Rhizobium huautlense sp. nov., a symbiont of Sesbania herbacea that has a close phylogenetic relationship with Rhizobium galegae

International Journal of Systematic Bacteriology

Volumn 48, Issue 3, 1998, Pages 687-699

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

^a INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

^b AGRICULTURAL RESEARCH SERVICE   (United States)

^c UNIVERSITY OF MARYLAND   (United States)

^d CHINA AGRICULTURAL UNIVERSITY   (China)

^e UNIVERSIDAD AUTÓNOMA DEL ESTADO DE MORELOS   (Mexico)

Author keywords

Nitrogen fixers; Rhizobium huautlense sp. nov.; Sesbania herbacea; Symbionts

Indexed keywords

RIBOSOME RNA; RNA 16S;

ARTICLE; MEXICO; NITROGEN FIXATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT GROWTH; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RHIZOBIUM; SEQUENCE HOMOLOGY; STRAIN DIFFERENCE; SYMBIOSIS;

AGROBACTERIUM VITIS; NEGIBACTERIA; RHIZOBIUM GALEGAE; RHIZOBIUM HUAUTLENSE; RHIZOBIUM LEGUMINOSARUM; SESBANIA; SESBANIA HERBACEA; VITIS;

EID: 0031853141     PISSN: 00207713     EISSN: None     Source Type: Journal    
DOI: 10.1099/00207713-48-3-687     Document Type: Article

References (62)

