A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extreme environments

The ISME Journal
Jacob H Munson-McGeeMark Young

Abstract

The application of viral and cellular metagenomics to natural environments has expanded our understanding of the structure, functioning, and diversity of microbial and viral communities. The high diversity of many communities, e.g., soils, surface ocean waters, and animal-associated microbiomes, make it difficult to establish virus-host associations at the single cell (rather than population) 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 National Park (YNP) hot spring microbial community. Leveraging the relatively low diversity of the YNP environment, we are able to overlay evidence at the single-cell level with contextualized viral and cellular community structure. Combining evidence from hexanucelotide analysis, single cell read mapping, network-based analytics, and CRISPR-based inference, we conservatively estimate that >60% of cells contain at least one virus type and a majority of these cells contain two or more virus types. Of the detected virus types, nearly 50% were found in more than 2 cellular clades, indicative of...Continue Reading

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Citations

Jul 6, 2018·Microbes and Environments·Hiroyuki Ogata
Nov 20, 2018·Environmental Microbiology·Ying LiuDavid Prangishvili
Mar 25, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Matthew D PaulyRachel J Whitaker
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May 26, 2021·Annual Review of Virology·Pacifica SommersGareth Trubl

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Methods Mentioned

BETA
MDA
amplicon sequencing

Software Mentioned

VirusHostMatcher
CR
BLASTn
trimmomatic
CheckM
SPAdes
Piler

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