Case of Localized Recombination in 23S rRNA Genes from Divergent Bradyrhizobium Lineages Associated with Neotropical Legumes

Applied and Environmental Microbiology

Volumn 67, Issue 5, 2001, Pages 2076-2082

  Parker, Matthew A ^a  

^a BINGHAMTON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ISOENZYME; NITROGENASE; RNA 16S; RNA 23S;

ARTICLE; BACTERIAL GENE; BRADYRHIZOBIUM; DNA SEQUENCE; ELECTROPHORESIS; GENETIC RECOMBINATION; GENETICS; LEGUME; MEDICINAL PLANT; METABOLISM; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; RNA GENE; TROPIC CLIMATE;

BASE SEQUENCE; BRADYRHIZOBIUM; ELECTROPHORESIS; FABACEAE; GENES, BACTERIAL; GENES, RRNA; ISOENZYMES; MOLECULAR SEQUENCE DATA; NITROGENASE; PHYLOGENY; PLANTS, MEDICINAL; RECOMBINATION, GENETIC; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 23S; SEQUENCE ANALYSIS, DNA; TROPICAL CLIMATE;

EID: 0035344698     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.67.5.2076-2082.2001     Document Type: Article

References (44)

1. Amarger, N., V. Macheret, and G. Laguerre. 1997. Rhizobium gallicum sp. nov. and Rhizubium giardinii sp. nov., from Phaseolus vulgaris nodules. Int. J. Syst. Bacteriol. 47:996-1006.
2. Barrera, L. L., M. E. Trujillo, M. Goodfellow, F. J. Garcia, I. Hernandez-Lucas, G. Davila, P. van Berkum, and E. Martinez-Romero. 1997. Biodiversity of bradyrhizohia nodulating Lupinus spp. Int. J. Syst. Bacteriol. 47:1086-1091.
3. Cohan, F. M. 1995. Does recombination constrain neutral divergence among bacterial taxa? Evolution 49:164-175.
4. Doyle, J. J., and J. L. Doyle. 1993. Chloroplast DNA phylogeny of the Papilionoid legume Tribe Phaseoleae. Syst. Bot. 18:309-327.
5. Doyle, J. J., J. L. Doyle, J. A. Ballenger, E. E. Dickson, T. Kajita, and H. Ohashi. 1997. A phylogeny of the chloroplast gene rbcL in the Leguminosae: taxonomic correlations and insights into the evolution of nodulation. Am. J. Bot. 84:541-554.
6. DuBose, R. F., D. E. Dykhuizen, and D. L. Hartl. 1988. Genetic exchange among natural isolates of bacteria: recombination within the phoA gene of Escherichia coli. Proc. Natl. Acad. Sci. USA 85:7036-7040.
7. Dupuy, N., A. Willems, B. Pot, D. Dewettinck, I. Vandenbruaene, G. Maestrojuan, B. Dreyfus, K. Kersters, M. D. Collins, and M. Gillis. 1994. Phenotypic and genotypic characterization of bradyrhizobia nodulating the leguminous tree Acacia albida. Int. J. Syst. Bacteriol. 44:461-473.
8. Dykhuizen, D. E., and L. Green. 1991. Recombination in Escherichia coli and the definition of biological species. J. Bacteriol. 173:7257-7268.
9. Eardly, B. D., F.-S. Wang, and P. van Berkum. 1996. Corresponding 16S rRNA gene segments in Rhizobiaceae and Aeromonas yield discordant phylogenies. Plant Soil 186:69-74.
10. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
11. Foster, R. B., and N. V. L. Brokaw. 1996. Structure and history of the vegetation on Barro Colorado Island, p. 67-81. In E. G. Leigh, A. S. Rand, and D. M. Windsor (ed.), The ecology of a tropical forest: seasonal rhythms and long-term changes, 2nd ed. Smithsonian Institution, Washington, D.C.
12. Graham, P. H., M. J. Sadowsky, H. H. Keyser, Y. M. Barnet, R. S. Bradley, J. E. Cooper, D. J. de Ley, B. D. W. Jarvis, E. B. Roslycky, B. W. Strijdom, and J. P. W. Young. 1991. Proposed minimum standards for the description of new genera and species of root- and stem-nodulating bacteria. Int. J. Syst. Bacteriol. 41:582-587.
13. Grassly, N. C., and E. C. Holmes. 1997. A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol. Biol. Evol. 14:239-247.
14. Lafay, B., and J. J. Burdon. 1998. Molecular diversity of rhizobia occurring on native shrubby legumes in southeastern Australia. Appl. Environ. Microbiol. 64:3989-3997.
15. Lawrence, J. G., and H. Ochman. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95:9413-9417.
16. Ludwig, W., R. Rossello-Mora, R. Aznar, S. Klugbauer, S. Spring, K. Reetz, C. Beimfohr, E. Brockmann, G. Kirchof, S. Dorn, M. Bachleitner, N. Klugbauer, N. Springer, D. Lane, R. Nietupsky, M. Weizenegger, and K.-H. Schleifer. 1995. Comparative sequence analysis of 23S rRNA from Proteobacteria. Syst. Appl. Microbiol. 18:164-188.
17. Molouba, F., J. Lorquin, A. Willems, B. Hoste, E. Giraud, B. Dreyfus, M. Gillis, P. de Lajudie, and C. Masson-Boivin. 1999. Photosynthetic bradyrhizobia from Aeschynomene spp. are specific to stem-nodulating species and form a separate 16S rihosomal DNA restriction fragment length polymorphism group. Appl. Environ. Microbiol. 65:3084-3094.
