Identification of genomic species in Agrobacterium biovar 1 by AFLP genomic markers

Applied and Environmental Microbiology

Volumn 72, Issue 11, 2006, Pages 7123-7131

  Portier, Perrine ^a   Fischer Le Saux, Marion ^b   Mougel, Christophe ^a,d   Lerondelle, Catherine ^a   Chapulliot, David ^a   Thioulouse, Jean ^c   Nesme, Xavier ^a  

^a University of Lyon   (France)

^b UNIVERSITÉ D'ANGERS   (France)

^c UNIVERSITÉ LYON 1   (France)

^d CEMAGREF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMARKERS; DNA; ECOLOGY; EPIDEMIOLOGY; GENETIC ENGINEERING;

CURRENT GENOME MISPAIRING (CGM); DNA-DNA HYBRIDIZATION; GENOME DIVERGENCE VALUES; GENOMIC SPECIES;

BACTERIA;

BACTERIUM; BIOTOPE; DNA FINGERPRINTING; GENETIC VARIATION; MARKING METHOD; STOCK IDENTIFICATION;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BIOTOPE; BIOTYPE; CROWN GALL; CURRENT GENOME MISPAIRING; DNA DNA HYBRIDIZATION; ECOLOGY; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; RELIABILITY; RHIZOBIUM; TAXON;

AGROBACTERIUM; AGROBACTERIUM TUMEFACIENS;

EID: 33751019669     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.00018-06     Document Type: Article

References (45)

