Plants produce a diversity of chemicals that mediate they way they interact with other plants, with animals, and with beneficial and pathogenic microogranisms. There are often fungi associated with plants that can stimulate the production of and/or modify chemicals produced by the plant, or the fungi may produce the chemicals themselves. These chemicals can help determine plant resistance to disease and environmental stress. Many of the details of how plants promote beneficial fungi, and how fungi interact with one another to affect plant defenses are not known. The goals of this project are to better understand these details using coffee plants, their relatives, and the fungal microbiomes associated with different plant species. Understanding the interactions of beneficial fungi in and on plant leaves will lead to improved strategies of disease management. Among the broader impacts of this project are botanical and microbial collections, and a database of plant and fungal genomic information that can serve as a resource for natural product discovery, and prevention and management of agricultural diseases. Additionally, students and postdocs will be trained in the various disciplines that are involved in this project, and an environmental genomics short course will be taught in two locations in the US and in Costa Rica.
This project will examine how secondary metabolites in foliar tissues define and are shaped by fungal endophyte communities, and how metabolite-defined niches and horizontal gene transfer of metabolic pathways promote species and genome diversity. Culture-dependent and culture-independent methods will be used to identify foliar endophyte communities associated with wild tropical Rubiaceae species, coffee plantation management strategies, and leaf metabolite profiles. Metabolomic analyses of leaves and endophyte competitive interactions will identify the roles of key fungi in the endophyte community and their contribution to the plant defense chemistry. Novel, genome-scale comparative analyses will identify gene clusters involved in the production and degradation of secondary metabolites, and the roles of these gene clusters in endophyte functional redundancy and fungal reproductive isolation will be investigated.
