Freshwater-derived Burkholderia vietnamiensis FBCC-B8049: Transcriptomic basis of antifungal activity and plant growth-promoting potential

Burkholderia vietnamiensis FBCC-B8049, isolated from a freshwater environment, exhibits strong antifungal activity against Colletotrichum spp. and Fusarium oxysporum, and effectively suppressed anthracnose disease in chili pepper fruits. In addition, FBCC-B8049 demonstrated multiple plant growth-promoting (PGP) activities, including siderophore production, phosphate solubilization, and indole-3-acetic acid (IAA) synthesis, which contributed to enhanced seed germination and seedling growth in chili pepper. To elucidate the molecular basis underlying this dual function, we performed in vitro transcriptome analysis of FBCC-B8049 under confrontation with C. acutatum. RNA-seq analysis revealed significant upregulation of PQQ biosynthesis genes (pqqBCDE) and periplasmic redox-related cytC3, suggesting enhanced activity of PQQ-dependent dehydrogenases and a functional link to phosphate solubilization. In contrast, a contiguous gene cluster (AK36_3727–AK36_3737) and several electron transport chain components were downregulated. These results indicate a branch-specific metabolic reprogramming strategy, whereby FBCC-B8049 selectively activates electron transfer chain (ETC) modules associated with antifungal redox activity while suppressing energetically costly or non-essential pathways. Taken together, this study provides transcriptomic insights into the dual-function mechanisms of B. vietnamiensis FBCC-B8049, highlighting its potential as a freshwater-derived biological control agent for sustainable agriculture.