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. 1996 Aug;62(8):2904–2909. doi: 10.1128/aem.62.8.2904-2909.1996

Amplification of 16S rRNA genes from Frankia strains in root nodules of Ceanothus griseus, Coriaria arborea, Coriaria plumosa, Discaria toumatou, and Purshia tridentata.

D R Benson 1, D W Stephens 1, M L Clawson 1, W B Silvester 1
PMCID: PMC168076  PMID: 8702283

Abstract

To study the global diversity of plant-symbiotic nitrogen-fixing Frankia strains, a rapid method was used to isolate DNA from these actinomycetes in root nodules. The procedure used involved dissecting the symbiont from nodule lobes; ascorbic acid was used to maintain plant phenolic compounds in the reduced state. Genes for the small-subunit rRNA (16S ribosomal DNA) were amplified by the PCR, and the amplicons were cycle sequenced. Less than 1 mg (fresh weight) of nodule tissue and fewer than 10 vesicle clusters could serve as the starting material for template preparation. Partial sequences were obtained from symbionts residing in nodules from Ceanothus griseus, Coriaria arborea, Coriaria plumosa, Discaria toumatou, and Purshia tridentata. The sequences obtained from Ceonothus griseus and P. tridentata nodules were identical to the sequence previously reported for the endophyte of Dryas drummondii. The sequences from Frankia strains in Coriaria arborea and Coriaria plumosa nodules were identical to one another and indicate a separate lineage for these strains. The Frankia strains in Discaria toumatou nodules yielded a unique sequence that places them in a lineage close to bacteria that infect members of the Elaeagnaceae.

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Selected References

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  1. Benson D. R. Isolation of frankia strains from alder actinorhizal root nodules. Appl Environ Microbiol. 1982 Aug;44(2):461–465. doi: 10.1128/aem.44.2.461-465.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Benson D. R., Silvester W. B. Biology of Frankia strains, actinomycete symbionts of actinorhizal plants. Microbiol Rev. 1993 Jun;57(2):293–319. doi: 10.1128/mr.57.2.293-319.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bloom R. A., Mullin B. C., Tate R. L., 3rd DNA restriction patterns and DNA-DNA solution hybridization studies of Frankia isolates from Myrica pennsylvanica (bayberry). Appl Environ Microbiol. 1989 Sep;55(9):2155–2160. doi: 10.1128/aem.55.9.2155-2160.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Maidak B. L., Larsen N., McCaughey M. J., Overbeek R., Olsen G. J., Fogel K., Blandy J., Woese C. R. The Ribosomal Database Project. Nucleic Acids Res. 1994 Sep;22(17):3485–3487. doi: 10.1093/nar/22.17.3485. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Mirza M. S., Hahn D., Dobritsa S. V., Akkermans A. D. Phylogenetic studies on uncultured Frankia populations in nodules of Datisca cannabina. Can J Microbiol. 1994 Apr;40(4):313–318. doi: 10.1139/m94-051. [DOI] [PubMed] [Google Scholar]
  7. Mirza M. S., Hameed S., Akkermans A. D. Genetic diversity of Datisca cannabina-compatible Frankia strains as determined by sequence analysis of the PCR-amplified 16S rRNA gene. Appl Environ Microbiol. 1994 Jul;60(7):2371–2376. doi: 10.1128/aem.60.7.2371-2376.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Newcomb W., Wood S. M. Morphogenesis and fine structure of Frankia (Actinomycetales): the microsymbiont of nitrogen-fixing actinorhizal root nodules. Int Rev Cytol. 1987;109:1–88. doi: 10.1016/s0074-7696(08)61719-2. [DOI] [PubMed] [Google Scholar]
  9. Nick G., Paget E., Simonet P., Moiroud A., Normand P. The nodular endophytes of Coriaria spp. form a distinct lineage within the genus Frankia. Mol Ecol. 1992 Oct;1(3):175–181. doi: 10.1111/j.1365-294x.1992.tb00173.x. [DOI] [PubMed] [Google Scholar]
  10. Normand P., Cournoyer B., Simonet P., Nazaret S. Analysis of a ribosomal RNA operon in the actinomycete Frankia. Gene. 1992 Feb 1;111(1):119–124. doi: 10.1016/0378-1119(92)90612-s. [DOI] [PubMed] [Google Scholar]
  11. Normand P., Orso S., Cournoyer B., Jeannin P., Chapelon C., Dawson J., Evtushenko L., Misra A. K. Molecular phylogeny of the genus Frankia and related genera and emendation of the family Frankiaceae. Int J Syst Bacteriol. 1996 Jan;46(1):1–9. doi: 10.1099/00207713-46-1-1. [DOI] [PubMed] [Google Scholar]
  12. Rouvier C., Prin Y., Reddell P., Normand P., Simonet P. Genetic diversity among Frankia strains nodulating members of the family Casuarinaceae in Australia revealed by PCR and restriction fragment length polymorphism analysis with crushed root nodules. Appl Environ Microbiol. 1996 Mar;62(3):979–985. doi: 10.1128/aem.62.3.979-985.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Simonet P., Bosco M., Chapelon C., Moiroud A., Normand P. Molecular characterization of Frankia microsymbionts from spore-positive and spore-negative nodules in a natural alder stand. Appl Environ Microbiol. 1994 Apr;60(4):1335–1341. doi: 10.1128/aem.60.4.1335-1341.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. 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]
  15. Soltis D. E., Soltis P. S., Morgan D. R., Swensen S. M., Mullin B. C., Dowd J. M., Martin P. G. Chloroplast gene sequence data suggest a single origin of the predisposition for symbiotic nitrogen fixation in angiosperms. Proc Natl Acad Sci U S A. 1995 Mar 28;92(7):2647–2651. doi: 10.1073/pnas.92.7.2647. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Thompson J. D., Higgins D. G., Gibson T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov 11;22(22):4673–4680. doi: 10.1093/nar/22.22.4673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol. 1991 Jan;173(2):697–703. doi: 10.1128/jb.173.2.697-703.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]

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