Abstract
Summary Protists play a crucial role for ecosystem function(ing) and oxygen is one of the strongest barriers against their local dispersal. However, protistan diversity in freshwater habitats with oxygen gradients received very little attention. We applied high‐throughput sequencing of the V9 region ( 18S rRNA gene) to provide a hitherto unique spatiotemporal analysis of protistan diversity along the oxygen gradient of a freshwater meromictic lake (Lake A latsee, SW G ermany). In the mixolimnion, the communities experienced most seasonal structural changes, with S tramenopiles dominating in autumn and D inoflagellata in summer. The suboxic interface supported the highest diversity, but only 23 OTUs 95% (mainly E uglenozoa, after quality check and removal of operational taxonomic units ( OTUs ) with less than three sequences) were exclusively associated with this habitat. Eukaryotic communities in the anoxic monimolimnion showed the most stable seasonal pattern, with C hrysophyta and B icosoecida being the dominant taxa. Our data pinpoint to the ecological role of the interface as a short‐term ‘meeting point’ for protists, contributing to the coupling of the mixolimnion and the monimolimnion. Our analyses of divergent genetic diversity suggest a high degree of previously undescribed OTUs . Future research will have to reveal if this result actually points to a high number of undescribed species in such freshwater habitats.