Ecological specificities of Agrobacterium fabrum : role of its specific genes in the interaction with the plant

Agrobacterium is a bacterial genus composed of many species capable of establishing commensal or pathogenic (by inducing the crown-gall disease) interactions. Field investigations showed that several species of agrobacteria generally co-exist in the same biotopes. To explain this biodiversity, we hypothesize that different species must have particular ecological niches allowing them to evade from competitions. Comparative genomics showed the existence of A. fabrum-specific genes clustered into genomic regions called “specific regions” encoding putative functional units related to metabolism or transport of plant compounds. This allowed us to predict a specific ecology related to bacteria-plant interactions and their implication in the specific niche construction of this bacteria. This study aims at verifying whether A. fabrum-specific regions are involved in adaptations to the plant in both lifestyles (commensal and pathogenic). For this purpose, we studied the effect of the specific regions on the bacterial fitness in planta and on the plant metabolome (rhizosphere and tumor). Competition tests reveal that almost all the A. fabrum-specific regions confer better fitness to bacteria. Some regions are more involved in one lifestyle more than the other, some in both. Metabolomic analyzes showed that A. fabrum is capable of modulating the content of phenolic compounds in roots and tumors, in particular flavonoids. This modulation was essentially linked to the specific regions. These results contribute to a better understanding of the ecological niche construction of A. fabrum highlighting the importance of its specific genes in the establishment of this fine-tuned interaction.