Note: Intro -- Copyright -- From the Series Editors -- Authors of Volume 45 -- Our Books -- Series Editors -- Contents -- Preface: A Brief Introduction to the Algae -- The Evolution of Photosynthesis -- The Evolution of Algae -- The Evolution of Eukaryotic Algae -- About the Editors -- Contributors -- Author Index -- Part I: Introductory Chapters -- Chapter 1: Recent Advances in the Photosynthesis of Cyanobacteria and Eukaryotic Algae -- I. Algal Systematics -- II. Cyanobacteria -- III. Crystal Structures -- IV. Light Harvesting -- V. Photoinhibition -- VI. Dinoflagellates and Coral Bleaching -- VII. Carbon Uptake and Metabolism (See Chap. 7 & -- 8) -- VIII. Water-Water Cycles (See Chap. 8) -- References -- Chapter 2: The Algal Tree of Life from a Genomics Perspective -- I. Introduction -- II. Why Inferring the Algal Tree of Life Is Non-trivial -- III. Examples of Reticulate Behavior Among Algal Genes -- IV. From Designer Datasets to Whole Genomes -- V. Conclusions -- Acknowledgments -- References -- Part II: Molecular Genetics of Algae -- Chapter 3: Chlorophyll-Xanthophyll Antenna Complexes: In Between Light Harvesting and Energy Dissipation -- I. Introduction -- II. Chromophores -- III. The Core Complexes of PSII and PSI -- IV. Light Harvesting -- A. Type I (LHCBM3, 4, 6, 8 and 9) -- B. Type II (LHCBM5) -- C. Type III (LHCBM2 and 7) -- D. Type IV (LHCBM1) -- V. Antenna Complexes of PSI -- VI. Fucoxanthin Chlorophyll Binding Proteins -- VII. Photoprotection -- VIII. Triggers of Quenching Reactions -- IX. Conclusions -- Acknowledgements -- References -- Chapter 4: The Dynamics of the Photosynthetic Apparatus in Algae -- I. Introduction -- II. Adaptation to Changes in Light Conditions -- A. State Transitions -- B. Non Photochemical Quenching (NPQ) -- C. PSII Repair Cycle. , III. Response of the Photosynthetic Apparatus to Micronutrient Depletion -- A. Copper Deficiency -- B. Iron Deficiency -- C. Sulfur Deprivation and Hydrogen Production -- D. Nitrogen Deprivation -- IV. Long Term Response: Changes in Nuclear and Chloroplast Gene Expression -- V. Conclusions and Perspectives -- Acknowledgements -- References -- Chapter 5: Biosynthesis of Chlorophyll and Bilins in Algae -- I. Introduction -- II. Diversity of Chlorophylls in Algae -- III. Diversity of Bilins in Algae -- IV. Overview of Biosynthesis of Bilins and Chlorophylls -- V. Biosynthesis of Protoporphyrin IX -- VI. Biosynthesis of Bilins from Protoporphyrin and Function of Bilin Lyases -- VII. Biosynthesis of Chlorophylls from Protoporphyrin IX -- VIII. Synthesis of Chlorophyll b, d and f -- IX. Concluding Remarks -- Bibliography -- Part III: Biochemistry and Physiology of Algae -- Chapter 6: Chloroplast Ion and Metabolite Transport in Algae -- I. Introduction -- II. Chloroplast Ion Transport -- A. Ion Channels -- 1. Voltage-Dependent Chloride Channels -- 2. Mechanosensitive Ion Channels -- 3. K+ Channels -- 4. Ca2+ Channels -- B. Ion Transporters -- 1. Phosphate Transporters -- 2. Sulfate Transporters -- 3. Nitrite Transporters -- 4. Potassium Proton Exchangers -- 5. Manganese and Calcium Transporters -- 6. Magnesium Transporters -- 7. Iron Transporters -- C. Ion Pumps (P-ATPases) -- D. ABC Transporters -- III. Chloroplast Metabolite Transport -- A. ATP Transporters -- 1. Plastidic Nucleotide Translocators -- 2. The Thylakoid ATP/ADP Carrier -- B. Plastidic Phosphate Transporters -- 1. Triose-Phosphate Transporters -- 2. Phosphoenolpyruvate Transporters -- 3. Glucose-6-Phosphate and Xylulose-5-Phosphate Translocators -- C. Bicarbonate Transporters -- D. Organic Acid Transporters -- E. Amino Acid Transporters -- F. Fatty Acid Transporters. , G. Lipid ABC Transporters -- IV. Strategies for Identification of Missing Algal Transporters -- V. Conclusions and Perspectives -- References -- Chapter 7: Structural and Biochemical Features of Carbon Acquisition in Algae -- I. Introduction -- II. Carbon Assimilation -- A. The Characteristics of Most Rubiscos Necessitate Operation of a CCM -- B. The PCRC and Other Pathways for C Assimilation -- III. Occurrence of CCMs -- IV. Mechanisms of CCMs Versus Diffusive CO2 Fluxes -- A. Definition of CCMs and What Do We Need in Order to Demonstrate Operation of CCMs? -- B. CCMs Based on Active Transport of Inorganic C Species -- C. C4 Photosynthesis as a CCM in Algae? -- V. Structural Aspects of CO2 Acquisition -- Acknowledgements -- References -- Chapter 8: Light-Driven Oxygen Consumption in the  Water-Water Cycles and Photorespiration, and Light Stimulated Mitochondrial Respiration -- I. Introduction -- II. The Evidence of Light-Dependent