Coral Reefs: An Ecosystem in Transition (eBook)

Preface 6
Contents 8
Part I:History and Perspective 12
Coral Research: Past Efforts and Future Horizons 13
1 Introduction 13
2 Early Coral Reef Research 14
3 Present Areas of Research and Future Directions 15
4 Future Horizons 17
References 19
Part II:Geology and Evolution 21
The Paleoecology of Coral Reefs 22
1 Introduction 22
1.1 What Is Paleoecology? 22
1.2 A Brief History of Reefs 22
1.3 The Past, The Present, and The Future 23
2 Constraints and Influences over Coral Reef Development 23
2.1 Local Controls 23
2.2 Regional and Global: Secular 23
2.3 Latitudinal Range Limits 23
2.4 Biotic Factors 24
2.5 Autecology of Reef Organisms 24
3 Reef Paleoproductivity 25
4 Biotic Interactions 25
5 Paleo Community Ecology 26
6 Global Change: Environmental Influences on Species Distribution Patterns 27
6.1 Reef Growth and Global Change 27
6.2 Range Expansions/Contractions 27
7 Diversity Through Time: Evolutionary Ecology and Biotic Turnover 28
7.1 Cenozoic Patterns 28
7.2 Deep Time 28
8 The History of Modern Biogeographic Patterns 29
9 Reef Paleoecology, Historical Ecology, and Conservation Biology 29
10 Proxies for Environmental Change 30
11 Summary 31
References 31
Remote Sensing of Coral Reef Processes 34
1 Introduction 34
2 Brief History of Coral Reef Remote Sensing 35
3 Remote Sensing Basics 36
4 Coral Reef Remote Sensing Considerations 37
5 Remote Sensing of Optically Shallow Waters 38
6 Coral Reef Remote Sensing Applications 40
7 Conclusion 42
References 42
Coral Taxonomy and Evolution 45
1 Taxonomy 45
1.1 Traditional Concepts of Species 45
1.2 Classification 45
1.2.1 Syngameons 46
2 Variation in Species 46
2.1 Environmental Variation 46
2.2 Geographic Variation 47
2.3 Genetic Links Among Populations 47
3 Taxonomic Issues 48
3.1 Taxonomic Certainty and Geographic Range 48
3.2 Arbitrary Decisions 48
3.3 Geographic Variation in Synonymies 49
4 Natural Organization 49
5 Evolutionary Mechanisms 49
5.1 Reticulate Evolution 49
5.2 Ocean Currents and Reticulate Patterns 50
5.3 Competing Hypotheses 51
5.3.1 Darwin’s Centers of Origin 51
5.3.2 Croizat’s Panbiogeography 51
5.3.3 Vicariance Biogeography 51
5.3.4 Dispersion and the Founder Principle 52
5.3.5 Equilibrium Theory 52
5.3.6 Competing Hypotheses in Summary 52
5.4 Where Reticulate Evolution and Darwinian Evolution Meet 52
Acknowledgments 53
References 53
The Coral Triangle 54
1 Introduction 54
2 Delineating the Coral Triangle 55
3 Hotspots of Biodiversity and Endemism 56
4 Characteristics of the Coral Triangle 57
5 Reasons for Existence of the Coral Triangle 58
5.1 Geological History 58
5.2 Dispersion 58
5.3 Biogeographic Patterns 59
5.4 Evolution 59
6 Future Impacts in the Coral Triangle 60
References 60
Part III:oral Biology: Symbiosis, Photosynthesisand Calcification 63
Sexual Reproduction of Scleractinian Corals 64
1 Introduction 64
2 Coral Life Cycle and Reproduction 65
2.1 Asexual Budding and Reproduction 65
3 Historical Perspectives on Coral Reproduction 67
4 Recent Advances in Coral Reproduction Research 68
4.1 Biogeographical Patterns of Coral Reproduction 68
4.2 Environmental Influences on Coral Reproduction 71
4.3 Molecular Perspectives on Coral Reproduction 74
5 Patterns of Sexual Reproduction 75
6 Sexual Patterns 75
6.1 Systematic Trends in Sexual Patterns 78
7 Mode of Development 79
8 Summary and Conclusions 80
References 81
Zooxanthellae: The Yellow Symbionts Inside Animals 91
