Uncovering soil amendment-induced genomic and functional divergence in soybean rhizosphere microbiomes during cadmium-contaminated soil remediation: Novel insights from field multi-omics

IF 7.3 2区环境科学与生态学 Q1 ENVIRONMENTAL SCIENCES Environmental Pollution Pub Date : 2025-02-03 DOI:10.1016/j.envpol.2025.125787

Zhongyi Cheng , Yan He , Nanxi Wang , Laosheng Wu , Jianming Xu , Jiachun Shi

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Abstract

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⁻¹ and 1950 kg ha⁻¹) 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.

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揭示镉污染土壤修复过程中大豆根际微生物组的基因组和功能差异：来自田间多组学的新见解

土壤改剂在降低镉（Cd）生物有效性及其在作物籽粒中的积累方面显示出巨大的潜力，但其对微生物特性（基因组性状和生态功能）的实际意义尚不清楚。本研究的目的是结合宏基因组学和亚转录组学，追踪在大田条件下使用低剂量和高剂量（975 kg ha-1和1950 kg ha-1） Mg-Ca-Si调节剂（CMC）修复cd污染土壤期间大豆根际细菌和病毒群落的动态。施用CMC增加了微生物基因组的平均大小，降低了鸟嘌呤-胞嘧啶（GC）含量，这些基因组受土壤pH和有效镉（ACd）的强烈影响。基因丰度和转录物丰度分析表明，CMC促进了携带编码Cd外排的czcC基因和编码二硫键氧化还原酶的dsbB基因的α变形菌宏基因组组装基因组（MAGs）的富集。这些基因与Cd抗性密切相关，并表现出显著的(p <；0.05)， cmc处理土壤中表达量增加。此外，与对照相比，低、高CMC添加量显著提高了病毒α多样性5.7%和9.6%，病毒活性分别提高了3.3%和7.8%。预测温带病毒为主要群体（64%），并与优势宿主积极联系，CMC的修改通过增强(p <；0.05)病毒编码的辅助代谢基因（AMGs）的丰度和转录活性通过“背驮式赢家”策略参与重金属抗性（ABC转运）、硫循环（cysH）和宿主代谢（galE和queD）。结构方程模型进一步揭示了CMC应用通过对土壤性质和根际微生物群的直接和间接影响影响大豆籽粒Cd积累，并强调了根际病毒在农业土壤修复中的潜在作用。

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来源期刊

Environmental Pollution 环境科学-环境科学

CiteScore

16.00

自引率

6.70%

发文量

2082

审稿时长

2.9 months

期刊介绍： Environmental Pollution is an international peer-reviewed journal that publishes high-quality research papers and review articles covering all aspects of environmental pollution and its impacts on ecosystems and human health. Subject areas include, but are not limited to: • Sources and occurrences of pollutants that are clearly defined and measured in environmental compartments, food and food-related items, and human bodies; • Interlinks between contaminant exposure and biological, ecological, and human health effects, including those of climate change; • Contaminants of emerging concerns (including but not limited to antibiotic resistant microorganisms or genes, microplastics/nanoplastics, electronic wastes, light, and noise) and/or their biological, ecological, or human health effects; • Laboratory and field studies on the remediation/mitigation of environmental pollution via new techniques and with clear links to biological, ecological, or human health effects; • Modeling of pollution processes, patterns, or trends that is of clear environmental and/or human health interest; • New techniques that measure and examine environmental occurrences, transport, behavior, and effects of pollutants within the environment or the laboratory, provided that they can be clearly used to address problems within regional or global environmental compartments.