The primary production by photosynthetic microbes in the sunlit upper ocean leads to the production of particulate organic matter that is transported and sequestered at depths by sinking. However, pico-plankton make up a large fraction of the planktonic biomass and, being too small to sink, are transported predominantly by the flow. We demonstrate through observations gathered in the Mediterranean Sea that subduction of water at ocean fronts generates three-dimensional intrusions with uncharacteristically high carbon, chlorophyll, and oxygen that extend below the sunlit photic-zone into the dark ocean. These intrusions contain picoplankton assemblages that resemble the photic-zone regions where the water originated, with the dominant biomass contribution from non-photosynthetic bacteria. Flow-driven intrusions are an important mechanism for transporting carbon to depth and for enhancing connectivity between the sunlit and dark oceanic ecosystems in stratified subtropical ocean environments that are expanding due to the warming climate.

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