Rootstock microbiome as a target for manipulation to combat apple replant disease

Apple replant disease (ARD) describes a phenomenon of reduction of crop productivity in the early years of orchard establishment in the sites previously planted to apple. Currently manipulation of soil microbiome by (bio)fumigation is the major approach to alleviate ARD. Adjustment of rootstock microbiome to harsh orchard soil biotic factors might be an alternative approach to combat ARD. In this study we evaluated differences in microbiome structure and composition between nursery rootstock and mature trees, grown in Nova Scotian apple orchards. We showed that mature apple tree roots possessed microbiome that dramatically differed in its diversity, structure and composition from that associated with saplings. Our research pointed to a single mycorrhizal fungus, Pteridiospora spinosispora , which should be further investigated as a potential nursery inoculum to prevent ARD development in re-planted apple orchards. The results of this study provide a foundation for development of a synthetic community which could be used in nurseries during rootstock propagation to improve saplings adaptation to ARD soils. This approach could deliver an ecologically safe and cost-efficient alternative to soil amendments to alleviate ARD consequences.