The St. Lawrence hydrographic system includes freshwater, brackish, and marine habitats, and is the largest waterway in North America by volume. The food-webs in these habitats are ultimately dependent on phytoplankton. Viral lysis is believed to be responsible for a major part of phytoplankton mortality. To better understand their role, we characterized the diversity and distribution of two viral taxa infecting phytoplankton: the picornaviruses and phycodnaviruses. Our study focused on the estuary transition zone, which is an important nursery for invertebrates and fishes. Both viral taxa were investigated by PCR amplification of conserved molecular markers and next-generation sequencing at six sites, ranging from freshwater to marine. Our results revealed few shared viral phylotypes between saltwater and freshwater sites. Salinity appeared to be the primary determinant of viral community composition. Moreover, our analysis indicated that the viruses identified in this region of the St. Lawrence diverge from classified viruses and homologous published environmental virotypes. These results suggest that DNA and RNA viruses infecting phytoplankton are likely active in the estuary transition zone, and that this region harbors its own unique viral assemblages.
Keywords: DNA Polymerase B; Phycodnaviridae; Picornavirales; RNA-dependent RNA polymerase; St. Lawrence Estuary; aquatic viruses; viral ecology.