Rapid vs. gradual changes in light significantly modulate diel photo‐acclimation strategy and can lead to changes in comparative physiology in the green algae <scp> <i>Micromonas commoda</i> </scp>

Abstract Variable chlorophyll a (Chl a ) fluorescence, a standard tool for assessing phytoplankton physiology, offers a wealth of information on photosynthetic performance and primary productivity through noninvasive means. However, a better understanding of diurnal patterns in photosynthesis is critically important as advanced fluorescence techniques are increasingly used to monitor coastal and oceanic primary productivity rates in situ. In this study, we coupled a custom‐made, Fast Repetition Rate Chl a fluorometer to an algal culture system (photobioreactor) to monitor the photosynthetic response of two strains of the green alga, Micromonas commoda , under highly regulated light and CO 2 conditions. When comparing diel profiles, our results reveal notable differences in the quantum yield of PSII and reoxidation kinetics across light patterns despite exposure to the same integrated photon dose per day. Specifically, CCMP2709 experienced a larger reduction in the quantum yield of PSII during the dark period, likely reflecting elevated chlororespiratory activity. This suggests that diel light patterns with rapid shifts in irradiance can bias phytoplankton toward the use of alternative electron pathways; such shifts can alter energetic budgets thereby leading to physiological changes. Our results also indicate a light‐profile dependent response to elevated CO 2 conditions, as reductions in cell size, relative Chl a fluorescence per cell, and side scatter are observed under the gradual, but not rapid changes in light intensity. These findings emphasize the utility of high‐resolution tools for monitoring photosynthetic performance in algal research, and the need to account for diel light patterns when comparing physiology among species and/or experimental conditions.