Effects of Trichoderma and Salicylic Acid/Methyl Jasmonate on the Growth, Development, and Lipid Metabolism of Codonopsis pilosula

Endophytic fungi and phytohormone signaling can jointly influence growth–defense trade-offs in medicinal plants by reprogramming metabolism in a stage-dependent manner. To elucidate how the endophytic fungus Trichoderma longibrachiatum FG and exogenous salicylic acid (SA) and methyl jasmonate (MJ) regulate Codonopsis pilosula (C. pilosula), seedlings were assigned to five treatments: control (CK), FG, SA, MJ, and SA + MJ (SM). Assessments were conducted at multiple growth stages using morphological measurements, photosynthetic and physiological assays, antioxidant profiling, and non-targeted metabolomics. All treatments promoted seedling growth, with SM producing the most pronounced improvements in biomass-related traits, including root growth and overall biomass accumulation. FG, SA, and MJ modified photosynthetic traits and redox status, as evidenced by changes in photosynthetic parameters, antioxidant enzyme activities, lipid peroxidation levels, and endogenous signaling molecules (SA, JA, NO), indicating coordinated regulation of primary physiology and stress-related responses. UHPLC/Q-TOF-based metabolomic profiling revealed temporally distinct patterns: FG induced limited early changes but triggered marked metabolic reprogramming at 50 days, whereas SA, MJ, and SM elicited stronger metabolite shifts at 15 days. Differential metabolites were predominantly lipids and lipid-like molecules, with steroid and steroid-derived pathways emerging as key responsive hubs; notably, FG at the late stage was associated with enrichment of intermediates linked to brassinosteroid biosynthesis. Overall, SA–MJ interactions were trait-dependent, showing clearer synergy in biomass-related performance, while FG primarily contributed to late-stage metabolic adjustments. These findings provide a mechanistic basis for optimizing high-quality cultivation and sustainable utilization of C. pilosula.