Diatom Photosynthesis

Johannes W. Goessling, PhD, is a researcher in the Department of Biology, Laboratory for Innovation and Sustainability of Marine Biological Resources, Centre for Environmental and Marine Studies, University of Aveiro, Portugal. He received his PhD in marine biology from the University of Copenhagen, with a foundational background in biology, specifically focusing on plant physiology and plant ecophysiology. His research is centered on diatom frustules, investigating their interactions with light, giving rise to photonic properties. His research is regularly published in the top journals in the field. João Serôdio, PhD, is an assistant professor in the Department of Biology at the University of Aveiro in Lisbon, Portugal. He received his PhD in biology from the University of Lisbon in 1999. His research focuses on the photobiology and ecophysiology of marine primary producers with a special emphasis on diatoms. He has authored more than 120 articles in international journals and has authored 7 peer-reviewed book chapters. Johann Lavaud, PhD, is a scientist in the Laboratory for Environmental Marine Sciences at the European Institute for Marine Studies, University of Western Brittany, France. He completed his PhD on the photosynthesis of diatoms in 2002 at the ENS-University of Paris VI. His research focuses on the diversity and productivity of how diatoms are impacted by the environment. His research has been published in more than 80 articles in peer-reviewed international journals.

Preface xxvii

Acknowledgements xxix

Part 1: Evolution and Genetics 1

1 Comparing Diatom Photosynthesis with the Green Lineage: Electron Transport, Carbon Fixation and Metabolism 3
Dany Croteau, Erik Jensen, Christian Wilhelm and Benjamin Bailleul

1.1 Introduction 5

1.2 Conservation and Diversity within Oxygenic Photosynthesis 6

1.3 Consequences of the Secondary Endosymbiosis and Thylakoid Ultrastructure 9

1.4 Different Modes of Photosynthetic Electron Flows 12

1.5 Regulation of CO2 Concentration, CO2 Fixation and Carbon Metabolism 18

1.6 General Response of Photosynthesis to Environmental Stresses 22

1.7 Conclusion 25

2 Genetic Regulation of Diatom Photosynthesis: Understanding and Exploiting Genetic Diversity 45
Charlotte Volpe, Marianne Nymark and Tore Brembu

2.1 Regulation of Photosynthesis 47

2.2 Diatom Genomes 48

2.3 Photosynthetic Components in Diatom Genomes 50

2.4 Responses to Changes in Light Intensity 54

2.5 Circadian Rhythmicity 57

2.6 Responses to Changes in Light Quality 58

2.7 Retrograde Signaling 59

2.8 Gene Editing for Functional Characterization and Commercial Applications 61

2.9 Conclusion 68

3 Evolution of Plastids and Mitochondria in Diatoms 81
Ansgar Gruber and Miroslav Oborník

3.1 Introduction 81

3.2 Origin and Evolution of Diatom Plastids 83

3.3 Derived States of Diatom Plastids 94

3.4 Consequences of Complex Plastid Acquisition 96

3.5 Conclusions and Outlook 100

4 Structure and Dynamics of the Diatom Chloroplast 113
Monika Bojko, Stanislaw Listwan, Reimund Goss and Dariusz Latowski

4.1 Evolution and Structure of Diatom Chloroplasts 114

4.2 Architecture of the Diatom Thylakoid Membrane 118

4.3 Molecular Dynamics and Structure of the Diatom Thylakoid Membrane Under Different Light Conditions 125

4.4 Molecular Dynamics and Structure of the Diatom Thylakoid Membrane Under Different Thermal Conditions 127

4.5 Conclusion 128

Part 2: Interaction with Light 137

5 Pigments in Diatoms: Light Absorption and Beyond 139
Paulina Kuczyñska, Ma³gorzata Jemio³a-Rzemiñska and Kazimierz Strza³ka

5.1 Environmental Factors Affect Pigments in Diatoms 139

5.2 Diatoms are Well Adapted to Changing Light Conditions 141

5.3 Photosynthetic Pigments in Diatoms are Chlorophylls and Carotenoids 143

5.4 The Main Pigment in Diatoms – Chlorophyll a Plays a Central Role in Photochemical Energy Conversion 148

5.5 Chlorophyll c Participates in Photosynthesis as an Accessory Pigment 150 

5.6 Fucoxanthin-Binding Proteins in Diatoms Play a Special Role 151

5.7 Regulation of Protochlorophyllide Oxidoreductases was Examined in Diatoms but Further Steps of Chlorophyll c Biosynthesis Remain Unclear 152

