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This dataset is referring to 2-year time series of particle flux, as measured by two deep moored sediment traps (P2, P3) located in the Southern Ocean (northern Scotia Sea sector), a globally important region of atmospheric CO2 drawdown containing both naturally iron-fertilised (P3) and iron-limited (P2) regimes. The dataset includes the main biogeochemical flux parameters (such as Bsi, POC and PIC) as well as the specific contribution of each part of the plankton calcifying community (pteropods, foraminifera, coccolithphores and ostracods) to the PIC within a period from April 2009 to February 2011. The dataset allows the estimation of the Carbonate Counter Pump (CCP), which causes an increase in surface ocean CO2 through the calcification and precipitation of carbonate.