Life at High Pressure: In the Deep Sea and Other Environments

Description

The book discusses the ways in which high hydrostatic pressure (i.e. water pressure) affects all grades of life which thrive at pressures much greater those in our normal environment. The deep sea is the best known high pressure environment, where pressures reach a thousand times greater than those at the surface, yet it is populated by a variety of animals and microorganisms. The earth’s crust supports microorganisms which live in water filled pores at high pressure. In addition, the load bearing joints of animals like ourselves experience pulses of hydrostatic pressure of a magnitude similar to the pressure at mid ocean depths. These pressures affect molecular structures and biochemical reactions. Basic cellular processes are drastically affected – the growth and division of cells, the way nerves conduct impulses and the chemical reactions which provide energy.  Adaptation to high pressure also occurs in complex physiological systems such as those which provide buoyancy.  Probably the greatest challenge to our understanding of adaptation to high pressure is the stabilisation of the nervous system of deep sea animals to avoid convulsions which pressure causes in shallow water animals. Additionally the book provides insight into the engineering required to study life at high pressure: equipment which can trap small deep sea animals and retrieve them at their high pressure, equivalent equipment for microorganisms, laboratory microscopes which can focus on living cells under high pressure, incubators for bacteria which require high pressure to grow, high pressure aquaria for marine animals and lastly and briefly, manned and unmanned submersible vessels, Landers and deep drill hole sampling. Rather like the organisms studied many laboratory instruments have been adapted to function at high pressure. Foreword Preface Contents 1: High Pressure and High-Pressure Environments 1.1 High-Pressure Environments 1.1.1 Measuring Pressure Box 1.1 Units Used to Measure Pressure 1.1.2 Negative Pressure 1.2 The Deep Ocean 1.2.1 The Ocean Depths and Their Inhabitants 1.2.2 Freshwater Lakes and Ice 1.3 The Deep Biosphere 1.3.1 Oceanic Crust 1.3.2 Continental Crust 1.4 High-Pressure Joints 1.5 The Modern Classification of Organisms Box 1.2 References 2: High Pressure: Molecules, Chemical Process and Cellular Structures 2.1 Water, Dissolved Salts and Proteins Box 2.1: Viscosity 2.2 Chemical Reactions in Solution, at High Pressure 2.2.1 Equilibria Box 2.2: Effect of Pressure on Dissociation 2.2.2 Rates of Reaction 2.2.2.1 Simple Reactions, Not Involving an Enzyme 2.2.2.2 Enzyme Catalysed Reactions Box 2.3: Measuring an Activation Volume (DeltaV*) and an Equilibrium Volume (DeltaV) 2.3 The Affinity of an Enzyme for Its Substrate Box 2.4: Measuring How High Pressure Affects the Affinity of an Enzyme for Its Substrate 2.4 Cells Under High Pressure 2.4.1 Cell Membranes Box 2.5: Measuring the Fluidity of Lipid Bilayers at High Pressure 2.4.2 Cytoplasm Box 2.6: Cytoplasm Under High Pressure 2.4.3 Cell Organelles 2.5 Prokaryotes 2.6 Proteins 2.6.1 Actin 2.6.2 Tubulin Box 2.7: Mitosis 2.6.3 A Special Enzyme, ATP Synthase 2.6.3.1 The ATP Synthase Under High Pressure References 3: The High Pressure Micro-environment of Vertebrate Load Bearing Joints 3.1 Introduction 3.2 Micro-pressures 3.3 Load Bearing Joints; Cartilage and Bone Cells Exist in Pressurised Environments 3.3.1 Bone 3.4 Experiments with Chondrocytes 3.4.1 The Response of Chondrocytes in Their Matrix to Physiological Pressures 3.5 Does High Hydrostatic Pressure Cause Pathological Effects? 