Plant miRNAs and amino acids interact to shape soil bacterial communities.

Abstract

Plants and microbes use many strategies to acquire soil amino acids. Recent findings suggest that genes related to amino acid metabolism and transport are influenced by plant miRNAs. This was the first report of a plant-derived molecule with the potential to modify microbial amino acid uptake. Here, we first show that Arabidopsis modifies its root miRNA content when fertilized with a mixture of 17 amino acids. The miRNAs that responded to amino acid fertilization and other rhizosphere-abundant miRNAs were applied to a simplified soil community, grown with diverse amino acid sources, to test if they interfered with microbial community growth, community composition and amino acid consumption. Plant miRNAs affected the communitys growth in over 70 % of the amino acid sources. The effectiveness of plant miRNAs also depended on the N source supplied to the microbial community, with the strongest effect observed with L-lysine. Specifically, ath-miR159a reduced the microbial consumption of L-lysine, further supporting that plant miRNAs can influence microbial amino acid uptake. Plant miRNAs also affected the relative abundance of specific bacterial taxa, which we subsequently isolated. All isolates were affected in terms of growth when exposed to miRNAs. Two out of three isolates were also impacted in their amino acid consumption. Surprisingly, while plant miRNAs inhibited amino acid consumption at both the community and isolate levels, they had mostly positive effects. Our results suggest that rhizospheric plant miRNAs might have a role in modulating the amino acid consumption of soil bacteria, but not necessarily in a competitive framework.