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 xviiPreface xxiii1 A Memorial to Frithjof Sterrenburg: The Importance of the Amateur Diatomist 1Janice L. Pappas1.1 Introduction 11.2 Background and Interests 31.3 The Personality of an Amateur Diatomist 71.4 The Amateur Diatomist and the Importance of Collections 111.5 The Amateur Diatomist as Expert in the Tools of the Trade 121.6 The Amateur Diatomist as Peer-Reviewed Scientific Contributor 151.7 Concluding Remarks 20Acknowledgments 21References 212 Alex Altenbach – In Memoriam of a Friend 29Wladyslaw AltermannReferences 313 The Beauty of Diatoms 33Mary Ann Tiffany and Stephen S. Nagy3.1 Early History of Observations of Diatoms 333.2 Live Diatoms 353.3 Shapes and Structures 353.4 Diatom Beauty at Various Scales 363.5 Valves During Morphogenesis 373.6 Jamin-Lebedeff Interference Contrast Microscopy 393.7 Conclusion 40Acknowledgments 40References 414 Current Diatom Research in China 43Yu Xin Zhang4.1 Diatoms for Energy Conversion and Storage 434.1.1 Introduction 434.1.2 Diatom Silica: Structure, Properties and Their Optimization 464.1.3 Diatoms for Lithium Ion Battery Materials 484.1.4 Diatoms for Energy Storage: Supercapacitors 514.1.5 Diatoms for Solar Cells 564.1.6 Diatoms for Hydrogen Storage 584.1.7 Diatoms for Thermal Energy Storage 594.2 Diatoms for Water Treatment 614.2.1 Support for Preparation of Diatomite-Based Adsorption Composites 614.2.2 Catalyst and Template for Preparation of Porous Carbon Materials 634.2.3 Modification of Surface and Porous Structure 664.2.4 Support for Preparation of Diatomite-Based Metal Oxide Composites 754.3 Study of Tribological Performances of Compound Dimples Based on Diatoms Shell Structures 86References 885 Cellular Mechanisms of Diatom Valve Morphogenesis 99Yekaterina D. Bedoshvili and Yelena V. Likhoshway5.1 Introduction 995.2 Valve Symmetry 1005.3 Valve Silification Order 1025.4 Silica Within SDV 1035.5 Macromorphogenesis Control 1045.6 Cytoskeletal Control of Morphogenesis 1065.7 The Role of Vesicles in Morphogenesis 1075.8 Valve Exocytosis and the SDV Origin 1085.9 Conclusion 110References 1106 Application of Focused Ion Beam Technique in Taxonomy-Oriented Research on Ultrastructure of Diatoms 115Andrzej Witkowski, Tomasz Płociński, Justyna Grzonka, Izabela Zgłobicka, Małgorzata Bąk, Przemysław Dąbek, Ana I. Gomes and Krzysztof J. Kurzydłowski6.1 Introduction 1166.2 Material and Methods 1176.3 Results 1176.3.1 Complex Stria Ultrastructure 1176.3.1.1 Biremis lucens (Hustedt) Sabbe, Witkowski & Vyverman 1995 1176.3.1.2 Olifantiella mascarenica Riaux-Gobin & Compere 2009 1206.4 Discussion 1236.4.1 Cultured Versus Wild Specimens 1246.5 Conclusions 124Acknowledgements 126References 1267 On Light and Diatoms: A Photonics and Photobiology Review 129Mohamed M. Ghobara, Nirmal Mazumder, Vandana Vinayak, Louisa Reissig, Ille C. Gebeshuber, Mary Ann Tiffany and Richard Gordon7.1 Introduction 1307.2 The Unique Multiscale Structure of the Diatom Frustules 1307.3 Optical Properties of Diatom Frustules 1397.3.1 The Frustule as a Box with Photonic Crystal Walls 1437.3.2 Light Focusing Phenomenon 1467.3.3 Photoluminescence Properties 1517.3.4 Probable Roles of the