Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
J Hazard Mater. 2024 Nov 5;479:135626. doi: 10.1016/j.jhazmat.2024.135626. Epub 2024 Aug 23.
The microbiome plays a crucial role in soil nitrogen (N) cycling and in regulating its bioavailability. However, the functional and genomic information of microorganisms encoding N cycling in response to copper (Cu) and cadmium (Cd) contamination is largely unknown. Here, metagenomics and genome binning were used to examine microbial N cycling in Cu and Cd co-contaminated red paddy soils collected from a polluted watershed in southern China. The results showed that soil Cu and Cd concentrations induced more drastic changes in microbial N functional and taxonomic traits than soil general properties. Soil Cu and Cd co-contamination stimulated microbial nitrification, denitrification, and dissimilatory nitrate reduction processes mainly by increasing the abundance of Nitrospira (phylum Nitrospirota), while inhibiting N fixation by decreasing the abundance of Desulfobacca. These contrasting changes in microbial N cycling processes suggested a potential risk of N loss in paddy soils. A high-quality genome was identified as belonging to Nitrospirota with the highest abundance in heavily contaminated soils. This novel Nitrospirota strain possessed metabolic capacities for N transformation and metal resistance. These findings elucidate the genetic mechanisms underlying soil N bioavailability under long-term Cu and Cd contamination, which is essential for maintaining agricultural productivity and controlling heavy metal pollution.
微生物组在土壤氮（N）循环中起着至关重要的作用，并调节其生物有效性。然而，对于编码响应铜（Cu）和镉（Cd）污染的 N 循环的微生物的功能和基因组信息，我们知之甚少。在这里，我们使用宏基因组学和基因组分箱技术来研究来自中国南方一个污染流域的 Cu 和 Cd 复合污染红稻田土壤中的微生物 N 循环。结果表明，土壤 Cu 和 Cd 浓度对微生物 N 功能和分类特征的影响比土壤一般性质更为剧烈。土壤 Cu 和 Cd 复合污染主要通过增加硝化螺旋菌（硝化螺旋菌门）的丰度来刺激微生物硝化、反硝化和异化硝酸盐还原过程，同时通过降低脱硫菌的丰度来抑制固氮作用。这些微生物 N 循环过程的相反变化表明稻田中存在 N 损失的潜在风险。鉴定出一个高质量的基因组属于硝化螺旋菌，在重度污染土壤中的丰度最高。这种新型硝化螺旋菌菌株具有 N 转化和金属抗性的代谢能力。这些发现阐明了长期 Cu 和 Cd 污染下土壤 N 生物有效性的遗传机制，这对于维持农业生产力和控制重金属污染至关重要。
