Skip to main content
SpringerLink
Log in

Overview of Fluorescence Protocols: Theory, Basic Concepts, and Practice

  • Chapter
  • First Online:
Chlorophyll a Fluorescence in Aquatic Sciences: Methods and Applications

Part of the book series: Developments in Applied Phycology ((DAPH,volume 4))

Abstract

At the request of the editors, this chapter is based on the book section written by Babin (2008), however, much of the manuscript has been revised and updated to address different readerships. While Babin (2008) is aimed at a more general audience interested in understanding the basis of the measurement and the current instruments available, this chapter is aimed at those who will use the fluorescence tool and are interested in understanding more of its underlying theory, as well as the assumptions associated with it. In short, while the first chapter was aimed more at a beginning user, this one is aimed more at an intermediate user. Nevertheless, some sections have seen little changes.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    Photosystem II is the location of the first photochemical reaction in the photosynthetic apparatus and location of water splitting and oxygen evolution (see Section 2.3.1).

  2. 2.

    Variation in the fluxes going to these alternative paths is the proposed mechanisms for the rapid fluorescence transients observed upon nutrient supply of nutrient stressed algae (see Chapter 11 – Shelly et al.).

  3. 3.

    β-carotene is thought to be involved in the de-excitation of active forms of oxygen that occur under high light and produce damage to the cell.

  4. 4.

    In prokaryotic phytoplankton, zeaxanthin is often present in larger concentration than chl a. However, it is located in the cell wall and, though it absorbs light, it does not appear to have a direct link to photosynthetic processes.

  5. 5.

    The rapid switch between xanthophylls associated with the so-called xanthophylls cycle is not considered a break down or de novo synthesis and is included within the process of regulation.

  6. 6.

    The presence of photodamage, which can arguably be considered a form of photoacclimation/photoprotection, should be conserved in this state. Removal of photodamage indeed requires break down and de novo synthesis of proteins.

  7. 7.

    In low-light acclimated/adapted cells, this fraction can increase to near 50% since the fraction going to non-photosynthetic pigments is reduced.

  8. 8.

    The model for the completely connected case (or lake model) is also expressed very simply as \({f}_{F}^{\prime }=\frac{{k}_{F}}{{k}_{F}+\mathbb{R}_{O}{k}_{P}+{k}_{D}+{k}_{qe}}\). It thus leads to equivalent expressions for the fluorescence yield when the reaction centres are all open (\(\mathbb{R}_{O}\) = 1) or all closed (\(\mathbb{R}_{O}\) = 0)

  9. 9.

    Rohacek uses a multiplicative factor to represent the increased heat dissipation under high light as \(d{k}_{D}\)where d is termed the “dissipation factor”. In our representation (which we used to portray two different types of dissipation) we use k D+k qe to describe the same processes. It follows that d=1+ k qe/k D.

  10. 10.

    The k qe is equivalent to what Oxborough and Baker (2000) call the “non-radiative decay through Stern-Volmer quenching”, instead of using a “variable rate constant”, they express it as a rate constant k SV multiplied by a concentration of quencher [SV]. The equivalence is k qe=k SV[SV].

  11. 11.

    The completely connected model is probably not appropriate in the case of damaged reaction centres as these are generally separated from the complex of connected PSII in the grana (when it exist) and transported to the stroma for resynthesis and reconstruction (Aro et al. 2005).

  12. 12.

    We assume that these photosystems are still capable of increased heat dissipation due to energy-dependent quenching as it seem to be regulated by events that are relatively far from the reaction centre, furthermore, there is no obvious reason why they couldn’t “feel” the transthylakoid pH gradient (see section 2.9.3 for more details).

  13. 13.

    Exception do arise, however, such as when the plastoquinone pool is reduced in the dark by chlororespiration, the maximal level of fluorescence is then observed in low light (see Kromkamp and Forster 2003 and references therein).

  14. 14.

    In this section we will describe the state of a reaction centre with respect to the reduction state of the two quinones QA and QB. The following successive states are possible from the dark-regulated (fully oxidized) state: no charge separation \({Q}_{A}{Q}_{B}\); one charge separation \({Q}_{A}^{-}{Q}_{B}\); \({Q}_{A}{Q}_{B}^{-}\); two charge separations: \({Q}_{A}^{-}{Q}_{B}^{-}\), \({Q}_{A}{Q}_{B}{H}_{2}\), three charge separations \({Q}_{A}^{-}{Q}_{B}{H}_{2}\). The inflexion points are, here, associated with the transfer of the electron from the state where most reaction centres are in the \({Q}_{A}\) reduced the state to the state where the \({\rm {Q\_B}}\) is reduced after one and two charge separations (the J and I inflexion respectively).

  15. 15.

    Light measured at the detector but not originating from the process that is being measured. In fluorometers, this can originate from, for example, scattered light in the measuring volume that is not perfectly filtered by the emission filter.

  16. 16.

    When phytoplankton samples are extracted in an organic solvent, these assumptions are generally met such that the method of chlorophyll determination in vitro is much more accurate once the influence of other fluorescing substances can be excluded (mostly chlorophyll b and pheopigments, Welschmeyer 1994).

  17. 17.

    We note that similar sources of variability are present for fluorometers designed to estimate the biomass of cyanobacteria (whether through phycobilosomes excitation or emission) in particular the presence of NPQ (Karapetyan 2007).

  18. 18.

    Kd(PAR) is the vertical diffuse attenuation coefficient for the downwelling planar irradiance. It is a good proxy of K(PAR) and much better described in the literature.

  19. 19.

    Here instead of defining these five measurements with respect to a protocol, we define them with respect to their theoretical meaning.

  20. 20.

    The fluorescence parameters in the recovery phase following illumination by an actinic light are usually denoted with double primes (e.g. \({F}_{m}^{\prime \prime }\)) this will not be discussed herein.

  21. 21.

    In the hypothetical case of non-quenching damaged reaction centers (kI = 0), F v /F m becomes a linear function of the fraction of damaged reaction centre.

  22. 22.

    The fully connected case also reduces to relatively simple expressions, while intermediate levels of connectivity, probably more true of the reality, are more complex.

  23. 23.

    It takes at least two photons per reaction centre to measure the fluorescence of a closed reaction center; the first photon closes the reaction centre and the second measures or “feels” its closed state. At sufficiently low irradiance the second photon arrives after the reaction centre has reopened.

  24. 24.

