Blue Planet, Red and Green Photosynthesis

Preface xi
Stephen Christopher MABERLY and Brigiette GONTERO

Chapter 1. An Introduction to Productivity and Carbon Cycling in Aquatic Ecosystems 1
Brigitte GONTERO, Timothy M. LENTON and Stephen Christopher MABERLY

1.1. Overview 1

1.2. Light and productivity on Earth 2

1.3. Converting light energy into chemical energy 4

1.3.1. Underwater light 4

1.3.2. The primary phase of photosynthesis 4

1.4. Carbon fixation 6

1.4.1. Inorganic carbon in air and water 6

1.4.2. Mechanisms of carbon fixation 10

1.5. The global carbon cycle 12

1.6. Perspectives 19

1.7. Acknowledgments 19

1.8. References 20

Chapter 2. Evolution of Aquatic Photoautotrophs 27
John A. RAVEN

2.1. Background 27

2.2. Anoxygenic photosynthetic bacteria 28

2.3. Cyanobacteria 30

2.4. Photosynthetic eukaryotes 32

2.5. References 36

Chapter 3. Biogeographical Patterns and Genomes of Aquatic Photoautotrophs 43
Juan José PIERELLA KARLUSICH, Charlotte NEF, Chris BOWLER and Richard G. DORRELL

3.1. Introduction - the changing face of algal genomes 43

3.2. Diversity of algae and their chloroplasts 46

3.3. Genomic insights into algal evolution 49

3.4. Limitations of cultured algal sequencing projects 50

3.5. History of omics-based approaches applied to environmental plankton samples 54

3.6. Biogeographical insights of algae from Tara Oceans metabarcoding 55

3.7. Functional studies of algae from Tara Oceans metagenomic and metatranscriptomic data 59

3.8. Applying genome-resolved metagenomics to phototrophic eukaryotes 61

3.9. Perspectives 63

3.10. Acknowledgments 66

3.11. References 67

Chapter 4. Inorganic Carbon Acquisition by Aquatic Primary Producers 81
Sebastian D. ROKITTA, Sven A. KRANZ and Björn ROST

4.1. Overview 81

4.2. Rubisco and the problem of its own success 82

4.3. Dissolved inorganic carbon and its behavior in water 84

4.4. Disequilibrium situations and implications of transport processes 88

4.5. CCM operation in cyanobacteria 93

4.6. CCM operation in green algae 96

4.7. CCM operation in diatoms 98

4.8. CCM operation in the coccolithophore Emiliania huxleyi 101

4.9. CCM operation in macroalgae, seagrasses and freshwater plants 105

4.10. CCM operation and its coupling with co-occurring processes 110

4.11. Future research foci 112

4.12. Acknowledgments 114

4.13. References 114

Chapter 5. Biochemical Carbon Dioxide Concentrating Mechanisms 133
Brigitte GONTERO and Stephen C. MABERLY

5.1. Introduction 133

5.2. Carbon-fixation by Rubisco in the C3 pathway 134

5.3. The C4 CO2 concentrating mechanism 138

5.3.1. C4 in terrestrial plants 138

5.3.2. C4 in aquatic plants and algae 141

5.4. The CAM CO2 concentrating mechanism 150

5.4.1. Terrestrial CAM 150

5.4.2. Aquatic CAM 150

5.5. Conclusions and perspectives 153

5.6. Acknowledgments 154

5.7. References 155

Chapter 6. Carbonic Anhydrase 167
Yusuke MATSUDA, Hermanus NAWALY, Kohei YONEDA

6.1. Overview 167

6.2. Introduction 168

6.3. Types of CA 169

6.3.1. Alpha CA 169

6.3.2. Beta CA 170

6.3.3. Gamma CA 172

6.3.4. Delta CA 173

6.3.5. Epsilon CA 174

6.3.6. Eta CA 174

6.3.7. Zeta CA 175

6.3.8. Theta CA 176

6.3.9. Iota CA 177

6.3.10. Subclasses and primary sequences 178

6.4. The functions of CAs in aquatic photoautotrophs 178

6.5. Regulation of CO2 efflux by CA at the chloroplast envelope 181

6.6. Summary: CAs in red and green photosynthesis 183

6.7. References 187

Chapter 7. Rubisco Microcompartments: The Function of Carboxysomes and Pyrenoids in Aquatic CO2-Concentrating Mechanisms 197
Moritz T. MEYER

