The effective absorption cross section for photochemistry of Photosystem II in the light (σ PSII ′ ) comprises the probability of light capture by Photosystem II and the quantum yield for subsequent photochemistry. σ PSII ′ is used to model photosynthesis and aquatic productivity, and phytoplankters regulate σ PSII ′ to mitigate over-or under-excitation of Photosystem II. We used diverse phytoplankton taxa to compare short and long term changes in σ PSII ′ with the induction of the yield of non-photochemical quenching (YNPQ) of chlorophyll fluorescence, a measure of regulated excitation dissipation. In two picocyanobacteria σ PSII ′ showed no decline upon induction of moderate YNPQ, above light levels sufficient for saturation of electron transport. In the eukaryotic chl a/b Ostreococcus and the chl a/c diatom Thalassiosira, induction of non-photochemical quenching was stronger after growth under saturating light, an acclimation attributable to increased xanthophyll cycle pigment content. Across short and longer-term light histories to induce or relax regulatory processes Ostreococcus and Thalassiosira showed proportional variations between the level of YNPQ and the down regulation of σ PSII ′ . The proportional down regulation of σ PSII ′ was, however, significantly smaller than the amplitude of YNPQ induction. For the eukaryotes we can predict changes in σ PSII ′ , useful for modeling electron transport, productivity and acclimation, from measures of YNPQ, which are accessible from fluorescence yield measures that do not include σ PSII ′ . This useful relation, however, does not extend to the tested prokaryotes, possibly as a result of differential violations of the rate constant assumptions that underlie the calculated YNPQ parameter.

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