Extraordinary diversity of viruses in deep-sea sediments as revealed by metagenomics without prior virion separation

Our current knowledge of the virosphere in deep-sea sediments remains rudimentary. Here we investigated viral diversity at both gene and genomic levels in deep-sea sediments of Southwest Indian Ocean. Analysis of 19 676 106 non-redundant genes from the metagenomic DNA sequences revealed a large number of unclassified viral groups in these samples. A total of 1106 high-confidence viral contigs were obtained after two runs of assemblies, and 217 of these contigs with sizes up to similar to 120 kb were shown to represent complete viral genomes. These contigs are clustered with no known viral genomes, and over 2/3 of the ORFs on the viral contigs encode no known functions. Furthermore, most of the complete viral contigs show limited similarity to known viral genomes in genome organization. Most of the classified viral contigs are derived from dsDNA viruses belonging to the orderCaudovirales, including primarily members of the familiesMyoviridae,PodoviridaeandSiphoviridae. Most of these viruses infectProteobacteriaand, less frequently,Planctomycetes,Firmicutes,Chloroflexi, etc. Auxiliary metabolic genes (AMGs), present in abundance on the viral contigs, appear to function in modulating the host ability to sense environmental gradients and community changes, and to uptake and metabolize nutrients.

Automated summary

Research on viral diversity in deep-sea sediments of Southwest Indian Ocean revealed a large number of unclassified viral groups, with most contigs belonging to dsDNA viruses in the order Caudovirales that primarily infect Proteobacteria. Auxiliary metabolic genes on viral contigs play a crucial role in modulating host responses to environmental changes and nutrient metabolism.