Integrated genomic and transcriptomic analysis reveals the biocontrol and plant growth-promoting mechanisms of Burkholderia gladioli PNB20-1 against peanut southern blight

Introduction Peanut southern blight, caused by Sclerotium rolfsii , is a devastating soilborne disease that threatens peanut production worldwide. Members of Burkholderia have attracted attention as biocontrol agents owing to their diverse secondary metabolites and plant growth-promoting (PGP) capacity. Methods We isolated B. gladioli PNB20-1 from the disease-healthy junction of peanut plants. Its biocontrol and PGP potential was evaluated by dual-culture, greenhouse pot, and biosafety assays, its genome was sequenced on the Oxford Nanopore platform, and host defense responses were profiled by RNA-Seq. Results PNB20-1 exhibited in vitro antagonism against S. rolfsii with a 52.7% inhibition rate and reduced sclerotial biomass by 19.3% after 4 weeks of co-culture. The complete genome of PNB20-1 comprised 8,278,972 bp across three circular replicons, encoding 6,923 CDSs and 21 biosynthetic gene clusters (BGCs). Among these, the ornibactin-type siderophore BGC and phosphate solubilization genes were supported by phenotypic assays. Transcriptomic profiling of PNB20-1-inoculated peanut roots identified 1,552 differentially expressed genes, of which 1,057 were upregulated and 495 downregulated. GO and KEGG enrichment analyses pointed to a coordinated defense response encompassing stilbenoid phytoalexin biosynthesis, cutin-, suberin-, and lignin-mediated apoplastic barrier reinforcement, and salicylic acid (SA)-dominated multi-hormonal signaling. Preliminary biosafety evaluation showed that PNB20-1 is non-hemolytic and lacks key virulence determinants of clinically significant Burkholderia species. Discussion These findings suggest that B. gladioli PNB20-1 is a promising biocontrol agent and provide insights into the molecular basis of Burkholderia -mediated disease suppression in peanut.