Viral metagenomic study of two freshwater Lakes.. Metavir

Viruses are known to be the most abundant biological entities in aquatic environment, where they are (i) important top-down regulation factors for microbial communities, (ii) known to interfere in major biogeochemical cycles, and (iii) thought to be an important source of genetic diversity. Yet, diversity and distribution of these viruses is still far from being understood, especially in freshwater ecosystems. Metagenomic analysis of two different temperate freshwater viral communities showed that most of the viral sequences were not similar to those in the current databases. A deep sequencing (1.5 billion sequences) associated to a large read size (400 bp) allowed us to assess, for the first time, the diversity in the main viral families through direct phylogenetic analysis of specific marker genes. The analysis of the major viral groups found in the two lakes shed light on a great diversity, and retrieved previously unknown clades among single-stranded DNA viruses (Microviridae, Circoviridae, Nanoviridae) and among Caudovirales. The absence of lake-specific clade indicated that the new viruses identified were ubiquitous, at least on a regional freshwater lake scale. Compared to the previously published viromes, a significant genetic similarity between viral communities of related environments was highlighted for the first time, despite the great geographical distances separating these different communities. Thus, viruses appear to be distributed worldwide, and are likely selected by the presence or absence of their hosts. Gene richness analysis assessed through rarefaction curves showed an extraordinary genetic diversity of viruses in each of the two lakes under study. Such diversity was never retrieved previously, even in the last generation of published viromes. The global virome is thereby a fantastic pool of unknown genes, which remains partially sampled and understood.