1887

Abstract

A Gram-staining-negative, catalase- and oxidase-positive, strictly aerobic, rod-shaped bacterial strain isolated from fresh water in Trabzon, Turkey and designated MK3 was characterized by phenotypic and molecular methods in order to determine its phylogenetic position. On the basis of 16S rRNA gene sequence similarity, strain MK3 was shown to belong to the genus , being most closely related to CECT 7184 (93.6 %). Sequence similarity with other species of the genus with validly published names was less than 91.6 %. Phenotypic and chemotaxonomic data supported the affiliation of strain MK3 to the genus . The only menaquinone was MK-6; the major fatty acids were iso-C (45.2 %), summed feature 9 (C 10-methyl and/or iso-Cω9; 20.4 %) and summed feature 3 (Cω7 and/or Cω6; 13.3 %) and the major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid and two unidentified phospholipids. The G+C content of the genomic DNA was 38.6 mol%. The results of physiological and biochemical tests allowed strain MK3 to be distinguished phenotypically from CECT 7184. Strain MK3, therefore, represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is MK3 ( = LMG 26441 = NCCB 100384). An emended description of is also proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.040394-0
2013-06-01
2024-05-13
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/6/2075.html?itemId=/content/journal/ijsem/10.1099/ijs.0.040394-0&mimeType=html&fmt=ahah

