Microbiomes: an important tool to elucidate the epidemiology of postharvest pathogens.

Postharvest diseases can be caused by latent pathogens infecting at different phenological phases in orchard. It is of great importance to understand the infection time, in order to intervene with preventive treatments in orchard. Microbiome analysis is a flexible tool to elucidate the epidemiology of plant pathogens. With the introduction of new apple varieties, dry lenticel rot, caused by Ramularia mali, and white haze, associated to Entylomatales and Golubeviales, are emerging. The epidemiology of these pathogens remains unclear. By using metabarcoding, we characterized both epiphytic and endophytic microbiomes of two apple cultivars from early fruit development up to the end of shelf life. R. mali developed in both cultivars as an endophyte at second fruit fall, then white haze symptoms appeared on fruit ripe for picking. This was confirmed in endophytic samples through qPCR specific for R. mali. Among the genera associated to white haze, Golubevia was the most abundant epiphyte from beginning of ripening to the end of shelf life. The analysis of the airborne mycobiome present in the orchard, by using a spore trap in orchard and metabarcoding, permitted to evaluate when fungal pathogen spores are released in orchard: Enylomatales started to occur at the end of the fruit development, whereas R. mali spores were released since flowering. Metabarcoding helps to elucidate the epidemiology of fungal pathogens and to design a targeted crop protection strategy.