1887

Abstract

Two Gram-negative, non-fermentative, non-denitrifying, non-pigmented, rod-shaped bacteria that were motile by means of polar flagella, designated strains KMM 330 and KMM 331, were isolated from a deep-sea sponge specimen and subjected to a polyphasic taxonomic study. The new isolates exhibited 16S rRNA gene sequence similarity of 99·9 %, and their mean level of DNA–DNA relatedness was 82 %. Phylogenetic analysis based on their 16S rRNA gene sequences placed the strains within the genus as an independent deep clade. Strain KMM 330 shared highest sequence similarity (96·3 %) with each of NRIC 0180, AJ 2129 and IAM 13000; sequence similarity to other recognized species of the genus was below 95·7 %. The marine sponge isolates KMM 330 and KMM 331 could be distinguished from the other recognized species based on a unique combination of their phenotypic characteristics, including growth in 8 or 10 % NaCl, the absence of pigments, the inability to denitrify and lack of carbohydrate utilization. On the basis of phylogenetic analysis, physiological and biochemical characterization, strains KMM 330 and KMM 331 should be classified as a novel species of the genus , for which the name sp. nov. is proposed. The type strain is KMM 330 (=JCM 12285=NRIC 0583=CCUG 46540).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.63176-0
2005-03-01
2019-10-17
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/55/2/ijs550919.html?itemId=/content/journal/ijsem/10.1099/ijs.0.63176-0&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, 249–251.[CrossRef]
    [Google Scholar]
  2. Anzai, Y., Kim, H., Park, J.-Y., Wakabayashi, H. & Oyaizu, H. ( 2000; ). Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 50, 1563–1589.[CrossRef]
    [Google Scholar]
  3. Baumann, P., Bouditch, R. D., Baumann, L. & Beaman, B. ( 1983; ). Taxonomy of marine Pseudomonas species: P. stanieri sp. nov.; P. perfectomarina sp. nov., nom. rev.; P. nautica; and P. doudoroffii. Int J Syst Bacteriol 33, 857–865.[CrossRef]
    [Google Scholar]
  4. Bennasar, A., Rosselló-Mora, R., Lalucat, J. & Moore, E. R. B. ( 1996; ). 16S rDNA sequence analysis relative to genomovars of Pseudomonas stutzeri and proposal of Pseudomonas balearica sp. nov. Int J Syst Bacteriol 49, 200–205.
    [Google Scholar]
  5. Brown, G. R., Sutcliffe, I. C. & Cummings, S. P. ( 2001; ). Reclassification of [Pseudomonas] doudoroffii ( Baumann et al., 1983 ) into the genus Oceanomonas gen. nov. as Oceanomonas doudoroffii comb. nov., and description of a phenol-degrading bacterium from estuarine water as Oceanomonas baumannii sp. nov. Int J Syst Evol Microbiol 51, 67–72.
    [Google Scholar]
  6. De Ley, J., Cattoir, H. & Reynaerts, A. ( 1970; ). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 133–142.[CrossRef]
    [Google Scholar]
  7. 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]
  8. 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]
  9. Hauser, E., Kämpfer, P. & Busse, H.-J. ( 2004; ). Pseudomonas psychrotolerans sp. nov. Int J Syst Evol Microbiol 54, 1633–1637.[CrossRef]
    [Google Scholar]
  10. Jukes, T. H. & Cantor, C. R. ( 1969; ). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21–132. Edited by H. N. Munro. New York: Academic Press.
  11. Kersters, K., Ludwig, W., Vancanneyt, M., De Vos, P., Gillis, M. & Schleifer, K.-H. ( 1996; ). Recent changes in the classification of pseudomonads: an overview. Syst Appl Microbiol 19, 465–477.[CrossRef]
    [Google Scholar]
  12. King, E. O., Ward, M. K. & Rainey, D. E. ( 1954; ). Two simple media for demonstration of pyocyanin and fluorescein. J Lab Clin Med 44, 301–307.
    [Google Scholar]
  13. Leifson, E. ( 1963; ). Determination of carbohydrate metabolism of marine bacteria. J Bacteriol 85, 1183–1184.
    [Google Scholar]
  14. Marmur, J. ( 1961; ). A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3, 208–218.[CrossRef]
    [Google Scholar]
  15. Marmur, J. & Doty, P. ( 1962; ). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5, 109–118.[CrossRef]
    [Google Scholar]
  16. Moore, E. R. B., Mau, M., Arnscheidt, A., Böttger, E. C., Hutson, R. A., Collins, M. D., van de Peer, Y., de Wachter, R. & Timmis, K. T. ( 1996; ). The determination and comparison of the 16S rDNA gene sequence of species of the genus Pseudomonas (sensu stricto) and estimation of the natural generic relationships. Syst Appl Microbiol 19, 478–492.[CrossRef]
    [Google Scholar]
  17. Owen, J., Hill, L. R. & Lapage, S. P. ( 1969; ). Determination of DNA base composition from melting profiles in dilute buffers. Biopolymers 7, 503–516.[CrossRef]
    [Google Scholar]
