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The Southern Ocean regulates the ocean's biological sequestration of CO2 and is widely suspected to underpin much of the ice age decline in atmospheric CO2 concentration, but the specific changes in the region are debated. Although more complete drawdown of surface nutrients by phytoplankton during the ice ages is supported by some sediment core-based measurements, the use of different proxies in different regions has precluded a unified view of Southern Ocean biogeochemical change. Here, we report measurements of the N-15/N-14 of fossil-bound organic matter in the stony deep-sea coral Desmophyllum dianthus, a tool for reconstructing surface ocean nutrient conditions. The central robust observation is of higher N-15/N-14 across the Southern Ocean during the Last Glacial Maximum (LGM), 18-25 thousand years ago. These data suggest a reduced summer surface nitrate concentration in both the Antarctic and Subantarctic Zones during the LGM, with little surface nitrate transport between them. After the ice age, the increase in Antarctic surface nitrate occurred through the deglaciation and continued in the Holocene. The rise in Subantarctic surface nitrate appears to have had both early deglacial and late deglacial/Holocene components, preliminarily attributed to the end of Subantarctic iron fertilization and increasing nitrate input from the surface Antarctic Zone, respectively.