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 xxvii1 Some Observations of Movements of Pennate Diatoms in Cultures and Their Possible Interpretation 1Thomas Harbich1.1 Introduction 21.2 Kinematics and Analysis of Trajectories in Pennate Diatoms with Almost Straight Raphe along the Apical Axis 31.3 Curvature of the Trajectory at the Reversal Points 91.4 Movement of Diatoms in and on Biofilms 131.5 Movement on the Water Surface 161.6 Formation of Flat Colonies in Cymbella lanceolata 231.7 Conclusion 29References 292 The Kinematics of Explosively Jerky Diatom Motility: A Natural Example of Active Nanofluidics 33Ahmet C. Sabuncu, Richard Gordon, Edmond Richer, Kalina M. Manoylov and Ali Beskok2.1 Introduction 342.2 Material and Methods 352.2.1 Diatom Preparation 352.2.2 Imaging System 352.2.3 Sample Preparation 362.2.4 Image Processing 362.3 Results and Discussion 412.3.1 Comparison of Particle Tracking Algorithms 412.3.2 Stationary Particles 422.3.3 Diatom Centroid Measurements 432.3.4 Diatom Orientation Angle Measurements 462.3.5 Is Diatom Motion Characterized by a Sequence of Small Explosive Movements? 492.3.6 Future Work 502.4 Conclusions 51Appendix 52References 593 Cellular Mechanisms of Raphid Diatom Gliding 65Yekaterina D. Bedoshvili and Yelena V. Likhoshway3.1 Introduction 653.2 Gliding and Secretion of Mucilage 673.3 Cell Mechanisms of Mucilage Secretion 683.4 Mechanisms of Gliding Regulation 713.5 Conclusions 72Acknowledgments 72References 734 Motility of Biofilm-Forming Benthic Diatoms 77Karen Grace Bondoc-Naumovitz and Stanley A. Cohn4.1 Introduction 774.2 General Motility Models and Concepts 864.2.1 Adhesion 874.2.2 Gliding Motility 894.2.3 Motility and Environmental Responsiveness 914.3 Light-Directed Vertical Migration 934.4 Stimuli-Directed Movement 944.4.1 Nutrient Foraging 944.4.2 Pheromone-Based Mate-Finding Motility 974.4.3 Prioritization Between Co-Occurring Stimuli 994.5 Conclusion 99References 1005 Photophobic Responses of Diatoms – Motility and Inter-Species Modulation 111Stanley A. Cohn, Lee Warnick and Blake Timmerman5.1 Introduction 1125.2 Types of Observed Photoresponses 1125.2.1 Light Spot Accumulation 1125.2.2 High-Intensity Light Responses 1145.3 Inter-Species Effects of Light Responses 1185.3.1 Inter-Species Effects on High Irradiance Direction Change Response 1195.3.2 Inter-Species Effects on Cell Accumulation into Light Spots 1235.4 Summary 123References 1316 Diatom Biofilms: Ecosystem Engineering and Niche Construction 135David M. Paterson and Julie A. Hope6.1 Introduction 1356.1.1 Diatoms: A Brief Portfolio 1356.1.2 Benthic Diatoms as a Research Challenge 1366.2 The Microphytobenthos and Epipelic Diatoms 1366.3 The Ecological Importance of Locomotion 1376.4 Ecosystem Engineering and Functions 1396.4.1 Ecosystem Engineering 1396.4.2 Ecosystem Functioning 1406.5 Microphytobenthos as Ecosystem Engineers 1416.5.1 Sediment Stabilization 1416.5.2 Beyond the Benthos 1436.5.3 Diatom Architects 1446.5.4 Working with Others: Combined Effects 1446.5.5 The Dynamic of EPS 1456.5.6 Nutrient Turnover and Biogeochemistry 1456.6 Niche Construction and Epipelic Diatoms 1466.7 Conclusion 149Acknowledgments 150References 1507 Diatom Motility: Mechanisms, Control and Adaptive Value 159João Serôdio7.1 Introduction 1597.2 Forms and Mechanisms of Motility in Diatoms 1607.2.1 Motility in Centric Diatoms 1607.2.2 Motility in Pennate Raphid