Involvement of miRNAs in plant-rhizosphere microbiota communication ; Implication des microARNs dans la communication plante-microbiote rhizosphérique

Here, thanks to small RNA sequencing, we have discovered the presence of miRNAs in the rhizosphere of Arabidopsis thaliana and Brachypodium distachyon. Through 16S/ITS sequencing of root and rhizosphere microbial communities of mutant plants, affected in the biosynthesis of small RNAs, we have observed the structuring rôle of the latter on the microbiota. We also confirmed this role using a more refined approach based on miRNA-endoded peptides (miPEPs), which make it possible to increase the specific production of a miRNA in planta. This methodology demonstrated the impact that a single rhizospheric miRNA can have on the composition of the microbiota. In order to assess the molecular mechanism behind this taxonomic shift, we developed a tool for predicting the targets of plant miRNAs in bacterial genomes. Biological confirmation of some target genes was done, first by exploring the transcriptome, by confronting a bacterial culture with a mixture of synthetic miRNAs, mimicking those of the rhizosphere; then, in a more refined way, by applying miPEP159c on A. thaliana seedlings, in parallel inoculated with Variovorax paradoxus EPS and by quantifying the target genes by qPCR. All these results demonstrate that plant miRNAs found in the rhizosphere have a role in modulating the composition and activity of the root and rhizosphere microbiota. ; Ici, grâce au séquençage petits ARNs, nous avons découvert la présence de miARNs dans la rhizosphère d’Arabidopsis thaliana et Brachypodium distachyon. A travers le séquençage 16S/ITS des communautés microbiennes des racines et de la rhizosphère de plantes mutantes, affectées dans la biosynthèse des petits ARNs, nous avons observé le rôle structurant de ces derniers sur le microbiote. Nous avons d’ailleurs confirmé ce rôle en utilisant une approche plus fine, à base de miRNA-endoded peptides (miPEPs), qui permettent d’augmenter la production spécifique d’un miARN in planta. Cette méthodologie a démontré l’impact que peut avoir un unique miARN rhizosphérique sur la composition ...