Changes in clover rhizosphere microbial community and diazotrophs in mercury-contaminated soils

Highlights: • High soil Hg content increased the abundance and diversity of diazotrophs. • Rhizobium acted as a biomarker at sites with high soil Hg contents. • Rhizosphere merA abundance was negatively correlated with clover shoot Hg content. Little is known about the response of the soil microbiome (including bacteria in the rhizosphere of legumes such as clover) to mercury (Hg) despite the toxicity of Hg to soil microorganisms. Here, Hg-contaminated soils collected from Guizhou province, southwest China, were divided into three groups according to their Hg contents and were planted with clover. High-throughput sequencing of bacterial 16S rRNA and nitrogenase (nifH) genes and quantitative polymerase chain reaction (qPCR) were used to study the response of bacteria and diazotrophs to soil Hg stress and the effects of Hg on the abundance of functional genes in rhizosphere soils. High concentrations of soil Hg decreased bacterial community abundance and diversity and increased the abundance and diversity of nitrogen-fixing bacteria. LEfSe analysis indicates that Rhizobium was a biomarker at sites with high soil Hg contents and the co-occurrence network results indicate a positive relationship between the abundance of the dominant module (from the co-occurrence network analysis) of Rhizobiaceae and soil Hg concentration. Structural equation modeling (SEM) indicates that the Hg content in the clover shoots (Shoot_Hg) was negatively correlated with the abundance of the mercury reductase (merA) gene (r = −0.26, P < 0.05) and the organomercury lyase (merB) gene (r = −0.23, P < 0.05) in rhizosphere soils. Moreover, correlation analysis and SEM indicate that soil total nitrogen (TN), nitrate‑nitrogen (NO₃⁻N), soil organic matter (SOM), and available molybdenum (Mo) contents were also important factors affecting the structure of the microbial community and the abundance of functional genes. The results provide a basis for further study of the mechanism(s) by which microorganisms may impart tolerance of clover to Hg in contaminated soils.