The importance of microorganisms in plant development, nutrition and stress resistance is consensus and has led to a more holistic approach of plant-microbe interactions, under the holobiont concept. The structure of plant microbiota is often described as hostdriven, especially in the rhizosphere, where microbial communities are shaped by diverse rhizodeposits. Gradually, this anthropogenic vision is fading and being replaced by the idea that plants and microorganisms co-shape the plant microbiota. Through coevolution, plants and microbes have developed cross-kingdom communication channels.We propose that microRNAs are crucial mediators of plant-microbe interactions and microbiota shaping in the rhizosphere. Moreover, we suggest, as an alternative to generally unsuccessful strategies based on microbial inoculants, microRNAs as a promising tool for novel holobiont engineering.

MicroRNAs (miRNAs) are small non-coding RNAs that control target gene expression, through sequence complementarity. Their roles in plants vary from regulating developmental processes to responding to abiotic and biotic stresses. Recently, small RNAs have been shown to play important roles in cross-kingdom communication, notably in plant-pathogen relationships. Plant miRNAs were even shown to regulate gene expression in the gut microbiota. Thus, we hypothesised that the same process happens in the rhizosphere which contributes to shaping plant microbial communities. To explore these questions, we performed small RNA sequencing in search of miRNAs in the rhizosphere of evolutionarily distant plants, Arabidopsis thaliana and Brachypodium distachyon. This revealed the presence of specific and shared rhizospheric plant miRNAs, which were all absent in unplanted soils. A subset of these miRNAs were also detected inside rhizospheric bacteria, but were missing in bacteria from unplanted soils, suggesting bacterial uptake of surrounding plant miRNAs. Furthermore, an in silico analysis indicated potential targets of these rhizospheric miRNAs in plant-associated bacterial genomes. To examine the function of these miRNAs, A. thaliana mutants, affected in their miRNA and/or siRNA (small interfering RNA) biosynthesis, were grown. Their rhizospheric microbial communities were significantly disrupted in comparison with wild-type plants. This work makes an important contribution to the field of rhizospheric plant-microbe interactions and offers some significant insights into the potential of plant miRNAs for microbiota engineering.