Blue Planet, Red and Green Photosynthesis

Stephen Christopher Maberly was the Head of the Lake Ecosystems Group and is now a Fellow at the UK Centre for Ecology & Hydrology (UKCEH). He is an expert in limnology, algal and aquatic plant ecophysiology, photosynthesis and inorganic carbon acquisition.Brigitte Gontero is Director of Research at CNRS, BIP, Marseille, France. She leads a group that studies algal metabolism, from CO2 fixation to lipid production. She is an expert in the mechanisms involved in protein–protein interactions and their consequences in photosynthetic organisms.

• Preface xiStephen Christopher MABERLY and Brigiette GONTEROChapter 1. An Introduction to Productivity and Carbon Cycling in Aquatic Ecosystems 1Brigitte GONTERO, Timothy M. LENTON and Stephen Christopher MABERLY1.1. Overview 11.2. Light and productivity on Earth 21.3. Converting light energy into chemical energy 41.3.1. Underwater light 41.3.2. The primary phase of photosynthesis 41.4. Carbon fixation 61.4.1. Inorganic carbon in air and water 61.4.2. Mechanisms of carbon fixation 101.5. The global carbon cycle 121.6. Perspectives 191.7. Acknowledgments 191.8. References 20Chapter 2. Evolution of Aquatic Photoautotrophs 27John A. RAVEN2.1. Background 272.2. Anoxygenic photosynthetic bacteria 282.3. Cyanobacteria 302.4. Photosynthetic eukaryotes 322.5. References 36Chapter 3. Biogeographical Patterns and Genomes of Aquatic Photoautotrophs 43Juan José PIERELLA KARLUSICH, Charlotte NEF, Chris BOWLER and Richard G. DORRELL3.1. Introduction – the changing face of algal genomes 433.2. Diversity of algae and their chloroplasts 463.3. Genomic insights into algal evolution 493.4. Limitations of cultured algal sequencing projects 503.5. History of omics-based approaches applied to environmental plankton samples 543.6. Biogeographical insights of algae from Tara Oceans metabarcoding 553.7. Functional studies of algae from Tara Oceans metagenomic and metatranscriptomic data 593.8. Applying genome-resolved metagenomics to phototrophic eukaryotes 613.9. Perspectives 633.10. Acknowledgments 663.11. References 67Chapter 4. Inorganic Carbon Acquisition by Aquatic Primary Producers 81Sebastian D. ROKITTA, Sven A. KRANZ and Björn ROST4.1. Overview 814.2. Rubisco and the problem of its own success 824.3. Dissolved inorganic carbon and its behavior in water 844.4. Disequilibrium situations and implications of transport processes 884.5. CCM operation in cyanobacteria 934.6. CCM operation in green algae 964.7. CCM operation in diatoms 984.8. CCM operation in the coccolithophore Emiliania huxleyi 1014.9. CCM operation in macroalgae, seagrasses and freshwater plants 1054.10. CCM operation and its coupling with co-occurring processes 1104.11. Future research foci 1124.12. Acknowledgments 1144.13. References 114Chapter 5. Biochemical Carbon Dioxide Concentrating Mechanisms 133Brigitte GONTERO and Stephen C. MABERLY5.1. Introduction 1335.2. Carbon-fixation by Rubisco in the C3 pathway 1345.3. The C4 CO2 concentrating mechanism 1385.3.1. C4 in terrestrial plants 1385.3.2. C4 in aquatic plants and algae 1415.4. The CAM CO2 concentrating mechanism 1505.4.1. Terrestrial CAM 1505.4.2. Aquatic CAM 1505.5. Conclusions and perspectives 1535.6. Acknowledgments 1545.7. References 155Chapter 6. Carbonic Anhydrase 167Yusuke MATSUDA, Hermanus NAWALY, Kohei YONEDA6.1. Overview 1676.2. Introduction 1686.3. Types of CA 1696.3.1. Alpha CA 1696.3.2. Beta