5.8 Fucoxanthin is the Main Light-Harvesting Carotenoid in Diatom 155

5.9 High Bioavailability and Bioactivity of Fucoxanthin Makes It a Desirable Compound Obtained by Extraction 158

5.10 Beneficial Effects of Fucoxanthin are Versatile 160

5.11 Diadinoxanthin and Diatoxanthin are Involved in Cyclic Changes, Ensuring Photoprotection 161

5.12 Diatoms Also Possess the Violaxanthin Cycle, but It is not the First Line of Defense Against Excessive Light Energy 163

5.13 Mechanisms of NPQ in Diatoms are Complex and Differ Depending on Species 163

5.14 Many Carotenogenic Enzymes and Genes in Diatoms Have not yet Been Revealed 165

5.15 Analysis and Production of Diatom Pigments are Challenging Tasks with Promising Prospects 167

5.16 Conclusions 170

6 Function, Structure and Organization of Light-Harvesting Proteins in Diatoms 191
Charlotte Volpe and Claudia Büchel

6.1 Introduction 192

6.2 The FCP Proteins 194

6.3 Structure, Pigmentation and Energy Transfer 195

6.4 Macroorganization of FCP-PSI/II Supercomplexes 198

6.5 Role of the Chloroplast Signal Recognition Particle Pathway (CpSRP) 201

6.6 Balancing Light Absorption and Photoprotection 202

6.7 Conclusion 206

7 Sensing Light Underwater: An Update on Photoreceptors in Diatoms 217
Manuel Serif and Per Winge

7.1 Introduction 219

7.2 Rhodopsins 221

7.3 Phytochromes 223

7.4 Cryptochrome/Photolyase Family 226

7.5 Aureochromes 231

7.6 Conclusion 235

8 Non-Invasive Biophysical Techniques to Monitor the Structural Plasticity of the Photosynthetic Machinery of Live Diatom Cells 245
Milán Szabó, Gergely Nagy and Gyözö Garab

8.1 Introduction 246

8.2 Circular Dichroism Spectroscopy 248

8.3 Small-Angle Neutron Scattering (SANS) 253

8.4 Electrochromic Shift Absorbance Transients 256

8.5 Conclusions and Outlook 259

9 Hypotheses on Frustule Functionalities: From Single Species Analysis to Systematic Approaches 267
Johannes W. Goessling, Matt P. Ashworth, Marianne Ellegaard, Joao Serôdio and Martin Lopez Garcia

9.1 Introduction 268

9.2 Frustule Fundamentals: Chemistry, Formation, Reproduction 271

9.3 Examples of Unique Frustule Systems 274

9.4 Physicochemical Properties 277

9.5 Physical Properties 279

9.6 Frustule as an Optical System 281

9.7 Conclusions and Outlook 289

Part 3: Primary Production and Ecology 301

10 Extracellular Polymeric Substance Production by Benthic Pennate Diatoms 303
Graham J. C. Underwood

10.1 Introduction 304

10.2 Types of EPS Produced by Benthic Diatoms 304

10.3 Functions of EPS in Benthic Diatoms in Relation to Chemical Composition 308

10.4 Metabolic Pathways of EPS Production and Regulation in Diatoms 310

10.5 Interactions Between Diatoms, EPS and Bacteria 313

10.6 Future Directions 315

11 Diatom Primary Production in Headwater Streams: A Limited but Essential Process 327
Joey Allen, Michael Danger, Carlos Eduardo Wetzel, Vincent Felten and Martin Laviale

11.1 Ecological Relevance of Headwater Stream Ecosystems 328

11.2 Diatom Primary Production is Highly Constrained in Headwater Streams 330

11.3 Diatoms as High-Quality Resources for Other Organisms 334

11.4 Anthropogenic Impacts on Diatom Contributions to Headwater Stream Functioning 336

11.5 Headwater Diatom Community Functioning is Supported by Unique Biodiversity 338

11.6 Conclusion and Perspectives 340

12 Present and Future Perspectives for Bioassessment of Running Water Using Diatoms 351
Salomé FP Almeida and Maria J. Feio

