RNA stable isotope probing in A. echinatior ants

Actinobacteria are ubiquitous in soil and well-known for producing antimicrobial compounds. Increasingly, members of this phylum are found to form symbiotic relationships 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 leafcutter ants transmit Pseudonocardia bacteria between generations and also recruit Streptomyces to their cuticular microbiome. These bacteria produce antibiotics on the ant cuticle and the ants use these compounds to protect their food fungus against infection. We show, using 13C RNA stable isotope probing, that ants supply cuticular resources to bacteria in their microbiome. Pseudonocardia, Streptomyces and several other actinobacterial genera were found to be present in heavier buoyant density fractions under the 13C treatment, indicating that ant-derived resources were publicly available to many bacteria on the cuticle. These resources may fuel interference competition between microbial species and therefore select for antibiotic-producing bacteria.