“…A large majority of aquatic viral ecological studies have been carried out in seawater (see Wommack & Colwell, 2000;Sime-Ngando et al, 2003;Weinbauer, 2004). Some freshwater systems have also been investigated, although less often, and these include rivers (Mathias, Kirschner & Velmirov, 1995;Farnell-Jackson & Ward, 2003), Antarctic lakes (Kepner, Wharton & Suttle, 1998;Laybourn-Parry, Hö fer & Sommaruga, 2001), oligotrophic lakes (Klut & Stockner, 1990;Tapper & Hicks, 1998;Hoffer & Sommaruga, 2001;Bettarel et al, 2003bBettarel et al, , 2004Vrede, Stensdotter & Lindströ m, 2003), mesotrophic lakes (Hennes & Simon, 1995;Maranger & Bird, 1995;Leff et al, 1999;Wilhelm & Smith, 2000), and eutrophic lakes (Sommaruga et al, 1995;Weinbauer & Höfle, 1998;Fischer & Velimirov, 2002;Bettarel et al, 2003a;Weinbauer et al, 2003;Bettarel et al, 2004), as well as lake sediments (Maranger & Bird, 1996). In France, the three largest natural freshwater ecosystems (Lakes Annecy, Bourget and Geneva) have not yet been investigated from this perspective and only the oligotrophic Lake Pavin and the eutrophic Lake Aydat and Sep Reservoir have received recent interest in France (Bettarel et al, 2003a(Bettarel et al, ,b, 2004Pradeep Ram et al, in press).…”