    The advantage of the high intensity of the flash is that fluorescence can be measured in low chlorophyll concentration as the fluorescence is proportional to the excitation light (see Eq. 2) while the short duration makes the flashlet subsaturating.

  25. 25.

    This corresponds to the “puddle” model.

  26. 26.

    This corresponds to the connected model and when fully connected often referred to the “lake” model.

  27. 27.

    The Fasttracka fluorometer shows a systematic artefactual transient in the measured fluorescence signal over the series of ∼100 flashes used to close reaction centres. This artefact can be observed using a fluorophore solution that shows no variable fluorescence (e.g. extracted chl a, rhodamine B).

  28. 28.

    Parkhill et al. (2001) make the following distinctions regarding the growth conditions and nutrient status of phytoplankton. When nutrients are available in concentrations that do not limit the growth rate and other environmental factors are constant, the physiological condition is said nutrient replete and phytoplankton assume balanced growth. That is, over a daily cycle the growth rate will be the same if measured by the concentrations of different cellular components (e.g. DNA, chlorophyll, carbon). When a nutrient is limiting growth, the physiological condition of phytoplankton is said to be nutrient stressed. This refers to two nutritional states: nutrient limitation and nutrient starvation . In the former, a nutrient is in short supply, but the fluxes are steady and sufficient to allow the phytoplankton to assume a balanced, albeit reduced, growth rate. Under nutrient starvation, the availability of the nutrient decreases with time relative to the demand so that phytoplankton cannot acclimate physiologically and their growth is unbalanced. Beyond nutrient stress, unbalanced growth is also generally assumed when environmental conditions change.

  29. 29.

    This protocol is in practice somewhat difficult to apply because some parameters cannot be estimated easily simply with fluorometry. The main advantage of the more recent version is that it does not require an estimate of the turnover time for electron transport through the photosynthetic chain and carbon fixation.

  30. 30.

    One recent alternative protocol was proposed by Smyth et al. (2004) using profiles of fluorescence properties.

  31. 31.

    We note that Suggett et al. (2003) interpret the formalism of Gorbunov et al. (2000) differently when forming the quantum yield of photochemistry.

References

  • Abbott MR, Richerson PJ, Powell TM (1982) In situ response of phytoplankton fluorescence to rapid variations in light. Limnol Oceanogr 27:218–225

    Google Scholar 

  • Ahn TK et al (2008) Architecture of a charge-transfer state regulating light harvesting in a plant antenna protein. Science 320:794–797

    CAS  Google Scholar 

  • Aro E-M, Ohad I (2003) Redox regulation of thylakoid protein phosphorylation. Antioxidants and Redox Signaling 5:55–67

    CAS  Google Scholar 

  • Aro E-M, Soursa M, Rokka A, Allahverdiyeva Y, Paakkarinen V, Saleem A, battchikova N, Rintamäki E (2005) Dynamics of photosystem II: a proteomics approach to thylakoid protein complexes. J Exp Bot 56:347–356

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  • Babin M (2008) Phytoplankton fluorescence: theory, current literature and in situ measurement. In: Babin M, Roesler CS, Cullen JJ (eds) Real-time coastal observing systems for marine ecosystem dynamics and harmful algal blooms. UNESCO Publishing, Paris. p 860

    Google Scholar 

  • Babin M, Morel A, Claustre H, Bricaud A, Kolber Z, Falkowski PG (1996a) Nitrogen- and irradiance-dependent variations of the maximum quantum yield of carbon fixation in eutrophic, mesotrophic and oligotrophic marine systems. Deep Sea Res I 43:1241–1272

    CAS  Google Scholar 

  • Babin M, Morel A, Gentili B (1996b) Remote sensing of sea surface sun-induced chlorophyll fluorescence: consequences of natural variations in the optical characteristics of phytoplankton and the quantum yield of chlorophyll a fluorescence. Int J Remote Sens 17:2417–2448

    Google Scholar 

  • Baker NR (2008) Chlorophyll fluorescence: a probe of photosynthesis in vivo. Annu Rev PlantBiol 59:89–113

    CAS  Google Scholar 

  • Barber J (2006) Photosystem II: an enzyme of global significance. Biochem Soc Trans 34:619–631

    CAS  Google Scholar 

  • Bassi R, Pineau B, Dainese P, Marquardt J (1993) Carotenoid-binding proteins of photosystem II. Eur J Biochem 212:297–303

    CAS  Google Scholar 

  • Behrenfeld MJ, Bale AJ, Kolber ZS, Aiken J, Falkowski PG (1996) Confirmation of iron limitation of phytoplankton photosynthesis in the equatorial Pacific Ocean. Nature 383:508–511

    CAS  Google Scholar 

  • Behrenfeld MJ, Boss E (2006) Beam attenuation and chlorophyll concentration as alternative optical indices of phytoplankton biomass. J Mar Res 64:431–451

    CAS  Google Scholar 

  • Behrenfeld MJ, Kolber Z (1999) Widespread iron limitation of phytoplankton in the South Pacific Ocean. Science 283:840–843

    CAS  Google Scholar 

  • Behrenfeld MJ, Prasil O, Babin M, Bruyant F (2004) In search of a physiological basis for covariations in light-limited and light-saturated photosynthesis. J Phycol 40:4–25

    CAS  Google Scholar 

  • Behrenfeld MJ, Worthington K, Sherrell RM, Chavez FP, Strutton P, McPhaden M, Shea DM (2006) Controls on tropical Pacific Ocean productivity revealed through nutrient stress diagnostics. Nature 442:1025–1028

    CAS  Google Scholar 

  • Beutler M, Wiltshire KH, Arp M, Kruse J, Moldaenke C, Hansen UP (2003) A reduced model of the fluorescence from cyanobacterial photosynthetic apparatus designed for the in situ detection of cyanobacteria. Biochim Biophys Acta 1604:33–46

    CAS  Google Scholar 

  • Beutler M, Wiltshire KH, Meyer B, Moldaenke C, Lüring C, Meyerhöfer M, Hansen UP, Dau H (2002) A fluorometric method for the differentiation of algal populations in vivo and in situ. Photosynth Res 72:39–53

    CAS  Google Scholar 

  • Beutler M, Wiltshire KH, Reineke C, Hansen UP (2004) Algorithms and practical fluorescence models of the photosynthetic apparatus of red cyanobacteria and Cryptophyta designed for the fluorescence detection of red cyanobacteria and cryptophytes. Aquat Microb Ecol 35:115–129