12.1 Introduction 352

12.2 Potential of Diatoms as Indicators in Running Water Quality Assessment 352

12.3 Water Quality Assessment Methods 353

12.4 Molecular-Based Methods 355

12.5 Transitioning from Morphology-Based to eDNA-Based Biomonitoring: Available Options 368

12.6 Conclusions 370

13 Photosynthetic and Growth Responses of Planktonic Diatoms to Ocean Global Changes 383
Peng Jin, John Beardall and Kunshan Gao

13.1 Introduction 384

13.2 The Effects of Elevated CO2 and Ocean Acidification 384

13.3 The Effects of Ocean Warming 388

13.4 The Effects of UVR 389

13.5 Combined Effects of Ocean Acidification and Warming 390

13.6 Combined Effects of Ocean Acidification and UVR 391

13.7 Combined Effects of Ocean Acidification and Deoxygenation 392

13.8 Ocean Acidification Effects Under Multiple Drivers 393

13.9 Ecological Implications 395

13.10 Conclusions and Recommendations 396

Part 4: Cultivation and Application 407

14 Culturing Diatoms 409
Daniel Vaulot, Gust Bilcke, Peter Chaerle, Angela Falciatore, Priscillia Gourvil, Michael W. Lomas, Ian Probert and Wim Vyverman

14.1 Introduction 409

14.2 Current Diversity of Diatoms in Culture 411

14.3 Isolation of Diatom Cultures 415

14.4 Culture of Diatoms 422

14.5 Life Cycles 424

14.6 Cryopreservation 426

14.7 Diatom Strains Amenable to Genetic Engineering 430

14.8 Conclusion 434

15 Diatom Biofilm: Ecology and Cultivation from Laboratory to Industrial Level 449
Mary Dianne Grace Arnaldo, Aurélie Mossion, Thierry Beignon, Hugo Vuillemin, Freddy Guihéneuf, Gaëtane Wielgosz-Collin and Vona Méléder

15.1 Introduction 449

15.2 Natural Biofilms 453

15.3 Artificial Algal Biofilm Systems 458

15.4 Conclusion and Perspective 467

16 Opportunities and Challenges of Diatom Cell Factory for Human Health 477
Clementina Sansone, Angelo Del Mondo, Luigi Pistelli, Arianna Smerilli, Maria Saggiomo and Christophe Brunet

16.1 Introduction 478

16.2 Carotenoids 479

16.3 Vitamins 485

16.4 Polyphenols 490

16.5 Phytosterols 494

16.6 Polysaccharides 496

16.7 Polar Diatoms: New Model for Biotechnology? 500

16.8 Filling the Gap between Diatoms Biological Traits and Biotechnological Use 503

16.9 Conclusions 507

17 Diatom-Based Bioproducts and the Potential of Frustules in Drug Delivery 529
Pankaj Kumar Singh, Abhishek Saxena and Archana Tiwari

17.1 Introduction 529

17.2 High-Value Products Derived from Diatoms 531

17.3 Diatom as Drug Delivery Carriers 535

17.4 Therapeutic Applications of Diatoms 540

17.5 Conclusion 542

Part 5: Diatoms as Representative Organisms for the Protection of Marine Genetic Resources 551

18 A Journey to Mars with Diatoms on Board 553
Louisa Reissig, Mohamed Ghobara, Christian Maibohm and Johannes W. Goessling

18.1 Introduction 554

18.2 The Living Diatom 556

18.3 The Diatom Frustule: A Sustainable Source of Porous Silica 561

18.4 The Evolving Diatom 568

18.5 Conclusion 571

19 Legal Regime of Marine Genetic Resources in Areas Beyond National Jurisdiction 583
Gemma Andreone, Valentina Rossi and Giovanni Ardito

19.1 Introduction 584

19.2 The Current Legal Framework 585

19.3 The Notion of Marine Genetic Resources 586

19.4 Bioprospecting and Marine Scientific Research: Access to and Collection of Marine Genetic Resources 589

19.5 Spatial Scope (High Seas-Area) and Legal Status of MGRs in ABNJ (Common Heritage of Mankind vs Freedom of the Seas) 593

19.6 Conclusion 597

Acknowledgments 598

References 598

Subject Index 601

Taxonomic Index 611