Endophytic fungi as biocontrol agents: A metabolite-driven approach to crop protection and sustainable agriculture

Abstract

The growing concerns over pesticide resistance, environmental pollution, and crop losses have increased the demand for sustainable and eco-friendly alternatives to chemical crop protection. Endophytic fungi, symbiotic microorganisms residing within plant tissues have emerged as promising biological control agents due to their ability to produce diverse bioactive secondary metabolites (SMs). These compounds, including alkaloids, terpenoids, polyketides, and peptides, exhibit potent antifungal, antibacterial, and insecticidal activities. This review consolidates current knowledge on the taxonomy, ecology, and colonization strategies of endophytic fungi, as well as their habitat-driven functional diversity. We explore the biosynthetic mechanisms underlying metabolite production, with an emphasis on the role of biosynthetic gene clusters (BGCs) in driving chemical diversity. Key classes of fungal metabolites are summarized based on their structure, biological activities, and role in plant protection. The review also discusses both direct and indirect mechanism through which endophytic fungi enhance plant immunity, including, competitive exclusion, antimicrobial compound production, defense responses activation, phosphate solubilization, siderophore production, and phytohormone modulations. Additionally, the significance of these endophytes in climate-resilient agriculture and post-harvest disease management is addressed. Despite promising advances, challenges such as inconsistent colonization, environmental variability, and regulatory barriers hinder their widespread application. This review aims to provide a comprehensive understanding of fungal endophyte-derived secondary metabolites as viable tools for sustainable crop protection and improved agricultural resilience.