Investigating the inoculum dynamics of Cladosporium on the surface of raspberry fruits and in the air

Raspberry production is under threat from the emerging fungal pathogenic genus Cladosporium. We used amplicon-sequencing, coupled with qPCR, to investigate how fruit age, fruit location within a polytunnel, polytunnel location and sampling date affected the fruit epiphytic microbiome. Fruit age was the most important factor impacting the fungal microbiome, followed by sampling date and polytunnel location. In contrast, polytunnel location and fruit age were important factors impacting the bacterial microbiome composition, followed by the sampling date. The within-tunnel location had a small significant effect on the fungal microbiome and no effect on the bacterial microbiome. As fruit ripened, fungal diversity increased and the bacterial diversity decreased. Cladosporium was the most abundant fungus of the fruit epiphytic microbiome, accounting for nearly 44% of all fungal sequences. Rotorod air samplers were used to study how the concentration of airborne Cladosporium inoculum (quantified by qPCR) varied between location (inside and outside the polytunnel) and time (daytime vs. nighttime). Quantified Cladosporium DNA was significantly higher during the day than the night and inside the polytunnel than the outside. This study demonstrated the dynamic nature of epiphytic raspberry fruit microbiomes and airborne Cladosporium inoculum within polytunnels, which will impact disease risks on raspberry fruit.Biotechnology and Biological Sciences Research Council, Grant/Award Number: BB/T509073/

From Endophyte Community Analysis to Field Application: Control of Apple Canker (<i>Neonectria ditissima</i>) with <i>Epicoccum nigrum</i> B14-1

Apple canker, caused by Neonectria ditissima (Tul. and C. Tul.) Samuels and Rossman, is a major disease of apples (Malus domestica) worldwide. N. ditissima infects through natural and artificial wounds. Infected wood develops canker lesions which girdle branches and main stems causing reduced yield and tree death. N. ditissima is difficult to control; removal of inoculum (cankers) is expensive and therefore seldom practiced, whilst effective chemical products are being banned and no biocontrol products have been found to be effective against N. ditissima. This study used cues from a previous apple endophyte community analysis to isolate and test fungal endophytes belonging to the genus Epicoccum as potential endophytic biocontrol agents. Epicoccum nigrum B14-1, isolated from healthy apple trees, antagonised N. ditissima in vitro and reduced the incidence of N. ditissima infections of leaf scars by 46.6% and pruning wounds by 5.3% in field conditions at leaf fall. Autumn application of B14-1 conidia increased E. nigrum abundance in apple tissues at 10–20 days post-inoculation by ca. 1.5×, but this returned to control levels after one year. E. nigrum B14-1 did not cause detrimental effects on apple foliage, buds, fruit, or growth and could therefore present a new biocontrol agent to manage N. ditissima in commercial apple production