    Google Scholar 

  • Bidigare RR, Ondrusek ME, Morrow JH, Kiefer DA (1990) In vivo absorption properties of algal pigments. In: Spinrad RW (ed) Ocean optics X. Proc SPIE 1302:290–302

    Google Scholar 

  • Blankenship RE (2002) Molecular mechanisms of photosynthesis. Blackwell Science, Oxford

    Google Scholar 

  • Boisvert S, Joly D, Carpentier R (2006) Quantitative analysis of the experimental O-J-I-P chlorophyll fluorescence induction kinetics. FEBS J 273:4770–4777

    CAS  Google Scholar 

  • Bricaud A, Claustre H, Ras J, Oubelkheir K (2004) Natural variability of phytoplankton absorption in oceanic waters: influence of the size structure of algal populations. J Geophys Res-Oceans 109:C11010. doi:11010.11029/12004JC002419

    Google Scholar 

  • Bricaud A, Morel A, Babin M, Allali K, Claustre H (1998) Variations of light absorption by suspended particles with the chlorophyll a concentration in oceanic (Case 1) waters: analysis and implications for bio-optical models. J Geophys Res-Oceans 103:31033–31044

    Google Scholar 

  • Bristow M, Nielsen D, Bundy D, Furtek R (1981) Use of water Raman emission to correct airborne laser fluorosensor data for effects of water optical attenuation. Appl Optics 20:2889–2906

    CAS  Google Scholar 

  • Browell EV (1977) Analysis of laser fluorosensor systems for remote algae detection and quantification. In: NASA technical note. National Aeronoutics and Space Administration, Washington, DC p 39

    Google Scholar 

  • Bruyant F, babin M, genty B, Prasil O, Behrenfeld MJ, Claustre H, Bricaud A, Garczarek L, Holtzendorff J, Koblizek M, Dousova H, Partensky F (2005) Diel variations in the photosynthetic parameters of Prochlorococcus strain PCC 9511: Combined effects of light and cell cycle. Limnol Oceanogr 50:850–863

    Google Scholar 

  • Bryant DA, Frigaard N-U (2006) Prokaryotic photosynthesis and phototrophy illuminated. Trends Microbiol 14:488–496

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  • Campbell D, Vaughan H, Clarke AK, Gustafsson P, Öquist G (1998) Chlorophyll fluorescence analysis of cyanobacterial photosynthesis and acclimation. Microbiol Mol Biol Rev 62:667–683

    CAS  Google Scholar 

  • Chamberlin WS, Booth CR, Kiefer DA, Morrow JH, Murphy RC (1990) Evidence for a simple relationship between natural fluorescence, photosynthesis and chlorophyll in the sea. Deep Sea Res 37:951–973

    CAS  Google Scholar 

  • Chekalyuk AM, Hafez M (2008) Advanced laser fluorometry of natural aquatic environments. Limnol Oceanogr Meth 6:591–609

    CAS  Google Scholar 

  • Chekalyuk AM, Hoge FE, Wright CW, Swift RN, Yungel JK (2000) Airborne test of laser pump-and-probe technique for assessment of phytoplankton photochemical characteristics. Photosynth Res 66:45–56

    CAS  Google Scholar 

  • Chow WS (2001) The photoinactivation of photosystem II in leaves: a personal perspective. J Photosci 2001:43–53

    Google Scholar 

  • Claustre H, Morel A, Babin M, Cailliau C, Marie D, Marty J-C, Taillez D, Vaulot D (1999) Variability in particle attenuation and chlorophyll fluorescence in the tropical Pacific: Scales, patterns, and biogeochemical implications. J Geophys Res 104:3401–3422

    CAS  Google Scholar 

  • Claustre H, Sciandra A, Vaulot D (2008) Introduction to the special section bio-optical and biogeochemical conditions in the South East Pacific in late 2004: the BIOSOPE program. Biogeosciences 5:679–691

    CAS  Google Scholar 

  • Clayton RK (1980) Photosynthesis. Cambridge University Press, Cambridge

    Google Scholar 

  • Collins DJ, Kiefer DA, SooHoo JB, McDermid IS (1985) The role of reabsorption in the spectral distribution of phytoplankton fluorescence emission. Deep Sea Res 32:983–1003

    Google Scholar 

  • Cowles TJ, Desiderio RA, Neuer S (1993) In situ characterization of phytoplankton from vertical profiles of fluorescence emission spectra. Mar Biol 115:217–222

    Google Scholar 

  • Cullen JJ, Davis RF (2003) The blank can make a big difference in oceanographic measurements. Limnol Oceanogr Bull 12:21–35

    Google Scholar 

  • Cullen JJ, Lewis MR (1995) Biological processes and optical measurements near the sea-surface: some issues relevant to remote sensing. J Geophys Res 100:13255–13266

    Google Scholar 

  • Cullen JJ, Renger EH (1979) Continuous measurement of the DCMU-induced fluorescence response of natural phytoplankton populations. Mar Biol 53:13–20

    CAS  Google Scholar 

  • Cullen JJ, Xiaolong Y, MacIntyre HL (1992) Nutrient limitation of marine photosynthesis. In: Falkowski PG (ed) Primary productivity and biogeochemical cycles in the sea. Plenum Press, NY, pp 69–88

    Google Scholar 

  • Cullen JJ, Yentsch CS, Cucci TL, MacIntyre HL (1988) Autofluorescence and other optical properties as tools in biological oceanography. Proc SPIE, Int Soci Opt Eng 925:149–156

    Google Scholar 

  • Dandonneau Y, Neveux J (1997) Diel variations of the in vivo fluorescence in the eastern equatorial Pacific: an unvarying pattern. Deep Sea Res II 44:1869–1880

    CAS  Google Scholar 

  • Demmig-Adams B, Adams WW III (1992) Photoprotection and other responses of plants to high light stress. Annu Rev Plant Physiol Plant Mol Biol 43:599–626

    CAS  Google Scholar 

  • Desiderio RA, Moore C, Lantz C, Cowles TJ (1997) Multiple excitation fluorometer for in situ oceanographic applications. Appl Optics 36:1289–1296

    CAS  Google Scholar 

  • Dubinsky Z, Falkowski PG, Wyman K (1986) Light Harvesting and utilization by phytoplankton. Plant Cell Physiol 27:1335–1349

    CAS  Google Scholar 

  • Exton RJ, Houghton WM, Esaias W, Harriss RC, Farmer FH, White HH (1983) Laboratory analysis of techniques for remote sensing of estuarine parameters using laser excitation. Appl Optics 22:54–64

