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1. The Non-Vent Deep Sea 1.1 The Physical Environment in the Deep Sea 1.2 The Deep-Sea Fauna 1.3 Deep-Sea Diversity 1.4 Biogeography and Population Genetics 1.5 Biochemical and Physiological Adaptations to the Deep-Sea Environment 1.6 Benthopelagic Coupling between Surface Productivity and the Deep Sea 1.7 Rates of Biological Processes in the Deep Sea 1.8 The Vent Contrast References 2. Geological Setting of Hydrothermal Vents 2.1 What Are Mid-Ocean Ridges? 2.1.1 How Spreading Rates for Ridge Axes Are Determined 2.1.2 Spreading Rates 2.1.3 Segmentation 2.1.4 Magma Supply and Spreading Rate 2.2 Back-Arc and Fore-Arc Spreading Centers 2.3 Seamounts 2.4 Volcanic and Tectonic Seafloor Features 2.4.1 Crustal Structure 2.4.2 Volcanic and Tectonic Fissures 2.4.3 Lava Lakes, Drainback Features, and Lava Pillars 2.4.4 Axial Boundary Faults 2.4.5 Lava Flow Morphologies 2.4.6 Emplacement of Lavas and the Time-Course of a Diking Event 2.4.7 Lava Dating 2.5 Deep-Sea Hydrothermal Fields 2.5.1 Missing Heat and Hydrothermal Cooling at Ridge Crests 2.5.2 Sulfide Deposits Morphological Variations Columnar Chimneys and Black Smokers White Smokers Beehives and Flanges Complex Sulfide Mounds Weathering of Seafloor Sulfides Dimensions and Ages of Active Hydrothermal Fields 2.5.3 Low-Temperature Diffuse Flows 2.5.4 Sediment-Hosted Hydrothermal Systems 2.5.5 Ophiolites Appendix References 3. Chemical and Physical Properties of Vent Fluids 3.1 Submarine Hydrothermal Circulation Cells: High-Temperature Reaction Zones 3.2 Phase Separation 3.3 Flow Rates, Transit Times, and Temperature of Formation 3.4 End-Member Fluids 3.4.1 Composition Basic Controls on Chemistry 3.4.2 Magmatic Inputs 3.4.3 Evolution of Vent-Fluid Chemistry 3.4.4 Back-Arc Fluid Chemistries 3.5 Thermal Radiation 3.6 Axial Low-Temperature, Diffuse-Flow Chemistry 3.6.1 Flow Rates, Temperature, and Temperature Variability 3.6.2 Silicate 3.6.3 Sulfide 3.6.4 Oxygen 3.6.5 Profiles of Oxygen, Sulfide, Silicate, and Temperature 3.6.6 Methane, Manganese, and Iron 3.6.7 Nitrogen and Phosphorus Compounds 3.7 Flank Low-Temperature Fluids 3.8 Global Fluxes and the Hydrothermal Influence on Ocean Chemistry and Currents References 4. Hydrothermal Plumes 4.1 Anatomy of a Black-Smoker Plume 4.1.1 Orifice 4.1.2 Buoyant Plume 4.1.3 Effluent Layer 4.2 Megaplumes 4.3 Spatial and Temporal Distributions of Plumes 4.3.1 Relationship between Plume Distributions and Geophysical Parameters 4.4 Plume-Driven Mesoscale Circulation 4.4.1 Plume Vortices 4.4.2 Advection and Downwelling 4.4.3 Basin-Scale Circulation 4.5 Diffuse-Flow Plumes References 5. Microbial Ecology 5.1 Autotrophic Organisms at Vents 5.1.1 Nomenclature 5.1.2 Aerobic and Anaerobic Chemoautotrophy at Vents Methanotrophy 5.1.3 Carbon Dioxide Fixation 5.1.4 Mixotrophy 5.1.5 Net Chemoautotrophic Production in Free-Living Hydrothermal-Vent Microorganisms Alternatives to Chemoautotrophy Organic Thermogenesis Hypothesis Detrital Thermal Alteration Hypothesis 5.2 Ecology of Free-Living Microorganisms 5.2.1 Microbial Habitats 5.2.2 Hyperthermophiles and Superthermophiles Flange Microbial Ecology and the Archaea Microorganisms in Black-Smoker Fluids The "Endeavour Model" The Subsurface