7.1. Introduction 197

7.2. The cyanobacterial CCM 199

7.2.1. Cyanobacteria accumulate bicarbonate through high- and low-affinity uptake systems 199

7.2.2. Carboxysomes belong to two distinct evolutionary lineages 201

7.2.3. Carboxysomes isolate Rubisco from the rest of the CBB cycle 203

7.2.4. Carboxysome shells are composed of thousands of self-assembling capsid proteins 204

7.2.5. Alpha and beta carboxysomes package the enzymatic cargo with different protein linkers 205

7.3. The algal CCM 207

7.3.1. The model alga Chlamydomonas has multiple acclimation states 207

7.3.2. Chlamydomonas has a cooperative CO2-HCO3 - uptake system 208

7.3.3. Chlamydomonas has a stromal vCA to capture CO2 209

7.3.4. Stromal HCO3 - is catalytically dehydrated to CO2 inside thylakoid lumen 210

7.3.5. The Chlamydomonas pyrenoid has a complex architecture 210

7.3.6. Rubisco and EPYC1 condense into a bimolecular complex 211

7.3.7. Rubisco is anchored to tubules and starch plates by proteins sharing a binding motif 211

7.4. Introducing an aquatic CCM into crops could increase biomass production 213

7.4.1. Proto-carboxysomes and proto-pyrenoids assemble in chloroplasts 213

7.4.2. Cyanobacterial and algal inorganic carbon transporters can be targeted to the chloroplast envelope 215

7.5. Conclusion 215

7.6. References 216

Chapter 8. Environmental Variability and Its Control of Productivity 225
Alessandra NORICI, Caterina GEROTTO, John BEARDALL and John A. RAVEN

8.1. Introduction 225

8.2. Macro- and micronutrients in aquatic environments during Earth's history and their biological functions 226

8.2.1. Nitrogen 227

8.2.2. Phosphorus 231

8.2.3. Sulfur 233

8.2.4. Silicon 235

8.2.5. Iron, copper, manganese, zinc, molybdenum, nickel 237

8.3. The ultimate element limiting productivity and cell stoichiometry 240

8.4. Light variability and effect on photosynthesis 243

8.4.1. Light-harvesting and photosynthetic electron transport 243

8.4.2. Photosynthesis versus irradiance (P vs. E) curves 246

8.4.3. Aquatic ecosystems: temporal and depth variations of light 247

8.4.4. Physiological processes associated with exposure to variable light intensities (acclimation and regulation of photosynthesis) 248

8.5. Photosynthesis and primary production in the water column 253

8.6. Glossary 256

8.7. Acknowledgments 257

8.8. References 257

Chapter 9. Future Responses of Marine Primary Producers to Environmental Changes 273
Kunshan GAO, Wenyan ZHAO and John BEARDALL

9.1. Introduction 273

9.2. Contemporary and future environmental changes 274

9.2.1. Ocean acidification 274

9.2.2. Ocean warming 275

9.2.3. Ultraviolet radiation 276

9.2.4. Ocean deoxygenation 276

9.3. Effects of CO2 rise and ocean acidification 277

9.3.1. Effects of ocean warming and its combination with OA 280

9.3.2. Effects of UV radiation and its combination with OA and warming 282

9.4. Other interactions 287

9.5. Summary 288

9.6. Perspectives 289

9.7. Acknowledgments 290

9.8. References 290

List of Authors 305

Index 309