Rhizobia-mediated soybean rhizosphere and nodule endophytic microorganisms reduce bioavailability of Cd and Cu in soil

Low-level bioavailable cadmium (Cd) and copper (Cu) in agricultural soils poses a severe threat to soil health and food safety; however, the mechanisms by which indigenous Cu-Cd tolerant rhizobia modulate plant-microbe-soil interactions remain poorly understood. In this field trial, the effects of two Cu-Cd tolerant strains, Sinorhizobium xinjiangense YN5 (RB) and Rhizobium pusense GF4 (RD), when inoculated individually and in combination (RC), were assessed with respect to soybean growth, heavy‑metal partitioning, rhizosphere and nodule endophytic microbiomes, and soil functional genes under bioavailable Cu-Cd stress. RB treatment significantly promoted aboveground growth parameters (plant height, node number, and pod per plant) and biomass accumulation, whereas RC treatment favored root development and maximized the reduction in soybean Cd accumulation. Rhizobia elevated Cu concentrations in leaves, while enhanced root sequestration curtailed Cd translocation to stems and pods, thereby diminishing Cd accumulation across all organs. Soil available nutrients, soil organic matter, and nitrogenase activity were significantly increased, whereas bioavailable Cd and Cu declined. Rhizobia strengthened cooperative interactions within the rhizosphere community, with positive associations accounting for 86.56% of network links under RB. Nodule symbiotic networks exhibited greater modularity and integration, and source tracking analysis revealed that RB markedly increased microbial transfer from the rhizosphere to nodules, reaching 85.2%. Rhizobia activated function associated with carbon and sulfur cycling genes. Collectively, indigenous Cu-Cd tolerant rhizobia mitigate heavy metal stress and strengthen nutrient cycling microbial functions, presenting a promising eco-compatible strategy to enhance legume productivity in agricultural soils facing low-level bioavailable heavy metal exposure.