1887

Abstract

Five strains of free-living diazotrophs isolated from rice were characterized by using a polyphasic approach. The strains were found to be very closely related, with 99–100 % 16S rRNA gene sequence similarity and DNA–DNA hybridization values greater than 70 %, suggesting that they represent a single species. When compared with other recognized species, they showed not more than 93 and 89 % similarity for the 16S rRNA and gene sequences, respectively. Phylogenetic distances showed that these isolates were distinct from other taxa within the -. Chemotaxonomic characteristics of these isolates included the DNA G+C content (62·1–63·1 mol%), the major quinone system (Q-10), predominant fatty acids (18 : 17, cyclo 19 : 08 and 16 : 0) and major hydroxy fatty acids (14 : 0 3-OH, 18 : 0 3-OH and 16 : 0 3-OH). Based on phylogenetic and phenotypic analyses, these isolates are considered to represent a novel genus and species, for which the name gen. nov., sp. nov. is proposed. The type strain is F-7 (=IAM 15079=ATCC BAA-940=DSM 16300).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.63406-0
2005-05-01
2020-01-25
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/55/3/ijs551233.html?itemId=/content/journal/ijsem/10.1099/ijs.0.63406-0&mimeType=html&fmt=ahah

References

  1. Barraquio, W. L., Revilla, L. & Ladha, J. K. ( 1997; ). Isolation of endophytic bacteria from wetland rice. Plant Soil 194, 15–24.[CrossRef]
    [Google Scholar]
  2. Bowman, J. P., Sly, L. I., Nichols, P. D. & Hayward, A. C. ( 1993; ). Revised taxonomy of the methanotrophs: description of Methylobacter gen. nov., emendation of Methylococcus, validation of Methylosinus and Methylocystis species, and a proposal that the family Methylococcaceae includes only the group I methanotrophs. Int J Syst Bacteriol 43, 735–753.[CrossRef]
    [Google Scholar]
  3. Chin, K. J., Hahn, D., Hengstmann, U., Liesack, W. & Janssen, P. H. ( 1999; ). Characterization and identification of numerically abundant culturable bacteria from the anoxic bulk soil of rice paddy microcosms. Appl Environ Microbiol 65, 5042–5049.
    [Google Scholar]
  4. Eckert, B., Weber, O. B., Kirchhof, G., Halbritter, A., Stoffels, M. & Hartmann, A. ( 2001; ). Azospirillum doebereinerae sp. nov., a nitrogen-fixing bacterium associated with the C4-grass Miscanthus. Int J Syst Evol Microbiol 51, 17–26.
    [Google Scholar]
  5. Elbeltagy, A., Nishioka, K., Sato, T., Suzuki, H., Ye, B., Hamada, T., Isawa, T., Mitsui, H. & Minamisawa, K. ( 2001; ). Endophytic colonization and in planta nitrogen fixation by Herbaspirillum sp. isolated from wild rice species. Appl Environ Microbiol 67, 5285–5293.[CrossRef]
    [Google Scholar]
  6. Engelhard, M., Hurek, T. & Reinhold-Hurek, B. ( 2000; ). Preferential occurrence of diazotrophic endophytes, Azoarcus spp., in wild rice species and land races of Oryza sativa in comparison with modern races. Environ Microbiol 2, 131–141.[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. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  9. Fujie, T., Huang, Y. D., Higashitani, A., Nishimura, Y., Iyama, S., Hirota, Y., Yoneyama, Y. & Dixon, R. A. ( 1987; ). Effect of inoculation with Klebsiella oxytoca and Enterobacter cloacae on dinitrogen fixation by rice–bacteria associations. Plant Soil 103, 221–226.[CrossRef]
    [Google Scholar]
  10. Hiraishi, A. & Ueda, Y. ( 1995; ). Isolation and characterization of Rhodovulum strictum sp. nov. and some other purple nonsulfur bacteria from colored blooms in tidal and seawater pools. Int J Syst Bacteriol 45, 319–326.[CrossRef]
    [Google Scholar]
