Host infection selects for sRNA variants that drive bacterial social cheating

Abstract Intra-strain variation in model bacterial pathogens can compromise experimental reproducibility and obscure biological interpretations. Dickeya solani , a necrotrophic potato pathogen, is widely studied using the type strain IPO 2222. However, phenotypic discrepancies among laboratories led us to investigate the genetic integrity of this reference stock. We identified at least three distinct IPO 2222 variants co-existing in the original stock, differing solely by mutations in the gene encoding the small regulatory RNA (sRNA) ArcZ. These findings resolve conflicting reports of antimicrobial activity in this strain described by Brual et al . (PLOS Genetics 19, e1010725, 2023) and Matilla et al . (mBio, e02472-22, 2022). We demonstrate that these are adaptive mutations rapidly selected in planta during host infection. Crucially, rather than systematically inactivating the gene, these mutations modulate the cellular levels of processed ArcZ. This modulation can uncouple virulence from antimicrobial activity. These variants behave as social cheaters, exhibiting a frequency-dependent fitness advantage over the cooperative wild-type strain during co-infection. These findings provide evidence that remodeling of a pleiotropic sRNA drives the emergence of bacterial cheaters within a plant host. The speed at which these mutants sweep through the population underscores the intense selective pressure acting on regulatory networks during infection, identifying sRNA modulation as a pivotal mechanism for rapid short-term adaptation. Significance Statement Bacterial pathogens often utilize cooperative behaviors, such as the secretion of communal “public goods,” to colonize hosts. We demonstrate that the plant pathogen Dickeya solani rapidly evolves “cheater” variants during infection through single-nucleotide mutations in the small regulatory RNA (sRNA) ArcZ. These mutations, concentrated within a 150-nucleotide region, modulate sRNA levels to uncouple virulence from antimicrobial production. This trade-off provides a significant fitness advantage during co-infection, revealing an evolutionarily accessible mechanism for social cheating. Our work highlights how minute noncoding elements serve as critical targets of selection, shaping both pathogenesis and microbial social dynamics.