Comparative genomics analysis reveals that antimicrobial activity in Pseudomonas protegens PBL3 is associated with gene clusters participating in multiple cellular functions

The environmental bacterium Pseudomonas protegens PBL3 has antagonistic activity against the bacterial pathogen Burkholderia glumae, the causal agent of the rice disease Bacterial Panicle Blight (BPB). The antimicrobial activity of the P. protegens PBL3 was found in the bacteria-free secreted fraction (secretome), but the specific molecules, as well as the genetic basis conferring activity, have not been identified. To elucidate the genes and biosynthetic pathways governing the antimicrobial activity of the P. protegens PBL3 secretome, we used comparative genomics, by leveraging six Pseudomonas spp. strains, with available genomic sequences and exhibiting contrasting antimicrobial activities against B. glumae. We hypothesized that Pseudomonas spp. strains with antimicrobial activity against B. glumae have conserved genes with P. protegens PBL3 and those genes are absent in the strains lacking activity. To test this hypothesis, we performed comparative genomics analysis across the six strains using two complementary approaches, anvio and progressiveMauve, and using P. protegens PBL3 as the reference genome. This analysis revealed 188 genes uniquely present in antimicrobial-producing strains. Seven of those genes were associated with biosynthetic gene clusters predicted to encode secondary metabolites; additional genes were grouped into twenty-five contiguous clusters with functions associated with secretion, signal transduction, regulation, transport/efflux, carbohydrate metabolism and one with additional uncharacterized function. Altogether, this study provided a complex and multi-functional network of candidate genes in antimicrobial-producing strains, suggesting that P. protegens PBL3 employs not only classical biosynthetic pathways but also integrated regulatory, metabolic, and export modules to synthesize and deploy antimicrobials. ImportanceBacterial plant diseases can be controlled through biological control, a strategy wherein beneficial microorganisms known as biological control agents (BCAs) interfere with the biological activities of pathogens through several mechanisms. One of these mechanisms is antibiosis, by which antimicrobial molecules produced by the BCA prevent pathogen multiplication or actively kill the pathogen. While this mechanism of antibiosis has been widely recognized, the specific molecules associated with the antimicrobial activity are not always identified, given their diverse and complex chemical structures as well as the unique and intricate biosynthetic pathways. This study unraveled different pathways underlying the antimicrobial activity in the environmental bacterium Pseudomonas protegens PBL3 to advance the discovery of effective antimicrobials to control bacterial plant diseases.