Phylogenetic placement of uncultured Ceanothus microsymbionts using 16S rRNA gene sequences

Canadian Journal of Botany

Volumn 77, Issue 9, 1999, Pages 1208-1213

  Ritchie, Nancy J ^a   Myrold, David D ^a  

^a OREGON STATE UNIVERSITY   (United States)

Author keywords

16S rDNA; Ceanothus; Frankia

Indexed keywords

CONSENSUS SEQUENCE; GENE SEQUENCING; MAXIMUM LIKELIHOOD METHOD; NODULATION; PARSIMONY ANALYSIS; PHYLOGENY; RIBOSOMAL DNA; RIBOSOMAL RNA; SEQUENCE ALIGNMENT; SYMBIOSIS;

ACTINORHIZAL PLANT; BACTERIUM; PHYLOGENETICS; SYMBIONT;

CEANOTHUS AMERICANUS; CEANOTHUS THYRSIFLORUS; DRYAS DRUMMONDII; FRANKIA;

EID: 0033494754     PISSN: 00084026     EISSN: None     Source Type: Journal    
DOI: 10.1139/cjb-77-9-1208     Document Type: Conference Paper

References (24)

1. 1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
2. 2. Baker, D.D., and Mullin, B.C. 1994. Diversity of Frankia nodule endophytes of the actinorhizal shrub Ceanothus as assessed by RFLP patterns from single nodule lobes. Soil Biol. Biochem. 26: 547-542.
3. 3. Benson, D.R., Stephens, D.W., Clawson, M.L., and Silvester, W.B. 1996. Amplification of 16S rRNA genes from Frankia strains in root nodules of Ceanothus griseus, Coriaria arborea, Coriaria plumosa, and Discaria toumatou, and Purshia tridentata. Appl. Environ. Microbiol. 62: 2904-2909.
4. 4. Benson, D.R., and Silvester, W.B. 1993. Biology of Frankia strains, actinomycete symbionts of actinorhizal plants. Microbiol. Rev. 57: 293-319.
5. 5. Clawson, M.L., Caru, M., and Benson, D.R. 1998. Diversity of Frankia strains in root nodules of plants from the families Elaeagnaceae and Rhamnaceae. Appl. Environ. Microbiol. 64: 3539-3543.
6. 6. Devereux, J., Haeberli, P., and Smithies, O. 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12: 387-395.
7. 7. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39: 783-791.
8. 8. Felsenstein, J. 1993. PHYLIP Phylogeny inference package, version 3.5. University of Washington, Seattle, Wash.
9. 9. Giovannoni, SJ. 1991. The polymerase chain reaction. In Sequencing and hybridization techniques in bacterial systematics. Edited by E. Stackebrandt and M. Goodfello. John Wiley & Sons, New York. pp. 177-201.
10. 10. Hahn, D., Lechevalier, M.P., Fischer, A., and Stackebrandt, E. 1989. Evidence for a close phylogenetic relationship between members of the genera Frankia Geodermatophilus, and "Blastococcus" and emendation of the family Frankiaceae. Syst. Appl. Microbiol. 11: 236-242.
11. 11. Hicks, R.E., Amann, R.I., and Stahl, D.A. 1992. Dual staining of natural bacterial plankton with 4′,6-diamidino-2 phenylindole and fluorescent oligonucleotide probes targeting kingdom-level 16S rRNA sequences. Appl. Environ. Microbiol. 58: 2158-2163.
12. 12. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120.
13. 13. Lane, D.J., Pace, B., Olsen, G.J., Stahl, D.A., Sogin, M.L., and Pace, N.R. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analysis. Proc. Natl. Acad. Sci. U.S.A. 82: 6955-6959.
14. 14. Mirza, M.S. 1993. Characterization of uncultured Frankia strains by 16S rRNA sequence analysis. Ph.D. thesis, Wageningen Agricultural University, Wageningen, The Netherlands.
15. 15. Murry, M.A., Konopka, A.S., Pratt, S.D., and Vandergon, T.L. 1997. The use of PCR-based typing methods to assess the diversity of Frankia nodule endophytes of the actinorhizal shrub Ceanothus. Physiol. Plant. 99: 714-721.
16. 16. Nazaret, S., Cournoyer, B., Normand, P., and Simonet, P. 1991. Phylogenetic relationships among Frankia genomic species determined by the use of amplified 16S rDNA sequences. J. Bacteriol. 173: 4072-4078.
17. 17. Nick, G., Paget, E., Simonet, P., Moiroud, A., and Normand, P. 1992. The nodular endophytes of Coriaria spp. form a distinct lineage within the genus Frankia. Mol. Ecol. 1: 175-181.
18. 18. Normand, P., Orso, S., Cournoyer, B., Jeannin, P., Chapelon, C., Dawson, J., Evtushenko, L., and Misra, K. 1996. Molecular phylogeny of the genus Frankia and related general and emendation of the family Frankiaceae. Int. J. Syst. Bacteriol. 46: 1-9.
19. 19. Page, R.D.M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12: 357-358.
20. - actinomycete. Can. J. Microbiol. 44: 140-148.
21. 21. Ritchie, N.J. 1999. Geographic distribution and genetic diversity of Ceanothus-mfective Frankia. Appl. Environ. Microbiol. 65: 1378-1383.
22. 22. Simonet, P., Grosjean, M.-C., Misra, A.K., Nazaret, S., Cournoyer, B., and Normand, P. 1991. Frankia genus-specific characterization by polymerase chain reaction. Appl. Environ. Microbiol. 57: 3278-3286.
23. 23. Swofford, D.L. 1991. PAUP: Phylogenetic analysis using parsimony, version 3.0. Illinois National History Survey, Champagne, Ill.
24. 24. Young, J.P., and Haukka, K.E. 1996. Diversity and phylogeny of rhizobia. New Phytol. 133: 87-94.