Distribution of Giant Viruses in Marine Environments

Abstract

Viruses are the most abundant biological entities in the sea. Infecting marine organisms from oxygen-producing phytoplankton to whales, viruses regulate the populations of many marine organisms and play important roles in global biogeochemical fluxes. Thanks to the recent improvement of sequencing technology, billions of bases of sequences from marine microbial communities are being determined by different groups of researchers.

Those environmental sequence data, or “metagenomes,” now provide unprecedented opportunities to reconstruct and characterize the composition and the dynamics of mostly unculturable microorganisms in different habitats.

We recently developed a new computational method called phylogenetic mapping to obtain a comprehensive picture of the distributions of microorganisms contained in environmental samples. We used our method to investigate the distributions of large DNA viruses represented in the Sorcerer II Global Ocean Sampling Expedition microbial metagenomic data set. Using DNA polymerase genes as a taxonomic marker, we identified 811 homologous sequences of likely viral origins. Most of these sequences corresponded to phages, being consistent with the large number of phage-like particles in marine environments. Interestingly, the second largest viral group corresponded to the one containing mimivirus, the largest known virus (with 1.2 Mb-genome), which infects amoeba. Albeit only recently discovered, giant viruses of the mimivirus family appear to constitute a diverse, quantitatively important, and geographically ubiquitous component of the population of large eukaryotic DNA viruses in the sea. We also identified several DNA polymerase homologs closely related to African swine fever virus, a large virus pathogenic to domestic animals and until now limited to terrestrial animal hosts.

Finally, our approach allowed the identification of a new combination of genes in viral-like sequences. In conclusion, high throughput metagenomics is becoming a technique of choice to follow the changes of marine microbial environments induced by climatic changes and/or human activities.