sp. nov., isolated from river water Free

Abstract

A bacterial strain, designated TMd3a3, was isolated from a freshwater sample collected from the Tamagawa River in Japan. The cells of strain TMd3a3 were facultatively anaerobic, Gram-stain-negative, non-spore-forming rods that showed gliding motility. This strain was capable of denitrification and anaerobic growth with nitrate. Cloned 16S rRNA gene sequences of strain TMd3a3 yielded three different sequences (similarity between the three sequences: 98.9–99.7 %). The 16S rRNA gene sequences of strain TMd3a3 showed high similarity to those of 435-08 (97.2–97.4 % similarity), BD-b365 (96.7–97.4 %), T9 (97.0–97.3 %), ST-82 (96.5–97.3 %), WB 1.1-56 (96.9–97.2 %), T16 (96.9–97.2 %) and LMG 22018 (96.4–97.0 %). Strain TMd3a3 contained menaquinone 6 as the sole respiratory quinone. The major cellular fatty acids were iso-C and summed feature 3 (C ω7 and/or C ω6). The polar lipids were phosphatidylethanolamine, five unidentified aminolipids and five unidentified polar lipids. The DNA G+C content was 36.5 mol %. The DNA–DNA relatedness values of strain TMd3a3with CCUG 60100, DSM 19382, JCM 19927, DSM 15094, DSM 18293, ATCC BAA-2541 and DSM 16141 were below 13 %. From the chemotaxonomic and physiological data and the levels of DNA–DNA relatedness, strain TMd3a3 should be classified as the representative of a novel species of the genus , for which the name sp. nov. (type strain TMd3a3=JCM 30987=DSM 100880) is proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001057
2016-08-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/8/2789.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001057&mimeType=html&fmt=ahah

