Metabolite-Mediated Rhizosphere–Endosphere Microbiome Shapes Genotype-Dependent Cadmium Accumulation via Coupled Chemical Immobilization and Microbial Detoxification

Cadmium (Cd) contamination threatens food safety, yet genotype-dependent Cd accumulation at the soil–root interface remains poorly understood. We integrated physiological profiling, metabolomics, density functional theory (DFT), and 16S rRNA sequencing to compare two amaranth cultivars, Quanhong (QH, low-Cd) and Liuye (LY, high-Cd). QH showed greater shoot biomass (6.84 g/plant) and stronger Cd exclusion (root/shoot Cd: 0.12/0.08 mg/kg), whereas LY developed a larger root system (1.42 vs 0.71 g/plant) and accumulated more Cd (0.26/0.16 mg/kg). QH promoted conversion of exchangeable Cd into stable residual fractions and enriched humic-like dissolved organic matter and 9-Oxo-ODE, which showed strong predicted Cd2+ binding (−22.34 kcal/mol), supporting its potential role in Cd immobilization. QH showed stronger host-associated microbial selection, enriching Bacillus and Streptomyces associated with sulfur metabolism and thiol-mediated metal sequestration, together with greater diversity and stability of root endophytes. These findings indicate coordinated chemical and microbial regulation contributing to the low-Cd phenotype of QH.