The aim of this new book series (Diatoms: Biology and Applications) is to provide a comprehensive and reliable source of information on diatom biology and applications. The first book of the series, Diatoms Fundamentals & Applications, is wide ranging, starting with the contributions of amateurs and the beauty of diatoms, to details of how their shells are made, how they bend light to their advantage and ours, and major aspects of their biochemistry (photosynthesis and iron metabolism). The book then delves into the ecology of diatoms living in a wide range of habitats, and look at those few that can kill or harm us. The book concludes with a wide range of applications of diatoms, in forensics, manufacturing, medicine, biofuel and agriculture. The contributors are leading international experts on diatoms. This book is for a wide audience researchers, academics, students, and teachers of biology and related disciplines, written to both act as an introduction to diatoms and to present some of the most advanced research on them.
Table of Contents
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
