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.

Anmerkung: Intro -- Algae for Biofuels and Energy -- Preface -- Contents -- Contributors -- 1: Energy from Microalgae: A Short History -- 1 Introduction -- 2 The Pioneers -- 3 The Early Years (1940s & -- 1950s) -- 4 The 1960s and 1970s -- 5 Commercial Production of Microalgae -- 6 The "Algae Species Programme" (USA) -- 7 The RITE Biological CO2 Fixation Programme (Japan) -- 8 Other Work -- 8.1 Botryococcus -- 8.2 Hydrogen -- 8.3 Closed Photobioreactors -- 8.4 Downstream Processing -- 9 Conclusion -- References -- 2: Algal Lipids and Their Metabolism -- 1 Introduction -- 2 Algal Lipids -- 2.1 Polar Glycerolipids -- 2.1.1 Phosphoglycerides -- 2.1.2 Glycosylglycerides -- 2.1.3 Betaine Lipids -- 2.1.3.1 Role of Polar Glycerolipids and Their Fatty Acids in Photosynthesis -- 2.2 Non-polar Storage Lipids -- 2.2.1 Triacylglycerols -- 2.2.2 Hydrocarbons -- 3 Biosynthesis of Glycerolipids -- 3.1 Fatty Acid and Polar Glycerolipid Biosynthesis -- 3.2 Biosynthesis of TAG -- 4 Factors Affecting Lipid Composition and Lipid Productivity of Algae -- 4.1 General Growth Conditions -- 4.1.1 Temperature -- 4.1.2 Light -- 4.1.3 Salt Concentrations -- 4.1.4 pH -- 4.1.5 Nutrients -- 5 Conclusion and Future Directions -- References -- 3: Hydrogenases, Nitrogenases, Anoxia, and H2 Production in Water-Oxidizing Phototrophs -- 1 Introduction -- 2 Structure, Function and Maturation of H2 -Producing Enzymes -- 3 [FeFe]-Hydrogenase Occurrence and Diversity -- 4 [FeFe]-Hydrogenase Structure and Function -- 5 [FeFe]-Hydrogenase Maturation -- 6 [NiFe]-Hydrogenase Phylogeny -- 7 [NiFe]-Hydrogenase Structure and Function -- 8 [NiFe]-Hydrogenase Maturation -- 9 Nitrogenase Genetic Diversity -- 10 Nitrogenase Structure and Function -- 11 Nitrogenase Maturation and FeMo-Cofactor Biosynthesis -- 12 Hydrogen Production in Phototrophic Organisms. , 13 Hydrogenase Activity in Eukaryotic Phototrophs -- 13.1 Hydrogen Production Pathways -- 13.2 Hydrogen Utilization Pathways -- 13.3 Hydrogen Production During Sulfur Deprivation -- 13.4 Hydrogenase Transcriptional Regulation -- 13.5 Hydrogenase Oxygen Sensitivity -- 13.6 Hydrogenase Activity Modulation -- 13.7 Fermentative Metabolism in C. reinhardtii -- 13.8 Genomics and Systems Biology in C. reinhardtii -- 14 Hydrogen Production in Cyanobacteria -- 14.1 Intrinsic Factors Studies -- 15 Engineering Approaches for Improved H2 Production -- 16 Glucose Oxidation for H2 Production -- 17 Outlook -- References -- 4: Species and Strain Selection -- 1 Introduction -- 2 Species and Strain Characteristics -- 2.1 Optimum Temperature and Temperature Tolerance -- 2.2 Carbon Supply, pH and Oxygen Tolerance -- 2.3 Respiration Rate -- 2.4 Salinity -- 2.5 Morphology -- 2.6 'Competitive' Strains -- 2.7 Lipid Composition and Quality -- 2.8 Co-products -- 3 Species or Strain? -- 4 Strain Selection In Situ -- 5 A Rapid Screening Approach -- 6 Strain Improvement -- 7 Maintenance of Cultures -- 8 Conclusion -- References -- 5: Limits to Phototrophic Growth in Dense