Note: Intro -- Preface -- Acknowledgements -- Contents -- Contributors -- Abbreviations and Acronyms -- 1: Coral Reefs at the Crossroads - An Introduction -- 1.1 Coming Together -- 1.2 Our Changing View -- 1.3 A Brief Look Back -- 1.4 Where Are WeNow? -- 1.5 Where Are We Headed? -- References -- 2: Coral Calcification and Ocean Acidification -- 2.1 Introduction -- 2.1.1 Basic Coral Anatomy and Physiology -- 2.1.2 Coral Morphology -- 2.1.3 Models of Light Enhanced Calcification (LEC) -- 2.1.4 Other Models of Coral Calcification -- 2.1.5 Chemistry of Ocean Acidification, Photosynthesis and Calcification -- 2.1.6 Conceptual Stumbling Blocks -- 2.1.7 The Concept of Aragonite Saturation State (Omegaarag) in Relation to Ocean Acidification (OA) -- 2.1.8 Relationship Between arag, the [DIC]:[H+] Ratio and Coral Calcification (Gnet) -- 2.1.9 Boundary Layers (BL) and Material Exchange Between the Water Column and the Coral -- 2.1.10 Material Fluxes -- 2.2 The Two-Compartment Proton Flux Model -- 2.2.1 Description of the Two-Compartment Proton Flux Model -- 2.2.2 Application of Model to Other Coral Morphologies -- 2.3 Ocean Acidification -- 2.3.1 Attempts to Explain How OA Reduces Coral Calcification -- 2.3.2 Shortcomings of the arag Model (i.e., CO32- Limitation) in Studies of Coral Calcification -- 2.3.3 Increasing Evidence that the arag Model for Coral and Coral Reefs Is Flawed -- 2.3.4 Future Changes in Oceanic Chemistry Due to Human Activity -- 2.3.5 Future Regional Changes in Reef Carbonate Production and Dissolution Rates Due to Increasing OA -- 2.4 Biological Control or Physical Control of Calcification? -- 2.5 Interaction Between Environmental and Biological Factors -- 2.5.1 Interaction Between OA and Coral-Growth Rate -- 2.5.2 Temperature and OA -- 2.5.3 Water Motion and Irradiance -- 2.6 Coral Nutrition -- 2.6.1 Inorganic Nutrients. , 2.6.2 Organic Nutrient Heterotrophy -- 2.6.3 Organic vs Inorganic Nutrients and Coral Calcification -- 2.7 Acclimatization and Adaptation -- 2.8 Resolving Unexplained Paradoxes with New Insights -- 2.8.1 Paradox of Decreasing Coral Growth Rate in the Face of Increasing HCO3- and Increasing DIC -- 2.8.2 Paradox of Rich Coral Reefs Growing Under Low arag Conditions -- 2.8.3 Paradox of Rapid LEC in Areas of The Coral Colony That Do Not Contain Photosynthetic Zooxanthellae -- 2.9 Alteration of Seawater Chemistry by Corals Over the Diurnal Cycle -- 2.9.1 Phase Shifts -- 2.9.2 Night Calcification -- 2.9.3 Diurnal Changes in Concentration of AT, pH, arag and DO -- 2.10 Back to the Basics -- 2.11 Conclusions -- 2.12 Future Research Directions -- References -- 3: Photosymbiosis in Past and Present Reefs -- 3.1 Introduction -- 3.2 Photosymbioses in Modern, Shallow-Water Carbonate Environments -- 3.2.1 Photosymbiosis in Reef Organisms -- 3.2.2 Photosymbiosis in Hypercalcifiers and Bleaching -- 3.3 Photosymbiosis in Ancient Fossils and Reef Environments -- 3.4 Important Photosymbiotic Taxa in Ancient Reef Ecosystems -- 3.4.1 Foraminifera -- 3.4.2 Calcified Sponges -- 3.4.3 Corals -- 3.4.4 Bryozoans -- 3.4.5 Brachiopods -- 3.4.6 Mollusks -- 3.5 Summary and Conclusions -- References -- 4: Bioerosion on Modern Reefs: Impacts and Responses Under Changing Ecological and Environmental Conditions -- 4.1 Introduction -- 4.2 The Reef Bioerosion Process: Key Species and Mechanisms of Bioerosion -- 4.3 Endolithic Bioerosion -- 4.3.1 Sponges -- 4.3.2 Molluscs -- 4.3.3 Polychaete and Sipunculan Worms -- 4.3.4 Microbioerosion -- 4.4 External Bioerosion -- 4.4.1 Echinoids -- 4.4.2 Parrotfish and Other Fishes -- 4.4.3 Molluscs - Gastropods/Chitons -- 4.5 Spatial Variations in Reef Bioerosion -- 4.5.1 Regional-Scale Variation -- 4.5.2 Habitat-Scale Variation. , 4.5.3 Intra-Habitat Variation -- 4.6 The Role of Bioerosion in Reef Structural Development -- 4.7 Impacts of Ecological and Environmental Change: Ecological Feedbacks and the Changing Role of Bioerosion in Contemporary R... -- 4.7.1 Impacts of Eutrophication -- 4.7.2 Impacts of Sedimentation -- 4.7.3 Impacts of Climatic Change -- 4.7.4 Other Ecological and Environmental Impacts -- 4.8 Quantifying the Role of Bioerosion: Carbonate Budgets and the Changing Face of Reef Accretion -- 4.9 Summary and Key Research Gaps -- References -- 5: Sponge Contributions to the Geology and Biology of Reefs: Past, Present, and Future -- 5.1 Introduction: Sponges and Reefs Have Been Linked from the Beginning -- 5.2 The Nature of Sponges -- 5.3 Species Diversity of Sponges on Present-Day Reefs -- 5.4 Geological Roles of Sponges: Reef Frame-Building and Fortifying -- 5.4.1 Archaeocyatha -- 5.4.2 Hypercalcified Sponges -- 5.4.3 Reef-Building Sponges with Siliceous Skeletons: Lithistids and Hexactinellids -- 5.5 Geological Roles of Sponges: Promoting Reef-Frame Integrity, Increasing Coral Survival, and Facilitating Repair -- 5.5.1 Increasing Coral Survival by Adhering Living Corals to the Reef and Protecting Exposed Skeletons Against Eroders -- 5.5.2 Rubble Stabilization: A Key Step in Reef Recovery After Physical Damage -- 5.5.3 Improving Reef Restoration by Harnessing the Ability of Sponges to Bind Rubble -- 5.6 Geological Roles of Sponges: Bioerosion -- 5.7 Biological Roles of Sponges: Overgrowth of Living and Dead Coral -- 5.8 Biological Roles of Sponges: Water-Column Influences -- 5.8.1 Maintaining Water Clarity -- 5.8.2 Influences on Dissolved Organic and Inorganic Water-Column Components -- 5.9 Biological Roles of Sponges: Providing Shelter and Food -- 5.9.1 Animal and Plant Guests of Sponges -- 5.9.2 Consumers of Sponges. , 5.10 Future of Sponges on Coral Reefs: Assessing and Ascribing Causes to Increases and Decreases -- 5.10.1 Inappropriate Methods for Assessing and Monitoring Sponges Yield Data That Are Difficult to Interpret -- 5.10.2 Lumping Together Sponges of Diverse Talents, Vulnerabilities, and Relationships with Corals -- 5.10.3 Are ``Sponges´´ Overwhelming Coral Reefs? -- 5.10.4 Data on Sponge Increases and Decreases -- 5.10.5 Sponge Dynamics Documented by Full Censuses in Time Series -- 5.11 Summary: What Would Happen to Coral Reefs if Sponges Were Entirely Deleted? -- References -- 6: The Changing Face of Reef Building -- 6.1 Introduction -- 6.1.1 Changing Perceptions Changing Strategies -- 6.1.2 The Road