Lakes represent less than 3% of terrestrial surface on Earth. Yet, they constitute a reservoir of biodiversity and provide major ecosystem services, notably by their crucial role in the carbon and other nutrients cycles and as important drinkable and uses resources of water. They are also considered as sentinels of climate changes they integrate inputs from surrounding terrestrial ecosystems. Human activities have amplified natural (seasonal) variations of the environment and amplify natural phenomena, such as eutrophication (allochthonous inputs of nutrients), leading to major changes in lake ecosystems functioning worldwide. Eutrophication has been shown to be a major driver of aquatic microbial communities, key contributors to ecosystem functioning, at various spatial and temporal scales. Yet, the interaction between these scales and the impact on microbial community function, more than taxa, changes remain poorly investigated.

With 12 million inhabitants, the Greater Paris offers a natural laboratory to explore the effects of eutrophication on freshwater lakes within a relatively restricted area. Here, a time-series was carried out during 18 months, to monitor planktonic microbial communities of nine lakes located within a 70 km radius around Paris (Île-de-France, France) with distinct trophic status (mesotrophic to hypereutrophic). During summer, lakes displayed major differences in prokaryotic taxa and functions despite their comparable morphologies. Trophic status was the main driver of the community structure and functional potential during the summer season (when the primary production peaks). Functional potential appeared much more stable than taxa composition within each lake, most of it being shared among all lakes. Phosphorus related processes contributed more than other BGC metabolisms to the difference between trophic statuses. Hypereutrophic lakes prokaryotic communities display the highest distinctiveness and heterogeneity over time, suggesting an alternative regime compared to lakes of lower trophic status. High eutrophication levels are sometimes assumed to be irreversible, so whether their driving effect and the hypothetical “regime shift” in hypereutrophic lakes continue in periods of lower primary production are being investigated. Besides, the identification of one lake dominated by non-bloom-forming Cyanobacteria over time without clear explanation shows that trophic status alone cannot explain all observations, pointing to the need to extend the considered top-down and bottom-up approaches (microbial eukaryotes, zooplankton, additional abiotic variables) in future studies.