  18. Oyaizu, H. & Komagata, K. ( 1983; ). Grouping of Pseudomonas species on the basis of cellular fatty acid composition and the quinone system with special reference to the existence of 3-hydroxy fatty acids. J Gen Appl Microbiol 29, 17–40.[CrossRef]
    [Google Scholar]
  19. Palleroni, N. J. ( 1984; ). Genus I. Pseudomonas Migula 1984, 237AL. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 141–199. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
  20. Pearson, W. & Lipman, D. J. ( 1988; ). Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 85, 2444–2448.[CrossRef]
    [Google Scholar]
  21. Peix, A., Rivas, R., Mateos, P. F., Martínez-Molina, E., Rodríguez-Barrueco, C. & Velásquez, E. ( 2003; ). Pseudomonas rhizosphaerae sp. nov., a novel species that actively solubilizes phosphate in vitro. Int J Syst Evol Microbiol 53, 2067–2072.[CrossRef]
    [Google Scholar]
  22. Rainey, P. B., Thompson, I. P. & Palleroni, N. J. ( 1994; ). Genome and fatty acid analysis of Pseudomonas stutzeri. Int J Syst Bacteriol 44, 54–61.[CrossRef]
    [Google Scholar]
  23. Rosselló, R. A., García-Valdés, E., Lalucat, J. & Ursing, J. ( 1991; ). Genotypic and phenotypic diversity of Pseudomonas stutzeri. Syst Appl Microbiol 14, 150–157.[CrossRef]
    [Google Scholar]
  24. Rosselló-Mora, R. A., García-Valdés, E. & Lalucat, J. ( 1993; ). Taxonomic relationship between Pseudomonas perfectomarina ZoBell and Pseudomonas stutzeri. Int J Syst Bacteriol 43, 852–854.[CrossRef]
    [Google Scholar]
  25. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  26. Shida, O., Takagi, H., Kadowaki, K., Nakamura, L. K. & Komagata, K. ( 1997; ). Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus. Int J Syst Bacteriol 47, 289–298.[CrossRef]
    [Google Scholar]
  27. Smibert, R. M. & Krieg, N. R. ( 1994; ). Phenotypic characterization. In Methods for General and Molecular Bacteriology, pp. 607–655. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
  28. Stackebrandt, E. & Goebel, B. M. ( 1994; ). Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846–849.[CrossRef]
    [Google Scholar]
  29. Svetashev, V. I., Vysotskii, M. V., Ivanova, E. P. & Mikhailov, V. V. ( 1995; ). Cellular fatty acids of Alteromonas species. Syst Appl Microbiol 18, 37–43.[CrossRef]
    [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, 4876–4882.[CrossRef]
    [Google Scholar]
  31. Uchino, M., Kosako, Y., Uchimura, T. & Komagata, K. ( 2000; ). Emendation of Pseudomonas straminea Iizuka and Komagata 1963. Int J Syst Evol Microbiol 50, 1513–1519.[CrossRef]
    [Google Scholar]
  32. Uchino, M., Shida, O., Uchimura, T. & Komagata, K. ( 2001; ). Recharacterization of Pseudomonas fulva Iizuka and Komagata 1963, and proposals of Pseudomonas parafulva sp. nov. and Pseudomonas cremoricolorata sp. nov. J Gen Appl Microbiol 46, 247–261.
    [Google Scholar]
  33. Vaskovsky, V. E. & Terekhova, T. A. ( 1979; ). HPTLC of phospholipid mixtures containing phosphatidylglycerol. J High Resolut Chromatogr 2, 671–672.[CrossRef]
    [Google Scholar]
  34. Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors ( 1987; ). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.[CrossRef]
    [Google Scholar]
  35. Wilkinson, S. G. ( 1988; ). Gram-negative bacteria. In Microbial Lipids, vol. I, pp. 299–488. Edited by C. Ratledge & S. G. Wilkinson. London: Academic Press.
  36. Yoon, J. H., Kim, H., Kang, K. H., Oh, T. K. & Park, Y. H. ( 2003; ). Transfer of Pseudomonas elongata Humm 1946 to the genus Microbulbifer as Microbulbifer elongatus comb. nov. Int J Syst Evol Microbiol 53, 1357–1361.[CrossRef]
    [Google Scholar]
  37. Yumoto, I., Yamazaki, K., Hishinuma, M., Nodasaka, Y., Suemori, A., Nakajima, K., Inoue, N. & Kawasaki, K. ( 2001; ). Pseudomonas alcaliphila sp. nov., a novel facultatively psychrophilic alkaliphile isolated from seawater. Int J Syst Evol Microbiol 51, 349–355.
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.63176-0
Loading
/content/journal/ijsem/10.1099/ijs.0.63176-0
Loading

Data & Media loading...

Supplements

Transmission electron micrographs of cells of sp. nov. KMM 330 . Bar, 1 µm.

IMAGE

Two-dimensional thin-layer chromatogram of polar lipids of strain KMM 330 . DPG, Diphosphatidylglycerol, PE, phosphatidylethanolamine, PG, phosphatidylglycerol, PL, unknown phospholipid. The same pattern was observed for strain KMM 331.

IMAGE

Phylogenic relationships of isolates KMM 330 and KMM 331 and some related species on the basis of 16S rRNA gene sequences. The branching pattern was generated by the maximum-likelihood method. [PDF](15 KB)

PDF

Most Cited This Month

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