Cheng Zhongyi, He Yan, Wang Nanxi, Wu Laosheng, Xu Jianming, Shi Jiachun
Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Hangzhou, 310058, China; Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, Ampère, UMR5005, Écully, 69134, France.
Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Hangzhou, 310058, China.
Environ Pollut. 2025 Mar 1;368:125787. doi: 10.1016/j.envpol.2025.125787. Epub 2025 Feb 3.
Soil amendments exhibit great potential in reducing cadmium (Cd) bioavailability and its accumulation in crop grains, but their practical implications on microbial characteristics (genomic traits and ecological functions) remain unclear. The objective of this study was to combine metagenomics and metatranscriptomics to track the dynamics of bacterial and viral communities in the soybean rhizosphere during the remediation of Cd-contaminated soil using a commercial Mg-Ca-Si conditioner (CMC), applied at low and high (975 kg ha and 1950 kg ha) rates under field conditions. Application of CMC increased the average size and decreased the guanine-cytosine (GC) content of microbial genomes, which were strongly shaped by soil pH and available Cd (ACd). Gene and transcript abundances analysis indicated that CMC promoted the enrichment of Alphaproteobacterial metagenome-assembled genomes (MAGs) carrying czcC gene encoding Cd efflux and dsbB gene encoding disulfide bond oxidoreductase. These genes are closely related to Cd resistance and exhibited notable (p < 0.05) increased expression in CMC-treated soils. Additionally, low and high CMC addition significantly increased viral alpha diversity by 5.7% and 9.6%, and viral activity by 3.3% and 7.8%, respectively, in comparison to the control. Temperate viruses were predicted as the major group (64%) and actively linked to the dominant host, and CMC amendment increased host metabolism and adaptability by enhancing (p < 0.05) the abundance and transcriptional activity of virus-encoded auxiliary metabolic genes (AMGs) involved in heavy metal resistance (ABC transport), sulfur cycling (cysH), and host metabolism (galE and queD) through "piggyback-the-winner" strategy. Structural equation modeling further revealed that CMC application influences Cd accumulation in soybean grains through its direct and indirect effects on soil properties and rhizosphere microbiomes, and highlighted the potential role of rhizosphere viruses in agricultural soil remediation.