Culture: CO2 Supply and Light -- 1 Introduction -- 2 Intrinsic Limitations to Growth -- 3 The End Product of Metabolism and the Production of Secondary Metabolites Can Impact on Growth Rate -- 4 Light Is Attenuated Exponentially in Cultures, So Is Potentially Growth Limiting -- 5 Diffusive Entry of CO2 Is Not Necessarily Limiting Under Air-Equilibrated Conditions, But Can Rapidly Become Limiting in Dense Cultures -- 6 The Kinetic Characteristics of Rubisco Potentially Limit Inorganic Carbon Acquisition Under Air-Equilibrated Conditions -- References -- 6: Genetic Engineering to Improve Algal Biofuels Production -- 1 Introduction. , 2 Tools and Techniques for Chlamydomonas reinhardtii Genetic Engineering -- 2.1 Chloroplast Engineering -- 2.1.1 The Chloroplast -- 2.1.2 Chloroplast Transformation -- 2.1.3 Translational and Transcriptional Control of Transgenes -- 2.1.4 Selection -- 2.1.5 Generating Stable Homoplasmic Lines -- 2.1.6 Chloroplasts as Protein Factories -- 2.2 Nuclear Engineering -- 2.2.1 The Nuclear Genome -- 2.2.2 Nuclear Transformation -- 2.2.3 Translational and Transcriptional Control of Transgenes -- 2.2.4 Selection -- 2.2.5 Expression of Foreign Genes -- 2.2.6 Gene Silencing in the Green Alga Chlamydomonas reinhardtii -- 3 Genetic Engineering of Other Algae -- 3.1 Green Algae -- 3.2 Diatoms -- 3.3 Dinoflagellates -- 3.4 Red Algae -- 3.5 Plastid Transformation -- 3.6 Inducible Systems -- 3.7 Riboswitches -- 4 Metabolic Engineering of Microalgae -- 4.1 Enhanced Lipid Production -- 4.2 Enhanced Hydrogen Production -- 4.3 Light-Harvesting Antennae Engineering -- 4.4 Trophic Conversion -- 4.5 Metabolic Engineering of Carotenoids -- 5 Other Areas Appropriate for Genetic Engineering for Algal Biofuels Production -- 5.1 Crop Protection -- 5.2 Co-Products -- 5.3 Altered Metabolic Profiles -- 5.4 Improved Harvestability -- 5.5 Improved Nutrient Utilization and Recycling -- 6 Concluding Remarks -- References -- 7: Photobioreactors for Microalgal Biofuel Production -- 1 Introduction -- 2.1 Flat Photobioreactors -- 2.2 Tubular Photobioreactors -- 2.3 Innovative Concepts -- 3 Energy Needs for Algae Biomass Production in a Disposable Panel Reactor -- 4 Economics of Algae Biofuel Production -- 5 Conclusions -- References -- 8: Open Pond Culture Systems -- 1 Introduction -- 2 Shallow Lagoons and Ponds -- 3 Inclined Systems -- 4 Circular Central-Pivot Ponds -- 5 Mixed Ponds -- 6 Raceway Ponds -- 6.1 Paddle-Wheels. , 6.2 Air-Lifts, Archimedes Screws, Propellers and Water Jets -- 7 Culture Management -- 7.1 CO2 Addition -- 7.2 Optimising Productivity -- 7.3 Management and Control of Contaminating Organisms -- 7.4 Recycling of the Medium -- 7.5 Using Waste Water -- 7.6 Productivity of Outdoor Open Pond Systems -- 8 Conclusion -- References -- 9: Wastewater Treatment and Algal Biofuel Production -- 1 Introduction -- 2 Wastewater Treatment Ponds -- 2.1 High Rate Algal Ponds -- 2.2 Algal Production in HRAPs -- 2.3 Algal Grazers and Pathogens -- 3 Wastewater Treatment in HRAPs -- 3.1 Aerobic Treatment -- 3.2 Nutrient