Pan-genome analysis identifies intersecting roles forPseudomonasspecialized metabolites in potato pathogen inhibition

Abstract Agricultural soil harbors a diverse microbiome that can form beneficial relationships with plants, including the inhibition of plant pathogens. Pseudomonas 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 Pseudomonas fluorescens population in commercial potato field soils and identify strong correlations between specialized metabolite biosynthetic pathways and antagonism of the potato pathogens Streptomyces scabies and Phytophthora infestans . Genetic and chemical analyses identified hydrogen cyanide and cyclic lipopeptides as key specialized metabolites associated with S. scabies inhibition. We show that a single potato field contains a hugely diverse and dynamic population of Pseudomonas bacteria, whose capacity to produce specialized metabolites is shaped both by plant colonization and defined environmental inputs.