Cyanobacteria Sustain Deep Ocean Carbon Sequestration Despite Eukaryotic Loss

The biological carbon pump exports phytoplankton-derived organic carbon to the deep ocean, regulating long-term carbon sequestration and climate. Yet how phytoplankton community composition controls the magnitude and efficiency of this process remains poorly understood. Using time-series sediment trap samples, we analyze compound-specific stable carbon isotopes of amino acids to trace taxon-specific sinking particulate organic carbon (POC), revealing stark contrasts in sequestration efficiency between cyanobacteria and eukaryotic microalgae. Despite pronounced seasonal variations in surface productivity and community structure, bulk POC sequestration efficiency remains statistically invariant. Mesopelagic sinking POC is persistently cyanobacteria-rich (67% ± 2%), even during high-productivity periods when surface dominant community shifts from cyanobacteria to eukaryotes. This decoupling arises because eukaryotic sequestration efficiency halves, while cyanobacterial efficiency nearly doubles. Elevated eukaryote-derived carbon, though produced by large ballasted algae, undergoes greater attenuation in the twilight zone, reflecting enhanced microbial remineralization. In contrast, small non-ballasted cyanobacteria benefit from aggregation–ballasting effects, thereby compensating for eukaryotic loss and stabilizing overall sequestration efficiency. Our findings challenge prevailing assumptions that overestimate eukaryotic contributions and highlight the pivotal, climate-sensitive role of cyanobacteria in marine carbon storage, underscoring the need for taxon-specific parameterization in modeling the ocean carbon sequestration capacity under global warming.