The abundance and composition of microbial communities were investigated during 2007 in Marennes Oléron Bay (France) in order to characterize the biological relationships governing the planktonic food web. Compared to the results of previous years, there was lower abundance and lower magnitude of variations in autotrophic and heterotrophic microbial entities in 2007. Using a Spearman rank correlation analysis, a significant link for biological abundance was only noted between bacteria and ciliates. However, an interesting relationship was highlighted between chlorophyll a and bacterial aminopeptidase and β-glucosidase exoenzymatic activities. Two characteristic periods of virus-bacteria uncoupling were observed in spring and autumn 2007. Using multivariate analysis, the clustering of monthly viral community structures (defined by RAPD-fingerprinting) was related to bacterial proteolysis activity and secondarily to flagellates. Spring and autumn were characterized by phytoplanktonic blooms of large cells (> 10µm) and small cells (< 10µm), respectively, during the virus-bacteria uncoupling phases. High predation by flagellates in the autumn, during a period of microbial food web activity, involved the highest viral fingerprint richness, inferring a top-down control in driving the number of virus-host systems. We discuss the proteolysis level as a descriptor in structuring viral assemblages and argue that changes in the quantity and quality of DOM may bridge phytoplankton to bacteria and reflect changes in phytoplankton composition.