References

  1. Aslam Z., Im W. T., Kim M. K., Lee S. T. ( 2005 ). Flavobacterium granuli sp. nov., isolated from granules used in a wastewater treatment plant. . Int J Syst Evol Microbiol 55, 747751. [View Article] [PubMed]
    [Google Scholar]
  2. Atlas R. M. ( 1993 ). Handbook of Microbiological Media. Edited by Parks L. C. . Boca Raton, FL:: CRC Press;.
    [Google Scholar]
  3. Baek S. H., Im W. T., Oh H. W., Lee J.-S., Oh H. M., Lee S. T. ( 2006 ). Brevibacillus ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field. . Int J Syst Evol Microbiol 56, 26652669. [View Article] [PubMed]
    [Google Scholar]
  4. Bergey D. H., Harrison F. C., Breed R. S., Hammer B. W., Huntoon F. M. (editors) ( 1923 ). Bergey’s Manual of Determinative Bacteriology. Baltimore:: The Williams & Wilkins Co;.
    [Google Scholar]
  5. 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. 112154. Edited by Whitman W. . Baltimore:: The Williams & Wilkins Co;.
    [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, 128148. [View Article]
    [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, 10491070. [View Article] [PubMed]
    [Google Scholar]
  8. 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, 18611868.[PubMed]
    [Google Scholar]
  9. Bowman J. P., Cavanagh J., Austin J. J., Sanderson K. ( 1996 ). Novel Psychrobacter species from Antarctic ornithogenic soils. . Int J Syst Bacteriol 46, 841848. [View Article] [PubMed]
    [Google Scholar]
  10. Brosius J., Palmer M. L., Kennedy P. J., Noller H. F. ( 1978 ). Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . . Proc Natl Acad Sci U S A 75, 48014805. [View Article] [PubMed]
    [Google Scholar]
  11. Chun J., Lee J.-H., Jung Y., Kim M., Kim S., Kim B. K., Lim Y.-W. ( 2007 ). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. . Int J Syst Evol Microbiol 57, 22592261. [View Article] [PubMed]
    [Google Scholar]
  12. Degryse E., Glansdorff N., Piérard A. ( 1978 ). A comparative analysis of extreme thermophilic bacteria belonging to the genus Thermus . . Arch Microbiol 117, 189196. [View Article] [PubMed]
    [Google Scholar]
  13. Dussault H. P. ( 1955 ). An improved technique for staining red halophilic bacteria. . J Bacteriol 70, 484485.[PubMed]
    [Google Scholar]
  14. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  15. Fitch W. M. ( 1971 ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [View Article]
    [Google Scholar]
  16. 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, 9598.
    [Google Scholar]
  17. Horn M. A., Ihssen J., Matthies C., Schramm A., Acker G., Drake H. L. ( 2005 ). Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov., Paenibacillus anaericanus sp. nov. and Paenibacillus terrae strain MH72, N2O-producing bacteria isolated from the gut of the earthworm Aporrectodea caliginosa . . Int J Syst Evol Microbiol 55, 12551265. [View Article] [PubMed]
    [Google Scholar]
  18. 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, 12351243.[PubMed]
    [Google Scholar]
  19. 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, 16451649. [View Article] [PubMed]
    [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, 111120. [View Article] [PubMed]
    [Google Scholar]
  21. Kirchman D. L. ( 2002 ). The ecology of Cytophaga–Flavobacteria in aquatic environments. . FEMS Microbiol Ecol 39, 91100.[PubMed]
    [Google Scholar]
  22. Kristjansson J. K., Alfredsson G. A. ( 1983 ). Distribution of Thermus spp. in Icelandic hot springs and a thermal gradient. . Appl Environ Microbiol 45, 17851789.[PubMed]
    [Google Scholar]
  23. Kuykendall L. D., Roy M. A., O’Neill J. J., Devine T. E. ( 1988 ). Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradirhyzobium japonicum . . Int J Syst Bacteriol 38, 358361. [View Article]
    [Google Scholar]
  24. Mandel M., Marmur J. ( 1968 ). Use of ultraviolet absorbance-temperature profile for determining the guanine plus cytosine content of DNA. . Methods Enzymol 12, 195206. [View Article]
    [Google Scholar]
  25. Marmur J. ( 1961 ). A procedure for the isolation of deoxyribonucleic acid from microorganisms. . J Mol Biol 3, 208218. [View Article]
    [Google Scholar]
  26. McCammon S. A., Bowman J. P. ( 2000 ). Taxonomy of Antarctic Flavobacterium species: description of Flavobacterium gillisiae sp. nov., Flavobacterium tegetincola sp. nov., and Flavobacterium xanthum sp. nov., nom. rev. and reclassification of [Flavobacterium] salegens as Salegentibacter salegens gen. nov., comb. nov. . Int J Syst Evol Microbiol 50, 10551063. [View Article] [PubMed]
    [Google Scholar]
  27. Miller L. T. ( 1982 ). Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. . J Clin Microbiol 16, 584586.[PubMed]
    [Google Scholar]
  28. 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, 37563758.[PubMed]
    [Google Scholar]
  29. Ryu S. H., Park M., Jeon Y., Lee J. R., Park W., Jeon C. O. ( 2007 ). Flavobacterium filum sp. nov., isolated from a wastewater treatment plant in Korea. . Int J Syst Evol Microbiol 57, 20262030. [View Article] [PubMed]
    [Google Scholar]
  30. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  31. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  32. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  33. 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, 519526. [View Article] [PubMed]
    [Google Scholar]
  34. Tamura K., Dudley J., Nei M., Kumar S. ( 2007 ). MEGA4: Molecular Evolutionary Genetics Analysis (mega) software version 4.0. . Mol Biol Evol 24, 15961599. [View Article] [PubMed]
    [Google Scholar]
  35. 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, 48764882. [View Article] [PubMed]
    [Google Scholar]
  36. Tindall B. J. ( 1990a ). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. . Syst Appl Microbiol 13, 128130. [View Article]
    [Google Scholar]
  37. Tindall B. J. ( 1990b ). Lipid composition of Halobacterium lacusprofundi . . FEMS Microbiol Lett 66, 199202. [View Article]
    [Google Scholar]
  38. Tindall B. J., Sikorski J., Smibert R. M., Krieg N. R. ( 2007 ). Phenotypic characterization and the principles of comparative systematics. . In Methods for General and Molecular Microbiology, , 3rd edn., pp. 330393. Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G., Schmidt T. M., Snyder L. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  39. Van Trappen S., Mergaert J., Van Eygen S., Dawyndt P., Cnockaert M. C., Swings J. ( 2002 ). Diversity of 746 heterotrophic bacteria isolated from microbial mats from ten Antarctic lakes. . Syst Appl Microbiol 25, 603610. [View Article] [PubMed]
    [Google Scholar]
  40. Vela A. I., Fernandez A., Sánchez-Porro C., Sierra E., Mendez M., Arbelo M., Ventosa A., Domínguez L., Fernández-Garayzábal J. F. ( 2007 ). Flavobacterium ceti sp. nov., isolated from beaked whales (Ziphius cavirostris). . Int J Syst Evol Microbiol 57, 26042608. [View Article] [PubMed]
    [Google Scholar]
  41. Yi H., Chun J. ( 2006 ). Flavobacterium weaverense sp. nov. and Flavobacterium segetis sp. nov., novel psychrophiles isolated from the Antarctic. . Int J Syst Evol Microbiol 56, 12391244. [View Article] [PubMed]
    [Google Scholar]
  42. Yoon J.-H., Kang S.-J., Oh T.-K. ( 2006 ). Flavobacterium soli sp. nov., isolated from soil. . Int J Syst Evol Microbiol 56, 9971000. [View Article] [PubMed]
    [Google Scholar]
  43. 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, 29212925. [View Article] [PubMed]
    [Google Scholar]
  44. Zhu F., Wang S., Zhou P. ( 2003 ). Flavobacterium xinjiangense sp. nov. and Flavobacterium omnivorum sp. nov., novel psychrophiles from the China No. 1 glacier. . Int J Syst Evol Microbiol 53, 853857. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.040394-0
Loading
/content/journal/ijsem/10.1099/ijs.0.040394-0
Loading

Data & Media loading...

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