Chen Tianyi, Deng Chunfang, Wu Zongzhi, Liu Tang, Zhang Yuanyan, Xu Xuming, Zhao Xiaohui, Li Jiarui, Li Shaoyang, Xu Nan, Yu Ke
Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; Environmental Microbiome and Innovative Genomics Laboratory, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; Environmental Microbiome and Innovative Genomics Laboratory, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
Water Res. 2023 Oct 15;245:120611. doi: 10.1016/j.watres.2023.120611. Epub 2023 Sep 10.
Enormous viral populations have been identified in activated sludge systems, but their ecological and biochemical roles in landfill leachate treatment plants remain poorly understood. To address this knowledge gap, we conducted an in-depth analysis using 36 metagenomic datasets that we collected and sequenced during a half-year time-series sampling campaign at six sites in a full-scale landfill leachate treatment plant (LLTP), elucidating viral distribution, virus‒host dynamics, virus-encoded auxiliary metabolic genes (AMGs), and viral contributions to the spread of virulence and antibiotic resistance genes. Our findings demonstrated that viral and prokaryotic communities differed widely among different treatment units, with stability over time. LLTP viruses were linked to various prokaryotic hosts, spanning 35 bacterial phyla and one archaeal phylum, which included the core microbes involved in biological treatments, as well as some of the less well-characterized microbial dark matter phyla. By encoding 2364 auxiliary metabolic genes (AMGs), viruses harbored the potential to regulate microbial nucleotide metabolism, facilitate the biodegradation of complex organic matter, and enhance flocculation and settling in biological treatment plants. The abundance distribution of AMGs varied considerably across treatment units and showed a lifestyle-dependent pattern with temperate virus-associated AMGs exhibiting a higher average abundance in downstream biological treatment units and effluent water. Meanwhile, temperate viruses tended to carry a higher load of virulence factor genes (VFGs), antibiotic resistance genes (ARGs), and biotic and metal resistance genes (BMRGs), and engaged in more frequent gene exchanges with prokaryotes than lytic viruses, thus acting as a pivotal contributor to the dissemination of pathogenicity and resistance genes in downstream LLTP units. This study provided a comprehensive profile of viral and prokaryotic communities in the LLTP and unveiled the varying roles of different-lifestyle viruses in biochemical processes and water quality safety.
在活性污泥系统中已发现大量病毒群体，但它们在垃圾渗滤液处理厂中的生态和生化作用仍知之甚少。为填补这一知识空白，我们利用36个宏基因组数据集进行了深入分析，这些数据集是我们在一家大型垃圾渗滤液处理厂（LLTP）的六个站点进行为期半年的时间序列采样活动期间收集并测序的，阐明了病毒分布、病毒-宿主动态、病毒编码的辅助代谢基因（AMG）以及病毒对毒力和抗生素抗性基因传播的贡献。我们的研究结果表明，不同处理单元之间的病毒和原核生物群落差异很大，且随时间保持稳定。LLTP病毒与各种原核宿主相关联，涵盖35个细菌门和1个古菌门，其中包括参与生物处理的核心微生物，以及一些特征不太明确的微生物暗物质门。通过编码2364个辅助代谢基因（AMG），病毒具有调节微生物核苷酸代谢、促进复杂有机物生物降解以及增强生物处理厂中絮凝和沉降的潜力。AMG的丰度分布在不同处理单元之间差异很大，并呈现出一种依赖生活方式的模式，与温和病毒相关的AMG在下游生物处理单元和出水中表现出更高的平均丰度。与此同时，温和病毒往往携带更高负荷的毒力因子基因（VFG）、抗生素抗性基因（ARG）以及生物和金属抗性基因（BMRG），并且比裂解病毒更频繁地与原核生物进行基因交换，因此成为下游LLTP单元中致病性和抗性基因传播的关键因素。这项研究提供了LLTP中病毒和原核生物群落的全面概况，并揭示了不同生活方式的病毒在生化过程和水质安全中的不同作用。
