Samples were collected as part of the Lake Mendota Microbial Observatory and North Temperate Lakes Long Term Ecological Research program. Surface samples were collected from spatial transects, filtered onto 0.22 um filters, and extracted DNA was sequenced using v3-v4 primers. A few of the Lake Mendota time series samples are also included, and these differ from the "limony" dataset because they were extracted separately and sequenced with different primers.