Anmerkung: Intro -- Chlorophyll a Fluorescence in Aquatic Sciences -- Preface -- Contents -- Contributors -- Chapter 1: Chlorophyll Fluorescence Terminology: An Introduction -- 1 Introduction -- 2 Light and Absorption -- 3 Fluorescence -- 3.1 Fast Phase (O-J-I-P) -- 3.1.1 Additional Features -- 3.2 Slow Phase (S-M-T) -- 3.3 The Saturation Pulse Method -- 3.4 Quantum Yield for PSII (FPSII) -- 3.5 Quenching -- 4 Conclusion -- References -- Chapter 2: In Situ Measurement of Variable Fluorescence Transients -- 1 Introduction -- 2 Phytoplankton Variable Fluorescence In Situ -- 2.1 Dynamical Protocols for Stimulating Variable Fluorescence -- 2.2 The Practical Relevance of the Single-turnover Time Scale In Situ -- 2.3 Issues Related to the Marine Light Field -- 2.4 Apparent Effects Resulting from Assemblage Composition -- 2.5 Effects Due to Optical Properties of Natural Waters -- 3 Conclusions and Future Directions -- References -- Chapter 3: Overview of Fluorescence Protocols: Theory, Basic Concepts, and Practice -- 1 Introduction -- 2 Theoretical Background -- 2.1 The Fluorescing Properties of Chlorophyll a -- 2.2 Source of Fluorescence in Seawater and Mathematical Description of Fluorescence Emission -- 2.3 The Functional Organization of the Photosynthetic Apparatus -- 2.3.1 Photosystem II -- 2.3.2 The Photosynthetic Chain -- 2.4 Adaptation, Acclimation, Regulation of Phytoplankton -- 2.5 Fates of Absorbed Photons Within PSII -- 2.6 A Simple Model of In Vivo Processes In PSII At Room Temperature -- 2.6.1 Quantum Yield of Fluorescence -- 2.7 Charge Separation at PSII -- 2.8 Photochemical Quenching of Fluorescence -- 2.9 Non-photochemical Quenching of Fluorescence -- 2.9.1 Energy-dependent Non-photochemical Quenching -- 2.9.2 Quenching Due to State Transitions -- 2.9.3 Quenching Linked to Inhibition -- 2.9.4 Reaction Center Quenching. , 2.10 Transient Changes in Fluorescence -- 3 Protocols for Measurement of In Vivo Phytoplankton Fluorescence, and the Use of Chl a Fluorescence to Study Phytoplankton -- 3.1 The Determination of Biomass In Vivo -- 3.1.1 Basic Principle -- 3.1.2 Instruments and Protocols -- 3.1.3 Validity of the Underlying Assumptions -- 3.1.4 Examples -- 3.2 Spectrofluorometry -- 3.2.1 Basic Principle -- 3.2.2 Instruments and Protocols -- 3.2.3 Validity of the Underlying Assumptions -- 3.2.4 Examples -- 3.3 Sun-induced Chlorophyll Fluorescence -- 3.3.1 Validity of the Underlying Assumptions -- 3.3.2 Examples -- 3.4 Flow Cytometry -- 3.5 Laser Excitation and LIDAR Fluorometry -- 3.6 Variable Fluorescence -- 3.6.1 Basic Principle -- 3.6.2 Instruments and Protocols -- Use of DCMU -- Pulse Amplitude Modulation -- Pump-and-Probe -- Fast Repetition Rate -- 3.6.3 Validity of the Underlying Assumptions -- 3.6.4 Examples -- 4 The Use of Chlorophyll Fluorescence to Estimate Primary Production -- 4.1 Variable Fluorescence -- 4.1.1 If is Available (FRRF and Pump and Probe Protocol) -- 4.1.2 When is not Available (PAM Protocol) -- 4.2 Sun-induced Chlorophyll Fluorescence -- 5 Conclusion -- 6 List of Symbols -- References -- Chapter 4: Fluorescence as a Tool to Understand Changes in Photosynthetic Electron Flow Regulation -- 1 Introduction -- 2 Electron Usage in Photosynthesis -- 2.1 Alternative Electron Cycling (AEC) -- 2.2 Electron Usage to Produce New Biomass -- 3 Effect of Light Stress on Fluorescence Signatures and their Interpretation -- 4 Use of Chemicals for the Differentiation of Photosynthetic Processes -- 4.1 Inhibitors of Linear Electron Transport -- 4.2 Inhibitors of Cyclic Electron Transport -- 4.3 Inhibitors of Alternative Electron Cycling (AEC) -- 4.4 Inhibitors of CO2 Fixation -- 4.5 Electron Transport Uncouplers -- 4.6 Electron Acceptors -- References. , Chapter 5: Microscopic Measurements of the Chlorophyll a Fluorescence Kinetics -- 1 Introduction -- 2 Fluorescence Techniques in High Resolution -- 3 Applications of Fluorescence Kinetic Microscopy -- References -- Chapter 6: Estimating Aquatic Productivity from Active Fluorescence Measurements -- 1 Fluorescence as a Probe for Photosynthesis -- 2 Overview of the Theory of Calculating ETRPSII -- 2.1 Measuring fPSII¢ and Calculating ETR -- 2.2 Examining Changes to the Quantum Yield Under Actinic Light -- 3 Light Absorption by Photosystem II -- 3.1 Bio-Physical Measures of PSII Absorption and Calculationof Chlorophyll-Specific ETR -- 3.2 Bio-Optical Based Determinationsof PSII Absorption -- 4 Reconciling Active Fluorescence-based Estimates of Productivity with Gas Exchange -- 4.1 Practical Constraints in Comparing Fluorescence- and Gas Exchange-Based Productivity Measurements -- 4.2 Are ETRs Indicative of Gross O2 Evolution? -- 