The epidemiology of fungal pathogens of apples unveiled by fruit microbiome: the case of dry lenticel rot and white haze.

Different methods, including cultural and molecular ones, can be used to study the epidemiology of postharvest pathogens. In recent years, metabarcoding is emerging as a flexible tool to elucidate the biology and epidemiology of pathogens. With the introduction of new apple varieties, emerging diseases emerged including dry lenticel rot and white haze. Dry lenticel rot symptoms are brown-to-black spots occurring on the fruit peel, caused by Ramularia mali. White haze is a waxy, opaque white film forming on the cuticle, associated with yeast-like basidiomycetes of Entylomatales and Golubeviales. The epidemiology of these pathogens remains unclear. In the present study, we used metabarcoding to characterize both epiphytic and endophytic microbial communities of two apple cultivars, ‘Opal’ and ‘Ambrosia’, across six time points from early fruit development up to the end of shelf life. Moreover, we measured fruit disease incidence and quality parameters. R. mali first developed in both cultivars as an endophyte at second fruit fall phenological phase, then it appeared as an epiphyte from fruit ripe for picking onward, when symptoms became visible. This was confirmed in endophytic samples through qPCR specific for R. mali: a higher amount of the pathogen was detected in June, lower in July and August, and the pathogen was not anymore detectable later. Among the genera associated to white haze, Golubevia was the most abundant epiphyte from beginning of ripening to the end of shelf life. Alpha and beta diversity analyses showed significant difference both in richness and composition among different tissue, time points and cultivars. The study helps to explain the epidemiology of white haze and dry lenticel rot, and to design a targeted crop protection strategy, reinforcing the hypothesis that fruit metabarcoding could be a valuable tool for assessment and prediction of postharvest diseases, before symptoms occurrence in fruit.