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The ocean plays a major role in controlling atmospheric carbon at decadal to millennial timescales, with benthic carbon representing the only geologic‐scale storage of oceanic carbon. Despite its importance, detailed benthic ocean observations are limited and representation of the benthic carbon cycle in ocean and Earth system models (ESMs) is mostly empirical with little prognostic capacity, which hinders our ability to properly understand the long‐term evolution of the carbon cycle and climate change‐related feedbacks. The Benthic Ecosystem and Carbon Synthesis (BECS) working group, with the support of the US Ocean Carbon & Biogeochemistry Program (OCB), identified key challenges limiting our understanding of benthic systems, opportunities to act on these challenges, and pathways to increase the representation of these systems in global modeling and observational efforts. We propose a set of priorities to advance mechanistic understanding and better quantify the importance of the benthos: (a) implementing a model intercomparison exercise with existing benthic models to support future model development, (b) data synthesis to inform both model parameterizations and future observations, (c) increased deployment of platforms and technologies in support of in situ benthic monitoring (e.g., from benchtop to field mesocosm), and (d) global coordination of a benthic observing program (“GEOSed”) to fill large regional data gaps and evaluate the mechanistic understanding of benthic processes acquired throughout the previous steps. Addressing these priorities will help inform solutions to both global and regional resource management and climate adaptation strategies. 

Abstract The oxygen concentration in marine ecosystems is influenced by production and consumption in the water column and fluxes across both the atmosphere–water and benthic–water boundaries. Each of these fluxes has the potential to be significant in shallow ecosystems due to high fluxes and low water volumes. This study evaluated the contributions of these three fluxes to the oxygen budget in two contrasting ecosystems, aZostera marina(eelgrass) meadow in Virginia, U.S.A., and a coral reef in Bermuda. Benthic oxygen fluxes were evaluated by eddy covariance. Water column oxygen production and consumption were measured using an automated water incubation system. Atmosphere–water oxygen fluxes were estimated by parameterizations based on wind speed or turbulent kinetic energy dissipation rates. We observed significant contributions of both benthic fluxes and water column processes to the oxygen mass balance, despite the often‐assumed dominance of the benthic communities. Water column rates accounted for 45% and 58% of the total oxygen rate, and benthic fluxes accounted for 23% and 39% of the total oxygen rate in the shallow (~ 1.5 m) eelgrass meadow and deeper (~ 7.5 m) reef site, respectively. Atmosphere–water fluxes were a minor component at the deeper reef site (3%) but a major component at the shallow eelgrass meadow (32%), driven by diel changes in the sign and strength of atmosphere–water gradient. When summed, the measured benthic, atmosphere–water, and water column rates predicted, with 85–90% confidence, the observed time rate of change of oxygen in the water column and provided an accurate, high temporal resolution closure of the oxygen mass balance.