Unraveling the Chemical Interactions of Fungal Endophytes for Exploitation as Microbial Factories

Endophytic fungi are a group of mutualistic fungi harbored in plant tissues that are known to provide a plethora of fitness benefits to host plants. It is now firmly established that fungal endophytes have a remarkable capability to produce bioactive secondary metabolites including valuable pharmaceutically relevant agents. Unfortunately, efforts to utilize endophytic fungi as sustainable microbial resources for industrial production of compounds have not yet been successful. Recent studies have revealed that endophytic fungi not only interact with their host plant but also engage in complex communication strategies with associated macro- and microorganisms in order to survive and function in their natural habitat. These multifaceted interactions are difficult to introduce and maintain in vitro under artificial fermentation conditions in the laboratory. Our emerging knowledge on the complex interaction between endophytic fungi and associated organisms as well as the host plants provides a silver lining toward industrial exploitation of endophytes. Herein, we highlight the importance of endophytes (particularly endophytic fungi) in plant-microbe associations and discuss future strategies that might be employed to investigate the chemical communication within endophytic microbial communities, which can lead the way toward sustainable industrial production of important compounds using endophytic fungi.