Secondary Metabolites from Plant-Associated Fungi: Diversity, Function and Applications

Plant-associated fungi, including endophytes, epiphytes, mycorrhizal symbionts, and plant pathogens, represent one of the richest and at the same time most underexplored sources of secondary metabolites. These compounds encompass a wide range of chemically and biologically active molecules, including antibiotics, antifungal and antibacterial agents, antivirals, cytotoxic and anticancer compounds, phytohormones, and signaling molecules involved in plant–microbe communication. Notably, many of these fungal metabolites exhibit potent antimicrobial activity and have historically contributed to the development of clinically and agriculturally important antimicrobial agents. In the context of the rapidly increasing global challenge of antimicrobial resistance, plant-associated fungi have gained renewed attention as promising sources of novel antimicrobials with alternative modes of action.With recent advances in analytical tools and omics-based approaches, this field has entered a phase of rapid discovery and conceptual expansion. Technologies such as high-resolution mass spectrometry, metabolomics, genome mining, next-generation sequencing, and bioinformatic prediction of biosynthetic gene clusters (BGCs) have significantly expanded our ability to identify and characterize novel fungal secondary metabolites, including antimicrobial compounds. At the same time, innovative experimental strategies—such as co-cultivation systems, epigenetic modifiers, and the simulation of environmental conditions—have enabled the activation of previously silent gene clusters, revealing a vast and largely untapped reservoir of bioactive metabolites with antimicrobial potential.Despite this progress, major questions remain unanswered. What ecological roles do antimicrobial and other secondary metabolites play in plant–fungal and multi-kingdom interactions? How are these compounds regulated at genetic and epigenetic levels? Which molecular mechanisms underlie their antimicrobial activity and specificity? And to what extent can these metabolites be harnessed to combat drug-resistant pathogens and support sustainable applications in agriculture, medicine, and biotechnology?This Research Topic aims to bring together leading and emerging perspectives on the diversity, function, biosynthesis, and application of secondary metabolites produced by plant-associated fungi, with particular emphasis on antimicrobial compounds. By integrating studies across molecular biology, chemistry, ecology, biotechnology, and systems biology, the topic seeks to provide a holistic overview of current developments and future directions in fungal natural product research and antimicrobial discovery.The scope of the Research Topic will include, but is not limited to:• Discovery and chemical characterization of secondary metabolites from endophytic, mycorrhizal, epiphytic, and pathogenic fungi• Identification, regulation, and functional analysis of biosynthetic gene clusters involved in antimicrobial metabolite production• Ecological functions of antimicrobial metabolites in plant defense, microbial competition, stress tolerance, and symbiosis• Molecular modes of action and resistance-related aspects of fungal-derived antimicrobial compounds• Crosstalk and signaling between fungi, host plants, and associated microbiota mediated by secondary metabolites• Advances in analytical, metabolomic, genomic, and bioinformatic approaches for antimicrobial natural product discovery• Activation of silent biosynthetic pathways (e.g. via co-cultures, epigenetic modification, or environmental cues) to uncover novel antimicrobials• Applied aspects, including biocontrol, plant health, sustainable agriculture, antimicrobial drug discovery, pharmaceutical potential, and industrial biotechnologyManuscripts focusing solely on screening of crude extracts, without chemical characterization of the active constituents or investigation of their molecular mechanisms of action, will be considered outside the scope of this Research Topic.We welcome the following article types: FAIR² Data, Hypothesis and Theory, Methods, Mini Review, Opinion, Original Research, Perspective, Review, Systematic Review, Technology and Code. The topic is intended for a broad scientific audience, including researchers in mycology, natural products chemistry, plant science, microbial ecology, molecular biology, biotechnology, agronomy, and antimicrobial research. Topic editors: Frank Surup Source: https://www.frontiersin.org/research-topics/74590/secondary-metabolites-from-plant-associated-fungi-diversity-function-and-applications