Dynamics and origin of endophyte communities in apple leaf scars

Effective management of European apple canker (Neonectria ditissima) is a key issue in commercial apple production. Recent research indicated that high relative abundance of a Sphingomonas taxon in apple leaf scar tissues is associated with reduced canker incidence. Roots of M9 rootstock plants were inoculated with six Sphingomonas strains at planting to investigate whether inoculation with Sphingomonas improved rootstock growth and influenced microbial communities in leaf scar tissues, roots and rhizosphere. Inoculation with Sphingomonas at potting did not significantly affect plant development in terms of plant height, girth and aboveground biomass. It also did not increase the relative abundance of aggregated Sphingomonas genus. Inoculation significantly microbial community structures in terms of within-sample diversity (appearing to reduce diversity), particularly in rhizosphere and roots-associated microbial communities. On the other hand, root inoculation did not significantly affect relative abundance of any taxon in rhizosphere and roots but affected relative abundance of many taxa in leaf scar tissues. There were reductions in the relative abundance of five fungal genera that are known to contain plant pathogens, including Gnomoniopsis and Phomopsis magnoliae. Furthermore, inoculation with Sphingomonas led to decreased abundance of other woody pathogens (Ilyonectria robusta, Neofabraea actinidiae and Perenniporia fraxinea). There were large differences in microbial communities in the leaf scar tissues between the top (younger) and base (older) positions, particularly the fungal community, suggesting aeroinocula as an importance source of endophytes in leaf scars. Further research is needed to develop application methods for increasing relative abundance of Sphingomonas in leaf scars.