Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 64, Issue Pt_11

sp. nov., isolated from a flooded rice field, and emended descriptions of , and Free

Abstract

A bacterial strain, designated Jyi-05, was isolated from a flooded rice field and characterized using a polyphasic taxonomic approach. Cells of strain Jyi-05 were Gram-stain-negative, strictly aerobic, bright-yellow-pigmented rods that were motile by gliding. Growth occurred at 10–30 °C (optimum 30 °C), at pH 6.5–7.5 (optimum pH 7.0) and with 0–2 % (w/v) NaCl (optimum 1 %, w/v, NaCl). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Jyi-05 belonged to the genus and was most closely related to DSM 1076 with sequence similarity of 97.6 %. Strain Jyi-05 contained iso-C (16.6 %), anteiso-C (10.8 %), summed feature 3 (Cω7 and/or Cω6; 10.3 %), iso-C 3-OH (9.2 %), C (7.3 %) and iso-C 3-OH (7.2 %) 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 genomic DNA G+C content of strain Jyi-05 was 34.2 mol%. The DNA–DNA relatedness of strain Jyi-05 with respect to recognized species of the genus was less than 70 %. On the basis of the phylogenetic inference and phenotypic data, strain Jyi-05 should be classified as a novel species, for which the name sp. nov. is proposed. The type strain is Jyi-05 ( = BCRC 80522 = LMG 27292 = KCTC 32240). Emended descriptions of , and are also presented.

  • Published Online:
© 2014 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.065524-0
2014-11-01
2025-03-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/11/3701.html?itemId=/content/journal/ijsem/10.1099/ijs.0.065524-0&mimeType=html&fmt=ahah

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. [View Article] [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, MD:: 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;. [View Article]
    [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 Krieg N. R., Ludwig W., Whitman W. B., Hedlund B. P., Paster B. J., Staley J. T., Ward N. L., Brown D. R., Parte A. . New York:: Springer;.
     [Google Scholar]
  5. 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. [View Article]
    [Google Scholar]
  6. 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]
  7. 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]
  8. 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 Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R. . Washington, DC:: American Society for Microbiology;.
     [Google Scholar]
  9. Busse J., Auling G. ( 1988 ). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . . Syst Appl Microbiol 11, 1–8. [View Article]
    [Google Scholar]
  10. 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. [View Article]
    [Google Scholar]
  11. 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. [View Article] [PubMed]
    [Google Scholar]
  12. 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. [View Article] [PubMed]
    [Google Scholar]
  13. 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 Res 37 (Suppl. 1), D141–D145. [View Article] [PubMed]
    [Google Scholar]
  14. 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]
  15. 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. [View Article] [PubMed]
    [Google Scholar]
  16. 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]
  17. 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]
  18. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368–376. [View Article] [PubMed]
    [Google Scholar]
  19. Felsenstein J. ( 1993 ). phylip (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  20. 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]
  21. 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]
  22. 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]
  23. Joung Y., Kim H., Ahn T. S., Joh K. ( 2012 ). Flavobacterium yonginense sp. nov. and Flavobacterium myungsuense sp. nov., isolated from a mesotrophic artificial lake. . Int J Syst Evol Microbiol 62, 806–810. [View Article] [PubMed]
    [Google Scholar]
  24. Joung Y., Kim H., Joh K. ( 2013 ). Flavobacterium jumunjinense sp. nov., isolated from a lagoon, and emended descriptions of Flavobacterium cheniae, Flavobacterium dongtanense and Flavobacterium gelidilacus . . Int J Syst Evol Microbiol 63, 3937–3943. [View Article] [PubMed]
    [Google Scholar]
  25. 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]
  26. 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]
  27. 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 Microbiol 62, 716–721. [View Article] [PubMed]
    [Google Scholar]
  28. Kimura M. ( 1983 ). The Neutral Theory of Molecular Evolution. Cambridge:: Cambridge University Press;. [View Article]
    [Google Scholar]
  29. Kluge A. G., Farris F. S. ( 1969 ). Quantitative phyletics and the evolution of anurans. . Syst Biol 18, 1–32. [View Article]
    [Google Scholar]
  30. 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 Microbiol 63, 3280–3286. [View Article] [PubMed]
    [Google Scholar]
  31. 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]
  32. 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. [View Article] [PubMed]
    [Google Scholar]
  33. 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]
  34. 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 Krieg N. R., Ludwig W., Whitman W. B., Hedlund B. P., Paster B. J., Staley J. T., Ward N. L., Brown D. R., Parte A. . New York:: Springer;.
     [Google Scholar]
  35. 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]
  36. Nokhal T. H., Schlegel H. G. ( 1983 ). Taxonomic study of Paracoccus denitrificans . . Int J Syst Bacteriol 33, 26–37. [View Article]
    [Google Scholar]
  37. 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]
  38. 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]
  39. 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]
  40. 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]
  41. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  42. 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]
  43. 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. [View Article] [PubMed]
    [Google Scholar]
  44. 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, F. cauense, F. terrae and F. aquatile . . Int J Syst Evol Microbiol 63, 2239–2247. [View Article] [PubMed]
    [Google Scholar]
  45. 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. [View Article] [PubMed]
    [Google Scholar]
  46. 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]
  47. 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 Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R. . Washington, DC:: American Society for Microbiology;. [View Article]
    [Google Scholar]
  48. van der Meulen H. J., Harder W., Veldkamp H. ( 1974 ). Isolation and characterization of Cytophaga flevensis sp. nov., a new agarolytic flexibacterium. . Antonie van Leeuwenhoek 40, 329–346. [View Article] [PubMed]
    [Google Scholar]
  49. 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 ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches of bacterial systematics. . Int J Syst Bacteriol 37, 463–464. [View Article]
    [Google Scholar]
  50. 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]
  51. 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 Biochem 35, 213–219. [View Article] [PubMed]
    [Google Scholar]
  52. 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]
/content/journal/ijsem/10.1099/ijs.0.065524-0
Loading
Flavobacterium oryzae sp. nov., isolated from a flooded rice field, and emended descriptions of Flavobacterium flevense, Flavobacterium yonginense and Flavobacterium myungsuense
Int J Syst Evol Microbiol 64, 3701 (2014); https://doi.org/10.1099/ijs.0.065524-0
/content/journal/ijsem/10.1099/ijs.0.065524-0
/content/journal/ijsem/10.1099/ijs.0.065524-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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