1887

Abstract

A Gram-stain-negative, yellow, facultatively-anaerobic, short, rod-shaped, non-spore-forming bacterium, designated PK15, was isolated from freshwater. Growth was observed at 4–40 °C (optimum, 30 °C), pH 6–9 (optimum, 8), and in the presence of 0–0.8 % (w/v) NaCl (optimum, 0.4 %). Strain PK15 exhibited both catalase and oxidase activities and was able to reduce nitrate. On the basis of 16S rRNA gene sequence similarities, strain PK15 was shown to belong to the genus Flavobacterium with close similarities to Flavobacterium palustre S44 (97.9 %) and Flavobacterium seoulense EM1321 (97.7 %). Menaquinone-6 (MK-6) was the major respiratory quinone, while the G+C content of the genomic DNA was 35.5 (±0.9) mol%. The major polar lipids were phosphatidylethanolamine, three unidentified aminolipids, one unidentified aminophospholipid and three unidentified polar lipids. The predominant cellular fatty acids (≥10 %) were anteiso-C15 : 0 (17.3 %), a summed feature comprising C16 : 1ω7c and/or C16 : 1ω6c (15.1 %) and iso-C15 : 0 (10.0 %). Chemotaxonomic data supported the affiliation of strain PK15 to the genus Flavobacterium . The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain PK15 from strains of closely related species. It was, therefore, evident that PK15 represents a novel species of the genus Flavobacterium , for which the name Flavobacterium commune sp. nov. is proposed with strain PK15 (=KCTC 52562=JCM 32115) as the type strain. Based on the results of the chemotaxonomic characterization in the present study, an emended description of Flavobacterium seoulense is also proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002463
2017-11-07
2019-12-08
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/1/93.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002463&mimeType=html&fmt=ahah

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 Baltimore: Williams and 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. Bernardet JF, 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 and Wilkins; 2011; pp. 112– 154
    [Google Scholar]
  7. Feng H, Zeng Y, Huang Y. Flavobacterium palustre sp. nov., isolated from soil of Xixi wetland in Zhejiang province, China. Int J Syst Evol Microbiol 2015; 65: 1003– 1007 [Crossref]
    [Google Scholar]
  8. Kolton M, Green SJ, Harel YM, Sela N, Elad Y et al. Draft genome sequence of Flavobacterium sp. strain F52, isolated from the rhizosphere of bell pepper (Capsicum annuum L. cv. Maccabi). J Bacteriol 2012; 194: 5462– 5463 [CrossRef] [PubMed]
    [Google Scholar]
  9. Fu Y, Tang X, Lai Q, Zhang C, Zhong H et al. Flavobacterium beibuense sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2011; 61: 205– 209 [CrossRef] [PubMed]
    [Google Scholar]
  10. Kim JH, Kim KY, Cha CJ. Flavobacterium chungangense sp. nov., isolated from a freshwater lake. Int J Syst Evol Microbiol 2009; 59: 1754– 1758 [CrossRef] [PubMed]
    [Google Scholar]
  11. Zamora L, Vela AI, Sánchez-Porro C, Palacios MA, Moore ER et al. Flavobacterium tructae sp. nov. and Flavobacterium piscis sp. nov., isolated from farmed rainbow trout (Oncorhynchus mykiss). Int J Syst Evol Microbiol 2014; 64: 392– 399 [CrossRef] [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 [CrossRef] [PubMed]
    [Google Scholar]
  13. Park M, Ryu SH, Vu TH, Ro HS, Yun PY et al. Flavobacterium defluvii sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2007; 57: 233– 237 [CrossRef] [PubMed]
    [Google Scholar]
  14. Ryu SH, Park M, Jeon Y, Lee JR, Park W et al. Flavobacterium filum sp. nov., isolated from a wastewater treatment plant in Korea. Int J Syst Evol Microbiol 2007; 57: 2026– 2030 [CrossRef] [PubMed]
    [Google Scholar]
  15. 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 [CrossRef] [PubMed]
    [Google Scholar]
  16. Sang MK, Kim KD. The volatile-producing Flavobacterium johnsoniae strain GSE09 shows biocontrol activity against Phytophthora capsici in pepper. J Appl Microbiol 2012; 113: 383– 398 [CrossRef] [PubMed]
    [Google Scholar]
  17. Kolton M, Sela N, Elad Y, Cytryn E. Comparative genomic analysis indicates that niche adaptation of terrestrial Flavobacteria is strongly linked to plant glycan metabolism. PLoS One 2013; 8: e76704 [CrossRef] [PubMed]
    [Google Scholar]
  18. Good C, Davidson J, Wiens GD, Welch TJ, Summerfelt S. Flavobacterium branchiophilum and F. succinicans associated with bacterial gill disease in rainbow trout Oncorhynchus mykiss (Walbaum) in water recirculation aquaculture systems. J Fish Dis 2015; 38: 409– 413 [CrossRef] [PubMed]
    [Google Scholar]
  19. 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 [CrossRef]
    [Google Scholar]
  20. Starliper CE. Bacterial coldwater disease of fishes caused by Flavobacterium psychrophilum. J Adv Res 2011; 2: 97– 108 [CrossRef]
    [Google Scholar]
  21. Declercq AM, Haesebrouck F, van den Broeck W, Bossier P, Decostere A. Columnaris disease in fish: a review with emphasis on bacterium-host interactions. Vet Res 2013; 44: 27 [CrossRef] [PubMed]
    [Google Scholar]
  22. Delong EF. Archaea in coastal marine environments. Proc Natl Acad Sci USA 1992; 89: 5685– 5689 [CrossRef] [PubMed]
    [Google Scholar]
  23. 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]
  24. 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 [CrossRef] [PubMed]
    [Google Scholar]
  25. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. (editor) Mammalian Protein Metabolism New York: Academic Press; 1969; pp. 21– 132 [Crossref]
    [Google Scholar]
  26. 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]
  27. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17: 368– 376 [CrossRef] [PubMed]
    [Google Scholar]
  28. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20: 406– 416 [CrossRef]
    [Google Scholar]
  29. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783– 791 [CrossRef] [PubMed]
    [Google Scholar]
  30. Baek SH, Im WT, Oh HW, Lee JS, Oh HM et al. Brevibacillus ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2006; 56: 2665– 2669 [CrossRef] [PubMed]
    [Google Scholar]
  31. 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]
  32. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp. 607– 654
    [Google Scholar]
  33. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes. 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
    [Google Scholar]
  34. 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 [CrossRef]
    [Google Scholar]
  35. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19: 161– 207 [Crossref]
    [Google Scholar]
  36. Gonzalez JM, Saiz-Jimenez C. A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 2002; 4: 770– 773 [PubMed] [Crossref]
    [Google Scholar]
  37. Shin SK, Goo H, Cho YJ, Kwon S, Yong D et al. Non-contiguous finished genome sequence and description of the gliding bacterium Flavobacterium seoulense sp. nov. Stand Genomic Sci 2014; 9: 34 [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002463
Loading
/content/journal/ijsem/10.1099/ijsem.0.002463
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error