  11. Imhoff, J. F. & Trüper, H. G. ( 1989; ). Purple nonsulfur bacteria (Rhodospirillaceae Pfennig and Trüper 1971, 17AL). In Bergey's Manual of Systematic Bacteriology, vol. 3, pp. 1658–1661. Edited by J. T. Staley, M. P. Bryant, N. Pfennig & J. G. Holt. Baltimore: Williams & Wilkins.
  12. Jordan, D. C. ( 1984; ). Family III. Rhizobiaceae Conn 1938, 321AL. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 234–235. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
  13. Kämpfer, P., Buczolits, S., Albrecht, A., Busse, H.-J. & Stackebrandt, E. ( 2003; ). Towards a standardized format for the description of a novel species (of an established genus): Ochrobactrum gallinifaecis sp. nov. Int J Syst Evol Microbiol 53, 893–896.[CrossRef]
    [Google Scholar]
  14. 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]
  15. Kirchhof, G., Eckert, B., Stoffels, M., Baldani, J. I., Reis, V. M. & Hartmann, A. ( 2001; ). Herbaspirillum frisingense sp. nov., a new nitrogen-fixing bacterial species that occurs in C4-fibre plants. Int J Syst Evol Microbiol 51, 157–168.
    [Google Scholar]
  16. Lechner, U., Baumbach, R., Becker, D., Kitunen, V., Auling, G. & Salkinoja-Salonen, M. ( 1995; ). Degradation of 4-chloro-2-methylphenol by an activated sludge isolate and its taxonomic description. Biodegradation 6, 83–92.[CrossRef]
    [Google Scholar]
  17. 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]
  18. Oyaizu-Masuchi, Y. & Komagata, K. ( 1988; ). Isolation of free-living nitrogen-fixing bacteria from the rhizosphere of rice. J Gen Appl Microbiol 34, 127–164.[CrossRef]
    [Google Scholar]
  19. Reinhold-Hurek, B. & Hurek, T. ( 2000; ). Reassessment of the taxonomic structure of the diazotrophic genus Azoarcus sensu lato and description of three new genera and new species, Azovibrio restrictus gen. nov., sp. nov., Azospira oryzae gen. nov., sp. nov. and Azonexus fungiphilus gen. nov., sp. nov. Int J Syst Evol Microbiol 50, 649–659.[CrossRef]
    [Google Scholar]
  20. 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]
  21. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  22. Sato, Y. (editor) ( 1994; ). Ecological–Genetic Studies on Wild and Cultivated Rice in Tropical Asia (4th Survey). Tropics 3, 189–245.
    [Google Scholar]
  23. Swofford, D. L. ( 1997; ). paup* – Phylogenetic Analysis Using Parsimony (*and other methods), version 4. Sunderland, MA: Sinauer Associates.
  24. 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]
  25. Tighe, S. W., de Lajudie, P., Dipietro, K., Lindström, K., Nick, G. & Jarvis, B. D. W. ( 2000; ). Analysis of cellular fatty acids and phenotypic relationships of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium species using the Sherlock Microbial Identification System. Int J Syst Evol Microbiol 50, 787–801.[CrossRef]
    [Google Scholar]
  26. 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]
  27. Xie, C. & Yokota, A. ( 2004; ). Phylogenetic analyses of the nitrogen-fixing genus Derxia. J Gen Appl Microbiol 50, 129–135.[CrossRef]
    [Google Scholar]
  28. Yokota, A., Akagawa-Matsushia, M., Hiraishi, A., Katayama, Y., Urakami, T. & Yamasato, K. ( 1992; ). Distribution of quinone systems in microorganisms: gram-negative eubacteria. Bull Jpn Fed Cult Coll 8, 136–171.
    [Google Scholar]
  29. 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.0.63406-0
Loading
/content/journal/ijsem/10.1099/ijs.0.63406-0
Loading

Data & Media loading...

Supplements

vol. , part 3, pp. 1233 - 1237

Neighbour-joining tree based on gene sequences showing relationships between strain F-7 and diazotrophs of the α- . [PDF](17 KB)



PDF

Most cited articles

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