Phenolic compounds in Medicago truncatula roots are under the influence of Agrobacterium fabrum through its species specific-genes regions

The impact of plant microbiota on the health and physiology of their host is increasingly studied and recognized. However, in the rhizosphere, the functions of most bacteria and the genetic determinants involved in the molecular dialogue between plant and bacteria are poorly understood. Agrobacteria are ubiquitous soil borne and rhizospheric bacteria able to establish commensal or even beneficial interactions with plant roots. The genomic species Agrobacterium fabrum harbor seven specific-regions (SpG8-1 to SpG8-7), whose annotation seems to indicate a close connection with the plant during plant-bacteria interactions. To evaluate the involvement of A. fabrum-specific regions in the plant-bacteria interaction, deletion mutant strains of each A. fabrum-specific region were inoculated on Medicago truncatula roots. Root metabolite profiles were compared by UHPLC-UV/DAD-ESI-MS QTOF analyses, and the highlighted discriminating metabolites were annotated by tandem mass spectrometry. Metabolomic analyses have shown that A. fabrum inoculation modulates the content of phenolic compounds in M. truncatula roots, in particular flavonoids. These root metabolite modulations observed with the wild-type strain often appear to be linked to at least one of the A. fabrum-specific genes, as almost all A. fabrum-specific regions showed an influence on one or more of these specialized root metabolites. In addition, our results underlined a putative cross-talk or coordinated effect of the A. fabrum-specific regions during the interaction of A. fabrum with M. truncatula, as all mutants except one induced similar modifications on flavonoids. 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.