    CAS  Google Scholar 

  • Falkowski PG, Fujita Y, Ley A, Mauzerall D (1986) Evidence for cyclic electron flow around photosystem-II in Chlorella pyrenoidosa. Plant Physiol 81:310–312

    CAS  Google Scholar 

  • Falkowski PG, Greene RM, Kolber Z (1995) Light utilization and photoinhibition of photosynthesis in marine phytoplankton. In: Baker NR, Bowyer JR (eds) Photoinhibition of photosynthesis from molecular mechanisms to the field Environmental plant biology. Bios Scientific Publishers, Oxford, pp 407–432

    Google Scholar 

  • Falkowski PG, Kiefer DA (1985) Chlorophyll a fluorescence in phytoplankton: relationship to photosynthesis and biomass. J Plankton Res 7:715–731

    CAS  Google Scholar 

  • Falkowski PG, LaRoche J (1991) Acclimation to spectral irradiance in algae. J Phycol 27:8–14

    Google Scholar 

  • Falkowski PG, Raven JA (2007) Aquatic photosynthesis. Princeton University Press, Princeton, NJ

    Google Scholar 

  • Falkowski PG, Ziemann D, Kolber Z, Bienfang PK (1991) Role of eddy pumping in enhancing primary production in the ocean. Nature 352:55–58

    Google Scholar 

  • Finazzi G, Rapaport F, Furia A, Fleischmann M, Rochaix J-D, Zito F, Forti G (2002) Involvement of state transitions in the switch between linear and cyclic electron flow in Chlamydomonas reihardtii. EMBO Reports 3:280–285

    CAS  Google Scholar 

  • Fisher J, Kronfeld U (1990) Sun-stimulated chlorophyll fluorescence 1: influence of oceanic properties. Int J Remote Sens 11:2125–2147

    Google Scholar 

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

    CAS  Google Scholar 

  • Fuchs E, Zimmerman RC, Jaffe JS (2002) The effect of elevated levels of phaeophytin in natural water on variable fluorescence measured from phytoplankton. J Plankton Res 24:1221–1229

    CAS  Google Scholar 

  • Geider RJ, Osborne BA (1992) Algal photosynthesis. Chapman & Hall, New York

    Google Scholar 

  • 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

    CAS  Google Scholar 

  • Gilmore AM, Govindjee (1999) How higher plants respond to excess light: energy dissipation in photosystem II. In: Singhal GS, Renger R, Sopory SK, Irrgang K-D, Govindjee (eds) Concepts in photobiology: photosynthesis and photomorphogenesis. Narosa-Publishing, New Delhi, pp 513–548

    Google Scholar 

  • Gorbunov MY, Falkowski PG, Kolber ZS (2000) Measurement of photosynthetic parameters in benthic organisms in situ using a SCUBA-based repetition rate fluorometer. Limnol Oceanogr 45:242–245

    Google Scholar 

  • Gorbunov MY, Kolber ZS, Falkowski PG (1999) Measuring phtosynthetic parameters in individual algal cells by Fast Repetition Rate fluorometry. Photosynth Res 62:141–153

    CAS  Google Scholar 

  • Gorbunov MY, Kolber ZS, Lesser MP, Falkowski PG (2001) Photosynthesis and photoprotection in symbiotic corals. Limnol Oceanogr 46:75–85

    CAS  Google Scholar 

  • Gordon HR (1979) Diffuse reflectance of the ocean: the theory of its augmentation by chlorophyll a fluorescence. Appl Optics 21:2489–2492

    Google Scholar 

  • Govindjee, Satoh K (1986) Fluorescence properties of chlorophyll b- and chlorophyll c-containing algae. In: Govindjee, Amesz J, Fork DC (eds) Light emission by plant and bacteria. Academic Press, Orlando, pp 497–537

    Google Scholar 

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

    CAS  Google Scholar 

  • Gower JFR, Brown L, Borstad GA (2004) Observations of chlorophyll fluorescence in west coast waters of Canada using the MODIS satellite sensor. Can J Remote Sens 30:17–25

    Google Scholar 

  • Gower JFR, Doerffer R, Borstad GA (1999) Interpretation of the 685 nm peak in water-leaving radiance spectra in terms of fluorescence, absorption and scattering, and its observation by MERIS. Int J Remote Sens 20:1771–1786

    Google Scholar 

  • Greene RM, Kolber ZS, Swift DG, Tindale NW, Falkowski PG (1994) Physiological limitation of phytoplankton photosynthesis in the eastern equatorial Pacific determined from variability in the quantum yield of fluorescence. Limnol Oceanogr 39:1061–1074

    CAS  Google Scholar 

  • Hall DO, Rao KK (1999) Photosynthesis, 6th edn. Cambridge University Press, Cambridge

    Google Scholar 

  • Han BP (2001) Photosynthesis-irradiance response at physiological level: A mechanistic model. J Theoret Biol 213:121–127

    CAS  Google Scholar 

  • Han BP (2002) A mechanistic model of algal photoinhibition induced by photodamage to Photosystem-II. J Theoret Biol 214:519–527

    CAS  Google Scholar 

  • Hankamer B, Barber J, Boekema EJ (1997) Structure and membrane organization of photosystem II in green plants. Annu Rev Plant Physiol Plant Mol Biol 48:641–671

    CAS  Google Scholar 

  • Havaux M, Strasser RJ, Greppin H (1991) A theoretical and experimental analysis of the qp and qn coefficients of chlorophyll fluorescence quenching and their relation to photochemical and nonphotochemical events. Photosynth Res 27:41–55

    CAS  Google Scholar 

  • Hofstraat JW, Rubelowsky K, Slutter S (1992) Corrected fluorescence excitation and emission spectra of phytoplankton: toward a more uniform approach to fluorescence measurements. J Plankton Res 14:625–636

    Google Scholar 

  • Hoge FE, Swift RN (1981) Airborne simultaneous spectroscopic detection of laser-induced water Raman backscatter and fluorescence from chlorophyll a and other naturally occurring pigments. Appl Optics 20:3197–3205

    CAS  Google Scholar 

  • Horton P, Ruban AV, Walters RG (1996) Regulation of light harvesting in green plants. Annu Rev Plant Physiol Plant Mol Biol 47:655–684

    CAS  Google Scholar 

  • Huot Y, Brown CA, Cullen JJ (2005) New algorithms for MODIS sun-induced chlorophyll fluorescence and a comparison with present data products. Limnol Oceanogr Meth 3:108–130

