The Southern Ocean plays a critical role for carbon sequestration in the oceans. The flux of carbon (C) and nitrogen (N) export to the deep ocean depends on the efficiency of the biological pump transporting biomass to depth, however the molecular mechanisms are not well understood. This study focuses on the impact of microbial communities in the C flux in the Ross Sea observed in the late austral summer of 2013 during the TRacing Algal Carbon Export in the Ross Sea (TRACERS) expedition. Programmed cell death (PCD) modulates the turnover of phytoplankton in the oceans, however few field data exist to demonstrate this phenomenon. We have characterized at taxonomical and functional level the primary groups of organisms undergoing PCD in the water column. PCD was observed to occur in both prokaryotic and eukaryotic cells, which dominated different regions and depths in the water column, specifically, we found Pelagibacter, Tenacibaculum and Psychrobacter as representative genera of the Bacteria, and Stylonychia, Emiliania and Chaetoceros of the Eukarya domain respectively. We observed higher occurrences of eukaryotic cells to undergo PCD in surface waters of a diatom bloom in the western Ross Sea, while prokaryotes undergoing PCD were found deeper in the water column and in regions outside of the bloom. We will also present new mechanistic insights about differentially active pathways among diatoms undergoing PCD. Finally, we discuss how PCD contributes to the production of free and assemble polymers gels, thus influencing carbon export.