Genotypic characterization of Bradyrhizobium strains nodulating endemic woody legumes of the canary islands by PCR-restriction fragment length polymorphism analysis of genes encoding 16S rRNA (16S rDNA) and 16S-23S rDNA intergenic spacers, repetitive extragenic palindromic PCR genomic fingerprinting, and partial 16S rDNA sequencing

Applied and Environmental Microbiology

Volumn 64, Issue 6, 1998, Pages 2096-2104

  Vinuesa, Pablo ^a   Rademaker, Jan L W ^b   De Bruijn, Frans J ^b,c   Werner, Dietrich ^a  

^a PHILIPPS UNIVERSITY MARBURG   (Germany)

^b MICHIGAN STATE UNIVERSITY   (United States)

^c NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NITROGEN; RIBOSOME DNA;

ARTICLE; BRADYRHIZOBIUM; CLUSTER ANALYSIS; DNA RESTRICTION; DNA SEQUENCE; GENE; GENOTYPE; LEGUME; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT SEED; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

ACACIA; BRADYRHIZOBIA; BRADYRHIZOBIUM; BRADYRHIZOBIUM JAPONICUM; BRADYRHIZOBIUM JAPONICUM USDA 110; BRADYRHIZOBIUM SP.; CENTROSEMA; CHAMAECYSTIS PALMENSIS; CHAMAECYTISUS PROLIFERUS; GLYCINE MAX; LEUCAENA LEUCOCEPHALA; LEUCOCEPHALA; MACROPTILIUM ATROPURPUREUM; PENDULA; PROKARYOTA; RHODOPSEUDOMONAS; VIGNA UNGUICULATA;

EID: 0031746448     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.64.6.2096-2104.1998     Document Type: Article

References (52)

