Zhou Zhichao, Tran Patricia Q, Martin Cody, Rohwer Robin R, Baker Brett J, McMahon Katherine D, Anantharaman Karthik
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
Institute for Advanced Study, Shenzhen University, Shenzhen, China.
Nat Microbiol. 2025 Jan;10(1):231-245. doi: 10.1038/s41564-024-01876-7. Epub 2025 Jan 3.
As freshwater lakes undergo rapid anthropogenic change, long-term studies reveal key microbial dynamics, evolutionary shifts and biogeochemical interactions, yet the vital role of viruses remains overlooked. Here, leveraging a 20 year time series from Lake Mendota, WI, USA, we characterized 1.3 million viral genomes across time, seasonality and environmental factors. Double-stranded DNA phages from the class Caudoviricetes dominated the community. We identified 574 auxiliary metabolic gene families representing over 140,000 auxiliary metabolic genes, including important genes such as psbA (photosynthesis), pmoC (methane oxidation) and katG (hydrogen peroxide decomposition), which were consistently present and active across decades and seasons. Positive associations and niche differentiation between virus-host pairs, including keystone Cyanobacteria, methanotrophs and Nanopelagicales, emerged during seasonal changes. Inorganic carbon and ammonium influenced viral abundances, underscoring viral roles in both 'top-down' and 'bottom-up' interactions. Evolutionary processes favoured fitness genes, reduced genomic heterogeneity and dominant sub-populations. This study transforms understanding of viral ecology and evolution in Earth's microbiomes.
随着淡水湖泊经历快速的人为变化，长期研究揭示了关键的微生物动态、进化转变和生物地球化学相互作用，但病毒的重要作用仍被忽视。在这里，我们利用来自美国威斯康星州门多塔湖的20年时间序列，对跨越时间、季节和环境因素的130万个病毒基因组进行了表征。长尾噬菌体纲的双链DNA噬菌体在群落中占主导地位。我们鉴定出574个辅助代谢基因家族，代表超过14万个辅助代谢基因，包括psbA（光合作用）、pmoC（甲烷氧化）和katG（过氧化氢分解）等重要基因，这些基因在数十年和季节中持续存在且活跃。在季节性变化期间，病毒-宿主对之间出现了正相关和生态位分化，包括关键的蓝细菌、甲烷营养菌和海洋微表层类群。无机碳和铵影响病毒丰度，凸显了病毒在“自上而下”和“自下而上”相互作用中的作用。进化过程有利于适应性基因，降低了基因组异质性并形成了优势亚群。这项研究改变了我们对地球微生物群落中病毒生态学和进化的理解。
