Spatial structuring of root-associated bacteria and metabolic landscapes in an endangered cliffside conifer <i>Thuja sutchuenensis</i> Franch

Abstract Understanding how plant–microbe–soil interactions vary across spatial scales is essential for elucidating belowground ecological dynamics, particularly in rare and ecologically sensitive species. Here, we investigated the diversity, function, and assembly of root-associated bacterial communities in Thuja sutchuenensis Franch. along continuous vertical gradients. Through an integrative multi-omics approach, morphological assessment, and soil physicochemical profiling, we uncovered a compartmentalized and spatially structured rhizosphere system. We observed a marked enrichment of soil nutrients, particularly carbon, nitrogen, and available phosphorus, in the rhizosphere compared with bulk soil. Bacterial diversity declined in the endosphere, accompanied by taxonomic and functional shifts, including enrichment of Proteobacteria and Actinobacteriota and metabolic pathways related to host interaction and xenobiotic degradation. Root and soil metabolomes also showed depth-specific signatures, with surface compartments enriched in flavonoids and defense compounds, and deeper layers characterized by core metabolic functions. Co-occurrence network and correlation analyses highlighted key bacterial hubs and revealed strong links between nutrient levels and bacterial diversity. Together, this study provides new insight into the organization of plant-soil ecosystems and offers a framework for conservation and ecological restoration strategies for endangered cliffside species.