Divergent genomic characteristics and convergent metabolic phenotypes associated with Cd tolerance and soil Cd immobilization in multifunctional bacteria

Heavy-metal-tolerant bacteria provide a sustainable, eco-friendly approach to remediate cadmium (Cd) contaminated soils, and elucidating their tolerance mechanisms is key for designing effective bio-remediation strategies. This study integrated whole-genome sequencing, untargeted metabolomics and multi-phenotypic analyses to reveal the Cd tolerance mechanisms and soil remediation effects of three plant-growth-promoting bacteria: Rhizobium sp. WW22, Burkholderia sp. WW13 and Pseudomonas sp. WW2. Results showed that three strains achieved Cd adsorption efficiencies of 60.27 %-99.56 % in 0.3–100 mg L-1 Cd solutions, with amino, carboxyl, hydroxyl, and amide groups on cell surfaces as major binding sites. They have evolved gene clusters related to metal transport/efflux and oxidative stress response, which synergistically maintain metabolic homeostasis under Cd stress. Among them, strain WW13 exhibited stronger Cd tolerance due to abundant unique gene clusters for antioxidant defense, siderophore synthesis, and putrescine metabolism. Notably, three strains showed convergent metabolic responses under Cd stress, with secretions (predominantly organic oxygen compounds, lipids/lipid-like molecules, benzenoids, and organoheterocyclic compounds) that significantly increased environmental pH. Key common upregulated secretions (itaconic acid, cis/trans-aconitic acid) increased soil pH by 0.01–0.32 units and reduced the proportion of exchangeable Cd by 2.22 %-9.19 % within 10 days. Pot experiments further confirmed that strains indirectly reduced Cd bioavailability by increasing soil pH, enriching hydroxyl/carboxyl/amino groups, regulating dissolved organic carbon/nitrogen, ammonium nitrogen, activities of β-glucosidase and N-acetyl-β- D -glucosaminidase. By day 14, the proportion of exchangeable Cd was reduced by 4.09 %-5.86 %. This study revealed multi-pathway Cd tolerance mechanisms in bacteria and their roles in soil Cd immobilization, providing theoretical basis and efficient strains for bioremediation of Cd-contaminated soils.