1. Boudon, S., C. Manceau, and J.-L. Nottéghem. 2005. Structure and origin of Xanthomonas arboricola pv. pruni populations causing bacterial spot of stone fruit trees in Western Europe. Phytopathology 95:1081-1088.
2. Bouzar, H. 1994. Request for a judicial opinion concerning the type species of Agrobacterium. Int. J. Syst. Bacteriol. 44:373-374.
3. Bouzar, H., and J. B. Jones. 2001. Agrobacterium larrymoorei sp. nov., a pathogen isolated from aerial tumours of Ficus benjamina. Int. J. Syst. Evol. Microbiol. 51:1023-1026.
4. Brenner, D. J., A. C. McWhorter, J. K. Leete Knutson, and A. G. Steigerwalt. 1982. Escherichia vulneris: a new species of Enterobacteriaceae associated with human wounds. J. Clin. Microbiol. 15:1133-1140.
5. Broothaerts, W., H. J. Mitchell, B. Weir, S. Kaines, L. M. Smith, W. Yang, J. E. Mayer, C. Roa-Rodriguez, and R. A. Jefferson. 2005. Gene transfer to plants by diverse species of bacteria. Nature 433:629-633.
6. Cohan, F. M. 2001. Bacterial species and speciation. Syst. Biol. 50:513-524.
7. Crosa, J. H., D. J. Brenner, and S. Falkow. 1973. Use of a single-strand-specific nuclease for analysis of bacterial and plasmid deoxyribonucleic acid homo- and heteroduplexes. J. Bacteriol. 115:904-911.
8. De Cleene, M., and J. De Ley. 1976. The host range of crown gall. Bot. Rev. 42:389-466.
9. De Ley, J. 1974. Phytogeny of procaryotes. Taxon 23:291-300.
10. De Ley, J., R. Tijtgat, J. De Smedt, and M. Michiels. 1973. Thermal stability of DNA:DNA hybrids within the genus Agrobacterium. J. Gen. Microbiol. 78:241-252.
11. Farrand, S. K., P. B. Van Berkum, and P. Oger. 2003. Agrobacterium is a definable genus of the family Rhizobiaceae. Int. J. Syst. Evol. Microbiol. 53:1681-1687.
12. Felsenstein, J. 2004. PHYLIP: Phytogeny Inference Package, version 3.6. Department of Genome Sciences, University of Washington, Seattle. [Online.] http://evolution.genetics.washington.edu/phylip.html.
13. Genetello, C., N. Van Larebeke, M. Holsters, A. De Picker, M. Van Montagu, and J. Schell. 1977. Ti plasmids of Agrobacterium tumefaciens as conjugative plasmids. Nature 265:561-563.
14. Gevers, D., F. M. Cohan, J. G. Lawrence, B. G. Spratt, T. Coenye, E. J. Feil, E. Stackebrandt, Y. van De Peerqq, P. Vandamme, F. L. Thompson, and J. Swings. 2005. Reevaluating prokaryotic species. Nat. Microbiol. Rev. 3:733-739.
15. Goodner, B., G. Hinkle, S. Gattung, N. Miller, M. Blanchard, B. Qurollo, B. S. Goldman, Y. Cao, M. Askenazi, C. Halling, L. Mullin, K. Houmiel, J. Gordon, M. Vaudin, O. Iartchouk, A. Epp, F. Liu, C. Wollam, M. Allinger, D. Doughty, C. Scott, C. Lappas, B. Markelz, C. Flanagan, C. Crowell, J. Gurson, C. Lome, C. Sear, G. Strub, C. Cielo, and S. Slater. 2001. Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 294:2323-2328.
16. Grimont, P. A. D., M. Y. Popoff, F. Grimont, C. Coynault, and M. Lemelin. 1980. Reproducibility and correlation study of three deoxyribonucleic acid hybridization procedures. Curr. Microbiol. 4:325-330.
17. Hooykaas P. J. J., P. M. Klapwyk, M. P. Nuti, R. A. Schilperoort, and A. Rorsh. 1977. Transfer of the Agrobacterium tumefaciens Ti-plasmid to avirulent agrobacteria and to Rhizobium ex-planta. J. Gen. Microbiol. 98:477-484.
18. Keane, P. J., A. Kerr, and P. B. New. 1970. Crown gall on stone fruits: identification and nomenclature of Agrobacterium isolates. Aust. J. Biol. Sci. 23:585-595.
19. Kersters, K., J. De Ley, P. H. A. Sneath, and M. Sackin. 1973. Numerical taxonomic analysis of Agrobacterium. J. Gen. Microbiol. 78:227-239.
20. Kersters, K., and J. De Ley. 1984. Agrobacterium Conn 1942, p. 244-254. In N. R. Krieg and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, vol. 1. Williams & Wilkins, Baltimore, Md.
21. 20a. Lapage, S. P., P. H. A. Sneath, E. F. Lessel, V. B. D. Skerman, H. P. R. Seeliger, and W. A. Clark (ed.). 1992. International code of nomenclature of bacteria. American Society for Microbiology, Washington, D.C.
22. Lindström, K., and M. E. Martinez-Romero. 2002. International Committee on Systematics of Prokaryotes, Subcommittee on the Taxonomy of Agrobacterium and Rhizobium, minutes of the meeting, 4th July 2001, Hamilton, Canada. Int. J. Syt. Evol. Microbiol. 52:2337.
23. Maiden, M. C., J. A. Bygraves, E. Feil, G. Morelli, J. E. Russell, R. Urwin, Q. Zhang, J. Zhou, K. Zurth, D. A. Caugant, I. M. Feavers, M. Achtman, and B. G. Spratt. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95:3140-3145.
24. Mougel, C., S. Teyssier, C. d'Angelo, K. Groud, M. Neyra, K. Sidi-Boumedine, A. Cloeckaert, M. Peloille, S. Baucheron, E. Chaslus-Dancla, S. Jarraud, H. Meugnier, F. Forey, F. Vandenesch, G. Lina, J. Etienne, J. Thioulouse, C. Manceau, P. Robbe, R. Nalin, J. Briolay, and X. Nesme. 2001. Experimental and theoretical evaluation of typing methods based upon random amplification of genomic restriction fragments (AFLP) for bacterial population genetics. Genet. Sci Evol. 33(Suppl. 1):S319-S338.
