The application of viral and cellular metagenomics to natural environments has expanded our understanding of viral diversity at the population level. Most natural environments are characterized by having a high diversity of microbial and viral communities. This diversity makes it difficult to establish a comprehensive understanding of virus-host associations at the single cell level, assign cellular hosts, or determine the extent of viral host range from metagenomics studies alone. Here we combine single-cell sequencing with environmental metagenomics to characterize the structure of virus-host associations in a Yellowstone hot spring microbial community. Leveraging the relatively low diversity of the environment, we are able to overlay evidence at the single-cell level with contextualized viral and cellular community structure. The new lens provided by the combination of metaviromics and single-cell genomics exposes the impact of viruses in extreme environments, supports the possibility that extensive host-virus associations are a common feature of many environments, and further expands the unseen impact of viruses.
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