Nonphotochemical fluorescence quenching was found to exist in the dark-adapted state in the diatom Pbaeodactyhm tricornutum. Pretreatment of cells with the uncoupler carbonylcyanide mchlorophenylhydrazone (CCCP) or with nigericin resulted in increases in dark-adapted minimum and maximum fluorescence yields. This suggests that a pH gradient exists across the thylakoid membrane in the dark, which serves to quench fluorescence levels nonphotochemically. The physiological processes involved in establishing this proton gradient were sensitive to anaerobiosis and antimycin A. Based on these results, it is likely that this energization of the thylakoid membrane is due in part to chlororespiration, which involves oxygen-dependent electron flow through the plastoquinone pool. Chlororespiration has been shown previously to occur in diatoms. In addition, we observed that cells treated with 3-(3,4-dichlorophenyI)-l,l-dimethylurea exhibited very strong nonphotochemical quenching when illuminated with actinic light.The rate and extent of this quenching were light-intensity dependent. This quenching was reversed upon addition of CCCP or nigericin and was thus due primarily to the establishment of a pH gradient across the thylakoid membrane. Preincubation of cells with CCCP or nigericin or antimycin A completely abolished this quenching. Cyclic electron transport processes around photosystem I may be involved in establishing this proton gradient across the thylakoid membrane under conditions where linear electron transport is inhibited. At steady state under normal physiological conditions, the qualitative changes in photochemical and nonphotochemical fluorescence quenching at increasing photon flux densities were similar to those in higher plants. However, important quantitative differences existed at limiting and saturating intensities. Dissimilarities in the factors that regulate fluorescence quenching mechanisms in these organisms may account for these differences.One process that competes directly with photochemistry for deactivation of excited-state energy is fluorescence emission from Chl a molecules of the PSII antenna. Changes in the proportion of excited states utilized for photochemistry will result in changes in fluorescence intensity. In recent years, it has been shown that both photochemical and nonphotochemical processes reduce the yield of fluorescence during photosynthesis (Krause et al., 1982). However, our current knowledge of these processes is based primarily on studies with higher plants and green algae. The components involved in qP are present in the PSII reaction center, which has been found to be highly conserved throughout evolution (Thornber, 1986). It is therefore likely that the mechanism of photochemical quenching has also been conserved. In contrast, a diverse group of underlying processes controls qN, whose primary site of action is thought to be in the lightharvesting antennae. With the extensive diversity in the composition of light-harvesting complexes among the algae, it is likely that the m...