1887

Abstract

A bacterial strain, designated CMJ-5, was isolated from a freshwater shrimp culture pond in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain CMJ-5 were Gram-stain-negative, strictly aerobic, non-motile, yellow-pigmented rods surrounded by a thick capsule. Growth occurred at 20–35 °C (optimum, 30 °C), at pH 6.5–8.0 (optimum, pH 7.0) and with 0–0.5 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CMJ-5 belonged to the genus and was related most closely to LQY-7 with sequence similarity of 94.4 %. Strain CMJ-5 contained iso-C (37.5 %), iso-C 3-OH (13.4 %), iso-C 3-OH (13.1 %) and iso-C G (11.2 %) 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 G+C content of the genomic DNA was 42.4 mol%. On the basis of phylogenetic inference and phenotypic data, strain CMJ-5 should be classified as a representative of a novel species, for which the name sp. nov. is proposed. The type strain is CMJ-5 ( = BCRC 80405 = LMG 26890 = KCTC 23915). Emended descriptions of , , and are also proposed.

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2013-06-01
2020-01-22
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References

  1. 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 Bacteriol 47:, 249–251. [CrossRef] [PubMed]
    [Google Scholar]
  2. Bergey D. H. , Harrison F. C. , Breed R. S. , Hammer B. W. , Huntoon F. M. . (editors) ( 1923; ). Genus II. Flavobacterium gen. nov. . In Bergey’s Manual of Determinative Bacteriology, pp. 97–117. Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  3. Bernardet J.-F. , Bowman J. P. . ( 2006; ). The genus Flavobacterium . . In The Prokaryotes: A Handbook on the Biology of Bacteria, , 3rd edn., vol. 7, pp. 481–531. Edited by Dworkin M. , Falkow S. , Rosenberg E. , Schleifer K. H. , Stackebrandt E. . . New York:: Springer;.
    [Google Scholar]
  4. Bernardet J.-F. , Bowman J. P. . ( 2011; ). Genus I. Flavobacterium Bergey et al. 1923. . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 4, pp. 112–154. Edited by Whitman W. . . Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  5. Bernardet J.-F. , Grimont P. A. D. . ( 1989; ). Deoxyribonucleic acid relatedness and phenotypic characterization of Flexibacter columnaris sp. nov., nom. rev., Flexibacter psychrophilus sp. nov., nom. rev., and Flexibacter maritimus Wakabayashi, Hikida, and Masumura 1986. . Int J Syst Bacteriol 39:, 346–354. [CrossRef]
    [Google Scholar]
  6. 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 Bacteriol 46:, 128–148. [CrossRef]
    [Google Scholar]
  7. 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 Microbiol 52:, 1049–1070. [CrossRef] [PubMed]
    [Google Scholar]
  8. Beveridge T. J. , Lawrence J. R. , Murray R. G. E. . ( 2007; ). Sampling and staining for light microscopy. . In Methods for General and Molecular Bacteriology, , 3rd edn., pp. 19–33. Edited by Beveridge T. J. , Breznak J. A. , Marzluf G. A. , Schmidt T. M. , Snyder L. R. . . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  9. 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 Microbiol 50:, 1861–1868.[PubMed]
    [Google Scholar]
  10. Breznak J. A. , Costilow R. N. . ( 2007; ). Physicochemical factors in growth. . In Methods for General and Molecular Bacteriology, , 3rd edn., pp. 309–329. Edited by Beveridge T. J. , Breznak J. A. , Marzluf G. A. , Schmidt T. M. , Snyder L. R. . . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  11. Busse H. J. , Auling G. . ( 1988; ). Polyamine pattern as chemotaxonomic marker within the Proteobacteria . . Syst Appl Microbiol 11:, 1–8. [CrossRef]
    [Google Scholar]
  12. Busse H. J. , Bunka S. , Hensel A. , Lubitz W. . ( 1997; ). Discrimination of members of the family Pasteurellaceae based on polyamine patterns. . Int J Syst Bacteriol 47:, 698–708. [CrossRef]
    [Google Scholar]
  13. 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 Microbiol 51:, 1729–1735. [CrossRef] [PubMed]
    [Google Scholar]
  14. 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 Microbiol 63:, 827–834.[PubMed] [CrossRef]
    [Google Scholar]
  15. Cole J. R. , Wang Q. , Cardenas E. , Fish J. , Chai B. , Farris R. J. , Kulam-Syed-Mohideen A. S. , McGarrell D. M. , Marsh T. et al. ( 2009; ). The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. . Nucleic Acids Res 37: (Database issue), D141–D145. [CrossRef] [PubMed]
    [Google Scholar]
  16. Collins M. D. . ( 1994; ). Isoprenoid quinones. . In Chemical Methods in Prokaryotic Systematics, pp. 265–309. Edited by Goodfellow M. , O’Donnell A. G. . . Chichester:: Wiley;.
    [Google Scholar]
  17. Cousin S. , Päuker O. , Stackebrandt E. . ( 2007; ). Flavobacterium aquidurense sp. nov. and Flavobacterium hercynium sp. nov., from a hard-water creek. . Int J Syst Evol Microbiol 57:, 243–249. [CrossRef] [PubMed]
    [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 Microbiol 62:, 1151–1157. [CrossRef] [PubMed]
    [Google Scholar]
  19. Embley T. M. , Wait R. . ( 1994; ). Structural lipids of eubacteria. . In Chemical Methods in Prokaryotic Systematics, pp. 121–161. Edited by Goodfellow M. , O’Donnell A. G. . . Chichester:: Wiley;.
    [Google Scholar]
  20. Felsenstein J. . ( 1981; ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17:, 368–376. [CrossRef] [PubMed]
