Multifaceted biodiversity changes of lake microeukaryote communities in response to nutrient enrichment and climate change

Microeukaryote communities ensure a large panel of ecological functions as autotrophs, predators, parasites and saprotrophs. Through the analysis of the sedimentary DNA from four peri‐alpine lakes with contrasting histories of nutrient enrichment, we reconstructed centennial‐scale ecological dynamics and assessed amplitude of change, resistance and resilience of microeukaryote communities in response to eutrophication and warming. Various biological metrics, including alpha‐ and beta‐diversity indices, and a trait‐based functional community approach were mobilized in order to depict the multi‐dimensional aspect of biodiversity changes. As the studied lakes switch from oligotrophic to meso‐oligotrophic condition, a uniform threshold response of the microeukaryote communities was observed across all lakes indicating that, in deep temperate lakes, increases in phosphorus concentration above a threshold of 10 µg l −1 , combined with declining bottom‐water oxygen conditions, can trigger early changes in the microeukaryote community, well before a lake become eutrophic. During the nutrient enrichment period, our diversity metrics indicate a decline in alpha diversity, and an increase in the turnover rate and richness difference, that might have arise from species loss. The amplitude of change in the microeukaryote community composition was lake‐dependant and not proportional to the intensity of eutrophication. Following the re‐oligotrophication of the lakes, the microeukaryote communities did not show signs of resilience. Indeed, although the communities recovered in terms of alpha diversity, the community composition did not return to pre‐disturbance composition. Instead, we observe a similar functional and structural reorganisation of the recent microeukaryote communities across all four lakes, likely driven by climate‐related processes. This multi‐metric analysis allowed to demonstrate the complex and multifaceted dimension of the biological response to environmental changes.