Biosphere 5.2.3 Plume Microbiology 5.2.4 Suspended Microbial Populations 5.2.5 Microbial Community Composition Dominance of a Single Bacterial Phylotype at a Mid-Atlantic Ridge Vent Diversity and Community Structure in Microbial Mats, Loihi Seamount Sulfur-Oxidizing Heterotrophs at Vents 5.2.6 Bacterial Blooms 5.2.7 Microbial Mats 5.2.8 The Link between Chemoautotrophic and Photosynthetic Processes 5.3 A Search for In Situ Bacterial Photosynthesis 5.4 Microbial Genesis of Hydrothermal Mineral Deposits 5.5 Microbial Exploitation of Particulate Sulfides 5.6 Biotechnology References 6. Symbiosis 6.1. Discovery 6.1.1 Sustenance of Gutless Tubeworms 6.1.2 Endosymbiotic Bacteria in Vent Mollusks 6.1.3 Episymbionts 6.2 Methanotrophic Symbioses 6.2.1 Dual Symbioses 6.2.2 Methanotrophs in Sponges 6.3 Adaptive Characteristics of Symbiosis 6.4 Host Nutrition 6.4.1 Digestive Enzymes 6.5 Symbiont Phylogeny 6.5.1 Endosymbiont Phylogeny and Host Fidelity 6.5.2 Episymbiont Phylogeny 6.6 Symbiont Acquisition References 7. Physiological Ecology 7.1 Novel Metabolic Demands 7.2 Riftia pachyptila 7.2.1 Anatomy of a Tubeworm 7.2.2 The Tubeworm Environment 7.2.3 Adaptations for Carbon Uptake and Transport in Riftia pachyptila Host Respiratory Inorganic Carbon Environmental Sources of Inorganic Carbon and the Role of Carbonic Anhydrase pH Regulation Carbon Transport Inorganic Carbon Capacity Carbon Fixation Rates 7.2.4 Sulfide Sulfide Toxicity Sulfide Uptake and Transport Coupling of Sulfide Detoxification and Energy Exploitation 7.2.5 Oxygen 7.2.6 Nitrogen Nitrate Respiration 7.3 Seep Vestimentiferans and Methanotrophic Pogonophorans 7.4 Vent and Seep Bivalve-Mollusk Symbioses 7.4.1 Calyptogena magnified 7.4.2 Bathymodiolid Mussels Bathymodiolus thermophilus Methanotrophic Mussels 7.4.3 Other Mollusk Symbioses 7.5 Physiological Ecology of Episymbiont-Invertebrate Associations 7.5.1 Alvinella pompejana 7.6 Sulfide Detoxification 7.7 Growth Rates 7.8 Thermal Adaptations 7.8.1 Indices of Thermal Tolerance and Adaptation Thermal Tolerance in Alvinellid Species 7.9 Heavy Metals and Petroleum Hydrocarbons 7.10 Sensory Adaptations 7.10.1 Novel Photoreceptors in Vent Shrimp 7.10.2 Chemoreception References 8. Trophic Ecology 8.1 The Food Web 8.1.1 The Rose Garden Food Web 8.2 Biological Sleuthing: Biomarker Assays 8.2.1 Stable Isotope Techniques Notation Stable Isotope Evidence for the Role of Free-Living Microorganisms in Vent Food Webs 8.2.2 Fatty Acids, Sterols, and Carotenoids Fatty-Acid Nomenclature Fatty-Acid Biomarkers Comparison of Lipid Characteristics of Tubeworms (Riftia pachyptila), Mussels (Bathymodiolus thermophilus), and Amphipods (Halice hesmonectes) on the East Pacific Rise Essential Fatty Acids Lipid-Condition Indices Sterols Carotenoids 8.3 Integrated Approaches to Trophic Ecology 8.3.1 Trophic Ecology of Vent Mussels, Bathymodiolus thermophilus 8.3.2 Trophic Ecology of Vent Shrimp, Rimicaris exoculata, and an Anecdote about Who Eats Them 8.4 Export of Chemosynthetic Production from Vents References 9. Reproductive Ecology 9.1 Gametogenesis 9.1.1 Evidence for Synchronous Gametogenesis Environmental Cues Recruited Synchrony 9.1.2 Evidence for Asynchronous Gametogenesis Release of Gametes and Larvae Riftia pachyptila