Diversity of rhizobia associated with Amorpha fruticosa isolated from Chinese soils and description of Mesorhizobium amorphae sp. nov.

International Journal of Systematic Bacteriology

Volumn 49, Issue 1, 1999, Pages 51-65

  Wang, E T ^a,c   Van Berkum, P ^b   Sui, X H ^c   Beyene, D ^b   Chen, W X ^c   Martinez Romero E ^a  

^a INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

^b AGRICULTURAL RESEARCH SERVICE   (United States)

^c CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

Amorpha fruticosa; Diversity; Mesorhizobium amorphae; Polyphasic taxonomy; Rhizobia

Indexed keywords

ARTICLE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; DNA DNA HYBRIDIZATION; GENE SEQUENCE; GENETIC VARIABILITY; MESORHIZOBIUM AMORPHAE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RHIZOBIACEAE; STRAIN DIFFERENCE;

AMORPHA FRUTICOSA; ANIMALIA; BACTERIA (MICROORGANISMS); MESORHIZOBIUM AMORPHAE; NEGIBACTERIA; RHIZOBIACEAE;

EID: 0032913488     PISSN: 00207713     EISSN: None     Source Type: Journal    
DOI: 10.1099/00207713-49-1-51     Document Type: Article

References (64)

1. Allen, O. N. & Allen, E. K. (1981). The Leguminosae: a Source Book of Characteristics, Uses, and Nodulation. Madison, WI: University of Wisconsin Press.
2. Amarger, N., Marcheret, V. & Laguerre, G. (1997). Rhizobium gallicum sp. nov. and Rhizobium giardinii sp. nov. from Phaseolus vulgar is nodules. Int J Syst Bacteriol 47, 996-1006.
3. van Berkum, P. (1990). Evidence for a third uptake hydrogenase phenotype among the soybean bradyrhizobia. Appl Environ Microbiol 56, 3835-3841.
4. van Berkum, P., Beyene, D. & Eardly, B. D. (1996). Phylogenetic relationships among Rhizobium species nodulating the common bean (Phaseolus vulgaris L.). Int J Syst Bacteriol 46, 240-244.
5. van Berkum, P., Beyene, D., Bao, G., Campbell, T. A. & Eardly, B. D. (1998a). 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.
6. van Berkum, P., Ruihua, F., Campbell, T. A. & Eardly, B. D. (1998b). Some issues of relevance in the taxonomy of rhizobia. In Highlights on Nitrogen Fixation Research. Edited by E. Martínez & G. Hernández. New York: Plenum (in press).
7. Brown, A. H. D., Feldman, M. W. & Nevo, E. (1980). Multilocus structure of natural populations of Hordeum spontaneum. Genetics 96, 523-536.
8. Caballero-Mellado, J. & Martínez-Romero, E. (1994). Limited genetic diversity in the endophytic sugarcane bacterium Acetobacter diazotrophicus. Appl Environ Microbiol 60, 1532-1537.
9. Chen, W. X., Wang, E. T, Wang, S. Y., Li, Y. B., Chen, X. Q. & Li, Y. (1995). Characterization of Rhizobium tianshanense sp. nov., a moderately and slowly growing root nodule bacterium isolated from an arid saline environment in Xinjiang, People's Republic of China. Int J Syst Bacteriol 45, 153-159.
10. Chen, W. X., Yan, G. H. & Li, J. L. (1988). Numerical taxonomic study of fast-growing soybean rhizobia and a proposal that Rhizobium fredii be assigned to Sinorhizobium gen. nov. Int J Syst Bacteriol 38, 392-398.
11. Chirgwin, J. M., Przybyla, A. E., MacDonald, R. J. & Rutter, W. J. (1979). Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease. Biochemistry 18, 5294-5299.
12. Cilia, V., Lafay, B. & Christen, R. (1996). Sequence heterogeneities among 16S ribosomal RNA sequences and their effect on phylogenetic analyses at the species level. Mol Biol Evol 13, 451-461.
13. De Ley, J. (1970). Re-examination of the association between melting point, buoyant density, and chemical base composition of DNA. J Bacteriol 101, 738-754.
14. Dreyfus, B., Garcia, J. L. & Gillis, M. (1988). Characterization of Azorhizobium caulinodans gen. nov., sp. nov., a stem-nodulating nitrogen-fixing bacterium isolated from Sesbania rostrata. Int J Syst Bacteriol 38, 89-98.
15. Eardly, B. D., Wang, F. S., Whittam, T. S. & Selander, R. K. (1995). Species limits in Rhizobium populations that nodulate the common bean (Phaseolus vulgaris). Appl Environ Microbiol 58, 1809-1815.
16. Eckhardt, T. (1978). A rapid method for the identification of plasmid deoxyribonucleic acid in bacteria. Plasmid 1, 584-588.
