Persistent antimicrobial resistance during soil remediation driven by residual heavy metal co-selection

Remediation of heavy metal-contaminated soil is a global priority, particularly as reclaimed land increasingly intersects with urban development and human exposure. However, the ecological consequences of soil remediation, especially its impact on antimicrobial resistance (AMR) as a global health threat, have remained poorly understood. Here, we combined single-cell Raman–D₂O probing with genome-resolved metagenomics to monitor the dynamics of phenotypic and genotypic resistance to metals and antibiotics during a 120-day remediation of soils with three contamination levels from a lead-zinc smelting site. Although chemical remediation substantially reduced bioavailable metals (by 42%–65%), AMR was not diminished. Instead, both phenotypic activity and gene abundance of metal- and antibiotic-resistant microorganisms increased, resulting in a two- to three-fold increase in AMR-associated health risks. Among 76 metagenome assembled genomes (MAGs) from phenotypic resistance communities, all Cd resistance-associated MAGs harbored multidrug resistance genes, half of which were colocalized with metal resistance determinants, and their prevalence continued to rise with remediation. These findings reveal that although remediation alleviates acute metal toxicity, residual low-concentration bioavailable metals sustain evolutionary selection for resistance, highlighting a disconnect between chemical recovery and biological safety. Moreover, the improved soil nutrient and physiochemical properties of remediated soils further promoted the proliferation of antibiotic-resistant bacteria. This study offers new ecological insights into the unintended consequences of anthropogenic interventions, underscoring the need to integrate biological safety into soil health and safety assessments.