Characterizing the antimicrobial activity of the beneficial bacterium Pseudomonas protegens PBL3 through comparative genomics

The environmental bacterium Pseudomonas protegens PBL3 has antagonistic activity against the bacterial pathogen Burkholderia glumae, the causal agent of the emerging 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 conferring that activity have not been identified. The objective of this research is to advance the characterization of the antimicrobial molecules produced by P. protegens PBL3 by comparative genomics. To achieve this objective, this work screened six sequenced Pseudomonas spp. strains, closely related to P. protegens PBL3, to evaluate their activity against B. glumae and identified three strains with activity and three strains without activity. We further retrieved the genomic sequences of these strains and reordered their contigs using P. protegens PBL3 as the reference genome. The six genomes, in addition to the genome of P. protegens PBL3, were then aligned to identify conserved regions present in the strains with antimicrobial activity but absent in those without activity. This approach revealed unique, previously uncharacterized biosynthetic genes and pathways specific to the strains with activity for further characterization by genetic and functional analyses. Identifying and characterizing the biosynthetic pathways responsible for the production of antimicrobials in P. protegens PBL3 will pave the way to developing sustainable strategies to control BPB.