Patterns of eukaryotic diversity from the surface to the deep-ocean sediment

Remote deep-ocean sediment (DOS) ecosystems are among the least explored biomes on Earth. Genomic assessments
of their biodiversity have failed to separate indigenous benthic organisms from sinking plankton. Here, we
compare global-scale eukaryotic DNA metabarcoding datasets (18S-V9) from abyssal and lower bathyal surficial
sediments and euphotic and aphotic ocean pelagic layers to distinguish plankton from benthic diversity in sediment
material. Based on 1685 samples collected throughout the world ocean, we show that DOS diversity is at
least threefold that in pelagic realms, with nearly two-thirds represented by abundant yet unknown eukaryotes.
These benthic communities are spatially structured by ocean basins and particulate organic carbon (POC) flux
from the upper ocean. Plankton DNA reaching the DOS originates from abundant species, with maximal deposition
at high latitudes. Its seafloor DNA signature predicts variations in POC export from the surface and reveals
previously overlooked taxa that may drive the biological carbon pump.