Integrative genomic and transcriptomic insights into the biocontrol activity of Pseudomonas sp. PF05 against Fusarium oxysporum

Microbial biological control agents (MBCAs) represent a sustainable alternative to chemical pesticides for the management of soil-borne fungal pathogens. Among them, fluorescent pseudomonads are widely recognized for their biocontrol potential, yet the precise mechanism of action and the molecular determinants underlying strain-specific antifungal activity remain incompletely understood. In this study, we investigated the genetic and transcriptional bases of biocontrol efficacy in Pseudomonas sp. PF05, a strain exhibiting strong antagonism against the phytopathogen Fusarium oxysporum, by integrating comparative genomics and transcriptomic analyses with those of a closely related but weakly antagonistic strain Pseudomonas frederiksbergensis PF4.89. Genome analyses revealed that strain PF05 harbors an expanded repertoire of genes associated with secondary metabolite biosynthesis, including phenazine metabolism, polyketide biosynthesis, and non-ribosomal peptide-related functions, compared with PF4.89. Transcriptomic profiling revealed that, during direct interaction with F. oxysporum, PF05 did not primarily activate canonical antifungal biosynthetic pathways, but instead mounted a coordinated adaptive response centered on efflux systems, metabolic reprogramming, detoxification processes, and regulatory networks. This response was accompanied by repression of respiratory activity, iron uptake, energy-intensive transport and secretion systems, indicating a strategic reprogramming aimed at stress tolerance and metabolic efficiency. In contrast, PF4.89 displayed a basal transcriptional profile characterized by a more limited regulatory engagement and reduced basal activation of pathways associated with microbial competition. Together, these results indicate that effective biocontrol in Pseudomonas sp. PF05 arises from the interplay between genomic potential and dynamic transcriptional regulation, rather than from the expression of individual antifungal genes alone. This work provides new insights into the multifaceted strategies underpinning microbial biocontrol and highlights regulatory and metabolic flexibility as key traits for the development of reliable MBCAs.