17. Geniaux, E., Flores, M., Palacios, R. & Martínez, E. (1995). Presence of megaplasmids in Rhizobium tropici and further evidence of differences between the two R. tropici subtypes. Int J Syst Bacteriol 45, 392-394.
18. Graham, P. H., Sadowsky, M. J., Keyser, H. H. & 8 other authors (1991). Proposed minimal standards for the description of new genera and species of root- and stem-nodulating bacteria. Int J Syst Bacteriol 41, 582-587.
19. Hynes, M. F. & McGregor, N. F. (1990). Two plasmids other than the nodulation plasmid are necessary for formation of nitrogen-fixing nodules by Rhizobium leguminosarum. Mol Microbiol 4, 567-574.
20. Jarvis, B. D. W., van Berkum, P., Chen, W. X., Nour, S. M., Fernandes, M. P., Cleyet-Marel, J. C. & Gillis, M. (1997). Transfer of Rhizobium loti, Rhizobium huakuii, Rhizobium ciceri, Rhizobium mediterraneum, and Rhizobium tianshanense to a new genus: Mesorhizobium. Int J Syst Bacteriol 47, 895-898.
21. Jordan, D. C. (1984). Family III. Rhizobiaceae. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 234-242. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
22. Jukes, T. H. & Cantor, C. R. (1969). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21-132. Edited by H. N. Munro. New York: Academic Press.
23. Konoshima, T., Terada, H., Kokumai, M., Kozuka, M., Tokuda, H., Estes, J. R., Li, L., Wang, H. K. & Lee, K. H. (1993). Studies on inhibitors of skin tumour promotion. XII. Rotenoids from Amorpha fruticosa. J Nat Prod (Lloydia) 56, 843-848.
24. Kumar, S., Tamura, K. & Nei, M. (1993). MEGA: Molecular Evolutionary Genetics Analysis, version 1.01. The Pennsylvania State University, University Park, PA 16802, USA.
25. Ladha, J. K. & So, R. B. (1994). Numerical taxonomy of photosynthetic rhizobia nodulating Aeschynomene species. Int J Syst Bacteriol 44, 62-73.
26. Laguerre, G., Allard, M., Revoy, F. & Amarger, N. (1994). Rapid identification of rhizobia by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl Environ Microbiol 61, 56-63.
27. 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.
28. de Lajudie, P., Willems, A., Nick, G. & 9 other authors (1998). Characterization of tropical tree rhizobia and description of Mesorhizobium plurifarium sp. nov. Int J Syst Bacteriol 48, 369-382.
29. Leonard, L. T. (1943). A simple assembly for use in the testing for cultures of rhizobia. J Bacteriol 45, 523-527.
30. Maidak, B. L., Larsen, N., McCaughey, M. J., Overbeek, R., Olsen, G. J., Fogel, K., Blandy, J. & Woese, C. R. (1994). The ribosomal database project. Nucleic Acids Res 22, 3485-3487.
31. Martínez, E., Palacios, R. & Sánchez, F. (1987). Nitrogen-fixing nodules induced by Agrobacterium tumefaciens harboring Rhizobium phaseoli plasmids. J Bacteriol 169, 2828-2834.
32. Martínez, E., Romero, D. & Palacios, R. (1990). The Rhizobium genome. Crit Rev Plant Sci 9, 59-93.
33. Martínez-Romero, E. & Caballero-Mellado, J. (1996). Rhizobium phylogenies and bacterial genetic diversity. Crit Rev Plant Sci 15, 113-140.
34. Martínez-Romero, E., Segovia, L., Mercante, F. M., Franco, A. A., Graham, P. & Pardo, M. A. (1991). Rhizobium tropici, a novel species nodulating Phaseolus vulgaris L. beans and Leucaena sp. trees. Int J Syst Bacteriol 41, 417-426.
35. Maynard Smith, J., Smith, N. H., O'Rourke, M. & Spratt, B. G. (1993). How clonal are bacteria? Proc Natl Acad Sci USA 90, 4384-4388.
36. Mitscher, L. A., Park, Y. H., Al-Shamma, A., Hudson, P. B. & Haas, T. (1981). Amorfrutin A and B, bibenzyl antimicrobial agents from Amorpha fruticosa. Phytochemistry 20, 781-785.
37. Morett, E., Moreno, S. & Espin, G. (1988). Transcription analysis of the three nifH genes of Rhizobium phaseoli with gene fusion. Mol Gen Genet 213, 499-504.
38. Navarro, R. B., Vargas, A. A. T., Schroder, E. C. & van Berkum, P. (1993). Uptake hydrogenase (Hup) in common bean (Phaseolus vulgaris) symbioses. Appl Environ Microbiol 60, 4162-4165.
39. Nei, M. & Li, W. H. (1979). Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76, 5269-5273.
40. Noel, K. D., Sánchez, F., Fernandez, F., Leemans, J. & Cevallos, A. (1984). Rhizobium phaseoli symbiotic mutants with transposon Tn5 insertions. J Bacteriol 158, 148-155.
