Surface Phytoplankton Shape Deep Ocean Prokaryotic Communities

Eplipelagic primary production determines the flux of carbon to microbes in the bathypelagic ocean, yet whether variations in surface phytoplankton communities control the assembly of deep-sea prokaryotes remains unexplored. Here we compare the taxonomic structure of free-living and particle-attached prokaryotic communities from 4000 m with surface phytoplankton assemblages across eight stations from the Atlantic, Pacific and Indian oceans. We show that bathypelagic prokaryotic communities mirror abundance variations in surface planktonic groups such as dinoflagellates and ciliates as well as gradients in surface primary productivity, but are less influenced by the bathypelagic physicochemical environment. The similarity between surface and bathypelagic prokaryotic communities increases towards productive surface waters likely due to intense particle-driven prokaryotic transport, resulting in particle-attached bathypelagic communities similar to those in surface waters, but we also detect a pool of endemic deep-sea taxa less influenced by surface processes which are potentially chemoautotrophs. Our results suggest a key role of phytoplankton composition and activity in structuring the global bathypelagic microbiome, likely through determining the nature of sinking particles and the associated prokaryotic communities.