Photosynthesis Research 79: 209–218, 2004. © 2004 Kluwer Academic Publishers. Printed in the Netherlands. 209 Short communication New fluorescence parameters for the determination of Q A redox state and excitation energy fluxes David M. Kramer 1,∗ , Giles Johnson 2 , Olavi Kiirats 3 & Gerald E. Edwards 3 1 Institute of Biological Chemistry, Washington State University, 289 Clark Hall, Pullman, WA 99163-6340,USA; 2 School of Biological Sciences, University of Manchester, Manchester, UK; 3 School of Biological Sciences, Washington State University, 289 Clark Hall, Pullman, WA 99164-6340, USA; ∗ Author for correspondence (e-mail: dkramer@wsu.edu; fax: +1-509-335-7643) Received 30 July 2003; accepted in revised form 3 November 2003 Key words: antenna, chlorophyll a fluorescence, electron transport, fluorimeter, photosynthetic unit, quantum yield Abstract A number of useful photosynthetic parameters are commonly derived from saturation pulse-induced fluorescence analysis. We show, that q P , an estimate of the fraction of open centers, is based on a pure ‘puddle’ antenna model, where each Photosystem (PS) II center possesses its own independent antenna system. This parameter is incompatible with more realistic models of the photosynthetic unit, where reaction centers are connected by shared antenna, that is, the so-called ‘lake’ or ‘connected units’ models. We thus introduce a new parameter, q L , based on a Stern–Volmer approach using a lake model, which estimates the fraction of open PS II centers. We suggest that q L should be a useful parameter for terrestrial plants consistent with a high connectivity of PS II units, whereas some marine species with distinct antenna architecture, may require the use of more complex parameters based on intermediate models of the photosynthetic unit. Another useful parameter calculated from fluorescence analysis is φ II , the yield of PS II. In contrast to q L , we show that the φ II parameter can be derived from either a pure ‘lake’ or pure ‘puddle’ model, and is thus likely to be a robust parameter. The energy absorbed by PS II is divided between the fraction used in photochemistry, φ II , and that lost non-photochemically. We introduce two additional parameters that can be used to estimate the flux of excitation energy into competing non-photochemical pathways, the yield induced by downregulatory processes, φ NPQ , and the yield for other energy losses, φ NO . Abbreviations: φ II – the quantum efficiency of Photosystem II estimated by fluorescence yield measurements based on a lake model for the PSU; φ IIi – the intrinsic yield of open PS II centers in a puddle model; fQ Aox – fraction of Q A in its oxidized state, also implying the fraction of PS II centers in open states; NPQ – light induced photoprotection through thermal dissipation of energy; PS – photosystem; PSU – photosynthetic unit; q – a generic term for the fraction of open PS II centers; q cu – a parameter estimating the fraction of PS II centers in open states based on a connected units model for the PSU; q L – a parameter estimating the fraction of PS II centers in open states based on a lake model for the PSU; q P – a parameter estimating the fraction of PS II centers in open states based on a puddle model for the PSU Introduction Steady-state chlorophyll a fluorescence yield has been a convenient and powerful tool for the study of higher plant photosynthesis. The vast majority of chlorophyll fluorescence studies focus on PS II and its related antenna. Events related to PS I photochemistry and its antenna are obscured by the fact that ‘closed’ PS I centers quench excitation energy as well as open centers, owing to the fact that P + 700 is as good a pho- tochemical trap as P 700 . The steady-state chlorophyll fluorescence has been described as a ‘rich’ signal