gen. nov., sp. nov., a member of the family , isolated from seawater Free

Abstract

A coccoid and amorphous-shaped, non-gliding, proteorhodopsin-containing, yellow bacterium, designated strain SG-18, was isolated from seawater in the western North Pacific Ocean near Japan. The strain was Gram-stain-negative, obligately aerobic, heterotrophic and oxidase-positive. It hydrolysed aesculin but not DNA, urea, gelatin or agar. Growth occurred in the presence of 1–5 % NaCl, with optimum growth at 2 % NaCl. The strain grew at 15–37 °C with an optimum temperature of 25–30 °C. The DNA G+C content of the genomic DNA of strain SG-18 was 47.0 mol% (HPLC). The predominant isoprenoid quinone was MK-6, and major cellular fatty acids were iso-C G, iso-C, iso-C 3-OH. Phylogenetic trees generated by using 16S rRNA gene sequences revealed that strain SG-18 belonged to the family and showed 92.7 % sequence similarity to the most closely related species, DOKDO 025. On the basis of phenotypic and phylogenetic features, strain SG-18 is classified as representing a novel species of a new genus within the family , for which the name gen. nov., sp. nov. is proposed. The type strain of the type species is SG-18 ( = NBRC 108814 = KCTC 23967).

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2013-05-01
2024-03-28
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References