    CAS  Google Scholar 

  • Huot Y, Brown CA, Cullen JJ (2007) Retrieval of phytoplankton biomass from simultaneous inversion of reflectance, the diffuse attenuation coefficient, and Sun-induced fluorescence in coastal waters. J Geophys Res 112. doi:10.1029/2006JC003794

    Google Scholar 

  • Ivanov AG, Hurry V, Prafullanchandra VS, Öquist G, Huner NPA (2008a) Reaction centre quenching of excess light energy and photoprotection of photosystem II. J Plant Biol 51:85–96

    CAS  Google Scholar 

  • Ivanov AG, Prafullanchandra VS, Hurry V, Öquist G, Huner NPA (2008b) Photosystem II reaction centre quenching: mechanisms and physiological role. Photosynth Res 98:565–574

    CAS  Google Scholar 

  • Jeffrey SW, Vesk M (1997) Introduction to marine phytoplankton and their pigment signature. In: Jeffrey SW, Mantoura RFC, Wright SW (eds) Phytoplankton pigments in oceanography. UNESCO Publishing, Rome

    Google Scholar 

  • Johnsen G, Prézelin BB, Jovine RVM (1997) Fluorescence excitation spectra and light utilization in two red tide dinoflagellates. Limnol Oceanogr 42:1166–1177

    CAS  Google Scholar 

  • Karapetyan NV (2007) Non-photochemical quenching of fluorescence in cyanobacteria. Biochemistry (Moscow) 72:1127–1135

    CAS  Google Scholar 

  • Kargul J, Barber J (2008) Photosynthetic acclimation: Structural reorganisation of light harvesting antenna - role of redox-dependent phophorylation of major and minor chlorophyll a/b binding proteins. FEBS J 275:1056–1068

    CAS  Google Scholar 

  • Kiefer DA (1973a) Chlorophyll a fluorescence in marine centric diatoms: responses of chloroplasts to light and nutrient stress. Mar Biol 23:39–46

    Google Scholar 

  • Kiefer DA (1973b) Fluorescence properties of natural phytoplankton populations. Mar Biol 22:263–269

    Google Scholar 

  • Kiefer DA, Chamberlin WS, Booth CR (1989) Natural fluorescence of chlorophyll a: relationship to photosynthesis and chlorophyll concentration in the western South Pacific gyre. Limnol Oceanogr 34:868–881

    CAS  Google Scholar 

  • Kiefer DA, Reynolds RA (1992) Advances in understanding phytoplankton fluorescence and photosynthesis. In: Falkowski PG (ed) Primary productivity and biogeochemical cycles in the sea. Plenum Press, New York, pp 155–174

    Google Scholar 

  • Kim HH (1973) New algae mapping technique by the use of an airborne laser fluorosensor. Appl Optics 12:1454–1459

    CAS  Google Scholar 

  • Kolber Z, Falkowski PG (1993) Use of active fluorescence to estimate phytoplankton photosynthesis in situ. Limnol Oceanogr 38:1646–1665

    CAS  Google Scholar 

  • Kolber Z, Wyman KD, Falkowski PG (1990) Natural variability in photosynthetic energy-conversion efficiency – A field-study in the Gulf of Maine. Limnol Oceanogr 35:72–79

    CAS  Google Scholar 

  • Kolber Z, Zehr JR, Falkowski PG (1988) Effects of growth irradiance and nitrogen limitation on photosynthetic energy conversion in photosystem II. Plant Physiol 88:923–929

    CAS  Google Scholar 

  • Kolber ZS, Barber RT, Coale KH, Fitzwater SE, Greene RM, Johnson S, Lindley KS, Falkowski PG (1994) Iron limitation of phytoplankton photosynthesis in the equatorial Pacific Ocean. Nature 371:145–149

    CAS  Google Scholar 

  • Kolber ZS, Prásil O, Falkowski PG (1998) Measurements of variable chlorophyll fluorescence using fast repetition rate techniques: defining methodology and experimental protocols. Biochim Biophys Acta 1367:88–106

    CAS  Google Scholar 

  • Kopf U, Heinze J (1984) 2, 7-Bis(diethylamino)phenazoxonium chloride as a quantum counter for emission measurements between 240 and 700 nm. Anal Chem 56:1931–1935

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  • Krause GH, Jahns P (2004) Non-photochemical energy dissipation determined by chlorophyll fluorescence quenching: characterization and function. In: Papageorgiou GC, Govindjee (eds) Chlorophyll a fluorescence: a signature of photosynthesis. Springer, Berlin, pp 463–495

    Google Scholar 

  • Krause GH, Weis E (1991) Chlorophyll fluorescence: the basics. Annu Rev Plant Physiol 42:313–349

    CAS  Google Scholar 

  • Kromkamp JC, Forster RM (2003) The use of variable fluorescence measurements in aquatic ecosystems: differences between multiple and single turnover measuring protocols and suggested terminology. Eur J Phycol 38:103–112

    Google Scholar 

  • Laney SR (2003) Assessing the error in photosynthetic properties determined by fast repetition rate fluorometry. Limnol Oceanogr 48:2234–2242

    Google Scholar 

  • Laney SR, Letelier RM (2008) Artifacts in measurements of chlorophyll fluorescence transients, with specific application to fast repetition rate fluorometry. Limnol Oceanogr Meth 6:40–50

    CAS  Google Scholar 

  • Lavaud J, Rousseau B, Etienne A-L (2004) General features of photoprotection by energy dissipation in planktonic diatoms (Bacillariophyceae). J Phycol 40:130–137

    Google Scholar 

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

    CAS  Google Scholar 

  • Laws EA (1991) Photosynthetic quotients, new production and net community production in the open ocean. Deep Sea Res Part A 38:143–167

    CAS  Google Scholar 

  • Lazar 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 Theoret Biol 220:469–503

    CAS  Google Scholar 

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

    Google Scholar 

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

    Google Scholar 

  • Letelier R, Abbott MR (1996) An analysis of chlorophyll fluorescence algorithms for the Moderate Resolution Imaging Spectrometer (MODIS). Remote Sens Environ 58:215–223

    Google Scholar 

  • Liu G, Janowitz GS, Kamykowski D (2001) A biophysical model of population dynamics of the autotrophic dinoflagellate Gymnodinium breve. Mar Ecol Prog Ser 210:101–124

    CAS  Google Scholar 

  • Loftus ME, Seliger HH (1975) Some limitations of the in vivo fluorescence technique. Chesapeake Sci 16:79–92

