LAUSR

Nonphotochemical quenching (NPQ) is known to depress in vivo fluorescence (IVF) of chlorophyll a (Chla) in aquatic environments, which makes it difficult to interpret the hour‐to‐hour variations in Chla measured by in situ fluorometers. We hypothesized that ratios between quenched and unquenched IVF are a function of both NPQ and photochemical quenching. In this study, two diatom model species Thalassiosira pseudonana (CCMP1335) and Thalassiosira weissflogii (CCMP1047) incubated under a sinusoidal light:dark cycle were studied; IVF was recorded continuously, and Chla and photo‐physiological variables were measured seven times a day. The maximal decline in Chla‐specific IVF (IVFB) attributable to quenching was 50% under the experimental settings. An NPQ and photochemical quenching‐based modeling equation exhibited a better match to the measured IVFB than equations representing the sole NPQ effect. Photochemical quenching induced by measuring light beam varied substantially during the day, and the part of the model for this process is excitation intensity‐dependent (which is differed between models of in situ fluorometers, implying no straightforward method to correct Chla for all instrument models, instrument‐specific parameterization is required). The forms of the IVFB‐light relationship are discussed as well. The findings foster a holistic understanding of NPQ effects on in vivo Chla fluorometry.