Exploring the diversity and evolution of giant viruses in deep sea sediments using genome-resolved metagenomics

Abstract: Viruses are the most abundant biological entities on this planet, which is impressive considering that they are completely dependent on their hosts for reproduction. Recently the idea of what viruses are has changed dramatically, with the discovery of giant viruses that belong to the Nucleocytoplasmic Large DNA Viruses (NCLDV), such as Mimiviridae, Marseilleviridae, and the proposed families Pandoraviruses, and Pithoviruses. Not only are some of these viruses as large as bacteria in size, their genomes also exceed the size of some prokaryotic genomes. The evolutionary path to viral giganticism is not yet fully understood, and several opposing theories have been proposed. The more examples of giant viruses we have to study, the clearer the picture becomes. The rate of discovery, however, is limited by the low capacity of culturing. In an effort to contribute through culture-independent methods, I used genome-resolved metagenomics to retrieve genomes of 23 new members of the NCLDV from deep sea sediment samples that were taken near Loki’s Castle hydrothermal vent field. This method has previously been used to study uncultured Bacteria and Archaea, but few successful cases of metagenomic binning of NCLDV have been documented. New methods for refinement and quality control of the binned genomes were developed, combining reads profiling with differential coverage binning, and composition-based cleaning of potentially contaminating sequences. The binned genomes represent several novel clades of NCLDV, the most noteworthy ones distantly related to Pithoviruses and Marseilleviridae, and greatly expand their overall diversity. Phylogenetic analysis of their genome content supports the independent evolution of viral giganticism from smaller viruses. Continued use of metagenomics to explore the presence of NCLDV in environmental samples will lead to new insights into their diversity, evolution, and biology.