    CAS  Google Scholar 

  • Lorenzen CJ (1966) A method for the continuous measurement of in vivo chlorophyll concentration. Deep Sea Res 13:223–227

    Google Scholar 

  • Lutz VA, Sathyendranath S, Head EJH, Li WKW (1998) Differences between in vivo absorption and fluorescence excitation spectra in natural samples of phytoplankton. J Phycol 34:214–227

    Google Scholar 

  • Lutz VA, Sathyendranath S, Head EJH, Li WKW (2001) Changes in the in vivo absorption and fluorescence excitation spectra with growth irradiance in three species of phytoplankton. J Plankton Res 23:555–569

    CAS  Google Scholar 

  • MacIntyre HL, Kana TM, Anning T, Geider RJ (2002) Photoacclimation of photosynthesis irradiance response curves and photosynthetic pigments in microalgae and cyanobacteria. J Phycol 38:17–38

    Google Scholar 

  • Maritorena S, Morel A, Gentili B (2000) Determination of the fluorescence quantum yield by oceanic phytoplankton in their natural habitat. Appl Optics 39:6725–6737

    CAS  Google Scholar 

  • Marshall HL, Geider RJ, Flynn KJ (2000) A mechanistic model of photoinhibition. New Phytol 145:347–359

    Google Scholar 

  • Mauzerall DC (1972) Light-induced changes in Chlorella, and the primary photoreaction for the production of oxygen. Proc Nat Acad Sci USA 69:1358–1362

    CAS  Google Scholar 

  • Mauzerall DC, Greenbaum NL (1989) The absolute size of a photosynthetic unit. Bioch Biophys Acta 974:119–140

    CAS  Google Scholar 

  • Melis A (1999) Photosystem-II damage and repair cycle in chloroplasts: what modulates the rate of photodamage in vivo. Trends Plant Sci 4:130–135

    Google Scholar 

  • Miller WL, Moran MA, Sheldon WM, Zepp RG, Opsahl S (2002) Determination of apparent quantum yield spectra for the formation of biologically labile photoproducts. Limnol Oceanogr 47:343–352

    CAS  Google Scholar 

  • Millie DF, Schofield OME, Kirkpatrick GJ, Johnsen G, Evens TJ (2002) Using absorbance and fluorescence spectra to discriminate microalgae. Eur J Phycol 37:313–322

    Google Scholar 

  • Mitchell BG, Kiefer DA (1988) Chlorophyll a specific absorption and fluorescence excitation spectra for light-limited phytoplankton. Deep Sea Res 35:639–663

    CAS  Google Scholar 

  • Mobley CD (1994) Light and water radiative transfer in natural waters, 1st edn. Academic Press, San Diego

    Google Scholar 

  • Moore CM, Suggett DM, Hickman AE, Kim Y-N, Tweddle JF, Sharples J, Geider RJ, Holligan PM (2006) Phytoplankton photoacclimation and photoadaptation in response to environmental gradients in a shelf sea. Limnol Oceanogr 51: 936–949

    Google Scholar 

  • Morel A (1988) Optical modeling of the upper ocean in relation to its biogenous matter content (case 1 waters). J Geophys Res-Oceans 93:10749–10768

    Google Scholar 

  • Morel A, Bricaud A (1981) Theoretical results concerning light absorption in a discrete medium, and application to specific absorption of phytoplankton. Deep-Sea Res 28:1375–1393

    Google Scholar 

  • Morel A, Bricaud A (1986) Inherent properties of algal cells including picoplankton: Theoretical and experimental results. In: Platt T, Li WKW (eds) Photosynthetic picoplankton. Can Bull Fish Aquat Sci 214:521–559

    Google Scholar 

  • Morel A, Prieur L (1977) Analysis of variations in ocean color. Limnol Oceanogr 22:709–722

    Google Scholar 

  • Morrison JR (2003) In situ determination of the quantum yield of phytoplankton chlorophyll a fluorescence: a simple algorithm, observations, and a model. Limnol Oceanogr 48:618–631

    Google Scholar 

  • Neale PJ, Cullen JJ, Yentsch CM (1989) Bio-optical inferences from chlorophyll a fluorescence: what kind of fluorescence is measured in flow cytometry? Limnol Oceanogr 34:1739–1748

    CAS  Google Scholar 

  • Nelson N, Yocum CF (2006) Structure and function of photosystems I and II. Annu Rev Plant Biol 57:521–565

    CAS  Google Scholar 

  • Neori A, Vernet M, Holm-Hansen O, Haxo FT (1986) Relationship between action spectra for chlorophyll a fluorescence and photosynthetic O2 evolution in algae. J Plankton Res 8:537–548

    CAS  Google Scholar 

  • Neori A, Vernet M, Holm-Hansen O, Haxo FT (1988) Comparison of chlorophyll far-red and red fluorescence excitation spectra with photosynthetic oxygen action spectra for photosystem II in algae. Mar Ecol Prog Ser 44:297–302

    CAS  Google Scholar 

  • Neville RA, Gower JFR (1977) Passive remote sensing of phytoplankton via chlorophyll fluorescence. J Geophys Res 82:3487–3493

    Google Scholar 

  • Niyogi KK (1999) Photoprotection revisited: Genetic and molecular approaches. Annu Rev Plant Physiol Plant Mol Biol 50:333–359

    CAS  Google Scholar 

  • Noctor G, Foyer CH (2000) Homeostasis of adenylate status during photosynthesis in a fluctuating environment. J Exp Bot 51:347–356

    CAS  Google Scholar 

  • Olaizola M, Geider RJ, Harrison WG, Graziano LM, Ferrari GM, Schlittenhardt PM (1996) Synoptic study of variations in the fluorescence-based maximum quantum efficiency of photosynthesis across the North Atlantic Ocean. Limnol Oceanogr 41:755–765

    CAS  Google Scholar 

  • Olaizola M, Yamamoto HY (1994) Short-term responses of the diadinoxanthin cycle and fluorescence yield in Chaetoceros muelleri. J Phycol 30:606–612

    CAS  Google Scholar 

  • Olson RJ, Chekalyuk AM, Sosik HM (1996) Phytoplankton photosynthetic characteristics from fluorescence induction assays of individual cells. Limnol Oceanogr 41:1253–1263

    Google Scholar 

  • Olson RJ, Sosik HM, Chekalyuk AM (1999) Photosynthetic characteristics of marine phytoplankton from pump-during-probe fluorometry of individual cells at sea. Cytometry 37:1–13

