LAUSR

Environmental partial pressure of CO2 (pCO2) variation can modify the responses of marine organisms to ocean acidification, yet the underlying mechanisms for this effect remain unclear. On coral reefs, environmental pCO2 fluctuates on a regular day–night cycle. Effects of future ocean acidification on coral reef fishes might therefore depend on their response to this diel cycle of pCO2. To evaluate the effects on the brain molecular response, we exposed two common reef fishes (Acanthochromis polyacanthus and Amphiprion percula) to two projected future pCO2 levels (750 and 1,000 µatm) under both stable and diel fluctuating conditions. We found a common signature to stable elevated pCO2 for both species, which included the downregulation of immediate early genes, indicating lower brain activity. The transcriptional programme was more strongly affected by higher average pCO2 in a stable treatment than for fluctuating treatments, but the largest difference in molecular response was between stable and fluctuating pCO2 treatments. This indicates that a response to a change in environmental pCO2 conditions is different for organisms living in a fluctuating than in stable environments. This differential regulation was related to steroid hormones and circadian rhythm (CR). Both species exhibited a marked difference in the expression of CR genes among pCO2 treatments, possibly accommodating a more flexible adaptive approach in the response to environmental changes. Our results suggest that environmental pCO2 fluctuations might enable reef fishes to phase‐shift their clocks and anticipate pCO2 changes, thereby avoiding impairments and more successfully adjust to ocean acidification conditions.