1. Acebes-Ginovés, J. R., M. del Arco-Aguilar, and W. Wildpret de la Torre. 1991. Revisión taxonómica de Chamaecytisus proliferus (L.Fil) Link en Canarias. Vieraea 20:191-202.
2. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. A. Smit, J. C. Seidman, and K. S. Struhl (ed.). 1994. Current protocols in molecular biology, section 2.4. John Wiley and Sons, New York, N.Y.
3. Bramwell, D. 1972. Endemism in the flora of the Canary Islands, p. 141-159. In D. H. Valentine (ed.), Taxonomy, phytogeography and evolution. Academic Press, London, United Kingdom.
4. Brosius, J., T. J. Dull, D. D. Sleeter, and H. F. Noller. 1981. Gene organisation and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol. 148:107-127.
5. de Bruijn, F. J. 1992. Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. Appl. Environ. Microbiol. 58:2180-2187.
6. Dommergues, Y. R., H. G. Diem, D. L. Gauthier, B. L. Dreyfus, and F. Cornet. 1984. Nitrogen-fixing trees in the tropics: potentialities and limitations, p. 7-8. In C. Veeger and W. E. Newton (ed.), Advances in nitrogen fixation research. Proceedings of the 5th International Symposium on Nitrogen Fixation. Martinus Nijhoff/Dr. W. Junk Publishers, Wageningen, The Netherlands.
7. Fox, G. E., J. D. Wisotzkey, and P. Jurtshuk. 1992. How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Bacteriol. 42:166-170.
8. Francisco-Ortega, J., M. T. Jackson, A. Santos-Guerra, and M. Fernández Galván. 1991. Historical aspects of the origin and distribution of tagasaste [Chamaecytisus proliferus (L.fil.) Link ssp. palmensis (Christ) G. Kunkel], a fodder tree from the Canary Islands. J. Adel. Bot. Gard. 14:67-76.
9. Francisco-Ortega, J., J. H. Newbury, and B. V. Ford-Lloyd. 1993. Numerical analysis of RAPD data highlights the origin of cultivated tagasaste (Chamecytisus proliferus ssp. palmensis) in the Canary Islands. Theor. Appl. Genet. 87:264-270.
10. Francisco-Ortega, J., M. T. Jackson, A. Santos-Guerra, M. Fernández-Galván, and B. V. Ford-Lloyd. 1994. The phytogeography of Chamaecytisus proliferus (L.fil.) Link complex (Fabaceae: Genisteae) in the Canary Islands: a multivariate analysis. Vegetatio 110:1-17.
11. Gault, R. R., A. Pilka, D. M. Hebb, and J. Brockwell. 1994. Nodulation studies on legumes exotic to Australia: symbiotic relationships between Chamaecytisus palmensis (tagasaste) and Lotus spp. Austr. J. Exp. Agric. 34:385-394.
12. Häne, B. G., K. Jäger, and H. Drexler. 1993. The Pearson product-moment correlation coefficient is better suited for identification of DNA fingerprint profiles than band matching algorithms. Electrophoresis 14:967-972.
13. Haukka, K., Lindström, and J. P. W. Young. 1996. Diversity of partial 16S rRNA sequences among and within strains of African rhizobia isolated from Acacia and Prosopis. System. Appl. Microbiol. 19:352-359.
14. Heyndrickx, M., L. Vauterin, P. Vandamme, K. Kersters, and P. De Vos. 1996. Applicability of combined amplified ribosomal DNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy. J. Microbiol. Methods 26:247-259.
15. Jordan, D. C. 1984. Family III. Rhizobiaceae Conn 1938, p. 234-244. In N. R. Krieg and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore, Md.
16. Judd, A. K., M. Schneider, M. J. Sadowsky, and F. J. de Bruijn. 1993. Use of repetitive sequences and the polymerase chain reaction technique to classify genetically related Bradyrhizobium japonicum serocluster 123 strains. Appl. Environ. Microbiol. 59:1702-1708.
17. Kündig, K., C. Beck, H. Hennecke, and M. Göttfert. 1995. A single rRNA gene region in Bradyrhizobium japonicum. J. Bacteriol. 177:5151-5154.
18. Kuykendall, L. D., B. Saxena, T. E. Devine, and S. E. Udell. 1992. Genetic diversity in Bradyrhizobium japonicum Jordan 1982 and a proposal for Bradyrhizobium elkanii sp. nov. Can. J. Microbiol. 38:501-505.
19. Laguerre, G., M. R. Allard, F. Revoy, and N. Amarger. 1994. Rapid identification of rhizobia by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl. Environ. Microbiol. 60:56-63.
20. Laguerre, G., P. Mavingui, M. R. Allard, M. P. Charnay, P. Louvrier, S. I. Mazurier, L. Rigottier-Gois, and N. Amarger. 1996. Typing of rhizobia by PCR and PCR-restriction fragment length polymorphism analysis of chromosomal and symbiotic gene regions: application to Rhizobium leguminosarum and its different biovars. Appl. Environ. Microbiol. 62:2029-2036.
21. León-Barrios, M., A. M. Gutiérrez-Navarro, R. Pérez-Galdona, and J. Corzo. 1991. Characterization of Canary Island isolates of Bradyrhizobium sp. (Chamaecytisus proliferus). Soil Biol. Biochem. 23:487-489.
22. Lindström, K., G. Laguerre, P. Normand, U. Rasmussen, T. Heulin, B. D. W. Jarvis, P. de Lajudie, E. Martínez. Romero and W.-X. Chen. 1998. Taxonomy and phylogeny of diazotrophs. In C. Elmerich, A. Kondorosi, and W. E. Newton (ed.), Biological nitrogen fixation for the 21st century. Proceedings of the 11th International Congress on Nitrogen Fixation, Paris, July 1997. Kluwer Academic Publishers, Dordrecht, The Netherlands.
23. Martínez-Romero, E., and J. Caballero-Mellado. 1996. Rhizobium phylogenies and bacterial genetic diversity. Crit. Rev. Plant Sci. 15:113-140.
24. Messing, J. 1988. M13, the universal primer and the polylinker. Focus (BRL) 10:21-26.
