Diatom Gliding Motility

Stanley Cohn is a Professor Emeritus of Biology at DePaul University, Chicago. His lab has been studying ecological conditions affecting diatom cell movement for over 30 years, focusing on the responses to changes in light, temperature, surface, and other ecological factors. He received the Royal Society of Arts Silver Medal and the DePaul University Excellence in Teaching Award. Kalina Manoylov is professor in Biology at Georgia College and State University and visiting professor at the University of Iowa Lakeside lab. She has a PhD in Zoology and Ecology, Evolutionary Biology and Behavior from Michigan State University. She uses algal-community data to understand environmental changes and anthropogenic effects in different aquatic environments. Her area of expertise is algal and diatom taxonomy and algal ecology. She has published more than 30 peer-reviewed articles, half of them with her students. She is the editor for PhytoKeys and Frontiers Plant Science. 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.

Preface xxvii

1 Some Observations of Movements of Pennate Diatoms in Cultures and Their Possible Interpretation 1
Thomas Harbich

1.1 Introduction 2

1.2 Kinematics and Analysis of Trajectories in Pennate Diatoms with Almost Straight Raphe along the Apical Axis 3

1.3 Curvature of the Trajectory at the Reversal Points 9

1.4 Movement of Diatoms in and on Biofilms 13

1.5 Movement on the Water Surface 16

1.6 Formation of Flat Colonies in Cymbella lanceolata 23

1.7 Conclusion 29

References 29

2 The Kinematics of Explosively Jerky Diatom Motility: A Natural Example of Active Nanofluidics 33
Ahmet C. Sabuncu, Richard Gordon, Edmond Richer, Kalina M. Manoylov and Ali Beskok

2.1 Introduction 34

2.2 Material and Methods 35

2.2.1 Diatom Preparation 35

2.2.2 Imaging System 35

2.2.3 Sample Preparation 36

2.2.4 Image Processing 36

2.3 Results and Discussion 41

2.3.1 Comparison of Particle Tracking Algorithms 41

2.3.2 Stationary Particles 42

2.3.3 Diatom Centroid Measurements 43

2.3.4 Diatom Orientation Angle Measurements 46

2.3.5 Is Diatom Motion Characterized by a Sequence of Small Explosive Movements? 49

2.3.6 Future Work 50

2.4 Conclusions 51

Appendix 52

References 59

3 Cellular Mechanisms of Raphid Diatom Gliding 65
Yekaterina D. Bedoshvili and Yelena V. Likhoshway

3.1 Introduction 65

3.2 Gliding and Secretion of Mucilage 67

3.3 Cell Mechanisms of Mucilage Secretion 68

3.4 Mechanisms of Gliding Regulation 71

3.5 Conclusions 72

Acknowledgments 72

References 73

4 Motility of Biofilm-Forming Benthic Diatoms 77
Karen Grace Bondoc-Naumovitz and Stanley A. Cohn

4.1 Introduction 77

4.2 General Motility Models and Concepts 86

4.2.1 Adhesion 87

4.2.2 Gliding Motility 89

4.2.3 Motility and Environmental Responsiveness 91

4.3 Light-Directed Vertical Migration 93

4.4 Stimuli-Directed Movement 94

4.4.1 Nutrient Foraging 94

4.4.2 Pheromone-Based Mate-Finding Motility 97

4.4.3 Prioritization Between Co-Occurring Stimuli 99

4.5 Conclusion 99

References 100

5 Photophobic Responses of Diatoms – Motility and Inter-Species Modulation 111
Stanley A. Cohn, Lee Warnick and Blake Timmerman