18. Nelson, K. E., R. A. Clayton, S. R. Gill, et al. 1999. Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature 399:323-329.
19. Parker, M. A. 1999. Relationships of bradyrhizobia from the legumes Apios americana and Desmodium glutinosum. Appl. Environ. Microbiol. 65:4914-4920.
20. Parker, M. A. 2000. Divergent Bradyrhizobium symbionts on Tachigali versi-color from Barro Colorado Island, Panama. Syst. Appl. Microbiol. 23:585-590.
21. Parker, M. A., and A. Lunk. 2000. Relationships of bradyrhizobia from Platypodium and Machaerium (Papilionoideae tribe Dalbergieae) on Barro Colorado Island. Panama. Int. J. Syst. Evol. Microbiol. 50:1179-1186.
22. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
23. Sawyer, S. 1989. Statistical tests for detecting gene conversion. Mol. Biol. Evol. 6:526-538.
24. Segovia, L., J. P. W. Young, and E. Martinez-Romero. 1993 Reclassification of American Rhizobium leguminosarum biovar phaseoli type I strains as Rhizobium etli sp. nov. Int. J. Syst. Bacteriol. 43:374-377.
25. Selander, R. K., D. A. Caugant, H. Ochman, J. M. Musser, M. N. Gilmour, and T. S. Whittam. 1986. Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl. Environ. Microbiol. 51:873-884.
26. Selenska-Pobell, S., and E. Evguenieva-Hackenberg. 1995. Fragmentation of the large-subunit rRNA in the family Rhizobiaceae. J. Bacteriol. 177:6993-6998.
27. Spoerke, J. M., H. H. Wilkinson, and M. A. Parker. 1996. Nonrandom genotypic associations in a legume-Bradyrhizobium mutualism. Evolution 50:146-154.
28. Spratt, B. G., and M. C. J. Maiden. 1999. Bacterial population genetics, evolution and epidemiology. Phil. Trans. R. Soc. Lond. B 354:701-710.
29. Stackebrandt, E., and B. M. Goebel. 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.
30. Sterner, J. P., and M. A. Parker. 1999. Diversity and relationships of bradyrhizobia from Amphicarpaea bracteata based on partial nod and ribosomal sequences. Syst. Appl. Microbiol. 22:387-392.
31. Thies, J. E., B. B. Bohlool, and P. W. Singleton. 1991. Subgroups of the cowpea miscellany: symbiotic specificity within Bradyrhizobium spp. for Vigna unguiculata, Phaseolus lunatis, Arachis hypogaea, and Macroptilium atropurpureum. Appl. Environ. Microbiol. 57:1540-1545.
32. Thompson, J. D., D. G. Higgans, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment thorugh sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
33. Turk, D., and H. H. Keyser. 1992. Rhizobia that nodulate tree legumes: specificity of the host for nodulation and effectiveness. Can. J. Microbiol. 38:451-460.
34. Vincent, J. M. 1970. A manual for the practical study of the root-nodule bacteria. Blackwell, Oxford, U.K.
35. Wang, E. T., P. van Berkum, X. H. Sui, D. Beyene, W. X. Chen, and E. Martinez-Romero. 1999. Diversity of rhizobia associated with Amorpha fruticosa isolated from Chinese soils and description of Mesorhizobium amorphae sp. nov. Int. J. Syst. Bacteriol. 49:51-65.
36. Wang, Y., and Z. Zhang. 2000. Comparative sequence analyses reveal frequent occurrence of short segments containing an abnormally high number of non-random base variations in bacterial rRNA genes. Microbiology 146: 2845-2854.
37. Wilkinson, H. H., J. M. Spoerke, and M. A. Parker. 1996. Divergence in symbiotic compatibility in a legume-Bradyrhizobium mutualism. Evolution 50:1470-1477.
38. Wilson, J. K. 1994. Preparation of genomic DNA from bacteria, p. 2.4.1-2.4.5. In F. M. Ausubel (ed.), Current protocols in molecular biology. John Wiley, New York, N.Y.
39. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.
40. 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.
41. Yap, W. H., Z. Zhang, and Y. Wang. 1999. Distinct types of rRNA operons exist in the genome of the acctinomycete Thermomonospora chromogena and evidence for horozontal transfer of an entire rRNA operon. J. Bacteriol. 181:5201-5209.
42. Young, J. P. W., and K. E. Haukka. 1996. Diversity and phylogeny of rhizobia. New Phytol. 133:87-94.
43. Zhou, J., L. D. Bowler, and B. G. Spratt. 1997. Interspecies recombination, and phylogenetic distortions, within the glutamine synthetase and shikimate dehydrogenase genes of Neisseria meningitidis and commensal Neisseria species. Mol. Microbiol. 23:799-812.
44. Zuker, M., D. H. Mathews, and D. H. Turner. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide, p. 11-43. In J. Barciszewski and B. F. C. Clark (ed.), RNA biochemistry and biotechnology. NATO ASI Series. Kluwer Academic Publishers, Amsterdam, The Netherlands.