Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics
Abstract
Virophages are small viruses that co-infect eukaryotic cells alongside giant viruses (Mimiviridae) and hijack their machinery to replicate. While two types of virophages have been isolated, their genomic diversity and ecology remain largely unknown. Here we use time series metagenomics to identify and study the dynamics of 25 uncultivated virophage populations, 17 of which represented by complete or near-complete genomes, in two North American freshwater lakes. Taxonomic analysis suggests that these freshwater virophages represent at least three new candidate genera. Ecologically, virophage populations are repeatedly detected over years and evolutionary stable, yet their distinct abundance profiles and gene content suggest that virophage genera occupy different ecological niches. Co-occurrence analyses reveal 11 virophages strongly associated with uncultivated Mimiviridae, and three associated with eukaryotes among the Dinophyceae, Rhizaria, Alveolata, and Cryptophyceae groups. Together, these findings significantly augment virophage databases, help refine virophage taxonomy, and establish baseline ecological hypotheses and tools to study virophages in nature.
- Authors:
-
- The Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Univ. of Wisconsin, Madison, WI (United States). Dept. of Bacteriology. Dept. of Civil and Environmental Engineering
- The Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology. Dept. of Civil, Environmental and Geodetic Engineering
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Science Foundation (NSF); Gordon and Betty Moore Foundation (United States)
- OSTI Identifier:
- 1459396
- Grant/Contract Number:
- AC02-05CH11231; MCB-0702395; DEB-1344254; DEB-1440297; OCE-1536989; GBMF #3790
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 8; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; freshwater ecology; metagenomics; microbial ecology; phage biology
Citation Formats
Roux, Simon, Chan, Leong-Keat, Egan, Rob, Malmstrom, Rex R., McMahon, Katherine D., and Sullivan, Matthew B. Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. United States: N. p., 2017.
Web. doi:10.1038/s41467-017-01086-2.
Roux, Simon, Chan, Leong-Keat, Egan, Rob, Malmstrom, Rex R., McMahon, Katherine D., & Sullivan, Matthew B. Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. United States. https://doi.org/10.1038/s41467-017-01086-2
Roux, Simon, Chan, Leong-Keat, Egan, Rob, Malmstrom, Rex R., McMahon, Katherine D., and Sullivan, Matthew B. Wed .
"Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics". United States. https://doi.org/10.1038/s41467-017-01086-2. https://www.osti.gov/servlets/purl/1459396.
@article{osti_1459396,
title = {Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics},
author = {Roux, Simon and Chan, Leong-Keat and Egan, Rob and Malmstrom, Rex R. and McMahon, Katherine D. and Sullivan, Matthew B.},
abstractNote = {Virophages are small viruses that co-infect eukaryotic cells alongside giant viruses (Mimiviridae) and hijack their machinery to replicate. While two types of virophages have been isolated, their genomic diversity and ecology remain largely unknown. Here we use time series metagenomics to identify and study the dynamics of 25 uncultivated virophage populations, 17 of which represented by complete or near-complete genomes, in two North American freshwater lakes. Taxonomic analysis suggests that these freshwater virophages represent at least three new candidate genera. Ecologically, virophage populations are repeatedly detected over years and evolutionary stable, yet their distinct abundance profiles and gene content suggest that virophage genera occupy different ecological niches. Co-occurrence analyses reveal 11 virophages strongly associated with uncultivated Mimiviridae, and three associated with eukaryotes among the Dinophyceae, Rhizaria, Alveolata, and Cryptophyceae groups. Together, these findings significantly augment virophage databases, help refine virophage taxonomy, and establish baseline ecological hypotheses and tools to study virophages in nature.},
doi = {10.1038/s41467-017-01086-2},
journal = {Nature Communications},
number = ,
volume = 8,
place = {United States},
year = {2017},
month = {10}
}
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Figures / Tables:
Fig. 1: Phylogeny and summarized gene content of virophage genomes. The maximum-likelihood phylogenetic tree was computed from a concatenated alignment of four core genes (major and minor capsid proteins, DNA packaging enzyme, and Cysteine protease). SH-like support are indicated on nodes, and branches with < 50% support are displayed asmore »
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