The effect of site, cold storage, and scion genotype on the apple root microbiome and its effect on apple canker (Neonectria ditissima) severity
The severity of European apple canker caused by Neonectria ditissima can vary between sites and between apple genotypes within a site. Root-associated microbial communities are also known to vary between sites and apple scion genotypes, but their role in canker susceptibility is unclear. We used quantitative PCR and 16S/ITS amplicon sequencing to investigate the degree to which planting site, cold storage of trees prior to planting, and scion genotype affect the diversity and composition of apple root-associated fungal and bacterial communities. In addition, we investigated whether differences in community diversity or relative abundance of specific taxa present on apple roots could be associated with the observed variance in number of cankers on each tree. Seven apple scion cultivars grafted onto M9 rootstocks were planted in December 2018 or stored at 2 ? until planting in April 2019 on three sites in Kent, UK, and canker lesion counts were assessed for 3 years. Root samples were collected in June 2021 from all cultivars across the sites and cold storage treatments. Site was the primary factor affecting root-associated community size, diversity, and composition. Cold storage—and its interaction with site—had small but significant effects on fungal microbiome size, fungal and bacterial ß-diversity, and the abundance of specific taxa, indicating that differences in microbial communities at planting can persist long-term. Scion genotype had a limited effect on root microbiome diversity, but affected the abundance of specific fungal and bacteria taxa, suggesting they may be partly under the control of the scion genotype. Greater fungal a-diversity and lower bacterial a-diversity of apple root-associated communities were associated with fewer canker lesions. The abundance of specific fungal and bacterial taxa were associated with the number of canker lesions across and within sites. For fungi, Clonostachys rosea were associated with fewer canker lesions and Alternaria alternata and Mortierella alpina were associated with more canker lesions. For bacteria, Bradyrhizobium was associated with more canker lesions and was affected by scion genotype, and different Streptomyces taxa were associated with either more or fewer canker lesions. These taxa could provide candidates for beneficial microbial soil amendments to reduce the impact of apple canker.