1 Introduction 91
2 Geological History 92
3 Cellular Anatomy and the Symbiosome 92
4 Division and Reproduction 94
5 Taxonomy from Morphology to Molecular Biology, Genus to Genotype 94
6 Inter- and Intrahost Transmission 95
7 Host Specificity 96
8 The Host Factor and the Nature of Translocated Compounds 97
9 Population Dynamics and Controls 99
10 Distribution Within Colony and Polyp 101
11 Photosynthesis 102
12 Ecology: Geography, Temperature, and Host Effects 104
References 105
Light as a Source of Information and Energy in Zooxanthellate Corals 111
1 Introduction 111
2 The Underwater Light Field to Which Corals are Exposed 111
3 Light as an Informational Signal in Corals 112
4 Fluorescent Proteins 113
5 Light as an Energy Source 113
6 The Zooxanthellae–Coral Association 114
7 Photoacclimation of the Zooxanthellae 115
8 Energy and Nutrient Fluxes 117
9 Colony Architecture 119
10 Conclusions 120
References 120
Coral Calcification, Cells to Reefs 123
1 Introduction 123
2 The Different Types of Biomineralization and the Coral Calcification 124
3 The Site of Coral Calcification: The Subcalicoblastic Extracellular Calcifying Medium 124
3.1 The Skeletogenic Tissue: The Calicoblastic Epithelium 125
3.2 The Subcalicoblastic Extracellular Calcifying Medium 126
3.3 ECM: Open or Closed Compartment? 127
3.4 Physicochemical Characteristics of the Subcalicoblastic Extracellular Calcifying Medium 127
3.5 Site of the Initial Mineral Deposition 128
4 Physiology of Coral Calcification 129
4.1 Coral Calcification: A Chemical Reaction with Four Molecules 129
4.2 Measurement of Coral Calcification 129
4.3 Ion Supply or Removal for Calcification: Paracellular and Passive or Transcellular and Active? 130
4.3.1 Ion Delivery to the Site of Mineralization: Three Possibilities 130
4.3.2 Energetic Dependence of Ion Transport 131
4.3.3 Calcium Transport 132
4.3.4 Dissolved Inorganic Carbon (DIC) 132
4.3.5 Removal of H+ 133
4.3.6 What About Other Mineralizing Organisms? 133
4.4 The First Mineral: Amorphous or Crystalline? 133
4.5 Carbonic Anhydrase: A Key Enzyme 134
4.6 The Key Role of Organic Matrix 135
4.6.1 Content in OM 136
4.6.2 Synthesis of OM 136
4.6.3 Biochemical Characterization of OM 136
4.6.4 Role of OM in Calcification 137
4.6.5 Interaction of OM and Calcium Carbonate 137
4.6.6 Comparison with OM from Other Invertebrates 138
4.6.7 Conclusions 139
4.7 The Cost of Calcification 139
5 Environmental Control of Calcification 140
5.1 Light 140
5.1.1 Background History of LEC 140
5.1.2 LEC During a Daily Cycle 140
5.1.3 Controversy on LEC 141
5.1.4 Hypothesis for LEC 141
LEC and Inorganic Chemistry 141
LEC and Inorganic Carbon 141
LEC and Supply of Ions 142
LEC and Removal of Phosphates 142
LEC and Organic Chemistry 142
LEC and Supply of Precursors for Organic Matrix Synthesis 142
LEC and Oxygen 143
LEC and Supply of ATP 143
LEC and Nitrogen 143
5.1.5 Paradox of LEC 143
5.1.6 Conclusion on LEC 143
5.2 Temperature 143
6 Unity and Diversity of Coral Skeletons 144
6.1 The Basic Mechanism: Fibers and Centers of Mineralization 144
6.2 Concentric Layers: Annual, Diel Patterns 145
6.3 Nanograins as Units of Mineralization? 145
7 Conclusions 147
References 147
Coral Calcification Under Ocean Acidification and Global Change 155
1 Introduction 155
1.1 The Ecological Importance of Coral Calcification 155
1.2 Global and Local Environmental Changes and Their Effects on Coral Reef Calcification 156