    [Google Scholar]
  21. Felsenstein, J. (1993). phylip (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  22. Frankland G. C. , Frankland P. F. . ( 1889; ). Ueber einige typische Mikroorganismen im Wasser und im Boden. . Z Med Mikrobiol Immunol 6:, 373–400. [CrossRef]
    [Google Scholar]
  23. Hall T. A. . ( 1999; ). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. . Nucleic Acids Symp Ser 41:, 95–98.
    [Google Scholar]
  24. Humphry D. R. , George A. , Black G. W. , Cummings S. P. . ( 2001; ). Flavobacterium frigidarium sp. nov., an aerobic, psychrophilic, xylanolytic and laminarinolytic bacterium from Antarctica. . Int J Syst Evol Microbiol 51:, 1235–1243.[PubMed]
    [Google Scholar]
  25. Kim O. S. , Cho Y. J. , Lee K. , Yoon S. H. , Kim M. , Na H. , Park S. C. , Jeon Y. S. , Lee J. H. et al. ( 2012; ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62:, 716–721. [CrossRef] [PubMed]
    [Google Scholar]
  26. Kimura M. . ( 1983; ). The Neutral Theory of Molecular Evolution. Cambridge:: Cambridge University Press;. [CrossRef]
    [Google Scholar]
  27. Kluge A. G. , Farris F. S. . ( 1969; ). Quantitative phyletics and the evolution of anurans. . Syst Zool 18:, 1–32. [CrossRef]
    [Google Scholar]
  28. 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 Microbiol 61:, 2734–2739. [CrossRef] [PubMed]
    [Google Scholar]
  29. 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 Microbiol 60:, 417–421. [CrossRef] [PubMed]
    [Google Scholar]
  30. Ludwig W. , Euzéby J. , Whitman W. B. . ( 2011; ). 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, pp. 21–24. Edited by Whitman W. . . Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  31. McCammon S. A. , Innes B. H. , Bowman J. P. , Franzmann P. D. , Dobson S. J. , Holloway P. E. , Skerratt J. H. , Nichols P. D. , Rankin L. M. . ( 1998; ). Flavobacterium hibernum sp. nov., a lactose-utilizing bacterium from a freshwater Antarctic lake. . Int J Syst Bacteriol 48:, 1405–1412. [CrossRef] [PubMed]
    [Google Scholar]
  32. 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 Bacteriol 39:, 159–167. [CrossRef]
    [Google Scholar]
  33. Nokhal T. H. , Schlegel H. G. . ( 1983; ). Taxonomic study of Paracoccus denitrificans . . Int J Syst Bacteriol 33:, 26–37. [CrossRef]
    [Google Scholar]
  34. Park M. , Lu S. , Ryu S. H. , Chung B. S. , Park W. , Kim C. J. , Jeon C. O. . ( 2006; ). Flavobacterium croceum sp. nov., isolated from activated sludge. . Int J Syst Evol Microbiol 56:, 2443–2447. [CrossRef] [PubMed]
    [Google Scholar]
  35. Park M. , Ryu S. H. , Vu T. H. , Ro H. S. , Yun P. Y. , Jeon C. O. . ( 2007; ). Flavobacterium defluvii sp. nov., isolated from activated sludge. . Int J Syst Evol Microbiol 57:, 233–237. [CrossRef] [PubMed]
    [Google Scholar]
  36. 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 Microbiol 61:, 3756–3758.[PubMed]
    [Google Scholar]
  37. 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 Microbiol 59:, 2666–2669. [CrossRef] [PubMed]
    [Google Scholar]
  38. Reichenbach H. . ( 1992; ). The order Cytophagales . . In The Prokaryotes, a Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, , 2nd edn., pp. 3631–3675. Edited by Balows A. , Trüper H. G. , Dworkin M. , Harder W. , Schleifer K. H. . . New York:: Springer;.
    [Google Scholar]
  39. Saitou N. , Nei M. . ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4:, 406–425.[PubMed]
    [Google Scholar]
  40. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  41. Schmidt K. , Connor A. , Britton G. . ( 1994; ). Analysis of pigments: carotenoids and related polyenes. . In Chemical Methods in Prokaryotic Systematics, pp. 403–461. Edited by Goodfellow M. , O’Donnell A. G. . . Chichester:: Wiley;.
    [Google Scholar]
  42. 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 Microbiol 61:, 1402–1407. [CrossRef] [PubMed]
    [Google Scholar]
  43. 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 Evol 28:, 2731–2739. [CrossRef] [PubMed]
    [Google Scholar]
  44. 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 Res 25:, 4876–4882. [CrossRef] [PubMed]
    [Google Scholar]
  45. Tindall B. J. , Sikorski J. , Smibert R. A. , Krieg N. R. . ( 2007; ). Phenotypic characterization and the principles of comparative systematics. . In Methods for General and Molecular Bacteriology, , 3rd edn., pp. 330–393. Edited by Beveridge T. J. , Breznak J. A. , Marzluf G. A. , Schmidt T. M. , Snyder L. R. . . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  46. Weisburg W. G. , Barns S. M. , Pelletier D. A. , Lane D. J. . ( 1991; ). 16S ribosomal DNA amplification for phylogenetic study. . J Bacteriol 173:, 697–703.[PubMed]
    [Google Scholar]
  47. 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 Microbiol 57:, 1594–1598. [CrossRef] [PubMed]
    [Google Scholar]
  48. Yoon J. H. , Kang S. J. , Lee J. S. , Oh T. K. . ( 2007; ). Flavobacterium terrigena sp. nov., isolated from soil. . Int J Syst Evol Microbiol 57:, 947–950. [CrossRef] [PubMed]
    [Google Scholar]
  49. 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 Microbiol 60:, 2882–2886. [CrossRef] [PubMed]
    [Google Scholar]
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