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Frequently asked questions about chlorophyll fluorescence, the sequel

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Frequently asked questions about chlorophyll fluorescence, the sequel

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Kalaji, H.; Schansker, G.; Brestic, M.; Bussotti, F.; Calatayud, A.; Ferroni, L.; Goltsev, V.... (2017). Frequently asked questions about chlorophyll fluorescence, the sequel. Photosynthesis Research. 132(1):13-66. https://doi.org/10.1007/s11120-016-0318-y

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Title: Frequently asked questions about chlorophyll fluorescence, the sequel
Author: Kalaji, Hazem Schansker, Gert Brestic, M. Bussotti, Filippo Calatayud, Angeles Ferroni, Lorenzo Goltsev, V. Guidi, Lucia Jajoo, Anjana Li, P.M. Losciale, P. Mishra, V. Misra, Amarendra Nebauer, Sergio G. Pancaldi, S. Penella-Casañ, Consuelo Pollastrini, M. Suresh, K. Tambussi, E. Yanniccari, M. Zivcak, M. Cetner, M. Zamborska, I.A. Stirbet, A. Olsovska, K. Kunderlikova, K. Shelonzek, H. Rusinowski, S. Baba, W.
UPV Unit: Universitat Politècnica de València. Departamento de Producción Vegetal - Departament de Producció Vegetal
Issued date:
Abstract:
[EN] Using chlorophyll (Chl) a fluorescence many aspects of the photosynthetic apparatus can be studied, both in vitro and, noninvasively, in vivo. Complementary techniques can help to interpret changes in the Chl a ...[+]
Subjects: Chl a fluorescence , Delayed fluorescence , Photochemical quenching , Energy partitioning , Area
Copyrigths: Reconocimiento (by)
Source:
Photosynthesis Research. (issn: 0166-8595 )
DOI: 10.1007/s11120-016-0318-y
Publisher:
Springer-Verlag
Publisher version: https://doi.org/10.1007/s11120-016-0318-y
Type: Artículo

References

Adams WW III, Demmig-Adams B (1992) Operation of the xanthophyll cycle in higher plants in response to diurnal changes in incident sunlight. Plant 186:390–398

Adams WW III, Demmig-Adams B (2004) Chlorophyll fluorescence as a tool to monitor plant response to the environment. In: Papageorgiou GC, Govindjee (eds) Advances in photosynthesis and respiration series chlorophyll fluorescence: a signature of photosynthesis, vol 19. Springer, Dordrecht, pp 583–604

Adams WW III, Demmig-Adams B, Winter K, Schreiber U (1990a) The ratio of variable to maximum chlorophyll fluorescence from photosystem II, measured in leaves at ambient temperature and at 77 K, as an indicator of the photon yield of photosynthesis. Planta 180:166–174 [+]
Adams WW III, Demmig-Adams B (1992) Operation of the xanthophyll cycle in higher plants in response to diurnal changes in incident sunlight. Plant 186:390–398

Adams WW III, Demmig-Adams B (2004) Chlorophyll fluorescence as a tool to monitor plant response to the environment. In: Papageorgiou GC, Govindjee (eds) Advances in photosynthesis and respiration series chlorophyll fluorescence: a signature of photosynthesis, vol 19. Springer, Dordrecht, pp 583–604

Adams WW III, Demmig-Adams B, Winter K, Schreiber U (1990a) The ratio of variable to maximum chlorophyll fluorescence from photosystem II, measured in leaves at ambient temperature and at 77 K, as an indicator of the photon yield of photosynthesis. Planta 180:166–174

Adams WW III, Winter K, Schreiber U, Schramel P (1990b) Photosynthesis and chlorophyll fluorescence characteristics in relationship to changes in pigment and element composition of leaves of Platanus occidentalis L. during autumnal senescence. Plant Physiol 93:1184–1190

Alfonso M, Montoya G, Cases R, Rodriguez R, Picorel R (1994) Core antenna complexes, CP43 and CP47, of higher plant photosystem II. Spectral properties, pigment stoichiometry, and amino acid composition. Biochemistry 33:10494–10500

Allakhverdiev SI (2011) Recent progress in the studies of structure and function of photosystem II. J Photochem Photobiol B Biol 104:1–8

Allakhverdiev SI, Klimov VV, Carpentier R (1994) Variable thermal emission and chlorophyll fluorescence in photosystem II particles. Proc Natl Acad Sci USA 491:281–285

Allakhverdiev SI, Los DA, Mohanty P, Nishiyama Y, Murata N (2007) Glycinebetaine alleviates the inhibitory effect of moderate heat stress on the repair of photosystem II during photoinhibition. Biochim Biophys Acta 1767:1363–1371

Allen JF (1992) Protein phosphorylation in regulation of photosynthesis. Biochim Biophys Acta 1098:275–335

Allen JF, Bennett J, Steinback KE, Arntzen CJ (1981) Chloroplast protein phosphorylation couples platoquinone redox state to distribution of excitation energy between photosystems. Nature 291:21–25

Amesz J, van Gorkom HJ (1978) Delayed fluorescence in photosynthesis. Annu Rev Plant Physiol 29:47–66

Ananyev GM, Dismukes GC (1996) Assembly of the tetra-Mn site of photosynthetic water oxidation by photoactivation: Mn stoichiometry and detection of a new intermediate. Biochemistry 35:4102–4109

Anderson JM, Chow WS, Goodchild DJ (1988) Thylakoid membrane organization in sun/shade acclimation. Aust J Plant Physiol 15:11–26

Andrizhiyevskaya EG, Chojnicka A, Bautista JA, Diner BA, van Grondelle R, Dekker JP (2005) Origin of the F685 and F695 fluorescence in photosystem II. Photosynth Res 84:173–180

Anithakumari AM, Nataraja KN, Visser RGF, van der Linden G (2012) Genetic dissection of drought tolerance and recovery potential by quantitative trait locus mapping of a diploid potato population. Mol Breed 30:1413–1429

Antal TK, Krendeleva TE, Rubin AB (2007) Study of photosystem 2 heterogeneity in the sulfur-deficient green alga Chlamydomonas reinhardtii. Photosynth Res 94:13–22

Antal TK, Matorin DN, Ilyash LV, Volgusheva AA, Osipov A, Konyuhow IV, Krendeleva TE, Rubin AB (2009) Probing of photosynthetic reactions in four phytoplanktonic algae with a PEA fluorometer. Photosynth Res 102:67–76

Araus JL, Amaro T, Voltas J, Nakkoul H, Nachit MM (1998) Chlorophyll fluorescence as a selection criterion for grain yield in durum wheat under Mediterranean conditions. Field Crops Res 55:209–223

Argyroudi-Akoyunoglou J (1984) The 77 K fluorescence spectrum of the Photosystem I pigment-protein complex CPIa. FEBS Lett 171:47–53

Arnold WA (1991) Experiments. Photosynth Res 27:73–82

Arnold WA, Thompson J (1956) Delayed light production by blue-green algae, red algae and purple bacteria. J Gen Physiol 39:311–318

Aro EM, Hundal T, Carlberg I, Andersson B (1990) In vitro studies on light-induced inhibition of PSII and D1-protein degradation at low temperatures. Biochim Biophys Acta 1019:269–275

Aro EM, Virgin I, Andersson B (1993) Photoinhibition of photosystem II. Inactivation protein damage and turnover. Biochim Biophys Acta 1143:113–134

Arsalane W, Parésys G, Duval JC, Wilhelm C, Conrad R, Büchel C (1993) A new fluorometric device to measure the in vivo chlorophyll a fluorescence yield in microalgae and its use as a herbicide monitor. Eur J Phycol 28:247–252

Asada K (1999) The water-water cycle in chloroplasts: scavenging of active oxygens and dissipation of excess photons. Annu Rev Plant Physiol Plant Mol Biol 50:601–639

Ashraf M, Harris PJC (2004) Potential biochemical indicators of salinity tolerance in plants. Plant Sci 166:3–16

Bailey S, Walters RG, Jansson S, Horton P (2001) Acclimation of Arabidopsis thaliana to the light environment: the existence of separate low light and high light responses. Planta 213:794–801

Baker NR (2008) Chlorophyll fluorescence: a probe of photosynthesis in vivo. Annu Rev Plant Biol 59:659–668

Baker NR, Rosenqvist E (2004) Applications of chlorophyll fluorescence can improve crop production strategies: an examination of future possibilities. J Exp Bot 55:1607–1621

Ballottari M, Dall’Osto L, Morosinotto T, Bassi R (2007) Contrasting behavior of higher plant photosystem I and II antenna systems during acclimation. J Biol Chem 282:8947–8958

Barbagallo RP, Oxborough K, Pallett KE, Baker NR (2003) Rapid, noninvasive screening for perturbations of metabolism and plant growth using chlorophyll fluorescence imaging. Plant Physiol 132:485–493

Barber J, Malkin S, Telfer A (1989) The origin of chlorophyll fluorescence in vivo and its quenching by the photosystem II reaction centre. Philos Trans R Soc Lond B 323:227–239

Barra M, Haumann M, Loja P, Krivanek R, Grundmeier A, Dau H (2006) Intermediates in assembly by photoactivation after thermally accelerated disassembly of the manganese complex of photosynthetic water oxidation. Biochemistry 45:14523–14532

Baumann HA, Morrison L, Stengel DB (2009) Metal accumulation and toxicity measured by PAM-chlorophyll fluorescence in seven species of marine macroalgae. Ecotoxicol Environ Safe 72:1063–1075

Bauwe H, Hagemann M, Fernie A (2010) Photorespiration: players, partners and origin. Trends Plant Sci 15:330–336

Beck WF, Brudvig GW (1987) Reactions of hydroxylamine with the electron-donor side of photosystem II. Biochemistry 26:8285–8295

Belgio E, Kapitonova E, Chmeliov J, Duffy CDP, Ungerer P, Valkunas L, Ruban AV (2014) Economic photoprotection in photosystem II that retains a complete light-harvesting system with slow energy traps. Nat Commun 5:4433. doi: 10.1038/ncomms5433

Bell DH, Hipkins MF (1985) Analysis of fluorescence induction curves from pea chloroplasts: photosystem II reaction centre heterogeneity. Biochim Biophys Acta 807:255–262

Bellafiore S, Barneche F, Peltier G, Rochaix J-D (2005) State transitions and light adaptation require chloroplast thylakoid protein kinase STN7. Nature 433:892–895

Belyaeva NE, Schmitt F-J, Paschenko VZ, Riznichenko GY, Rubin AB (2015) Modeling of the redox state dynamics in photosystem II of Chlorella pyrenoidosa Chick cells and leaves of spinach and Arabidopsis thaliana from single flash-induced fluorescence quantum yield changes on the 100 ns–10 s time scale. Photosynth Res 125:123–140

Bennett J (1977) Phosphorylation of chloroplast membrane polypeptides. Nature 269:344–346

Bennett J (1983) Regulation of photosynthesis by reversible phosphorylation of the light-harvesting chlorophyll a/b protein. Biochem J 212:1–13

Bennett J, Shaw EK, Michel H (1988) Cytochrome b6f complex is required for phosphorylation of light-harvesting chlorophyll a/b complex II in chloroplast photosynthetic membranes. Eur J Biochem 171:95–100

Bennoun P (2002) The present model for chlororespiration. Photosynth Res 73:273–277

Bennoun P, Li Y-S (1973) New results on the mode of action of 3,-(3,4-dichlorophenyl)-1,1-dimethylurea in spinach chloroplasts. Biochim Biophys Acta 292:162–168

Berden-Zrimec M, Drinovec L, Zrimec A (2011) Delayed fluorescence. In: Suggett DJ, Borowitzka M, Prášil O (eds) Chlorophyll a fluorescence in aquatic sciences: methods and applications, developments in applied phycology, vol 4. Springer, The Netherlands, pp 293–309

Berger S, Sinha AK, Roitsch T (2007) Plant physiology meets phytopathology: plant primary metabolism and plant-pathogen interactions. J Exp Bot 58:4019–4026

Bernacchi CJ, Leakey ADB, Heady LE, Morgan PB, Dohleman FG, McGrath JM, Gillespie GM, Wittig VE, Rogers A, Long SP, Ort DR (2006) Hourly and seasonal variation in photosynthesis and stomatal conductance of soybean grown at future CO2 and ozone concentrations for 3 years under fully open-air field conditions. Plant Cell Environ 29:2077–2090

Betterle N, Ballotari M, Zorzan S, de Bianchi S, Cazzaniga S, Dall’Osto L, Morosinotto T, Bassi R (2009) Light-induced dissociation of an antenna hetero-oligomer is needed for non-photochemical quenching induction. J Biol Chem 284:15255–15266

Bielczynski LW, Schansker G, Croce R (2016) Effect of light acclimation on the organization of photosystem II super and sub-complexes in Arabidopsis thaliana. Front Plant Sci. doi: 10.3389/fpls.2016.00105

Björkman O, Demmig-Adams B (1995) Regulation of photosynthetic light energy capture, conversion, and dissipation in leaves of higher plants. In: Schulze ED, Caldwell MM (eds) Ecophysiology of photosynthesis. Springer, Berlin, pp 17–47

Blubaugh DJ, Cheniae GM (1990) Kinetics of photoinhibition in hydroxylamine-extracted photosystem II membranes: relevance to photoactivation and site of electron donation. Biochemistry 29:5109–5118

Bock A, Krieger-Liszkay A, Ortiz de Zarate IB, Schönknecht G (2001) Cl—channel inhibitors of the arylaminobenzoate type act as photosystem II herbicides: a functional and structural study. Biochemistry 40:3273–3281

Bode S, Quentmeier CC, Liao P-N, Hafi N, Barros T, Wilk L, Bittner F, Walla PJ (2009) On the regulation of photosynthesis by excitonic interactions between carotenoids and chlorophylls. Proc Natl Acad Sci USA 106:12311–12316

Boekema EJ, Van Roon H, Van Breemen JFL, Dekker JP (1999) Supramolecular organization of photosystem II and its light-harvesting antenna in partially solubilized photosystem II membranes. Eur J Biochem 266:444–452

Bolhar-Nordenkampf HR, Long SP, Baker NR, Öquist G, Schreiber U, Lechner EG (1989) Chlorophyll fluorescence as a probe of the photosynthetic competence of leaves in the field: a review of current Instrumentation. Funct Ecol 3:497–514

Bonaventura C, Myers J (1969) Fluorescence and oxygen evolution from Chlorella pyrenoidosa. Biochim Biophys Acta 189:366–383

Bonfig KB, Schreiber U, Gabler A, Roitsch T, Berger S (2006) Infection with virulent and avirulent P. syringae strains differentially affects photosynthesis and sink metabolism in Arabidopsis leaves. Planta 225:1–12

Bouges-Bocquet B (1980) Kinetic models for the electron donors of photosystem II of photosynthesis. Biochim Biophys Acta 594:85–103

Bradbury M, Baker NR (1981) Analysis of the slow phases of the in vivo chlorophyll fluorescence induction curve; changes in the redox state of photosystem II electron acceptors and fluorescence emission from photosystem I and II. Biochim Biophys Acta 635:542–551

Brestič M, Živčák M (2013) PSII fluorescence techniques for measurement of drought and high temperature stress signal in crop plants: protocols and applications. In: Das AB, Rout GR (eds) Molecular stress physiology of plants. Springer, New Dehli, pp 87–131

Brestič M, Cornic G, Fryer MJ, Baker NR (1995) Does photorespiration protect the photosynthetic apparatus in French bean leaves from photoinhibition during drought stress? Planta 196:450–457

