Phenotypic and genotypic characterization of rhizobia from diverse geographical origin that nodulate Pachyrhizus species

Systematic and Applied Microbiology

Volumn 27, Issue 6, 2004, Pages 737-745

  Rodríguez Navarro, Dulce N ^a   Camacho, María ^a   Leidi, Eduardo O ^b   Rivas, Raúl ^c   Velázquez, Encarna ^c  

^a Ctro de Invest y Formacion Agraria   (Spain)

^b INSTITUTO DE RECURSOS NATURALES Y AGROBIOLOGÍA DE SEVILLA   (Spain)

^c UNIVERSITY OF SALAMANCA   (Spain)

Author keywords

Bradyrhizobia biodiversity; LPS profiles; Pachyrhizus ahipa; SDS PAGE analysis; TP RAPD fingerprinting ITS sequencing

Indexed keywords

BACTERIAL RNA; INTERNAL TRANSCRIBED SPACER;

ARTICLE; BACTERIAL STRAIN; BRADYRHIZOBIUM; CONTROLLED STUDY; CULTURE MEDIUM; GENE SEQUENCE; GENOTYPE; GEOGRAPHY; MICROBIAL DIVERSITY; MICROBIOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; RANDOM AMPLIFIED POLYMORPHIC DNA; RHIZOBIACEAE; SEQUENCE ANALYSIS; SYMBIOSIS; YAM;

BACTERIA (MICROORGANISMS); BRADYRHIZOBIUM BETAE; BRADYRHIZOBIUM ELKANII; BRADYRHIZOBIUM JAPONICUM; BRADYRHIZOBIUM LIAONINGENSE; BRADYRHIZOBIUM YUANMINGENSE; DIOSCOREA ALATA; PACHYRHIZUS; PACHYRHIZUS AHIPA; PHASEOLUS (ANGIOSPERM); RHIZOBIACEAE;

EID: 9944238298     PISSN: 07232020     EISSN: None     Source Type: Journal    
DOI: 10.1078/0723202042369839     Document Type: Article

References (49)