1.2.1 Global Warming and Bleaching 156
1.2.2 Eutrophication 156
1.2.3 Coral Breakage by Tourism, Boating, and Fishing 157
1.2.4 Ocean Acidification 157
2 Basics of Coral Calcification Relevant to Ocean Acidification 157
2.1 Light and Dark Calcification, the Effect of the Symbiotic Algae, and the Classical Calcification Hypothesis of Goreau 157
2.2 Direct Supply of Seawater to the Biomineralization Site 158
2.3 Information from Shell Chemistry and Isotopes 159
3 Sensitivity of Corals and Coral Reefs to Changes in the Carbonate Chemistry of the Water 159
3.1 Carbonate Chemistry of Seawater and the Use of Variable Experimental Techniques 159
3.2 The Effects of Ocean Acidification on Individual Corals and the Connection to Cell- and Tissue-Level Processes 166
3.2.1 Direct Effects on Coral Calcification 166
3.2.2 Potential Effect on Symbiotic Algae 169
3.2.3 Direct Effect of CO2 170
3.2.4 pH-Mediated Effects 171
3.2.5 Change in the Buffering Capacity 172
3.2.6 Conclusion: Origins of the Sensitivity of Corals to Ocean Acidification 172
3.3 Ocean Acidification and Coral Reefs at the Community Level 172
3.3.1 Community Calcification as a Function of Warag 173
3.3.2 CaCO3 Dissolution in Coral Reefs 173
3.4 Implications for the Future Existence of Coral Reefs 175
4 General Conclusions 175
References 176
Simulating and Quantifying the Environmental Influence on Coral Colony Growth and Form 181
1 Introduction 181
2 Three-Dimensional Images of Coral Colonies Obtained Using Computer Tomography Scanning 184
3 Morphometrics of Three-Dimensional Complex-Shaped Branching Colonies 184
4 The Accretive Growth Model 185
5 Comparison Between Coral Colony Morphologies and Simulated Forms 187
References 188
Physiological Adaptation to Symbiosis in Cnidarians 190
1 The Coral/Zooxanthella Holobiont: A Chimera? 190
2 First Adaptation: A Marine Microalgae Living in an Intracellular Medium 191
3 Second Adaptation: The Need of a Permanent Supply of CO2 for Symbiont Photosynthesis 191
4 Third Adaptation: Withstand Hyperoxia 193
4.1 High Diversity of Enzymatic Antioxidative Defense is a Consequence of Symbiosis 193
4.2 Nonenzymatic Antioxidative Mechanisms 194
5 Fourth Adaptation: Withstand Solar Radiations 194
5.1 Ultraviolet Screens 194
5.2 Host and Symbiont Pigments 195
6 Conclusion 195
References 195
Part IV:The Coral Reef Ecosystem: Bacteria, Zooplankton,Algae, Invertebrates, Fishes and Model 199
Biogeochemistry of Nutrients 200
1 Introduction 200
2 Summary of Reviews 200
3 Nutrient Pool Sizes 202
4 Productivity 202
5 Mass Transfer 204
6 Implications of Mass Transfer and Questions Revisited 205
7 Summary: A Mass Transfer Interpretation of Coral Reef Biogeochemistry 205
References 206
The Role of Dissolved Organic Nitrogen (DON) in Coral Biology and Reef Ecology 208
1 Significance and Newly Raised Questions Regarding DON 208
2 Concentration and Distribution of DON, DIN, and PON in Coral Reef Water 209
3 Behavior of DON in Coral Reef Water 209
4 Nitrogen Compounds in DON 210
4.1 Urea 210
4.2 Dissolved Free Amino Acids (DFAA) 210
4.3 Dissolved Combined Amino Acids (DCAA) 211
4.4 Humic Acid and Fulvic Substances 211
4.5 Nitrogen Fixation 211
5 Role of DON in the Coral Reef Ecosystem 212
References 214
The Role of Plankton in Coral Trophodynamics 216
1 Introduction 216
2 Effect of Heterotrophy on Coral Physiology 217
2.1 Effect of Heterotrophy on Tissue Growth 217
