1887

Abstract

A bacterial strain, designated Npb-02, was isolated from a freshwater river in Taiwan and characterized in a taxonomic study using a polyphasic approach. Cells of strain Npb-02 were Gram-stain-negative, aerobic, poly-β-hydroxybutyrate-accumulating, rod-shaped and non-motile. Growth occurred at 15–40 °C (optimum 25–30 °C), at pH 7.0–8.0 (optimum pH 7.0) and with 0–1 % NaCl (optimum 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Npb-02 belonged to the genus and was most closely related to DS-28 with sequence similarity of 98.3 %. Strain Npb-02 contained summed feature 3 (comprising Cω7 and/or Cω6) and C as the major fatty acids. The major respiratory quinone was Q-8.The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminophospholipid and an uncharacterized phospholipid. The genomic DNA G+C content of strain Npb-02 was 64.1 mol%. The DNA–DNA hybridization values for strain Npb-02 with DS-28, 389 and GR13 were less than 25 %. On the basis of phylogenetic inference and phenotypic data, strain Npb-02 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is Npb-02 ( = BCRC 80887 = LMG 28419 = KCTC 42195).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000467
2015-10-01
2024-12-14
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/10/3634.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000467&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 249251 [View Article] [PubMed].
    [Google Scholar]
  2. 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. 1933. Edited by Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R. Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  3. 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]. [CrossRef]
    [Google Scholar]
  4. Breznak J.A., Costilow R.N. ( 2007;). Physicochemical factors in growth. . In Methods for General and Molecular Bacteriology , 3rd edn.., pp. 309329. Edited by 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 17291735 [View Article] [PubMed].
    [Google Scholar]
  6. Chou Y.J., Chou J.H., Lin M.C., Arun A.B., Young C.C., Chen W.M. ( 2008;). Vogesella perlucida sp. nov., a non-pigmented bacterium isolated from spring water. Int J Syst Evol Microbiol 58 26772681 [View Article] [PubMed].
    [Google Scholar]
  7. Chou J.H., Chou Y.J., Arun A.B., Young C.C., Chen C.A., Wang J.T., Chen W.M. ( 2009;). Vogesella lacus sp. nov., isolated from a soft-shell turtle culture pond. Int J Syst Evol Microbiol 59 26292632 [View Article] [PubMed].
    [Google Scholar]
  8. 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 D141D145 [View Article] [PubMed].
    [Google Scholar]
  9. Collins M.D. ( 1994;). Isoprenoid quinones. . In Chemical Methods in Prokaryotic Systematics, pp. 265309. Edited by Goodfellow M., O'Donnell A. G. Chichester: Wiley;.
    [Google Scholar]
  10. Embley T.M., Wait R. ( 1994;). Structural lipids of eubacteria. . In Chemical Methods in Prokaryotic Systematics, pp. 121161. Edited by Goodfellow M., O'Donnell A. G. Chichester: Wiley;.
    [Google Scholar]
  11. 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 224229 [View Article].
    [Google Scholar]
  12. Felsenstein J. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 368376 [View Article] [PubMed].
    [Google Scholar]
  13. Felsenstein J. ( 1993;). phylip (phylogeny inference package) version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington; Seattle, USA:.
    [Google Scholar]
  14. Grimes D.J., Woese C.R., MacDonell M.T., Colwell R.R. ( 1997;). Systematic study of the genus Vogesella gen. nov. and its type species, Vogesella indigofera comb. nov. Int J Syst Bacteriol 47 1927 [View Article] [PubMed].
    [Google Scholar]
  15. 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]
  16. Jørgensen N.O.G., Brandt K.K., Nybroe O., Hansen M. ( 2010;). Vogesella mureinivorans sp. nov., a peptidoglycan-degrading bacterium from lake water. Int J Syst Evol Microbiol 60 24672472 [View Article] [PubMed].
    [Google Scholar]
  17. 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]
  18. Kimura M. ( 1983). The Neutral Theory of Molecular Evolution Cambridge: [View Article] Cambridge University Press;.
    [Google Scholar]
  19. Kluge A.G., Farris J.S. ( 1969;). Quantitative phyletics and the evolution of anurans. Syst Zool 18 132 [View Article].
    [Google Scholar]
  20. Krieg N.R. ( 2005;). Genus Vogesella . . In Bergey's Manual of Systematic Bacteriology , 2nd edn., vol. 2., pp. 858859. Edited by Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. New York: [View Article] Springer;.
    [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. 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]
  23. Saitou N., Nei M. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 406425 [PubMed].
    [Google Scholar]
  24. Sasser M. ( 1990). Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI Inc;.
    [Google Scholar]
  25. Schlegel H.G., Lafferty R., Krauss I. ( 1970;). The isolation of mutants not accumulating poly-β-hydroxybutyric acid. Arch Mikrobiol 71 283294 [View Article] [PubMed].
    [Google Scholar]
  26. Sheu S.Y., Chen J.C., Young C.C., Chen W.M. ( 2013;). Vogesella fluminis sp. nov., isolated from a freshwater river, and emended description of the genus Vogesella. Int J Syst Evol Microbiol 63 30433049 [View Article] [PubMed].
    [Google Scholar]
  27. 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 7380 [View Article] [PubMed].
    [Google Scholar]
  28. Subhash Y., Tushar L., Sasikala Ch., Ramana ChV. ( 2013;). Vogesella alkaliphila sp. nov., isolated from an alkaline soil, and emended description of the genus Vogesella. Int J Syst Evol Microbiol 63 23382343 [View Article] [PubMed].
    [Google Scholar]
  29. 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 27312739 [View Article] [PubMed].
    [Google Scholar]
  30. 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]
  31. 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. 330393. Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R. Washington, D.C.: [View Article] American Society for Microbiology;.
    [Google Scholar]
  32. 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 463464 [View Article].
    [Google Scholar]
  33. 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]
  34. 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 213219 [View Article] [PubMed].
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.000467
Loading
/content/journal/ijsem/10.1099/ijsem.0.000467
Loading

Data & Media loading...

Supplements

Supplementary Data

PDF
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