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High-throughput single virus genomics unveil reference viral genomes in marine epipelagic ambients at global scale


Francisco J. Martínez-Hernández1, Òscar Fornás2, Mónica Lluesma Gomez1, Joaquín Martínez-Martínez3, Josefa Antón1, Matthew Sullivan4, Francisco Rodriguez-Valera5, Josep M. Gasol6, Dolors Vaqué6, Silvia G. Acinas6, Manuel Martinez-Garcia1

1Department of Physiology, Genetics and Microbiology, University of Alicante., Alicante, Spain
2Flow Citometry Unit, Centre for Genomic Regulation-Barcelona Biomedical Research Park., Barcelona, Spain
3Bigelow Laboratory for Ocean Sciences., Maine, United States
4Department of Ecology and Evolutionary Biology, University of Arizona., Tucson, United States
5Microbiology Division, Miguel Hernandez University, San Juan de Alicante, Spain
6Department of Marine Biology and Oceanography, Institut de Ciències del Mar—CSIC, Barcelona, Spain


Viruses are ubiquitous and the most numerous and diverse biological entities in nature. Recently, Brum and colleagues (2015) confirmed by metagenomics that "the most abundant and widespread viral population lack culture representative"in marine systems. To circumvent culture and metaviromic limitations to deliver reference genomes, we will present the usefulness of Single Virus Genomics (SVG) to unveil unknown, uncultured and ubiquitous marine viruses at global scale. We first sorted 3984 single viruses from the epipelagic zone of the Mediterranean Sea. Then, whole genome was amplified by multiple displacement amplification and sequenced single amplified viral genomes (SAVs). Metaviromic fragment recruitment with Tara Oceans expedition, Pacific Ocean Virome and Mediterranean datasets demonstrated that SAVs provided the highest recruitment rate among all publicly available marine viruses including marine virus isolates (n=180), viral fosmids (n=1149) and virus genomes assembled from TARA metaviromes (n=3018, surface) and single amplified prokaryote genomes (n=20). Most of generated SAVs were Caudovirales and unexpectedly, results indicated that the most putatively abundant virus in surface marine environment, the phage 37-F6 (mean recruitment rate over Pelagiphages ≈40-fold) was not related with Pelagiphage isolates, but the closest phages (≈55% of nucleotide identity, whole genome alignment) were those found in single cells of Verrucomicrobia (AAA164-I21) and Flavobacteria (AAA160-P02), both considered as active members of bacterioplankton (Martínez-Garcia et al., 2012). Furthermore, the analysis of a metaproteome from the Oregon Coast bacterioplankton and comparison with metaviromes confirmed that peptide signatures of structural proteins of virus 37-F6 were widespread in all oceans. Thus, overall, our results demonstrated that SVG rises as a powerful approach to unveil the genomics of uncultured viruses and open new ways to formulate and contrast hypothesis in microbial ecology, such as the predominance of virus 37-F6 and the total contribution of viruses predating on low abundant but active taxa to total viral production.






Reference:
Viral Ecology-T01-Oft-03
Session:
Viral Ecology in Natural Environments
Presenters:
Francisco J. Martínez-Hernández
Session:
Viral ecology in natural environments
Presentation type:
Offered talk - 15 min
Room:
Main Auditorium
Chair/s:
Willie Wilson
Date:
Tuesday, 19 July 2016
Time:
09:25 - 09:40