2.1.1 Animal Tissue Fraction 217
2.1.2 Algal Fraction 220
2.2 Effect of Heterotrophy on Rates of Photosynthesis 220
2.3 Effect of Heterotrophy on Skeletal Growth 221
3 Energetic Inputs from Heterotrophy 223
4 Perspectives and Directions for Future Research 225
5 Conclusions 226
References 227
Fish or Germs? Microbial Dynamics Associated with Changing Trophic Structures on Coral Reefs 231
1 Introduction 231
2 Trophic Structure on Coral Reefs 231
3 Herbivores 231
4 Dissolved Inorganic Nitrogen and Soluble Reactive Phosphorus 232
5 Dissolved Organic Carbon and Coral Reef Microbes 232
6 Microbes and the Coral Holobiont 233
7 Local Connections Between Coral Disease, Fishing, and Fleshy Algae 233
8 Large-Scale Connections Between Coral Disease, Fishing, Fleshy Algae, and Eutrophication 234
9 The DDAMed Model 236
10 The Future 236
References 237
Coral Reef Algae 241
1 Importance of Coral Reef Algae 241
2 Diversity 242
3 Distribution and Abundance 244
4 Ecological Processes Controlling Algal Populations and Communities 245
4.1 Factors Limiting Settlement and Growth: Suitable Substrate 245
4.2 Factors Limiting Settlement and Growth: Light 245
4.3 Factors Limiting Settlement and Growth: Nutrients 247
4.3.1 Allochthonous Versus Autochthonous Sources of Nutrients 247
4.3.2 N Versus P Limitation of Coral Reef Algae 248
4.3.3 Efficient Nutrient Uptake by Coral Reef Algae 248
4.3.4 Nutrient Storage and Retention by Coral Reef Algae 250
4.3.5 Recycling of Nutrients by Coral Reef Algae: Turnover Rates 250
4.4 Factors Causing Removal: The Importance of Herbivory in Limiting Algal Proliferation 250
4.5 Factors Causing Removal: Chemical Defenses and Interactions 251
4.6 Benthic-Community-Level Interactions: Nutrient Supply Shapes Community Structure 253
4.7 Benthic-Community-Level Interactions: Positive Algal Cues for Coral Larvae 254
4.8 Benthic-Community-Level Interactions: Negative Algal Cues for Coral Larvae 254
4.9 Benthic-Community-Level Interactions: Algal/Coral Competition 255
4.10 Benthic-Community-Level Interactions: Invasive Species 256
4.11 Climate Change 258
5 Phase Shifts, Alternative Stable States, and the Stability of Algal-Dominated Tropical Reefs 261
5.1 The Nature of Transitions to Algal Domination of Tropical Reefs: Phase Shifts Versus Alternative Stable States 261
References 264
Invertebrates and Their Roles in Coral Reef Ecosystems 273
1 Introduction 273
2 Historical Overview 273
3 Overview of Major Invertebrate Taxa 276
3.1 Major Taxa 276
3.2 Minor Taxa 291
3.2.1 Epibenthic Consumers 291
3.2.2 Infaunal Consumers 291
3.2.3 Parasites 291
3.2.4 Microphagous Microbenthos and Meiofauna 291
4 Invertebrate Reef Habitats 292
4.1 The Cryptic Reef Habitat 292
4.1.1 Classification 292
4.1.2 Cryptic Environment 293
4.2 Habitat Providers 293
4.2.1 Porifera 293
4.2.2 Scleractinia 294
4.2.3 Alcyoniina (Gorgonacea) 294
4.2.4 Actiniaria 294
4.2.5 Antipatharia 295
4.2.6 Millepora 296
4.2.7 Polychaeta 296
4.2.8 Crinoidea 296
4.2.9 Ascidiacea 296
4.2.10 Motile Taxa 296
4.3 Bioerosion 297
4.4 Framework Consolidation 297
4.5 Growth Form Modification 298
5 Biotic Interactions 299
5.1 Predation 299
5.1.1 Corallivores 299
5.1.2 Other Kinds of Predators 302
5.2 Herbivory 303
5.3 Other Consumers 303
5.4 Symbiosis 304
5.4.1 Mutualisms and commensalisms 304
5.4.2 Parasitism 305
5.5 Competition 307
5.6 Indirect Effects 307
6 Trophic Interactions 308
6.1 Guilds and Reef Invertebrates 308
6.2 Food Webs 309
