Diatom Gliding Motility

DIATOM GLIDING MOTILITY Moving photosynthetic organisms are still a great mystery for biologists and this book summarizes what is known and reports the current understanding and modeling of those complex processes. The book covers a broad range of work describing our current state of understanding on the topic, including: historic knowledge and misconceptions of motility; evolution of diatom motility; diatom ecology & physiology; cell biology and biochemistry of diatom motility, anatomy of motile diatoms; observations of diatom motile behavior; diatom competitive ability, unique forms of diatom motility as found in the genus Eunotia; and models of motility. This is the first book attempting to gather such information surrounding diatom motility into one volume focusing on this single topic. Readers will be able to gather both the current state of understanding on the potential mechanisms and ecological regulators of motility, as well as possible models and approaches used to help determine how diatoms accomplish such varied behaviors as diurnal movements, accumulation into areas of light, niche partitioning to increase species success. Given the fact that diatoms remain one of the most ecologically crucial cells in aquatic ecosystems, we hope that this volume will act as a springboard towards future research into diatom motility and even better resolution of some of the issues in motility. Audience Diatomists, phycologists, aquatic ecologists, cellular physiologists, environmental biologists, biophysicists, diatom nanotechnologists, algal ecologists, taxonomists.

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