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Metagenomic exploration of viral diversity and virus-host interactions in a deep freshwater lake

View ORCID ProfileYusuke Okazaki, View ORCID ProfileYosuke Nishimura, View ORCID ProfileTakashi Yoshida, View ORCID ProfileHiroyuki Ogata, View ORCID ProfileShin-ichi Nakano
doi: https://doi.org/10.1101/655167
Yusuke Okazaki
Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, JapanBioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305–8566, Japan
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  • For correspondence: okazaki.yusuke.e31@kyoto-u.jp
Yosuke Nishimura
Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, JapanInstitute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, JapanAtmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
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Takashi Yoshida
Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan
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Hiroyuki Ogata
Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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Shin-ichi Nakano
Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
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Abstract

The use of metagenomics has dramatically expanded the known virosphere, but freshwater viral diversity and the ecological relationships between viruses and hosts remain poorly understood. In this study, we conducted a large-scale metagenomic exploration of planktonic dsDNA prokaryotic viruses by sequencing both virion (<0.22 μm) and cellular (0.22–5.0 μm) fractions collected spatiotemporally from a deep freshwater lake (Lake Biwa, Japan). This simultaneously reconstructed 183 complete (i.e., circular) viral genomes and 57 bacterioplankton metagenome-assembled genomes. Spatiotemporal, intra- and extra-cellular dynamics of individual viruses assessed through metagenomic read coverage revealed a hypolimnion-specific viral community analogous to the vertically-stratified bacterioplankton community. The hypolimnetic community was generally stable during stratification, but occasionally shifted abruptly due to lysogenic induction, presumably reflecting low bacterial productivity in the hypolimnion. Genes involved in assimilatory sulfate reduction were encoded in 20 (10.9%) viral genomes, including those of dominant viruses, and may aid viral propagation in sulfur-limited freshwater systems. Hosts were predicted for 40 (21.9%) viral genomes, encompassing 10 phyla (or classes of Proteobacteria) including ubiquitous freshwater bacterioplankton lineages (e.g., LD12 and Ca. Nitrosoarchaeum). Comparison with published metagenomes revealed phylogeographic connectivity of viral communities in geographically isolated habitats, probably following the phylogeographic connectivity of their hosts. Notably, analogous to their hosts, actinobacterial viruses were among the most diverse, ubiquitous, and abundant viral groups in freshwater systems, with high lytic replication rates in surface waters. This result suggested that freshwater Actinobacteria are under high viral lytic pressure, which likely facilitated their genomic micro-diversification to elude viral recognition.

Significance Statement Metagenomics allows for the reconstruction of bacterial and viral genomes without cultivation, contributing substantially to elucidation of bacterial and viral diversity and their key ecological roles. In this study, we report the largest-scale metagenomic exploration of freshwater prokaryotic viruses to date. We investigated the hypolimnion of a deep freshwater lake and tracked viruses throughout their life cycles, including both intra- and extra-cellular phases. This method allowed us to reconstruct both viral and host genomes and characterize numerous novel virus-host interactions, including those involving ubiquitous freshwater bacterial lineages. When the data were compared with published metagenomic datasets, we uncovered genome-resolved phylogeographic connectivity among viruses from geographically isolated habitats and identified ecologically important viral groups that are ubiquitous in aquatic habitats.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted May 31, 2019.
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Metagenomic exploration of viral diversity and virus-host interactions in a deep freshwater lake
Yusuke Okazaki, Yosuke Nishimura, Takashi Yoshida, Hiroyuki Ogata, Shin-ichi Nakano
bioRxiv 655167; doi: https://doi.org/10.1101/655167
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Metagenomic exploration of viral diversity and virus-host interactions in a deep freshwater lake
Yusuke Okazaki, Yosuke Nishimura, Takashi Yoshida, Hiroyuki Ogata, Shin-ichi Nakano
bioRxiv 655167; doi: https://doi.org/10.1101/655167

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