Genome mining and comparative genome analysis of Pseudomonas fluorescens revealed diverse biosynthetic and metabolic potential

Abstract

Bacterial genome sequencing has been used to identify a myriad of bioactive compounds that have yet to be characterised. Pseudomonas fluorescens is a widely distributed Gram-negative bacterium known for its plant growth-promoting traits and production of diverse secondary metabolites. P. fluorescens genome harbours several biosynthetic gene clusters (BGCs), and it is challenging to link many of these BGCs with their respective product under laboratory conditions. The current study employed a bioinformatic approach to gain in-depth genomic insight into the distribution, evolution, and diversity of these BGCs in P. fluorescens, facilitating the exploration of cryptic biosynthetic capabilities. In addition, to understand the genomic landscape and evolutionary dynamics, core pan-genome analysis was conducted for P. fluorescens species. We identified a total of 2098 BGCs across the high-quality targeted genomes (n = 174), including non-ribosomal peptide synthetases (NRPSs), ribosomal-synthesised and post-translationally modified peptides (RiPPs), polyketides (PKSs), Terpenes, siderophores, and arylpolyenes, which were the most prevalent. Several low similarity clusters (n = 14) were identified that encode putative novel metabolites. Core Pan-genome analysis revealed an “open pan-genome” and large accessory genome enriched in secondary metabolism genes, supporting the biosynthetic versatility of P. fluorescens. This work enhances our understanding of the metabolic capabilities and genomic landscape of the P. fluorescens species, providing a foundation for natural product discovery using bioinformatic approaches.