1887

Abstract

Four Gram-stain-negative, non-endospore-forming, non-motile strains were found in soil, South Korea. Based on their 16S rRNA gene sequences, strains UCM-R15 and UCM-R21 are most closely related to DK69 (97.4–97.5 %, pairwise similarity) while strains UCM-R36 and UCM-46 are most closely related to GH29-5 (97.5 % and 98.3 %, respectively), with all four strains sharing less than 97 % pairwise similarity to the type strain of any other species of the genus . None of the four strains can reduce/digest nitrate or urea. The only menaquinone detected was MK-6 and the major fatty acids were iso-C, iso-C 3-OH, iso-C G and summed feature 9 in all the type strains. Phosphatidylethanolamine was found in three strains as the major polar lipid, phosphatidylserine was found in both strains UCM-R15 and UCM-R36, but not UCM-46, and phosphatidylmonomethylethanolamine only occurred in strain UCM-R15. The genomic DNA G+C content values of strains UCM-R15, UCM-R21, UCM-R36 and UCM-46 were 35.3–39.0  mol%. Taking into account their physiological and biochemical characteristics, we suggest that three of the strains are novel members of the genus . We propose the names sp. nov. for type strain UCM-R15(=KACC 18666=NBRC 111764), and strain UCM-R21 as an additional strain sp. nov. for type strain UCM-R36 (=KACC 18668=NBRC 111765), and sp. nov. for type strain UCM-46 (=KACC 18575=NBRC 111657).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001154
2016-08-01
2022-01-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/8/3108.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001154&mimeType=html&fmt=ahah