O2 Uptake -- III. Possible Mechanisms of Light-Driven O2 Uptake -- A. Water-Water Cycles -- B. The Mehler Ascorbate Peroxidase (MAP) Reactions Involving PSI and PSII -- C. Flavodiiron Protein Involving PSI and PSII -- D. Plastid (Plastoquinol) Terminal Oxidase (PTOX) Involving PSII but not PSI -- E. Photorespiration -- F. Mitochondrial Respiration -- G. Allocation of O2 Uptake Among the Five Pathways -- IV. Functions of the Light-Driven O2 Uptake Processes -- V. Conclusions -- Acknowledgements -- References -- Chapter 9: The Algal Pyrenoid -- I. Introduction -- A. A Pyrenoid Timeline - From Microscopic Curiosity to a Key Factor in the Earth's Carbon Cycle -- B. Pyrenoid Prevalence -- C. Independent Origins but Convergent Structures -- D. Diversity -- II. Pyrenoid Structure & -- Function: Lessons from Chlamydomonas -- A. Structure and Organisation. , B. Functional Integration of Pyrenoid Proteome and CCM Activity -- C. Integrating Transcriptomics and Pyrenoid-Associated Processes -- III. When, Where, How and Whither: From Paleo-Origins to Future Synthetic Biology -- References -- Part IV: Light-Harvesting Systems in Algae -- Chapter 10: Light-Harvesting in Cyanobacteria and Eukaryotic Algae: An Overview -- I. Introduction -- II. The Photosynthetic Pigments of Cyanobacteria and Eukaryotic Algae -- A. Chlorophylls -- 1. Chlorophyll a -- 2. Chlorophyll b -- 3. Chlorophyll c and MgDVD -- 4. Chlorophyll d -- 5. Chlorophyll f -- 6. Summary Comments on the Chlorophylls -- B. Carotenoids -- 1. Carotenes -- 2. Xanthophylls -- C. Phycobiliproteins -- III. The Evolution of Protists with Plastids (Algae) -- A. Algae with Primary Plastids -- 1. Glaucophyceae -- 2. Rhodophyceae -- 3. Chlorophyceae -- B. Secondary and Tertiary Plastids -- 1. Diatoms (Bacillariophyceae) and Related Phyla Including the Phaeophyceae -- 2. Related Phyla -- 3. Dinoflagellates -- 4. Cryptophytes (Cryptophyceae) -- 5. Other Stramenopiles, Haptophytes and Apicomplexans -- IV. The Need for Light-Harvesting Antennas -- V. Light-Harvesting Antennas in Cyanobacteria and Eukaryotic Algae -- VI. Control of Energy Supply to PSI and PSII: State Transitions, Absorption Cross-Sectional Changes and Spillover -- A. Overview -- B. State Transitions -- 1. State Transitions in Chlamydomonas -- 2. An Aside on Cyclic Electron Transport (CET) -- 3. State Transitions in Other Algae -- C. Absorption Cross-Sectional Changes -- D. Spillover -- E. Complementary Chromatic Adaptation -- F. Non-photochemical Quenching - Sensu Lato -- VII. Non-photochemical Quenching -- A. The Xanthophyll Cycle -- B. pH Quenching -- C. Orange Carotenoid Protein -- VIII. Reactive Oxygen Species (ROS) and Other Photoprotective Mechanisms -- Acknowledgements. , References -- Chapter 11: Light Harvesting by Long-Wavelength Chlorophyll Forms (Red Forms) in Algae: Focus on their Presence, Distribution and Function -- I. Long Wavelength ("Red") Chlorophyll a Forms: Historical Perspective on Their Discovery and General Overview -- II. Long Wavelength Chlorophyll Forms Associated to Photosystem I -- A. Photosystem I Core Red Forms -- B. Photosystem I External Antenna Red Forms -- C. Nature of Long Wavelength Chlorophyll Forms -- III. Long Wavelength Chlorophyll Forms Associated to Photosystem II -- A. PSII-Associated Long Wavelength Chlorophylls in Algae -- IV. Survey of Cyanobacterial and Algal Species for the Presence of Long-Wavelength Chlorophyll Forms -- A. Physiological and Environmental Consequences of the Presence of Red Forms (or Their Absence) -- V. Effect of Long Wavelength Chlorophyll Forms on the Photochemical Quantum Efficiency -- A. Simulations of the Impact of Red Forms on Excited State Energy Trapping -- 1.. Photosystem I -- 2.. Photosystem II -- VI. Concluding Remarks -- Acknowledgements -- References -- Chapter 12: Diversity in Photoprotection and Energy Balancing in Terrestrial and Aquatic Phototrophs -- I. Introduction -- II. Energy Storage and Regulation in Oxygenic Photosynthesis -- III. The pmf Paradigm for Regulation of the Photosynthetic Light Reactions -- IV. The Need to Coordinate qE and Photosynthetic Control -- V. The Critical Need to Balance the Chloroplast Energy Budget -- VI. Regulation of CEF -- VII. Modulation of pmf Feedback Regulation and Its Impact on Energy Balancing -- VIII. How Diverse Photoprotective Mechanisms Challenge the pmf Paradigm and Open Up New Questions -- IX. Coping with ATP Excess or NADPH Deficit -- A. Energy Balancing by Interactions Between Photosynthetic and Respiratory Machinery -- X. Conclusions and Perspective -- Acknowledgements. , References.