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

Authors: Yurgel, Svetlana; AJEETHAN, NIVETHIKA - Dalhousie University; ALI, SHAWKAT - Aafc Lethrdge Research Center

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/4/2025
Publication Date: 7/2/2025
Citation: Yurgel, S., Ajeethan, N., Ali, S. 2025. Rootstock microbiome as a target for manipulation to combat apple replant disease. Scientific Reports. 15. Article 23498. https://doi.org/10.1038/s41598-025-05837-w.
DOI: https://doi.org/10.1038/s41598-025-05837-w

Interpretive Summary: Apple replant disease (ARD) describes a phenomenon of a reduction of crop productivity in the early years of orchard establishment in sites previously planted to apple. Soil fumigation is the dominant way to control ARD in the USA. However, this approach is labor intensive, imposes substantial financial burdens, and causes considerable damage to the environment. On the other hand, manipulation of microbial communities in apple rootstock to improve the tree adaption to hostile orchard soil environment could deliver an ecologically safe and cost-efficient alternative to soil amendments to alleviate ARD consequences. In this study we evaluated differences in microbial composition between nursery rootstock and mature trees grown in Nova Scotian apple orchards. As a result, we identified a mycorrhizal fungus, Pteridiospora spinosispora, which was preferentially enriched in mature tree roots and potentially provides protection from diseases. This fungus 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 the development of a synthetic community that could be used in nurseries during rootstock propagation to improve sapling adaptation to ARD soils

Technical Abstract: Apple replant disease (ARD) describes a phenomenon of reduction of crop productivity in the early years of orchard establishment in sites previously planted to apple. Currently manipulation of the soil microbiome by (bio)fumigation is the major approach to alleviate ARD. However, adjustment of rootstock microbiomes 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 six Nova Scotian apple orchards. We showed that mature apple tree roots possessed a microbiome that dramatically differed in its diversity, structure and composition from that associated with saplings. This was reflected in (i) the significant effect of origin factor (tree vs. rootstock) on the overall bacterial and fungal community structure; (ii) the strong hierarchical clustering pattern separating tree and rootstock microbiomes onto two clusters; (iii) the differences in the intensity of microbial collaboration between tree and rootstock microbiomes; (iv) the large number of differentially represented taxa across the niches; and (v) the variation in microbiome function across root types. 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 that could be used in nurseries during rootstock propagation to improve saplings adaptation to ARD soils. This approach could deliver a more ecologically safe and cost-efficient alternative to soil amendments for alleviating ARD consequences.