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Variable fluorescence methods are becoming popular in studies related to aquatic photosynthesis. In natural ocean water, phytoplankton co-exist with their zooplankton and flagellate predators, viral parasites and the waste products of digested phytoplankton cells that contain phaeophytin (a chromophore produced by digestion of chlorophyll a). Fast repetition rate fluorometry, a technique mainly applied in phytoplankton studies, was used to evaluate and quantify the effect of phaeophytin abundance in sea water on variable fluorescence parameters: the photochemical quantum yield, Φ F (also known as F v /F m ), and the functional cross-section of photosystem 2 (PS2), σ PS2 . If the value of Φ F determined is lower than that it actually is, phytoplankton may be labeled as less healthy (or productive) than their true condition. Results were compared with data collected using another widely used variable fluorescence technique: pulse amplitude modulation (PAM). Our study concludes that for significantly elevated levels of phaeophytin in the water, the measured values of Φ F should be corrected to avoid misinterpretation. This conclusion is independent of the measuring instrument. In waters with phaeophytin levels that constitute less than ∼30% of the total measured pigment, no correction is required (<5% change in Φ F is expected). However, as phaeophytin levels rise, the effect on Φ F increases and becomes more significant (e.g. Φ F appears 25% lower when the phaeophytin to total pigment ratio is ∼70%). High concentrations of phaeophytin are not often reported in the open ocean. However, in highly productive coastal waters, high levels of phaeophytin can be encountered. The functional cross-section (σ PS2 ) measurements are not affected by the presence of phaeophytin in the water.

The effect of elevated levels of phaeophytin in natural water on variable fluorescence measured from phytoplankton