Plants release miRNAs in the rhizosphere, targeting microbial genes

Harriet Middleton (1, 2) , Cécile Monard (2) , Virginie Daburon (2) , Emmanuel Clostres (2) , Julien Tremblay (3) , Étienne Yergeau (1) , Abdelhak El Amrani (2)

1 INRS - Institut National de la Recherche Scientifique [Québec]
2 ECOBIO - Ecosystèmes, biodiversité, évolution [Rennes]
3 CNRC - Conseil National de Recherches Canada

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.

Domaines: Ecologie, Environnement

Harriet Middleton, Cécile Monard, Virginie Daburon, Emmanuel Clostres, Julien Tremblay, et al.. Plants release miRNAs in the rhizosphere, targeting microbial genes. 2022. ⟨hal-03843674⟩