Data and scripts related to manuscript entitled: The effects of root amendment with Sphingomonas strains on apple (Malus domestica) rootstock physiology and associated microbiota

This repository contains the data used in statistical analysis and the analaysis scripts for the publication described below. Abstract of the manuscript: Background European apple canker, caused by Neonectria ditissima, remains a major constraint to sustainable apple production, with limited chemical control options and no microbiome-based solutions currently available. Recent correlative studies link high relative abundance of Sphingomonas taxa in leaf scar tissues with reduced canker severity, suggesting a potential role for targeted microbiome manipulation. However, whether Sphingomonas can establish in planta, affect plant growth and influence resident microbial communities across plant compartments remains unresolved. Results Apple ‘M9’ rootstocks were inoculated at planting with consortia of apple-derived Sphingomonas strains, and effects on plant growth and microbial communities in roots, rhizosphere, and leaf scars were assessed. Inoculation did not enhance plant growth (height, girth, biomass) nor increase the relative abundance of Sphingomonas in any compartment. Nevertheless, significant shifts in microbial alpha diversity were observed, particularly in root and rhizosphere communities, indicating a measurable impact on community structure despite the lack of detectable inoculant establishment. These changes occurred without significant effects on beta diversity or on the relative abundance of taxa belowground. In contrast, root inoculation significantly altered fungal community composition in leaf scar tissues, reducing the relative abundance of several genera containing known plant pathogens, including Gnomoniopsis, Phomopsis, Ilyonectria robusta, Neofabraea actinidiae, and Perenniporia fraxinea. Marked differences between younger and older leaf scar tissues further indicated a strong influence of external inoculum sources on aboveground microbiota. Conclusions This study demonstrates that root-applied microbiome amendments can exert cross-compartment effects on aboveground fungal communities in a perennial crop, even in the absence of sustained colonisation by the inoculated taxa. The observed reduction in potential pathogens in leaf scars provides a plausible mechanistic link to previously reported associations between Sphingomonas abundance and reduced apple canker severity. More broadly, the results reveal a decoupling between inoculant persistence and microbiome restructuring, highlighting a new possibility for microbiome engineering in woody hosts. Optimising delivery strategies and understanding temporal colonisation dynamics will be critical for translating microbiome-based interventions into effective disease management tools.