria. In Chemical Methods in Prokaryotic Systematics pp121–161Edited by Goodfellow M., O'Donnell A. G.. Chichester: Wiley;
    [Google Scholar]
  21. Ezaki T., Hashimoto Y., Yabuuchi E.. 1989; 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 Bacteriol39:224–229 [CrossRef]
    [Google Scholar]
  22. Felsenstein J.. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  23. Felsenstein J.. 1993; phylip (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA
  24. Fujii D., Nagai F., Watanabe Y., Shirasawa Y.. 2014; 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 Microbiol64:1488–1494 [CrossRef][PubMed]
    [Google Scholar]
  25. Glaeser S. P., Galatis H., Martin K., Kämpfer P.. 2013; Flavobacterium cutihirudinis sp. nov., isolated from the skin of the medical leech Hirudo verbana . Int J Syst Evol Microbiol63:2841–2847 [CrossRef][PubMed]
    [Google Scholar]
  26. Gómez E., Méndez J., Cascales D., Guijarro J. A.. 2014; Flavobacterium psychrophilum vaccine development: a difficult task. Microb Biotechnol7:414–423 [CrossRef][PubMed]
    [Google Scholar]
  27. Gunasinghe R. N., Ikiriwatte C. J., Karunaratne A. M.. 2004; The use of Pantoea agglomerans and Flavobacterium sp. to control banana pathogens. J Hortic Sci Biotechnol79:1002–1006[CrossRef]
    [Google Scholar]
  28. Hall T. A.. 1999; BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser41:95–98
    [Google Scholar]
  29. Kämpfer P., Lodders N., Martin K., Avendaño-Herrera R.. 2012; Flavobacterium chilense sp. nov. and Flavobacterium araucananum sp. nov., isolated from farmed salmonid fish. Int J Syst Evol Microbiol62:1402–1408 [CrossRef][PubMed]
    [Google Scholar]
  30. Kang J. Y., Chun J., Jahng K. Y.. 2013; Flavobacterium aciduliphilum sp. nov., isolated from freshwater, and emended description of the genus Flavobacterium . Int J Syst Evol Microbiol63:1633–1638 [CrossRef][PubMed]
    [Google Scholar]
  31. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H., other authors. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  32. Kimura M.. 1983; The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; [CrossRef]
    [Google Scholar]
  33. Kluge A. G., Farris F. S.. 1969; Quantitative phyletics and the evolution of anurans. Syst Zool18:1–32 [CrossRef]
    [Google Scholar]
  34. Kuo I., Saw J., Kapan D. D., Christensen S., Kaneshiro K. Y., Donachie S. P.. 2013; Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai'i, and emended description of the genus Flavobacterium . Int J Syst Evol Microbiol63:3280–3286 [CrossRef][PubMed]
    [Google Scholar]
  35. Li A., Liu H., Sun B., Zhou Y., Xin Y.. 2014; Flavobacterium lacus sp. nov., isolated from a high-altitude lake, and emended description of Flavobacterium filum . Int J Syst Evol Microbiol64:933–939 [CrossRef][PubMed]
    [Google Scholar]
  36. Lim C. S., Oh Y. S., Lee J. K., Park A. R., Yoo J. S., Rhee S. K., Roh D. H.. 2011; Flavobacterium chungbukense sp. nov., isolated from soil. Int J Syst Evol Microbiol61:2734–2739 [CrossRef][PubMed]
    [Google Scholar]
  37. Liu Y., Jin J.-H., Zhou Y.-G., Liu H.-C., Liu Z.-P.. 2010; Flavobacterium caeni sp. nov., isolated from a sequencing batch reactor for the treatment of malachite green effluents. Int J Syst Evol Microbiol60:417–421 [CrossRef][PubMed]
    [Google Scholar]
  38. Ludwig W., Euzéby J., Whitman W. B.. 2010; Taxonomic outlines of the phyla Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes . In Bergey's Manual of Systematic Bacteriology, 2nd edn.vol. 4 pp21–24Edited by Krieg N. R., Ludwig W., Whitman W., Hedlund B. P., Paster B. J., Staley J. T., Ward N., Brown D., Parte A.. New York: Springer;
    [Google Scholar]
  39. Mesbah M., Premachandran U., Whitman W. B.. 1989; Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol39:159–167 [CrossRef]
    [Google Scholar]
  40. Murray R. G. E., Doetsch R. N., Robinow C. F.. 1994; Determinative and cytological light microscopy. In Methods for General and Molecular Bacteriology pp21–41Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R.. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  41. Powers E. M.. 1995; Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol61:3756–3758[PubMed]
    [Google Scholar]
  42. Qu J. H., Yuan H. L., Li H. F., Deng C. P.. 2009; Flavobacterium cauense sp. nov., isolated from sediment of a eutrophic lake. Int J Syst Evol Microbiol59:2666–2669 [CrossRef][PubMed]