1. Alschul, S. F., Gish, W., Miller, W., Myers, E. W., Lipman, D. J.: Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
2. Barrera, L. L., Trujillo, M. E., Goodfellow, M., García, F. J., Hernández-Lucas, I., Dávila, G., van Berkum, P., Martínez-Romero, E.: Biodiversity of bradyrhizobia nodulating Lupinus spp. Int. J. Syst. Bacteriol. 47, 1086-1091 (1997).
3. Camacho, M., Santamaría, C., Temprano, F., Rodríguez- Navarro, D. N., Daza, A., Espuny, R., Bellogín, R., Ollero, F. J., Lyra, M. C. C. P., Buendía-Clavería, A., Zhou, J., Li, F. D., Mateos, C., Velázquez, E. Vinardell, J. M., Ruiz-Sainz, J. E.: Soils of the Chinese Hubei province show a very high diversity of Sinorhizobium fredii strains. System. Appl. Microbiol. 25, 592-602 (2002).
4. Casella, S., Rossi, N., Toffanin, A.: Cell surface lipopolysaccharides of different rhizobia. FEMS Microbiol. Lett. 93, 213-220 (1993).
5. Fuentes, J. B., Abe, M., Uchiumi, Y., Suzuki, A., Higashi, S.: Symbiotic root nodule bacteria isolated from yam bean (Pachyrhizus erosus). J. Gen. Appl. Microbiol. 48 (4), 181-191 (2002).
6. Fuhrman, J.: Serological distribution of Bradyrhizobium japonicum as influenced by soybean cultivar and sampling location. Soil Biol. Biochem. 21, 1079-1081 (1989).
7. Grum, M.: Pachyrhizus (yam bean) symbiosis with Rhizobium bacteria: genetic variation and performance. Final Report IPGR (1994).
8. Halafihi, M., Grum, M., Stolen, O., Sørensen, M.: Biological nitrogen fixation in Pachyrhizus Rich. Ex DC., pp. 215-225. In: Proceedings of the First International Symposium on Tuber Legumes. Gualdalupe. (M. Sørensen, ed.) DSR Tryk, Denmark 1994.
9. Jarabo-Lorenzo, A., Velázquez, E., Pérez-Galdona, R., Vega-Hernández, M. C., Martínez-Molina, E., Mateos, P. F., Vinuesa, P., Martinez-Romero, E., Leon-Barrios, M.: Restriction Fragment Length Polymorphism analysis of PCR-amplified 16S rDNA and Low Molecular Weight RNA profiling in the characterisation of rhizobial isolates from shrubby legumes endemic to the Canary Islands. Syst. Appl. Microbiol. 23, 4-18 (2000).
10. Jarabo-Lorenzo, A., Pérez-Galdona, R. Donate-Correa, J., Rivas, R., Velázquez, E., Hernández, M., Temprano, F., Martínez-Molina, E., Ruiz-Argüeso, T., León-Barrios, M.: Genetic diversity of bradyrhizobial populations from diverse geographic origins that nodulate Lupinus spp. and Ornithopus spp. Syst. Appl. Microbiol. 26, 611-623. (2003).
11. Jordan, D. C.: Transfer of Rhizobium japonicum to Bradyrhizobium gen. nov., a genus of slow-growing, root nodule bacteria from leguminous plants. Int. J. Syst. Bacteriol. 32, 136-139 (1982).
12. Kimura, M.: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120 (1980).
13. Kjaer, S.: Biological nitrogen fixation in Pachyrhizus ahipa [Wedd.] Parodi, Annals of Botany 70, 11-17 (1992).
14. Kumar, S., Tamura, K., Jakobsen, I. B., Nei, M.: Molecular Evolutionary Genetics Analysis software. Arizona State University. Tempe, Arizona. USA (2001).
15. Kuykendall, L. D., Saxena, B., Devine, T. E., Udell, S. E.: Genetic diversity in Bradyrhizobium japonicum Jordan 1982 and a proposal for Bradyrhizobium elkanii sp. nov. Can J. Microbiol. 38, 501-505 (1992).
16. Ladha, J. K., So, R. B.: Numerical taxonomy of photosynthetic rhizobia nodulating Aeschynomene species. Int. J. Syst. Bacteriol. 44, 62-73 (1994).
17. Laemmli, U. K.: Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680-685 (1970).
18. 2, pp. 431-440. In: Proceedings of 2nd International Symposium on Tuberous Legumes, Celaya, Gto., Mexico 58 (M. Sørensen, J. E. Estrella, O. J. Hamann, S. A. Ríos Ruíz, eds.). MacKenzie Press, København 1998.
19. Leidi, E. O., Sarmiento, R., Rodríguez-Navarro, D. N.: Ahipa (Pachyrhizus ahipa [Wedd.] Parodi): an alternative legume crop for sustainable production of starch, oil and protein. Industrial Crops and Products 17, 27-37 (2003).
20. Macedo-Lemos, E. G., Carareto-Alves, L. M.: Electrophoretic patterns of lipopolysaccharides and antigenic analysis of soybean bradyrhizobia. World J. Microbiol. Biotechnol. 15, 205-215 (1999).
21. Novikova, N., Pavlova, E. A., Vorobjev, N. I., Limeshchenko, E. V.: Numerical taxonomy of Rhizobium strains from legumes of the temperate zone. Int. J. Syst. Bacteriol. 44 (4), 734-742 (1994).
22. Parker, M. A.: Genetic markers for analysing symbiotic relationships and lateral gene transfer in Neotropical bradyrhizobia. Mol. Ecol. 12, 2447-2455 (2003).
23. Quatrini, P., Scaglione, G., Cardinale, M., Caradonna, F., Puglia, A. M. Bradyrhizobium sp. nodulating the Mediterranean shrub Spanish broom (Spartium junceum) J. App. Microbiol. 92, 13-21 (2002).
24. Rigaud, J., Puppo, A.: Indole-3-acetic acid catabolism by soybean bacteroids. J. Gen. Microbiol. 88, 223-228 (1975).
25. Rivas, R., Velázquez, E., Valverde, A., Mateos, P. F., Martínez-Molina, E.: A two primers random amplified polymorphic DNA procedure to obtain polymerase chain reaction fingerprints of bacterial species. Electrophoresis 22, 1086-1089 (2001).
