Zhu Ying, Li Ruili, Yan Shuang, Li Yangyang, Xie Shuguang
State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; Guangdong Mangrove Engineering Technology Research Center, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
J Hazard Mater. 2025 Jun 15;490:137870. doi: 10.1016/j.jhazmat.2025.137870. Epub 2025 Mar 6.
Phages have garnered increasing attention due to their potential roles in biogeochemical cycling. However, their impacts on nitrogen cycling have primarily been inferred from the presence of putative auxiliary metabolic genes (AMGs) and the virus-host linkage, despite of very limited direct experimental evidence. In this study, a series of microcosms were established with the inoculation of either native or non-native phages to simulate coastal wetlands with different phage sources and different levels of copper (Cu) contamination. Metagenomics and metatranscriptomics were combined to reveal phages' regulation on microbially-driven nitrogen cycling and to explore how the effects were mediated by Cu stress. Phages significantly impacted denitrification-related genes, with their effects depending on Cu level. Phages inhibited nirK-type denitrification under Cu stress but led to up-regulation of nirS gene in the treatments without Cu addition. Non-native phages also promoted the transcription of genes related to nitrogen assimilation and organic nitrogen transformation. Detection of viral AMGs involved in glutamate synthesis suggested that horizontal gene transfer may be a crucial pathway for phages to facilitate microbial nitrogen uptake. Overall, these findings enhance the understanding of phages' impact on biogeochemical metabolism in coastal wetland, offering novel insights into the links of phages' regulation on microbial nitrogen cycling with Cu stress.
噬菌体因其在生物地球化学循环中的潜在作用而受到越来越多的关注。然而，尽管直接实验证据非常有限，但它们对氮循环的影响主要是通过推定的辅助代谢基因（AMGs）的存在和病毒-宿主联系推断出来的。在本研究中，通过接种本地或非本地噬菌体建立了一系列微观世界，以模拟具有不同噬菌体来源和不同铜（Cu）污染水平的沿海湿地。宏基因组学和宏转录组学相结合，以揭示噬菌体对微生物驱动的氮循环的调控，并探索铜胁迫如何介导这些影响。噬菌体对反硝化相关基因有显著影响，其影响取决于铜水平。在铜胁迫下，噬菌体抑制nirK型反硝化作用，但在不添加铜的处理中导致nirS基因上调。非本地噬菌体还促进了与氮同化和有机氮转化相关基因的转录。对参与谷氨酸合成的病毒AMGs的检测表明，水平基因转移可能是噬菌体促进微生物氮吸收的关键途径。总体而言，这些发现增进了对噬菌体对沿海湿地生物地球化学代谢影响的理解，为噬菌体对微生物氮循环的调控与铜胁迫之间的联系提供了新的见解。
