Plant-associated Fungi: Methods for Taxonomy, Diversity, and Bioactive Secondary Metabolite Bioprospecting

Plants harbor a large reservoir of fungal diversity, encompassing endophytic, epiphytic, phytopathogenic, and rhizosphere-associated fungi. Despite this diversity, relatively few fungal species have been characterized as sources of bioactive secondary metabolites. The role of secondary metabolites is still not fully understood; however, it is suggested that these metabolites play important roles in defense mechanisms and fungal interactions with other organisms. Hence, fungal secondary metabolites have potential biotechnological applications as prototype molecules for the development of therapeutic drugs. In this chapter, we describe the main methods used for routine fungi isolation, production of crude fungal extracts, and chemical characterization of bioactive compounds. In addition, explicative notes about the steps described are provided to explore the diversity of the endophytic, phytopathogenic, epiphytic, and rhizosphere fungi and to evaluate the biotechnological potential of each group.