Seasonal variations in PCR-DGGE fingerprinted viruses infecting phytoplankton in large and deep peri-alpine lakes

Double-stranded DNA viruses infecting eukaryotic algae (e.g., phycodnaviruses) and cyanobacteria (e.g., cyanophages) are now recognized as widespread and ubiquitous in aquatic environments. However, both the diversity and functional roles of these viruses in fresh waters are still poorly understood. We conducted a year-long study in 2011 of the community structure of planktonic virus groups in the upper lit layer of two important freshwater natural ecosystems in France, Lake Annecy (oligotrophic) and Lake Bourget (oligo-mesotrophic). Using PCR-DGGE to target a number of different structural and functional signature genes, i.e.,g20, g23, psbA, polB, and mcp, the phytoplankton viruses were shown to display temporal and spatial variability. There were marked seasonal changes in community structure for all viral groups in Lake Bourget, but only for T4-like myoviruses and psbA-containing cyanophages in Lake Annecy. The multivariate statistical analyses revealed that (1) various environmental factors can directly or indirectly explain the community structure observed for each phytoplankton viral group, and (2) temporal patterns of T4-like myovirus community structure were similar between the two lakes. In general, our results (1) suggest that the observed algal virus patterns were associated with significant shifts in phytoplankton biomass and/or structure, which in turn were shaped by the abiotic environment, and (2) support the Bank model proposed by Breitbart and Rohwer (Trends Microbiol 13:278–284, 2005). This study provides new evidence that freshwater lakes contain a significant diversity of algal viruses, and that the distribution of these viruses strongly mirrors that of their hosts.