Brestič M, Živčák M, Kalaji HM, Allakhverdiev SI, Carpentier R (2012) Photosystem II thermo-stability in situ: environmentally induced acclimation and genotype-specific reactions in Triticum aestivum L. Plant Physiol Biochem 57:93–105

Brody SS, Rabinowitch E (1957) Excitation lifetime of photosynthetic pigments in vitro and in vivo. Science 125:555–563

Brudvig GW, Casey JL, Sauer K (1983) The effect of temperature on the formation and decay of the multiline EPR signal species associated with photosynthetic oxygen evolution. Biochim Biophys Acta 723:366–371

Bukhov NG, Boucher N, Carpentier R (1997) The correlation between the induction kinetics of the photoacoustic signal and chlorophyll fluorescence in barley leaves is governed by changes in the redox state of the photosystem II acceptor side; a study under atmospheric and high CO2 concentrations. Can J Bot 75:1399–1406

Bukhov N, Egorova E, Krendeleva T, Rubin A, Wiese C, Heber U (2001) Relaxation of variable chlorophyll fluorescence after illumination of dark-adapted barley leaves as influenced by the redox states of electron carriers. Photosynth Res 70:155–166

Buschmann C, Koscányi L (1989) Light-induced heat production correlated with chlorophyll fluorescence and its quenching. Photosynth Res 21:129–136

Bussotti F (2004) Assessment of stress conditions in Quercus ilex L. leaves by O-J-I-P chlorophyll a fluorescence analysis. Plant Biosystems 13:101–109

Bussotti F, Agati G, Desotgiu R, Matteini P, Tani C (2005) Ozone foliar symptoms in woody plants assessed with ultrastructural and fluorescence analysis. New Phytol 166:941–955

Bussotti F, Desotgiu R, Cascio C, Pollastrini M, Gravano E, Gerosa G, Marzuoli R, Nali C, Lorenzini G, Salvatori E, Manes F, Schaub M, Strasser RJ (2011a) Ozone stress in woody plants assessed with chlorophyll a fluorescence. A critical reassessment of existing data. Environ Exp Bot 73:19–30

Bussotti F, Pollastrini M, Cascio C, Desotgiu R, Gerosa G, Marzuoli R, Nali C, Lorenzini G, Pellegrini E, Carucci MG, Salvatori E, Fusaro L, Piccotto M, Malaspina P, Manfredi A, Roccotello E, Toscano S, Gottardini E, Cristofori A, Fini A, Weber D, Baldassarre V, Barbanti L, Monti A, Strasser RJ (2011b) Conclusive remarks. Reliability and comparability of chlorophyll fluorescence data from several field teams. Environ Exp Bot 73:116–119

Butler WL (1978) Energy distribution in the photochemical apparatus of photosynthesis. Annu Rev Plant Physiol 29:345–378

Byrdin M, Rimke I, Schlodder E, Stehlik D, Roelofs TA (2000) Decay kinetics and quantum yields of fluorescence in photosystem I from Synechococcus elongatus with P700 in the reduced and oxidized state: Are the kinetics of excited state decay trap-limited or transfer-limited? Biophys J 79:992–1007

Caffarri S, Croce R, Cattivelli L, Bassi R (2004) A look within LHCII: differential analysis of the Lhcb1-3 complexes building the major trimeric antenna complex of higher-plant photosynthesis. Biochemistry 43:9467–9476

Calatayud A, Ramirez JW, Iglesias DJ, Barreno E (2002) Effects of ozone on photosynthetic CO2 exchange, chlorophyll a fluorescence and antioxidant systems in lettuce leaves. Physiol Plant 116:308–316

Cascio C, Schaub M, Novak K, Desotgiu R, Bussotti F, Strasser RJ (2010) Foliar responses to ozone of Fagus sylvatica L. seedlings grown in shaded and in full sunlight conditions. Environ Exp Bot 68:188–197

Cazzaniga S, Dall’Osto L, Kong S-G, Wada M, Bassi R (2013) Interaction between avoidance of photon absorption, excess energy dissipation and zeaxanthin synthesis against photooxidative stress in Arabidopsis. Plant J 76:568–579

Ceppi MG, Oukarroum A, Çiçek N, Strasser RJ, Schansker G (2012) The IP amplitude of the fluorescence rise OJIP is sensitive to changes in the photosystem I content of leaves: a study on plants exposed to magnesium and sulfate deficiencies, drought stress and salt stress. Physiol Plant 144:277–288

Chaudhary N, Singh S, Agrawal SB, Agrawal M (2013) Assessment of six Indian cultivars of mung bean against ozone by using foliar injury index and changes in carbon assimilation, gas exchange, chlorophyll fluorescence and photosynthetic pigments. Environ Monit Assess 185:7793–7807

Chen J, Kell A, Acharya K, Kupitz C, Fromme P, Jankowiak R (2015) Critical assessment of the emission spectra of various photosystem II core complexes. Photosynth Res 124:253–265

Cheng L, Fuchigami LH, Breen PJ (2000) Light absorption and partitioning in relation to nitrogen content ‘Fuji’ apple leaves. J Am Soc Hortic Sci 125:581–587

Choi CJ, Berges JA, Young EB (2012) Rapid effects of diverse toxic water pollutants on chlorophyll a fluorescence: variable responses among freshwater microalgae. Water Res 46:2615–2626

Chow WS, Aro EM (2005) Photoinactivation and mechanisms of recovery. In: Wydrzynski T, Satoh K (eds) Photosystem II: the light-driven water: plastoquinone oxidoreductase, advances in photosynthesis and respiration, vol 22. Springer, Dordrecht, pp 627–648

Chow WS, Fan DY, Oguchi R, Jia H, Losciale P, Youn-Il P, He J, Öquist G, Shen YG, Anderson JM (2012) Quantifying and monitoring functional photosystem II and the stoichiometry of the two photosystems in leaf segments: approaches and approximations. Photosynth Res 113:63–74

Christensen MG, Teicher HB, Streibig JC (2003) Linking fluorescence induction curve and biomass in herbicide screening. Pest Manag Sci 59:1303–1310

Codrea CM, Aittokallio T, Keränen M, Tyystjärvi E, Nevalainen OS (2003) Feature learning with a genetic algorithm for fluorescence fingerprinting of plant species. Pattern Recognit Lett 24:2663–2673

Conjeaud H, Mathis P (1980) The effect of pH on the reduction kinetics of P-680 in tris-treated chloroplasts. Biochim Biophys Acta 590:353–359

Conrad R, Büchel C, Wilhelm C, Arsalane W, Berkaloff C, Duval JC (1993) Changes in yield of in-vivo fluorescence of chlorophyll a as a tool for selective herbicide monitoring. J Appl Phycol 5:505–516

Cornic G, Massacci A (1996) Leaf photosynthesis under drought stress. In: Baker NR (ed) Photosynthesis and the environment. Kluwer Academic Publisher, Dordrecht, pp 347–366

Cornic G, Fresneau C (2002) Photosynthetic carbon reduction and carbon oxidation cycles are the main electron sinks for photosystems II during a mild drought. Ann Bot 89:887–894

Correia MJ, Chaves MMC, Pereira JS (1990) Afternoon depression in photosynthesis in grapevine leaves—evidence for a high light stress effect. J Exp Bot 41:417–426

Cotrozzi L, Remorini D, Pellegrini E, Landi M, Massai R, Nali C, Guidi L, Lorenzini G (2016) Variations in physiological and biochemical traits of oak seedlings grown under drought and ozone stress. Physiol Plant 157:69–84

Croce R, Zucchelli G, Garlaschi FM, Bassi R, Jennings RC (1997) Excited state equilibration in the photosystem I-light-harvesting I complex: P700 is almost isoenergetic with its antenna. Biochemistry 35:8572–8579

Cser K, Vass I (2007) Radiative and non-radiative charge recombination pathways in photosystem II studied by thermoluminescence and chlorophyll fluorescence in the cyanobacterium Synechocystis 6308. Biochim Biophys Acta 1767:233–243

Czyczyło-Mysza I, Tyrka M, Marcińska Skrzypek E, Karbarz M, Dziurka M, Hura T, Dziurka K, Quarrie SA (2013) Quantitative trait loci for leaf chlorophyll fluorescence parameters, chlorophyll and carotenoid contents in relation to biomass and yield in bread wheat and their chromosome deletion bin assignments. Mol Breed 32:189–210

D’Haene SE, Sobotka R, Bučinská L, Dekker JP, Komenda J (2015) Interaction of the PsbH subunit with a chlorophyll bound to histidine 114 of CP47 is responsible for the red 77 K fluorescence of Photosystem II. Biochim Biophys Acta 1847:1327–1334

Dang NC, Zazubovich V, Reppert M, Neupane B, Picorel R, Seibert M, Jankowiak R (2008) The CP43 proximal antenna complex of higher plant photosystem II revisited: modeling and hole burning study. J Phys Chem B 112:9921–9933

Dau H (1994) Molecular mechanisms and quantitative models of variable Photosystem II fluorescence. Photochem Photobiol 60:1–23

Dau H, Sauer K (1992) Electric field effect on the picosecond fluorescence of photosystem II and its relation to the energetics and kinetics of primary charge separation. Biochim Biophys Acta 1102:91–106

Dau H, Zaharieva I, Haumann M (2012) Recent developments in research on water oxidation by photosystem II. Curr Opin Chem Biol 16:3–10

de Wijn R, van Gorkom HJ (2001) Kinetics of electron transfer from QA to QB in photosystem II. Biochemistry 40:11912–11922

de Wijn R, van Gorkom HJ (2002) The rate of charge recombination in photosystem II. Biochim Biophys Acta 1553:302–308

Debus RJ (1992) The manganese and calcium ions of photosynthetic oxygen evolution. Biochim Biophys Acta 1102:269–352

Degl’Innocenti E, Guidi L, Soldatini GF (2002) Characterization of the photosynthetic response of tobacco leaves to ozone: CO2 assimilation and chlorophyll fluorescence. J Plant Physiol 159:845–853

Dell’Aquila AR, Van der Schoor R, Jalink H (2002) Application of chlorophyll fluorescence in sorting controlled deteriorated white cabbage (Brassica oleracea L.) seeds. Seed Sci Technol 30:689–695

Demeter S, Zs Rósza, Vass I, Sallai A (1985) Thermoluminescence study of charge recombination in photosystem II at low temperatures. I. Characterization of the Zv and A thermoluminescence bands. Biochim Biophys Acta 809:369–378

Demeter S, Goussias Ch, Bernát G, Kovács L, Petrouleas V (1993) Participation of the g = 1.9 and g = 1.82 EPR forms of the semiquinone-iron complex, Q A − Fe2+ of photosystem II in the generation of the Q and C thermoluminescence bands, respectively. FEBS Lett 336:352–356

Demetriou G, Neonaki C, Navakoudis E, Kotzabasis K (2007) Salt stress impact on the molecular structure and function of the photosynthetic apparatus—the protective role of polyamines. Biochim Biophys Acta 1767:272–280

Demmig B, Winter K (1988) Characterisation of three components of non-photochemical fluorescence quenching and their response to photoinhibition. Aust J Plant Physiol 15:163–177

Demmig-Adams B, Adams WW III, Barker DH, Logan BA, Bowling DR, Verhoeven AS (1996) Using chlorophyll fluorescence to assess the fraction of absorbed light allocated to thermal dissipation of excess excitation. Physiol Plant 98:253–264

Demmig-Adams B, Cohu CM, Muller O, Adams WW III (2012) Modulation of photosynthetic energy conversion efficiency in nature: from seconds to seasons. Photosynth Res 113:75–88

Demmig-Adams B, Garab G, Adams WW III, Govindjee (2014) Non-photochemical quenching and energy dissipation in plants, algae and cyanobacteria. Advances in photosynthesis and respiration, vol 40. Springer, Dordrecht

Depège N, Bellafiore S, Rochaix J-D (2003) Role of chloroplast protein kinase Stt7 in LHCII phosphorylation and state transition in Chlamydomonas. Science 299:1572–1575

Desotgiu R, Cascio C, Pollastrini M, Gerosa G, Marzuoli R, Bussotti F (2012a) Short and long term photosynthetic adjustments in sun and shade leaves of Fagus sylvatica L., investigated by fluorescence transient (FT) analysis. Plant Biosystems 146:206–216

Desotgiu R, Pollastrini M, Cascio C, Gerosa G, Marzuoli R, Bussotti F (2012b) Chlorophyll a fluorescence analysis along a vertical gradient of the crown in a poplar (Oxford clone) subjected to ozone and water stress. Tree Physiol 32:976–986

Desotgiu R, Pollastrini M, Cascio C, Gerosa G, Marzuoli R, Bussotti F (2013) Responses to ozone on Populus “Oxford” clone in an open top chamber experiment assessed before sunrise and in full sunlight. Photosynthetica 51:267–280

DeVault D, Govindjee, Arnold W (1983) Energetics of photosynthetic glow peaks. Proc Natl Acad Sci USA 80:983–987

Dorigo U, Leboulanger C (2001) A pulse-amplitude modulated fluorescence-based method for assessing the effects of photosystem II herbicides on freshwater periphyton. J Appl Phycol 13:509–515

Doschek WW, Kok B (1972) Photon trapping in photosystem II of photosynthesis; the fluorescence rise curve in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea. Biophys J 12:832–838

Ducruet JM (1999) Relation between the heat-induced increase of F0 fluorescence and a shift in the electronic equilibrium at the acceptor side of photosystem 2. Photosynthetica 37:335–338

Ducruet J-M, Miranda T (1992) Graphical and numerical analysis of thermoluminescence and fluorescence F0 emission in photosynthetic material. Photosynth Res 33:15–27

Ducruet JM, Vavilin D (1999) Chlorophyll high-temperature thermoluminescence emission as an indicator of oxidative stress: perturbating effects of oxygen and leaf water content. Free Radical Res 31:S187–S192

Ducruet JM, Vass I (2009) Thermoluminescence: experimental. Photosynth Res 101:195–204

Ducruet J-M, Peeva V, Havaux M (2007) Chlorophyll thermofluorescence and thermoluminescence as complementary tools for the study of temperature stress in plants. Photosynth Res 93:159–171

Duysens LNM, Sweers HE (1963) Mechanisms of two photochemical reactions in algae as studied by means of fluorescence. In: Mahlis L (ed) Studies on microalgae and photosynthetic bacteria, special issue of plant cell physiol. Japanese Society of Plant Physiologists, University of Tokyo Press, Tokyo, pp 353–372

Duysens LNM, Amesz J, Kamp BM (1961) Two photochemical systems in photosynthesis. Nature 190:510–511

Ebenhöh O, Fucile G, Finazzi G, Rochaix J-D, Goldschmidt-Clermont M (2014) Short-term acclimation of the photosynthetic electron transfer chain to changing light: a mathematical model. Philos Trans R Soc B 369:20130223

Edwards GE, Baker NR (1993) Can CO2 assimilation in maize leaves be predicted accurately from chlorophyll fluorescence analysis? Photosynth Res 37:89–102

Edwards G, Walker D (1983) C3, C4: mechanisms, and cellular and environmental regulation, of photosynthesis. University of California Press, California

Ehleringer J, Pearcy RW (1983) Variation in quantum yield for CO2 uptake among C3 and C4 plants. Plant Physiol 73:555–559

Eichelmann H, Talts E, Oja V, Padu E, Laisk A (2009) Rubisco in planta kcat is regulated in balance with photosynthetic electron transport. J Exp Bot 60:4077–4088

