sp. nov., a facultatively anaerobic bacterium isolated from a tidal flat sediment Free

Abstract

A novel Gram-negative, facultatively anaerobic, non-sporulating, non-motile, catalase- and oxidase-positive, rod-shaped bacterium (strain JSM 061001) was isolated from a tidal flat in the South China Sea, China. Growth occurred with 0–5 % (w/v) NaCl [optimum, 0.5–1 % (w/v) NaCl], at pH 5.0–10.0 (optimum, pH 7.0) and at 4–35 °C (optimum, 25–30 °C). The major cellular fatty acids were C, cyclo C, C 7 and C. Strain JSM 061001 contained ubiquinone Q-8 as the predominant respiratory quinone, and phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as the polar lipids. The genomic DNA G+C content was 65.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 061001 belongs to the family and was related most closely to the type strains of the two recognized species of the genus . The three strains formed a robust cluster in the neighbour-joining, maximum-parsimony and maximum-likelihood phylogenetic trees. Levels of DNA–DNA relatedness between strain JSM 061001 and the type strains of and were 15.8 and 10.5 %, respectively. The combination of phylogenetic analysis, DNA–DNA hybridization data, phenotypic characteristics and chemotaxonomic differences supported the view that strain JSM 061001 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is JSM 061001 (=CCTCC AA207034=KCTC 22165).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.002949-0
2009-03-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/59/3/521.html?itemId=/content/journal/ijsem/10.1099/ijs.0.002949-0&mimeType=html&fmt=ahah

References

  1. Blümel, S., Mark, B., Busse, H.-J., Kämpfer, P. & Stolz, A.(2001).Pigmentiphaga kullae gen. nov., sp. nov., a novel member of the family Alcaligenaceae with the ability to decolorize azo dyes aerobically. Int J Syst Evol Microbiol 51, 1867–1871.[CrossRef] [Google Scholar]
  2. Chen, Y.-G., Cui, X.-L., Pukall, R., Li, H.-M., Yang, Y.-L., Xu, L.-H., Wen, M.-L., Peng, Q. & Jiang, C.-L.(2007).Salinicoccus kunmingensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, southwest China. Int J Syst Evol Microbiol 57, 2327–2332.[CrossRef] [Google Scholar]
  3. Cowan, S. T. & Steel, K. J.(1965).Manual for the Identification of Medical Bacteria. London: Cambridge University Press.
  4. Cui, X.-L., Mao, P.-H., Zeng, M., Li, W.-J., Zhang, L.-P., Xu, L.-H. & Jiang, C.-L.(2001).Streptomonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol 51, 357–363. [Google Scholar]
  5. De Ley, J., Segers, P., Kersters, K., Mannheim, W. & Lievens, A.(1986). Intra- and intergeneric similarities of the Bordetella ribosomal ribonucleic acid cistrons: proposal for a new family, Alcaligenaceae. Int J Syst Bacteriol 36, 405–414.[CrossRef] [Google Scholar]
  6. 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.[CrossRef] [Google Scholar]
  7. Felsenstein, J.(1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368–376.[CrossRef] [Google Scholar]
  8. Felsenstein, J.(1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef] [Google Scholar]
  9. Felsenstein, J.(1993).phylip (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  10. Gregersen, T.(1978). Rapid method for distinction of Gram-negative from Gram-positive bacteria. Eur J Appl Microbiol Biotechnol 5, 123–127.[CrossRef] [Google Scholar]
  11. Groth, I., Schumann, P., Weiss, N., Martin, K. & Rainey, F. A.(1996).Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol 46, 234–239.[CrossRef] [Google Scholar]
  12. Hopwood, D. A., Bibb, M. J., Chater, K. F., Kieser, T., Bruton, C. J., Kieser, H. M., Lydiate, D. J., Smith, C. P. & Ward, J. M.(1985). Preparation of chromosomal, plasmid and phage DNA. In Genetic Manipulation of Streptomyces. A Laboratory Manual, pp. 79–80. Norwich: John Innes Foundation.
  13. Kimura, M.(1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120.[CrossRef] [Google Scholar]
  14. Kluge, A. G. & Farris, J. S.(1969). Quantitative phyletics and the evolution of anurans. Syst Zool 18, 1–32.[CrossRef] [Google Scholar]
  15. Komagata, K. & Suzuki, K.(1987). Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161–207. [Google Scholar]
  16. Kumar, S., Tamura, K. & Nei, M.(2004).mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef] [Google Scholar]
  17. Lányí, B.(1987). Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19, 1–67. [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.[CrossRef] [Google Scholar]
  19. 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, 233–241.[CrossRef] [Google Scholar]
  20. Saitou, N. & Nei, M.(1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425. [Google Scholar]
  21. Sasser, M.(1990).Identification of bacteria by gas chromatography of cellular fatty acids. Newark, DE: MIDI Inc.
  22. Shirling, E. B. & Gottlieb, D.(1966). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313–340.[CrossRef] [Google Scholar]
  23. 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.[CrossRef] [Google Scholar]
  24. 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 to bacterial systematics. Int J Syst Bacteriol 37, 463–464.[CrossRef] [Google Scholar]
  25. Yoon, J.-H., Kang, S.-J., Kim, W. & Oh, T.-K.(2007).Pigmentiphaga daeguensis sp. nov., isolated from wastewater of a dye works, and emended description of the genus Pigmentiphaga. Int J Syst Evol Microbiol 57, 1188–1191.[CrossRef] [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.002949-0
Loading
/content/journal/ijsem/10.1099/ijs.0.002949-0
Loading

Data & Media loading...

Supplements

Maximum-parsimony and maximum-likelihood phylogenetic trees based on 16S rRNA gene sequences showing the position of strain JSM 061001 among other related taxa. [PDF](20 KB)

PDF

Fatty acid compositions of strain JSM 061001 and members of the genus . [PDF](63 KB)

PDF

Most cited Most Cited RSS feed