Heavy metals (HMs) and pesticides disrupt aquatic biodiversity and microbial communities, contributing to antibiotic resistance via cross-resistance and co-selection mechanisms. This study investigates the relationship between organophosphorus pesticides (OPs), HMs, microbial diversity, and antibiotic resistance genes (ARGs) in eight lakes and wetlands. Microbial communities were analyzed via metagenomics methods, and data were processed using CLC Genomics Workbench 22. ARGs, including tetA, tetB, qnrA, qnrS, CIT, Fox, KPC, CTX-M1, DHA, GES, OXA, IMP, VEB, NDM1, SHV, TEM, CTX-M, PER, and MOX, were identified through polymerase chain reaction (PCR). Element concentrations and pesticide were quantified using inductively coupled plasma mass spectrometry and gas chromatography-mass spectrometry, respectively. The results indicate that environmental elements and pesticides significantly influence microbial diversity. Proteobacteria (Gamma, Beta, Alpha) dominate over other bacteria in all locations. β-Lactamase resistance genes have a significant positive correlations with the concentrations of boron, iron, lithium, magnesium, sodium, and phosphorus (P-value<0.05). Positive correlations between phosphorus, iron, and beta-lactamase genes suggest that higher concentrations of these elements may increase resistance likelihood by promoting resistant bacterial growth or facilitating gene transfer. Additionally, tetA and tetB exhibited a significant positive correlation with parathion concentration. The results showed that OPs and HMs increase antibiotic resistance by causing gene mutations, altering gene expression, and promoting horizontal gene transfer, resulting in multidrug-resistant strains. This highlights the need for monitoring these pollutants as they affect microbial diversity and accelerate antibiotic resistance. Targeted measures, such as bioremediation and pollution control, are essential to mitigate risks to the environment and public health.

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