Emerson R, Lewis CM (1943) The dependence of the quantum yield of Chlorella photosynthesis on wavelength of light. Am J Bot 30:165–178

Etienne A-L, Ducruet J-M, Ajlani G, Vernotte C (1990) Comparative studies on electron transfer in photosystem II of herbicide-resistant mutants from different organisms. Biochim Biophys Acta 1015:435–440

Eyles A, Smith D, Pinkard EA, Smith I, Corkrey R, Elms S, Beadle C, Mohammed C (2011) Photosynthetic responses of field-grown Pinus radiata trees to artificial and aphid-induced defoliation. Tree Physiol 31:592–603

Fai PB, Grant A, Reid B (2007) Chlorophyll a fluorescence as a biomarker for rapid toxicity assessment. Environ Toxicol Chem 26:1520–1531

Faller P, Pascal A, Rutherford AW (2001) β-Carotene redox reactions in photosystem II: electron transfer pathway. Biochemistry 40:6431–6440

Falster DS, Westoby M (2003) Leaf size and angle vary widely across species: what consequences for light interception? New Phytol 158:509–525

Felle HH, Hanstein S, Steinmeyer R, Hedrich R (2000) Dynamics of ionic activities in the apoplast of the sub-stomatal cavity of intact Vicia faba leaves during stomatal closure evoked by ABA and darkness. Plant J 24:297–304

Feller U, Crafts-Brandner SJ, Salvucci E (1998) Moderately high temperatures inhibit ribulose-1,5-bisphosphate carboxylase/oxygenase activase mediated activation of Rubisco. Plant Physiol 116:539–546

Ferroni L, Baldisserotto C, Giovanardi M, Pantaleoni L, Morosinotto T, Pancaldi S (2011) Revised assignment of room-temperature chlorophyll fluorescence emission bands in single living cells of Chlamydomonas reinhardtii. J Bioenergy Biomembr 43:163–173

Ferroni L, Pantaleoni L, Baldisserotto C, Aro EM, Pancaldi S (2013) Low photosynthetic activity is linked to changes in the organization of photosystem II in the fruit of Arum italicum. Plant Physiol Biochem 63:140–150

Ferroni L, Angeleri M, Pantaleoni L, Pagliano C, Longoni P, Marsano F, Aro EM, Suorsa M, Baldisserotto C, Giovanardi M, Cella R, Pancaldi S (2014) Light-dependent reversible phosphorylation of the minor photosystem II antenna Lhcb6 (CP24) occurs in lycophytes. Plant J 77:893–905

Ferroni L, Suorsa M, Aro EM, Baldisserotto C, Pancaldi S (2016) Light acclimation in the lycophyte Selaginella martensii depends on changes in the amount of photosystems and on the flexibility of LHCII antenna association to both photosystems. New Phytol 211:554–568

Flexas J, Medrano H (2002) Energy dissipation in C3 plants under drought. Funct Plant Biol 29:1209–1215

Flexas J, Escalona JM, Medrano H (1999) Water stress induces different levels of photosynthesis and electron transport rate regulation in grapevines. Plant Cell Environ 22:39–48

Flexas J, Escalona JM, Evain S, Gulías J, Moya I, Osmond CB, Medrano H (2002) Steady-state chlorophyll fluorescence (Fs) measurements as a tool to follow variations of net CO2 assimilation and stomatal conductance during water-stress in C3 plants. Physiol Plant 114:231–240

Flood PJ, Harbinson J, Aarts MGM (2011) Natural genetic variation in plant photosynthesis. Trends Plant Sci 16:327–335

Foyer CH, Noctor G (2009) Redox regulation in photosynthetic organisms: signaling, acclimation, and practical implications. Antioxid Redox Signal 11:861–905

Fracheboud Y, Leipner J (2003) The application of chlorophyll fluorescence to study light, temperature, and drought stress. In: DeEll JR, Toivonen PMA (eds) Practical applications of chlorophyll fluorescence in plant biology. Kluwer Academic Publishers, Dordrecht, pp 125–150

Fracheboud Y, Ribaut J-M, Vargas M, Messmer R, Stamp P (2002) Identification of quantitative trait loci for cold-tolerance of photosynthesis in maize (Zea mays L.). J Exp Bot 53:1967–1977

Fracheboud Y, Jompuk C, Ribaut JM, Stamp P, Leipner J (2004) Genetic analysis of cold-tolerance of photosynthesis in maize. Plant Mol Biol 56:241–253

Franck F, Juneau P, Popovich R (2002) Resolution of the photosystem I and photosystem II contributions to chlorophyll fluorescence of intact laves at room temperature. Biochim Biophys Acta 1556:239–246

Franco AC, Herzog B, Hübner C, de Mattos EA, Scarano FR, Ball E, Lüttge U (1999) Diurnal changes in chlorophyll a fluorescence, CO2-exchange and organic acid decarboxylation in the tropical CAM tree Clusia hilariana. Tree Physiol 19:635–644

Froux F, Ducrey M, Epron D, Dreyer E (2004) Seasonal variations and acclimation potential of the thermostability of photochemistry in four Mediterranean conifers. Ann For Sci 61:235–241

Fuerst EP, Nakatani HY, Dodge AD, Penner D, Arntzen CJ (1985) Paraquat resistance in conyza. Plant Physiol 77:984–989

Fufezan C, Rutherford AW, Krieger-Liszkay A (2002) Singlet oxygen production in herbicide-treated photosystem II. FEBS Lett 532:407–410

Gaevsky NA, Morgun VN (1993) Use of variable and delayed chlorophyll fluorescence for the study of plant photosynthesis. Fiziol Rast 40:136–145 [in Russian]

García-Plazaola JI, Faria T, Abaía J, Abadía A, Chaves MM, Pereira JS (1997) Seasonal changes in xanthophyll composition and photosynthesis of cork oak (Quercus suber L.) leaves under mediterranean climate. J Exp Bot 48:1667–1674

Garnier J, Maroc J, Guyon D (1986) Low-temperature fluorescence emission spectra and chlorophyll-protein complexes in mutants of Chlamydomonas reinhardtii: evidence for a new chlorophyll-a-protein complex related to photosystem I. Biochim Biophys Acta 85:395–406

Genty B, Harbinson J (2004) The regulation of light utilization for photosynthetic electron transport. In: Baker NR (ed) Photosynthesis and environment. Advances in photosynthesis and respiration, vol 5. Kluwer Academic Publisher, Dordrecht, pp 67–99

Genty B, Briantais J-M, Baker NR (1989) The relationship between the quantum yield of photosynthetic electron transport and quenching of chlorophyll fluorescence. Biochim Biophys Acta 990:87–92

Genty B, Harbinson J, Baker NR (1990a) Relative quantum efficiencies of the two photosystems of leaves in photorespiratory and non-photorespiratory conditions. Plant Physiol Biochem 28:1–10

Genty B, Wonders J, Baker NR (1990b) Non-photochemical quenching of F O in leaves is emission wavelength dependent. Consequences for quenching analysis and its interpretation. Photosynth Res 26:133–139

Gibasiewicz K, Croce R, Morosinotto T, Ihalainen JA, van Stokkum IHM, Dekker JP, Bassi R, van Grondelle R (2005) Excitation energy transfer pathways in Lhca4. Biophys J 88:1959–1969

Gilmore AM, Shinkarev VP, Hazlett TL, Govindjee (1998) Quantitative analysis of the effects of intrathylakoid pH and xanthophyll cycle pigments on chlorophyll a fluorescence lifetime distributions and intensity in thylakoids. Biochemistry 37:13582–13593

Gitelson AA, Buschmann C, Lichtenthaler HK (1998) Leaf chlorophyll fluorescence corrected for re-absorption by means of absorption and reflectance measurements. J Plant Physiol 152:283–296

Goldschmidt-Clermont M, Bassi R (2015) Sharing light between two photosystems: mechanism of state transitions. Curr Opin Plant Biol 25:71–78

Goltsev V, Yordanov I (1997) Mathematical model of prompt and delayed chlorophyll fluorescence induction kinetics. Photosynthetica 33:571–586

Goltsev V, Zaharieva I, Lambrev P, Yordanov I, Strasser R (2003) Simultaneous analysis of prompt and delayed chlorophyll a fluorescence in leaves during the induction period of dark to light adaptation. J Theor Biol 225:171–183

Goltsev V, Chernev P, Zaharieva I, Lambrev P, Strasser RJ (2005) Kinetics of delayed chlorophyll a fluorescence registered in milliseconds time range. Photosynth Res 84:209–215

Goltsev V, Zaharieva I, Chernev P, Strasser RJ (2009) Delayed fluorescence in photosynthesis. Photosynth Res 101:217–232

Goltsev V, Zaharieva I, Chernev P, Kouzmanova M, Kalaji H, Yordanov I, Krasteva V, Alexandrov V, Stefanov D, Allakhverdiev S, Strasser RJ (2012) Drought-induced modifications of photosynthetic electron transport in intact leaves: analysis and use of neural networks as a tool for a rapid non-invasive estimation. Biochim Biophys Acta 1817:1490–1498

Gorbe E, Calatayud A (2012) Applications of chlorophyll fluorescence imaging technique in horticultural research: a review. Sci Hortic 138:24–35

Gorbunov MY, Kolber ZS, Falkowski PG (1999) Measuring photosynthetic parameters in individual algal cells by fast repetition rate fluorometry. Photosynth Res 62:141–153

Govindjee, Jursinic PA (1979) Photosynthesis and fast changes in light emission by green plants. In: Smith KC (ed) Photochemical and photobiological reviews, vol 4. Plenum Press, New York, pp 125–205

Govindjee (1995) Sixty years since Kautsky: chlorophyll a fluorescence. Aust J Plant Physiol 22:131–160

Govindjee (1999) On the requirement of minimum number of four versus eight quanta of light for the evolution of one molecule of oxygen in photosynthesis: a historical note. Photosynth Res 59:249–254

Govindjee, Papageorgiou G (1971) Chlorophyll fluorescence and photosynthesis: fluorescence transients. Photophysiol 6:1–50

Govindjee R, Rabinowitch E, Govindjee (1968) Maximum quantum yield and action spectrum of photosynthesis and fluorescence in Chlorella. Biochim Biophys Acta 162:539–544

Govindjee, Amesz J, Fork DJ (1986) Light emission by plants and bacteria. Academic Press, New York

Grabolle M, Dau H (2005) Energetics of primary and secondary electron transfer in photosystem II membrane particles of spinach revisited on basis of recombination-fluorescence measurements. Biochim Biophys Acta 1708:209–218

Grabolle M, Dau H (2007) Efficiency and role of loss processes in light-driven water oxidation by PSII. Physiol Plant 131:50–63

Greaves JA, Wilson JM (1987) Chlorophyll fluorescence analysis—an aid to plant breeders. Biologist 34:209–214

Grieco M, Tikkanen M, Paakkarinen V, Kangasjärvi S, Aro E-M (2012) Steady-state phosphorylation of light-harvesting complex II proteins preserves photosystem I under fluctuating white light. Plant Physiol 160:1896–1910

Grieco M, Suorsa M, Jajoo A, Tikkanen M, Aro EM (2015) Light-harvesting II antenna trimers connect energetically the entire photosynthetic machinery—including both photosystems II and I. Biochim Biophys Acta 1847:607–619

Groot ML, Frese RN, de Weerd FL, Bromek K, Petterson Å, Peterman EJG, van Stokkum IHM, van Grondelle R, Dekker JP (1999) Spectroscopic properties of the CP43 core antenna protein of photosystem II. Biophys J 77:3328–3340

Grouneva I, Jakob T, Wilhelm C, Goss R (2009) The regulation of xanthophyll cycle activity and of non-photochemical fluorescence quenching by two alternative electron flows in the diatoms Phaeodactylum tricornutum and Cyclotella meneghiniana. Biochim Biophys Acta 1787:929–938

Guidi L, Calatayud A (2014) Non-invasive tools to estimate stress-induced changes in photosynthetic performance in plants inhabiting Mediterranean areas. Environ Exp Bot 103:42–52

Guidi L, Nali C, Ciompi S, Lorenzini G, Soldatini GF (1997) The use of chlorophyll fluorescence and leaf gas exchange as methods for studying the different responses to ozone of two bean cultivars. J Exp Bot 48:173–179

Guidi L, Tonini M, Soldatini GF (2000) Effects of high light and ozone fumigation on photosynthesis in Phaseolus vulgaris. Plant Physiol Biochem 38:717–725

Guidi L, Degl’Innocenti E, Giordano C, Biricolti S, Tattini M (2010) Ozone tolerance in Phaseolus vulgaris depends on more than one mechanism. Environ Pollut 158:3164–3171

Guidi L, Degl’Innocenti E, Remorini D, Biricolti S, Fini A, Ferrini F, Nicese FP, Tattini M (2011) The impact of UV-radiation on the physiology and biochemistry of Ligustrum vulgare exposed to different visible-light irradiance. Environ Exp Bot 70:88–95

Guo P, Baum M, Varshney RK, Graner A, Grando S, Ceccarelli S (2008) QTLs for chlorophyll and chlorophyll fluorescence parameters in barley under post-flowering drought. Euphytica 163:203–214

Hall JL (2002) Cellular mechanisms for heavy metal detoxification and tolerance. J Exp Bot 53:1–11

Harbinson J, Hedley CL (1993) Changes in P-700 oxidation during the early stages of the induction of photosynthesis. Plant Physiol 103:649–660

Harbinson J, Rosenqvist E (2003) An introduction to chlorophyll fluorescence. In: DeEll J, Toivonen PMA (eds) Practical applications of chlorophyll fluorescence in plant biology. Kluwer Academic Publishers, Dordrecht, pp 1–30

Harbinson J, Genty B, Foyer CH (1990) Relationship between photosynthetic electron transport and stromal enzyme activity in pea leaves toward an understanding of the nature of photosynthetic control. Plant Physiol 94:545–553

Haynes D, Ralph P, Prange J, Dennison W (2000) The impact of the herbicide diuron on photosynthesis in three species of tropical seagrass. Mar Pollut Bull 41:288–293

Heber U, Walker D (1992) Concerning a dual function of coupled cyclic electron transport in leaves. Plant Physiol 100:1621–1626

Heber U, Neimanis S, Dietz K-J (1988) Fractional control of photosynthesis by the QB protein, the cytochrome f/b6 complex and other components of the photosynthetic apparatus. Planta 173:267–274

Henriques FS (2009) Leaf chlorophyll fluorescence: background and fundamentals for plant biologists. Bot Rev 75:249–270

Hermans C, Smeyers M, Maldonado-Rodriguez R, Eyletters M, Strasser RJ, Delhaye P-J (2003) Quality assessment of urban trees: a comparative study of physiological characterisation, airborne imaging and on site fluorescence by the OJIP-test. J Plant Physiol 160:81–90

Hess FD (2000) Light-dependent herbicides: an overview. Weed Sci 48:160–170

Hideg E, Schreiber U (2007) Parallel assessment of ROS formation and photosynthesis in leaves by fluorescence imaging. Photosynth Res 92:103–108

Hideg E, Vass I (1993) The 75 °C thermoluminescence band of green tissues: chemiluminescence from membrane-chlorophyll interaction. Photochem Photobiol 58:280–283

Hideg E, Sass L, Barbato R, Vass I (1993) Interaction of photosynthetic oxygen evolution by UV-B irradiation: a thermoluminescence study. Photosynth Res 38:455–462