    CAS  Google Scholar 

  • Olson RJ, Zettler ER, Chisholm SW, Dusenberry JA (1991) Flow cytometry in oceanography. In: Demers S (ed) Particle analysis in oceanography. Springer, Berlin, pp 351–399

    Google Scholar 

  • Ostrowska M, Darecki M, Wozniak B (1997) An attempt to use measurements of sun-induced chlorophyll fluorescence to estimate chlorophyll a concentration in the Baltic Sea. Proc SPIE, Int Soci Optical Eng 3222:528–537

    CAS  Google Scholar 

  • Ostrowska M, Majchrowski R, Matorin DN, Wozniak B (2000a) Variability of the specific fluorescence of chlorophyll in the ocean. Part 1. Theory of classical in situ chlorophyll fluorometry. Oceanologia 42:203–219

    Google Scholar 

  • Ostrowska M, Matorin DN, Ficek D (2000b) Variability of the specific fluorescence of chlorophyll in the ocean. Part 2. Fluorometric method of chlorophyll a determination. Oceanologia 42:221–229

    Google Scholar 

  • Oxborough K, Baker NR (2000) An evaluation of the potential triggers of photoinactivation of photosystem II in the context of a Stern-Volmer model for downregulation and the reversible radical pair equilibrium. Phil Trans Roy Soc London 355:1489–1498

    CAS  Google Scholar 

  • Park Y-I, Chow WS, Anderson JM (1995) Light inactivation of functional photosystem II in leaves of peas grown in moderate light depends on photon exposure. Planta 196:401–411

    CAS  Google Scholar 

  • Parkhill J-P, Maillet G, Cullen JJ (2001) Fluorescence-based maximal quantum yield for PSII as a diagnostic of nutrient stress. J Phycol 37:517–529

    Google Scholar 

  • Poole LR, Esaias WE (1982) Water Raman normalization of airborn laser fluorosensor measurements: a computer model study. Appl Optics 21:1982

    Google Scholar 

  • Prézelin BB (1981) Light reactions in photosynthesis. In: Platt T (ed) Physiological bases of phytoplankton ecology. Can Bull Fish Aquat Sciences 210:1–43

    Google Scholar 

  • Prezelin BB, Boczar BA (1986) Molecular bases of cell absorption and fluorescence in phytoplankton: potential applications to studies in optical oceanography. Prog Phycol Res 4:349–464

    CAS  Google Scholar 

  • Raateoja M, Seppälä J, Ylöstalo P (2004) Fast repetition rate fluorometry is not applicable to studies of filamentous cyanobacteria from the Baltic Sea. Limnol Oceanogr 49:1006–1012

    Google Scholar 

  • Raven JA, Geider RJ (2003) Adaptation, acclimation and regulation in algal phtosynthesis. In: Larkum AWD, Douglas SE, Raven JA (eds) Photosynthesis in algae. Kluwer, Dordrecht, pp 385–412

    Google Scholar 

  • Roesler CS, Perry MJ (1995) In situ phytoplankton absorption, fluorescence emission, and particulate backscattering spectra determined from reflectance. J Geophys Res 100:13279–13294

    Google Scholar 

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

    Google Scholar 

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

    Google Scholar 

  • Roy S, Legendre L (1979) DCMU-enhanced fluorescence as an index of photosynthetic activity of phytoplankton. Mar Biol 55:93–101

    CAS  Google Scholar 

  • Ruban AV Berera R, Ilioaia C, van Stokkum IHM, Kennis JTM, Pascal AA, van Amerongen H, Robert B, Horton P, van Grondelle R (2007) Identification of a mechanism of photoprotective energy dissipation in higher plants. Nature 450:575–578

    CAS  Google Scholar 

  • Ruban AV, Lavaud J, Rousseau B, Guglielmi G, Horton P, Etienne A-L (2004) The super-excess energy dissipation in diatom algae: comparative analysis with higher plants. Photosynth Res 82:165–175

    CAS  Google Scholar 

  • Sakshaug E, Johnsen G, Andresen K, Vernet M (1991) Modeling of light-dependent algal photosynthesis and growth: experiments with the Barents Sea diatoms Thalassiosira nordenskioeldii and Chaetoceros furcellatus. Deep Sea Res A 38:415–430

    Google Scholar 

  • Sathyendranath S, Platt T, Irwin B, Horne E, Borstad G, Stuart V, Payzant L, Maass H, Kepkay P, Li P, Spry J, Gower J (2004) A multispectral remote sensing study of coastal waters off Vancouver Island. Int J Remote Sens 25:893–919

    Google Scholar 

  • Schallenberg C, Lewis MR, Kelley DE, Cullen JJ (2008) The inferred influence of nutrient availability on the relationship between sun-induced fluorescence and incident irradiance in the Bering Sea. J Geophys Res 113:C07046. doi:07010.01029/02007JC004355

    Google Scholar 

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

    CAS  Google Scholar 

  • 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

    CAS  Google Scholar 

  • Sciandra A, Lazzara L, Claustre H, Babin M (2000) Responses of growth rate, pigment composition and optical properties of Cryptomonas sp. to light and nitrogen stresses. Mar Ecol Prog Ser 201:107–120

    CAS  Google Scholar 

  • Smyth TJ, Pemberton KL, Aiken J, Geider RJ (2004) A methodology to determine primary production and phytoplankton photosynthetic parameters from fast repetition rate fluorometry. J Plankton Res 26:1337–1350

    CAS  Google Scholar 

  • SooHoo JB, Kiefer DA (1982) Vertical distribution of phaeopigments — II. Rates of production and kinetics of photooxidation. Deep-Sea Res 29:1553–1563

    CAS  Google Scholar 

  • Sosik HM, Mitchell BG (1995) Light absorption by phytoplankton, photosynthetic pigments and detritus in the California Current System. Deep Sea Res I 42:1717–1748

    Google Scholar 

  • Sosik HM, Olson JS, Neubert MG, Shalapyonok A, Solow AR (2003) Growth rates of coastal phytoplankton from time-series measurements with a submersible flow cytometer. Limnol Oceanog 48:1756–1765

    Google Scholar 

  • Stegmann PM, Lewis MR, Davis CO, Cullen JJ (1992) Primary production estimates from recordings of solar-stimulated fluorescence in the Equatorial Pacific at 150˚W. J Geophys Res 97:627–638

    Google Scholar 

  • Stirbet A, Govindjee SBJ, Strasser RJ (1998) Chlorophyll a fluorescence induction in higher plants: modelling and numerical simulation. J Theoret Biol 193:131–151