4.3 Estimating Net O2 Production and C-Fixation from ETRs -- 4.4 Reconciliation of ETRPSII : O2 : CO2 Estimates -- 5 Future Application of ETRs to Primary Productivity Studies -- References -- Chapter 7: Taxonomic Discrimination of Phytoplankton by Spectral Fluorescence -- 1 Introduction -- 2 The Principles of Taxonomy by Spectral Fluorescence -- 2.1 Energy Transfer Between Pigments -- 2.2 Taxonomic Differences in Fluorescence Spectra -- 2.3 Taxonomic Discrimination by Spectral Fluorescence -- 3 Variation in Chlorophyll-specific Fluorescence, FChl -- 3.1 Inter-Specific Variability -- 3.2 Intra-specific Variability -- 3.3 Short-Term Quenching -- 4 Optical Indices and Application of the SFS Approach in the Field -- 4.1 Bias in SFS by Background Absorption and Scattering -- 4.2 Quenching In Situ and Taxonomic Assessment -- 5 A Field Test of the SFS Approach -- 6 Conclusion -- References. , Chapter 8: Flow Cytometry in Phytoplankton Research -- 1 Introduction -- 2 Background and Historical Perspective -- 3 Select Research Applications -- 3.1 Picophytoplankton Community Structure and Dynamics -- 3.2 Time Resolved Pulses for Physiological and Ecological Studies -- 3.3 Cell Sorting for Physiology and Diversity -- 3.4 Interpretation of Optical Variability in the Ocean -- 4 Emerging Approaches and Applications -- References -- Chapter 9: The Use of the Fluorescence Signal in Studies of Seagrasses and Macroalgae -- 1 Introduction -- 2 Major Achievements Using the Chlorophyll a Fluorescence Signal in Seagrass and Macroalgae Studies -- 2.1 Quenching Analysis -- 2.2 Analysis of Quenching Components: Use of Chemicals -- 3 Protocols Used, Limitations and Specific Modifications for Aquatic Macrophytes -- 3.1 Determination of the Variation in Fv/Fm and DF/Fm¢ -- 3.2 Limitation of the Use of Rapid Light Curves (RLC) -- 3.3 The Importance of Photosynthesis Induction -- 3.4 Determination of Absorptance, PSII Effective Absorption Cross-Section and the Number of Reaction Centers -- 3.5 Use of Relative ETR Values (rETR) -- 3.6 The Use of Electron Transport Rates Values (ETR) as Descriptors of Gross Photosynthesis (GPS) -- 4 Final Comments -- References -- Chapter 10: Chlorophyll Fluorescence in Reef Building Corals -- 1 Introduction -- 2 Natural Patterns of Fluorescence -- 2.1 Multiple and Single Turnover Instrumentation -- 2.2 Non-Photochemical Quenching -- 3 Detecting Stress -- 4 Protocols and Pitfalls -- 4.1 Dark Acclimation, Sample Area and Related Matters -- 4.2 Electron Transport Rate -- 5 Conclusion -- References -- Chapter 11: Assessing Nutrient Status of Microalgae Using Chlorophyll a Fluorescence -- 1 Introduction -- 2 Defining Nutrient Limitation -- 3 The Effects of Nutrient Limitation on Phytoplankton -- 3.1 Nitrogen -- 3.2 Phosphorus. , 3.3 Iron -- 4 Measuring Nutrient Limitation -- 4.1 Nutrient Enrichment Bioassays -- 4.2 Chlorophyll a Fluorescence as a Measure of Nutrient Stress -- 4.3 Natural Population Enrichments and Chlorophyll a Fluorescence -- 5 NIFTS -- 5.1 What is a NIFT? -- 5.2 How to Measure NIFTs -- 5.3 The Characteristics of the NIFT Response are Dependent on the Limiting Nutrient -- 5.4 NIFT Responses of Different Taxa -- 5.5 Mechanisms Behind NIFTs -- 6 Conclusion -- References -- Chapter 12: The Application of Variable Chlorophyll Fluorescence to Microphytobenthic Biofilms -- 1 Introduction to Benthic Biofilms -- 2 The Effects of Subsurface Signal -- 2.1 Microphytobenthic Biofilms on Soft Sediments -- 2.2 Stromatolites - the effect of "layered" biofilms -- 2.3 Deconvolution of Depth Integrated Signals -- 3 Down Regulation Through Non-photochemical Quenching -- 3.1 NPQ and the Xanthophyll Cycle in Diatoms -- 3.2 NPQ in the Dark -- 4 The Quantification of the Microalgal Biomass Using Fluorescence -- 5 Calculation of Electron Transport Rate: ETR v rETR -- 5.1 Multiple and Single Turnover Methods -- 5.2 The MT-method -- 5.3 The ST-method -- 5.4 Assumptions and Uncertainties -- 5.5 Calculation of ETR in Microphytobenthos Studies -- 6 Light Response Curves -- 6.1 A Brief Overview of Methodology -- 6.2 Steady State Light Curves -- 6.3 Rapid Light Curves -- 6.4 Non-sequential Light Curves -- 6.5 Light Curves Summary -- 7 Comparison of Fluorescence with Other Methodologies -- 8 General Summary -- References -- Chapter 13: Chlorophyll Fluorescence Applications in Microalgal Mass Cultures -- 1 Preface -- 2 Historical Overview of Using Chl Fluorescence in Microalgal Mass Cultures -- 3 Microalgae Grown for Commercial Purposes and Cultivation Systems -- 4 Principles of Microalgae Mass Culturing -- 4.1 Culture Maintenance. , 5 Interpretation of Chl Fluorescence Parameters in MicroalgaeMass Cultures.