3.6 Conclusion References 4: Effects of High Pressure on the Activity of Ordinary Animals, Including Humans, and on the Function of Their Excitable Cell... 4.1 Early and Modern Observations, Mostly on Invertebrates Box 4.1: The Problem of Very Small Hydrostatic Pressures 4.2 Effects of Pressure on the Activity of Fish 4.3 Effects of Pressure on the Activity of Air-Breathing Vertebrates 4.3.1 The Pressure Tolerance of Aquatic and Air-Breathing Vertebrates 4.3.2 HPNS 4.3.3 Free Escape from Submarines 4.4 Reflexes 4.5 Excitable Membranes 4.5.1 Effects of Pressure on Isolated Neurons Box 4.2: The Resting Potential 4.5.2 Measuring Ionic Currents by Different Methods 4.5.3 How High Pressure Affects Excitable Membranes 4.5.3.1 Single Channel Recording at High Pressure 4.6 Effects of Pressure on Synapses Box 4.3: The Working Synapse Box 4.4 4.7 Post Script 4.8 Conclusion References 5: The Effects of Decompression and Subsequent Re-compression on the Activity of Deep-Sea Animals and Eukaryote Cells. The Iso... 5.1 Deep-Sea Amphipods 5.1.1 Amphipods Collected with Decompression 5.1.2 Amphipods from Lake Baikal 5.2 The Isobaric Collection of Deep-Sea Animals: Retrieval Without Decompression 5.2.1 The Isobaric Trap 5.2.2 Other Isobaric Collections 5.2.3 When to Use Isobaric Collecting Equipment? 5.2.4 The Isobaric Collection of Deep-Sea Fish 5.3 Resuscitation of Animals and Their Tissues from the Effects of Hydraulic Decompression 5.3.1 The Resuscitation of Deep-Sea Fish by High Pressure 5.3.1.1 Fish from Lake Baikal 5.3.2 The Resuscitation of Isolated Fish Tissue by High Pressure 5.3.2.1 Fish Swimming Muscle 5.3.2.2 Fish Heart Muscle 5.3.3 Fish Neurons 5.4 The Tolerance of Other Deep-Sea Animals to Decompression 5.4.1 Animals from Great and Moderate Depths 5.4.2 The Antioxidative Defences of Deep-Sea Animals 5.4.3 Deep-Sea Fish Cells and Tissues In Vitro 5.5 Other Deep-Sea Animals 5.6 Microbial Eukaryotes 5.6.1 Protists 5.6.2 Fungi 5.7 Conclusion References 6: Molecular Adaptation to High Pressure: Proteins in Deep-Sea Animals 6.1 Protein Adaptation 6.1.1 Intrinsic Adaption of Proteins to High Pressure 6.1.1.1 Structural Proteins 6.1.1.2 Enzymes 6.1.1.3 Visual Pigments Box 6.1 Opsins 6.2 Extrinsic Adaptation of Proteins to High Pressure 6.2.1 Pressure Protection 6.2.2 Compatible Solutes 6.2.3 TMAO in Deep-Sea Animals 6.2.4 Some Implications of the Extrinsic Adaptation of Proteins to High Pressure 6.3 How Does TMAO Counteract the Effects of High Pressure on Proteins? 6.4 Conclusions References 7: Molecular Adaptation to High Pressure: Membranes 7.1 Homeoviscous Adaptation 7.2 Membranes from Deep-sea Fish 7.2.1 The Fluidity of the Lipid Bilayer in Deep-sea Fish Membranes 7.2.2 The Lipid Composition of Deep-sea Fish Membranes 7.3 Homeoviscous Adaptation in the Membranes of Deep-sea Bacteria 7.3.1 Some Physiological Functions Related to the Membranes of Marine Bacteria 7.4 Bacteria in the Deep Biosphere 7.4.1 Sample Collection 7.4.2 Membrane Lipids in Bacteria From the Deep Biosphere 7.5 Homeoviscous Adaptation: Other Aspects 7.6 Do Shallow Water Cells Show Homeoviscous Adaptation When Exposed to High Pressure? References 8: Prokaryotes at High Pressure in the Oceans and Deep Biosphere 8.1 Microorganisms in the Deep Sea and Their Collection 8.2 Effects of Decompression on Deep-Sea Bacteria 8.2.1 Bacteria Decompressed During Collection and Recompressed 8.2.2 Isobaric Samples 8.2.3 Bacteria from the Hadal Zone 8.3 Growing Bacteria at High Pressure 8.3.1 Continuous Culture Methods 8.4 Pressure Experienced by Sinking Particles 8.5 Eukaryotic Microorganisms 8.6 Viruses 8.7 Microorganisms in the Deep Biosphere 8.7.1 The Presence and Activity of Microorganisms in the Deep Biosphere 8.7.2 Growth in High-Pressure Gases 8.7.3 High Partial Pressures of Helium, Hydrogen and Methane 8.7.4 Gases Important in the Deep Biosphere 8.8 Isobaric Samples from the Deep Biosphere 8.8.1 CORKs and FLOCS 8.8.2 Pollution in Deep Environments: Hydrocarbons and Other Toxic Compounds 8.9 Adaptations of the Enzymes of Deep Sea and Deep Biosphere Microorganisms to High Pressure 8.9.1 Intrinsic Adaptation of Microbial Proteins to High Pressure 8.9.2 Extrinsic Adaptations of Proteins 8.10 Conclusion References 9: Hydrothermal Vents: The Inhabitants, Their Way of Life and Their Adaptation to High Pressure 9.1 Hydrothermal Vents: Physical Conditions 9.2 Geobiochemistry and the Origin of Life Box 9.1 Extraterrestrial Life 9.3 The Inhabitants of the Vent Sites 9.3.1 Animals 9.3.1.1 The Tubeworm Riftia 9.3.1.2 Other Worms 9.3.1.3 