6.3 Quantitative Modeling 310
6.4 Prey for Fishes 311
7 Outlook and Implications 311
7.1 Major Recent Developments 311
7.2 Likely Future Research Foci 312
References 313
Coral Reef Fishes: Opportunities, Challenges and Concerns 326
1 Introduction 326
2 Biases in Knowledge of Coral Reef Fishes 327
3 The Human Element in Study and Exploitation of Coral Reef Fishes 330
4 Complexity in the Early Life History of Coral Reef Fishes 331
4.1 Eggs 331
4.2 Pelagic Larvae 333
4.3 Post-Settlement Larvae and Juveniles 336
5 Topics in the Lives of Adult Coral Reef Fishes 338
5.1 Trophic Links on Coral Reefs 338
5.2 Coral Reef Fishes as Habitats 339
6 Crises in Management and Conservation of Coral Reef Fishes 340
7 Perspectives 341
References 342
Competition Among Sessile Organisms on Coral Reefs 346
1 Introduction 346
2 Methods of Studying Competition Among Sessile Organisms on Reefs 347
2.1 Field Surveys at a Single Point in Time 347
2.2 Long-Term Field Monitoring 348
2.3 Field Experiments 350
2.4 Laboratory Experiments 352
2.5 Mathematical Modeling 353
3 Mechanisms of Competition 354
3.1 Cnidarians 354
3.2 Other Sessile Invertebrates 358
3.3 Macroalgae 359
4 Factors That Alter Competition Among Sessile Reef Organisms 361
5 Effects of Competition Among Sessile Organisms 363
5.1 Effects on Individuals 363
5.2 Effects on Populations and Communities 365
6 Conclusions and Directions for Future Research 366
References 367
Scaling Up Models of the Dynamics of Coral Reef Ecosystems:An Approach for Science-Based Management of Global Change 371
1 Introduction 371
1.1 The Coral Reef Crisis 371
1.2 The Rise of Modeling 373
1.3 The Challenges of Complexityand Complicatedness 373
2 Modeling Local-Scale Dynamics 373
2.1 The Need for Local Models to IncludePhase Shifts 374
3 Connecting Processes at Localand Regional Scales 375
4 Coupling of Ecological and Social Systems 378
5 Ecosystem-Based Models 380
5.1 Bottom-Up Effects on Ecosystem Function 380
5.2 Top-Down Effects on Ecosystem Function 382
6 Conclusions and Outlook 383
7 Summary 383
References 384
Part V:Disturbances 387
The Impact of Climate Change on Coral Reef Ecosystems 388
1 Introduction 388
2 The Coral Reef Environment 388
3 The Influence of Rising Atmospheric Carbon Dioxide and Other Greenhouse Gases 389
4 Changes to Tropical/Sub-tropical Oceans 391
5 Impacts on Coral Reefs 392
5.1 Impacts of Thermal Stress 392
5.2 Impacts of Ocean Acidification 393
5.3 Other Factors Associated with Climate Change 395
5.4 Ecosystem Responses and Outcomes 396
6 The Role of Acclimation and Adaptation in Altering Projections of the State of Coral Reefs Under Climate Change 396
7 Prospects for Coral Reefs and Dependent Societies in the Coming Decades and Century 397
8 Conclusions and Future Directions 398
References 399
Coral Bleaching: Causes and Mechanisms 401
1 Introduction 401
2 Causes of Coral Bleaching 402
3 Mechanisms of Coral Bleaching 403
4 Acclimatization/Adaptation of Host and Zooxanthellae 409
5 Conclusions and Future Directions 411
References 411
The Potential for Temperature Acclimatisation of Reef Corals in the Face of Climate Change 416
Box 1 – Terms and Concepts Usedin Considering ResistanceAdaptations of Corals 416
Terminology 416
Resistance Adaptations 416
Measuring Thermal Resistance 417
1 Historical Perspectives on Coral Acclimatisation and Acclimation 418
2 Organisms Living Close to their Lethal Limits are more Vulnerable to the Effects of Climate Change 418
