Host-mediated selection drives compartment-specific core root microbiome assembly and function

Aims Plants evolve with persistent core microbiomes that extend host functional repertoires, yet the assembly patterns and functions of these communities remain insufficiently understood, limiting their application in enhancing plant performance. Methods We investigated bacterial communities in the bulk soil, rhizosphere and root endosphere of various Cd-hyperaccumulators growing under controlled and field conditions, and identified core microbes linked to key plant traits using 16S rRNA gene sequencing and synthetic community (SynCom). Results Microbiome assembly along the soil-root continuum was predominantly shaped by plant species and compartment type rather than by soil type and pollution level, with host selection intensifying from the rhizosphere to the root endosphere. Stochastic processes dominated the assembly of endosphere generalists (59%), but less so for rhizosphere generalists (45%). We identified 24 rhizosphere and 9 root endophytic generalist species as core microbiomes, which were more strongly driven by host selection than non-core taxa. These core microbiomes were markedly enriched in their respective compartments, with over 60% consistently detected across controlled and field settings. Endophytic core microbes conferred greater biotic connectivity in co-occurrence networks and were stronger predictors of plant metal accumulation than soil-derived cores, whereas rhizosphere cores were more closely associated with plant biomass production and nitrogen and phosphorus acquisition. These compartment-specific contributions to plant phenotypic properties were further validated through SynComs with isolates of core microbes. Conclusions This study provides empirical insights into host selection and the compartment-specific functions of metal-hyperaccumulator core microbiota, laying the foundation for developing microbiome-based strategies for accelerating metal-contaminated soil restoration.