Crabs and Mussels 9.3.1.4 Shrimps 9.3.1.5 Fish 9.3.2 Microorganisms 9.3.2.1 Eukaryote Microorganisms 9.3.2.2 Protists 9.4 Prokaryotes 9.4.1 Archaea 9.4.2 Bacteria 9.4.2.1 Bacteria Growing on Substrates 9.4.2.2 Bacteria in Water Samples 9.5 Viruses and Other Mobile Genetic Elements 9.6 Homeoviscous Adaptation in Hydrothermal Vent Organisms 9.6.1 Animals 9.6.2 Bacteria 9.6.3 Archaea 9.6.3.1 Archaeal Lipids 9.6.3.2 Methanococcus janaschii 9.6.3.3 Thermococcus barophilus 9.7 The Dispersal from, and the Colonisation of, Hydrothermal Vents 9.7.1 Dispersal from Hydrothermal Vents 9.7.2 Abyssal and Benthic Animals Also Produce Planktonic Larva 9.7.3 Pelagic Adults and Larvae 9.7.4 Colonisation References 10: Buoyancy at Depth 10.1 Densities of Sea Water and Cell Constituents 10.2 Small Planktonic Organisms 10.3 Buoyancy in Larger Animals Living at Significant Pressures 10.3.1 Ionic Regulation in Bathypelagic Squid 10.4 Gas Phase Buoyancy 10.4.1 Cephalopods Box 10.1 Solute Coupled Water Transport in Nautilus 10.4.2 The Gas-Filled Swim Bladder of Bony Fishes Box 10.2 Hydrostatic pressure affects gas solubility 10.4.3 Other Functions of the Swim Bladder 10.5 Buoyancy Provided by Oil and Lipid 10.5.1 The Sperm Whale 10.5.2 Fish Buoyed by Oil and Lipids 10.5.2.1 Cartilaginous Fish 10.5.2.2 Bony Fish References 11: Divers: Air-Breathing Animals, Including Humans, at High Pressure 11.1 Breath-Hold Diving 11.1.1 Humans 11.1.2 Specialised Deep-Diving Birds and Mammals 11.2 Deep-Diving Lungs Under Pressure 11.2.1 Consequences of Gas Dissolved in Tissues Under Pressure 11.2.1.1 Nitrogen 11.2.1.2 Oxygen 11.3 Pressure Effects on Some Cells in Diving Animals 11.3.1 Muscle Enzymes 11.3.2 Red Cells 11.3.3 Platelets 11.3.4 Excitable Cells 11.4 Human Diving Supported by a Self-Contained Gas Supply 11.4.1 Gases Breathed at High Pressure 11.4.2 Oxygen 11.4.3 Nitrogen and Other Anaesthetic Inert Gases 11.4.3.1 Anaesthesia and Inert Gas Narcosis Are Reversed by Pressure Box 11.1 11.5 The High-Pressure Neurological Syndrome, HPNS 11.6 Decompression 11.7 Conclusion References 12: Adaptation to High Pressure in the Laboratory 12.1 Microorganisms 12.1.1 Escherichia coli 12.1.2 Other Examples of Organisms Surviving Very High Pressures 12.1.3 Photobacterium profundum 12.1.4 Other Microorganisms 12.1.5 Yeast, Saccharomyces sp., a Eukaryote Microorganism 12.2 Animals 12.2.1 Shallow Water Animals 12.2.1.1 The Design of Experiments Eliciting Stress Responses and the Expression of Other Genes 12.2.2 Animals from Deeper Water: Acclimation to Atmospheric Pressure 12.2.3 Genetic Adaptation 12.2.4 The Eel, Anguilla anguilla 12.3 Conclusion References 13: High-Pressure Equipment for Use in the Laboratory, at Sea and at Depth 13.1 Generating High Pressure 13.1.1 Pumps 13.1.2 Generating Pressure by Centrifugation 13.2 High-Pressure Plumbing 13.3 Pressure Vessels 13.4 Safety 13.5 Examples of High-Pressure Experimental Apparatus 13.5.1 Experiments with Small Animals 13.5.2 Electrical Recording at High Pressure (Fig. 13.2) 13.5.2.1 Patch Clamp Recording at High Pressure 13.5.3 Other High-Pressure Apparatus 13.5.3.1 Stopping a Reaction at High Pressure 13.5.3.2 Starting a Physiological Reaction at High Pressure 13.5.3.3 Measuring High Hydrostatic Pressure in Load-Bearing Joints 13.6 High-Pressure Windows 13.6.1 Small High-Pressure Windows 13.6.2 Large High-Pressure Windows 13.7 The Isobaric Collection and Transfer of Organisms from High-Pressure Environments Box 13.1 Isobaric Collection of Small Deep-Sea Animals 13.7.1 Isobaric Collection of Deep-Sea Animals Using Equipment Operated from a Surface Ship 13.7.1.1 Isobaric Trapping of Benthic Animals 13.7.2 Isobaric Collection of Fish from a Surface Ship 13.7.3 The Isobaric Collection of Animals Using a Submersible 13.8 The Isobaric Collection of Microorganisms 13.8.1 Meso and Bathy Pelagic Microorganisms 13.8.2 DEEPBATH 13.8.3 Microorganisms from Deep-Sea Animals 13.8.4 Fluid and Dissolved Gas Samplers 13.9 Isobaric Recovery from the Deep Biosphere 13.9.1 Isobaric Drill Cores 13.9.2 CORKS and FLOCS: Drill Hole Sampling References Index