We aimed to explore the community composition and turnover of eukaryotic and bacterial microorganisms associated with ice-associated and sinking algal aggregates, as well as their similarity to potential source communities of sea ice, water and deep-sea sediments using Illumina tag sequencing. We sampled algae aggregates growing in melt ponds on sea ice, deposited algae aggregates at the seafloor in more than 4000 m water depth, sea ice, upper water column, sediment surface and the gut content of holothurians feeding on the deposits.