Besides the lethal effect of viruses on the microbial community (typically the bacteria and the phytoplankton), the viral activity can affect significantly not only the structure of this community but also the cycling of carbon and other nutrients within aquatic ecosystems. Due to their activities, viruses could maintain the prokaryotic community diversity by lysing the most dominant populations then allowing the development of the minor groups. Also, viruses constitute the major driver of horizontal gene transfer between bacterial species or genus and therefore they could be the principal actor in the diversification of microbial communities. The viral lysis which induces the transformation of the biomass into dissolved organic matter pool could stimulate the microbial respiration and reduce the transfer of carbon to higher trophic levels as well as the sedimentation of organic particles towards the bottom. At last, aquatic viruses may generate an important interest for applied issues, typically the phagotherapy for aquaculture, even if an important effort remains to be done in the comprehension of the real efficiency of this therapy and the possible underlying resistance phenomena.
Keywords: aquatic ecosystems; biogeochemical cycle; ecology; microbial diversity; phagotherapy; virus.