Hogewoning SW, Harbinson J (2007) Insights on the development, kinetics, and variation of photoinhibition using chlorophyll fluorescence imaging of a chilled, variegated leaf. J Exp Bot 58:453–463

Hogewoning SW, Wientjes E, Douwstra P, Trouwborst G, van Ieperen W, Croce R, Harbinson J (2012) Photosynthetic quantum yield dynamics: from photosystems to leaves. Plant Cell 24:1921–1935

Holzwarth AR, Miloslavina Y, Nilkens M, Jahns P (2009) Identification of two quenching sites active in the regulation of photosynthetic light-harvesting studied by time-resolved fluorescence. Chem Phys Lett 483:262–267

Horton P, Hague A (1988) Studies on the induction of chlorophyll fluorescence in isolated barley protoplasts: IV. Resolution of nonphotochemical quenching. Biochim Biophys Acta 932:107–115

Hund A, Frascaroli E, Leipner J, Jompuk C, Stamp P, Fracheboud Y (2005) Cold tolerance of the photosynthetic apparatus: pleiotropic relationship between photosynthetic performance and specific leaf area of maize seedlings. Mol Breed 16:321–331

Ilík P, Schansker G, Kotabová E, Váczi P, Strasser RJ, Bartak M (2006) A dip in the chlorophyll fluorescence induction at 0.2–2 s in Trebouxia-possessing lichens reflects a fast reoxidation of photosystem I. A comparison with higher plants. Biochim Biophys Acta 1757:12–20

Ioannidis N, Schansker G, Barynin VV, Petrouleas V (2000) Interaction of nitric oxide with the oxygen evolving complex of photosystem II and manganese catalase: a comparative study. J Bioinorg Chem 5:354–363

Ishida A, Toma T, Marjenah (1999) Leaf gas exchange and chlorophyll fluorescence in relation to leaf angle, azimuth, and canopy position in the tropical pioneer tree, Macaranga conifer. Tree Physiol 9:117–124

Itoh S, Murata N (1973) Correlation between delayed light emission and fluorescence of chlorophyll a in system II particles derived from spinach chloroplasts. Photochem Photobiol 18:209–218

Itoh S, Katoh S, Takamiya A (1971) Studies on the delayed light emission in spinach chloroplasts; II. Participation of primary electron donor and acceptor of photoreaction II in producing the delayed light emission. Biochim Biophys Acta 245:121–128

Iwai M, Takahashi Y, Minagawa J (2008) Molecular remodeling of photosystem II during state transitions in Chlamydomonas reinhardtii. Plant Cell 20:2177–2189

Jahns P, Holzwarth AR (2012) The role of the xanthophyll cycle and of lutein in photoprotection of photosystem II. Biochim Biophys Acta 1817:182–193

Jalink H, Van der Schoor R, Frandas A, Van Pijlen JG (1998) Chlorophyll fluorescence of Brassica oleracea seeds as a non-destructive marker for seed maturity and seed performance. Seed Sci Res 8:437–443

Jifon JL, Syvertsen JP (2003) Moderate shade can increase net gas exchange and reduce photoinhibition in citrus leaves. Tree Physiol 23:119–127

Johnson GN (2011) Physiology of PSI cyclic electron transport in higher plants. Biochim Biophys Acta 1807:384–389

Johnson MP, Goral TK, Duffy CD, Brain AP, Mullineaux CW, Ruban AV (2011) Photoprotective energy dissipation involves the reorganization of photosystem II light-harvesting complexes in the grana membranes of spinach chloroplasts. Plant Cell 23:1468–1479

Joliot A, Joliot P (1964) Étude cinétique de la reaction photochimique libérant l’oxygène au cours de la photosynthèse. C R Acad Sci Paris 258:4622–4625

Joliot P, Joliot A (2002) Cyclic electron transfer in plant leaf. Proc Natl Acad Sci USA 99:10209–10214

Joliot P, Joliot A, Bouges B, Barbieri G (1971) Studies of system II photocenters by comparative measurements of luminescence, fluorescence, and oxygen emission. Photochem Photobiol 14:287–305

Judy BM, Lower WR, Ireland FA, Krause GF (1991) A seedling chlorophyll fluorescence toxicity assay. In: Gorsuch JW, Lower WR, Lewis MA, Wang W (eds) Plants for toxicity assessment. ASTM, Philadelphia, pp 146–158

Juneau P, Dewez D, Matsui S, Kim SG, Popovic R (2001) Evaluation of different algal species sensitivity to mercury and metolachlor by PAM-fluorometry. Chemosphere 45:589–598

Jung H-S, Niyogi KK (2009) Quantitative genetic analysis of thermal dissipation in Arabidopsis. Plant Physiol 150:977–986

Jursinic P (1986) Delayed fluorescence: current concepts and status. In: Amesz J, Fork DJ, Govindjee (eds) Light emission by plants and bacteria. Academic Press, New York, pp 291–328

Jursinic P, Govindjee (1982) Effects of hydroxylamine and silicomolybdate on the decay in delayed light emission in the 6–100 µs range after a single 10 ns flash in pea thylakoids. Photosynth Res 3:161–177

Kalaji MH, Guo P (2008) Chlorophyll fluorescence: A useful tool in barley plant breeding programs. In: Sánchez A, Gutierrez SJ (eds) Photochemistry research progress. Nova Science Publishers, New York, pp 439–463

Kalaji MH, Łoboda T (2007) Photosystem II of barley seedlings under cadmium and lead stress. Plant Soil Environ 53:511–516

Kalaji MH, Pietkiewicz S (1993) Salinity effects on plant growth and other physiological processes. Acta Physiol Plant 15:89–124

Kalaji MH, Pietkiewicz S (2004) Some physiological indices to be exploited as a crucial tool in plant breeding. Plant Breed Seeds Sci 49:19–39

Kalaji MH, Bosa K, Kościelniak J, Hossain Z (2011a) Chlorophyll a fluorescence—a useful tool for the early detection of temperature stress in spring barley (Hordeum vulgare L.). OMICS 15:925–934

Kalaji MH, Govindjee, Bosa K, Kościelniak J, Żuk-Gołaszewska K (2011b) Effects of salt stress on photosystem II efficiency and CO2 assimilation of two Syrian barley landraces. Environ Exper Bot 73:64–72

Kalaji MH, Carpentier R, Allakhverdiev SI, Bosa K (2012a) Fluorescence parameters as early indicators of light stress in barley. J Photochem Photobiol B 112:1–6

Kalaji MH, Govindjee, Goltsev V, Bosa K, Allakhverdiev SI, Strasser R (2012b) Experimental in vivo measurements of light emission in plants: a perspective dedicated to David Walker. Photosynth Res 114:69–96

Kalaji MH, Oukarroum A, Alexandrov V, Kouzmanova M, Brestič M, Živčák M, Samborska IA, Cetner MD, Allakhverdiev SI, Vasilij Goltsev V (2014a) Identification of nutrient deficiency in maize and tomato plants by in vivo chlorophyll a fluorescence measurements. Plant Physiol Biochem 81:16–25

Kalaji HM, Schansker G, Ladle RJ, Goltsev V, Bosa K, Allakhverdiev SI, Brestič M, Bussotti F, Calatayud A, Dąbrowski Elsheery NI, Ferroni L, Guidi L, Hogewoning SW, Jajoo A, Misra AN, Nebauer SG, Pancaldi S, Penella C, Poli DB, Pollastrini M, Romanowska-Duda ZB, Rutkowska B, Serôdio J, Suresh K, Szulc W, Tambussi E, Yanniccari M, Živčák M (2014b) Frequently Asked Questions about chlorophyll fluorescence: practical issues. Photosynth Res 122:121–158

Kalaji HM, Goltsev VN, Żuk-Golaszewska K, Živčák M, Brestič M (2016) Application of Chlorophyll Fluorescence in Understanding Plant Performance. CRC Press, Florida

Kaňa R, Spundová P, Ilík P, Lazár D, Klem K, Tomek P, Naus J, Prásil O (2004) Effect of herbicide clomazone on photosynthetic processes in primary barley (Hordeum vulgare L.) leaves. Pestic Biochem Physiol 78:161–170

Karapetyan NV (2004) Interaction of pigment-protein complexes within aggregates stimulates dissipation of excess energy. Biochem (Moscow) 69:1299–1304

Karapetyan NV, Bolychevtseva YV, Yurina NP, Terekhova IV, Shubin VV, Brecht M (2014) Long-wavelength chlorophylls in photosystem I of cyanobacteria: origin, localization, and functions. Biochem (Moscow) 79:213–220

Kasajima I, Takahara K, Kawai-Yamada M, Uchimiya H (2009) Estimation of the relative sizes of rate constants for chlorophyll de-excitation processes through comparison of inverse fluorescence intensities. Plant Cell Physiol 50:1600–1616

Katsumata M, Takeuchi A, Kazumura K, Koike T (2008) New feature of delayed luminescence: preillumination-induced concavity and convexity in delayed luminescence decay curve in the green alga Pseudokirchneriella subcapitata. J Photochem Photobiol B 90:152–162

Kautsky H, Hirsch A (1931) Neue Versuche zur Kohlensäureassimilation. Naturwissenschaften 19:964 [in German]

Kautsky H, Appel W, Amann H (1960) Chlorophyllfluoreszenz und Kohlensäure-assimilation: XIII. Die Fluoreszenzkurve und die Photochemie der Pflanze. Biochem Z 322:277–292 [in German]

Keränen M, Aro E-M, Tyystjärvi E (2003) Automatic plant identification with chlorophyll fluorescence fingerprinting. Precis Agric 4:53–67

Kiani SP, Maury P, Sarrafi A, Grieu P (2008) QTL analysis of chlorophyll fluorescence parameters in sunflower (Helianthus annuus L.) under well-watered and water-stressed conditions. Plant Sci 175:565–573

Kirchhoff H, Horstmann S, Weis E (2000) Control of the photosynthetic electron transport by PQ diffusion microdomains in thylakoids of higher plants. Biochim Biophys Acta 1459:148–168

Kirchhoff H, Hinz HJ, Rösgen J (2003) Aggregation and chlorophyll a fluorescence quenching of the light harvesting complex II from spinach in vitro. Biochim Biophys Acta 1606:105–116

Kirova M, Ceppi G, Chernev P, Goltsev V, Strasser R (2009) Using artificial neural networks for plant taxonomic determination based on chlorophyll fluorescence induction curves. Biotechnol Biotechnol Equip 23:941–945

Klughammer C, Schreiber U (1994) An improved method, using saturating light pulses, for the determination of photosystem I quantum yield via P700+-absorbance changes at 830 nm. Planta 192:261–268

Knoetzel J, Bossmann B, Grimme H (1998) Chlorina and viridis mutants of barley (Hordeum vulgare L.) allow assignment of long-wavelength chlorophyll forms to individual Lhca proteins of Photosystem I in vivo. FEBS Lett 436:339–342

Kok B, Forbush B, McGloin M (1970) Cooperation of charges in photosynthetic O2 evolution; I. A linear four-step mechanism. Photochem Photobiol 11:467–475

Komayama K, Khatoon M, Takenaka D, Horie J, Yamashita A, Yoshioka M, Nakayama Y, Yoshida M, Ohira S, Morita N, Velitchkova M, Enami I, Yamamoto Y (2007) Quality control of photosystem II: cleavage and aggregation of heat-damaged D1 protein in spinach thylakoids. Biochim Biophys Acta 1767:838–846

Kong S-G, Wada M (2014) Recent advances in understanding the molecular mechanism of chloroplast photorelocation movement. Biochim Biophys Acta 1837:522–530

Konishi A, Eguchi A, Hosoi F, Omasa K (2009) 3D monitoring spatio–temporal effects of herbicide on a whole plant using combined range and chlorophyll a fluorescence imaging. Funct Plant Biol 36:874–879

Konstantinova P, Van der Schoor R, van den Bulk RW, Jalink H (2002) Chlorophyll fluorescence sorting as a method for improvement of barley (Hordeum vulgare L.) seed health and germination. Seed Sci Technol 30:411–421

Kopriva S, Rennenberg H (2004) Control of sulphate assimilation and glutathione synthesis: interaction with N and C metabolism. J Exp Bot 55:1831–1842

Kornyeyev D, Hendrickson L (2007) Energy partitioning in photosystem II complexes subjected to photoinhibitory treatment. Funct Plant Biol 34:214–220

Kornyeyev D, Guadagno CR, D’Ambrosio N (2013) Assessment of energy partitioning in PSII complexes using chlorophyll fluorescence: reviewing the different approaches toward the definition of a unified method. Photosynthetica 51:477–480

Kotakis C, Kyeridou A, Manetas Y (2014) Photosynthetic electron flow during leaf senescence: evidence for a preferential maintenance of photosystem I activity and increased cyclic electron flow. Photosynthetica 52:413–420

Krall JP, Edwards GE (1990) Quantum yields of photosystem II electron transport and carbon dioxide fixation in C4 plants. Aust J Plant Physiol 17:579–588

Krall JP, Edwards GE (1992) Relationship between photosystem II activity and CO2 fixation in leaves. Physiol Plant 86:180–187

Kramer DM, Robinson HR, Crofts AR (1990) A portable multi-flash kinetic fluorimeter for measurement of donor and acceptor reactions of photosystems 2 in leaves of intact plants under field conditions. Photosynth Res 26:181–193

Kramer DM, Sacksteder CA, Cruz JA (1999) How acidic is the lumen? Photosynth Res 60:151–163

Kramer DM, Avenson TJ, Edwards GE (2004a) Dynamic flexibility in the light reactions of photosynthesis governed by both electron and proton transfer reactions. Trends Plant Sci 9:349–357

Kramer DM, Johnson G, Kiirats O, Edwards GE (2004b) New fluorescence parameters for the determination of QA redox state and excitation energy fluxes. Photosynth Res 79:209–218

Krause G, Weis E (1991) Chlorophyll fluorescence and photosynthesis: the basics. Annu Rev Plant Physiol Plant Mol Biol 42:313–349

Krause GH, Vernotte C, Briantais J-M (1982) Photoinduced quenching of chlorophyll fluorescence in intact chloroplasts and algae; resolution into two components. Biochim Biophys Acta 679:116–124

Krausz E, Hughes JL, Smith PJ, Pace RJ, Peterson Årsköld S (2005) Assignment of the low-temperature fluorescence in oxygen-evolving photosystem II. Photosynth Res 84:193–199

Krieger A, Weis E, Demeter S (1993) Low-pH-induced Ca2+ ion release in the water-splitting system is accompanied by a shift in the midpoint redox potential of the primary quinone acceptor QA. Biochim Biophys Acta 1144:411–418

Krieger-Liszkay A (2004) Singlet oxygen production in photosynthesis. J Exp Bot 56:337–346

Krieger-Liszkay A, Rutherford AW (1998) Influence of herbicide binding on the redox potential of the quinone acceptor in photosystem II: relevance to photodamage and phytotoxicity. Biochemistry 37:17339–17344

Krieger-Liszkay A, Fufezan C, Trebst A (2008) Singlet oxygen production in photosystem II and related protetction mechanism. Photosynth Res 98:551–564

Kromer S (1995) Respiration during photosynthesis. Annu Rev Plant Physiol Plant Mol Biol 46:45–70

Ku MSB, Wu J, Dai Z, Scott RA, Chu C, Edwards GE (1991) Photosynthetic and photorespiratory characteristics of Flaveria species. Plant Physiol 96:518–528

