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ISME J. 2018 May;12(5):1287-1295. doi: 10.1038/s41396-018-0052-x. Epub 2018 Jan 30.

Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan.

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Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan.
Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan.
School of Life Science and Technology, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan.
Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, 442, Shakudo, Habikino, Osaka, Japan.
Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France.
Database Center for Life Science, Joint-Support Center for Data Science Research, Research Organization of Information and Systems, Wakashiba, Kashiwa, Chiba, 277-0871, Japan.


Viruses infecting microorganisms are ubiquitous and abundant in the ocean. However, it is unclear when and where the numerous viral particles we observe in the sea are produced and whether they are active. To address these questions, we performed time-series analyses of viral metagenomes and microbial metatranscriptomes collected over a period of 24 h at a Japanese coastal site. Through mapping the metatranscriptomic reads on three sets of viral genomes ((i) 878 contigs of Osaka Bay viromes (OBV), (ii) 1766 environmental viral genomes from marine viromes, and (iii) 2429 reference viral genomes), we revealed that all the local OBV contigs were transcribed in the host fraction. This indicates that the majority of viral populations detected in viromes are active, and suggests that virions are rapidly diluted as a result of diffusion, currents, and mixing. Our data further revealed a peak of cyanophage gene expression in the afternoon/dusk followed by an increase of genomes from their virions at night and less-coherent infectious patterns for viruses putatively infecting various groups of heterotrophs. This suggests that cyanophages drive the diel release of cyanobacteria-derived organic matter into the environment and viruses of heterotrophic bacteria might have adapted to the population-specific life cycles of hosts.

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