Diatoms 1617.2.3 Motility in Other Substrate-Associated Diatoms 1627.2.4 Vertical Migration in Diatom-Dominated Microphytobenthos 1637.3 Controlling Factors of Diatom Motility 1647.3.1 Motility Responses to Vectorial Stimuli 1647.3.1.1 Light Intensity 1647.3.1.2 Light Spectrum 1657.3.1.3 UV Radiation 1667.3.1.4 Gravity 1667.3.1.5 Chemical Gradients 1677.3.2 Motility Responses to Non-Vectorial Stimuli 1677.3.2.1 Temperature 1677.3.2.2 Salinity 1687.3.2.3 pH 1687.3.2.4 Calcium 1687.3.2.5 Other Factors 1697.3.2.6 Inhibitors of Diatom Motility 1697.3.3 Species-Specific Responses and Interspecies Interactions 1697.3.4 Endogenous Control of Motility 1707.3.5 A Model of Diatom Vertical Migration Behavior in Sediments 1707.4 Adaptive Value and Consequences of Motility 1727.4.1 Planktonic Centrics 1727.4.2 Benthic Pennates 1737.4.3 Ecological Consequences of Vertical Migration 1757.4.3.1 Motility-Enhanced Productivity 1757.4.3.2 Carbon Cycling and Sediment Biostabilization 176Acknowledgments 176References 1768 Motility in the Diatom Genus Eunotia Ehrenb. 185Paula C. Furey8.1 Introduction 1858.2 Accounts of Movement in Eunotia 1888.3 Motility in the Context of Valve Structure 1948.3.1 Motility and Morphological Characteristics in Girdle View 1948.3.2 Motility and Morphological Characteristics in Valve View 1968.3.3 Motility and the Rimoportula 1988.4 Motility and Ecology of Eunotia 1988.4.1 Substratum-Associated Environments 1998.4.2 Planktonic Environments 2018.5 Motility and Diatom Evolution 2028.6 Conclusion and Future Directions 203Acknowledgements 204References 2059 A Free Ride: Diatoms Attached on Motile Diatoms 211Vincent Roubeix and Martin Laviale9.1 Introduction 2119.2 Adhesion and Distribution of Epidiatomic Diatoms on Their Host 2139.3 The Specificity of Host-Epiphyte Interactions 2159.4 Cost-Benefit Analysis of Host-Epiphyte Interactions 2179.5 Conclusion 219References 21910 Towards a Digital Diatom: Image Processing and Deep Learning Analysis of Bacillaria paradoxa Dynamic Morphology 223Bradly Alicea, Richard Gordon, Thomas Harbich, Ujjwal Singh, Asmit Singh and Vinay Varma10.1 Introduction 22410.1.1 Organism Description 22410.1.2 Research Motivation 22710.2 Methods 22810.2.1 Video Extraction 22810.2.2 Deep Learning 23010.2.3 DeepLabv3 Analysis 23410.2.4 Primary Dataset Analysis 23410.2.5 Data Availability 23510.3 Results 23510.3.1 Watershed Segmentation and Canny Edge Detection 23510.3.2 Deep Learning 23610.4 Conclusion 243Acknowledgments 245References 24511 Diatom Triboacoustics 249Ille C. Gebeshuber, Florian Zischka, Helmut Kratochvil, Anton Noll, Richard Gordon and Thomas HarbichGlossary 24911.1 State-of-the-Art 25111.1.1 Diatoms and Their Movement 25111.1.2 The Navier-Stokes Equation 25211.1.3 Low Reynolds Number 25311.1.4 Reynolds Number for Diatoms 25411.1.5 Further Thoughts About Movement of Diatoms 25411.1.6 Possible Reasons for Diatom Movement 25511.1.7 Underwater Acoustics, Hydrophones 25611.1.7.1 Underwater Acoustics 25611.1.7.2 Hydrophones 25711.2 Methods 25711.2.1 Estimate of the Momentum of a Moving Diatom 25711.2.2 On the Speed of Expansion of the Mucopolysaccharide Filaments 25811.2.2.1 Estimation of Radial Expansion 25811.2.2.2 Sound Generation 26111.2.3 Gathering Diatoms 26611.2.3.1 Purchasing Diatom Cultures 26711.2.3.2 Diatoms from the Wild 26711.2.4 Using a Hydrophone to Detect Possible Acoustic Signals from Diatoms 26911.2.4.1 First