1. Allen, O. N. & Allen, E. K. (1980). The Leguminosae: a source book of characteristics, uses, and nodulation. The University of Wisconsin Press, Madison, WI.
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.
3. Becker, M., Ladha, J. K. & Ottow, J. C. (1988). Stem-nodulating legumes as green manure for lowland rice. Philipp J Crop Sci 13, 121-127.
4. Brenner, D. J., Fanning, G. R., Rake, A. V. & Johnson, K. E. (1969). A batch procedure for thermal elution of DNA from hydroxyapatite. Anal Biochem 28, 447-460.
5. Britten, R. J. & Kohne, D. E. (1966). Nucleotide sequence repetition in DNA. Carnegie Instit Wash Year Book 65, 78-106.
6. Brown, A. H. D., Feldman, M. W. & Nevo, E. (1980). Multilocus structure of natural populations of Hordeum spontaneum. Genetics 96, 523-536.
7. Caballero-Mellado, J. & Martínez-Romero, E. (1994). Limited genetic diversity in the endophytic sugarcane bacterium Acetobacter diazotrophicus. Appl Environ Microbiol 61, 1532-1537.
8. 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, 392-397.
9. 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.
10. de Faria, S. M., Lewis, G. P., Sprent, J. I. & Sutherland, J. M. (1989). Occurrence of nodulation in the Leguminosae. New Phytol 111, 617-629.
11. 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.
12. De Ley, J. (1970). Reexamination of the association between melting point, buoyant density, and chemical base composition of DNA. J Bacteriol 101, 738-754.
13. Dreyfus, B. L. & Dommergues, Y. R. (1981). Nitrogen-fixing nodules induced by Rhizobium on the stem of the tropical legume Sesbania rostrata. FEMS Microbiol Lett 10, 313-317.
14. 2 as the sole nitrogen source. Appl Environ Microbiol 45, 711-713.
15. 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.
16. Elkan, G. H. (1992). Taxonomy of the rhizobia. Can J Microbiol 38, 446-450.
17. Felsenstein, J. (1993). PHYLIP (phylogenetic inference package) version 3.5c. Department of Genetics, University of Washington, Seattle.
18. Frank, B. (1889). Ueber die Pilzsymbiose der Leguminosen. Ber Dtsch Bot Ges 7, 332-346
19. 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.
20. 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.
21. Jarvis, B. D. W., van Berkum, P., Chen, W. X., Nour, S. M., Fernandez, 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.
22. 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.
23. Kaijalainen, S. & Lindström, K. (1989). Restriction fragment length polymorphism analysis of Rhizobium galegae strains. J Bacteriol 171, 5562-5566.
24. Kumar, S., Tamura, K. & Nei, M. (1993). MEGA: Molecular Evolutionary Genetics Analysis, version 1.01. The Pennsylvania State University, University Park, PA 16802.
25. Ladha, J. K., Pareek, R. P. & Becker, M. (1992). Stem-nodulating legame-Rhizobium symbiosis and its agronomic use in lowland rice. Adv Soil Sci 20, 147-192.
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. Leonard, L. T. (1943). A simple assembly for use in the testing for cultures of rhizobia. J Bacteriol 45, 523-527.
28. Lindström, K. (1989). Rhizobium galegae, a new species of legume root nodule bacteria. Int J Syst Bacteriol 39, 365-367.
29. Lindström, K. & Jarvis, B. D. W. (1983). DNA homology, phage-typing, and cross-nodulation studies of rhizobia infecting Galega species. Can J Microbiol 29, 781-789.
30. Martínez, E., Palacios, R. & Sanchez, F. (1987). Nitrogen-fixing nodules induced by Agrobacterium tumefaciens harboring Rhizobium phaseoli plasmids. J Bacteriol 169, 2828-2834.
31. 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, 411-426.
32. Maynard Smith, J., Smith, N. H., O'Rourke, M. & Spratt, B. J. (1993). How clonal are bacteria? Proc Natl Acad Sci USA 90, 4384-4388.
33. McArthur, J. V., Kovacic, D. A. & Smith, M. H. (1988). Genetic diversity in natural populations of a soil bacterium across a landscape gradient. Proc Natl Acad Sci USA 85, 9621-9624.
34. 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.
35. Moyer, C. L., Tiedje, J. M., Dobbs, F. C. & Karl, D. M. (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.
36. Navarro, R. B., Vargas, A. A. T., Schröder, E. C. & van Berkum, P. (1993). Uptake hydrogenase (Hup) in common bean (Phaseolus vulgaris) symbioses. Appl Environ Microbiol 60, 4162-4165.
37. 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.
38. Noel, K. D., Sánchez, F., Fernandez, L., Leemans, J. & Cevallos, M. A. (1984). Rhizobium phaseoli symbiotic mutants with transposon Tn5 insertions. J. Bacteriol 158, 148-155.
39. Novikova, N. I., Pavlova, E. A., Vorobjev, N. I. (1994). Numerical taxonomy of Rhizobium strains from legumes of the temperate zone. Int J Syst Bacteriol 44, 734-742.
40. Novikova, N. I. & Safronova, V. (1992). Transconjugants of Agrobacterium radiobacter harbouring sym genes of R. galegae can form an effective symbiosis with Medicago sativa. FEMS Microbiol Lett 93, 262-268.
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. Rana, D. & Krishnan, H. B. (1995). A new root-nodulating symbiont of the tropical legume Sesbania, Rhizobium sp. SIN-1, is closely related to R. galegae, a species that nodulates temperate legumes. FEMS Microbiol Lett 134, 19-25.
43. Rhoads, D. D. & Roufa, D. J. (1989). Seqaid II (tm) version 3.5. Molecular Genetics Laboratory, Kansas State University.
44. Rinaudo, G., Orenga, S., Fernandez, M. P., Meugnier, H. & Bardin, R. (1991). DNA homologies among members of the genus Azorhizobium and other stem-nodulating bacteria isolated from the tropical legume Sesbania rostrata. Int J Syst Bacteriol 41, 114-120.
45. Romero, D., Brom, S., Martínez-S., 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. Sawada, H., Ieki, H., Oyaizu, H. & Matsumoto, S. (1993). Proposal for rejection of Agrobacterium tumefaciens and revised descriptions for the genus Agrobacterium and for Agrobacterium radiobacter and Agrobacterium rhizogenes. Int J Syst Bacteriol 43, 694-702.
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. Int 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. Selander, R. K., McKinney, R. M., Whittam, T. S., Bibb, W. F., Brenner, D. J., Nolte, F. S. & Pattison, P. E. (1985). Genetic structure of populations of Legionella pneumophila. J Bacteriol 163, 1021-1037.
50. Souza, V., Eguiarte, L., Avila, G., Cappello, R., Gallardo, C., Montoya, J. & Piñero, D. (1994). Genetic structure of Rhizobium etli biovar phaseoli associated with wild and cultivated bean plants (Phaseolus vulgaris and Phaseolus coccineus) in Morelos, Mexico. Appl Environ Microbiol 61, 1261-1268.
51. 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.
52. Suomnen, L., Jugens, G., Roos, C., Paulin, L. & Lindström, K. (1995). Identification of nodulation gene clusters in Phizobium galegae strain HAMBI 1174. In Nitrogen Fixation: Fundamentals and Applications, p. 333. Edited by I. A. Tikhonovich, N. A. Provorov, V. I. Romanov & W. E. Newton. Dordrecht, The Netherlands: Kluwer.
53. van Berkum, P. (1990). Evidence for a third uptake hydrogenase phenotype among the soybean bradyrhizobia. Appl Environ Microbiol 56, 3835-3841.
54. van Berkum, P., Beyene, D. & Eardly, B. D. (1996). Phylogenetic relationships among Rhizobium species nodulating the common bean (Phaseolus vulgaris L.). Int J Bacteriol 46, 240-244.
55. 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.
56. Vincent, J. M. (1970). A manual for the practical study of root-nodule bacteria. IBP handbook 15. Oxford: Blackwell Scientific Publications.
57. Wedlock, D. N. & Jarvis, B. D. W. (1986). DNA homologies between Rhizobium fredii, rhizobia that nodulate Galega sp., and other Rhizobium and Bradyrhizobium species. Int J Syst Bacteriol 36, 550-558.
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. Whittam, T. S., Ochman, H. & Selander, R. K. (1983). Multilocus genetic structure in natural populations of Escherichia coli. Proc Natl Acad Sci USA 80, 1751-1755.
60. Willems, A. & Collins, M. D. (1993). Phylogenetic analysis of rhizobia and agrobacteria based on 16S rRNA gene sequence. Int J Syst Bacteriol 43, 305-313.
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. Young, J. P. W. & Haukka, K. E. (1996). Diversity and phytogeny of rhizobia. New Phytol 133, 87-94.