Raspeberry fruit epiphyte microbiome

Raspberries are delicate fruits and susceptible to a range of fungal and bacterial diseases. One such fungal pathogen, Cladosporium, is becoming more prevalent in the UK, coinciding with the movement of raspberry production to under polythene. We first used amplicon-sequencing to investigate how fruit age, location of fruit within a polytunnel, polytunnel location and sampling date affected the raspberry fruit epiphytic microbiome. Fruit age was the most important factor impacting the fungal microbiome, followed by sampling date and polytunnel location; the location of fruit within a tunnel had a small, albeit significant, effect on the overall fungal microbiome composition. In contrast, polytunnel location and fruit age were both important factors impacting the bacterial microbiome composition, followed by the sampling date. The within-tunnel location had no significant effect on the bacterial microbiome. As fruit ripened, more fungal genera were detected; the opposite was true for bacteria. Cladosporium was the most abundant fungus of the fruit epiphytic microbiome, accounting for nearly 44% of all fungal sequences.