A natural bacterial pathogen of C. elegans uses a small RNA to induce transgenerational inheritance of learned avoidance

C . elegans can learn to avoid pathogenic bacteria through several mechanisms, including bacterial small RNA-induced learned avoidance behavior, which can be inherited transgenerationally. Previously, we discovered that a small RNA from a clinical isolate of Pseudomonas aeruginosa , PA14, induces learned avoidance and transgenerational inheritance of that avoidance in C . elegans . Pseudomonas aeruginosa is an important human pathogen, and there are other Pseudomonads in C . elegans’ natural habitat, but it is unclear whether C . elegans ever encounters PA14-like bacteria in the wild. Thus, it is not known if small RNAs from bacteria found in C . elegans’ natural habitat can also regulate host behavior and produce heritable behavioral effects. Here we screened a set of wild habitat bacteria, and found that a pathogenic Pseudomonas vranovensis strain isolated from the C . elegans microbiota, GRb0427, regulates worm behavior: worms learn to avoid this pathogenic bacterium following exposure, and this learned avoidance is inherited for four generations. The learned response is entirely mediated by bacterially-produced small RNAs, which induce avoidance and transgenerational inheritance, providing further support that such mechanisms of learning and inheritance exist in the wild. We identified Pv1, a small RNA expressed in P . vranovensis , that has a 16-nucleotide match to an exon of the C . elegans gene maco-1 . Pv1 is both necessary and sufficient to induce learned avoidance of Grb0427. However, Pv1 also results in avoidance of a beneficial microbiome strain, P . mendocina . Our findings suggest that bacterial small RNA-mediated regulation of host behavior and its transgenerational inheritance may be functional in C . elegans’ natural environment, and that this potentially maladaptive response may favor reversal of the transgenerational memory after a few generations. Our data also suggest that different bacterial small RNA-mediated regulation systems evolved independently, but define shared molecular features of bacterial small RNAs that produce transgenerationally-inherited effects.