SignificanceSilica-shelled diatoms dominate marine phytoplankton blooms and play a key role in ocean ecology and the global carbon cycle. We show how differences in ecological traits of dominant Southern Ocean diatom species, observed during the in situ European Iron Fertilization Experiment (EIFEX), can influence ocean carbon and silicon cycles. We argue that the ecology of thick-shelled diatom species, selected for by heavy copepod grazing, sequesters silicon relative to other nutrients in the deep Southern Ocean and underlying sediments to the detriment of diatom growth elsewhere. This evolutionary arms race provides a framework to link ecology with biogeochemistry of the ocean.