StratFreshDB v1.1 doi-10-17044-scilifelab-13005311-0 https://doi.org/10.17044/SCILIFELAB.13005311 Swedish National Data Service Svensk nationell datatjänst Landing page StratFreshDB v1.1 doi-10-17044-scilifelab-13005311-0 https://doi.org/10.17044/SCILIFELAB.13005311 Buck, Moritz Swedish National Data Service Svensk nationell datatjänst Landing page Stratified lakes and ponds that feature steep oxygen gradients are known to be significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the resident microbial communities, especially in the oxygen-depleted hypolimnetic compartments are poorly known. In this paper, we present a comprehensive metagenome dataset including shotgun metagenomes from 29 stratified lakes and 12 ponds mainly located in the boreal and subarctic regions but also including one reservoir from tropical Puerto Rico and one Swiss lake from the temperate zone. For most lakes and ponds, the data includes a vertical sample set spanning the oxic surface waters to anoxic bottom layers. In addition to the metagenomic sequences, the dataset includes environmental variables for the samples, such as oxygen, nutrient, and carbon concentrations. The dataset is ideal for further exploring the microbial taxonomic and functional diversity in freshwater environments and climate change impacts on the functioning of these ecosystems. Access to data through an external actor. Åtkomst till data via extern aktör.