References

  1. Ao L., Zeng X. C., Nie Y., Mu Y., Zhou L., Luo X. 2014; Flavobacterium arsenatis sp. nov., a novel arsenic-resistant bacterium from high-arsenic sediment. Int J Syst Evol Microbiol 64:3369–3374 [View Article][PubMed]
    [Google Scholar]
  2. 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]
  3. Bernardet J. F., Bowman J. P. 2010; The genus Flavobacterium . In Bergey's Manual of Systematic Bacteriology, 2nd edn. Vol. 4 pp. 112–155 Edited by Whitman W. B., Parte A. C. New York, Dordrecht, Heidelberg, London: Springer;
    [Google Scholar]
  4. 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]
  5. Duchaud E., Boussaha M., Loux V., Bernardet J. F., Michel C., Kerouault B., Mondot S., Nicolas P., Bossy R. et al. 2007; Complete genome sequence of the fish pathogen Flavobacterium psychrophilum . Nat Biotechnol 25:763–769 [View Article][PubMed]
    [Google Scholar]
  6. 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 Evol Microbiol 39:224–229 [View Article]
    [Google Scholar]
  7. Fautz E., Reichenbach H. 1980; A simple test for flexirubin-type pigments. FEMS Microbiol Lett 8:87–91 [View Article]
    [Google Scholar]
  8. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [View Article][PubMed]
    [Google Scholar]
  9. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  10. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 [View Article]
    [Google Scholar]
  11. Frank J. A., Reich C. I., Sharma S., Weisbaum J. S., Wilson B. A., Olsen G. J. 2008; Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 74:2461–2470 [View Article][PubMed]
    [Google Scholar]
  12. 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 Microbiol 63:2841–2847 [View Article][PubMed]
    [Google Scholar]
  13. Hatayama K., Kuno T. 2015; Spirosoma fluviale sp. nov., isolated from river water. Int J Syst Evol Microbiol 65:3447–3450 [View Article]
    [Google Scholar]
  14. Jacin H., Mishkin A. R. 1965; Separation of carbonhydrates on borate-impregnated silica gel G plates. J Chromatogr 18:170–173 [View Article]
    [Google Scholar]
  15. Jit S., Dadhwal M., Prakash O., Lal R. 2008; Flavobacterium lindanitolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil. Int J Syst Evol Microbiol 58:1665–1669 [View Article][PubMed]
    [Google Scholar]
  16. 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 Microbiol 62:1402–1408 [View Article][PubMed]
    [Google Scholar]
  17. Khianngam S., Akaracharanya A., Lee J. S., Lee K. C., Kim K. W., Tanasupawat S. 2014; Flavobacterium arsenitoxidans sp. nov., an arsenite-oxidizing bacterium from Thai soil. Antonie Van Leeuwenhoek 106:1239–1246 [View Article][PubMed]
    [Google Scholar]
  18. Kim B. Y., Weon H. Y., Cousin S., Yoo S. H., Kwon S. W., Go S. J., Stackebrandt E. 2006; Flavobacterium daejeonense sp. nov. and Flavobacterium suncheonense sp. nov., isolated from greenhouse soils in Korea. Int J Syst Evol Microbiol 56:1645–1649 [View Article][PubMed]
    [Google Scholar]
  19. Kim J. H., Choi B. H., Jo M., Kim S. C., Lee P. C. 2014; Flavobacterium faecale sp. nov., an agarase-producing species isolated from stools of Antarctic penguins. Int J Syst Evol Microbiol 64:2884–2890 [View Article][PubMed]
    [Google Scholar]
  20. 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 [View Article][PubMed]
    [Google Scholar]
  21. Kimura M. 1983 The Neutral Theory of Molecular Evolution Cambridge, UK: Cambridge University Press; [CrossRef]
    [Google Scholar]
  22. Krieg N. R., Padgett P. J. 2011; Phenotypic and physiological characterization methods. In Methods in Microbiology, 1st edn. Vol. 38 pp. 15–60 Edited by Rainey F. , Oren A. . Oxford, UK: Elsevier Academic Press;
    [Google Scholar]
  23. Lata P., Lal D., Lal R. 2012; Flavobacterium ummariense sp. nov., isolated from hexachlorocyclohexane-contaminated soil, and emended description of Flavobacterium ceti Vela et al. 2007. Int J Syst Evol Microbiol 62:2674–2679 [View Article]
    [Google Scholar]
  24. Lee K., Park S. C., Yi H., Chun J. 2013; Flavobacterium limnosediminis sp. nov., isolated from sediment of a freshwater lake. Int J Syst Evol Microbiol 63:4784–4789 [View Article][PubMed]
    [Google Scholar]
  25. Lee S., Oh J. H., Weon H. Y., Ahn T. Y. 2012a; Flavobacterium cheonhonense sp. nov., isolated from a freshwater reservoir. J Microbiol 50:562–566 [View Article]
    [Google Scholar]
  26. Lee S., Weon H.-Y., Han K., Ahn T.-Y. 2012b; 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 62:2378–2382 [View Article]
    [Google Scholar]
  27. 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 Microbiol 64:933–939 [View Article][PubMed]
    [Google Scholar]
  28. 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]
  29. 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 [View Article]