    [Google Scholar]
  43. Reichenbach H.. 1992; The order Cytophagales . In The Prokaryotes, 2nd edn. pp3631–3675Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K. H.. New York: Springer;[CrossRef]
    [Google Scholar]
  44. Riffel A., Brandelli A.. 2002; Isolation and characterization of a feather-degrading bacterium from the poultry processing industry. J Ind Microbiol Biotechnol29:255–258 [CrossRef][PubMed]
    [Google Scholar]
  45. Rodgers M., Flanigan D., Pfaller S., Jakubowski W., Kinkle B.. 2003; Identification of a flavobacterium strain virulent against Giardia lamblia cysts. World J Microbiol Biotechnol19:703–709 [CrossRef]
    [Google Scholar]
  46. Saitou N., Nei M.. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol4:406–425[PubMed]
    [Google Scholar]
  47. Sang M. K., Kim K. D.. 2012; The volatile-producing Flavobacterium johnsoniae strain GSE09 shows biocontrol activity against Phytophthora capsici in pepper. J Appl Microbiol113:383–398 [CrossRef][PubMed]
    [Google Scholar]
  48. Sasser M.. 1990; Identification of bacteria by gas chromatography of cellular fatty acids Newark, DE:http://www.microbialid.com/PDF/TechNote_101.pdf MIDI Inc;
    [Google Scholar]
  49. Schmidt K., Connor A., Britton G.. 1994; Analysis of pigments: carotenoids and related polyenes. In Chemical Methods in Prokaryotic Systematics pp403–461Edited by Goodfellow M., O'Donnell A. G.. Chichester: Wiley;
    [Google Scholar]
  50. Sheu S. Y., Chiu T. F., Young C. C., Arun A. B., Chen W. M.. 2011; Flavobacterium macrobrachii sp. nov., isolated from a freshwater shrimp culture pond. Int J Syst Evol Microbiol61:1402–1407 [CrossRef][PubMed]
    [Google Scholar]
  51. Sheu S. Y., Lin Y. S., Chen W. M.. 2013; 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 Microbiol63:2239–2247 [CrossRef][PubMed]
    [Google Scholar]
  52. Singh P., Singh S. M., Dhakephalkar P.. 2014; Diversity, cold active enzymes and adaptation strategies of bacteria inhabiting glacier cryoconite holes of High Arctic. Extremophiles18:229–242 [CrossRef][PubMed]
    [Google Scholar]
  53. Soares F.L., Jr, Melo I. S., Dias A. C., Andreote F. D.. 2012; Cellulolytic bacteria from soils in harsh environments. World J Microbiol Biotechnol28:2195–2203 [CrossRef][PubMed]
    [Google Scholar]
  54. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S.. 2011; mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol28:2731–2739 [CrossRef][PubMed]
    [Google Scholar]
  55. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G.. 1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res25:4876–4882 [CrossRef][PubMed]
    [Google Scholar]
  56. Tindall B. J., Sikorski J., Smibert R. A., Krieg N. R.. 2007; Phenotypic characterization and the principles of comparative systematic. In Methods for General and Molecular Bacteriology, 3rd edn. pp330–393Edited by Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R.. Washington, DC: American Society for Microbiology; [CrossRef]
    [Google Scholar]
  57. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E., other authors. 1987; Report of the ad hoc committee on reconciliation of approaches of bacterial systematics. Int J Syst Bacteriol37:463–464 [CrossRef]
    [Google Scholar]
  58. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J.. 1991; 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol173:697–703[PubMed]
    [Google Scholar]
  59. Wen C. M., Tseng C. S., Cheng C. Y., Li Y. K.. 2002; Purification, characterization and cloning of a chitinase from Bacillus sp. NCTU2. Biotechnol Appl Biochem35:213–219 [CrossRef][PubMed]
    [Google Scholar]
  60. Weon H. Y., Song M. H., Son J. A., Kim B. Y., Kwon S. W., Go S. J., Stackebrandt E.. 2007; Flavobacterium terrae sp. nov. and Flavobacterium cucumis sp. nov., isolated from greenhouse soil. Int J Syst Evol Microbiol57:1594–1598 [CrossRef][PubMed]
    [Google Scholar]
  61. Yoon J. H., Kang S. J., Lee J. S., Oh T. K.. 2007; Flavobacterium terrigena sp. nov., isolated from soil. Int J Syst Evol Microbiol57:947–950 [CrossRef][PubMed]
    [Google Scholar]
  62. Zhang J., Jiang R. B., Zhang X. X., Hang B. J., He J., Li S. P.. 2010; Flavobacterium haoranii sp. nov., a cypermethrin-degrading bacterium isolated from a wastewater treatment system. Int J Syst Evol Microbiol60:2882–2886 [CrossRef][PubMed]
    [Google Scholar]
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