Introduction of active chlorophyll a fluorescence protocols, in particular fast repetition rate (FRR) fluorometry, to oceanography and limnology 15 yr ago has enabled rapid assessment of photosynthetic physiology in situ. The FRR protocol generates simultaneous measurements of Photosystem II (PSII) effective absorption cross sections (termed sigma(PSII),l) and photochemical efficiency (termed F-v/F-m). Both F-v/F-m and sigma(PSII) measurements have been utilised to examine the effects of physiological stress on the photosynthetic apparatus of phytoplankton in an ever growing number of fluorescence-based studies. However, it is now becoming clearer that in situ values of F-v/F-m, and sigma(PSII) also contain taxonomic information. Here, we present a synthesis of previously unpublished and published data, which show that F-v/F-m and sigma(PSII) vary principally with broad-scale changes in community structure. These patterns observed in situ conform to trends observed in la boratory-grown cultures of a range of phytoplankton taxa. The magnitudes of variability in Fv/F-m and sigma(PSII) driven by changes in phytoplankton community structure often exceed that induced by nutrient limitation (as determined from controlled nutrient addition experiments). An exception to this general trend occurs in high-nutrient, low-chlorophyll a (HNLC) regions, where strong phenotypic changes in F-v/F-m and sigma(PSII) have been repeatedly demonstrated on relief of iron limitation. Overall, FRR fluorescence measurements of both F-v/F-m, and sigma(PSII) in natural populations represent a combination of the taxonomic 'signature' (values of F-v/F-m and sigma(PSII) determined by the taxa present) within the phytoplankton community that is further modified according to the (photo-) physiological status. As such, fluorescence-based investigations of mixed populations must account for potential variations in phytoplankton community structure before interpretations of physiological status are made
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