Skip to main content
NCBI home page
Applied and Environmental Microbiology logoLink to Applied and Environmental Microbiology
. 1997 Feb;63(2):574–580. doi: 10.1128/aem.63.2.574-580.1997

Fast and accurate identification of Xenorhabdus and Photorhabdus species by restriction analysis of PCR-amplified 16S rRNA genes.

B Brunel 1, A Givaudan 1, A Lanois 1, R J Akhurst 1, N Boemare 1
PMCID: PMC168349  PMID: 9023937

Abstract

Thirteen bacterial strains of Xenorhabdus and 14 strains of Photorhabdus originating from a wide range of geographical and nematode host sources were typed by analyzing 16S rRNA gene (rDNA) restriction patterns obtained after digestion of PCR-amplified 16S rDNAs. Eight tetrameric restriction endonucleases were examined. A total of 17 genotypes were identified, forming two heterogeneous main clusters after analysis by the unweighted pair-group method using arithmetic averages: group I included all Xenorhabdus species and strains, symbionts of Steinernema, whereas group II encompassed the Photorhabdus strains, symbionts of Heterorhabditis. To identify the four valid species of Xenorhabdus and unclassified strains and all the genotypes of Photorhabdus luminescens, three restriction enzymes are required: CfoI, AluI, and HaeIII. Our results, in substantial agreement with DNA-DNA pairing and 16S rDNA sequence data, indicate that amplified 16S rDNA restriction analysis is a simple and accurate tool for identifying entomopathogenic nematode bacterial symbionts.

Full Text

The Full Text of this article is available as a PDF (1.2 MB).

Selected References

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

  1. Akhurst R. J., Boemare N. E. A numerical taxonomic study of the genus Xenorhabdus (Enterobacteriaceae) and proposed elevation of the subspecies of X. nematophilus to species. J Gen Microbiol. 1988 Jul;134(7):1835–1845. doi: 10.1099/00221287-134-7-1835. [DOI] [PubMed] [Google Scholar]
  2. Akhurst R. J., Mourant R. G., Baud L., Boemare N. E. Phenotypic and DNA relatedness between nematode symbionts and clinical strains of the genus Photorhabdus (Enterobacteriaceae). Int J Syst Bacteriol. 1996 Oct;46(4):1034–1041. doi: 10.1099/00207713-46-4-1034. [DOI] [PubMed] [Google Scholar]
  3. Akhurst R. J. Neoaplectana species: specificity of association with bacteria of the genus Xenorhabdus. Exp Parasitol. 1983 Apr;55(2):258–263. doi: 10.1016/0014-4894(83)90020-6. [DOI] [PubMed] [Google Scholar]
  4. Farmer J. J., 3rd, Jorgensen J. H., Grimont P. A., Akhurst R. J., Poinar G. O., Jr, Ageron E., Pierce G. V., Smith J. A., Carter G. P., Wilson K. L. Xenorhabdus luminescens (DNA hybridization group 5) from human clinical specimens. J Clin Microbiol. 1989 Jul;27(7):1594–1600. doi: 10.1128/jcm.27.7.1594-1600.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Fox G. E., Wisotzkey J. D., Jurtshuk P., Jr How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol. 1992 Jan;42(1):166–170. doi: 10.1099/00207713-42-1-166. [DOI] [PubMed] [Google Scholar]
  6. Givaudan A., Baghdiguian S., Lanois A., Boemare N. Swarming and Swimming Changes Concomitant with Phase Variation in Xenorhabdus nematophilus. Appl Environ Microbiol. 1995 Apr;61(4):1408–1413. doi: 10.1128/aem.61.4.1408-1413.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Grenier E., Bonifassi E., Abad P., Laumond C. Use of species-specific satellite DNAs as diagnostic probes in the identification of Steinernematidae and Heterorhabditidae entomopathogenic nematodes. Parasitology. 1996 Nov;113(Pt 5):483–489. doi: 10.1017/s0031182000081555. [DOI] [PubMed] [Google Scholar]
  8. Grimont P. A. Use of DNA reassociation in bacterial classification. Can J Microbiol. 1988 Apr;34(4):541–546. doi: 10.1139/m88-092. [DOI] [PubMed] [Google Scholar]
  9. Gurtler V., Wilson V. A., Mayall B. C. Classification of medically important clostridia using restriction endonuclease site differences of PCR-amplified 16S rDNA. J Gen Microbiol. 1991 Nov;137(11):2673–2679. doi: 10.1099/00221287-137-11-2673. [DOI] [PubMed] [Google Scholar]
  10. Laguerre G., Allard M. R., Revoy F., Amarger N. Rapid Identification of Rhizobia by Restriction Fragment Length Polymorphism Analysis of PCR-Amplified 16S rRNA Genes. Appl Environ Microbiol. 1994 Jan;60(1):56–63. doi: 10.1128/aem.60.1.56-63.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Leclerc M. C., Boemare N. E. Plasmids and phase variation in Xenorhabdus spp. Appl Environ Microbiol. 1991 Sep;57(9):2597–2601. doi: 10.1128/aem.57.9.2597-2601.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Martinez-Murcia A. J., Benlloch S., Collins M. D. Phylogenetic interrelationships of members of the genera Aeromonas and Plesiomonas as determined by 16S ribosomal DNA sequencing: lack of congruence with results of DNA-DNA hybridizations. Int J Syst Bacteriol. 1992 Jul;42(3):412–421. doi: 10.1099/00207713-42-3-412. [DOI] [PubMed] [Google Scholar]
  13. Moureaux N., Karjalainen T., Givaudan A., Bourlioux P., Boemare N. Biochemical Characterization and Agglutinating Properties of Xenorhabdus nematophilus F1 Fimbriae. Appl Environ Microbiol. 1995 Jul;61(7):2707–2712. doi: 10.1128/aem.61.7.2707-2712.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Nei M., Li W. H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5269–5273. doi: 10.1073/pnas.76.10.5269. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Rainey F. A., Ehlers R. U., Stackebrandt E. Inability of the polyphasic approach to systematics to determine the relatedness of the genera Xenorhabdus and Photorhabdus. Int J Syst Bacteriol. 1995 Apr;45(2):379–381. doi: 10.1099/00207713-45-2-379. [DOI] [PubMed] [Google Scholar]
  16. Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuchi R., Horn G. T., Mullis K. B., Erlich H. A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 1988 Jan 29;239(4839):487–491. doi: 10.1126/science.2448875. [DOI] [PubMed] [Google Scholar]
  17. 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]
  18. Smigielski A. J., Akhurst R. J., Boemare N. E. Phase Variation in Xenorhabdus nematophilus and Photorhabdus luminescens: Differences in Respiratory Activity and Membrane Energization. Appl Environ Microbiol. 1994 Jan;60(1):120–125. doi: 10.1128/aem.60.1.120-125.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Sneath P. H. Evidence from Aeromonas for genetic crossing-over in ribosomal sequences. Int J Syst Bacteriol. 1993 Jul;43(3):626–629. doi: 10.1099/00207713-43-3-626. [DOI] [PubMed] [Google Scholar]
  20. Vandamme P., Pot B., Gillis M., de Vos P., Kersters K., Swings J. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev. 1996 Jun;60(2):407–438. doi: 10.1128/mr.60.2.407-438.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. 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]

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

RESOURCES