Revisiting the Ocean's Metabolic Balance: Correcting Biases in Bottle Incubations Reveals a More Autotrophic and Dynamic Ocean

Abstract

The ocean's metabolic state—reflecting the balance between organic carbon production and consumption—is fundamental to understanding carbon sequestration potential. Yet, whether the ocean is net autotrophic or heterotrophic remains actively debated. Classic light-dark bottle incubations often suggest net heterotrophy, whereas geochemical tracer-based assessments indicate widespread autotrophy. Here, we show that bottle incubations systematically overestimate heterotrophy by artificially exacerbating bacterial activity, especially in oligotrophic waters. Applying a correction to global incubation data reduces the fraction of areas exhibiting net heterotrophy from 66% to 12% and shifts the euphotic zone carbon budget from a deficit of −9 ± 2.4 Pg C yr⁻¹ to a surplus of +12 ± 3.5 Pg C yr⁻¹. Moreover, our revisited estimate reveals that oligotrophic gyres are seasonally dynamic, oscillating between net autotrophy and heterotrophy, yet remain net autotrophic on an annual scale. These results help partly reconcile the long-standing methodological discrepancy in ocean metabolic balance and highlight the need to reassess biologically mediated carbon flux estimates in other aquatic systems broadly reliant on incubation-based measurements.