Frustule in Diatom Photobiology 1527.4 Diatom Photobiology 1537.4.1 Underwater Light Field 1537.4.2 Cell Cycle Light Regulation 1547.4.3 The Phototactic Phenomenon in Pennates 1547.4.4 Chloroplast Migration (Karyostrophy) 1567.4.5 Blue Light and Its Effects on Microtubules of Cells 1577.4.6 Strategies for Photoregulation Under High Light Intensity 1597.4.7 Strategies for Photoregulation Under Ultraviolet Radiation (UV) Exposure 1597.4.8 Diatoms and Low Light 1607.4.9 Diatoms and No Light 1617.4.10 Light Piping and Cellular Vision 1617.5 Diatom and Light Applications 1627.5.1 In Photocatalysis 1627.5.2 Bio-Based UV Filters 1647.5.3 In Solar Cells 1657.5.4 Applications Based on Luminescence Properties 1677.5.5 Cloaking Diatoms 1677.6 Conclusion 169Acknowledgement 169Glossary 169References 1718 Photosynthesis in Diatoms 191Matteo Scarsini, Justine Marchand, Kalina M. Manoylov and Benoît Schoefs8.1 Introduction 1918.2 The Chloroplast Structure Reflects the Two Steps Endosymbiosis 1948.3 Photosynthetic Pigments 1968.3.1 Chlorophylls 1968.3.2 Carotenoids 1978.4 The Organization of the Photosynthetic Apparatus 1978.5 Non-Photochemical Quenching (NPQ) 2008.6 Carbon Uptake and Fixation 2028.7 Conclusions and Perspectives 204Acknowledgment 205References 2059 Iron in Diatoms 213John A. Raven9.1 Introduction 2139.2 Fe Acquisition by Diatoms 2149.3 Fe-Containing Proteins in Diatoms and Economy of Fe Use 2149.4 Iron Storage 2199.5 Conclusions and Prospects 220Acknowledgements 220References 22010 Diatom Symbioses with Other Photoauthotroph 225Rosalina Stancheva and Rex Lowe10.1 Introduction 22510.2 Diatoms with a N2-Fixing Coccoid Cyanobacterial Endosymbiont 22610.3 Diatoms with N2-Fixing Filamentous Heterocytous Cyanobacterial Endosymbionts 23310.4 Epiphytic, Endogloeic and Endophytic Diatoms 23510.5 Diatom Endosymbionts in Dinoflagellates 238Acknowledgements 239References 23911 Diatom Sexual Reproduction and Life Cycles 245Aloisie Poulíčková and David G. Mann11.1 Introduction 24511.2 Centric Diatoms 24711.2.1 Life Cycle and Reproduction 24711.2.2 Gametogenesis and Gamete Structure 25011.2.3 Spawning 25111.3 Pennate Diatom Life Cycles and Reproduction 25211.4 Auxospore Development and Structure 25711.4.1 Incunabula 25911.4.2 Perizonium 26011.5 Induction of Sexual Reproduction 261Acknowledgments 262References 26312 Ecophysiology, Cell Biology and Ultrastructure of a Benthic Diatom Isolated in the Arctic 273Ulf Karsten, Rhena Schumann and Andreas Holzinger12.1 Introduction 27412.2 Environmental Settings in the Arctic 27412.3 Growth as Function of Temperature 27512.4 Growth After Long-Term Dark Incubation 27712.5 Cell Biological Traits After Long-Term Dark Incubation 27912.6 Ultrastructural Traits 28212.7 Conclusions 283Acknowledgements 284References 28413 Ecology of Freshwater Diatoms – Current Trends and Applications 289Aloisie Poulíčková and Kalina Manoylov13.1 Introduction 28913.2 Diatom Distribution 29213.3 Diatom Dispersal Ability 29213.4 Functional Classification in Diatom Ecology 29413.5 Spatial Ecology and Metacommunities 29613.6 Aquatic Ecosystems Biomonitoring 29913.7 Conclusions 301References 30114 Diatoms from Hot Springs of the Kamchatka Peninsula (Russia) 