Abstract : The main goal of this thesis was to assess qualitative, quantitative and functional significance of viruses in Lake Pavin, by taking into account the depth-related gradients in the water column. Specifically, we have examined the (i) spatio temporal dynamics of viral community diversity, (ii) significance of depth-related gradients in seasonal variations of viral abundance and lytic activity and (iii) relative significance of lysogenic 'life style'. From an original concentration protocol, we have shown that the dynamics of viral diversity in the lake was strongly linked to those of microbial communities. Similar for variations in viral seasonal abundance and lytic activity. Through the entire water column, microbial trophic network structure and the role of viruses in this network depended strongly on depth, with a simplification of trophic modes, of biological organization levels of communities, and of trophic interactions with depth. Biological limnology of the deep layers is reducte to viruses and prokaryotes, and is thus governed by the viral loop processes. Finally, up to 16 % of bacterioplankton could be lysogens. This way of life, antagonist with lytic one, depended on host availability and could be more a mechanism for the maintenance of viral traits, than can further have significant incidences on the evolutionary ecology of host communities. Overall, our results show that viruses are essential in the diversification and ecology of microbial communities, and in the matter and energy flows in the lake water column.