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Investigating the species and strain diversity of agrobacteria by MLSA: toward a phylogenetically relevant redefinition of the genus Agrobacterium.

Abstract : Agrobacteria is the name usually given to bacteria inducing the crown gall disease to numerous crops. Agrobacteria belong to different species that appeared phylogenetically intermingled with species of rhizobia, the symbiotic bacteria that induce nitrogen fixing nodules to Fabaceae, leading authors to propose the inclusion of agrobacteria within the genus Rhizobium. This proposal was contested by other authors who suggested to keep the early division in Agrobacterium and Rhizobium up to a clarification of the phylogeny. In the present work, we applied the multi-locus sequence analysis method to construct a robust phylogeny of agrobacteria and close relatives in order to clarify their taxonomic positions. Results allowed the clear assignation of bacteria to clades that fit to bona fide species previously defined by genomic methods (i.e. genomospecies). As a consequence MLSA could be used as a proxy to delineate novel species that virtually fit with the genomic definition of a species. Plant pathogenic agrobacteria were found to belong to different genomospecies distributed into three clades. Two clades encompasses species that are either bona fide Rhizobium species such as R. tropici for R. rhizogenes or more different taxa such as R. taibainensis and Allorhizobium undicola for R. vitis. A third clade encompasses all other plant pathogenic agrobacteria as well as benign plant commensals, plant growth promoting rhizobacteria, industrial strains and human opportunists. We propose to consider this large clade for a novel delineation of the genus Agrobacterium. As such, Agrobacterium spp. would include A. rubi, A. larrymooreii, A. skierniewicense (formerly R. skierniewicense), A. viscosum, A. radiobacter (i.e. the genomospecies G4 of Agrobacterium), A. fabrum, A. nepotum (formerly R. nepotum), A. pusense (formerly R. pusense) as well as bona fide genomospecies that have not yet received Latin binominals. An unifying trait of Agrobacterium members is their unique genome architecture characterized by the presence of a linear chromid (e.g. secondary chromosome) and the consequential occurrence in their genome of telA, the gene that encodes the protelomerase required to process the replication of the linear chromid. These particular traits strongly support the present proposal for a renewed definition of the genus Agrobacterium.
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Submitted on : Friday, March 27, 2020 - 5:58:38 PM
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  • HAL Id : hal-02522212, version 1



X. Nesme, D. Costechareyre, M. H. R. Bahena, Daniel Muller, J. Nesme, et al.. Investigating the species and strain diversity of agrobacteria by MLSA: toward a phylogenetically relevant redefinition of the genus Agrobacterium.. Frontiers in Plant-Microbe Interaction, 2013. ⟨hal-02522212⟩



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