Multi-omics elucidates how humic acid-biochar composite empowers sulfate-reducing bacteria for efficient biomineralization of cadmium and lead.

The HA&BC-SRB composite, formed by immobilizing sulfate-reducing bacteria (SRB) onto a hybrid of humic acid (HA) and biochar (BC), achieved effective remediation of cadmium (Cd) and lead (Pb) through synergistic physicochemical and biological processes. The carrier provided a favorable microenvironment for bacterial activity (3.82 × 10⁸ CFU g⁻¹), with maximum adsorption capacities of 210.92 mg g⁻¹ for Pb and 137.04 mg g⁻¹ for Cd. Removal occurred primarily via monolayer chemisorption, involving sulfate reduction, extracellular polymeric substance complexation, and enzymatic electron transfer leading to stable sulfide precipitation. Immobilization induced substantial transcriptional reprogramming of metal detoxification and metabolic genes, accompanied by a metabolomic shift characterized by enhanced tricarboxylic acid cycle activity, oxidative phosphorylation, and glutathione metabolism. These changes collectively bolstered energy supply and antioxidant capacity. A strong correlation between differentially expressed genes and altered metabolites revealed a well-coordinated molecular network supporting biomineralization while preserving cellular integrity. This gene-metabolite coupling directly fuels the energy-intensive processes of sulfide precipitation and metal efflux, thereby enhancing biomineralization efficiency. Multi-omics integration confirmed that the carbon carrier primes SRB into a metabolically pre-adapted state, enabling a rapid and robust stress response. In soil trials, the system effectively transformed bioavailable heavy metals into stable residual fractions, reducing Cd and Pb accumulation in pakchoi plants by up to 85.12% and 66.88% respectively. These findings demonstrate that inducing a pre-adapted state in SRB through a functionalized carbon carrier offers a promising strategy to enhance bioremediation efficacy in metal-contaminated soils.