Investigating the leaf microbiome as a means of disease resistance against coffee leaf rust (CLR, Hemileia vastatrix) in Hawaii

Coffee is the second most economically important agricultural crop in Hawaii, with an estimated value of $131 million for roasted and $60 million for green coffee annually. The recent arrival of coffee leaf rust (CLR), a disease caused by the obligate parasitic fungal pathogen Hemileia vastatrix, has had a profound impact on Hawaii’s coffee industry with yield losses estimated at 30-70%. While significant progress has been made in the development of an integrated pest management (IPM) strategy for CLR in Hawaii over the last 5 years, much remains to be explored in terms of understanding this disease under Hawaii’s unique agroecological conditions. For example, little is known about how the leaf microbiome may influence the presence and severity of CLR. Microbiome-mediated disease resistance may occur through the secretion of antimicrobial chemicals, or by indirectly activating the plant’s immune system. Our work proposes to characterize the epiphytic microbiome on healthy and CLR-infected leaves, as well as in three coffee cultivars with different levels of susceptibility to CLR. We will combine field sampling with genomic methods to characterize bacterial and fungal communities on coffee leaves and describe any shifts in taxonomic and functional diversity as CLR infection progresses. The results of this research will help to determine if the coffee leaf microbiome plays a significant role in the plant’s ability to respond to or resist this devastating disease.