Amplicon sequencing data set of bacterial and phytoplankton communities during a record low-ice winter in the North American Great Lakes

Bacterial and phytoplankton communities were profiled across a record low ice-cover winter (2024) and adjacent shoulder seasons in Lakes Erie, Huron, Superior, and St. Clair using 16S and 18S rRNA gene sequencing. Eukaryotic communities were dominated by diatoms and zooplankton, with Lake Superior exhibiting a distinct taxonomic composition.