Microbial eukaryotes communities from freshwater Lake Pavin (France)

As reservoirs of microbial biodiversity, aquatic ecosystems play a central role in global biogeochemical cycles. However, the specific and functional diversity of microorganisms inhabiting these ecosystems remain largely unknown. This is particularly true for microbial eukaryotes, which have complex metabolisms and whose physiologies may vary upon environmental conditions. Focusing on the microbial eukaryotic community of the meromictic Lake Pavin, we provide a comprehensive -omic dataset that includes raw reads from amplicon-based (18S rDNA regions V4 and V9), metagenomic, metatranscriptomic and single amplified genomes (SAG) datasets. The lake Pavin is located in Auvergne (France), characterised by a mixed oxygenated upper layer (top to ca. 60 m) and a permanent anoxic deep layer (ca. 60–92 m). Water sampling was carried out in both layers (at 9 m and 80 m) by day and night, at four distinct times throughout 2018 (April, June, September, and November) and for two size classes (0.65-10 and 10-50 µm).