Global cooling with the onset of Antarctic glaciation ca. 34 Ma across the Eocene–Oligocene transition (EOT) terminated the early Cenozoic greenhouse climate state and marked the beginning of icehouse conditions. Although a pCO2 decline is considered to have been a major cause of this climate shift, the associated carbon-sequestration mechanism remains unclear. Here, we assessed ocean production and circulation changes across the EOT using numerical simulations combined with a novel proxy, namely, bacterial magnetofossils, the abundance and morphology of which are sensitive to sedimentary organic matter accumulation and oxygenation. We detected production and oxygenation declines in the equatorial Pacific Ocean coeval with increased biological production in the Southern Ocean after the EOT. Corroborated by simulation results and evidence from the Subantarctic region, we interpret this counterintuitive combination as a result of enhanced bottom-water formation and biological pump efficiency in the Southern Ocean due to Antarctic glacial buildup across the EOT. These results provide key evidence for deep Pacific Ocean deoxygenation and increased respired carbon concentrations, which amplified CO2 decline across the EOT.

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