Ahead -- 6.2 What Do We (Think We) ``Know´´? -- 6.2.1 Reefs Without Us: The Late Quaternary -- 6.2.2 The Variable Nature of Sea-Level Rise -- 6.2.3 Looking to the Future: How Good Are Our Reef Models? -- 6.2.4 So What Do We Still Need to Know? -- 6.3 Carbonate Cycling and Reef Building -- 6.4 A Review of Sea-Level Basics -- 6.4.1 Phanerozoic Sea Level -- 6.4.2 Sea Level in the Holocene -- 6.4.3 Historic Sea-Level Change -- 6.4.4 Regional Variations in Recent Sea-Level Rise -- 6.4.5 The Lessons to Be Learned -- 6.5 Corals Grow Reefs Build -- 6.5.1 Changing Perspectives -- 6.5.2 How Fast Do Reefs Build? -- 6.5.3 Water Depth and Reef Building -- 6.5.4 A Possible Role for Bioerosion -- 6.5.5 Sediment Redistribution and Export -- 6.5.6 Relevance to the Carbonate Budget -- 6.5.7 The Zonation Conundrum -- 6.6 The Path Forward -- 6.6.1 What Should We Be Measuring? -- 6.6.2 Can Reefs Keep Up? -- 6.6.3 How Will This Impact Those Who Depend on Reefs? -- 6.6.4 Now More Than Ever -- References -- 7: Stability of Reef-Coral Assemblages in the Quaternary -- 7.1 Introduction -- 7.2 Stability and Persistence of Coral Reefs -- 7.3 The Pattern -- 7.4 The Problem. , 7.5 Climatic Variability in the Tropics During Glacial-Interglacial Cycles -- 7.6 Temperature -- 7.7 Reefs on the Edge -- 7.8 Sea Level -- 7.9 A Coral´s-Eye View -- 7.10 The Shattering of Ecological and Evolutionary Stability? -- 7.11 Summary -- References -- 8: Reefs Through Time: An Evolutionary View -- 8.1 Introduction -- 8.1.1 What Are Carbonate Reefs and Platforms? -- 8.1.2 Are Reefs Fragile Ecosystems? -- 8.2 Ancient Reefs -- 8.2.1 Precambrian Reefs: Earth´s Most Ancient Photosynthetic Reefs (3.4-0.541Ga) -- 8.2.2 Early Paleozoic Reefs: The Beginnings of Reefs (541-443Ma) -- 8.2.3 Mid-Paleozoic Reefs. The First Coral-Reef Ecosystems (443-359Ma) -- 8.2.4 Late Paleozoic Reefs After Extinction (359-252my) -- 8.2.5 Mesozoic Reefs: The First Modern Coral Reefs? (252-66Ma) -- 8.2.6 Cenozoic Reefs (66Ma-Present) -- 8.3 Extinction of Reef Organisms and the Reefs They Built in Geologic Time -- 8.3.1 Extraterrestrial Impacts -- 8.3.2 Sea-Level Changes -- 8.3.3 CO2 Decline and Climate Cooling -- 8.3.4 Volcanism, CO2 Increases, Climate Warming, Ocean Acidification and Anoxia -- 8.3.5 The Role of Photoendosymbiosis in Extinctions and Diversifications -- 8.3.6 Extinctions -- 8.4 The Future of Reefs -- References -- 9: Climate Change, Ocean Chemistry, and the Evolution of Reefs Through Time -- 9.1 Introduction -- 9.2 Physical, Chemical, and Biological Drivers of Reef Building -- 9.2.1 Light, Turbidity, and Sedimentation -- 9.2.2 Temperature -- 9.2.3 Nutrients, Herbivory, and Bioerosion -- 9.2.4 Water Motion and Storm Damage -- 9.2.5 Carbonate Chemistry -- 9.2.6 Sea-Level Rise -- 9.3 The Rise and Fall of Reefs Through Time -- 9.3.1 The First Reefs -- 9.3.2 The Paleozoic Rise of Metazoan Reefs -- 9.3.3 Origination and Diversification of the Scleractinia -- 9.3.4 Reef Building Through the Mesozoic -- 9.3.5 Coral-Reef Building Through the Cenozoic. , 9.4 Climate Change and Reef Building in the Past.

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