Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition

Agricultural soil harbors a diverse microbiome that can form beneficial relationships with plants, including the inhibition of plant pathogens. are one of the most abundant bacterial genera in the soil and rhizosphere and play important roles in promoting plant growth and preventing disease. However, the genetic determinants of this beneficial activity are only partially understood, especially in relation to specialized metabolite production. Here, we genetically and phenotypically characterize the population in commercial potato field soils and identify strong correlations between specialized metabolite biosynthetic pathways and antagonism of the potato pathogens and . Genetic and chemical analyses identified hydrogen cyanide and cyclic lipopeptides as key specialized metabolites associated with inhibition. We show that a single potato field contains a hugely diverse and dynamic population of bacteria, whose capacity to produce specialized metabolites is shaped both by plant colonization and defined environmental inputs.