5.1 Introduction 112

5.2 Types of Observed Photoresponses 112

5.2.1 Light Spot Accumulation 112

5.2.2 High-Intensity Light Responses 114

5.3 Inter-Species Effects of Light Responses 118

5.3.1 Inter-Species Effects on High Irradiance Direction Change Response 119

5.3.2 Inter-Species Effects on Cell Accumulation into Light Spots 123

5.4 Summary 123

References 131

6 Diatom Biofilms: Ecosystem Engineering and Niche Construction 135
David M. Paterson and Julie A. Hope

6.1 Introduction 135

6.1.1 Diatoms: A Brief Portfolio 135

6.1.2 Benthic Diatoms as a Research Challenge 136

6.2 The Microphytobenthos and Epipelic Diatoms 136

6.3 The Ecological Importance of Locomotion 137

6.4 Ecosystem Engineering and Functions 139

6.4.1 Ecosystem Engineering 139

6.4.2 Ecosystem Functioning 140

6.5 Microphytobenthos as Ecosystem Engineers 141

6.5.1 Sediment Stabilization 141

6.5.2 Beyond the Benthos 143

6.5.3 Diatom Architects 144

6.5.4 Working with Others: Combined Effects 144

6.5.5 The Dynamic of EPS 145

6.5.6 Nutrient Turnover and Biogeochemistry 145

6.6 Niche Construction and Epipelic Diatoms 146

6.7 Conclusion 149

Acknowledgments 150

References 150

7 Diatom Motility: Mechanisms, Control and Adaptive Value 159
João Serôdio

7.1 Introduction 159

7.2 Forms and Mechanisms of Motility in Diatoms 160

7.2.1 Motility in Centric Diatoms 160

7.2.2 Motility in Pennate Raphid Diatoms 161

7.2.3 Motility in Other Substrate-Associated Diatoms 162

7.2.4 Vertical Migration in Diatom-Dominated Microphytobenthos 163

7.3 Controlling Factors of Diatom Motility 164

7.3.1 Motility Responses to Vectorial Stimuli 164

7.3.1.1 Light Intensity 164

7.3.1.2 Light Spectrum 165

7.3.1.3 UV Radiation 166

7.3.1.4 Gravity 166

7.3.1.5 Chemical Gradients 167

7.3.2 Motility Responses to Non-Vectorial Stimuli 167

7.3.2.1 Temperature 167

7.3.2.2 Salinity 168

7.3.2.3 pH 168

7.3.2.4 Calcium 168

7.3.2.5 Other Factors 169

7.3.2.6 Inhibitors of Diatom Motility 169

7.3.3 Species-Specific Responses and Interspecies Interactions 169

7.3.4 Endogenous Control of Motility 170

7.3.5 A Model of Diatom Vertical Migration Behavior in Sediments 170

7.4 Adaptive Value and Consequences of Motility 172

7.4.1 Planktonic Centrics 172

7.4.2 Benthic Pennates 173

7.4.3 Ecological Consequences of Vertical Migration 175

7.4.3.1 Motility-Enhanced Productivity 175

7.4.3.2 Carbon Cycling and Sediment Biostabilization 176

Acknowledgments 176

References 176

8 Motility in the Diatom Genus Eunotia Ehrenb. 185
Paula C. Furey

8.1 Introduction 185

8.2 Accounts of Movement in Eunotia 188

8.3 Motility in the Context of Valve Structure 194

8.3.1 Motility and Morphological Characteristics in Girdle View 194

8.3.2 Motility and Morphological Characteristics in Valve View 196

8.3.3 Motility and the Rimoportula 198

8.4 Motility and Ecology of Eunotia 198

8.4.1 Substratum-Associated Environments 199

8.4.2 Planktonic Environments 201

8.5 Motility and Diatom Evolution 202

8.6 Conclusion and Future Directions 203

Acknowledgements 204

References 205

9 A Free Ride: Diatoms Attached on Motile Diatoms 211
Vincent Roubeix and Martin Laviale

9.1 Introduction 211

9.2 Adhesion and Distribution of Epidiatomic Diatoms on Their Host 213

9.3 The Specificity of Host-Epiphyte Interactions 215

9.4 Cost-Benefit Analysis of Host-Epiphyte Interactions 217

9.5 Conclusion 219

References 219

10 Towards a Digital Diatom: Image Processing and Deep Learning Analysis of Bacillaria paradoxa Dynamic Morphology 223
Bradly Alicea, Richard Gordon, Thomas Harbich, Ujjwal Singh, Asmit Singh and Vinay Varma

10.1 Introduction 224

10.1.1 Organism Description 224

10.1.2 Research Motivation 227

10.2 Methods 228

10.2.1 Video Extraction 228

10.2.2 Deep Learning 230

10.2.3 DeepLabv3 Analysis 234

10.2.4 Primary Dataset Analysis 234

10.2.5 Data Availability 235

10.3 Results 235

10.3.1 Watershed Segmentation and Canny Edge Detection 235

10.3.2 Deep Learning 236

10.4 Conclusion 243

Acknowledgments 245

References 245

11 Diatom Triboacoustics 249
Ille C. Gebeshuber, Florian Zischka, Helmut Kratochvil, Anton Noll, Richard Gordon and Thomas Harbich

