The interplay between scion genotype, root microbiome, and Neonectria ditissima apple canker

Severity of European apple canker caused by Neonectria ditissima can vary between locations and apple genotypes. We investigated how location, cold storage/planting season, and apple scion genotype affect root-associated microbial communities. Additionally, we investigated whether differences in abundance of specific taxa could be associated with canker lesion counts. Seven scion cultivars grafted onto M9 rootstocks were inoculated with N. ditissima in the nursery and then planted in December 2018 or stored at 2°C until planting in April 2019 at three sites in Kent, UK. We assessed canker lesions and collected root samples in June 2021. Quantitative polymerase chain reaction (qPCR) and internal transcribed spacer (ITS)/16S rRNA gene amplicon sequencing was used to analyse microbial communities. Site was the primary factor affecting microbiome size, diversity, and composition. Cold storage/planting season had small but significant effects, indicating that differences in the microbiome at planting can persist long-term. Scion genotype had a limited effect on diversity but did influence the abundance of specific root-associated taxa. Bacterial α-diversity was associated with canker count in a site-dependent manner. Increased abundances of particular fungal (Rhizophagus irregularis and Epicoccum nigrum) and bacterial (Amycolatopsis and Bradyrhizobium) root-associated taxa were associated with fewer cankers.