References

  1. Bergey D. H., Harrison F. C., Breed R. S., Hammer B. W., Huntoon F. M. 1923; Genus II. Flavobacterium gen. nov. In Bergey’s Manual of Determinative Bacteriology pp. 97–117 Baltimore: Williams & Wilkins;
    [Google Scholar]
  2. 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]
  3. 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 Krieg N. R., Staley J. T., Brown D. R., Hedlund B. P., Paster B. J., Ward N. L., Ludwig W., Whitman W. B. New York: Springer;
    [Google Scholar]
  4. 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 [View Article][PubMed]
    [Google Scholar]
  5. Bligh E. G., Dyer W. J. 1959; A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37:911–917 [View Article][PubMed]
    [Google Scholar]
  6. Buck J. D. 1982; Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993[PubMed]
    [Google Scholar]
  7. 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 [View Article][PubMed]
    [Google Scholar]
  8. 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 Microbiol 63:886–892 [View Article][PubMed]
    [Google Scholar]
  9. 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 Bacteriol 39:224–229 [View Article]
    [Google Scholar]
  10. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  11. Feng Q., Gao Y., Nogi Y., Tan X., Han L., Zhang Y., Lv J. 2015; Flavobacterium maotaiense sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 65:171–176 [View Article][PubMed]
    [Google Scholar]
  12. Finster K. W., Herbert R. A., Lomstein B. A. 2009; Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov., isolated from a high Arctic permafrost soil, and emended description of the genus Spirosoma . Int J Syst Evol Microbiol 59:839–844 [View Article][PubMed]
    [Google Scholar]
  13. 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 Microbiol 64:1488–1494 [View Article][PubMed]
    [Google Scholar]
  14. Hatayama K. 2014; Comamonas humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 64:3976–3982 [View Article]
    [Google Scholar]
  15. Hatayama K., Kuno T. 2015a; Spirosoma fluviale sp. nov., isolated from river water. Int J Syst Evol Microbiol 65:3447–3450 [View Article]
    [Google Scholar]
  16. Hatayama K., Kuno T. 2015b; Croceifilum oryzae gen. nov., sp. nov., isolated from rice paddy soil. Int J Syst Evol Microbiol 65:4061–4065 [View Article]
    [Google Scholar]
  17. 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 Microbiol 63:1633–1638 [View Article][PubMed]
    [Google Scholar]
  18. Kim J.-J., Kanaya E., Weon H.-Y., Koga Y., Takano K., Dunfield P. F., Kwon S.-W., Kanaya S. 2012a; Flavobacterium compostarboris sp. nov., isolated from leaf-and-branch compost, and emended descriptions of Flavobacterium hercynium, Flavobacterium resistens and Flavobacterium johnsoniae . Int J Syst Evol Microbiol 62:2018–2024 [CrossRef]
    [Google Scholar]
  19. 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. 2012b; 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]
    [Google Scholar]
  20. Kimura M. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120 [View Article][PubMed]
    [Google Scholar]
  21. 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 [View Article][PubMed]
    [Google Scholar]
  22. Loch T. P., Faisal M. 2014; Flavobacterium spartansii sp. nov., a pathogen of fishes, and emended descriptions of Flavobacterium aquidurense and Flavobacterium araucananum . Int J Syst Evol Microbiol 64:406–412 [View Article][PubMed]
    [Google Scholar]
  23. Minnikin D. E., O'Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H. 1984; An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241 [View Article]
    [Google Scholar]
  24. Pei A. Y., Oberdorf W. E., Nossa C. W., Agarwal A., Chokshi P., Gerz E. A., Jin Z., Lee P., Yang L. et al. 2010; Diversity of 16S rRNA genes within individual prokaryotic genomes. Appl Environ Microbiol 76:3886–3897 [View Article][PubMed]
    [Google Scholar]
  25. Reasoner D. J., Geldreich E. E. 1985; A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 49:1–7[PubMed]
    [Google Scholar]
  26. Ryu S. H., Park J. H., Moon J. C., Sung Y., Lee S.-S., Jeon C. O. 2008; Flavobacterium resistens sp. nov., isolated from stream sediment. Int J Syst Evol Microbiol 58:2266–2270 [View Article][PubMed]
    [Google Scholar]
  27. 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]
  28. Skerman V. B. D., McGowan V., Sneath P. H. A. 1980; Approved lists of bacterial names. Int J Syst Bacteriol 30:225–420 [CrossRef]
    [Google Scholar]
  29. Tamaki H., Hanada S., Kamagata Y., Nakamura K., Nomura N., Nakano K., Matsumura M. 2003; Flavobacterium limicola sp. nov., a psychrophilic, organic-polymer-degrading bacterium isolated from freshwater sediments. Int J Syst Evol Microbiol 53:519–526 [View Article][PubMed]
    [Google Scholar]
  30. Tamaoka J., Komagata K. 1984; Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125–128 [View Article]
    [Google Scholar]
  31. Tamura K., Nei M. 1993; Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526[PubMed]
    [Google Scholar]
  32. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. 2013; MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  33. 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 [View Article][PubMed]
    [Google Scholar]
  34. Van Trappen S., Vandecandelaere I., Mergaert J., Swings J. 2005; Flavobacterium fryxellicola sp. nov. and Flavobacterium psychrolimnae sp. nov., novel psychrophilic bacteria isolated from microbial mats in Antarctic lakes. Int J Syst Evol Microbiol 55:769–772 [View Article][PubMed]
    [Google Scholar]
  35. Větrovský T., Baldrian P. 2013; The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS One 8:e57923 [View Article][PubMed]
    [Google Scholar]
  36. 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. et al. 1987; Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [CrossRef]
    [Google Scholar]
  37. Zamora L., Vela A. I., Sánchez-Porro C., Palacios M. A., Moore E. R. B., Domínguez L., Ventosa A., Fernández-Garayzábal J. F. 2014; Flavobacterium tructae sp. nov. and Flavobact erium piscis sp. nov., isolated from farmed rainbow trout (Oncorhynchus mykiss). Int J Syst Evol Microbiol 64:392–399 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001057
Loading
/content/journal/ijsem/10.1099/ijsem.0.001057
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed