Diatoms

Professor J. Seckbach is a retired senior academician at The Hebrew University of Jerusalem, Israel. He earned his MSc. & PhD from the University of Chicago. He was appointed to the Hebrew University, Jerusalem (as a senior Lecturer) and spent sabbaticals at UCLA and Harvard University. He served at Louisiana State University (LSU), Baton Rouge, LA, USA, as the first selected Chair for the Louisiana Sea Grant and Technology transfer. He has edited over 35 scientific books and ~ 140 scientific articles on plant ferritin–phytoferritin, cellular evolution, acidothermophilic algae, and life in extreme environments and on astrobiology. Richard Gordon's involvement with diatoms goes back to 1970 with his capillarity model for their gliding motility, published in the Proceedings of the National Academy of Sciences of the United States of America. He later worked on a diffusion limited aggregation model for diatom morphogenesis, which led to the first paper ever published on diatom nanotechnology in 1988. He organized the first workshop on diatom nanotech in 2003. His other research is on computed tomography algorithms, HIV/AIDS prevention, and embryogenesis.

Foreword xvii

Preface xxiii

1 A Memorial to Frithjof Sterrenburg: The Importance of the Amateur Diatomist 1
Janice L. Pappas

1.1 Introduction 1

1.2 Background and Interests 3

1.3 The Personality of an Amateur Diatomist 7

1.4 The Amateur Diatomist and the Importance of Collections 11

1.5 The Amateur Diatomist as Expert in the Tools of the Trade 12

1.6 The Amateur Diatomist as Peer-Reviewed Scientific Contributor 15

1.7 Concluding Remarks 20

Acknowledgments 21

References 21

2 Alex Altenbach – In Memoriam of a Friend 29
Wladyslaw Altermann

References 31

3 The Beauty of Diatoms 33
Mary Ann Tiffany and Stephen S. Nagy

3.1 Early History of Observations of Diatoms 33

3.2 Live Diatoms 35

3.3 Shapes and Structures 35

3.4 Diatom Beauty at Various Scales 36

3.5 Valves During Morphogenesis 37

3.6 Jamin-Lebedeff Interference Contrast Microscopy 39

3.7 Conclusion 40

Acknowledgments 40

References 41

4 Current Diatom Research in China 43
Yu Xin Zhang

4.1 Diatoms for Energy Conversion and Storage 43

4.1.1 Introduction 43

4.1.2 Diatom Silica: Structure, Properties and Their Optimization 46

4.1.3 Diatoms for Lithium Ion Battery Materials 48

4.1.4 Diatoms for Energy Storage: Supercapacitors 51

4.1.5 Diatoms for Solar Cells 56

4.1.6 Diatoms for Hydrogen Storage 58

4.1.7 Diatoms for Thermal Energy Storage 59

4.2 Diatoms for Water Treatment 61

4.2.1 Support for Preparation of Diatomite-Based Adsorption Composites 61

4.2.2 Catalyst and Template for Preparation of Porous Carbon Materials 63

4.2.3 Modification of Surface and Porous Structure 66

4.2.4 Support for Preparation of Diatomite-Based Metal Oxide Composites 75

4.3 Study of Tribological Performances of Compound Dimples Based on Diatoms Shell Structures 86

References 88

5 Cellular Mechanisms of Diatom Valve Morphogenesis 99
Yekaterina D. Bedoshvili and Yelena V. Likhoshway

5.1 Introduction 99

5.2 Valve Symmetry 100

5.3 Valve Silification Order 102

5.4 Silica Within SDV 103

5.5 Macromorphogenesis Control 104

5.6 Cytoskeletal Control of Morphogenesis 106

5.7 The Role of Vesicles in Morphogenesis 107

5.8 Valve Exocytosis and the SDV Origin 108

5.9 Conclusion 110

References 110

6 Application of Focused Ion Beam Technique in Taxonomy-Oriented Research on Ultrastructure of Diatoms 115
Andrzej Witkowski, Tomasz Płociński, Justyna Grzonka, Izabela Zgłobicka, Małgorzata Bąk, Przemysław Dąbek, Ana I. Gomes and Krzysztof J. Kurzydłowski

6.1 Introduction 116

6.2 Material and Methods 117

6.3 Results 117

6.3.1 Complex Stria Ultrastructure 117

6.3.1.1 Biremis lucens (Hustedt) Sabbe, Witkowski & Vyverman 1995 117

6.3.1.2 Olifantiella mascarenica Riaux-Gobin & Compere 2009 120

6.4 Discussion 123

6.4.1 Cultured Versus Wild Specimens 124

6.5 Conclusions 124

Acknowledgements 126

References 126

7 On Light and Diatoms: A Photonics and Photobiology Review 129
Mohamed M. Ghobara, Nirmal Mazumder, Vandana Vinayak, Louisa Reissig, Ille C. Gebeshuber, Mary Ann Tiffany and Richard Gordon

7.1 Introduction 130

7.2 The Unique Multiscale Structure of the Diatom Frustules 130

7.3 Optical Properties of Diatom Frustules 139

7.3.1 The Frustule as a Box with Photonic Crystal Walls 143

7.3.2 Light Focusing Phenomenon 146

7.3.3 Photoluminescence Properties 151

7.3.4 Probable Roles of the Frustule in Diatom Photobiology 152

7.4 Diatom Photobiology 153

7.4.1 Underwater Light Field 153

7.4.2 Cell Cycle Light Regulation 154

7.4.3 The Phototactic Phenomenon in Pennates 154

7.4.4 Chloroplast Migration (Karyostrophy) 156

7.4.5 Blue Light and Its Effects on Microtubules of Cells 157

7.4.6 Strategies for Photoregulation Under High Light Intensity 159

7.4.7 Strategies for Photoregulation Under Ultraviolet Radiation (UV) Exposure 159

7.4.8 Diatoms and Low Light 160

7.4.9 Diatoms and No Light 161

7.4.10 Light Piping and Cellular Vision 161

7.5 Diatom and Light Applications 162

7.5.1 In Photocatalysis 162

7.5.2 Bio-Based UV Filters 164

7.5.3 In Solar Cells 165

7.5.4 Applications Based on Luminescence Properties 167

7.5.5 Cloaking Diatoms 167

7.6 Conclusion 169

Acknowledgement 169

Glossary 169

References 171

8 Photosynthesis in Diatoms 191
Matteo Scarsini, Justine Marchand, Kalina M. Manoylov and Benoît Schoefs

8.1 Introduction 191

8.2 The Chloroplast Structure Reflects the Two Steps Endosymbiosis 194

8.3 Photosynthetic Pigments 196

8.3.1 Chlorophylls 196

8.3.2 Carotenoids 197

8.4 The Organization of the Photosynthetic Apparatus 197

8.5 Non-Photochemical Quenching (NPQ) 200

8.6 Carbon Uptake and Fixation 202

8.7 Conclusions and Perspectives 204

Acknowledgment 205

References 205

9 Iron in Diatoms 213
John A. Raven

9.1 Introduction 213

9.2 Fe Acquisition by Diatoms 214

9.3 Fe-Containing Proteins in Diatoms and Economy of Fe Use 214

9.4 Iron Storage 219

9.5 Conclusions and Prospects 220

Acknowledgements 220

References 220

10 Diatom Symbioses with Other Photoauthotroph 225
Rosalina Stancheva and Rex Lowe

10.1 Introduction 225

10.2 Diatoms with a N2-Fixing Coccoid Cyanobacterial Endosymbiont 226

10.3 Diatoms with N2-Fixing Filamentous Heterocytous Cyanobacterial Endosymbionts 233

10.4 Epiphytic, Endogloeic and Endophytic Diatoms 235

10.5 Diatom Endosymbionts in Dinoflagellates 238

Acknowledgements 239

References 239

11 Diatom Sexual Reproduction and Life Cycles 245
Aloisie Poulíčková and David G. Mann

11.1 Introduction 245

11.2 Centric Diatoms 247

11.2.1 Life Cycle and Reproduction 247

11.2.2 Gametogenesis and Gamete Structure 250

11.2.3 Spawning 251

11.3 Pennate Diatom Life Cycles and Reproduction 252

11.4 Auxospore Development and Structure 257

11.4.1 Incunabula 259

11.4.2 Perizonium 260

11.5 Induction of Sexual Reproduction 261

Acknowledgments 262

References 263

12 Ecophysiology, Cell Biology and Ultrastructure of a Benthic Diatom Isolated in the Arctic 273
Ulf Karsten, Rhena Schumann and Andreas Holzinger

12.1 Introduction 274

12.2 Environmental Settings in the Arctic 274

12.3 Growth as Function of Temperature 275

12.4 Growth After Long-Term Dark Incubation 277

12.5 Cell Biological Traits After Long-Term Dark Incubation 279

12.6 Ultrastructural Traits 282

12.7 Conclusions 283

Acknowledgements 284

References 284

13 Ecology of Freshwater Diatoms – Current Trends and Applications 289
Aloisie Poulíčková and Kalina Manoylov

13.1 Introduction 289

13.2 Diatom Distribution 292

13.3 Diatom Dispersal Ability 292

13.4 Functional Classification in Diatom Ecology 294

13.5 Spatial Ecology and Metacommunities 296

13.6 Aquatic Ecosystems Biomonitoring 299

13.7 Conclusions 301

References 301

14 Diatoms from Hot Springs of the Kamchatka Peninsula (Russia) 311
Tatiana V. Nikulina, E. G. Kalitina, N. A. Kharitonova, G. A. Chelnokov, Elena A. Vakh and O. V. Grishchenko

14.1 Introduction 311

14.2 Materials and Methods 313

14.3 Description of Sampling Sites 313

14.3.1 Malkinsky Geothermal Field 314

14.3.2 Nachikinsky Geothermal Field 317

14.3.3 Verkhnaya-Paratunka Geothermal Field 317

14.3.3.1 Goryachaya Sopka Hot Spring 318

14.3.3.2 Karimshinsky Hot Spring 318

14.3.4 Mutnovsky Geothermal Field 318

14.3.4.1 Dachny Hot Springs 319

14.3.4.2 Verkhne-Vilyuchinsky Hot Spring 319

14.4 Results 320

14.4.1 Malkinsky Geothermal Field 320

14.4.2 Nachikinsky Geothermal Field 320

14.4.3 Verkhnaya-Paratunka Geothermal Field 326

14.4.3.1 Goryachaya Sopka Hot Spring 326

14.4.3.2 Karimshinsky Hot Spring 326

14.4.4 Mutnovsky Geothermal Field 326

14.4.4.1 Dachny Hot Springs 326

14.4.4.2 Verkhne-Vilyuchinsky Hot Spring 327

14.5 Summary 330

References 331

15 Biodiversity of High Mountain Lakes in Europe with Special Regards to Rila Mountains (Bulgaria) and Tatra Mountains (Poland) 335
Nadja Ognjanova-Rumenova, Agata Z. Wojtal, Elwira Sienkiewicz, Ivan Botev and Teodora Trichkova

15.1 Introduction 335

15.1.1 Factors Which Control the Diatom Distribution 336

15.1.2 Biodiversity Assessment 337

15.2 Recent Datom Biodiversity in High Mountain Lakes in bulgaria and Poland 338

15.2.1 The Rila Lakes, Bulgaria 338

15.2.2 The Tatra Lakes, Poland 339

15.3 Diatom Community Changes in High-Mountain Lakes in Bulgaria and Poland from Pre-Industrial Times to Present Day 340

15.3.1 The Rila Mts. 340

15.3.2 Tatra Mts. 342

15.4 Monitoring Data ‘2015’ and Correlations Between the Data Sets of the Rila Mts. and the Tatra Mts. 344

15.4.1 The Rila Lakes 344

15.4.2 The Tatra Lakes 346

15.5 Red-List Data: Cirque “Sedemte Ezera”, Rila Mts. and Tatra Mts. 349

15.5.1 Cirque “Sedemte Ezera”, Rila Mts. 349

15.5.2 Tatra Mts. 349

15.6 Summary 349

Acknowledgements 351

References 351

16 Diatoms of the Southern Part of the Russian Far East 355
Tatiana V. Nikulina and Lubov A. Medvedeva

16.1 History of the Study of Freshwater Algae of the Southern Part of the Russian Far East 355

16.1.1 The Primorye Territory 357

16.1.1.1 Lakes and Reservoirs 357

16.1.1.2 Rivers and Streams 358

16.1.2 The Amur Region 360

16.1.2.1 The Upper Amur 360

16.1.2.2 The Middle Amur 360

16.1.3 The Jewish Autonomous Region 361

16.1.4 The Khabarovsk Territory 361

16.1.4.1 The Middle Amur 361

16.1.4.2 The Lower Amur 361

16.1.5 The Sakhalin Region 362

16.1.5.1 Sakhalin Island 362

16.1.5.2 Moneron Island 363

16.1.5.3 The Kuril Islands 363

16.2 Diatom Flora of the Southern Part of the Russian Far East 363

References 377

17 Toxic and Harmful Marine Diatoms 389
Stephen S. Bates, Nina Lundholm, Katherine A. Hubbard, Marina Montresor and Chui Pin Leaw

17.1 Introduction 390

17.2 Harmful Diatoms 391

17.2.1 How Diatoms May Cause Harm 391

17.2.2 Diatom Oxylipins 391

17.2.2.1 Polyunsaturated Aldehydes (PUAs) 391

17.2.2.2 Oxylipin Production by Pseudo-nitzschia 396

17.3 Toxic Diatoms 397

17.3.1 Diatoms That Produce Β-N-Methylamino-L-Alanine (BMAA) 397

17.3.2 Nitzschia navis-varingica 400

17.3.3 Nitzschia bizertensis 400

17.3.4 Pseudo-nitzschia spp 401

17.3.4.1 New Species 401

17.3.4.2 Distribution 401

17.3.4.3 Sexual Reproduction 401

17.3.4.4 Genomic Insights Into Pseudo-nitzschia and Its Population Genetic Structure 410

17.3.4.5 New Knowledge of Pseudo-nitzschia 411

17.3.5 Identification of Toxic Diatoms 414

17.3.5.1 Classical Methods 414

17.3.5.2 Molecular Approaches 415

17.4 Gaps in Knowledge and Thoughts for Future Directions 417

References 418

18 Diatoms in Forensics: A Molecular Approach to Diatom Testing in Forensic Science 435
Vandana Vinayak and S. Gautam

18.1 Introduction 435

18.2 Postmortem Forensic Counter Measures 438

18.3 Differences in Drowned Victims vs Those that Die of Other Causes 439

18.4 Techniques to Identify Diatoms in Biological Sample 440

18.4.1 Morphological Analysis of Water Samples 441

18.4.2 Role of Site Specific Diatoms 442

18.5 Case Studies 443

18.5.1 Case 1 443

18.5.2 Case 2 443

18.5.3 Case 3 444

18.6 Identification of Diatom Using Molecular Tools in Tissue and Water Samples 446

18.7 Differentiation of Diatom DNA in the Tissue of a Drowned Victim 447

18.8 Polymerase Chain Reaction (PCR) 448

18.9 Diatom DNA Extraction from Biological Samples of a Drowned Victim 448

18.9.1 Biological Samples 448

18.9.2 Plankton/Diatom Isolation from Tissues Using Colloidal Silica Gradient and Phenol Chloroform Method for DNA Extraction 454

18.10 Best Barcode Markers for Diatoms to Diagnose Drowning 454

18.10.1 Cytochrome C Oxidase Subunit 1 (COI) 455

18.10.2 Nuclear rDNA ITS Region 456

18.10.3 Nuclear Small Subunit rRNA Gene 457

18.11 DNA Sequencing 457

18.12 Advancement in Sequencing Leads to Advancement of Data Interpretation 458

18.13 Conclusion and Future Perspectives 459

Acknowledgements 459

List of Abbreviations Used 460

References 460

19 Diatomite in Use: Nature, Modifications, Commercial Applications and Prospective Trends 471
Mohamed M. Ghobara and Asmaa Mohamed

19.1 The Nature of Diatomite 471

19.1.1 Diatomite Formation 472

19.1.2 Diatom Frustule’s Resistance Against Dissolution (The Reason for Their Preservation Over Millions of Years) 473

19.2 The History of Discovery and Ancient Applications 475

19.3 Diatomite Occurrence and Distribution 476

19.4 Diatomite Mining and Processing 477

19.5 Diatomite Characterization 479

19.6 Diatom Frustules Modifications 480

19.7 Diatomite in Use 481

19.7.1 Diatomite-Based Filtration 482

19.7.1.1 Water Filtration 483

19.7.1.2 Beer Filtration 484

19.7.1.3 Recent Trends in Diatomite-Based Separation Techniques 485

19.7.1.4 Reuse of Spent DE Filter Media 485

19.7.2 Diatomite for Thermal Insulation 485

19.7.3 Diatomite-Based Building Materials 487

19.7.4 Diatomaceous Earth as an Insecticide 488

19.7.5 Diatomaceous Earth as a soil amendment 488

19.7.6 Diatomaceous Earth as a Filler 489

19.7.7 Diatomaceous Earth as Abrasive Material 490

19.7.8 Diatomaceous Earth as Animals’ and Human’s Food Additives 490

19.7.9 Diatomaceous Earth and Nanotechnology 491

19.7.9.1 Diatomaceous Earth in Solar Energy Harvesting Systems 491

19.7.9.2 Diatomaceous Earth-Based Superhydrophobic Surfaces 491

19.7.9.3 Diatomaceous Earth Composites as Catalysts 492

19.7.9.4 Diatomaceous Earth-Based Supercapacitors 492

19.7.9.5 Diatomaceous Earth-Based Pharmaceutical and Biomedical Applications 492

19.7.9.6 Diatomaceous Earth-Based Lab-on-a-Chip 494

19.7.10 Non-Industrial Applications 494

19.8 Diatomite Fabrication and Future Aspects 495

19.9 Conclusion 495

Acknowledgements 496

References 496

20 Diatom Silica for Biomedical Applications 511
Shaheer Maher, Moom Sin Aw and Dusan Losic

20.1 Introduction 511

20.2 Diatoms: Natural Silica Microcapsules for Therapeutics Delivery 513

20.2.1 Structure 513

20.2.2 Surface Modification of Diatoms 514

20.2.3 Diatoms Applications as Drug Carriers 516

20.2.4 Diatoms as a Source of Biodegradable Carriers for Drug Delivery Applications 522

20.2.4.1 Diatoms as a Source of Biodegradable Silicon Micro and Nano Carriers for Drug Delivery 525

20.2.5 Diatom Silica for Other Biomedical Applications 527

20.2.5.1 Tissue Engineering 527

20.2.5.2 Haemorrhage Control 528

20.3 Conclusions 530

Acknowledgements 531

References 531

21 Diafuel™(Diatom Biofuel) vs Electric Vehicles, a Basic Comparison: A High Potential Renewable Energy Source to Make India Energy Independent 537
Vandana Vinayak, Khashti Ballabh Joshi and Priyangshu Manab Sarma

21.1 Introduction 538

21.2 Debate on Relation of Green House Gas Emissions (GHG) with CO2 and Temperature 539

21.3 Outcomes of Paris Agreement 2015 541

21.4 Energy Demands for India 542

21.5 Critics Talking About Entry of EV in Market 545

21.6 Comparison Between Electric Vehicles vs Vehicles with Diafuel™ at Large 546

21.6.1 Electric Vehicles 546

21.6.1.1 Status of EV in India 548

21.6.1.2 Predicted Impact of EV on Global and Indian Network Versus Their Energy Sources 549

21.6.2 Diafuel™ 550

21.6.2.1 Diafuel™ Industrial Production 552

21.6.2.2 Designing an Energy Self-Sufficient Indian House Producing Diafuel™ 554

21.6.2.3 Working Prototype of Diatom Panels for the Indian House 555

21.6.2.4 Advantages of Diafuel™ 556

21.7 Source for Generation of Electricity to Drive EVs 557

21.7.1 Resources with Zero Carbon Emission 558

21.7.1.1 Nuclear Power 559

21.7.1.2 Solar Energy for Faster Adoption and Manufacturing of Electric & Hybrid Vehicles in India 559

21.7.1.3 Wind Power 560

21.7.1.4 Barriers for Wind and Solar Energy 561

21.8 CO2 Emissions by Electric Vehicle vs Gasoline Driven Vehicles 562

21.9 Depletion of Earth Metals to Run EV’s vs Abundant Resources for Diafuel™ 564

21.9.1 Can Diafuel™ be the Answer 566

21.9.2 Harvesting Diafuel™ from Diatoms 566

21.10 Current Status 567

21.10.1 Data Analysis and Comparison Between EV and Diafuel™ 569

21.11 Conclusions 569

Acknowledgement 574

List of Abbreviations Used 574

References 574

22 Bubble Farming: Scalable Microcosms for Diatom Biofuel and the Next Green Revolution 583
Richard Gordon, Clifford R Merz, Shawn Gurke and Benoît Schoefs

22.1 Introduction 584

22.1.1 The Bubble Farming Concept 588

22.1.2 Bubble Injection, Sampling, Harvesting and Sealing, Maybe by Drones 592

22.1.3 Approach 594

22.2 Mechanical Properties 594

22.2.1 Optimal Bubble Size 596

22.3 Optical Properties 597

22.4 Surface Properties 599

22.4.1 Gas Exchange Properties 599

22.5 Toxicity Restrictions 609

22.5.1 Algal Oil Droplet Properties 611

22.6 Biofilms 611

22.7 Bacterial Symbionts 612

22.7.1 Soil as a Source of CO2 613

22.8 Demand 614

22.8.1 The Choice of Diatoms vs Other Algae 614

22.9 Exponential Growth vs Stationary Phase 617

22.10 Carbon Recycling 619

22.11 Packaging 619

22.11.1 Crop Choice by Farmers 620

22.11.2 Bubble Farming vs Photobioreactors and Raceways 620

22.12 Summary 620

Acknowledgements 626

References 626

Index 655