Kuang TY, Argyroudi-Akoyunoglou JH, Nakatani HY, Watson J, Arntzen CJ (1984) The origin of the long-wavelength fluorescence emission band (77 K) from photosystem I. Arch Biochem Biophys 235:618–627

Kumar K, Dahms H, Lee J, Kim H, Lee W, Shin K (2014) Algal photosynthetic responses to toxic metals and herbicides assessed by chlorophyll a fluorescence. Ecotoxicol Environ Safety 104:51–71

Kvíderová J (2010) Rapid algal toxicity assay using variable chlorophyll fluorescence for Chlorella kessleri (chlorophyta). Environ Toxicol 25:554–563

Kyle DJ, Baker NR, Arntzen CJ (1983) Spectral characterization of photosystem I fluorescence at room temperature using thylakoid protein phosphorylation of Chlamydomonas reinhardtii. Photobiochem Photobiophys 5:71–78

Laisk A, Edwards GE (1998) Oxygen and electron flow in C4 photosynthesis: Mehler reaction, photorespiration and CO2 concentration in the bundle sheath. Planta 205:632–645

Laisk A, Oja V (1998) Dynamics of leaf photosynthesis. CSIRO Publishing, Collingwood

Laisk A, Nedbal L, Govindjee (2009) Photosynthesis in Silico; understanding complexity from molecules to ecosystems. Advances in Photosynthesis and Respiration, vol 25. Springer, Dordrecht

Lange OL, Lösch R, Schulze E-D, Kappen L (1971) Responses of stomata to changes in humidity. Planta 100:76–86

Larcher W (2000) Temperature stress and survival ability of Mediterranean sclerophyllous plants. Plant Biosyst 134:279–295

Latimer P, Bannister TT, Rabinowitch E (1956) Quantum yields of fluorescence of plant pigments. Science 124:585–586

Lavergne J, Trissl H-W (1995) Theory of fluorescence induction in photosystem II: derivation of analytical expression in a model including exciton-radical-pair equilibrium and restricted energy transfer between photosynthetic units. Biophys J 68:2474–2492

Lavergne J, Bouchaud J-P, Joliot P (1992) Plastoquinone compartmentation in chloroplasts. II. Theoretical aspects. Biochim Biophys Acta 1101:13–22

Lavorel J (1975) Luminescence. In: Govindjee (ed) Bioenergetics of photosynthesis. Academic Press, New York, pp 223–317

Lavorel J, Lavergne J, Etienne AL (1982) A reflection of several problems of luminescence in photosynthetic systems. Photobiochem Photobiophys 3:287–314

Law RD, Crafts-Brandner SJ (1999) Inhibition and acclimation of photosynthesis to heat stress is closely correlated with activation of ribulose-1,5-bisphosphate carboxylase/oxygenase. Plant Physiol 120:173–181

Lazár D (1999) Chlorophyll a fluorescence induction. Biochim Biophys Acta 1412:1–28

Lazár D (2003) Chlorophyll a fluorescence rise induced by high light illumination of dark-adapted plant tissue studied by means of a model of photosystem II and considering photosystem II heterogeneity. J Theor Biol 220:469–503

Lazár D (2006) The polyphasic chlorophyll a fluorescence rise measured under high intensity of exciting light. Funct Plant Biol 33:9–30

Lazár D (2013) Simulations show that a small part of variable chlorophyll a fluorescence originates in photosystem I and contributes to overall fluorescence rise. J Theor Biol 335:249–264

Lazár D (2015) Parameters of photosynthetic energy partitioning. J Plant Physiol 175:131–147

Lazár D (2016) A word or two about chlorophyll fluorescence and its relation to photosynthesis research; a text for Ph.D. students. doi:10.13140/RG.2.1.4243.0329

Lazár D, Ilík P (1997) High-temperature induced chlorophyll fluorescence changes in barley leaves; comparison of the critical temperatures determined from fluorescence induction and from fluorescence temperature curve. Plant Sci 124:159–164

Lazár D, Nauš J (1998) Statistical properties of chlorophyll fluorescence induction parameters. Photosynthetica 35:121–127

Lazár D, Pospíšil P (1999) Mathematical simulation of chlorophyll a fluorescence rise measured with 3-(3′,4′-dichlorophenyl)-1,1-dimethylurea-treated barley leaves at room and high temperatures. Eur Biophys J 28:468–477

Lazár D, Schansker G (2009) Models of chlorophyll a fluorescence transients. In: Laisk A, Nedbal L, Govindjee (eds) Photosynthesis in silico; understanding complexity from molecules to ecosystems. Advances in photosynthesis and respiration, vol 25. Springer, Dordrecht, pp 85–123

Lazár D, Ilík P, Nauš J (1997a) An appearance of K-peak in fluorescence induction depends on the acclimation of barley leaves to higher temperatures. J Luminesc 72–74:595–596

Lazár D, Nauš J, Matoušková M, Flašarová M (1997b) Mathematical modeling of changes in chlorophyll fluorescence induction caused by herbicides. Pest Biochem Physiol 57:200–210

Lazár D, Brokeš M, Nauš J, Dvořák L (1998) Mathematical modelling of 3-(3′,4′-dichlorophenyl)-1,1-dimethylurea action in plant leaves. J Theor Biol 191:79–86

Lazár D, Tomek P, Ilík P, Nauš J (2001) Determination of the antenna heterogeneity of Photosystem II by direct simultaneous fitting of several fluorescence rise curves measured with DCMU at different light intensities. Photosynth Res 68:247–257

Lazár D, Sušila P, Nauš J (2005) Statistical properties of parameters evaluated from the O-J-I-P chlorophyll a fluorescence transients and their change upon high temperature stress. In: van Est A, Bruce D (eds) Photosynthesis: fundamental aspects to global perspectives. Allen Press, Lawrence, pp 563–566

Legendre P, Legendre L (2012) Numerical ecology, vol 3. Elsevier, Amsterdam

Leipner J, Oxborough K, Baker NR (2001) Primary sites of ozone-induced perturbations of photosynthesis in leaves: identification and characterization in Phaseolus vulgaris using high resolution chlorophyll fluorescence imaging. J Exp Bot 52:1689–1696

Leustek T, Martin MN, Bick J-A, Davies JP (2000) Pathways and regulation of sulfur metabolism revealed through molecular and genetic studies. Annu Rev Plant Physiol Plant Mol Biol 51:141–165

Lewis S, Donkin ME, Depledge MH (2001) Hsp70 expression in Enteromorpha intestinalis (Chlorophyta) exposed to environmental stress. Aquat Bot 51:277–291

Lichtenthaler HK (1988) Applications of chlorophyll fluorescence. Kluwer Academic, Dordrecht

Lichtenthaler HK (2013) Chlorophyll fluorescence kinetics, photosynthetic activity, and pigment composition of blue-shade and half-shade leaves as compared to sun and shade leaves of different trees. Photosynth Res 117:355–366

Lichtenthaler HK, Buschmann C, Döll M, Fietz HJ, Bach T, Kozel U, Meier D, Rahmsdorf U (1981) Photosynthetic activity, chloroplast ultrastructure, and leaf characteristics of high-light and low-light plants and of sun and shade leaves. Photosynth Res 2:115–141

Lichtenthaler HK, Buschmann C, Rinderle U, Schmuck G (1986) Application of chlorophyll fluorescence in ecophysiology. Radiat Environmental Biophys 25:297–308

Lichtenthaler HK, Buschmann C, Knapp M (2005a) How to correctly determine the different chlorophyll fluorescence parameters and the chlorophyll fluorescence decrease ratio RFd of leaves with the PAM fluorometer. Photosynthetica 43:379–393

Lichtenthaler HK, Langsdorf G, Lenk S, Buschmann C (2005b) Chlorophyll fluorescence imaging of photosynthetic activity with the flash-lamp fluorescence imaging system. Photosynthetica 43:355–369

Lichtenthaler HK, Ač A, Marek MV, Kalina J, Urban O (2007) Differences in pigment composition, photosynthetic rates and chlorophyll fluorescence images of sun and shade leaves of four tree species. Plant Physiol Biochem 45:577–588

Logan BA, Adams WW, Demmig-Adams B (2007) Viewpoint: avoiding common pitfalls of chlorophyll fluorescence analysis under field conditions. Funct Plant Biol 34:853–859

Long SP, Humphries S (1994) Photoinhibition of photosynthesis in nature. Annu Rev Plant Physiol Plant Mol Biol 45:633–662

Long SP, Ainsworth EA, Leakey ADB, Nösberger J, Ort DR (2006) Food for thought: lower-than-expected crop yield stimulation with rising CO2 concentrations. Science 312:1918–1921

Losciale P, Oguchi R, Hendrickson L, Hope AB, Corelli Grappadelli L, Chow WS (2008) A rapid, whole-tissue determination of the functional fraction of photosystem II after photoinhibition of leaves based on flash-induced P700 redox kinetics. Physiol Plant 132:23–32

Losciale P, Chow WS, Corelli Grappadelli L (2010) Modulating the light environment with the peach ‘asymmetric orchard’: effects on gas exchange performances, photoprotection, and photoinhibition. J Exp Bot 61:1177–1192

Losciale P, Manfrini L, Morandi B, Pierpaoli E, Zibordi M, Stellaci AM, Salvati L, Grappadelli LC (2015) A multivariate approach for assessing leaf photo-assimilation performance using the IPL index. Physiol Plant 154:609–620

Lu C, Zhang J (1998) Effects of water stress on photosynthesis, chlorophyll fluorescence and photoinhibition in wheat plants. Aust J Plant Physiol 25:883–892

Lu C, Zhang J (1999) Effects of water stress on photosystem II photochemistry and its thermostability in wheat plants. J Exp Bot 50:1199–1206

Lu Q, Lu C, Zhang J, Kuang T (2002) Photosynthesis and chlorophyll a fluorescence during flag leaf senescence of field-grown wheat plants. J Plant Physiol 159:1173–1178

Lunde C, Jensen PE, Haldrup A, Knoetzel J, Scheller HV (2000) The PSI-H subunit of photosystem I is essential for state transitions in plant photosynthesis. 408:613–615

Macinnis-Ng CMO, Ralph PJ (2003) Short-term response and recovery of Zostera capricorni photosynthesis after herbicide exposure. Aqua Bot 76:1–15

Maldonado-Rodriguez R, Pavlov S, Gonzalez A, Oukarroum A, Strasser RJ (2003) Can machines recognise stress in plants? Environ Chem Lett 1:201–205

Malenovsky Z, Mishra KB, Zemek F, Rascher U, Nedbal L (2009) Scientific and technical challenges in remote sensing of plant canopy reflectance of fluorescence. J Exp Bot 60:2987–3004

Malkin S (1966) Fluorescence induction studies in isolated chloroplasts. I. Kinetic analysis of the fluorescence intensity dependence on time. Biochim Biophys Acta 126:433–442

Malkin S (1979) Delayed luminescence. In: Trebst A, Avron M (eds) Photosynthesis I. Photosynthetic Electron Transport and Photophosphorylation. Academic Press, New York, pp 473–491

Malkin S, Barber J (1978) Induction patterns of delayed luminescence from isolated chloroplasts. I. Response of delayed luminescence to changes in the prompt fluorescence yield. Biochim Biophys Acta 502:524–541

Malkin S, Bilger W, Schreiber U (1994) The relationship between millisecond luminescence and fluorescence in tobacco leaves during the induction period. Photosynth Res 39:57–66

Mar T, Brebner J, Roy G (1975) Induction kinetics of delayed light emission in spinach chloroplasts. Biochim Biophys Acta 376:345–353

Martínez-Ferri E, Manrique E, Valladares F, Balaguer L (2004) Winter photoinhibition in the field involves different processes in four co-occurring Mediterranean tree species. Tree Physiol 24:981–990

Marwood CA, Solomon KR, Greenberg BM (2001) Chlorophyll fluorescence as a bioindicator of effects on growth in aquatic macrophytes from mixtures of polycyclic aromatic hydrocarbons. Environ Toxicol Chem 20:890–898

Matsubara S, Chow WS (2004) Population of photoinactivated Photosystem II reaction centers characterized by chlorophyll a fluorescence lifetime in vivo. Proc Natl Acad Sci USA 101:18234–18239

Matsubara S, Chen Y-C, Caliandro R, Govindjee, Clegg RM (2011) Photosystem II fluorescence lifetime imaging in avocado leaves: contributions of the lutein-epoxide and violaxanthin cycles to fluorescence quenching. J Photochem Photobiol B 104:271–284

Maxwell K, Johnson GN (2000) Chlorophyll fluorescence—a practical guide. J Exp Bot 51:659–668

McCormac DJ, Bruce D, Greenberg BM (1994) State transitions, light-harvesting antenna phosphorylation and light-harvesting antenna migration in vivo in the higher plant Spirodela oligorrhiza. Biochim Biophys Acta 1187:301–312

McCree KJ (1972) The action spectrum, absorptance and quantum yield of photosynthesis in crop plants. Agric Meteorol 9:191–216

Medrano H, Escalona JM, Bota J, Gulías J, Flexas J (2002) Regulation of photosynthesis of C3 plants in response to progressive drought: stomatal conductance as a reference parameter. Ann Bot 89:895–905

Melgar JC, Guidi L, Remorini Agati G, Degl’Innocenti E, Castelli S, Baratto MC, Faraloni C, Tattini M (2009) Antioxidant defences and oxidative damage in salt-treated olive plants under contrasting sunlight irradiance. Tree Physiol 29:1187–1198

Melis A, Homann PH (1975) Kinetic analysis of the fluorescence induction in 3-(3,4- dichlorophenyl)-1,1-dimethylurea poisoned chloroplasts. Photochem Photobiol 21:431–437

Melis A, Homann PH (1976) Heterogeneity of the photochemical centers in system II of chloroplasts. Photochem Photobiol 23:343–350

Merkell U, Rathke GW, Schuster C, Warnstorff K, Diepenbrock W (2004) Use of glufosinate-ammonium to control cruciferous weed species in glufosinate-resistant winter oilseed rape. Field Crop Res 85:237–249

Merz D, Geyer M, Moss DA, Ache HJ (1996) Chlorophyll fluorescence biosensor for the detection of herbicides. Fresenius J Anal Chem 354:299–305

Messinger J, Renger G (1990) The reactivity of hydrazine with photosystem II strongly depends on the redox state of the water oxidizing system. FEBS Lett 277:141–146

Messinger J, Renger G (1993) Generation, oxidation by the oxidized form of the tyrosine of polypeptide D2, and possible electronic configuration of the redox states S0, S-1, and S-2 of the water oxidase in isolated spinach thylakoids. Biochemistry 32:9379–9386

Meyer S, Genty B (1999) Heterogeneous inhibition of photosynthesis over the leaf surface of Rosa rubiginosa L. during water stress and abscisic acid treatment: induction of a metabolic component by limitation of CO2 diffusion. Planta 210:126–131

Misra AN, Biswal AK (2000) Thylakoid membrane protein kinase activity as a signal transduction pathway in chloroplasts. Photosynthetica 38:323–332

Misra AN, Srivastava A, Strasser RJ (2001a) Fast chlorophyll a fluorescence kinetic analysis for the assessment of temperature and light effects: a dynamic model for stress recovery phenomena. Photosynthesis: PS2001. CSIRO Publ., Melbourne, Australia S3-007

Misra AN, Srivastava A, Strasser RJ (2001b) Utilisation of fast chlorophyll a fluorescence technique in assessing the salt/ion sensitivity of mung bean and brassica seedlings. J Plant Physiol 158:1173–1181

