Multimedia profiling of metal resistance genes in the Yangtze Estuary: Biofilm dominance and community-driven regulatory pathways

Biofilms are critical microbial assemblages that function as sinks and potential reservoirs of metal resistance genes (MRGs) in contaminated aquatic systems. In this study, metagenomic sequencing and environmental profiling were employed to characterize MRGs distribution, heavy metal contamination, and microbial community structure across water, sediment, and biofilm samples in the Yangtze Estuary. Biofilms exhibited significantly higher concentrations of heavy metals and MRGs than other matrices, particularly for key genes such as corS (Cu-resistance), nrsS (Ni-resistance), and pbrA (Pb-resistance). Ecological risk assessment identified cadmium as the primary risk contributor, especially in biofilms. Partial redundancy analysis revealed that microbial community composition was the dominant factor shaping MRGs distribution, rather than metal concentrations alone. Network and canonical correspondence analyses further demonstrated strong co-occurrence patterns between MRGs and antibiotic resistance genes (ARGs), regulated by eutrophication (TN, Chl-a) and heavy metals (Pb, Cd, Cu). Notably, Pb-resistance genes in biofilm communities were significantly enriched and closely associated with Cyanobacteria and Proteobacteria, reflecting a multi-stage co-occurrence pattern potentially involving pbrT , pbrA , cadD , and czcD . These findings highlight the ecological significance of biofilms in MRGs enrichment, dissemination, and risk propagation in estuarine ecosystems under combined pollution stress. • MRGs were profiled across biofilm, sediment, and water in the Yangtze Estuary. • Biofilms showed the highest MRG and metal levels among all environmental media. • Microbial communities, not metal levels, primarily shaped MRG distribution patterns. • MRGs co-occurred with ARGs under eutrophication and heavy metal stress conditions. • Pb resistance involved multiple genes regulated by cyanobacterial taxa in biofilms.