Genomic characterization and antifungal properties of Paenibacillus polymyxa YF, a promising biocontrol agent against Fusarium oxysporum pathogen of codonopsis root rot

Ying Li ¹ Xu Su ² Wenjie Xi ^1* Yanli Zheng ¹ Yang Liu ^1* Wangshan Zheng ^1* Shiyu Wei ^1* Yan Leng ^1* Yongqiang Tian ^1*

• ¹ School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, Gansu Province, China
• ² Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Xizang Plateau in Qinghai Province, Qinghai Normal University, Xining, China

Root rot, a destructive soil-borne disease, poses a significant threat to a wide range of economically important crops. Codonopsis, a high value medicine plant, is particularly susceptible to substantial production losses caused by Fusarium oxysporum-induced root rot. In this study, we identified a promising biocontrol agent for codonopsis root rot, Paenibacillus polymyxa YF. In-vitro assay demonstrated that the strain YF exhibited a 70.69% of the inhibition ration against F. oxysporum, and broad-spectrum antifungal activities against the selected six postharvest pathogens. Additionally, strain YF demonstrated significant plant growth-promoting properties. Subsequent in vivo inoculation assays revealed that strain YF effectively mitigated disease symptoms of F. oxysporum-induced root rot in codonopsis, even achieving a complete disease prevention efficacy rate of 100%. Our findings further elucidated that the robust biocontrol capacity of strain YF against F. oxysporum is mediated through multiple mechanisms, including inhibition of fusaric acid secretion, downregulation of virulence-associated genes in F. oxysporum, and the production of multiple hydrolytic enzymes. Genomic analysis showed that strain YF has a 5.62 Mb single circular chromosome with 5,138 protein-coding genes. Comprehensive genome mining of strain YF also identified numerous genes and gene clusters involved in bio-fertilization, resistance inducers synthesis, plant colonization, biofilm formation, and antimicrobial activity. These findings provide insights into the biocontrol mechanisms of strain YF and offer substantial potential for its further exploration and application in crop production.