311Tatiana V. Nikulina, E. G. Kalitina, N. A. Kharitonova, G. A. Chelnokov, Elena A. Vakh and O. V. Grishchenko14.1 Introduction 31114.2 Materials and Methods 31314.3 Description of Sampling Sites 31314.3.1 Malkinsky Geothermal Field 31414.3.2 Nachikinsky Geothermal Field 31714.3.3 Verkhnaya-Paratunka Geothermal Field 31714.3.3.1 Goryachaya Sopka Hot Spring 31814.3.3.2 Karimshinsky Hot Spring 31814.3.4 Mutnovsky Geothermal Field 31814.3.4.1 Dachny Hot Springs 31914.3.4.2 Verkhne-Vilyuchinsky Hot Spring 31914.4 Results 32014.4.1 Malkinsky Geothermal Field 32014.4.2 Nachikinsky Geothermal Field 32014.4.3 Verkhnaya-Paratunka Geothermal Field 32614.4.3.1 Goryachaya Sopka Hot Spring 32614.4.3.2 Karimshinsky Hot Spring 32614.4.4 Mutnovsky Geothermal Field 32614.4.4.1 Dachny Hot Springs 32614.4.4.2 Verkhne-Vilyuchinsky Hot Spring 32714.5 Summary 330References 33115 Biodiversity of High Mountain Lakes in Europe with Special Regards to Rila Mountains (Bulgaria) and Tatra Mountains (Poland) 335Nadja Ognjanova-Rumenova, Agata Z. Wojtal, Elwira Sienkiewicz, Ivan Botev and Teodora Trichkova15.1 Introduction 33515.1.1 Factors Which Control the Diatom Distribution 33615.1.2 Biodiversity Assessment 33715.2 Recent Datom Biodiversity in High Mountain Lakes in bulgaria and Poland 33815.2.1 The Rila Lakes, Bulgaria 33815.2.2 The Tatra Lakes, Poland 33915.3 Diatom Community Changes in High-Mountain Lakes in Bulgaria and Poland from Pre-Industrial Times to Present Day 34015.3.1 The Rila Mts. 34015.3.2 Tatra Mts. 34215.4 Monitoring Data ‘2015’ and Correlations Between the Data Sets of the Rila Mts. and the Tatra Mts. 34415.4.1 The Rila Lakes 34415.4.2 The Tatra Lakes 34615.5 Red-List Data: Cirque “Sedemte Ezera”, Rila Mts. and Tatra Mts. 34915.5.1 Cirque “Sedemte Ezera”, Rila Mts. 34915.5.2 Tatra Mts. 34915.6 Summary 349Acknowledgements 351References 35116 Diatoms of the Southern Part of the Russian Far East 355Tatiana V. Nikulina and Lubov A. Medvedeva16.1 History of the Study of Freshwater Algae of the Southern Part of the Russian Far East 35516.1.1 The Primorye Territory 35716.1.1.1 Lakes and Reservoirs 35716.1.1.2 Rivers and Streams 35816.1.2 The Amur Region 36016.1.2.1 The Upper Amur 36016.1.2.2 The Middle Amur 36016.1.3 The Jewish Autonomous Region 36116.1.4 The Khabarovsk Territory 36116.1.4.1 The Middle Amur 36116.1.4.2 The Lower Amur 36116.1.5 The Sakhalin Region 36216.1.5.1 Sakhalin Island 36216.1.5.2 Moneron Island 36316.1.5.3 The Kuril Islands 36316.2 Diatom Flora of the Southern Part of the Russian Far East 363References 37717 Toxic and Harmful Marine Diatoms 389Stephen S. Bates, Nina Lundholm, Katherine A. Hubbard, Marina Montresor and Chui Pin Leaw17.1 Introduction 39017.2 Harmful Diatoms 39117.2.1 How Diatoms May Cause Harm 39117.2.2 Diatom Oxylipins 39117.2.2.1 Polyunsaturated Aldehydes (PUAs) 39117.2.2.2 Oxylipin Production by Pseudo-nitzschia 39617.3 Toxic Diatoms 39717.3.1 Diatoms That Produce Β-N-Methylamino-L-Alanine (BMAA) 39717.3.2 Nitzschia navis-varingica 40017.3.3 Nitzschia bizertensis 40017.3.4 Pseudo-nitzschia spp 40117.3.4.1 New Species 40117.3.4.2 Distribution 40117.3.4.3 Sexual Reproduction 40117.3.4.4 Genomic Insights Into Pseudo-nitzschia and Its Population Genetic Structure 41017.3.4.5 New Knowledge of Pseudo-nitzschia 41117.3.5 Identification of Toxic Diatoms 41417.3.5.1 Classical Methods 41417.3.5.2 Molecular Approaches 41517.4 Gaps in Knowledge and Thoughts for Future Directions 417References 41818 Diatoms in Forensics: A Molecular Approach to Diatom Testing in Forensic Science 435Vandana Vinayak and S. Gautam18.1 Introduction 43518.2 Postmortem Forensic Counter Measures 43818.3 Differences in Drowned Victims vs Those that Die of Other Causes 43918.4 Techniques to Identify Diatoms in Biological Sample 44018.4.1 Morphological Analysis of Water Samples 44118.4.2 Role of Site Specific Diatoms 44218.5 Case Studies 44318.5.1 Case 1 44318.5.2 Case 2 44318.5.3 Case 3 44418.6 Identification of Diatom Using Molecular Tools in Tissue and Water Samples 44618.7 Differentiation of Diatom DNA in the Tissue of a Drowned Victim 44718.8 Polymerase Chain Reaction (PCR) 44818.9 Diatom DNA Extraction from Biological Samples of a Drowned Victim 44818.9.1 Biological Samples 44818.9.2 Plankton/Diatom Isolation from Tissues Using Colloidal Silica Gradient and Phenol Chloroform Method for DNA Extraction 45418.10 Best Barcode Markers for Diatoms to Diagnose Drowning 45418.10.1 Cytochrome C Oxidase Subunit 1 (COI) 45518.10.2 Nuclear rDNA ITS Region 45618.10.3 Nuclear Small Subunit rRNA Gene 45718.11 DNA Sequencing 45718.12 Advancement in Sequencing Leads to Advancement of Data Interpretation 45818.13 Conclusion and Future Perspectives 459Acknowledgements 459List of Abbreviations Used 460References 46019 Diatomite in Use: Nature, Modifications, Commercial Applications and Prospective Trends 471Mohamed M. Ghobara and Asmaa Mohamed19.1 The Nature of Diatomite 47119.1.1 Diatomite Formation 47219.1.2 Diatom Frustule’s Resistance Against Dissolution (The Reason for Their Preservation Over Millions of Years) 47319.2 The History of Discovery and Ancient Applications 47519.3 Diatomite Occurrence and Distribution 47619.4 Diatomite Mining and Processing 47719.5 Diatomite Characterization 47919.6 Diatom Frustules Modifications 48019.7 Diatomite in Use 48119.7.1 Diatomite-Based Filtration 48219.7.1.1 Water Filtration 48319.7.1.2 Beer Filtration 48419.7.1.3 Recent Trends in Diatomite-Based Separation Techniques 48519.7.1.4 Reuse of Spent DE Filter Media 48519.7.2 Diatomite for Thermal Insulation 48519.7.3 Diatomite-Based Building Materials 48719.7.4 Diatomaceous Earth as an Insecticide 48819.7.5 Diatomaceous Earth as a soil amendment 48819.7.6 Diatomaceous Earth as a Filler 48919.7.7 Diatomaceous Earth as Abrasive Material 49019.7.8 Diatomaceous Earth as Animals’ and Human’s Food Additives 49019.7.9 Diatomaceous Earth and Nanotechnology 49119.7.9.1 Diatomaceous Earth in Solar Energy Harvesting Systems 49119.7.9.2 Diatomaceous Earth-Based Superhydrophobic Surfaces 49119.7.9.3 Diatomaceous Earth Composites as Catalysts 49219.7.9.4 Diatomaceous Earth-Based Supercapacitors 49219.7.9.5 Diatomaceous Earth-Based Pharmaceutical and Biomedical Applications 49219.7.9.6 Diatomaceous Earth-Based Lab-on-a-Chip 49419.7.10 Non-Industrial Applications 49419.8 Diatomite Fabrication and Future Aspects 49519.9 Conclusion 495Acknowledgements 