    [Google Scholar]
  30. 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]
  31. Nedashkovskaya O. I., Balabanova L. A., Zhukova N. V., Kim S. J., Bakunina I. Y., Rhee S. K. 2014; Flavobacterium ahnfeltiae sp. nov., a new marine polysaccharide-degrading bacterium isolated from a Pacific red alga. Arch Microbiol 196:745–752 [View Article][PubMed]
    [Google Scholar]
  32. Ngo H. T., Kook M., Yi T. H. 2015; Flavobacterium daemonensis sp. nov., isolated from Daemo Mountain soil. Int J Syst Evol Microbiol 65:983–989 [View Article][PubMed]
    [Google Scholar]
  33. Pitcher D. G., Saunders N. A., Owen R. J. 1989; Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8:151–156 [View Article]
    [Google Scholar]
  34. 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 [View Article][PubMed]
    [Google Scholar]
  35. Rohde M. 2011; Microscopy. In Methods in Microbiology, 1st edn. Vol. 38 pp. 61–100 Edited by Rainey F., Oren A. London: Elsevier Academic Press;
    [Google Scholar]
  36. Ross H. N. M., Grant W. D. 1985; Lipids in archaebacterial taxonomy. In Chemical Methods in Bacterial Systematics pp. 289–299 Edited by Goodfellow M., Minnikin D. E. New York: Academic Press;
    [Google Scholar]
  37. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  38. Sasser M. 1990 Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101 Newark, DE: MIDI Inc;
    [Google Scholar]
  39. Starliper C. E. 2011; Bacterial coldwater disease of fishes caused by Flavobacterium psychrophilum . J Adv Res 2:97–108 [View Article]
    [Google Scholar]
  40. 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]
  41. 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]
  42. 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]
  43. Tindall B. J., Sikorki J., Smibert R. A., Kried N. R., Snyder L. R. 2007; Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology, 3rd edn. pp. 330–394 Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M. Washington, DC: ASM press;
    [Google Scholar]
  44. Tschech A., Pfennig N. 1984; Growth yield increase linked to caffeate reduction in Acetobacterium woodii . Arch Microbiol 137:163–167 [View Article]
    [Google Scholar]
  45. 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]
    [Google Scholar]
  46. Wakabayashi H., Huh G. J., Kimura N. 1989; Flavobacterium branchiophila sp. nov., a causative agent of bacterial gill disease of freshwater fishes. Int J Syst Bacteriol 39:213–216 [CrossRef]
    [Google Scholar]
  47. Wang Z. W., Liu Y. H., Dai X., Wang B. J., Jiang C. Y., Liu S. J. 2006; Flavobacterium saliperosum sp. nov., isolated from freshwater lake sediment. Int J Syst Evol Microbiol 56:439–442 [View Article]
    [Google Scholar]
  48. Weeks O. B., Andrewes A. G., Brown B. O., Weedon B. C. 1969; Occurrence of C40 and C45 carotenoids in the C50 carotenoid system of Flavobacterium dehydrogenans . Nature 224:879–882 [View Article][PubMed]
    [Google Scholar]
  49. Wheater D. M. 1955; The characteristics of Lactobacillus acidophilus and Lactobacillus bulgaricus . J Gen Microbiol 12:123–132 [View Article]
    [Google Scholar]
  50. Widdel F., Kohring G. W., Mayer F. 1983; Studies on dissimilatory sulfate-reducing bacteria that decompose fatty acids III. Characterization of the filamentous gliding Desulfonema limicola gen. nov. sp. nov., and Desulfonema magnum sp. nov. Arch Microbiol 134:286–294 [View Article]
    [Google Scholar]
  51. Yi H., Oh H. M., Lee J. H., Kim S. J., Chun J. 2005; Flavobacterium antarcticum sp. nov., a novel psychrotolerant bacterium isolated from the Antarctic. Int J Syst Evol Microbiol 55:637–641 [View Article]
    [Google Scholar]
  52. Yoon H. S., Aslam Z., Song G. C., Kim S. W., Jeon C. O., Chon T. S., Chung Y. R. 2009; Flavobacterium sasangense sp. nov., isolated from a wastewater stream polluted with heavy metals. Int J Syst Evol Microbiol 59:1162–1166 [View Article]
    [Google Scholar]
  53. Zhang D. C., Wang H. X., Liu H. C., Dong X. Z., Zhou P. J. 2006; Flavobacterium glaciei sp. nov., a novel psychrophilic bacterium isolated from the China No.1 glacier. Int J Syst Evol Microbiol 56:2921–2925 [View Article][PubMed]
    [Google Scholar]
  54. 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 [View Article][PubMed]
    [Google Scholar]
  55. Zhu L., Liu Q., Liu H., Zhang J., Dong X., Zhou Y., Xin Y. 2009; Flavobacterium noncentrifugens sp. nov., a psychrotolerant bacterium isolated from glacier meltwater. Int J Syst Evol Microbiol 63:2032–2037 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001154
Loading
/content/journal/ijsem/10.1099/ijsem.0.001154
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited this month Most Cited RSS feed

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