Abstract
Community composition of freshwater prokaryotes and protists varies through time. Few studies contemporarily investigate temporal variation of these freshwater communities for more than 1 year. We compared the temporal patterns of prokaryotes and protists in three distinct habitats for 4 years (2014–2017) in Lake Tovel, a cold‐water lake. This lake showed a marked temperature increase in 2017 linked to altered precipitation patterns. We investigated whether microbial communities reflected this change across habitats and whether changes occurred at the same time and to the same extent. Furthermore, we tested the concept of hydrological year emphasizing the ecological effect of water renewal on communities for its explanatory power of community changes. Microbe diversity was assessed by Illumina sequencing of the V3–V4 hypervariable region of the 16S rRNA gene and 18S rRNA gene, and we applied co‐inertia analysis and asymmetric eigenvector maps modelling to infer synchrony and temporal patterns of prokaryotes and protists. When considering community composition, microbes were invariable in synchrony across habitats and indicated a temporal gradient linked to decreasing precipitation; however, when looking at temporal patterns, the extent of synchrony was reduced. Small‐scale patterns were similar across habitats and microbes and linked to seasonally varying environmental variables, while large‐scale patterns were different and partially linked to an ecosystem change as indicated by increasing water transparency and temperature and decreasing dissolved oxygen. Our advanced statistical approach outlined the multifaceted aspect of synchrony when linked to community composition and temporal patterns.