41. Oyaizu, H., Matsumoto, S., Minamisawa, K. & Gamou, T. (1993). Distribution of rhizobia in leguminous plants surveyed by phylogenetic identification. J Gen Appl Microbiol 39, 339-354.
42. Pérez-Ramirez, N. O., Rogel-Hernández, M. A., Wang, E. T. & Martínez-Romero, E. (1998). Seeds of Phaseolus vulgaris bean carry Rhizobium etli. FEMS Microbiol Ecol 26, 289-296.
43. Piñero, D., Martínez, E. & Selander, R. K. (1988). Genetic diversity and relationships among isolates from Rhizobium leguminosarum biovar phaseoli. Appl Environ Microbiol 54, 2825-2832.
44. Rhoads, D. D. & Roufa, D. J. (1989). Seqaid II (tm) version 3.5. Molecular Genetics Laboratory, Kansas State University, KS, USA.
45. Romero, D., Brom, S., Martínez-Salazar, J., de Lourdes Girard, M., Palacios, R. & Davila, G. (1991). Amplification and deletion of a nod-nif region in the symbiotic plasmid of Rhizobium phaseoli. J Bacteriol 173, 2435-2441.
46. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
47. Segovia, L., Young, J. P. W. & Martínez-Romero, E. (1993). Reclassification of American Rhizobium leguminosarum biovar phaseoli type I strains as Rhizobium etli sp. nov. InI J Syst Bacteriol 43, 374-377.
48. Selander, R. K., Caugant, D. A., Ochman, H., Musser, J. M., Gilmour, M. N. & Whittam, T. S. (1986). Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl Environ Microbiol 51, 873-884.
49. Sneath, P. H. A. & Sokal, R. R. (1973). Numerical Taxonomy. San Francisco: Freeman.
50. Souza, V., Nguyen, T. T., Hudson, R. R., Piñero, D. & Lenski, R. E. (1992). Hierarchical analysis of linkage disequilibrium in Rhizobium populations: evidence for sex? Proc Natl Acad Sci USA 89, 8389-8393.
51. 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.
52. Sullivan, J. T., Patrick, H. N., Lowther, W. L., Barry Scott, D. & Ronson, C. W. (1995). Nodulating strains of Rhizobium loti arise through chromosomal symbiotic gene transfer in the environment. Proc Natl Acad Sci USA 92, 8985-8989.
53. Sullivan, J. T., Eardly, B. D., van Berkum, P. & Ronson, C. W. (1996). Four unnamed species of nonsymbiotic rhizobia isolated from the rhizosphere of Lotus corniculatus. Appl Environ Microbiol 62, 2818-2825.
54. Tan, Z. Y., Xu, X. D., Wang, E. T., Gao, J. L., Martínez-Romero, E. & Chen, W. X. (1997). Phylogenetic and genetic relationships of Mesorhizobium tianshanense and related rhizobia. Int J Syst Bacteriol 47, 874-879.
55. Vincent, J. M. (1970). A Manual for the Practical Study of Root-nodule Bacteria. IBP handbook 15. Oxford: Blackwell Scientific Publications.
56. Wang, Y., Zhang, Z. & Ramanan, N. (1997). The actinomycete Thermobispora bispora contains two distinct types of transcriptionally active 16S rRNA genes. J Bacteriol 179, 3270-3276.
57. Wang, E. T., van Berkum, P., Beyene, D., Sui, X. H., Dorado, O., Chen, W. X. & Martínez-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.
58. Weisburg, W. G., Barns, S. M., Pelletier, D. A. & Lane, D. J. (1991). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173, 697-703.
59. Willems, A. & Collins, D. (1993). Phylogenetic analysis of rhizobia and agrobacteria based on 16S rRNA gene sequence. Int J Syst Bacteriol 43, 305-313.
60. Xu, Y. & Murooka, Y. (1995). A large plasmid isolated from Rhizobium huakuii bv Renge that includes genes for both nodulation of Astragalus sinicus cv. Japan and nitrogen-fixation. J Ferment Bioeng 80, 276-279.
61. Yanagi, M. & Yamasato, K. (1993). Phylogenetic analysis of the family Rhizobiaceae and related bacteria by sequencing of 16S rRNA gene using PCR and DNA sequencer. FEMS Microbiol Lett 107, 115-120.
62. Yelton, M. M., Yang, S. S., Edie, S. A. & Lim, S. T. (1983). Characterization of an effective salt-tolerant, fast-growing strain of Rhizobium japonicum. J Gen Microbiol 129, 1537-1547.
63. Young, J. P. W. (1985). Rhizobium population genetics: enzyme polymorphism in isolates from peas, clover, beans and lucerne grown in the same site. J Gen Microbiol 131, 2389-2408.
64. Young, J. P. W. & Haukka, K. E. (1996). Diversity and phylogeney of rhizobia. New Phytol 133, 87-94.