Today, the key role played by the ocean in Earth’s carbon cycle is widely accepted. The important interface to consider is not the one between ocean and atmosphere, across which the CO2 concentration gradient is small, but rather the seasonal and permanent thermoclines at ~ 20–300-m depth. Though both physical and biological pumps act to increase the amount of carbon stored in the deep sea, this workshop focused on the biological pump. More than 90% of the organic carbon annually exported from surface waters (~ 10 GTC/yr, as compiled in Boyd and Trull, 2007) is respired back to CO2 in mesopelagic waters (the region below the euphotic zone extending to about 1000 m, also known as the “twilight zone”). This respiration limits the penetration of carbon to the deeper ocean and sediments, and thus limits the extent of carbon sequestration from the atmosphere. The mechanisms controlling both the magnitude of carbon export and its fate in the twilight zone are not yet well enough understood to assess the impact of ongoing climate and ocean circulation changes on this carbon sequestration.