26. Rivas, R., Velázquez, E., Palomo, J. L., Mateos, P., García-Benavides, P., Martínez-Molina, E.: Rapid identification of Clavibacter michiganensis subspecies sepedonicus using two primers random amplified polymorphic DNA (TP-RAPD) fingerprints. Eur. J. Plant Pathol. 108, 179-184 (2002).
27. Rivas, R., Velázquez, E., Willems A., Vizcaíno N., SubbaRao N. S., Mateos P. F., Gillis M., Dazzo F. B., Martínez-Molina E.: A new species of Devosia that forms a nitrogen-fixing root-nodule symbiosis with the aquatic legume Neptunia natans (L. f.) Druce. Appl. Environ. Microbiol. 68, 5217-5222 (2002).
28. Rivas, R., Willems, A., Palomo, J. L., García-Benavides, P., Mateos, P. F., Martínez-Molina, E., Gillis, M., Velázquez, E. Bradyrhizobium betae sp. nov. isolated from roots of Beta vulgaris affected by tumor-like deformations. Int. J. Syst. Evol. Microbiol. IJSEM Papers in Press, published online DOI 10.1099/ijs.0.02971-0 (2004).
29. Rodríguez-Navarro, D. N., Camacho, M., Daza, A., Santamaría, C., Temprano, F., Lourenço A. P. M. S., Leidi, E.: Symbiotic performance of Bradyrhizobium sp. [Pachyrhizus ahipa (Wedd.) Parodi] strains under controlled conditions, pp.315. In: 4th European Nitrogen Fixation Conference, Sevilla (Spain) 2000.
30. Rodríguez-Navarro, D. N., Buendía, A. M., Camacho, M., Lucas, M. M., Santamaría, C.: Characterization of Rhizobium spp. bean isolates from South-West Spain. Soil Biol. Biochem. 32, 1601-1613 (2000).
31. Sadowsky, M. J., Bohlool, B. B., Keyser, H. H.: Serological relatedness of Rhizobium fredii to other rhizobia and to the bradyrhizobia. Appl. Environ. Microbiol. 41, 679-685 (1987).
32. Saitou, N., Nei, M.: A neighbour-joining method: a new method for reconstructing phylogenetics trees. Mol. Biol. Evol. 44, 406-425 (1987).
33. Santamaría, M., Agius, F., Monza, J., Gutiérrez-Navarro, A. M., Corzo, J.: Comparative performance of enterobacterial repetitive intragenic consensus-polymerase chain reaction and lipopolysaccharide electrophoresis for identification of Bradyrhizobium sp. (Lotus) strains. FEMS Microbiol. Ecol. 28, 163-168 (1999).
34. Sørensen, M.: A taxonomic revision of the genus Pachyrhizus (Fabacea-Phaseolae). Nordic J. Botany 8, 167-192 (1988).
35. Sørensen, M.: Yam bean Pachyrhizus DC. Promoting the Conservation and Use of under-utilised and neglected Crops 2. Institute of Plant Genetics and Crop Plant Research, Gatersleben/IPGR Institute, Rome (1996).
36. Switzer, R. C., Merril, C. R., Shifrin, S.: A highly sensitive silver stain for detecting proteins and peptides in polyacrylamide gels. Anal. Biochem. 98, 231-237 (1979).
37. Sylla, S. N., Samba, R. T., Neyra, M., Ndoye, I., Giraud, E., Willems, A., de Lajudie, P., Dreyfus, B. Phenotypic and genotypic diversity of rhizobia nodulating Pterocarpus erinaceus and P. lucens in Senegal. Syst. Appl. Microbiol. 25, 572-583 (2002).
38. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., Higgins, D. G.: The clustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acid Res. 24, 4876-4882 (1997).
39. Tsai, C. M., Frasch, C. E.: A sensitive silver staining for detecting lipopolysaccharides in polyacrylamide gels. Anal. Biochem. 119, 115-119 (1982).
40. van Berkum, P., Fuhrmann, J. J.: Evolutionary relationships among the soybean bradyrhizobia reconstructed from 16S rRNA gene and internally transcribed spacer region sequence divergence. Int. J. Syst. Evol. Microbiol. 50, 2165-2172 (2000).
41. van Berkum, P., Terefework, Z., Paulin, L., Suomalainen, S., Lindström, K., Eardly, B.: Discordant phylogenies within the rnn loci of rhizobia. J. Bacteriol. 185, 2988-2998 (2003).
42. th Caribbean Food Crops Society Meeting (L. Degras, ed.), Publication INRA Antilles-Suyane 1989.
43. Vincent, J. M.: A Manual for the Practical Study of Root-Nodule Bacteria. Blackwell Scientific Publications, Oxford, 1970.
44. Willems, A., Coopman, R. Gillis, M.: Comparison of sequence analysis of 16S - 23S rDNA spacer regions, AFLP analysis, and DNA-DNA hybridizations in Bradyrhizobium. Int. J. Syst. Evol. Microbiol. 51, 623-632 (2001).
45. Willems, A., Doignon-Bourcier, F., Goris, J., Coopman, R., De Lajudie, P., Gillis, M.: DNA-DNA hybridization study of Bradyrhizobium strains. Int. J. Syst. Evol. Microbiol. 51, 1315-1322 (2001)
46. Willems, A., Munive, A., de Lajudie, P., Gillis, M.: In most Bradyrhizobium groups sequence comparison of 16S-23S rDNA internal transcribed spacer regions corroborates DNA-DNA hybridizations. Syst. Appl. Microbiol. 26, 203-210 (2003).
47. Xu, L. M., Ge, C., Cui, Z., Li, J., Fan, H.: Bradyrhizobium liaoningense sp. nov., isolated from the root nodules of soybeans. Int. J. Syst. Bacteriol. 45, 706-711 (1995).
48. Yao, Z. Y., Kan, F. L., Wang, E. T., Chen, W. X.: Characterization of rhizobia that nodulate legume species within the genus Lespedeza and description of Bradyrhizobium yuanmingense sp. nov. Int. J. Syst. Evol. Microbiol. 52, 2219-2230 (2002).
49. Zhang, X., Kaijalainen, N. G., Terefework, S., Paulin, L., Tighe, S. W., Graham, P. H., Lindström, K. Phylogeny and Diversity of Bradyrhizobium strains isolated from the root nodules of peanut (Arachis hypogaea) in Sichuan, China. Syst. Appl. Microbiol. 22, 378-386 (1999).