Fungal endophytes and their secondary metabolites for crop protection

Abstract Fungal endophytes have emerged as a promising strategy for sustainable crop management, due to their remarkable ability to synthesize a wide array of secondary metabolites with beneficial effects on plants. These microorganisms establish asymptomatic relationships within plant tissues and can produce bioactive compounds with biocidal properties. Despite promising advances, the mechanisms of symbiosis remain unclear and there is a lack of in-depth analysis on the chemical characterization of their metabolites. This review compiles and discusses the current discoveries on 180 metabolites summarized according to their biological activities (insecticidal, antifungal, phytotoxic, nematicidal and antibacterial), highlighting their potential applications as biocontrol agents for integrated crop protection strategies. As a future perspective, the use of next-generation sequencing (NGS) technologies such as metagenomics in endophytic fungi research is emphasized for its promise in elucidating complex plant–microbe interactions and guiding bioprospecting efforts to identify fungal taxa capable of producing agriculturally relevant bioactive compounds. This review aims to summarize recent advances in the field, highlighting the potential uses of endophytic compounds in plant health, disease suppression, and resistance enhancement, while also identifying current limitations and outlining future research directions to further expand this promising area.