Seasonal restructuring of heterotrophic microbial communities is differentially affected by glacier type in Greenland fjords

This dataset investigates seasonal (spring–summer) variation in heterotrophic microbial communities in two adjacent fjords of southwest Greenland, Nuup Kangerlua (marine-terminating glacier-influenced) and Ameralik (land-terminating glacier-influenced). Environmental DNA samples were collected across multiple stations and depths and analyzed using 18S rRNA gene metabarcoding for heterotrophic protists and 16S rRNA gene metabarcoding for bacterial communities. The high-throughput sequence data have been deposited in the NCBI SRA under BioProject accession PRJNA1457328 (eukaryotes) and PRJNA1466576 (bacteria). These data were complemented by imaging approaches (imaging flow cytometry, iFCM, and FlowCAM) to quantify microbial abundance, size structure, and carbon biomass. Environmental variables, including hydrographic parameters and nutrient concentrations, were integrated to examine their relationships with microbial community composition. The dataset provides a comparative framework to evaluate how contrasting glacial regimes influence the seasonal dynamics and coupling of bacterial and heterotrophic protist communities in Arctic fjord ecosystems.