The chemical ecology of protective microbiomes in plant roots and leafcutter ants

Actinobacteria are ubiquitous in soil and well-known for producing antimicrobial compounds. Increasingly, members of this phylum are found to form symbiotic relationships, for example with plants and insects, and are thought to provide protection against host infection. However, it remains poorly understood how Actinobacteria are recruited to microbiomes and whether secondary metabolites are produced in vivo. Acromyrmex echinatior leaf cutter ants transmit Pseudonocardia bacteria between generations and also recruit Streptomyces to their cuticular microbiome. We show that Pseudonocardia species isolated from the ant cuticle inhibit the fungal nest pathogen Escovopsisweberi and dual RNA-sequencing confirmed that Pseudonocardia secondary metabolite gene clusters are expressed in vivo on the ant cuticle. RNA stable isotope probing showed that ants supply cuticular resources to their microbiome which may fuel interference competition and select for antibiotic-producing bacteria. Similar to leaf cutter ants we also show that plant roots recruit growth-promoting and antibiotic-producing Streptomyces bacteria, but appear not to transmit them via their seeds. Root exudates are hypothesized to play a major role in root microbiome recruitment and DNA stable isotope probing coupled with Illumina sequencing showed that these were actively metabolized by many bacterial genera. However, Streptomyces appeared to be outcompeted by more abundant Proteobacteria, despite the fact that isolates could grow on purified exudates in the absence of competition. Streptomyces root exudate preferences are now being evaluated using comparative metabolomics. Defining the factors that influence the competitiveness of protective bacteria when colonizing microbiomes has implications for the development of more consistent biocontrol strategies and prebiotic techniques.