25. Mougel, C., J. Thioulouse, G. Perriere, and X. Nesme. 2002. A mathematical method for determining genome divergence and species delineation using AFLP. Int. J. Syst. Evol. Microbiol 52:573-586.
26. Nesme, X., M. F. Michel, and B. Digat. 1987. Population heterogeneity of Agrobacterium tumefaciens in galls of Populus L. from a single nursery. Appl Environ. Microbiol. 53:655-659.
27. Nesme, X., C. Ponsonnet, C. Picard, and P. Normand. 1992. Chromosomal and pTi genotypes of Agrobacterium strains isolated from Populus tumors in two nurseries. FEMS Microbiol. Ecol. 101:189-196.
28. Ophel, K., and A. Kerr. 1990. Agrobacterium vitis sp. nov. for strains of Agrobacterium biovar 3 from grapevines. Int. J. Syst. Bacteriol. 40:236-241.
29. Pionnat, S., H. Keller, D. Héricher, A. Bettachini, Y. Dessaus, X. Nesme, and C. Poncet. 1999. Ti plasmid from Agrobacterium characterizes rootstock clones that initiate spread of crown gall disease in Mediterranean countries. Appl Environ. Microbiol. 65:4197-4206.
30. Popoff, M. Y., K. Kersters, M. Kiredjian, I. Miras, and C. Coynault. 1984. Taxonomic position of Agrobacterium strains of hospital origin. Ann. Microbiol. 135:427-442.
31. Raio, A., R. Peluso, X. Nesme, and A. Zoina. 2004. Chromosomal and plasmid diversity of Agrobacterium populations isolated from Ficus benjamina tumors. Eur. J. Plant Pathol. 109:163-173.
32. Sawada, H., H. Ieki, H. Oyaizu, and S. Matsumoto. 1993. Proposal for rejection of Agrobacterium tumefaciens and revised descriptions for the genus Agrobacterium and for Agrobacterium radiobacter and Agrobacterium rhizogenes. Int. J. Syst. Bacteriol. 43:694-702.
33. Stackebrandt, E., W. Frederiksen, G. M. Garrity, P. A. Grimont, P. Kampfer, M. C. Maiden, X. Nesme, R. Rossello-Mora, J. Swings, H. G. Truper, L. Vauterin, A. C. Ward, and W. B. Whitman. 2002. Report of the Ad Hoc Committee for the Re-evaluation of the Species Definition in Bacteriology. Int. J. Syst. Evol. Microbiol. 52:1043-1047.
34. Starr, M. P., and J. E. Weiss. 1943. Growth of phytopathogenic bacteria in a synthetic asparagin medium. Phytopathology 33:314-318.
35. Teyssier-Cuvelle, S., C. Mougel, and X. Nesme. 1999. Direct conjugal transfers of Ti plasmid to soil microflora. Mol. Ecol. 8:1273-1284.
36. Teyssier-Cuvelle S., P. Oger, C. Mougel, K. Groud, S. Farrand, and X. Nesme. 2004. A highly selectable and highly transferable Ti plasmid to study conjugal host range and Ti plasmid dissemination in complex ecosystems. Microb. Ecol. 48:10-18.
37. Van Larebeke, N., G. Engler, M. Holsters, S. Van den Elsacker, I. Zaenen, R. A. Schilperoort, and J. Schell. 1974. Large plasmid in Agrobacterium tumefaciens essential for crown gall-inducing ability. Nature 252:169-170.
38. Van Valen, L. 1976. Ecological species, multispecies, and oaks. Taxon 25:233-239.
39. Vos, P., R. Hogers, M. Bleeker, M. Reijans, T. Van De Lee, M. Homes, A. Frijters, J. Pot, J. Peleman, and M. Kuiper. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23:4407-4414.
40. Vulic, M., F. Dionisio, F. Taddei, and M. Radman. 1997. Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria. Proc. Natl. Acad. Sci. USA 94:9763-9767.
41. Wayne, L. G., D. J. Brenner, R. R. Colwell, P. A. D. Grimont, O. Kandler, M. I. Krichevisky, L. H. Moore, W. E. C. Moore, R. G. E. Murray, E. Stackebrandt, M. P. Starr, and H. G. Truper. 1987. Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int. J. Syst. Bacteriol. 37:463-464.
42. Wood, D. W., J. C. Setubal, R. Kaul, D. E. Monks, J. P. Kitajima, V. K. Okura, Y. Zhou, L. Chen, G. E. Wood, N. F. Almeida, Jr., L. Woo, Y. Chen, I. T. Paulsen, J. A. Eisen, P. D. Karp, D. Bovee, Sr., P. Chapman, J. Clendenning, G. Deatherage, W. Gillet, C. Grant, T. Kutyavin, R. Levy, M. J. Li, E. McClelland, A. Palmieri, C. Raymond, G. Rouse, C. Saenphimmachak, Z. Wu, P. Romero, D. Gordon, S. Zhang, H. Yoo, Y. Tao, P. Biddle, M. Jung, W. Krespan, M. Perry, B. Gordon-Kamm, L. Liao, S. Kim, C. Hendrick, Z. Y. Zhao, M. Dolan, F. Chumley, S. V. Tingey, J. F. Tomb, P. G. Milton, V. O. Maynard, and W. E. Nester. 2001. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294:2317-2323.
43. Young, J. M., L. D. Kuykendall, E. Martinez-Romero, A. Kerr, and H. Sawada. 2001. A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola De Lajudie et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis. Int. J. Syst. Evol. Microbiol. 51:89-103.
44. Young, J. M., L. D. Kuykendall, E. Martinez-Romero, A. Kerr, and H. Sawada. 2003. Classification and nomenclature of Agrobacterium and Rhizobium - a reply to Farrand et al. 2003. Int. J. Syst. Evol. Microbiol. 53:1689-1695
45. Young, J. M., S. R. Pennycook, and D. R. W. Watson. 2006. Proposal that Agrobacterium radiobacter has priority over Agrobacterium tumefaciens. Request for an opinion. Int. J. Syst. Evol. Microbiol. 56:491-493.