Abstract

The remediation of agricultural soils contaminated with heavy metal complexes is a critical and urgent challenge, in which microbial-based approaches play a pivotal role. However, the bacterial response mechanisms under co-contamination conditions with Fe-Cd (Iron, Cadmium) remain incompletely elucidated. This study investigated the adsorption and detoxification mechanisms in complex environments using multi-omics analysis of Stenotrophomonas maltophilia HC89—a strain capable of adsorbing 200   mg·L⁻¹ Cd within 36   h. Gene_1_253, gene_1_1548, gene_1_1645, gene_1_2035 and gene_1_4296 encoded Cd-resistant proteins (two of which were implicated in Cd adsorption functionality). Notably, gene_1_1645, gene_1_2035 and gene_1_4296 encoded novel putative proteins. The Fe/S system synergistically enhanced Cd adsorption efficiency. Co-exposure to Fe and Cd resulted in a 16.95% elevation in ROS (reactive oxygen species) levels over Cd exposure alone. The characterization experiments suggested that the Fe treatment led to the formation of Fe-Cd-biofilm composite to enhance bacterial adsorption. Metabolomic profiling revealed that Fe treatment upregulated metabolites associated with quorum sensing, phosphate/amino acid transporters, and tyrosine metabolism. In contrast, sulfur treatment reduced siderophore that were chelated with Cd and reduced ROS level by 27.65%. Microcosm simulations experiments further confirmed that inoculation with HC89 altered soil microbial community composition, increased pH from 6.37 to 7.93 in sterilized soil and to 7.63 in unsterilized soil, and significantly reduced heavy metal bioavailability. These findings clarify microbial adaptive strategies under dual-metal condition and establish novel bioremediation approaches for complex heavy metal contamination in agricultural systems.