Diatoms with their fast growth rates and obligate requirement for Si have a unique relationship to the oceanic Si cycle with the potential for controlling the nutrient and CO2 environment of large important areas of the ocean. The new production of diatoms based on both new nitrogen and Si sources is described using a Si-pump based upon the differential regeneration of the two elements. This approach, applied to the eastern equatorial Pacific, showed diatoms to respond as in a Si-limited chemostat, to the low source Si(OH)4 in the Equatorial UnderCurrent. Increased Si(OH)4 results in increased diatom productivity, suppression of non-diatom populations and decreased surface pCO2. The deficiency in source concentrations of Si(OH)4 results from low Si(OH)4:NO3 water originating in the vicinity of the Antarctic Polar Front, a consequence of the extraordinary trapping of Si by the Southern Ocean. In glacial periods this trapping is reduced several fold and likely results in increased Si(OH)4 export to the north, and increased Si(OH)4 production and deposition at the equatorial Pacific which can be expected to reduce surface pCO2. The connections between the eastern equatorial Pacific export production and Southern Ocean Si trapping may provide a major biogeochemical feedback system with implications for contemporary and paleoclimatology.