Abstract Microbial communities form the base of food webs in freshwater ecosystems, yet the interactions within these diverse assemblages are poorly understood. Based on evidence showing that primary production and respiration follow diurnal trends in lakes, we hypothesized that gene expression in freshwater microbes would have similar diel cycles. We used three 2‐d time series of metatranscriptomes to test this hypothesis in a eutrophic lake, an oligotrophic lake, and a humic lake.
