Skip to main content
PMC home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1991 Jul;173(13):4072–4078. doi: 10.1128/jb.173.13.4072-4078.1991

Phylogenetic relationships among Frankia genomic species determined by use of amplified 16S rDNA sequences.

S Nazaret 1, B Cournoyer 1, P Normand 1, P Simonet 1
PMCID: PMC208055  PMID: 2061287

Abstract

Actinomycetes of the genus Frankia establish a nitrogen-fixing symbiosis with a large number of woody dicotyledonous plants. Hundreds of strains isolated from various actinorhizal plants growing in different geographical areas have recently been classified into at least nine genomic species by use of the DNA-DNA hybridization technique (M.P. Fernandez, H. Meugnier, P.A.D. Grimont, and R. Bardin, Int. J. Syst. Bacteriol. 39:424-429, 1989). A protocol based on the amplification and sequencing of 16S ribosomal DNA segments was used to classify and estimate the phylogenetic relationships among eight different genomic species. A good correlation was established between the grouping of strains according to their 16S ribosomal DNA sequence homology and that based on total DNA homology, since most genomic species could be characterized by a specific sequence. The phylogenetic tree showed that strains belonging to the Alnus infectivity group are closely related to strains belonging to the Casuarina infectivity group and that strains of these two infectivity groups are well separated from strains of the Elaeagnus infectivity group, which also includes atypical strains isolated from the Casuarina group. This phylogenetic analysis was also very efficient for classifying previously unclassified pure cultures or unisolatable strains by using total DNA extracted directly from nodules.

Full text

PDF
4074

Selected References

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

  1. Benson D. R. The genus Frankia: actinomycete symbionts of plants. Microbiol Sci. 1988 Jan;5(1):9–12. [PubMed] [Google Scholar]
  2. Brosius J., Dull T. J., Sleeter D. D., Noller H. F. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol. 1981 May 15;148(2):107–127. doi: 10.1016/0022-2836(81)90508-8. [DOI] [PubMed] [Google Scholar]
  3. Callaham D., Deltredici P., Torrey J. G. Isolation and Cultivation in vitro of the Actinomycete Causing Root Nodulation in Comptonia. Science. 1978 Feb 24;199(4331):899–902. doi: 10.1126/science.199.4331.899. [DOI] [PubMed] [Google Scholar]
  4. Devereux R., He S. H., Doyle C. L., Orkland S., Stahl D. A., LeGall J., Whitman W. B. Diversity and origin of Desulfovibrio species: phylogenetic definition of a family. J Bacteriol. 1990 Jul;172(7):3609–3619. doi: 10.1128/jb.172.7.3609-3619.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Fitch W. M., Margoliash E. Construction of phylogenetic trees. Science. 1967 Jan 20;155(3760):279–284. doi: 10.1126/science.155.3760.279. [DOI] [PubMed] [Google Scholar]
  6. Gardes M., Bousquet J., Lalonde M. Isozyme Variation among 40 Frankia Strains. Appl Environ Microbiol. 1987 Jul;53(7):1596–1603. doi: 10.1128/aem.53.7.1596-1603.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Lane D. J., Pace B., Olsen G. J., Stahl D. A., Sogin M. L., Pace N. R. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985 Oct;82(20):6955–6959. doi: 10.1073/pnas.82.20.6955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Li W. H. Simple method for constructing phylogenetic trees from distance matrices. Proc Natl Acad Sci U S A. 1981 Feb;78(2):1085–1089. doi: 10.1073/pnas.78.2.1085. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Mullis K. B., Faloona F. A. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol. 1987;155:335–350. doi: 10.1016/0076-6879(87)55023-6. [DOI] [PubMed] [Google Scholar]
  10. Normand P., Bousquet J. Phylogeny of nitrogenase sequences in Frankia and other nitrogen-fixing microorganisms. J Mol Evol. 1989 Nov;29(5):436–447. doi: 10.1007/BF02602914. [DOI] [PubMed] [Google Scholar]
  11. Normand P., Simonet P., Bardin R. Conservation of nif sequences in Frankia. Mol Gen Genet. 1988 Aug;213(2-3):238–246. doi: 10.1007/BF00339587. [DOI] [PubMed] [Google Scholar]
  12. Pernodet J. L., Boccard F., Alegre M. T., Gagnat J., Guérineau M. Organization and nucleotide sequence analysis of a ribosomal RNA gene cluster from Streptomyces ambofaciens. Gene. 1989 Jun 30;79(1):33–46. doi: 10.1016/0378-1119(89)90090-5. [DOI] [PubMed] [Google Scholar]
  13. Prager E. M., Wilson A. C. Ancient origin of lactalbumin from lysozyme: analysis of DNA and amino acid sequences. J Mol Evol. 1988;27(4):326–335. doi: 10.1007/BF02101195. [DOI] [PubMed] [Google Scholar]
  14. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. doi: 10.1093/oxfordjournals.molbev.a040454. [DOI] [PubMed] [Google Scholar]
  15. Simonet P., Normand P., Moiroud A., Bardin R. Identification of Frankia strains in nodules by hybridization of polymerase chain reaction products with strain-specific oligonucleotide probes. Arch Microbiol. 1990;153(3):235–240. doi: 10.1007/BF00249074. [DOI] [PubMed] [Google Scholar]
  16. Winship P. R. An improved method for directly sequencing PCR amplified material using dimethyl sulphoxide. Nucleic Acids Res. 1989 Feb 11;17(3):1266–1266. doi: 10.1093/nar/17.3.1266. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Woese C. R., Gutell R., Gupta R., Noller H. F. Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol Rev. 1983 Dec;47(4):621–669. doi: 10.1128/mr.47.4.621-669.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES