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 xxviiAcknowledgements xxixPart 1: Evolution and Genetics 11 Comparing Diatom Photosynthesis with the Green Lineage: Electron Transport, Carbon Fixation and Metabolism 3Dany Croteau, Erik Jensen, Christian Wilhelm and Benjamin Bailleul1.1 Introduction 51.2 Conservation and Diversity within Oxygenic Photosynthesis 61.3 Consequences of the Secondary Endosymbiosis and Thylakoid Ultrastructure 91.4 Different Modes of Photosynthetic Electron Flows 121.5 Regulation of CO2 Concentration, CO2 Fixation and Carbon Metabolism 181.6 General Response of Photosynthesis to Environmental Stresses 221.7 Conclusion 252 Genetic Regulation of Diatom Photosynthesis: Understanding and Exploiting Genetic Diversity 45Charlotte Volpe, Marianne Nymark and Tore Brembu2.1 Regulation of Photosynthesis 472.2 Diatom Genomes 482.3 Photosynthetic Components in Diatom Genomes 502.4 Responses to Changes in Light Intensity 542.5 Circadian Rhythmicity 572.6 Responses to Changes in Light Quality 582.7 Retrograde Signaling 592.8 Gene Editing for Functional Characterization and Commercial Applications 612.9 Conclusion 683 Evolution of Plastids and Mitochondria in Diatoms 81Ansgar Gruber and Miroslav Oborník3.1 Introduction 813.2 Origin and Evolution of Diatom Plastids 833.3 Derived States of Diatom Plastids 943.4 Consequences of Complex Plastid Acquisition 963.5 Conclusions and Outlook 1004 Structure and Dynamics of the Diatom Chloroplast 113Monika Bojko, Stanislaw Listwan, Reimund Goss and Dariusz Latowski4.1 Evolution and Structure of Diatom Chloroplasts 1144.2 Architecture of the Diatom Thylakoid Membrane 1184.3 Molecular Dynamics and Structure of the Diatom Thylakoid Membrane Under Different Light Conditions 1254.4 Molecular Dynamics and Structure of the Diatom Thylakoid Membrane Under Different Thermal Conditions 1274.5 Conclusion 128Part 2: Interaction with Light 1375 Pigments in Diatoms: Light Absorption and Beyond 139Paulina Kuczyñska, Ma³gorzata Jemio³a-Rzemiñska and Kazimierz Strza³ka5.1 Environmental Factors Affect Pigments in Diatoms 1395.2 Diatoms are Well Adapted to Changing Light Conditions 1415.3 Photosynthetic Pigments in Diatoms are Chlorophylls and Carotenoids 1435.4 The Main Pigment in Diatoms – Chlorophyll a Plays a Central Role in Photochemical Energy Conversion 1485.5 Chlorophyll c Participates in Photosynthesis as an Accessory Pigment 150 5.6 Fucoxanthin-Binding Proteins in Diatoms Play a Special Role 1515.7 Regulation of Protochlorophyllide Oxidoreductases was Examined in Diatoms but Further Steps of Chlorophyll c Biosynthesis Remain Unclear 1525.8 Fucoxanthin is the Main Light-Harvesting Carotenoid in Diatom 1555.9 High Bioavailability and Bioactivity of Fucoxanthin Makes It a Desirable Compound Obtained by Extraction 1585.10 Beneficial Effects of Fucoxanthin are Versatile 1605.11 Diadinoxanthin and Diatoxanthin are Involved in Cyclic Changes, Ensuring Photoprotection 1615.12 Diatoms Also Possess the Violaxanthin Cycle, but It is not the First Line of Defense Against Excessive Light Energy 1635.13 Mechanisms of NPQ in Diatoms are Complex and Differ Depending on Species 1635.14 Many Carotenogenic Enzymes and Genes in Diatoms Have not yet Been Revealed 1655.15 Analysis and Production of Diatom Pigments are Challenging Tasks with Promising Prospects 1675.16 Conclusions 1706 Function, Structure and Organization of Light-Harvesting Proteins in Diatoms 191Charlotte Volpe and Claudia Büchel6.1 Introduction 1926.2 The FCP Proteins 1946.3 Structure, Pigmentation and Energy Transfer 1956.4 Macroorganization of FCP-PSI/II Supercomplexes 1986.5 Role of the Chloroplast Signal Recognition Particle Pathway (CpSRP) 2016.6 Balancing Light Absorption and Photoprotection 2026.7 Conclusion 2067 Sensing Light Underwater: An Update on Photoreceptors in Diatoms 217Manuel Serif and Per Winge7.1 Introduction 2197.2 Rhodopsins 2217.3 Phytochromes 2237.4 Cryptochrome/Photolyase Family 2267.5 Aureochromes 2317.6 Conclusion 2358 Non-Invasive Biophysical Techniques to Monitor the Structural Plasticity of the Photosynthetic Machinery of Live Diatom Cells 245Milán Szabó, Gergely Nagy and Gyözö Garab8.1 Introduction 2468.2 Circular Dichroism Spectroscopy 2488.3 Small-Angle Neutron Scattering (SANS) 2538.4 Electrochromic Shift Absorbance Transients 2568.5 Conclusions and Outlook 2599 Hypotheses on Frustule Functionalities: From Single Species Analysis to Systematic Approaches 267Johannes W. Goessling, Matt P. Ashworth, Marianne Ellegaard, Joao Serôdio and Martin Lopez Garcia9.1 Introduction 2689.2 Frustule Fundamentals: Chemistry, Formation, Reproduction 2719.3 Examples of Unique Frustule Systems 2749.4 Physicochemical Properties 2779.5 Physical Properties 2799.6 Frustule as an Optical System 2819.7 Conclusions and Outlook 289Part 3: Primary Production and Ecology 30110 Extracellular Polymeric Substance Production by Benthic Pennate Diatoms 303Graham J. C. Underwood10.1 Introduction 30410.2 Types of EPS Produced by Benthic Diatoms 30410.3 Functions of EPS in Benthic Diatoms in Relation to Chemical Composition 30810.4 Metabolic Pathways of EPS Production and Regulation in Diatoms 31010.5 Interactions Between Diatoms, EPS and Bacteria 31310.6 Future Directions 31511 Diatom Primary Production in Headwater Streams: A Limited but Essential Process 327Joey Allen, Michael Danger, Carlos Eduardo Wetzel, Vincent Felten and Martin Laviale11.1 Ecological Relevance of Headwater Stream Ecosystems 32811.2 Diatom Primary Production is Highly Constrained in Headwater Streams 33011.3 Diatoms as High-Quality Resources for Other Organisms 33411.4 Anthropogenic Impacts on Diatom Contributions to Headwater Stream Functioning 33611.5 Headwater Diatom Community Functioning is Supported by Unique Biodiversity 33811.6 Conclusion and Perspectives 34012 Present and Future Perspectives for Bioassessment of Running Water Using Diatoms 351Salomé FP Almeida and Maria J. Feio12.1 Introduction 35212.2 Potential of Diatoms as Indicators in Running Water Quality Assessment 35212.3 Water Quality Assessment Methods 35312.4 Molecular-Based Methods 35512.5 Transitioning from Morphology-Based to eDNA-Based Biomonitoring: Available Options 36812.6 Conclusions 37013 Photosynthetic and Growth Responses of Planktonic Diatoms to Ocean Global Changes 383Peng Jin, John Beardall and Kunshan Gao13.1 Introduction 38413.2 The Effects of Elevated CO2 and Ocean Acidification 38413.3 The Effects of Ocean Warming 38813.4 The Effects of UVR 38913.5 Combined Effects of Ocean Acidification and Warming 39013.6 Combined Effects of Ocean Acidification and UVR 39113.7 Combined Effects of Ocean Acidification and Deoxygenation 39213.8 Ocean Acidification Effects Under Multiple Drivers 39313.9 Ecological Implications 39513.10 Conclusions and Recommendations 396Part 4: Cultivation and Application 40714 Culturing Diatoms 409Daniel Vaulot, Gust Bilcke, Peter Chaerle, Angela Falciatore, Priscillia Gourvil, Michael W. Lomas, Ian Probert and Wim Vyverman14.1 Introduction 40914.2 Current Diversity of Diatoms in Culture 41114.3 Isolation of Diatom Cultures 41514.4 Culture of Diatoms 42214.5 Life Cycles 42414.6 Cryopreservation 42614.7 Diatom Strains Amenable to Genetic Engineering 43014.8 Conclusion 43415 Diatom Biofilm: Ecology and Cultivation from Laboratory to Industrial Level 449Mary Dianne Grace Arnaldo, Aurélie Mossion, Thierry Beignon, Hugo Vuillemin, Freddy Guihéneuf, Gaëtane Wielgosz-Collin and Vona Méléder15.1 Introduction 44915.2 Natural Biofilms 45315.3 Artificial Algal Biofilm Systems 45815.4 Conclusion and Perspective 46716 Opportunities and Challenges of Diatom Cell Factory for Human Health 477Clementina Sansone, Angelo Del Mondo, Luigi Pistelli, Arianna Smerilli, Maria Saggiomo and Christophe Brunet16.1 Introduction 47816.2 Carotenoids 47916.3 Vitamins 48516.4 Polyphenols 49016.5 Phytosterols 49416.6 Polysaccharides 49616.7 Polar Diatoms: New Model for Biotechnology? 50016.8 Filling the Gap between Diatoms Biological Traits and Biotechnological Use 50316.9 Conclusions 50717 Diatom-Based Bioproducts and the Potential of Frustules in Drug Delivery 529Pankaj Kumar Singh, Abhishek Saxena and Archana Tiwari17.1 Introduction 52917.2 High-Value Products Derived from Diatoms 53117.3 Diatom as Drug Delivery Carriers 53517.4 Therapeutic Applications of Diatoms 54017.5 Conclusion 542Part 5: Diatoms as Representative Organisms for the Protection of Marine Genetic Resources 55118 A Journey to Mars with Diatoms on Board 553Louisa Reissig, Mohamed Ghobara, Christian Maibohm and Johannes W. Goessling18.1 Introduction 55418.2 The Living Diatom 55618.3 The Diatom Frustule: A Sustainable Source of Porous Silica 56118.4 The Evolving Diatom 56818.5 Conclusion 57119 Legal Regime of Marine Genetic Resources in Areas Beyond National Jurisdiction 583Gemma Andreone, Valentina Rossi and Giovanni Ardito19.1 Introduction 58419.2 The Current Legal Framework 58519.3 The Notion of Marine Genetic Resources 58619.4 Bioprospecting and Marine Scientific Research: Access to and Collection of Marine Genetic Resources 58919.5 Spatial Scope (High Seas-Area) and Legal Status of MGRs in ABNJ (Common Heritage of Mankind vs Freedom of the Seas) 59319.6 Conclusion 597Acknowledgments 598References 598Subject Index 601Taxonomic Index 611