Bythograea sp. Calyptogena soyae 9.2 Larval Development 9.2.1 Vestimentifera 9.2.2 Bathymodiolid Mussels 9.2.3 Bythograeid Crabs 9.2.4 Alvinocarid Shrimp 9.3 Larval Dispersal and Retention 9.3.1 Alvinellid Dispersal Model 9.3.2 Plume Dispersal 9.3.3 Megaplume Dispersal 9.3.4 Mesoscale Flows 9.3.5 Dispersal by Non-Larval Stages 9.4 Settlement Cues 9.5 Recruitment Appendix References 10. Community Dynamics 10.1 The Early Work 10.2 Dynamic Succession at Northeast Pacific Vents 10.2.1 High-Resolution Time-Series Studies on the Juan de Fuca Ridge 10.3 Community Dynamics on the Mid-Atlantic Ridge 10.4 Eruptions 10.4.1 The 9°N Event 10.4.2 The CoAxial Event 10.4.3 Sweepstakes versus Predictable Sequences References 11. Evolution and Biogeography 11.1 Origins of Vent Fauna 11.1.1 Immigrants from the Surrounding Deep Sea 11.1.2 Immigrants with Close Shallow-Water Relatives 11.1.3 Vent Taxa Shared with Other Chemosynthetic Ecosystems Taxonomic Position and Origin of the Vestimentifera 11.1.4 Vent Taxa Shared with Both Other Chemosynthetic Ecosystems and Nonchemosynthetic Habitats 11.1.5 Specialized Taxa Found Only at Hydrothermal Vents 11.1.6 The "Ancient" Taxa Ancient Barnacles Ancient Mollusks 11.1.7 The Newman and McLean Hypothesis of Relict Vent Faunas Hickman's Counterhypothesis 11.2 Fossil Vent Communities 11.3 Vent Ecosystems as Refuges from Major Planetary Extinction Events 11.4 Species Diversity 11.5 Taxonomic Cautionary Tales 11.5.1 Cryptic Species 11.5.2 Phenotypic Plasticity 11.5.3 Ontogenetic Stages 11.6 Biogeography 11.6.1 Pacific Biogeographic Patterns Missing Mussels {Bathymodiolus thermophilus) Centers of Diversity along Linear Arrays of Habitat North America as a Biogeographical Barrier Mariana Hydrothermal-Vent Fauna 11.6.2 Paleotectonic Controls on the Atlantic Vent Fauna 11.6.3 Similarities among Global Vent Biogeographic Provinces 11.6.4 Biogeography of Fast- versus Slow-Spreading Centers 11.6.5 Physical Oceanography and Bathymetry The Romanche Fracture Zone 11.6.6 Shallow-Water Vents 11.7 Gene Flow and Genetic Diversity References 12. Cognate Communities 12.1 Atlantic Sites 12.1.1 Florida Escarpment (Gulf of Mexico) 12.1.2 Louisiana Slope Hydrocarbon and Brine Seeps (Gulf of Mexico) 12.1.3 The Laurentian Fan 12.1.4 Barbados Subduction Zone 12.1.5 North Sea Pockmarks 12.1.6 Skagerrak Methane Seep 12.1.7 The Francois Vieljeux 12.1.8 Coral Reefs 12.2 Pacific Sites 12.2.1 Cascadia Subduction Zone 12.2.2 Western Pacific Subduction Zones Kaiko Project Sagami Bay 12.2.3 Peruvian Subduction Zone 12.2.4 Monterey Canyon 12.2.5 Northern California Methane Hydrate Field 12.2.6 Guaymas Basin Transform Margin Seeps 12.2.7 Shallow-Water Hydrocarbon Seeps 12.2.8 British Columbia Fjords 12.2.9 Aleutian Subduction Zone 12.3 Whale Skeletons 12.4 Fossil Seeps References 13. Hydrothermal Systems and the Origin of Life 13.1 Earth's Early Environment 13.2 Evolution of Hydrothermal Systems 13.3 Heterotrophic versus Chemosynthetic Hypotheses for the Origin of Life 13.4 Evidence for Thermophilic, Autotrophic Ancestors 13.4.1 Wachterhauser's Outline for the Origin and Evolution of Life 13.4.2 Synthesis of Organic Compounds in Hydrothermal Systems 13.5 Extraterrestrial Hydrothermal Systems and the Search for Life in Outer Space