Skip to main content
NCBI home page
Applied and Environmental Microbiology logoLink to Applied and Environmental Microbiology
. 1994 Aug;60(8):2772–2778. doi: 10.1128/aem.60.8.2772-2778.1994

Genetic Structure of Rhizobium leguminosarum biovar trifolii and viciae Populations Found in Two Oregon Soils under Different Plant Communities †

Steven R Strain 1,2, Kamtin Leung 1, Thomas S Whittam 3, Frans J de Bruijn 4, Peter J Bottomley 1,2,*
PMCID: PMC201722  PMID: 16349348

Abstract

An investigation was carried out to determine the genetic structure in soil populations of Rhizobium leguminosarum bv. trifolii and viciae at each of two Oregon sites (A and C) that were 1 km apart. Although the soils were similar, the plant communities were quite different because grazing by domestic animals had been allowed (site A) or prevented (site C). Analysis of allelic variation at 13 enzyme-encoding loci by multilocus enzyme electrophoresis delineated 202 chromosomal types (ETs) among a total of 456 isolates representing two populations of R. leguminosarum bv. trifolii (AT and CT) and two populations of R. leguminosarum bv. viciae (AV and CV). Regardless of their site of origin or biovar affiliation, isolates of the same ET were confirmed to be more closely related to each other than to isolates of other ETs by repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus sequences and the PCR technique. Despite the wide range in densities of the Rhizobium populations (<102 to >105/g of soil), their overall genetic diversities were similar (mean genetic diversity, 0.45 to 0.51), indicating that low-density populations of soil-borne bacterial species are not necessarily of little genetic diversity. Linkage disequilibrium analysis revealed significant multilocus structure (nonrandom associations of alleles) within each of the four populations. From a combination of cluster and linkage disequilibrium analyses, a total of eight distinct groups of ETs were defined in the four populations. Two groups (I and III) contributed significant numbers of ETs and isolates to each population. The two populations of R. leguminosarum bv. viciae (AV and CV) exhibited similar genetic structures despite existing at different densities, in different plant communities, and in the presence (CV) or absence (AV) of their local Vicia hosts. In contrast, total linkage disequilibrium was partitioned differently in two biovar populations occupying the same soil (AV and AT), with disequilibrium in the latter being due entirely to the presence of group V.

Full text

PDF
2772

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Almendras A. S., Bottomley P. J. Influence of Lime and Phosphate on Nodulation of Soil-Grown Trifolium subterraneum L. by Indigenous Rhizobium trifolii. Appl Environ Microbiol. 1987 Sep;53(9):2090–2097. doi: 10.1128/aem.53.9.2090-2097.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bottomley P. J., Dughri M. H. Population Size and Distribution of Rhizobium leguminosarum bv. trifolii in Relation to Total Soil Bacteria and Soil Depth. Appl Environ Microbiol. 1989 Apr;55(4):959–964. doi: 10.1128/aem.55.4.959-964.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Brown A. H., Feldman M. W., Nevo E. Multilocus Structure of Natural Populations of HORDEUM SPONTANEUM. Genetics. 1980 Oct;96(2):523–536. doi: 10.1093/genetics/96.2.523. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Brown A. H., Feldman M. W. Population structure of multilocus associations. Proc Natl Acad Sci U S A. 1981 Sep;78(9):5913–5916. doi: 10.1073/pnas.78.9.5913. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Demezas D. H., Reardon T. B., Watson J. M., Gibson A. H. Genetic Diversity among Rhizobium leguminosarum bv. Trifolii Strains Revealed by Allozyme and Restriction Fragment Length Polymorphism Analyses. Appl Environ Microbiol. 1991 Dec;57(12):3489–3495. doi: 10.1128/aem.57.12.3489-3495.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Istock C. A., Duncan K. E., Ferguson N., Zhou X. Sexuality in a natural population of bacteria--Bacillus subtilis challenges the clonal paradigm. Mol Ecol. 1992 Aug;1(2):95–103. doi: 10.1111/j.1365-294x.1992.tb00161.x. [DOI] [PubMed] [Google Scholar]
  7. Leung K., Strain S. R., de Bruijn F. J., Bottomley P. J. Genotypic and Phenotypic Comparisons of Chromosomal Types within an Indigenous Soil Population of Rhizobium leguminosarum bv. trifolii. Appl Environ Microbiol. 1994 Feb;60(2):416–426. doi: 10.1128/aem.60.2.416-426.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Leung K., Yap K., Dashti N., Bottomley P. J. Serological and Ecological Characteristics of a Nodule-Dominant Serotype from an Indigenous Soil Population of Rhizobium leguminosarum bv. trifolii. Appl Environ Microbiol. 1994 Feb;60(2):408–415. doi: 10.1128/aem.60.2.408-415.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Levin B. R. Periodic selection, infectious gene exchange and the genetic structure of E. coli populations. Genetics. 1981 Sep;99(1):1–23. doi: 10.1093/genetics/99.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Nei M. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics. 1978 Jul;89(3):583–590. doi: 10.1093/genetics/89.3.583. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Nei M. F-statistics and analysis of gene diversity in subdivided populations. Ann Hum Genet. 1977 Oct;41(2):225–233. doi: 10.1111/j.1469-1809.1977.tb01918.x. [DOI] [PubMed] [Google Scholar]
  12. Selander R. K., Caugant D. A., Ochman H., Musser J. M., Gilmour M. N., Whittam T. S. Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl Environ Microbiol. 1986 May;51(5):873–884. doi: 10.1128/aem.51.5.873-884.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Selander R. K., Levin B. R. Genetic diversity and structure in Escherichia coli populations. Science. 1980 Oct 31;210(4469):545–547. doi: 10.1126/science.6999623. [DOI] [PubMed] [Google Scholar]
  14. Smith J. M., Smith N. H., O'Rourke M., Spratt B. G. How clonal are bacteria? Proc Natl Acad Sci U S A. 1993 May 15;90(10):4384–4388. doi: 10.1073/pnas.90.10.4384. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Souza V., Eguiarte L., Avila G., Cappello R., Gallardo C., Montoya J., Piñero D. 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. 1994 Apr;60(4):1260–1268. doi: 10.1128/aem.60.4.1260-1268.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Souza V., Nguyen T. T., Hudson R. R., Piñero D., Lenski R. E. Hierarchical analysis of linkage disequilibrium in Rhizobium populations: evidence for sex? Proc Natl Acad Sci U S A. 1992 Sep 1;89(17):8389–8393. doi: 10.1073/pnas.89.17.8389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Whittam T. S., Ochman H., Selander R. K. Geographic components of linkage disequilibrium in natural populations of Escherichia coli. Mol Biol Evol. 1983 Dec;1(1):67–83. doi: 10.1093/oxfordjournals.molbev.a040302. [DOI] [PubMed] [Google Scholar]
  18. Whittam T. S., Ochman H., Selander R. K. Multilocus genetic structure in natural populations of Escherichia coli. Proc Natl Acad Sci U S A. 1983 Mar;80(6):1751–1755. doi: 10.1073/pnas.80.6.1751. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Young J. P., Demetriou L., Apte R. G. Rhizobium Population Genetics: Enzyme Polymorphism in Rhizobium leguminosarum from Plants and Soil in a Pea Crop. Appl Environ Microbiol. 1987 Feb;53(2):397–402. doi: 10.1128/aem.53.2.397-402.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. de Bruijn F. J. 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. 1992 Jul;58(7):2180–2187. doi: 10.1128/aem.58.7.2180-2187.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Applied and Environmental Microbiology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES