1887

Abstract

A polyphasic study was carried out to determine the taxonomic position of two aerobic, cyanide-degrading bacterial strains, designated L61 and L22, which had been isolated from a bioreactor for the treatment of nickel-complexed cyanide. The two isolates exhibited almost identical taxonomic characteristics. Phylogenetic analysis inferred from comparative 16S rRNA gene sequences indicated that the isolates fall in a sublineage of the genus comprising the type strains of , , , , , , , and . Cells of the two isolates are Gram-negative, aerobic, motile and non-spore-forming rods (0·6–0·7×1·1–1·3 μm), with peritrichous flagella. The DNA G+C content is 60·1–60·9 mol%. Cellular fatty acids are C (2·2–3·3 %), C (2·1–3·2 %), C cyclo 8 (9·9–16·8 %), C 6,9,12 (2·7–3·3 %), summed feature 3 (7·2–7·7 %) and summed feature 7 (67·8–73·7 %). The strains formed nodules on a legume plant, . A gene encoding denitrogenase reductase, the key component of the nitrogenase enzyme complex, was detected in L61 by PCR amplification by using a -specific primer system. Strains L61 and L22 were distinguished from the type strains of recognized species in the same sublineage based on low DNA–DNA hybridization values (2–4 %) and/or a 16S rRNA gene sequence similarity value of less than 96 %. Moreover, some phenotypic properties with respect to substrate utilization as a carbon or nitrogen source, antibiotic resistance and growth conditions could be used to discriminate L61 and L22 from species in the same sublineage. Based on the results obtained in this study, L61 and L22 are considered to be representatives of a novel species of , for which the name sp. nov. is proposed. The type strain is L61 (=KCTC 12121=IAM 15042=CCBAU 10050).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.63667-0
2005-11-01
2019-10-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/55/6/2543.html?itemId=/content/journal/ijsem/10.1099/ijs.0.63667-0&mimeType=html&fmt=ahah

