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Applied and Environmental Microbiology, November 2006, p. 7123-7131, Vol. 72, No. 11
0099-2240/06/$08.00+0     doi:10.1128/AEM.00018-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Identification of Genomic Species in Agrobacterium Biovar 1 by AFLP Genomic Markers{triangledown}

Perrine Portier,1 Marion Fischer-Le Saux,2 Christophe Mougel,1,{dagger} Catherine Lerondelle,1 David Chapulliot,1 Jean Thioulouse,3 and Xavier Nesme1*

Ecologie Microbienne, UMR CNRS 5557/USC INRA 1193, Université Claude Bernard-Lyon 1, Villeurbanne, France,1 Pathologie Végétale, INRA, UMR ENITH-Université d'Angers, Beaucouzé, France,2 Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard-Lyon 1, Villeurbanne, France3

Received 4 January 2006/ Accepted 14 August 2006

Biovar 1 of the genus Agrobacterium consists of at least nine genomic species that have not yet received accepted species names. However, rapid identification of these organisms in various biotopes is needed to elucidate crown gall epidemiology, as well as Agrobacterium ecology. For this purpose, the AFLP methodology provides rapid and unambiguous determination of the genomic species status of agrobacteria, as confirmed by additional DNA-DNA hybridizations. The AFLP method has been proven to be reliable and to eliminate the need for DNA-DNA hybridization. In addition, AFLP fragments common to all members of the three major genomic species of agrobacteria, genomic species G1 (reference strain, strain TT111), G4 (reference strain, strain B6, the type strain of Agrobacterium tumefaciens), and G8 (reference strain, strain C58), have been identified, and these fragments facilitate analysis and show the applicability of the method. The maximal infraspecies current genome mispairing (CGM) value found for the biovar 1 taxon is 10.8%, while the smallest CGM value found for pairs of genomic species is 15.2%. This emphasizes the gap in the distribution of genome divergence values upon which the genomic species definition is based. The three main genomic species of agrobacteria in biovar 1 displayed high infraspecies current genome mispairing values (9 to 9.7%). The common fragments of a genomic species are thus likely "species-specific" markers tagging the core genomes of the species.

* Corresponding author. Mailing address: Ecologie Microbienne, Université Claude Bernard-Lyon 1, Domaine scientifique de La Doua, 16 rue Raphaël Dubois, 69622 Villeurbanne cedex, France. Phone: 33 4 72 44 82 89. Fax: 33 4 72 43 12 23. E-mail: nesme{at}biomserv.univ-lyon1.fr.

{triangledown} Published ahead of print on 25 August 2006.

{dagger} Present address: INRA, Dijon, France.

Applied and Environmental Microbiology, November 2006, p. 7123-7131, Vol. 72, No. 11
0099-2240/06/$08.00+0     doi:10.1128/AEM.00018-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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