Dark septate endophyte as an effective synergistic approach to enhance growth and flavonoid accumulation in Cyclocarya paliurus

Abstract Traditional cultivation of medicinal Cyclocarya paliurus has consistently failed to resolve the growth-secondary metabolism trade-off, affecting yield and quality. Utilizing dark septate endophyte, which induces host plant endogenous hormone synthesis and enhance stress resistance, offers a feasible and effective method to balance this trade-off relationship. In this study, sterile Cyclocarya paliurus seedlings were subjected to dark septate endophyte inoculation, jasmonic acid spraying, and jasmonic acid inhibitor treatments. We demonstrated that dark septate endophyte inoculation increased seedling height by 59.46% and biomass by 15.94%. This treatment established an antioxidant barrier in plants, maintained reactive oxygen species homeostasis, and alleviated membrane lipid peroxidation, thereby boosting plant stress resistance. ITS gene sequencing confirmed that dark septate endophyte enhanced root fungal diversity. Integrated multi-omics analysis revealed that dark septate endophyte promoted flavonoid biosynthesis (total flavonoids increased by 15.30%) through triggering the jasmonic acid signaling pathway to activate MYC2-mediator complex subunit 25, significantly increasing vitexin content. Our results identify dark septate endophyte as a pivotal metabolic checkpoint for synergistically enhancing medicinal plant yield and quality. This study provides novel insights into eco-efficient cultivation strategies and lays the foundation for the broader application of beneficial dark septate endophyte in agroforestry practices.