Apple leaf scar endophytes metabarcoding canker samples

Bacterial and fungal endophytes may help their host in terms of improved tolerance to plant pathogens. Neonectria ditissima infects apple trees through artificial or natural wounds, including leaf scars, picking wounds, and pruning cuts, causing the European apple canker disease. Specific apple endophytes may partially contribute to the observed cultivar resistance/tolerance to the pathogen and thus could be used for disease management. We assessed the relative effects of large and small spatial scale, sampling time, and rootstock and scion genotypes on the overall bacterial and fungal endophyte community structures around the apple leaf scar tissues of current-season extension shoots. Apple leaf scar tissues were sampled three times over two seasons (one spring and two autumn times) for 16 scion-rootstock combinations at two locations. Both 16S and ITS regimes were sequence with the Illumina MiSeq platform. The results showed that endophyte composition was primarily affected by location and sampling time effects. There was a crush crash in the microbial population size in the spring as well as considerable turnover in microbial groups between spring and autumn, particularly for fungal endophytes. The effects of scion genotypes were limited, albeit statistically significant, primarily through its interaction with sampling time. Rootstock genotypes in general did not significantly affect endophyte composition around leaf scar tissues. Thus, a large proportion of endophytes around leaf scars of new shoots is likely to have originated from the surrounding environment, suggesting annual augmentation of specific endophytes may be necessary to protect leaf scars from infection in the autumn.