Setup 26911.2.4.2 Second Setup 27111.3 Results and Discussion 27211.3.1 Spectrograms 27211.3.2 Discussion 27711.4 Conclusions and Outlook 277Acknowledgements 279References 27912 Movements of Diatoms VIII: Synthesis and Hypothesis 283Jean Bertrand12.1 Introduction 28312.2 Review of the Conditions Necessary for Movements 28412.3 Hypothesis 28512.4 Analysis – Comparison with Observations 28812.4.1 Translational Apical Movement 28812.4.2 The Transapical Toppling Movement 29012.4.3 Diverse Pivoting 29012.5 Conclusion 291Acknowledgments 292References 29213 Locomotion of Benthic Pennate Diatoms: Models and Thoughts 295Jiadao Wang, Ding Weng, Lei Chen and Shan Cao13.1 Diatom Structure 29513.1.1 Ultrastructure of Frustules 29513.1.2 Bending Ability of Diatoms 29713.2 Models for Diatom Locomotion 30013.2.1 Edgar Model for Diatom Locomotion 30013.2.2 Van der Waals Force Model (VW Model) for Diatom Locomotion 30213.2.2.1 Locomotion Behavior of Diatoms 30213.2.2.2 Moving Organelles and Pseudopods 30413.2.2.3 Chemical Properties of Mucilage Trails 30713.2.2.4 Mechanical Properties of Mucilage Trails 31013.2.2.5 VW Model for Diatom Locomotion 31413.3 Locomotion and Aggregation of Diatoms 31913.3.1 Locomotion Trajectory and Parameters of Diatoms 31913.4 Simulation on Locomotion, Aggregation and Mutual Perception of Diatoms 32313.4.1 Simulation Area and Parameters 32313.4.2 Diatom Life Cycle and Modeling Parameters 32313.4.3 Simulation Results of Diatom Locomotion Trajectory with Mutual Perception 32613.4.4 Simulation Results of Diatom Adhesion with Mutual Perception 32713.4.5 Adhesion and Aggregation Mechanism of Diatoms 331References 33214 The Whimsical History of Proposed Motors for Diatom Motility 335Richard Gordon14.1 Introduction 33614.2 Historical Survey of Models for the Diatom Motor 33814.2.1 Diatoms Somersault via Protruding Muscles (1753) 33814.2.2 Vibrating Feet or Protrusions Move Diatoms (1824) 33814.2.3 Diatoms Crawl Like Snails (1838) 34214.2.4 The Diatom Motor is a Jet Engine (1849) 34414.2.5 Rowing Diatoms (1855) 34614.2.6 Diatoms Have Protoplasmic Tank Treads (1865) 35014.2.7 Diatoms as the Flame of Life: Capillarity (1883) 35414.2.8 Bellowing Diatoms (1887) 35514.2.9 Jelly Powered Jet Skiing Diatoms (1896) 35514.2.10 Bubble Powered Diatoms (1905) 35814.2.11 Diatoms Win: “I Have No New Theory to Offer and See No Reason to Use Those Already Abandoned” (1940) 36014.2.12 Is Diatom Motility a Special Case of Cytoplasmic Streaming? (1943) 36014.2.13 Diatom Adhesion as a Sliding Toilet Plunger (1966) 36514.2.14 Diatom as a Monorail that Lays Its Own Track (1967) 36614.2.15 The Diatom as a “Compressed Air” Coanda Effect Gliding Vehicle (1967) 36814.2.16 The Electrokinetic Diatom (1974) 37114.2.17 The Diatom Clothes Line or Railroad Track (1980) 37214.2.18 Diatom Ion Cyclotron Resonance (1987) 37414.2.19 Diatoms Do Internal Treadmilling (1998) 37514.2.20 Surface Treadmilling, Swimming and Snorkeling Diatoms (2007) 37614.2.21 Acoustic Streaming: The Diatom as Vibrator or Jack Hammer (2010) 37814.2.22 Propulsion of Diatoms Via Many Small Explosions (2020) 37914.2.23 Diatoms Walk Like Geckos (2019) 38014.3 Pulling What We Know and Don’t Know Together, about the Diatom Motor 38114.4 Membrane Surfing: A New Working Hypothesis for the Diatom Motor (2020) 393Acknowledgments 397References 397Appendix 420Index 421

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