References

  1. Adjei, M. D. & Ohta, Y. ( 1999; ). Isolation and characterization of a cyanide-utilizing Burkholderia cepacia strain. World J Microbiol Biotechnol 15, 699–704.[CrossRef]
    [Google Scholar]
  2. Amarger, N., Macheret, V. & Laguerre, G. ( 1997; ). Rhizobium gallicum sp. nov. and Rhizobium giardinii sp. nov., from Phaseolus vulgaris nodules. Int J Syst Bacteriol 47, 996–1006.[CrossRef]
    [Google Scholar]
  3. Beringer, J. E. ( 1974; ). R-Factor transfer in Rhizobium leguminosarum. J Gen Microbiol 84, 188–198.[CrossRef]
    [Google Scholar]
  4. Bouzar, H. & Jones, J. B. ( 2001; ). Agrobacterium larrymoorei sp. nov., a pathogen isolated from aerial tumours of Fucus benjamina. Int J Syst Evol Microbiol 51, 1023–1026.[CrossRef]
    [Google Scholar]
  5. de Lajudie, P., Willems, A., Pot, B. & 7 other authors ( 1994; ). Polyphasic taxonomy of rhizobia: emendation of the genus Sinorhizobium and description of Sinorhizobium meliloti comb. nov., Sinorhizobium saheli sp. nov., and Sinorhizobium teranga sp. nov. Int J Syst Bacteriol 44, 715–733.[CrossRef]
    [Google Scholar]
  6. de Lajudie, P., Laurent-Fulele, E., Willems, A., Torck, U., Coopman, R., Collins, M. D., Kersters, K., Dreyfus, B. & Gillis, M. ( 1998; ). Allorhizobium undicola gen. nov., sp. nov., nitrogen-fixing bacteria that efficiently nodulate Neptunia natans in Senegal. Int J Syst Bacteriol 48, 1277–1290.[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. Frank, B. ( 1889; ). Ueber die Pilzsymbiose der Leguminosen. Ber Dtsch Bot Ges 7, 332–346 (in German).
    [Google Scholar]
  10. Gao, J. L., Sun, J. G., Li, Y., Wang, E. T. & Chen, W. X. ( 1994; ). Numerical taxonomy and DNA relatedness of tropical rhizobia isolated from Hainan province, China. Int J Syst Bacteriol 44, 151–158.[CrossRef]
    [Google Scholar]
  11. 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]
  12. Harris, R. & Knowles, C. J. ( 1983; ). Isolation and growth of a Pseudomonas species that utilizes cyanide as a source of nitrogen. J Gen Microbiol 129, 1005–1011.
    [Google Scholar]
  13. Ingvorsen, K., Højer-Pedersen, B. & Godtfredsen, S. E. ( 1991; ). Novel cyanide-hydrolyzing enzyme from Alcaligenes xylosoxidans subsp. denitrificans. Appl Environ Microbiol 57, 1783–1789.
    [Google Scholar]
  14. Jarvis, B. D. W., Sivakumaran, S., Tighe, S. W. & Gillis, M. ( 1996; ). Identification of Agrobacterium and Rhizobium species based on cellular fatty acid composition. Plant Soil 184, 143–158.[CrossRef]
    [Google Scholar]
  15. Kimura, M. ( 1983; ). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  16. Kumar, S., Tamura, K., Jacobsen, I. B. & Nei, M. ( 2001; ). mega2: molecular evolutionary genetics analysis software. Bioinformatics 17, 1244–1245.[CrossRef]
    [Google Scholar]
  17. Lindström, K. ( 1989; ). Rhizobium galegae, a new species of legume root nodule bacteria. Int J Syst Bacteriol 39, 365–367.[CrossRef]
    [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. Poly, E., 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]
  20. Rome, S., Fernandez, M. P., Brunel, B., Norman, P. & Cleyet-Marel, J.-C. ( 1996; ). Sinorhizobium medicae sp. nov., isolated from annual Medicago spp. Int J Syst Bacteriol 46, 972–980.[CrossRef]
    [Google Scholar]
  21. Rzhetsky, A. & Nei, M. ( 1992; ). A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 9, 945–967.
    [Google Scholar]
  22. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  23. Sasser, M. ( 1990; ). Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. Newark, DE: MIDI Inc.
  24. Smibert, R. M. & Krieg, N. R. ( 1981; ). General characterization. In Manual of Methods for General Bacteriology, pp. 409–443. Edited by P. Gerhardt, R. G. E. Murray, R. N. Costilow, E. W. Nester, W. A. Wood, N. R. Krieg & G. B. Phillips, Washington, DC: American Society for Microbiology.
  25. Stackebrandt, E., Frederiksen, W., Garrity, G. M. & 10 other authors ( 2002; ). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043–1047.[CrossRef]
    [Google Scholar]
  26. Swofford, D. L. ( 1993; ). paup: Phylogenetic Analysis Using Parsimony, version 3.1.1. Champaign, IL: Illinois Natural History Survey.
  27. 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]
  28. van Berkum, P., Beyene, D., Bao, G., Campbell, T. A. & Eardly, B. D. ( 1998; ). Rhizobium mongolense sp. nov. is one of three rhizobial genotypes identified which nodulate and form nitrogen-fixing symbioses with Medicago ruthenica [(L.) Ledebour]. Int J Syst Bacteriol 48, 13–22.[CrossRef]
    [Google Scholar]
  29. Vincent, J. M. ( 1970; ). A Manual for the Practical Study of Root Nodule Bacteria. Oxford: Blackwell Scientific.
  30. Wang, E. T., van Berkum, P., Beyene, D., Sui, X. H., Dorado, O., Chen, W. X. & Martinez-Romero, E. ( 1998; ). Rhizobium huautlense sp. nov., a symbiont of Sesbania herbacea that has a close phylogenetic relationship with Rhizobium galegae. Int J Syst Bacteriol 48, 687–699.[CrossRef]
    [Google Scholar]
  31. 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]
  32. Wei, G. H., Tan, Z. Y., Zhu, M. E., Wang, E. T., Han, S. Z. & Chen, W. X. ( 2003; ). Characterization of rhizobia isolated from legume species within the genera Astragalus and Lespedeza grown in the Loess Plateau of China and description of Rhizobium loessense sp. nov. Int J Syst Evol Microbiol 53, 1575–1583.[CrossRef]
    [Google Scholar]
  33. White, L. O. ( 1972; ). The taxonomy of the crown gall organism Agrobacterium tumefaciens and its relationship to rhizobia and other agrobacteria. J Gen Microbiol 72, 565–574.[CrossRef]
    [Google Scholar]
  34. Young, J. M., Kuykendall, L. D., Martínez-Romero, E., Kerr, A. & Sawada, H. ( 2001; ). A revision of Rhizobium Frank 1889 , with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis. Int J Syst Evol Microbiol 51, 89–103.
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.63667-0
Loading
/content/journal/ijsem/10.1099/ijs.0.63667-0
Loading

Data & Media loading...

Supplements

Morphological features of strain L61 grown on YMA for 3 days, observed by transmission electron microscopy. Bar, 1 µm.

IMAGE

Minimum-evolution tree showing the phylogenetic relationships of strains L61 and L22, species and other related species of the ‘ ’. [PDF](16 KB)

PDF

Cellular fatty acid composition of strains L61 and L22 and related species. [PDF](50 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