Single-virus genomics reveals hidden cosmopolitan and abundant viruses

Francisco Martinez-Hernandez, Oscar Fornas, Monica Lluesma Gomez, Benjamin Bolduc, Maria Jose de la Cruz Peña, Joaquín Martínez Martínez, Josefa Anton, Josep M. Gasol, Riccardo Rosselli, Francisco Rodriguez-Valera, Matthew B. Sullivan, Silvia G. Acinas and Manuel Martinez-Garcia ()
Additional contact information
Francisco Martinez-Hernandez: Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig
Oscar Fornas: Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST)
Monica Lluesma Gomez: Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig
Benjamin Bolduc: The Ohio State University
Maria Jose de la Cruz Peña: Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig
Joaquín Martínez Martínez: Bigelow Laboratory for Ocean Sciences
Josefa Anton: Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig
Josep M. Gasol: Institut de Ciències del Mar (ICM)
Riccardo Rosselli: Evolutionary Genomics Group, Universidad Miguel Hernández
Francisco Rodriguez-Valera: Evolutionary Genomics Group, Universidad Miguel Hernández
Matthew B. Sullivan: The Ohio State University
Silvia G. Acinas: Institut de Ciències del Mar (ICM)
Manuel Martinez-Garcia: Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig

Nature Communications, 2017, vol. 8, issue 1, 1-13

Abstract: Abstract Microbes drive ecosystems under constraints imposed by viruses. However, a lack of virus genome information hinders our ability to answer fundamental, biological questions concerning microbial communities. Here we apply single-virus genomics (SVGs) to assess whether portions of marine viral communities are missed by current techniques. The majority of the here-identified 44 viral single-amplified genomes (vSAGs) are more abundant in global ocean virome data sets than published metagenome-assembled viral genomes or isolates. This indicates that vSAGs likely best represent the dsDNA viral populations dominating the oceans. Species-specific recruitment patterns and virome simulation data suggest that vSAGs are highly microdiverse and that microdiversity hinders the metagenomic assembly, which could explain why their genomes have not been identified before. Altogether, SVGs enable the discovery of some of the likely most abundant and ecologically relevant marine viral species, such as vSAG 37-F6, which were overlooked by other methodologies.

Date: 2017
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DOI: 10.1038/ncomms15892

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