Misra AN, Latowski D, Strzalka K (2006) The xanthophyll cycle activity in kidney bean and cabbage leaves under salinity stress. Russ J Plant Physiol 53:102–109

Misra AN, Misra M, Singh R (2012) Chlorophyll fluorescence in plant biology. In: Misra AN (ed) Biophysics. Intech Europe, Croatia, pp 171–192

Mittler R (2002) Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci 7:405–410

Mohanty N, Vass I, Demeter S (1989) Copper toxicity affects photosystem II electron transport at the secondary quinone acceptor, QB. Plant Physiol 90:175–179

Mukerji I, Sauer K (1990) Optical Spectroscopy on a Photosystem I Antenna Complex. In: Baltscheffsky M (ed) Current research in photosynthesis, vol II. Kluwer Academic Publishers, Dordrecht, pp 321–324

Mulkidjanian AY (2010) Activated Q cycle as a common mechanism for cytochrome bc1 and cytochrome b6f complexes. Biochim Biophys Acta 1797:1858–1868

Muller R, Schreiber U, Escher BI, Quayle P, Bengtson Nash SM, Mueller JF (2008) Rapid exposure assessment of PSII herbicides in surface water using a novel chlorophyll a fluorescence imaging assay. Sci Total Environ 401:51–59

Müller P, Li X-P, Niyogi KK (2001) Non-photochemical quenching; a response to excess light energy. Plant Physiol 125:1558–1566

Mullet JE, Burke JJ, Arntzen CJ (1980) Chlorophyll proteins of photosystem I. Plant Physiol 65:814–822

Munday JC, Govindjee (1969) Light-induced changes in the fluorescence yield of chlorophyll a in vivo; III. The dip and the peak in the fluorescence transient of Chlorella pyrenoidosa. Biophys J 9:1–21

Munekage YN, Eymery F, Rumeau D, Cuiné S, Oguri M, Nakamura N, Yakota A, Genty B, Peltier G (2010) Elevated expression of PGR5 and NDH-H in bundle sheath chloroplasts in C4 Flaveria species. Plant Cell Physiol 51:664–668

Murakami Y, Tsuyama M, Kobayashi Y, Kodama H, Iba K (2000) Trienoic fatty acids and plant tolerance of high temperature. Science 287:476–479

Murata N, Nishimura M, Takamiya A (1966a) Fluorescence of chlorophyll in photosynthetic systems; II. Induction of fluorescence in isolated spinach chloroplasts. Biochim Biophys Acta 120:23–33

Murata N, Nishimura M, Takamiya A (1966b) Fluorescence of chlorophyll in photosynthetic systems. III. Emission and action spectra of fluorescence–three emission bands of chlorophyll a and the energy transfer between two pigment systems. Biochim Biophys Acta 126:234–243

Murchie EH, Lawson T (2013) Chlorophyll fluorescence analysis: a guide to good practice and understanding some new applications. J Exp Bot 64:3983–3998

Nagy V, Tengölics R, Schansker G, Rákhely G, Kovács KL, Garab G, Tóth SZ (2012) Stimulatory effect of ascorbate, the alternative electron donor of photosystem II, on the hydrogen production of Chlamydomonas reinhardtii. Int J Hydrog Energ 37:8864–8871

Nakatani HY, Ke B, Dolan E, Arntzen CJ (1984) Identity of the photosystem II reaction center polypeptide. Biochim Biophys Acta 765:347–352

Nauš J, Šmecko S, Špundová M (2016) Chloroplast avoidance movement as a sensitive indicator of relative water content during leaf dessication in the dark. Photosynth Res 129:217–225

Nedbal L, Whitmarsh J (2004) Chlorophyll fluorescence imaging of leaves and fruits. In: Papageorgiou GC, Govindjee (eds) Advances in photosynthesis and respiration series chlorophyll fluorescence: a signature of photosynthesis, vol 19. Springer, Dordrecht, pp 389–407

Nedbal L, Soukupová J, Whitmarsh J, Trtílek M (2000) Postharvest imaging of chlorophyll fluorescence from lemons can be used to predict fruit quality. Photosynthetica 38:571–579

Nejad AR, Harbinson J, van Meeteren U (2006) Dynamics of spatial heterogeneity of stomatal closure in Tradescantia virginiana altered by growth at high relative humidity. J Exp Bot 57:3669–3678

Neubauer C, Schreiber U (1987) The polyphasic rise of chlorophyll fluorescence upon onset of the strong continuous illumination: I. Saturation characteristics and partial control by the photosystem II acceptor side. Z Naturforsch 42c:1246–1254

Neyra CH, Hageman RH (1974) Dependence of nitrite reduction on electron transport in chloroplasts. Plant Physiol 54:480–484

Nilkens M, Kress E, Lambrev P, Miloslavina Y, Müller M, Holzwarth AR, Jahns P (2010) Identification of a slowly inducible zeaxanthin-dependent component of non-photochemical quenching of chlorophyll fluorescence generated under steady-state conditions in Arabidopsis. Biochim Biophys Acta 1797:466–475

Noctor G, Foyer CH (1998) Ascorbate and glutathione: keeping active oxygen under control. Annu Rev Plant Physiol Plant Mol Biol 49:249–279

Oberhuber W, Dai Z-Y, Edwards GE (1993) Light dependence of quantum yields photosystem II and CO2 fixation in C3 and C4 plants. Photosynth Res 35:265–274

Ögren E, Rosenqvist E (1992) On the significance of photoinhibition of photosynthesis in the field and its generality among species. Photosynth Res 33:63–71

Oh M-H, Moon Y-H, Lee C-H (2003) Increased stability of LHCII by aggregate formation during dark-induced leaf senescence in the Arabidopsis mutant ore10. Plant Cell Physiol 44:1368–1377

Oja V, Laisk A (2012) Photosystem II antennae are not energetically connected: evidence based on flash-induced O2 evolution and chlorophyll fluorescence in sunflower leaves. Photosynth Res 114:15–28

Olesen CF, Cedergreen N (2010) Glyphosate uncouples gas exchange and chlorophyll fluorescence. Pest Manag Sci 66:536–542

Oukarroum A, El Madidi S, Schansker G, Strasser RJ (2007) Probing the responses of barley cultivars (Hordeum vulgare L.) by chlorophyll a fluorescence OLKJIP under drought stress and re-watering. Environ Exp Bot 60:438–446

Oukarroum A, Schansker G, Strasser RJ (2009) Drought stress effects on photosystem I content and photosystem II thermotolerance analyzed using Chl a fluorescence kinetics barley varieties differing in their drought tolerance. Physiol Plant 137:188–199

Oukarroum A, Strasser RJ, Schansker G (2012) Heat stress response of the lichen Parmelia tiliacea in the dry and the wet state: differences and similarities with the heat stress response of higher plants. Photosynth Res 111:303–314

Oxborough K (2004) Using chlorophyll a fluorescence imaging to monitor photosynthetic performance. In: Papageorgiou GC, Govindjee (eds) Chl a fluorescence: a signature of photosynthesis, advances in photosynthesis and respiration, vol 19. Springer, Dordrecht, pp 409–428

Oxborough K, Baker NR (1997) Resolving chlorophyll a fluorescence images of photosynthetic efficiency into photochemical and non-photochemical components: calculation of qP and Fv’/Fm’ without measuring Fo’. Photosynth Res 54:135–142

Pålsson LO, Tjus SE, Andersson B, Gillbro T (1995) Energy-transfer in photosystem-I: time-resolved fluorescence of the native photosystem-I complex and its core complex. Chem Phys 194:291–302

Pantaleoni L, Ferroni L, Baldisserotto C, Aro EM, Pancaldi S (2009) Photosystem II organisation in chloroplasts of Arum italicum leaf depends on tissue location. Planta 230:1019–1031

Pantazi XE, Moshou D, Mouazen AM, Kuang B, Alexandridis T (2014) Application of supervised self organising models for wheat yield prediction. In: Iliadis L, Maglogiannis I, Papadopoulos H (eds) Artificial intelligence applications and innovations. Springer, Berlin, pp 556–565

Papageorgiou GC, Govindjee (eds) (2004) Chl a fluorescence: a signature of photosynthesis, advances in photosynthesis and respiration, vol 19. Springer, Dordrecht

Pastenes C, Horton P (1996) Effect of high temperature on photosynthesis in beans. 1. Oxygen evolution and chlorophyll fluorescence. Plant Physiol 112:1245–1251

Paul M, Foyer CH (2001) Sink regulation of photosynthesis. J Exp Bot 52:1383–1400

Penella C, Landi M, Guidi L, Nebauer SG, Pellegrini E, San Bautista A, Remorini D, Nali C, Lopez-Galarza S, Calatayud A (2016) Salt-tolerant rootstock increases yield of pepper under salinity through maintenance of photosynthetic performance and sink strength. J Plant Physiol 193:1–11

Perreault F, Oukarroum A, Pirastru L, Sirois L, Matias GW, Popovic R (2010) Evaluation of copper oxide nanoparticles toxicity using chlorophyll a fluorescence imaging in Lemna gibba. J Bot. doi: 10.1155/2010/763142

Pesaresi P, Hertle A, Pribil M, Kleine T, Wagner R, Strissel H, Ihnatowicz A, Bonardi V, Scharfenberg M, Schneider A, Pfannschmidt T, Leister D (2009) Arabidopsis STN7 kinase provides a link between short- and long-term photosynthetic acclimation. Plant Cell 21:2402–2423

Peterson RB, Havir EA (2003) Contrasting modes of regulation of PS II light utilization with changing irradiance in normal and psbS mutant leaves of Arabidopsis thaliana. Photosynth Res 75:57–70

Peterson RB, Havir EA (2004) The multiphasic nature of nonphotochemical quenching: implications for assessment of photosynthetic electron transport based on chlorophyll fluorescence. Photosynth Res 82:95–107

Peterson RB, Oja V, Laisk A (2001) Chlorophyll fluorescence at 680 and 730 nm and leaf photosynthesis. Photosynth Res 70:185–196

Peterson RB, Oja V, Eichelmann H, Bichele I, Dall’Osto L, Laisk A (2014) Fluorescence F0 of photosystems II and I in developing C3 and C4 leaves, and implications on regulation of excitation balance. Photosynth Res 122:41–56

Petrouleas V, Crofts AR (2005) The iron-quinone acceptor complex. In: Wydrzynski TJ, Satoh K (eds) Photosystem II: the light-driven water:plastoquinone oxidoreductase, advances in photosynthesis and respiration, vol 22. Springer, Dordrecht, pp 177–206

Pfündel E (1998) Estimating the contribution of photosystem I to total leaf chlorophyll fluorescence. Photosynth Res 56:185–195

Pfündel E, Pfeffer M (1997) Modification of photosystem I light harvesting of bundle-sheath chloroplasts occurred during the evolution of NADP-malic enzyme C4 photosynthesis. Plant Physiol 114:145–152

Pfündel EE, Klughammer C, Meister A, Cerovic ZG (2013) Deriving fluorometer-specific values of relative PSI fluorescence intensity from quenching of F0 fluorescence in leaves of Arabidopsis thaliana and Zea mays. Photosynth Res 114:189–206

Pogson BJ, Niyogio KK, Björkman O, DellaPenna D (1998) Altered xanthophyll compositions adversely affect chlorophyll accumulation and nonphotochemical quenching in Arabidopsis mutants. Proc Natl Acad Sci USA 95:13324–13329

Pollastrini M, Di Stefano V, Ferretti M, Agati G, Grifoni D, Zipoli G, Orlandini S, Bussotti F (2011) Influence of different light intensity regimes on leaf features of Vitis vinifera L. in ultraviolet radiation filtered condition. Environ Exp Bot 73:108–115

Pollastrini M, Desotgiu R, Camin F, Ziller L, Marzuoli R, Gerosa G, Bussotti F (2013) Intra-annual pattern of photosynthesis, growth and stable isotope partitioning in a poplar clone subjected to ozone and water stress. Water Air Soil Pollut 224:1761–1772

Pollastrini M, Holland V, Brüggemann W, Koricheva J, Jussila I, Scherer-Lorenzen M, Berger S, Bussotti F (2014) Interactions and competition processes among tree species in young experimental mixed forests, assessed with chlorophyll fluorescence and leaf morphology. Plant Biol 16:323–331

Pollet B, Steppe K, van Labeke M-C, Lemeur R (2009) Diurnal cycle of chlorophyll fluorescence in Phalaenopsis. Photoynthetica 47:309–312

Popovic R, Dewez D, Juneau P (2003) Applications of chlorophyll fluorescence in ecotoxicology: heavy metals, herbicides, and air pollutants. In: DeEll JR, Toivonen PMA (eds) Practical applications of chlorophyll fluorescence in plant biology. Kluwer Academic Publishers, Dordrecht, pp 151–184

Porcar-Castell A, Tyystjärvi E, Atherton J, van der Tol C, Flexas J, Pfündel EE, Moreno J, Frankenberg C, Berry JA (2014) J Exp Bot 65:4065–4095

Pospíčil P, Haumann M, Dittmer J, Solé VA, Dau H (2003) Stepwise transition of the tetra-manganese complex of photosystem II to a binuclear Mn2(µ-O)2 complex in response to a temperature jump: a time-resolved structural investigation employing X-ray absorption spectroscopy. Biophys J 84:1370–1386

Quick WP, Horton P (1984) Studies on the induction of chlorophyll fluorescence in barley protoplasts; II. Resolution of fluorescence quenching by redox state and the transthylakoid pH gradient. Proc R Soc Lond B 220:371–382

Quick WP, Stitt M (1989) An examination of factors contributing to non-photochemical quenching of chlorophyll fluorescence in barley leaves. Biochim Biophys Acta 977:287–296

Quilliam RS, Swarbrick PJ, Scholes JD, Rolfe SA (2006) Imaging photosynthesis in wounded leaves of Arabidopsis thaliana. J Exp Bot 57:55–69

Radenovic C, Markovic D, Jeremic M (1994) Delayed chlorophyll fluorescence in plant models. Photosynthetica 30:1–24

Raghavendra AS, Padmasree K (2003) Beneficial interactions of mitochondrial metabolism with photosynthetic carbon assimilation. Trends Plant Sci 8:546–553

Ralph PJ, Burchett MD (1998) Photosynthetic response of Halophila ovalis to heavy metal stress. Environ Pollut 103:91–101

Ralph PJ, Gademann R (2005) Rapid light curves: a powerful tool to assess photosynthetic activity. Aquat Bot 82:222–237

Ralph PJ, Durako MJ, Enríquez S, Collier CJ, Doblin MA (2007) Impact of light limitation on seagrasses. J Exp Mar Biol Ecol 350:176–193

Reale L, Ferranti F, Mantilacci S, Corboli M, Aversa S, Landucci F, Baldisserotto C, Ferroni L, Pancaldi S, Venanzini R (2016) Cyto-histological and morpho-physiological responses of common duckweed (Lemna minor L.) to chromium. Chemosphere 145:98–105

Renger T, Schlodder E (2011) Optical properties, excitation energy and primary charge transfer in photosystem II: theory meets experiment. J Photochem Photobiol B 104:126–141

Reppert M, Acharya K, Neupane B, Jankowiak R (2010) Lowest electronic states of the CP47 antenna protein complex of photosystem II: simulation of optical spectra and revised structural assignments. J Phys Chem B 114:11884–11898

