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Volume 63, Issue Pt_11

sp. nov., isolated from a freshwater spring Free

Abstract

A bacterial strain designated Orc-4 was isolated from a freshwater spring in Taiwan and characterized using the polyphasic taxonomic approach. Cells of strain Orc-4 were facultatively anaerobic, Gram-reaction-negative, poly-β-hydroxybutyrate-accumulating, non-motile rods surrounded by a thick capsule and forming cream–white colonies. Growth occurred at 15–40 °C (optimum, 25–30 °C), at pH 6.0–9.0 (optimum, pH 7.0) and with 0–1 % NaCl (optimum, 0–0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Orc-4 belonged to the genus within the family of the class and its most closely related neighbour was JS43 with sequence similarity of 97.8 %. Strain Orc-4 contained Cω7 as the predominant fatty acid. The major respiratory quinone was Q-10. The DNA G+C content of the genomic DNA was 63.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one uncharacterized aminolipid and several uncharacterized phospholipids. The DNA–DNA relatedness of strain Orc-4 with respect to recognized species of the genus was less than 48 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Orc-4 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is Orc-4 ( = BCRC 80378 = LMG 26667 = KCTC 23714).

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2013-11-01
2024-04-19
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References

  1. Anil Kumar P., Srinivas T. N. R., Sasikala Ch., Ramana Ch. V. ( 2007 ). Rhodobacter changlensis sp. nov., a psychrotolerant, phototrophic alphaproteobacterium from the Himalayas of India. . Int J Syst Evol Microbiol 57, 2568–2571. [View Article] [PubMed]
    [Google Scholar]
  2. 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]
  3. Beveridge T. J., Lawrence J. R., Murray R. G. E. ( 2007 ). Sampling and staining for light microscopy. . In Methods for General and Molecular Bacteriology, , 3rd edn., pp. 19–33. 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]
  4. 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]
  5. 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]
  6. Chen W. M., Cho N. T., Huang W. C., Young C. C., Sheu S. Y. ( 2013 ). Description of Gemmobacter fontiphilus sp. nov., isolated from a freshwater spring, reclassification of Catellibacterium nectariphilum as Gemmobacter nectariphilus comb. nov., Catellibacterium changlense as Gemmobacter changlensis comb. nov., Catellibacterium aquatile as Gemmobacter aquaticus nom. nov., Catellibacterium caeni as Gemmobacter caeni comb. nov., Catellibacterium nanjingense as Gemmobacter nanjingensis comb. nov., and emended description of the genus Gemmobacter and of Gemmobacter aquatilis . . Int J Syst Evol Microbiol 63, 470–478. [View Article] [PubMed]
    [Google Scholar]
  7. 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 (Database issue), D141–D145. [View Article] [PubMed]
    [Google Scholar]
  8. 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]
  9. 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]
  10. Ezaki T., Hashimoto Y., Yabuuchi E. ( 1989 ). Fluorometric DNA-DNA 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]
  11. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368–376. [View Article] [PubMed]
    [Google Scholar]
  12. Felsenstein, J. (1993). phylip (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  13. 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]
  14. 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]
  15. Kimura M. ( 1983 ). The Neutral Theory of Molecular Evolution. Cambridge:: Cambridge University Press;. [View Article]
    [Google Scholar]
  16. Kluge A. G., Farris F. S. ( 1969 ). Quantitative phyletics and the evolution of anurans. . Syst Zool 18, 1–32. [View Article]
    [Google Scholar]
  17. Liu Y., Xu C. J., Jiang J. T., Liu Y. H., Song X. F., Li H., Liu Z. P. ( 2010 ). Catellibacterium aquatile sp. nov., isolated from fresh water, and emended description of the genus Catellibacterium Tanaka et al. 2004. . Int J Syst Evol Microbiol 60, 2027–2031. [View Article] [PubMed]
    [Google Scholar]
  18. 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]
  19. Nokhal T. H., Schlegel H. G. ( 1983 ). Taxonomic study of Paracoccus denitrificans . . Int J Syst Bacteriol 33, 26–37. [View Article]
    [Google Scholar]
  20. Pfennig N., Trüper H. G. ( 1974 ). The phototrophic bacteria. . In Bergey’s Manual of Systematic Bacteriology, , 8th edn., pp. 24–75. Edited by Buchanan R. E., Gibbons N. E. . Baltimore:: Williams & Wilkins;.
     [Google Scholar]
  21. 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]
  22. Rothe B., Fischer A., Hirsch P., Sittig M., Stackebrandt E. ( 1987 ). The phylogenetic position of the budding bacteria Blastobacter aggregatus and Gemmobacter aquatilis gen., nov. sp. nov.. Arch Microbiol 147, 92–99. [View Article]
    [Google Scholar]
  23. 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]
  24. Schlegel H. G., Lafferty R., Krauss I. ( 1970 ). The isolation of mutants not accumulating poly-β-hydroxybutyric acid. . Arch Mikrobiol 71, 283–294. [View Article] [PubMed]
    [Google Scholar]
  25. Sheu S. Y., Sheu D. S., Sheu F. S., Chen W. M. ( 2013 ). Gemmobacter tilapiae sp. nov., a poly-β-hydroxybutyrate-accumulating bacterium isolated from a freshwater pond. . Int J Syst Evol Microbiol 63, 1550–1556. [View Article] [PubMed]
    [Google Scholar]
  26. Spiekermann P., Rehm B. H. A., Kalscheuer R., Baumeister D., Steinbüchel A. ( 1999 ). A sensitive, viable-colony staining method using Nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds. . Arch Microbiol 171, 73–80. [View Article] [PubMed]
    [Google Scholar]
  27. 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]
  28. Tanaka Y., Hanada S., Manome A., Tsuchida T., Kurane R., Nakamura K., Kamagata Y. ( 2004 ). Catellibacterium nectariphilum gen. nov., sp. nov., which requires a diffusible compound from a strain related to the genus Sphingomonas for vigorous growth. . Int J Syst Evol Microbiol 54, 955–959. [View Article] [PubMed]
    [Google Scholar]
  29. 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]
  30. 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 . J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R. . Washington, DC:: American Society for Microbiology;.
     [Google Scholar]
  31. 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 ). Report of the ad hoc committee on reconciliation of approaches of bacterial systematics. . Int J Syst Bacteriol 37, 463–464. [View Article]
    [Google Scholar]
  32. 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]
  33. Zhang J., Chen S. A., Zheng J. W., Cai S., Hang B. J., He J., Li S. P. ( 2012 ). Catellibacterium nanjingense sp. nov., a propanil-degrading bacterium isolated from activated sludge, and emended description of the genus Catellibacterium . . Int J Syst Evol Microbiol 62, 495–499. [View Article] [PubMed]
    [Google Scholar]
  34. Zheng J. W., Chen Y. G., Zhang J., Ni Y. Y., Li W. J., He J., Li S. P. ( 2011 ). Description of Catellibacterium caeni sp. nov., reclassification of Rhodobacter changlensis Anil Kumar et al. 2007 as Catellibacterium changlense comb. nov. and emended description of the genus Catellibacterium . . Int J Syst Evol Microbiol 61, 1921–1926. [View Article] [PubMed]
    [Google Scholar]
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Gemmobacterlanyuensis sp. nov., isolated from a freshwater spring
Int J Syst Evol Microbiol 63, 4039 (2013); https://doi.org/10.1099/ijs.0.052399-0
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