1887

Abstract

The aim of this study was to clarify the taxonomic position of the nitrogen-fixing and hydrogen-oxidizing bacteria strains IAM 12599, IAM 12664 and IAM 12665 and IAM 14368. It was found that the type strain of , IAM 12599, showed 99·9 and 96·1 % 16S rRNA gene sequence similarity to strains IAM 12665 and IAM 12664, respectively. A comparison using DNA–DNA hybridization suggested that strains IAM 12599 and IAM 12665 belong to a single species (89·7 %) and that strain IAM 12664 (35·1 %) forms a separate species. The phenotypic characteristics also support the conclusion that these bacteria should be identified as two species of a new genus: gen. nov., comb. nov. (type strain IAM 12599=DSM 1122=LMG 3321=ATCC 29712; reference strain IAM 12665=DSM 1123=LMG 3325=ATCC 29714) and sp. nov. (type strain IAM 12664=DSM 1124=LMG 3324=ATCC 29713). IAM 14368 was found to be closely related to the phototrophic bacterium , with 96·8 % 16S rRNA gene sequence similarity, but the two bacteria are quite different with respect to their metabolism and some significant phenotypic characteristics, suggesting that they cannot be included in a single genus. Further studies on their gene sequences, G+C content of the DNA and cellular fatty acid composition confirm that should be reclassified: the name gen. nov., comb. nov. is proposed, with the type strain IAM 14368 (=LMG 2256=ATCC 15946).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.63733-0
2005-11-01
2019-10-22
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/55/6/2419.html?itemId=/content/journal/ijsem/10.1099/ijs.0.63733-0&mimeType=html&fmt=ahah

References

  1. Amakata, D., Matsuo, Y., Shimono, K., Park, J. K., Yun, C. S., Matsuda, H., Yokota, A. & Kawamukai, M. ( 2005; ). Mitsuaria chitosanitabida gen. nov., sp. nov., an aerobic, chitosanase-producing member of the ‘Betaproteobacteria’. Int J Syst Evol Microbiol 55, 1927–1932.[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. Barraquio, W. L., Padre, B. C., Jr, Watanabe, I. & Knowles, R. ( 1986; ). Nitrogen fixation by Pseudomonas saccharophila Douforoff ATCC 15946. J Gen Microbiol 132, 237–241.
    [Google Scholar]
  4. Doudoroff, M. ( 1940; ). The oxidative assimilation of sugars and related substances by Pseudomonas saccharophila with a contribution to the problem of the direct respiration of di- and polysaccharides. Enzymologia 9, 59–72.
    [Google Scholar]
  5. 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]
  6. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  7. Hiraishi, A., Ueda, Y., Ishihara, I. & Kamata, H. ( 1996; ). Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42, 457–469.[CrossRef]
    [Google Scholar]
  8. Kersters, K. & De Ley, J. ( 1984; ). Genus Alcaligenes Castellani and Chalmers 1919, 936AL. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 361–373. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
  9. 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]
  10. Malik, K. A., Jung, C., Claus, D. & Schlegel, H. G. ( 1981; ). Nitrogen fixation by the hydrogen-oxidizing bacterium Alcaligenes latus. Arch Microbiol 129, 254–256.[CrossRef]
    [Google Scholar]
  11. Marmur, J. ( 1961; ). A procedure of the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3, 208–218.[CrossRef]
    [Google Scholar]
  12. Moulin, L., Munive, A., Dreyfus, B. & Boivin-Masson, C. ( 2001; ). Nodulation of legumes by members of the β-subclass of Proteobacteria. Nature 411, 948–950.[CrossRef]
    [Google Scholar]
  13. Palleroni, N. J. ( 1984; ). Genus I. Pseudomonas Migula 1894, 237AL. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 141–199. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
  14. Palleroni, N. J. & Palleroni, A. ( 1978; ). Alcaligenes latus, a new species of hydrogen-utilizing bacteria. Int J Syst Bacteriol 28, 416–424.[CrossRef]
    [Google Scholar]
  15. Poly, F., Monrozier, L. J. & Bally, R. ( 2001; ). Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. Res Microbiol 152, 95–103.[CrossRef]
    [Google Scholar]
  16. Rosado, A. S., Duarte, G. F., Seldin, L. & Van Elsas, L. D. ( 1998; ). Genetic diversity of nifH gene sequences in Paenibacillus azotofixans strains and soil samples analyzed by denaturing gradient gel electrophoresis of PCR-amplified gene fragments. Appl Environ Microbiol 64, 2770–2779.
    [Google Scholar]
  17. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  18. 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]
  19. Suyama, T., Shigematsu, T., Takaichi, S., Nodasaka, Y., Fujikawa, S., Hosoya, H., Tokiwa, Y., Kanagawa, T. & Hanada, S. ( 1999; ). Roseateles depolymerans gen. nov., sp. nov., a new bacteriochlorophyll a-containing obligate aerobe belonging to the β-subclass of the Proteobacteria. Int J Syst Bacteriol 49, 449–457.[CrossRef]
    [Google Scholar]
  20. Swofford, D. L. ( 1998; ). paup* – phylogenetic analysis using parsimony* and other methods, version 4. Sunderland, MA: Sinauer Associates.
  21. Thompson, J. D., Higgins, D. G. & Gibson, T. J. ( 1994; ). clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.[CrossRef]
    [Google Scholar]
  22. Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 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]
  23. Willems, A., Gillis, M. & De Ley, J. ( 1991; ). Transfer of Rhodocyclus gelatinosus to Rubrivivax gelatinosus gen. nov., comb. nov., and phylogenetic relationships with Leptothrix, Sphaerotilus natans, Pseudomonas saccharophila, and Alcaligenes latus. Int J Syst Bacteriol 41, 65–73.[CrossRef]
    [Google Scholar]
  24. Xie, C. & Yokota, A. ( 2003; ). Phylogenetic analysis of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 49, 345–349.[CrossRef]
    [Google Scholar]
  25. Xie, C. & Yokota, A. ( 2004; ). Phylogenetic analysis of the nitrogen-fixing genus Derxia. J Gen Appl Microbiol 50, 129–135.[CrossRef]
    [Google Scholar]
  26. Young, J. P. W. ( 1992; ). Phylogenetic classification of nitrogen-fixing organisms. In Biological Nitrogen Fixation, pp. 43–86. Edited by G. Stacey, R. H. Burris & H. J. Evans. New York: Chapman & Hall.
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.63733-0
Loading
/content/journal/ijsem/10.1099/ijs.0.63733-0
Loading

Data & Media loading...

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