Phytoplankton communities in upwelling regions experience a wide range of light and nutrient conditions as a result of upwelling cycles. These cycles can begin with a bloom at the surface followed by cells sinking to depth when nutrients are depleted. Cells can then be transported back to the surface with upwelled waters to seed another bloom. In spite of the physicochemical extremes associated with these cycles, diatoms consistently outcompete other phytoplankton when upwelling events occur. Here we simulated the conditions of a complete upwelling cycle with a common diatom, Chaetoceros decipiens, and coccolithophore, Emiliania huxleyi. We show that while both organisms exhibited physiological and transcriptomic plasticity, the diatom displayed a distinct response enabling it to rapidly shiftup growth and nitrate assimilation when returned to light and nutrients. As observed in natural diatom communities, C. decipiens frontloads key transcriptional and nitrate assimilation genes coordinating its rapid response. Low iron simulations showed that C. decipiens is capable of maintaining this response when iron is limiting whereas E. huxleyi could not. Differential expression between iron treatments further revealed molecular mechanisms used by each organism under low iron availability. Overall, these results highlight the responses of two dominant phytoplankton groups to upwelling cycles, providing insight into the mechanisms fueling diatom success during upwelling events in current and future oceans. Correspondence: amarchetti@unc.edu Lampe et al. | bioRχiv | May 1, 2020 | 1-11 Low Light, High Nutrients (T2, T3) High Light, High Nutrients (Shift-up; T4) High Light, Low Nutrients (Shift-Down; T6) Sinking Balanced Growth (T1, T5)