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a synthesis of previously unpublished and published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