Abrupt pH changes overestimate the responses of Chaetoceros muelleri to ocean acidification

Ocean acidification, characterized by a gradual seawater pH decline, influences marine primary producers such as diatoms, which contribute substantially to oceanic carbon fixation. Experimental studies aiming to project climate change impacts often simulate acidification via abrupt pH shifts, potentially misrepresenting ecological and evolutionary responses. Here we conduct a long-term evolution experiment with the marine diatom Chaetoceros muelleri, comparing abrupt and gradual CO2 increases from 440 to 1000 ppm over 1100 generations. Integrating evolutionary genomics, physiological assays, elemental stoichiometry, and Earth System Modeling, we find that abrupt acidification exaggerates diatom growth and carbon fixation responses by up to 15%, driven by enhanced divergent genomic signals and persistent gene expression changes. Gradual acidification elicits weaker phenotypic and genomic shifts, aligning more closely with natural ocean conditions. These findings suggest that models based on abrupt CO2 increases may overestimate the contribution of Chaetoceros muelleri and maybe also other diatoms to productivity and biogeochemical cycling under ocean acidification, highlighting the importance of gradual pH decline in experimental designs to accurately predict marine ecosystem responses. Ocean acidification influences diatom carbon fixation, yet most experiments use abrupt pH shifts. This study’s 1100-generation experiment finds that abrupt pH reduction overestimates Chaetoceros muelleri responses to ocean acidification at the physiological, transcriptomic, and genomic levels.