Relative contribution of season, site, scion and rootstock genotype, and susceptibility to European canker to the variability in bacterial and fungal communities in apple leaf scar tissues

Neonectria ditissima infects apple trees through wounds, causing European canker. In the UK, the most important entry site for N. ditissima is leaf scar. Specific apple endophytes may contribute to cultivar resistance/tolerance to the pathogen. We assessed the relative effect of location, sampling time (season), and rootstock/scion genotype on bacterial and fungal endophyte communities in the apple leaf scar tissues of current‐season extension shoots and identified Operational Taxonomic Units (OTUs) with differential abundance between canker resistant and susceptible scions, and between rootstocks. Leaf scar tissues were sampled from two orchards at three times (10/2018, 06/2019 and 10/2019) for eight scion cultivars, each grafted onto two rootstocks, for profiling 16S and ITS rRNA regions. Endophyte composition was primarily affected by season (autumn vs. spring) and location (sites and blocks within site). There was a significant reduction in the community size in the spring, particularly for fungi, and species turnover between autumn and spring. This seasonal dynamics suggest that to protect leaf scars from N. ditissima infection in the autumn specific endophytes suppressing canker may have to be augmented annually around the leaf‐fall time. Scion and rootstock genotypes had limited effects on the endophyte community. A group of resistant cultivars differed from a group of susceptible ones in the relative abundance of many bacterial and fungal OTUs, most of which had low reads numbers. Nevertheless, several OTUs with high reads numbers differed in their relative abundance between resistant and susceptible scions, including OTUs from Sphingomonas, Methylobacterium, Vishniacozyma and Rhodotorula babjevae, and warrant further investigation for their potential role in host resistance/tolerance against N. ditissima. Composition of endophyte around the apple leaf scars was primarily affected by season and planting location. There was a significant reduction in the community size in the spring, particularly for fungi, and species turnover between autumn and spring. Scion and rootstock genotypes had limited effects on the endophyte community. A group of resistant cultivars differed from a group of susceptible ones in the relative abundance of many bacterial and fungal OTUs, including OTUs from Sphingomonas, Methylobacterium, Vishniacozyma and Rhodotorula babjevae.