  1. Bae S. S., Kwon K. K., Yang S. H., Lee H. S., Kim S. J., Lee J. H. ( 2007 ). Flagellimonas eckloniae gen. nov., sp. nov., a mesophilic marine bacterium of the family Flavobacteriaceae, isolated from the rhizosphere of Ecklonia kurome . . Int J Syst Evol Microbiol 57, 10501054. [View Article] [PubMed]
    [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 & Tait 1978). . Int J Syst Bacteriol 46, 128148. [View Article]
    [Google Scholar]
  3. 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]
  4. Brettar I., Christen R., Höfle M. G. ( 2004 ). Aquiflexum balticum gen. nov., sp. nov., a novel marine bacterium of the CytophagaFlavobacteriumBacteroides group isolated from surface water of the central Baltic Sea. . Int J Syst Evol Microbiol 54, 23352341. [View Article] [PubMed]
    [Google Scholar]
  5. Bruns A., Rohde M., Berthe-Corti L. ( 2001 ). Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. . Int J Syst Evol Microbiol 51, 19972006. [View Article] [PubMed]
    [Google Scholar]
  6. Cottrell M. T., Kirchman D. L. ( 2000 ). Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization. . Appl Environ Microbiol 66, 51165122. [View Article] [PubMed]
    [Google Scholar]
  7. Dittmer J. C., Lester R. L. ( 1964 ). A simple, specific spray for the detection of phospholipids on thin-layer chromatograms. . J Lipid Res 15, 126127.[PubMed]
    [Google Scholar]
  8. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  9. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  10. Glöckner F. O., Fuchs B. M., Amann R. ( 1999 ). Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. . Appl Environ Microbiol 65, 37213726.[PubMed]
    [Google Scholar]
  11. Guindon S., Gascuel O. ( 2003 ). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. . Syst Biol 52, 696704. [View Article] [PubMed]
    [Google Scholar]
  12. 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, 716721. [View Article] [PubMed]
    [Google Scholar]
  13. Kimura M. ( 1983 ). The Neutral Theory of Molecular Evolution. Cambridge:: Cambridge University Press;. [View Article]
    [Google Scholar]
  14. Kirchman D. L. ( 2002 ). The ecology of CytophagaFlavobacteria in aquatic environments. . FEMS Microbiol Ecol 39, 91100.[PubMed]
    [Google Scholar]
  15. Komagata K., Suzuki K. ( 1987 ). Lipid and cell-wall analysis in bacterial systematics. . Methods Microbiol 19, 161207. [View Article]
    [Google Scholar]
  16. Kwon K. K., Lee Y. K., Lee H. K. ( 2006 ). Costertonia aggregata gen. nov., sp. nov., a mesophilic marine bacterium of the family Flavobacteriaceae, isolated from a mature biofilm. . Int J Syst Evol Microbiol 56, 13491353. [View Article] [PubMed]
    [Google Scholar]
  17. Lane D. J. ( 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115147. Edited by Stackebrandt E., Goodfellow M. . New York:: Wiley;.
    [Google Scholar]
  18. Lee H.-S., Kwon K. K., Yang S.-H., Bae S. S., Park C. H., Kim S.-J., Lee J.-H. ( 2008 ). Description of Croceitalea gen. nov. in the family Flavobacteriaceae with two species, Croceitalea eckloniae sp. nov. and Croceitalea dokdonensis sp. nov., isolated from the rhizosphere of the marine alga Ecklonia kurome . . Int J Syst Evol Microbiol 58, 25052510. [View Article] [PubMed]
    [Google Scholar]
  19. Lucena T., Pascual J., Giordano A., Gambacorta A., Garay E., Arahal D. R., Macián M. C., Pujalte M. J. ( 2010 ). Euzebyella saccharophila gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae . . Int J Syst Evol Microbiol 60, 28712876. [View Article] [PubMed]
    [Google Scholar]
  20. Marmur J. ( 1961 ). A procedure for the isolation of deoxyribonucleic acid from microorganisms. . J Mol Biol 3, 208218. [View Article]
    [Google Scholar]
  21. 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, 159167. [View Article]
    [Google Scholar]
  22. 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, 233241. [View Article]
    [Google Scholar]
  23. Murray R. G. E., Doetsch R. N., Robinow F. ( 1994 ). Determinative and cytological light microscopy. . In Methods for General and Molecular Bacteriology, pp. 2141. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  24. Nakagawa Y., Yamasato K. ( 1993 ). Phylogenetic diversity of the genus Cytophaga revealed by 16S rRNA sequencing and menaquinone analysis. . J Gen Microbiol 139, 11551161.[PubMed] [CrossRef]
    [Google Scholar]
  25. Nedashkovskaya O. I., Suzuki M., Lee J. S., Lee K. C., Shevchenko L. S., Mikhailov V. V. ( 2009 ). Pseudozobellia thermophila gen. nov., sp. nov., a bacterium of the family Flavobacteriaceae, isolated from the green alga Ulva fenestrata . . Int J Syst Evol Microbiol 59, 806810. [View Article] [PubMed]
    [Google Scholar]
  26. O’Sullivan L. A., Weightman A. J., Fry J. C. ( 2002 ). New degenerate CytophagaFlexibacterBacteroides-specific 16S ribosomal DNA-targeted oligonucleotide probes reveal high bacterial diversity in River Taff epilithon. . Appl Environ Microbiol 68, 201210. [View Article] [PubMed]
    [Google Scholar]
  27. Reichenbach H. ( 1992 ). The order Cytophagales . . In The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, , 2nd edn., pp. 36313675. Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K. H. . New York:: Springer;.
    [Google Scholar]
  28. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  29. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc.;
  30. 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]
  31. 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]
  32. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. ( 1991 ). 16S ribosomal DNA amplification for phylogenetic study. . J Bacteriol 173, 697703.[PubMed]
    [Google Scholar]
  33. Worliczek H. L., Kämpfer P., Rosengarten R., Tindall B. J., Busse H. J. ( 2007 ). Polar lipid and fatty acid profiles – re-vitalizing old approaches as a modern tool for the classification of mycoplasmas?. Syst Appl Microbiol 30, 355370. [View Article] [PubMed]
    [Google Scholar]
  34. Yoon B. J., Oh D. C. ( 2012 ). Spongiibacterium flavum gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the marine sponge Halichondria oshoro, and emended descriptions of the genera Croceitalea and Flagellimonas . . Int J Syst Evol Microbiol 62, 11581164. [View Article] [PubMed]
    [Google Scholar]
  35. Yoshizawa S., Kawanabe A., Ito H., Kandori H., Kogure K. ( 2012 ). Diversity and functional analysis of proteorhodopsin in marine Flavobacteria . . Environ Microbiol 14, 12401248. [View Article] [PubMed]
    [Google Scholar]
  36. Yu Y., Li H. R., Zeng Y. X., Sun K., Chen B. ( 2012 ). Pricia antarctica gen. nov., sp. nov., a member of the family Flavobacteriaceae, isolated from Antarctic intertidal sediment. . Int J Syst Evol Microbiol 62, 22182223. [View Article] [PubMed]
    [Google Scholar]
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