496References 49620 Diatom Silica for Biomedical Applications 511Shaheer Maher, Moom Sin Aw and Dusan Losic20.1 Introduction 51120.2 Diatoms: Natural Silica Microcapsules for Therapeutics Delivery 51320.2.1 Structure 51320.2.2 Surface Modification of Diatoms 51420.2.3 Diatoms Applications as Drug Carriers 51620.2.4 Diatoms as a Source of Biodegradable Carriers for Drug Delivery Applications 52220.2.4.1 Diatoms as a Source of Biodegradable Silicon Micro and Nano Carriers for Drug Delivery 52520.2.5 Diatom Silica for Other Biomedical Applications 52720.2.5.1 Tissue Engineering 52720.2.5.2 Haemorrhage Control 52820.3 Conclusions 530Acknowledgements 531References 53121 Diafuel™(Diatom Biofuel) vs Electric Vehicles, a Basic Comparison: A High Potential Renewable Energy Source to Make India Energy Independent 537Vandana Vinayak, Khashti Ballabh Joshi and Priyangshu Manab Sarma21.1 Introduction 53821.2 Debate on Relation of Green House Gas Emissions (GHG) with CO2 and Temperature 53921.3 Outcomes of Paris Agreement 2015 54121.4 Energy Demands for India 54221.5 Critics Talking About Entry of EV in Market 54521.6 Comparison Between Electric Vehicles vs Vehicles with Diafuel™ at Large 54621.6.1 Electric Vehicles 54621.6.1.1 Status of EV in India 54821.6.1.2 Predicted Impact of EV on Global and Indian Network Versus Their Energy Sources 54921.6.2 Diafuel™ 55021.6.2.1 Diafuel™ Industrial Production 55221.6.2.2 Designing an Energy Self-Sufficient Indian House Producing Diafuel™ 55421.6.2.3 Working Prototype of Diatom Panels for the Indian House 55521.6.2.4 Advantages of Diafuel™ 55621.7 Source for Generation of Electricity to Drive EVs 55721.7.1 Resources with Zero Carbon Emission 55821.7.1.1 Nuclear Power 55921.7.1.2 Solar Energy for Faster Adoption and Manufacturing of Electric & Hybrid Vehicles in India 55921.7.1.3 Wind Power 56021.7.1.4 Barriers for Wind and Solar Energy 56121.8 CO2 Emissions by Electric Vehicle vs Gasoline Driven Vehicles 56221.9 Depletion of Earth Metals to Run EV’s vs Abundant Resources for Diafuel™ 56421.9.1 Can Diafuel™ be the Answer 56621.9.2 Harvesting Diafuel™ from Diatoms 56621.10 Current Status 56721.10.1 Data Analysis and Comparison Between EV and Diafuel™ 56921.11 Conclusions 569Acknowledgement 574List of Abbreviations Used 574References 57422 Bubble Farming: Scalable Microcosms for Diatom Biofuel and the Next Green Revolution 583Richard Gordon, Clifford R Merz, Shawn Gurke and Benoît Schoefs22.1 Introduction 58422.1.1 The Bubble Farming Concept 58822.1.2 Bubble Injection, Sampling, Harvesting and Sealing, Maybe by Drones 59222.1.3 Approach 59422.2 Mechanical Properties 59422.2.1 Optimal Bubble Size 59622.3 Optical Properties 59722.4 Surface Properties 59922.4.1 Gas Exchange Properties 59922.5 Toxicity Restrictions 60922.5.1 Algal Oil Droplet Properties 61122.6 Biofilms 61122.7 Bacterial Symbionts 61222.7.1 Soil as a Source of CO2 61322.8 Demand 61422.8.1 The Choice of Diatoms vs Other Algae 61422.9 Exponential Growth vs Stationary Phase 61722.10 Carbon Recycling 61922.11 Packaging 61922.11.1 Crop Choice by Farmers 62022.11.2 Bubble Farming vs Photobioreactors and Raceways 62022.12 Summary 620Acknowledgements 626References 626Index 655