CA 1706.3.3. Gamma CA 1726.3.4. Delta CA 1736.3.5. Epsilon CA 1746.3.6. Eta CA 1746.3.7. Zeta CA 1756.3.8. Theta CA 1766.3.9. Iota CA 1776.3.10. Subclasses and primary sequences 1786.4. The functions of CAs in aquatic photoautotrophs 1786.5. Regulation of CO2 efflux by CA at the chloroplast envelope 1816.6. Summary: CAs in red and green photosynthesis 1836.7. References 187Chapter 7. Rubisco Microcompartments: The Function of Carboxysomes and Pyrenoids in Aquatic CO2-Concentrating Mechanisms 197Moritz T. MEYER7.1. Introduction 1977.2. The cyanobacterial CCM 1997.2.1. Cyanobacteria accumulate bicarbonate through high- and low-affinity uptake systems 1997.2.2. Carboxysomes belong to two distinct evolutionary lineages 2017.2.3. Carboxysomes isolate Rubisco from the rest of the CBB cycle 2037.2.4. Carboxysome shells are composed of thousands of self-assembling capsid proteins 2047.2.5. Alpha and beta carboxysomes package the enzymatic cargo with different protein linkers 2057.3. The algal CCM 2077.3.1. The model alga Chlamydomonas has multiple acclimation states 2077.3.2. Chlamydomonas has a cooperative CO2–HCO3 - uptake system 2087.3.3. Chlamydomonas has a stromal vCA to capture CO2 2097.3.4. Stromal HCO3 - is catalytically dehydrated to CO2 inside thylakoid lumen 2107.3.5. The Chlamydomonas pyrenoid has a complex architecture 2107.3.6. Rubisco and EPYC1 condense into a bimolecular complex 2117.3.7. Rubisco is anchored to tubules and starch plates by proteins sharing a binding motif 2117.4. Introducing an aquatic CCM into crops could increase biomass production 2137.4.1. Proto-carboxysomes and proto-pyrenoids assemble in chloroplasts 2137.4.2. Cyanobacterial and algal inorganic carbon transporters can be targeted to the chloroplast envelope 2157.5. Conclusion 2157.6. References 216Chapter 8. Environmental Variability and Its Control of Productivity 225Alessandra NORICI, Caterina GEROTTO, John BEARDALL and John A. RAVEN8.1. Introduction 2258.2. Macro- and micronutrients in aquatic environments during Earth’s history and their biological functions 2268.2.1. Nitrogen 2278.2.2. Phosphorus 2318.2.3. Sulfur 2338.2.4. Silicon 2358.2.5. Iron, copper, manganese, zinc, molybdenum, nickel 2378.3. The ultimate element limiting productivity and cell stoichiometry 2408.4. Light variability and effect on photosynthesis 2438.4.1. Light-harvesting and photosynthetic electron transport 2438.4.2. Photosynthesis versus irradiance (P vs. E) curves 2468.4.3. Aquatic ecosystems: temporal and depth variations of light 2478.4.4. Physiological processes associated with exposure to variable light intensities (acclimation and regulation of photosynthesis) 2488.5. Photosynthesis and primary production in the water column 2538.6. Glossary 2568.7. Acknowledgments 2578.8. References 257Chapter 9. Future Responses of Marine Primary Producers to Environmental Changes 273Kunshan GAO, Wenyan ZHAO and John BEARDALL9.1. Introduction 2739.2. Contemporary and future environmental changes 2749.2.1. Ocean acidification 2749.2.2. Ocean warming 2759.2.3. Ultraviolet radiation 2769.2.4. Ocean deoxygenation 2769.3. Effects of CO2 rise and ocean acidification 2779.3.1. Effects of ocean warming and its combination with OA 2809.3.2. Effects of UV radiation and its combination with OA and warming 2829.4. Other interactions 2879.5. Summary 2889.6. Perspectives 2899.7. Acknowledgments 2909.8. References 290List of Authors 305Index 309