In 2012 Arctic sea ice declined to a record minimum. As a consequence of the melting, large sub-ice filaments of the diatom Melosira arctica were released and sank to the seafloor, resulting in a widespread deposition of fresh ice-algal material at 4400 m water depth. Elevated rates of oxygen consumption in sediments with algal deposits indicated remineralization by bacteria and evidenced a response of the entire ecosystem down to the deep sea to elevated carbon flux rates (Boetius et al. 2013, Science 339: 1430-1432). Bacteria play essential roles in carbon and nutrient cycling not only at the seafloor but also in the sea ice and in the water column, contributing significantly to Arctic ecosystem functioning. We sampled a wide range of Arctic environments from the surface to the deep sea, in order to compare bacterial communities from sea ice, melt ponds, surface seawater, deep-sea sediment with and without algal aggregates. Structure and composition of bacterial communities showed strong environmental specificity, with distinct differences between surface and deep-sea environments. Yet, some taxa were shared between algae aggregates from the surface and the seafloor, suggesting a transport of surface-derived bacteria to the deep ocean, as a consequence of rapid sea-ice melt.