Apple rootstock (Malus domestica) root amendment with Sphingomonas strains affected host microbiota below and aboveground

European apple canker ( Neonectria ditissima ) is major constraint to apple production, with limited chemical control and no microbiome-based solutions currently available. Recent studies linked Sphingomonas taxa in leaf scar tissues with reduced canker severity, suggesting a potential for targeted microbiome manipulation. However, whether Sphingomonas can establish in planta and influence resident host microbiomes remains unresolved. Apple ‘M9’ rootstocks were inoculated at planting with consortia of apple-derived Sphingomonas strains. Inoculation did not affect plant height, girth or biomass, nor increase the relative abundance of Sphingomonas in roots, rhizosphere or leaf-scar compartments. Nevertheless, Sphingomonas inoculation affected alpha diversity in roots and rhizosphere without significant effects on beta diversity and relative abundance of taxa belowground. In contrast, root inoculation significantly altered fungal community composition in leaf scar tissues, reducing the relative abundance of known plant pathogenic genera including Gnomoniopsis , Phomopsis , Ilyonectria , Neofabraea , and Perenniporia . This study demonstrates that root-applied microbiome amendments can exert cross-compartment effects on microbial communities in a perennial crop, even in the absence of sustained colonisation by the inoculated taxa. Sphingomonas induced reduction in potential fungal pathogens in leaf scars reveal a decoupling between inoculant persistence and microbiome restructuring, highlighting a new possibility for microbiome engineering in woody hosts.