    CAS  Google Scholar 

  • Strasser RJ, Srivastava A, Govindgee (1995) Polyphasic chlorophyll a fluorescence transient in plants and cyanobacteria. Photochem Photobiol 61:32–42

    CAS  Google Scholar 

  • Suggett DJ, Kraay G, Holligan P, Davey M, Aiken J, Geider RJ (2001) Assessment of photosynthesis in a spring cyanobacterial bloom by use of a fast repetition rate fluorometer. Limnol Oceanogr 46:802–810

    Google Scholar 

  • Suggett DJ, MacIntyre HL, Geider RJ (2004) Evaluation of biophysical and optical determination of light absorption by photosystem II in phytoplankton. Limnol Oceanogr Meth 2:316–332

    Google Scholar 

  • Suggett DJ, Moore CM, Hickman AE, Geider RJ (2009) Interpretation of fast repetition rate (FRR) fluorescence: signature of phytoplankton community structure versus physiological state. Mar Ecol Prog Ser 376:1–19

    Google Scholar 

  • Suggett DJ, Oxborough K, Baker NR, MacIntyre HL, Kana TM, Geider RJ (2003) Fast repetition rate and pulse amplitude modulation chlorophyll a fluorescence measurements for assessment of photosynthetic electron transport in marine phytoplankton. Eur J Phycol 38:371–384

    Google Scholar 

  • Timmermans KR, van der Woerd HJ, Wernand MR, Sligting M, Uitz J, de Baar HJW (2008) In situ and remote-sensed chlorophyll fluorescence as indicator of the physiological state of phytoplankton near the Isles Kerguelen (Souther Ocean). Polar Biol 31:617–628

    Google Scholar 

  • Ting CS, Rocap G, King J, Chisholm SW (2002) Cyanobacterial photosynthesis in the oceans: the origins and significance of divergent light-harvesting strategies. Trends Microbiol 10:134–142

    CAS  Google Scholar 

  • Trees CC, Clark DK, Bidigare RR, Ondrusek ME, Mueller JL (2000) Accessory pigments versus chlorophyll a concentrations within the euphotic zone: A ubiquitous relationship. Limnol Oceanogr 45:1130–1143

    CAS  Google Scholar 

  • 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

    CAS  Google Scholar 

  • Vaulot D, Marie D (1999) Diel variability of photosynthetic picolankton in the equatorial Pacific. J Geophys Res 104:3297–3310

    CAS  Google Scholar 

  • Vermotte C, Etienne A-L, Briantais J-M (1979) Quenching of the system II chlorophyll fluorescence by the plastoquinone pool. Biochim Biophys Acta 545:519–527

    Google Scholar 

  • Vincent WF (1981) Photosynthetic capacity measured by DCMU-induced chlorophyll fluorescence in an oligotrophic lake. Freshw Biol 11:61–78

    Google Scholar 

  • Welschmeyer NA (1994) Fluorometric analysis of chlrophyll a in the presence of chlorophyll b and pheopigments. Limnol Oceanogr 39:1985–1992

    CAS  Google Scholar 

  • Westberry TK, Siegel DA (2003) Phytoplankton natural fluorescence variability in the Sargasso Sea. Deep Sea Res I 50:417–434

    Google Scholar 

  • 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

    CAS  Google Scholar 

  • Whitmarsh J, Govindjee (1999) The photosynthetic process. In: Singhal GS, Renger R, Sopory SK, Irrgang K-D, Govindjee (eds) Concepts in photobiology: photosynthesis and photomorphogenesis. Narosa-Publishing, New Delhi, pp 11–51

    Google Scholar 

  • Yentsch CM, Horan PK, Muirhead K, Dortch Q, Haugen E, Legendre L, Muphy LS, Perry MJ, Phinney DA, pomponi SA, Spinrad RW, Wood M, Yentsch CS Zahoranec BJ (1983) Flow cytometry and cell sorting: a technique for analysis and sorting of aquatic particles. Limnol Oceanogr 28:1275–1280

    Google Scholar 

  • Yentsch CS, Menzel DW (1963) A method for the determination of phytoplankton chlorophyll and phaeophytin by fluorescence. Deep Sea Res 10:221–231

    CAS  Google Scholar 

  • Yentsch CS, Phinney DA (1985) Spectral fluorescence: a taxonomic tool for studying the structure of phytoplankton populations. J Plankton Res 7:617–632

    CAS  Google Scholar 

  • Yentsch CS, Yentsch CA (1979) Fluorescence spectral signatures: the characterization of phytoplankton populations by the use of excitation and emission. J Mar Res 37:471–483

    CAS  Google Scholar 

  • Zonneveld C (1997) Modelling the effects of photoadaptation on the photosynthesis-irradiance curve. J Theoret Biol 186:381–388

    CAS  Google Scholar 

  • Zouni A, Witt HT, Fromme P, Krauss N, Saenger W, Orth P (2001) Crystal structure of photosystem II from Synechococcus elongatus a 3.8Å resolution. Nature 409:739–743

    CAS  Google Scholar 

Download references

Acknowledgements

We are very thankful to John Cullen for sharing with us his insights on chlorophyll fluorescence over the years. This work was funded by a CNES grant to M. Babin and a CNES fellowship to Y. Huot.

Author information

Authors and Affiliations

  1. Département de Géomatique Appliquée, Université de Sherbrooke, Sherbrooke, J1K 2R1, Québec, Canada

    Yannick Huot

  2. Laboratoire d’Océanographie de Villefranche, UMR 7093, Université Pierre et Marie Curie-Paris 6, Paris, France

    Marcel Babin

Authors
  1. Yannick Huot
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marcel Babin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yannick Huot .

Editor information

Editors and Affiliations

  1. , Department of Biological Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom

    David J. Suggett

  2. Institute of Microbiology, Opatovciky mlyn, Trebon, 379 81, Czech Republic

    Ondrej Prášil

  3. Murdoch University, School of Biological Sciences and Biotec, Algae R&D Center, Murdoch, 6150, West Australia, Australia

    Michael A. Borowitzka

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer Netherlands

About this chapter

Cite this chapter

Huot, Y., Babin, M. (2010). Overview of Fluorescence Protocols: Theory, Basic Concepts, and Practice. In: Suggett, D., Prášil, O., Borowitzka, M. (eds) Chlorophyll a Fluorescence in Aquatic Sciences: Methods and Applications. Developments in Applied Phycology, vol 4. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-9268-7_3

Download citation

Publish with us

Policies and ethics

Search

Navigation