Viral metagenomics: a new and complementary tool for environmental quality assessment

Metagenomic sequencing of nucleic acids from environmental or other complex samples can be successfully used as a powerful tool for environmental quality assessment. Being a culture-independent approach, it does not rely on the presence or absence of specific organisms or genes, and can even identify novel organisms. When focused on viruses, metagenomics can help to shed light on their involvement in ecosystem functioning, due to their dependence on their hosts and their ability to respond quickly to environmental changes. Moreover, viral metagenomics can show the impact of contamination on different natural ecosystems, highlighting putative sources and potential pathogens.