25. Moyer, C. L., J. M. Tiedje, F. C. Dobbs, and D. M. Karl. 1996. A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature. Appl. Environ. Microbiol. 62:2501-2507.
26. 2-fixation, nodule efficiency and biomass accumulation after two years in three Chilean legume trees and tagasaste Chamaecytisus proliferus subsp. palmensis. Plant Soil 179:131-140.
27. Oyaizu, H., S. Matsumoto, K. Minamisawa, and T. Gamou. 1993. Distribution of rhizobia in leguminous plants surveyed by phylogenetic identification. J. Gen. Appl. Microbiol. 39:339-354.
28. Rademaker, J. L. W., and F. J. de Bruijn. 1997. Characterization and classification of microbes by rep-PCR genomic fingerprinting and computer assisted pattern analysis, p. 151-171. In G. Caetano-Anollés and P. M. Gresshoff (ed.), DNA markers: protocols, applications and overviews. John Wiley and Sons, Inc., New York, N.Y.
29. Rademaker, J. L. W., F. J. Louws, and F. J. de Bruijn. 1998. Characterization of the diversity of ecologically important microbes by rep-PCR fingerprinting, p. 1-26. In A. D. L. Akkermans. J. D. van Elsas, and F. J. de Bruijn (ed.), Molecular microbial ecology manual, suppl. 3. Kluwer Academic Publishers, Dordrecht, The Netherlands.
30. Regunath, B. R., J. Francisco-Ortega, H. J. Newbury, and B. V. Ford-Lloyd. 1993. Methods for increasing the efficiency of seed germination in the fodder legumes tagasaste and escobon [Chamaecytisus proliferus (L.fil.) Link sensu lato] Seed Sci. Technol. 21:225-235.
31. Sambrook, J., E. F. Fritsch, and T. A. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
32. Santamaría, M., J. Corzo, M. León-Barrios, and A. M. Gutiérrez-Navarro. 1997. Characterization and differentiation of indigenous rhizobia isolated from Canarian shrub legumes of agricultural and ecological interest. Plant Soil 190:143-152.
33. So, R. B., J. K. Ladha, and J. P. W. Young. 1994. Photosynthetic symbionts of Aeschynomene spp. form a cluster with bradyrhizobia on the basis of fatty acid and rRNA analyses. Int. J. Syst. Bacteriol. 44:392-403.
34. Sokal, R. R., and C. D. Michener. 1958. A statistical method for evaluating systematic relationships. Univ. Kans. Sci. Bull. 38:1409-1438.
35. Somasegaran, P., and H. J. Hoben. 1994. Handbook for rhizobia - methods in legume-Rhitzobium technology. Springer-Verlag, Heidelberg, Germany.
36. Streit, W., K. Kosch, and D. Werner. 1992. Nodulation competitiveness of Rhizobium leguminosarum bv. phaseoli and Rhizobium tropici strains measured by glucuronidase (gus) gene fusion. Biol. Fertil. Soils 14:140-144.
37. Townsend, R. J., and J. E. Radcliffe. 1990. Tagasaste forage production systems. N. Z. J. Agric. Res. 33:627-634.
38. Triplett, E. W., and M. J. Sadowsky. 1992. Genetics of competition for nodulation of legumes. Annu. Rev. Microbiol. 46:399-428.
39. Tyler, K. D., G. Wang, S. D. Tyler, and W. M. Johnson. 1997. Factors affecting reliability and reproducibility of amplification-based DNA fingerprinting of representative bacterial pathogens. J. Clin. Microbiol. 35:339-346.
40. van Rhijn, P., and J. Vanderleyden. 1995. The Rhizobium-plant symbiosis. Microbiol. Rev. 59:124-142.
41. van Rossum, D., F. P. Schuurmans, M. Gillis, A. Muyotcha, H. W. van Verseveld, A. H. Stouthamer, and F. C. Boogerd. 1995. Genetic and phenetic analyses of Bradyrhizobium strains nodulating peanut (Arachis hypogaea L.) roots. Appl. Environ. Microbiol. 61:1599-1609.
42. Versalovic, J., M. Schneider, F. J. de Bruijn, and J. R. Lupski. 1994. Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol. Cell. Biol. 5:25-40.
43. Vinuesa, P. Unpublished results.
44. Vinuesa-Fleischmann, P., M. A. Negrín, M. C. Jaizme-Vega, and J. M. Hernández-Moreno. 1996. Arbuscular mycorrhizal tagasaste plants mediate transformations on the P pools in an andisol, p. 599-602. In C. Azcón-Aguila, and J. M. Barea (ed.), Proceedings of the 4th European Symposium on Mycorrhizas 1994. Office for Official Publications of the European Communities, Brussels, Belgium.
45. Weisburg, W. G., S. M. Barns, D. A. Pelletier, and D. J. Lane. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173:697-703.
46. Welsh, J., and M. McClelland. 1990. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 18:7213-7218.
47. Werner, D., J. Wilcockson, and E. Zimmermann. 1975. Adsorption and selection of rhizobia by ion exchange papers. Arch. Microbiol. 105:27-32.
48. Willems, A., and M. D. Collins. 1993. Phylogenetic analysis of rhizobia and agrobacteria based on 16S rRNA gene sequences. Int. J. Syst. Bacteriol. 43:305-313.
49. Xu, L. M., C. Ge, Z. Cui, J. Li, and H. Fan. 1995. Bradyrhizobium liaoningense sp. nov., isolated from the root nodules of soybeans. Int. J. Syst. Bacteriol. 45:706-711.
50. Young, J. P. W., H. L. Downer, and B. D. Eardly. 1991. Phylogeny of the phototrophic Rhizobium strain BTAi1 by polymerase chain reaction-based sequencing of a 16S rRNA gene segment. J. Bacteriol. 173:2271-2277.
51. Young, J. P. W., and K. E. Haukka. 1996. Diversity and phylogeny of rhizobia. New Phytol. 133:87-94.
52. Zhang, X., R. Harper, M. Karsito, and K. Lindström. 1991. Diversity of Rhizobium bacteria isolated from the root nodules of leguminous trees. Int. J. Syst. Bacteriol. 41:104-113.