The genetic basis of predation resistance in Pseudomonas species associated with the bactivorous soil amoeba Dictyostelium discoideum.

Predation is likely to influence the function of bacterial communities and the evolution of bacterial pathogens, because characteristics that permit escape from predators often overlap with traits used for biocontrol of plant pathogens, virulence, or even bioremediation. Soil bacteria are preyed upon by a variety of microorganisms, including the amoeba Dictyostelium discoideum, which has led some strains to evolve resistance. We identified genes required for three Pseudomonas species associated with D. discoideum to evade predation by screening more than 6,000 transposon mutants for loss of resistance. One species required a variety of genes including toxins and secondary metabolism genes, but the other two appear to have functionally redundant mechanisms of resistance, since disruption of genes with pleiotropic effects was required to render them susceptible. We determined that GacA, which positively regulates secondary metabolism, is required for resistance in all three species. Predation resistance also appears to be a social trait based on enrichment of cooperative genes in one species and rescue of mutants by wild type in another. Many genes required for resistance are conserved among both resistant and susceptible species, but several are found in few genomes and some of these have homologs in distantly related species. Gain and loss of resistance appears to be a dynamic process in which regulatory and structural genes are well conserved across species, the specific toxins they regulate may be lost in the absence of predators, and new toxins may be acquired through horizontal gene transfer.