Research on the Regulatory Mechanism of Endophytic Fungi on Active Components of Root-Derived Medicinal Plants: A Review

Root-derived medicinal plants are vital sources of bioactive molecules for traditional medicine and modern drug development, with their therapeutic effects relying on specialized secondary metabolites. Endophytic fungi, symbiotic microorganisms colonizing root tissues, play a key mediating role in regulating the biosynthesis and accumulation of these active components. While individual case studies of fungal-mediated metabolite enhancement have been extensively reported, a critical, comparative synthesis of regulatory efficacy, mechanistic conservation, and evidence robustness remains a major gap in the field. This review systematically summarizes research progress on endophytic fungi-root medicinal plant interactions. It elaborates the taxonomic diversity of root endophytic fungi (predominantly Ascomycota and Basidiomycota) with distinct host specificity, and clarifies their colonization dynamics and molecular mechanisms involving chemical signaling, enzymatic action and immune regulation, with a critical evaluation of methodological limitations in current detection approaches. The review focuses on fungal regulatory effects on major active components (terpenoids, saponins, alkaloids, flavonoids) via direct synthesis or upregulating host biosynthetic pathways, and provides a quantitative comparison of regulatory efficacy across different fungal genera, alongside a graded assessment of evidence strength for supporting studies. It dissects underlying mechanisms from signal exchange, hormone network modulation, gene regulation and enzymatic biotransformation, and elucidates the evolutionary basis for the conservation of core pathways across plant-fungus systems. It also discusses influential factors including host traits, fungal characteristics, abiotic conditions and biotic interactions, resolves key contradictory findings in the field, and highlights research areas based on weak or inconsistent evidence. Finally, it presents current challenges as well as future directions such as Holo-omics and metabolic engineering. This work provides a critical theoretical framework and practical guidance for using endophytic fungi to promote sustainable medicinal plant production and novel drug discovery.