Rintamäki E, Martinsuo P, Pursiheimo S, Aro E-M (2000) Cooperative regulation of light-harvesting complex II phosphorylation via the plastoquinol and ferredoxin-thioredoxin system in chloroplasts. Proc Natl Acad Sci USA 97:11644–11649

Robakowski P (2005) Susceptibility to low-temperature photoinhibition in three conifers differing in successional status. Tree Physiol 25:1151–1160

Robinson HH, Crofts AR (1983) Kinetics of the oxidation-reduction reactions of photosystem II quinone acceptor complex, and the pathway for deactivation. FEBS Lett 153:221–226

Roháček K (2002) Chlorophyll fluorescence parameters: the definitions, photosynthetic meaning, and mutual relationships. Photosynthetica 40:13–29

Roháček K, Barták M (1999) Technique of the modulated chlorophyll fluorescence: basic concepts, useful parameters, and some applications. Photosynthetica 37:339–363

Roháček K, Soukupová J, Barták M (2008) Chlorophyll fluorescence: a wonderful tool to study plant physiology and plant stress. Res Signpost 37(661):41–104

Romanowska-Duda B, Kalaji MH, Strasser RJ (2005) The use of PSII activity of Spirodela oligorrhiza plants as an indicator for water toxicity. In: Van der Est A, Bruce D (eds) Photosynthesis: fundamental aspects to global perspectives. Allen Press, Lawrence, KS, pp 585–587

Romanowska-Duda ZB, Grzesik M, Kalaji MH (2010) Physiological activity of energy plants fertilized with sewage sludge and usefulness of the Phytotoxkit test in practice. Environ Prot Eng 36:73–81

Rosenqvist E, van Kooten O (2003) Chlorophyll fluorescence: a general description and nomenclature. In: DeEll JR, Toivonen PMA (eds) Practical applications of chlorophyll fluorescence in plant biology. Kluwer Academic Publishers, Dordrecht, pp 31–77

Rosyara UR, Subedi S, Sharma RC, Duveiller E (2010) The effect of spot blotch and heat stress in variation of canopy temperature depression, chlorophyll fluorescence and chlorophyll content of hexaploid wheat genotypes. Euphytica 174:377–390

Rousseau C, Belin E, Bove E, Rousseau D, Fabre F, Berruyer R, Guillaumès J, Manceau C, Jacques M-A, Boureau T (2013) High throughput quantitative phenotyping of plant resistance using chlorophyll fluorescence image analysis. Plant Methods 9:17. doi: 10.1186/1746-4811-9-17

Ruban AV, Horton P (1992) Mechanism of delta-pH-dependent dissipation of absorbed excitation-energy by photosynthetic membranes. 1. Spectroscopic analysis of isolated light-harvesting complexes. Biochim Biophys Acta 1102:30–38

Rutherford AW, Govindjee, Inoue Y (1984) Charge accumulation and photochemistry in leaves studied by thermoluminescence and delayed light emission. Proc Natl Acad Sci USA 81:1107–1111

Sacksteder CA, Kanazawa A, Jacoby ME, Kramer DM (2000) The proton to electron stoichiometry of steady-state photosynthesis in living plants: in proton-pumping Q cycle is continuously engaged. Proc Natl Acad Sci USA 97:14283–14288

Salvucci ME, Crafts-Brandner SJ (2004) Inhibition of photosynthesis by heat stress: the activation state of Rubisco as a limiting factor in photosynthesis. Physiol Plant 120:179–186

Samborska IA, Alexandrov V, Sieczko L, Kornatowska B, Goltsev V, Cetner MD, Kalaji MH (2014) Artificial neural networks and their application in biological and agricultural research. Signpost Open Access J NanoPhotoBioSciences 2:14–30

Samson G, Bruce D (1996) Origins of the low yield of chlorophyll a fluorescence induced by a single turnover flash in spinach thylakoids. Biochim Biophys Acta 1276:147–153

Sarvikas P, Tyystjärvi T, Tyystjärvi E (2010) Kinetics of prolonged photoinhibition revisited: photoinhibited photosystem II centres do not protect the active ones against loss of oxygen evolution. Photosynth Res 103:7–17

Satoh K (1981) Fluorescence induction and activity of ferredoxin-NADP+ reductase in Bryopsis chloroplasts. Biochim Biophys Acta 638:327–333

Saura P, Quiles MJ (2009) Assessment of photosynthesis tolerance to herbicides, heat and high illumination by fluorescence. Open Plant Sci J 3:7–13

Savikhin S (2006) Ultrafast optical spectroscopy of photosystem I. In: Golbeck JH (ed) Photosystem I: the light-driven plastocyanin: ferredoxin oxidoreductase. Springer, Dordrecht, pp 155–175

Sazanov LA, Burrows PA, Nixon PJ (1998) The chloroplast Ndh complex mediates the dark reduction of the plastoquinone pool in response to heat stress in tobacco leaves. FEBS Lett 429:115–118

Schaller S, Latowski D, Jemioła-Rzemińska M, Dawood A, Wilhelm C, Strzałka K, Goss R (2011) Regulation of LHCII aggregation by different thylakoid membrane lipids. Biochim Biophys Acta 1807:326–335

Schansker G, Strasser RJ (2005) Quantification of non-QB-reducing centers in leaves using a far-red pre-illumination. Photosynth Res 84:145–151

Schansker G, Goussias C, Petrouleas V, Rutherford AW (2002) Reduction of the Mn cluster of the water-oxidizing enzyme by nitric oxide: formation of an S-2 state. Biochem US 41:3057–3064

Schansker G, Srivastava A, Strasser RJ (2003) Characterization of the 820-nm transmission signal paralleling the chlorophyll a fluorescence rise (OJIP) in pea leaves. Funct Plant Biol 30:785–796

Schansker G, Tóth SZ, Strasser RJ (2005) Methylviologen and dibromothymoquinone treatments of pea leaves reveal the role of photosystem I in the Chl a fluorescence rise OJIP. Biochim Biophys Acta 1706:250–261

Schansker G, Tóth SZ, Strasser RJ (2006) Dark-recovery of the Chl a fluorescence transient (OJIP) after light adaptation: the qT-component of non-photochemical quenching is related to an activated photosystem I acceptor side. Biochim Biophys Acta 1757:787–797

Schansker G, Yuan Y, Strasser RJ (2008) Chl a fluorescence and 820 nm transmission changes occurring during a dark-to-light transition in pine needles and pea leaves: a comparison. In: Allen JF, Osmond B, Golbeck JH, Gantt E (eds) Photosynthesis. Energy from the sun. Springer, Dordrecht, pp 951–955

Schansker G, Tóth SZ, Kovács L, Holzwarth AR, Garab G (2011) Evidence for a fluorescence yield change driven by a light-induced conformational change within photosystem II during the fast chlorophyll a fluorescence rise. Biochim Biophys Acta 1807:1032–1043

Schansker G, Tóth SZ, Holzwarth AR, Garab G (2014) Chlorophyll a fluorescence: beyond the limits of the QA-model. Photosynth Res 120:43–58

Scharte J, Schön H, Weis E (2005) Photosynthesis and carbohydrate metabolism in tobacco leaves during an incompatible interaction with Phytophthora nicotianae. Plant Cell Environ 28:1421–1435

Schatz GH, Brock H, Holzwarth AR (1988) Kinetic and energetic model for the primary processes in photosystem II. Biophys J 54:397–405

Scheibe R, Backhausen JE, Emmerlich V, Holtgrefe S (2005) Strategies to maintain redox homeostasis during photosynthesis under changing conditions. J Exp Bot 56:1481–1489

Schreiber U (1986) Detection of rapid induction kinetics with a new type of high-frequency modulated chlorophyll fluorometer. Photosynth Res 9:261–272

Schreiber U, Berry JA (1977) Heat-induced changes of chlorophyll fluorescence in intact leaves correlated with damage of the photosynthetic apparatus. Planta 136:233–238

Schreiber U, Bilger W (1987) Rapid assessment of stress effects on plant leaves by chlorophyll fluorescence measurements. In: Tenhunen JD, Catarino FM, Lange OL, Oechel WC (eds) Plant response to stress, NATO ASI series, vol 15. Springer, Berlin, pp 27–53

Schreiber U, Krieger A (1996) Two fundamentally different types of variable chlorophyll fluorescence in vivo. FEBS Lett 397:131–135

Schreiber U, Neubauer C (1987) The polyphasic rise of chlorophyll fluorescence upon onset of strong continuous illumination: II. Partial control by the photosystem II donor side and possible ways of interpretation. Z Naturforsch 42c:1255–1264

Schreiber U, Schliwa U, Bilger W (1986) Continuous recording of photochemical and non-photochemical chlorophyll fluorescence quenching with a new type of modulation fluorometer. Photosynth Res 10:51–62

Schreiber U, Endo T, Mi H, Asada K (1995) Quenching analysis of chlorophyll fluorescence by the saturation pulse method: particular aspects relating to the study of eukaryotic algae and cyanobacteria. Plant Cell Physiol 36:873–882

Schreiber U, Klughammer C, Kolbowski J (2012) Assessment of wavelength-dependent parameters of photosynthetic electron transport with a new type of multi-color PAM chlorophyll fluorometer. Photosynth Res 113:127–144

Schultz HR (1996) Leaf absorptance of visible radiation in Vitis vinifera L.: estimates of age and shade effects with a simple field method. Sci Hortic 66:93–102

Schulze ED (1986) Carbon dioxide and water vapor exchange in response to drought in the atmosphere and in the soil. Annu Rev Plant Physiol 37:247–274

Sharkey TD, Zhang R (2010) High temperature effects on electron and proton circuits of photosynthesis. J Integr Plant Biol 52:712–722

Shikanai T (2014) Central role of cyclic electron transport around photosystem I in the regulation of photosynthesis. Curr Opin Biotechnol 26:25–30

Shinkarev VP (2005) Flash-induced oxygen evolution in photosynthesis: simple solution for the extended S-state model that includes misses, double-hits, inactivation, and backward-transitions. Biophys J 88:412–421

Shubin VV, Bezsmertnaya IN, Karapetyan NV (1992) Isolation from Spirulina membranes of two photosystem I-type complexes, one of which contains chlorophyll responsible for the 77 K fluorescence band at 760 nm. FEBS Lett 309:340–342

Shubin VV, Terekhova IN, Kirillova BA, Karapetyan NV (2008) Quantum yield of P700+ photodestruction in isolated photosystem I complexes of the cyanobacterium Arthrospira platensis. Photochem Photobiol Sci 7:956–962

Šiffel P, Braunová Z (1999) Release and aggregation of the light harvesting complex in intact leaves subjected to strong CO2 deficit. Photosynth Res 61:217–226

Šimić D, Lepeduš H, Jurković V, Antunović J, Cesar V (2014) Quantitative genetic analysis of chlorophyll a fluorescence parameters in maize in the field environments. J Integr Plant Biol 56:695–708

Sinclair J, Spence SM (1990) Heterogeneous photosystem 2 activity in isolated spinach chloroplasts. Photosynth Res 24:209–220

Skotnica J, Fiala J, Ilík P, Dvořk L (1999) Thermally induced chemiluminescence of barley leaves. Photochem Photobiol 69:211–217

Smit MF, van Heerden PDR, Pienaar JJ, Weissflog L, Strasser RJ, Krüger GHJ (2009) Effect of trifluoroacetate, a persistent degradation product of fluorinated hydrocarbons, on Phaseolus vulgaris and Zea mays. Plant Physiol Biochem 47:623–634

Snel JFH, Dassen HHA (2000) Measurement of light and pH dependence of single-cell photosynthesis by fluorescence microscopy. J Fluoresc 10:269–273

Snel JFH, Kooijman M, Vredenberg WJ (1990) Correlation between chlorophyll fluorescence and photoacoustic signal transients in spinach leaves. Photosynth Res 25:259–268

Søbye KW, Streibig JC, Cedergreen N (2011) Prediction of joint herbicide action by biomass and chlorophyll a fluorescence. Weed Res 51:23–32

Solymosi K (2012) Plastid structure, diversification and interconversions. I. Algae. Curr Chem Biol 6:167–186

Sonneveld A, Rademaker H, Duysens LNM (1980) Microsecond delayed fluorescence of photosystem II of photosynthesis in various algae: emission spectra and uphill energy transfer. FEBS Lett 113:323–327

Srivastava A, Greppin H, Strasser RJ (1995) Acclimation of land plants to diurnal changes in temperature and light. In: Mathis P (ed) Photosynthesis: from light to biosphere, vol IV. Kluwer, Dordrecht, pp 909–912

Srivastava A, Guissé B, Greppin H, Strasser RJ (1997) Regulation of antenna structure and electron transport in Photosystem II of Pisum sativum under elevated temperature probed by the fast polyphasic chlorophyll a fluorescence transient: OKJIP. Biochim Biophys Acta 1320:95–106

Srivastava A, Strasser RJ, Govindjee (1999) Greening of peas: parallel measurements of 77 K emission spectra, OJIP chlorophyll a fluorescence transient, period four oscillation of the initial fluorescence level, delayed light emission, and P700. Photosynthetica 37:365–392

StatSoft, Inc. (2011). STATISTICA (data analysis software system), version 10. www.statsoft.com

Steffen R, Christen G, Renger G (2001) Time-resolved monitoring of flash-induced changes of fluorescence quantum yield and decay of delayed light emission in oxygen-evolving photosynthetic organisms. Biochemistry 40:163–180

Steffen R, Eckert H-J, Kelly AA, Dörmann P, Renger G (2005) Investigations on the reaction pattern of photosystem II in leaves from Arabidopsis thaliana by time-resolved fluorometric analysis. Biochemistry 44:3123–3133

Stewart DW, Costa C, Dwyer LM, Smith DL, Hamilton RI, Ma BL (2003) Canopy structure, light interception, and photosynthesis in maize. Agronom J 95:1465–1474

Stirbet A (2013) Excitonic connectivity between photosystem II units: what is it, and how to measure it? Photosynth Res 116:189–214

Stirbet A, Govindjee (2012) Chlorophyll a fluorescence induction: a personal perspective of the thermal phase, the J-I-P rise. Photosynth Res 113:15–61

Stirbet A, Govindjee (2016) The slow phase of chlorophyll a fluorescence induction in silico: origin of the S-M fluorescence rise. Photosynth Res 130:193–213

Strand M, Lundmark T (1987) Effects of low night temperature and light on chlorophyll fluorescence of field-grown seedlings of Scots pine (Pinus sylvestris L.). Tree Physiol 3:211–224

Strasser RJ (1978) The grouping model of plant photosynthesis. In: Akoyunoglou G, Argyroudi-Akoyunoglou (eds) Chloroplast development. Elsevier/North Holland Biomedical Press, The Netherlands, pp 513–524

Strasser RJ, Butler WL (1977) Fluorescence emission spectra of photosystem I, photosystem II and the light-harvesting chlorophyll a/b complex of higher plants. Biochim Biophys Acta 462:307–313

Strasser RJ, Stirbet A (2001) Estimation of the energetic connectivity of PS II centres in plants using the fluorescence rise O-J-I-P: fitting of experimental data to three different PS II models. Math Comput Simul 56:451–462

Strasser BJ, Strasser RJ (1995) Measuring fast fluorescence transients to address environmental questions: The JIP test. In: Mathis P (ed) Photosynthesis: from light to biosphere, vol V. Kluwer Acadamic Publishers, Dordrecht, pp 977–980

Strasser BJ, Strasser RJ (1998) Oscillations of the chlorophyll a fluorescence related to the S-states of the oxygen evolving complex. In: Garab G (ed) Photosynthesis: mechanisms and effects, vol V. Kluwer, Dordrecht, pp 4325–4328

