Metagenomic insights into the ecological risks of multiple heavy metals on soil bacterial communities and resistance-related genes.

The simultaneous contamination of soils by various heavy metals (HMs) significantly disrupts microbial ecosystems, leading to notable shifts in bacterial community structures and the prevalence of resistance-related genes, including metal resistance genes (MRGs) and antibiotic resistance genes (ARGs). Conventional indices, such as the Nemerow Integrated Pollution Index (NIPI), primarily assess contamination from a chemical standpoint but often overlook the complex ecological responses elicited by multiple HMs. In this study, we used metagenomic analyses, network assessments, and neutral community models to investigate the agricultural soils near a nonferrous metal smelter, aiming to elucidate the collective influence of seven representative HMs (cadmium, chromium, copper, nickel, lead, zinc and arsenic) on bacterial communities and resistance-related gene dynamics. Our findings revealed that elevated levels of the seven HMs are pivotal in reshaping microbial assemblages and resistance profiles in soils. Notably, nonlinear correlations between NIPI of the seven HMs and bacterial indices suggested threshold-dependent microbial responses to HM mixtures. Among various indicators, the total relative abundance of MRGs emerged as a superior indicator for assessing the ecological risks associated with combined HM contamination, surpassing traditional bacterial diversity metrics and ARG prevalence. Furthermore, random forest modeling identified specific MRG subtypes as robust biomarkers, a discovery validated through controlled microcosm experiments. This study provides a systematic framework for evaluating the ecological risks in agricultural soils under multiple HM contamination, highlighting the intricate interplay between pollutant mixtures and microbial community dynamics.