Glaciers archive time-structured information on climates and ecosystems, including microorganisms. However, the long-term ecogenomic dynamics or biogeography of the preserved viruses and their palaeoclimatic connections remain uninvestigated. Here we use metagenomes to reconstruct viral genomes from nine time horizons, spanning three cold-to-warm cycles over the past >41,000 years, preserved in an ice core from Guliya Glacier, Tibetan Plateau. We recover genomes of 1,705 approximately species-level viral operational taxonomic units. Viral communities significantly differ during cold and warm climatic conditions, with the most distinct community observed ~11,500 years ago during the major climate transition from the Last Glacial Stage to the Holocene. In silico analyses of virus–host interactions reveal persistently high viral pressure on Flavobacterium (a common dominant glacier lineage) and historical enrichment in the metabolism of cofactors and vitamins that can contribute to host adaptation and virus fitness under extreme conditions. Biogeographic analyses show that approximately one-fourth of Guliya viral operational taxonomic units overlap with the global dataset, primarily with the Tibetan Plateau metagenomes, suggesting regional associations of a subset of the Guliya-preserved viruses over time. We posit that the cold-to-warm variations in viral communities might be attributed to distinct virus sources and/or environmental selections under different temperature regimes.

冰川存档有关气候和生态系统（包括微生物）的时间结构信息。然而，保存的病毒的长期生态基因组动力学或生物地理学及其古气候联系仍未得到研究。在这里，我们使用宏基因组来重建九个时间范围内的病毒基因组，跨越过去 >41,000 年的三个冷到暖周期，保存在青藏高原古里雅冰川的冰芯中。我们恢复了 1,705 个大约物种级病毒操作分类单位的基因组。病毒群落在寒冷和温暖的气候条件下存在显着差异，其中最明显的群落是在约 11,500 年前从末次冰期到全新世的主要气候转变期间观察到的。病毒与宿主相互作用的计算机分析揭示了黄杆菌（一种常见的优势冰川谱系）的持续高病毒压力以及辅助因子和维生素代谢的历史富集，这有助于宿主在极端条件下的适应和病毒适应性。生物地理学分析表明，大约四分之一的古里雅病毒操作分类单元与全球数据集重叠，主要是与青藏高原宏基因组重叠，这表明古里雅保存的病毒的一个子集随着时间的推移存在区域关联。我们认为病毒群落的从冷到暖的变化可能归因于不同的病毒来源和/或不同温度条件下的环境选择。