Glossary 249

11.1 State-of-the-Art 251

11.1.1 Diatoms and Their Movement 251

11.1.2 The Navier-Stokes Equation 252

11.1.3 Low Reynolds Number 253

11.1.4 Reynolds Number for Diatoms 254

11.1.5 Further Thoughts About Movement of Diatoms 254

11.1.6 Possible Reasons for Diatom Movement 255

11.1.7 Underwater Acoustics, Hydrophones 256

11.1.7.1 Underwater Acoustics 256

11.1.7.2 Hydrophones 257

11.2 Methods 257

11.2.1 Estimate of the Momentum of a Moving Diatom 257

11.2.2 On the Speed of Expansion of the Mucopolysaccharide Filaments 258

11.2.2.1 Estimation of Radial Expansion 258

11.2.2.2 Sound Generation 261

11.2.3 Gathering Diatoms 266

11.2.3.1 Purchasing Diatom Cultures 267

11.2.3.2 Diatoms from the Wild 267

11.2.4 Using a Hydrophone to Detect Possible Acoustic Signals from Diatoms 269

11.2.4.1 First Setup 269

11.2.4.2 Second Setup 271

11.3 Results and Discussion 272

11.3.1 Spectrograms 272

11.3.2 Discussion 277

11.4 Conclusions and Outlook 277

Acknowledgements 279

References 279

12 Movements of Diatoms VIII: Synthesis and Hypothesis 283
Jean Bertrand

12.1 Introduction 283

12.2 Review of the Conditions Necessary for Movements 284

12.3 Hypothesis 285

12.4 Analysis – Comparison with Observations 288

12.4.1 Translational Apical Movement 288

12.4.2 The Transapical Toppling Movement 290

12.4.3 Diverse Pivoting 290

12.5 Conclusion 291

Acknowledgments 292

References 292

13 Locomotion of Benthic Pennate Diatoms: Models and Thoughts 295
Jiadao Wang, Ding Weng, Lei Chen and Shan Cao

13.1 Diatom Structure 295

13.1.1 Ultrastructure of Frustules 295

13.1.2 Bending Ability of Diatoms 297

13.2 Models for Diatom Locomotion 300

13.2.1 Edgar Model for Diatom Locomotion 300

13.2.2 Van der Waals Force Model (VW Model) for Diatom Locomotion 302

13.2.2.1 Locomotion Behavior of Diatoms 302

13.2.2.2 Moving Organelles and Pseudopods 304

13.2.2.3 Chemical Properties of Mucilage Trails 307

13.2.2.4 Mechanical Properties of Mucilage Trails 310

13.2.2.5 VW Model for Diatom Locomotion 314

13.3 Locomotion and Aggregation of Diatoms 319

13.3.1 Locomotion Trajectory and Parameters of Diatoms 319

13.4 Simulation on Locomotion, Aggregation and Mutual Perception of Diatoms 323

13.4.1 Simulation Area and Parameters 323

13.4.2 Diatom Life Cycle and Modeling Parameters 323

13.4.3 Simulation Results of Diatom Locomotion Trajectory with Mutual Perception 326

13.4.4 Simulation Results of Diatom Adhesion with Mutual Perception 327

13.4.5 Adhesion and Aggregation Mechanism of Diatoms 331

References 332

14 The Whimsical History of Proposed Motors for Diatom Motility 335
Richard Gordon

14.1 Introduction 336

14.2 Historical Survey of Models for the Diatom Motor 338

14.2.1 Diatoms Somersault via Protruding Muscles (1753) 338

14.2.2 Vibrating Feet or Protrusions Move Diatoms (1824) 338

14.2.3 Diatoms Crawl Like Snails (1838) 342

14.2.4 The Diatom Motor is a Jet Engine (1849) 344

14.2.5 Rowing Diatoms (1855) 346

14.2.6 Diatoms Have Protoplasmic Tank Treads (1865) 350

14.2.7 Diatoms as the Flame of Life: Capillarity (1883) 354

14.2.8 Bellowing Diatoms (1887) 355

14.2.9 Jelly Powered Jet Skiing Diatoms (1896) 355

14.2.10 Bubble Powered Diatoms (1905) 358

14.2.11 Diatoms Win: “I Have No New Theory to Offer and See No Reason to Use Those Already Abandoned” (1940) 360

14.2.12 Is Diatom Motility a Special Case of Cytoplasmic Streaming? (1943) 360

14.2.13 Diatom Adhesion as a Sliding Toilet Plunger (1966) 365

14.2.14 Diatom as a Monorail that Lays Its Own Track (1967) 366

14.2.15 The Diatom as a “Compressed Air” Coanda Effect Gliding Vehicle (1967) 368

14.2.16 The Electrokinetic Diatom (1974) 371

14.2.17 The Diatom Clothes Line or Railroad Track (1980) 372

14.2.18 Diatom Ion Cyclotron Resonance (1987) 374

14.2.19 Diatoms Do Internal Treadmilling (1998) 375

14.2.20 Surface Treadmilling, Swimming and Snorkeling Diatoms (2007) 376

14.2.21 Acoustic Streaming: The Diatom as Vibrator or Jack Hammer (2010) 378

14.2.22 Propulsion of Diatoms Via Many Small Explosions (2020) 379

14.2.23 Diatoms Walk Like Geckos (2019) 380

14.3 Pulling What We Know and Don’t Know Together, about the Diatom Motor 381

14.4 Membrane Surfing: A New Working Hypothesis for the Diatom Motor (2020) 393

Acknowledgments 397

References 397

Appendix 420

Index 421