Removal -- 3.3 Disinfection -- 4 Wastewater Treatment HRAP Design -- 5 Harvest of Wastewater Treatment HRAP Algae -- 6 Economic and Environmental Benefits of Wastewater Treatment HRAP Algal Production -- 7 Wastewater Algal Biofuel Production -- 7.1 Biogas Methane -- 7.2 Biodiesel -- 7.3 Bioethanol -- 7.4 Bio-Crude Oil -- 7.5 Other Algal Uses -- 7.5.1 Feeds -- 7.5.2 High Value Products -- 8 Greenhouse Gas (GHG) Emission Abatement -- 8.1 Offset Equivalent Fossil Fuel Use GHG Emissions -- 8.2 Reduced CO2 Emissions from Wastewater Treatment Through Lower Electricity Use -- 9 Fertiliser Recovery -- 10 Conclusions -- References -- 10: Harvesting, Thickening and Dewatering Microalgae Biomass -- 1 Introduction -- 2 Coagulation and Flocculation -- 2.1 Inorganic (Chemical) Coagulation and Flocculation -- 2.2 Organic (Chemical) Coagulation and Flocculation -- 2.3 Autoflocculation -- 2.4 Bioflocculation -- 2.5 Ultrasound -- 2.6 Electrocoagulation -- 2.7 Flocculation Summary -- 3 Liquid Constrained Systems -- 3.1 Sedimentation -- 3.1.1 Gravity Thickeners -- 3.1.2 Enhanced Gravity Sedimentation -- 3.2 Centrifugation -- 3.3 Flotation -- 3.3.1 Dispersed Air Flotation -- 3.3.2 Dissolved Air Flotation (DAF). , 3.3.3 Suspended Air Flotation (SAF) -- 3.3.4 Auto otation -- 4 Particle Constrained Systems -- 4.1 Filtration -- 4.1.1 Filter Presses -- 4.1.2 Tangential (Cross) Flow Filtration -- 4.1.3 Gravity Belt Filters -- 4.1.4 Combined Gravity Belt Thickener and Dewatering -- 4.1.5 Vacuum Filters (Rotary Drum) -- 4.1.5.1 Mechanical Presses -- 4.1.6 Linear Electro-dewatering (EDW) -- 4.1.7 Filtration Summary -- 4.2 Attachment -- 4.3 Drying -- 4.4 Process Equipment Selection -- 4.4.1 Laboratory Testing -- 4.4.2 Specification and Shortlist -- 4.4.3 Pilot-Plant and Computer Simulation -- 4.4.4 Scale-Up, Construction and Operational Considerations -- 4.5 Conclusion -- References -- 11: Solvent Extraction for Microalgae Lipids -- 1 Introduction -- 2 Thermodynamics of Solvent Extraction -- 3 Ideal Solvent Characteristics -- 4 Cell Wall and Plasma Membrane of Microalgae -- 5 Biomass Pretreatment -- 6 Extraction of Lipid from Microalgae -- 7 Lipid Fractionation -- 8 Lipid Extraction from Dry Microalgae Biomass -- 9 Fatty Acid Extraction by Direct Saponification of Dry Microalgae Biomass -- 10 Optimization of Lipid and Fatty Acid Extraction from Paste Microalgae Biomass -- 11 Fractionation of Fatty Acids -- 12 Direct Transesterification of Wet Biomass for Producing Fatty Acid Methyl Esters (FAMEs) -- 13 Case Study -- 14 Concluding Remarks -- References -- 12: Production and Properties of Biodiesel from Algal Oils -- 1 Introduction -- 2 General Aspects of Biodiesel -- 2.1 Biodiesel Production. General Aspects -- 2.2 Biodiesel Production from Algae -- 2.3 Fatty Acid Profile and Fuel Properties of Biodiesel. General Aspects -- 2.3.1 Cetane Number and Combustion -- 2.3.2 Kinematic Viscosity -- 2.3.3 Oxidative Stability -- 2.3.4 Cold Flow -- 2.3.5 Summary. , 2.4 Fatty Acid Profiles of Algae-Derived Biodiesel and Effect on Fuel Properties.