Burkholderia cepacia NB-13: Biocontrol efficacy and medium-driven metabolic regulation.

Fusarium oxysporum, the primary pathogen causing lily root rot, severely impairs lily yield and quality, threatening the sustainable development of the lily industry. Conventional chemical control strategies are associated with drawbacks such as pesticide residues, environmental pollution, and pathogen resistance, emphasizing the urgent need for eco-friendly biological control strategies. In this study, an antagonistic bacterial strain Burkholderia cepacia NB-13 was isolated from healthy lily rhizosphere tissues, which exhibited 80.76% inhibition rate against F. oxysporum mycelial growth and was identified as B. cepacia through morphological and molecular verification. Whole-genome sequencing was performed to predict antifungal metabolites, while integrated transcriptome analysis and targeted pyrrolnitrin quantification elucidated the regulatory mechanism underlying differential antifungal substance production, with a significantly higher pyrrolnitrin yield in King's B Medium supported by the upregulation of prnA biosynthetic genes and ED pathway activation. In vitro and field experiments indicated that the strain achieved an in vitro control efficacy of 91.66%. Application of B. cepacia NB-13 combined with conventional field management delivered excellent biocontrol efficacy, raising the survival rate of lily to 89.58% after field treatment. The strain also showed good compatibility with organic fertilizers. Microbial diversity analysis indicated that B. cepacia NB-13 regulated the rhizosphere microenvironment without altering α-diversity. Collectively, our findings demonstrate that B. cepacia NB-13 possesses excellent biocontrol potential against F. oxysporum-induced lily root rot, providing a promising candidate for green biological control in agricultural production.