Most of the Specific Genomic Regions of Agrobacterium fabrum Shape Phenolics Content of Medicago truncatula Roots

The impact of plant microbiota on host is increasingly recognized, yet specific bacterial functions and genetic determinants in rhizosphere interactions remain largely unknown. Agrobacteria, common soil and rhizospheric bacteria, establish root interactions. The species Agrobacterium fabrum harbour seven specific-gene regions, whose annotation indicates a close connection with the plant. To evaluate the involvement of these specific regions in the plant-bacteria interaction, deletion mutant strains of each 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. A. fabrum inoculation modulates the content of root phenolic compounds, in particular flavonoids. These root metabolite modulations appear to be linked to at least one of the A. fabrum-specific genes, as almost all specific regions showed an influence on one or more of these metabolites. Furthermore, our results suggested a putative cross-talk of the specific regions during the interaction of A. fabrum with M. truncatula, as all mutants except one induced similar modifications on flavonoids. These findings enhance our understanding of A. fabrum's ecological niche construction, highlighting the importance of specific genes in the establishment of this fine-tuned interaction.