The persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle in disentangling the complex web of ecological interactions spun by a diverse assortment of participants (pro- and eukaryotes and their viruses). In aquatic microbial communities, the numerically most abundant actors, the viruses, remain the most elusive, and especially in freshwaters their identities and ecology remain unknown. Here, using ultra-deep metagenomic sequencing from pelagic freshwater habitats, we recovered complete genomes of > 2000 phages, including small "miniphages" and large "megaphages" infecting iconic freshwater prokaryotic lineages. For instance, abundant freshwater Actinobacteria support infection by a very broad size range of phages (13-200 Kb). We describe many phages encoding genes that likely afford protection to their host from reactive oxygen species (ROS) in the aquatic environment and in the oxidative burst in protist phagolysosomes (phage-mediated ROS defense). Spatiotemporal abundance analyses of phage genomes revealed evanescence as the primary dynamic in upper water layers, where they displayed short-lived existences. In contrast, persistence was characteristic for the deeper layers where many identical phage genomes were recovered repeatedly. Phage and host abundances corresponded closely, with distinct populations displaying preferential distributions in different seasons and depths, closely mimicking overall stratification and mixis.

中文翻译：

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通过超深度宏基因组学揭示了水生生态系统中以噬菌体为中心的生态相互作用。

从水生生态系统培养环境丰富的微生物的能力的持续惯性，是解开由各种参与者（原核生物和真核生物及其病毒）纺成的复杂的生态相互作用网的障碍。在水生微生物群落中，数量最多的行为者（病毒）仍然最难以捉摸，尤其是在淡水中，其身份和生态仍然未知。在这里，使用来自中上层淡水生境的超深度宏基因组测序，我们回收了> 2000个噬菌体的完整基因组，包括感染标志性淡水原核生物谱系的小“小噬菌体”和大“巨噬细胞”。例如，丰富的淡水放线菌支持非常大范围的噬菌体（13-200 Kb）感染。我们描述了许多噬菌体编码的基因，它们有可能在水生环境和原生质吞噬溶酶体的氧化性爆发（噬菌体介导的ROS防御）中为宿主提供保护，使其免受活性氧（ROS）的侵害。噬菌体基因组的时空丰度分析显示，e逝是上层水层的主要动力，它们表现出短暂的存在。相反，持久性是深层的特征，在深层中许多相同的噬菌体基因组被重复回收。噬菌体和宿主的丰度紧密对应，不同的种群在不同的季节和深度显示出优先的分布，紧密地模仿了整体分层和混血。