Strasser RJ, Srivastava A, Tsimilli-Michael M (2000) The fluorescence transient as a tool to characterize and screen photosynthetic samples. In: Yunus M, Pathre U, Mohanty P (eds) Probing photosynthesis: mechanisms, regulation and adaptation. Tayor & Francis, London, pp 445–483

Strasser RJ, Schansker G, Srivastava A, Govindjee (2001) Simultaneous measurement of photosystem I and photosystem II probed by modulated transmission at 820 nm and by chlorophyll a fluorescence in the sub ms to second time range. In: Proceedings of the 12th international congress on photosynthesis. CSIRO Publishing, Collingwood, Australia, S14-003

Strasser RJ, Tsimilli-Michael M, Srivastava A (2004) Analysis of the chlorophyll a fluorescence transient. In: Papageorgiou G, Govindjee (eds) Chlorophyll a Fluorescence: a signature of photosynthesis, advances in photosynthesis and respiration. Springer, Dordrecht, pp 321–362

Strasser RJ, Tsimilli-Michael M, Qiang S, Goltsev V (2010) Simultaneous in vivo recording of prompt and delayed fluorescence and 820-nm reflection changes during drying and after rehydration of the resurrection plant Haberlea rhodopensis. Biochim Biophys Acta 1797:1313–1326

Strehler BL, Arnold WA (1951) Light production by green plants. J Gen Physiol 34:809–820

Sun R, Liu K, Dong L, Wu Y, Paulsen H, Yang C (2015) Direct energy transfer from the major antenna to the photosystem II core complexes in the absence of minor antennae in liposomes. Biochim Biophys Acta 1847:248–261

Suorsa M, Jarvi S, Grieco M, Nurmi M, Pietrzykowska M, Rantala M, Kangasjarvi S, Paakkarinen V, Tikkanen M, Jansson S, Aro EM (2012) PROTON GRADIENT REGULATION5 is essential for proper acclimation of Arabidopsis photosystem I to naturally and artificially fluctuating light conditions. Plant Cell 24:2934–2948

Suorsa M, Rantala M, Mamedov F, Lespinasse M, Trotta A, Grieco M, Vuorio E, Tikkanen M, Järvi S, Aro EM (2015) Light acclimation involves dynamic re-organisation of the pigment-protein megacomplexes in non-appressed thylakoid domains. Plant J 84:360–373

Suresh K, Nagamani C, Kantha DL, Kumar MK (2012) Changes in photosynthetic activity in five common hybrids of oil palm (Elaeis guineensis Jacq.) seedlings under water deficit. Photosynthetica 50:549–556

Swoczyna T, Kalaji MH, Pietkiewicz S, Borowski J, Zaraś-Januszkiewicz E (2010a) Photosynthetic apparatus efficiency of eight tree taxa as an indicator of their tolerance to urban environments. Dendrobiology 63:65–75

Swoczyna T, Kalaji MH, Pietkiewicz S, Borowski J, Zaraś-Januszkiewicz E (2010b) Monitoring young urban trees tolerance to roadside conditions by application of chlorophyll fluorescence technique. Zesz Probl Post N Rol 545:303–309

Tallman G (2004) Are diurnal patterns of stomatal movement the result of alternating metabolism of endogenous guard cell ABA and accumulation of ABA delivered to the apoplast around guard cells by transpiration? J Exp Bot 55:1963–1976

Tikkanen M, Aro EM (2014) Integrative regulatory network of plant thylakoid energy transduction. Trends Plant Sci 19:10–17

Tikkanen M, Mekala NR, Aro E-M (2014) Photosystem II photoinhibition-repair cycle protects photosystem I from irreversible damage. Biochim Biophys Acta 1837:210–215

Tikkanen M, Rantala S, Aro E-M (2015) Electron flow from PSII to PSI under high light is controlled by PGR5 but not by PSBS. Front Plant Sci 6:521. doi: 10.3389/fpls.2015.00521

Tiwari A, Mamedov F, Grieco M, Suorsa M, Jajoo A, Styring S, Tikkanen M, Aro E-M (2016) Photodamage of iron–sulphur clusters in photosystem I induces non-photochemical energy dissipation. Nat Plants. doi: 10.1038/NPLANTS.2016.35

Tóth SZ, Strasser RJ (2005) The specific rate of QA reduction increases as a function of the initial Q A − concentration. In: van Est A, Bruce D (eds) Photosynthesis: fundamental aspects to global perspectives. Allen Press, Lawrence, pp 198–200

Tóth SZ, Schansker G, Kissimon J, Kovács L, Garab G, Strasser RJ (2005a) Biophysical studies of photosystem II-related recovery processes after a heat pulse in barley seedling (Hordeum vulgare L.). J Plant Physiol 162:181–194

Tóth SZ, Schansker G, Strasser RJ (2005b) In intact leaves, the maximum fluorescence level (F M ) is independent of the redox state of the plastoquinone pool: a DCMU-inhibition study. Biochim Biophys Acta 1708:275–282

Tóth SZ, Schansker G, Garab G, Strasser RJ (2007a) Photosynthetic electron transport activity in heat-treated barley leaves: the role of internal alternative electron donors to photosystem II. Biochim Biophys Acta 1767:295–305

Tóth SZ, Schansker G, Strasser RJ (2007b) A non-invasive assay of the plastoquinone pool redox state based on the OJIP-transient. Photosynth Res 93:193–203

Tóth SZ, Puthur JT, Nagy V, Garab G (2009) Experimental evidence for ascorbate-dependent electron transport in leaves with inactive oxygen-evolving complexes. Plant Physiol 149:1568–1578

Tóth SZ, Schansker G, Garab G (2013) The physiological roles and metabolism of ascorbate in chloroplasts. Physiol Plant 148:161–175

Trissl H-W, Lavergne J (1995) Fluorescence induction from photosystem II: analytical equations for the yields of photochemistry and fluorescence derived from analysis of a model including exciton-radical pair equilibrium and restricted energy transfer between photosynthetic units. Aust J Plant Physiol 22:183–193

Trissl HW, Wilhelm C (1993) Why do thylakoid membranes from higher plants form grana stacks? Trends Biochem Sci 18:415–419

Tuba Z, Saxena DK, Srivastava K, Singh S, Sz Czebol, Kalaji MH (2010) Chlorophyll a fluorescence measurements for validating the tolerant bryophytes for heavy metal (Pb) biomapping. Curr Sci 98:1505–1508

Tyystjärvi E, Aro EM (1996) The rate constant of photoinhibition, measured in lincomycin-treated leaves, is directly proportional to light intensity. Proc Natl Acad Sci USA 93:2213–2218

Tyystjärvi E, Vass I (2004) Light emission as a probe of charge separation and recombination in the photosynthetic apparatus: relation of prompt fluorescence to delayed light emission and thermoluminescence. In: Papageorgiou GC, Govindjee (eds) Chlorophyll a fluorescence: a signature of photosynthesis. Advances in photosynthesis and respiration, vol 19. Springer, Dordrecht, pp 363–388

Tyystjärvi E, Koski A, Keränen M, Nevalainen O (1999) The Kautsky curve is a built-in barcode. Biophys J 77:1159–1167

van der Weij-de Wit CD, Ihalainen JA, van Grondelle R, Dekker JP (2007) Excitation energy transfer in native and unstacked thylakoid membranes studied by low temperature and ultrafast fluorescence spectroscopy. Photosynth Res 93:173–182

van Dorssen RJ, Breton J, Plijter JJ, Satoh K, van Gorkom HJ, Amesz J (1987) Spectroscopic properties of the reaction center and of the 47 kDa chlorophyll protein of photosystem II. Biochim Biophys Acta 893:267–274

van Grondelle R, Gobets B (2004) Transfer and trapping of excitations om plant photosystems. In: Papageorgiou GC, Govindjee (eds) Chlorophyll a fluorescence: a signature of photosynthesis. Advances in photosynthesis and respiration, vol 19. Springer, Dordrecht, pp 107–132

van Kooten O, Snel JFH (1990) The use of chlorophyll fluorescence nomenclature in plant stress physiology. Photosynth Res 25:147–150

van Rensen JJS, Vredenberg WJ, Rodrigues GC (2007) Time sequence of the damage to the acceptor and donor sides of photosystem II by UV-B radiation as evaluated by chlorophyll a fluorescence. Photosynth Res 94:291–297

Vass I (2003) The history of photosynthetic thermoluminescence. Photosynth Res 76:303–318

Vass I, Govindjee (1996) Thermoluminescence from the photosynthetic apparatus. Photosynth Res 48:117–126

Vass I, Horváth G, Herczeg T, Demeter S (1981) Photosynthetic energy conservation investigated by thermoluminescence; activation energies and half-lives of thermoluminescence bands of chloroplasts determined by mathematical resolution of glow curves. Biochim Biophys Acta 634:140–152

Vass I, Kirilovski D, Etienne A-L (1999) UV-B radiation-induced donor- and acceptor-side modifications of photosystem II in the cyanobacterium Synechocystis sp. PCC 6803. Biochemistry 38:12786–12794

Velthuys BR, Visser JWM (1975) The reactivation of EPR signal II in chloroplasts treated with reduced dichlorophenol-indophenol: evidence against a dark equilibrium between two oxidation states of the oxygen evolving system. FEBS Lett 55:109–112

Vermaas WFJ, Renger G, Dohnt G (1984) The reduction of the oxygen-evolving system in chloroplasts by thylakoid components. Biochim Biophys Acta 764:194–202

Veselovskii V, Veselova T (1990) Plant Luminescence: theoretical and practical aspects. Nauka, Moscow [in Russian]

von Caemmerer S (2000) Biochemical models of photosynthesis. Techniques in plant sciences, vol 2. CSIRO Publications, Collingwood

Vos MH, van Gorkom HJ, van Leeuwen PJ (1991) An electroluminescence study of stabilization reactions in the oxygen-evolving complex of photosystem II. Biochim Biophys Acta 1056:27–39

Vredenberg WJ (2008) Analysis of initial chlorophyll fluorescence induction kinetics in chloroplasts in terms of rate constants of donor side quenching release and electron trapping in photosystem II. Photosynth Res 96:83–97

Wagner R, Dietzel L, Bräutigam K, Fischer W, Pfannschmidt T (2008) The long-term response to fluctuating light quality is an important and distinct light acclimation mechanism that supports survival of Arabidopsis thaliana under low light conditions. Planta 228:573–587

Warburg O, Negelein E (1923) Über den Einfluss der Wellenlänge auf den Energieumsatz bei der Kohlensäureassimilation. Z Physik Chem 106:191–218 [in German]

Weis E, Berry JA (1987) Quantum efficiency of photosystem II in relation to ‘energy’-dependent quenching of chlorophyll fluorescence. Biochim Biophys Acta 894:198–208

White AJ, Critchley C (1999) Rapid Light Curves: a new fluorescence method to assess the state of the photosynthetic apparatus. Photosynth Res 59:63–72

Wientjes E, van Amerongen H, Croce R (2013a) Quantum yield of charge separation in photosystem II: functional effect of changes in the antenna size upon light acclimation. J Phys Chem B 117:11200–11208

Wientjes E, van Amerongen H, Croce R (2013b) LHCII is an antenna of both photosystems after long-term acclimation. Biochim Biophys Acta 1827:420–426

Wilson KG, Ralph PJ (2012) Laboratory testing protocol for the impact of dispersed petrochemicals on seagrass. Mar Pollut Bull 64:2421–2427

Wingler A, Brownhill E, Portau N (2005) Mechanisms of the light-dependent induction of cell death in tobacco plants with delayed senescence. J Exp Bot 56:2897–2905

Witt HT (1979) Energy conversion in the functional membranes of photosynthesis analysis by light pulse and electric pulse methods. Biochim Biophys Acta 505:355–427

Wraight CA, Crofts AR (1971) Delayed fluorescence and the high-energy state of chloroplasts. Eur J Biochem 19:386–397

Yamane Y, Kashino Y, Koike H, Satoh K (1998) Effects of high temperatures on the photosynthetic systems in spinach: oxygen-evolving activities, fluorescence characteristics and the de-naturation process. Photosynth Res 57:51–59

Yamauchi Y, Sugimoto Y (2010) Effect of protein modification by malondialdehyde on the interaction between the oxygen-evolving complex 33 kDa protein and photosystem II core proteins. Planta 231:1077–1088

Yang DL, Jing RL, Chang XP, Li W (2007) Quantitative trait loci mapping for chlorophyll fluorescence and associated traits in wheat (Triticum aestivum). OMICS 49:646–654

Yanniccari M, Tambussi E, Istilart C, Castro AM (2012) Glyphosate effects on gas exchange and chlorophyll fluorescence responses of two Lolium perenne L. biotypes with differential herbicide sensitivity. Plant Physiol Biochem 57:210–217

Yin Z, Meng F, Song H, He X, Xu X, Yu D (2010) Mapping quantitative trait loci associated with chlorophyll a fluorescence parameters in soybean (Glycine max (L.) Merr.). Planta 231:875–885

Yocum CF (2008) The calcium and chloride requirements of the O2 evolving complex. Coord Chem Rev 252:296–305

Yokono M, Takabayashi A, Akimoto S, Tanaka A (2015) A megacomplex composed of both photosystem reaction centres in higher plants. Nat Commun 6:6675. doi: 10.1038/ncomms7675

Yoshida K, Terashima I, Noguchi K (2007) Up-regulation of mitochondrial alternative oxidase concomitant with chloroplast over-reduction by excess light. Plant Cell Physiol 48:606–614

Yusuf MA, Kumar D, Rajwanshi R, Strasser RJ, Tsimilli-Michael M, Govindjee, Sarin NM (2010) Overexpression of y-tocopherol methyl transferase gene in transgenic Brassica juncea plants alleviates abiotic stress: physiological and chlorophyll fluorescence measurements. Biochim Biophys Acta 1791:428–438

Zaharieva I, Goltsev V (2003) Advances on photosystem II investigation by measurement of delayed chlorophyll fluorescence by a phosphoroscopic method. Photochem Photobiol 77:292–298

Zhang ZB, Xu P, Jia JZ, Zhou RH (2010) Quantitative trait loci for leaf chlorophyll fluorescence traits in wheat. Aust J Crop Sci 4:571–579

Živčák M, Brestič M, Olšovská K (2008a) Physiological parameters useful in screening for improved tolerance to drought in winter wheat (Triticum aestivum L.). Cereal Res Commun 36:1943–1946

Živčák M, Brestič M, Olšovská K (2008b) Application of photosynthetic parameters in screening of wheat (Triticum aestivum L.) genotypes for improved drought and high temperature tolerance. In: Allen JF, Gantt E, Goldbeck JH, Osmond B (eds) Photosynthesis. Energy from the sun. Springer, Dordrecht, pp 1247–1250

Živčák M, Brestič M, Olšovská K, Slamka P (2008c) Performance Index as a sensitive indicator of water stress in Triticum aestivum. Plant Soil Environ 54:133–139

Živčák M, Brestič M, Balatová Z, Drevenaková P, Olsovska K, Kalaji HM, Allakhverdiev SI (2013) Photosynthetic electron transport and specific photoprotective responses in wheat leaves under drought stress. Photosynth Res 117:529–546

Živčák M, Kalaji HM, Shao HB, Olšovská K, Brestič M (2014) Photosynthetic proton and electron transport in wheat leaves under prolonged moderate drought stress. J Photochem Photobiol B 137:107–115

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