Soil mercury (Hg) contamination is a serious threat to local ecology and public health. Exogenous selenium (Se) supplementation can effectively reduce the toxicity of Hg. However, the mechanisms affecting the changes in soil Hg speciation, soil properties and the microbial Hg-resistant system during the Se–Hg interaction after exogenous Se supplementation are not clear. Therefore, in this study, soil culture experiments were conducted to analyze the effects of different Se additions on the transformation of Hg speciation, soil properties and Hg-resistant microorganisms and resistant genes (mer operon). The results indicated that Se supplementation facilitated the transformation of soil Hg from bioavailable (exchangeable and carbonate-bound) to stable forms (organic material-bound and residual), significantly reducing Hg bioavailability. Se supplementation notably decreased the electrical conductivity of Hg-contaminated soil, but had no significant effect on the soil pH, organic matter content, cation exchange capacity or alkaline phosphatase and catalase activities. The maximum activity levels of soil sucrase and urease were observed when 1 mg kg−1 Se was added. Se significantly inhibited soil peroxidase and ascorbate oxidase activities, thereby alleviating the oxidative stress in the soil system caused by Hg. Additionally, Se significantly activated the Hg-resistant system in soil microorganisms by either decreasing or increasing the regulatory genes merD and merR, and it significantly upregulated the cytoplasmic protein gene merP and the membrane protein genes merC, merF and merT. This further increased the abundance of the organomercury lyase gene merB and the mercuric reductase gene merA, promoting the conversion of Hg species to Hg⁰. Furthermore, the abundance of mer operon-containing microorganisms, such as Thiobacillus ferrooxidants, Pseudomonas, Streptomyces and Cryptococcus, significantly increased with Se addition, explaining the role of soil microorganisms in mitigating soil Hg stress via Se supplementation.
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