Genome Sequencing, In Vitro Assays, and Metabolomics Reveals Biocontrol and PGP Traits of a Rhizobacterium, Streptomyces cavourensis SAI-25

A rice rhizosphere Streptomyces strain SAI-25 was previously reported to exhibit bicontrol activity against a limited range of agricultural pests, leaving its broader agricultural potential unexplored. In this study, we performed whole genome sequencing, untargeted metabolomics and in-vitro assays to examine its full agricultural potential. Genome similarity confidently re-assigned SAI-25 as a new strain of S. cavourensis. The comparative genome analysis revealed the presence of unique proteins and genomic islands with diverse functions highlighting its genomic novelty. Among the predicted Biosynthetic Gene Clusters (BGCs) for secondary metabolites, majority were annotated having biocontrol and plant growth promoting (PGP) activities. Three of them were detected in untargeted metabolomics of secretome on Iron deficiency or Salinity stress, which includes a siderophore (desferrioxamine B), an osmoprotectant (ectoine), and a broad-spectrum antimicrobial (valinomycin). Beyond the annotated BGCs, at least eight additional agriculturally relevant secondary metabolites were also detected. For the previously reported insecticidal diketopiperazine derivative produced by SAI-25, two key enzymes capable of diketopiperazine core biosynthesis were predicted. Finally, the in-vitro assays revealed its broad range PGP activities. Overall, the SAI-25’s versatile secondary metabolites and potent PGP enzymes highlight its potential as a promising biopesticide/biofertilizer candidate.