Fruit microbiome: A powerful tool to study the epidemiology of dry lenticel rot and white haze – Emerging postharvest diseases of apple

With the introduction of new apple varieties, emerging diseases have been recorded including dry lenticel rot and white haze. Ramularia mali has been identified as the causal agent of dry lenticel rot, whereas species of Golubevia, Tilletiopsis and Entyloma have been associated to white haze, but the epidemiology of these pathogens remains unclear. In the present study, we measured fruit disease incidence and quality parameters, and we used metabarcoding to characterize both epiphytic and endophytic microbial communities of apple fruit of two commercial cultivars, ‘Opal’ and ‘Ambrosia’, across six time points from early fruit development up to the end of shelf life. R. mali first develops in both cultivars as an endophyte at BBCH (Biologische Bundesanstalt, Bundessortenamt and CHemical industry) phenological phase 73 (10–11% relative abundance), BBCH 77 (26–33% relative abundance) and BBCH 81 (1–7% relative abundance), then it appears as an epiphyte from BBCH 87 onward (1–2% relative abundance), when symptoms start to be visible. 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 (2–4%) from BBCH 81 to the end of shelf life. Alpha and beta diversity analyses unveiled the presence of significant difference both in richness and composition among different tissue, time points and cultivars. In conclusion, 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. •‘Ambrosia’ apples had 20% and 15% incidence of white haze and dry lenticel rot•Time point, cultivar and tissue influenced microbial richness and composition•Golubevia emerged as the main fungal genus associated to white haze•Ramularia was found first as an endophyte and later as an epiphyte•Ramularia abundance and development trend were verified through qPCR