3 Has Coral Bleaching Increased in Intensity and Frequency in Recent Years? 420
4 Recent Work on Phenotypic Resistance Adaptations to Thermal/Irradiance Stresses in Reef Corals 421
5 Genomics Approaches to Stress Responses in Corals 424
6 Epigenetics and Its Significance for Coral Acclimatisation to Elevated Temperature 425
7 Summary and Conclusions 426
References 426
Reef Bioerosion: Agents and Processes 429
1 Introduction 429
2 Agents of Bioerosion 429
2.1 Internal Agents 430
2.1.1 Microborers 430
2.1.2 Macroborers 431
2.2 External Agents 433
3 Geological History 434
4 Interactions and Ecological Impact of Bioeroding Agents on Coral Reefs 435
5 Effects of Anthropogenic and Climatic Changes on Bioerosion Processes 438
5.1 Direct Effects 438
5.2 Indirect Effects 439
6 Perspectives 440
References 440
Microbial Diseases of Corals: Pathology and Ecology 444
1 Introduction 444
2 The Bacterial Bleaching Disease 444
2.1 Vibrio shiloi 444
2.2 Infection of O. patagonica by V. shiloi 445
2.3 Development of Resistance ofO. patagonica to V. shiloi 445
2.4 Vibrio coralliilyticus 446
2.5 Mass Bleaching 447
3 Black Band Disease 448
3.1 Environmental Factors 448
3.2 What is the Causative Agent(S) of BBD? 449
4 Aspergillosis of Gorgonians 449
4.1 Disease Signs 449
4.2 Identification of the Pathogen 449
4.3 Source of the Pathogen 449
5 White Plague Diseases 449
6 White Band Diseases 450
7 White Pox Disease 451
8 Yellow Band Disease 451
9 Brown Band Disease 452
10 Porites Trematodiasis 452
11 Skeletal Eroding Band 452
12 Coral Resistance to Disease 453
12.1 The Surface Mucus Layer as a Barrierto Infection 453
12.2 Coral Production of Antibacterials 453
12.3 Circulating Amoebocytes 453
12.4 Production of Free Radicalsand Antibacterial Biochemicals 454
12.5 Bacteriophages (Phages) 454
References 454
Coral Reef Diseases in the Atlantic-Caribbean 458
1 Introduction 458
2 Historical Perspective 461
2.1 Black Band Disease 461
2.2 White Plague Diseases 461
2.3 White Band Disease and Diadema 461
2.4 White Patches and Octocoral Mortalities 464
2.5 Dark Spots Disease 464
2.6 Caribbean Yellow Band Disease 465
2.7 Caribbean Ciliate Infection 465
2.8 Aspergillosis and Purple Spots 465
2.9 Other Diseases 465
3 Current Status of Coral Diseases 466
3.1 Pathogenesis 467
3.2 Geographic Distribution 468
3.3 Depth Distribution 469
3.4 Prevalence, Incidence, and Virulence 470
3.5 Host Ranges 471
3.6 Vectors and Reservoirs 474
4 Environmental Drivers 475
5 Consequences and Management Implications 476
6 Summary 478
References 479
Factors Determining the Resilience of Coral Reefs to Eutrophication: A Review and Conceptual Model 485
1 Introduction 485
2 Responses of Reef Organisms to Eutrophication 486
2.1 Hard Corals 486
2.2 Coral Recruitment 488
2.3 Crustose Coralline Algae 488
2.4 Macroalgae 489
2.5 Crown-of-Thorns Starfish (Acanthaster planci) 489
2.6 Filter-Feeders, Macrobioeroders, and Suspension Feeders 489
2.6.1 Fishes 490
3 Factors Influencing the Susceptibility of Reefs to Eutrophication 490
4 The Conceptual Model 492
5 Discussion 493
References 495
Part VI:Conservation and Management 498
The Resilience of Coral Reefs and Its Implications for Reef Management 499
1 Introduction 499
2 The Concept of Resilience: Definitionsand History 500
3 Resistance and Recovery 501
4 Calculating Resilience by Combining Disturbance and Recovery into a Single Framework 501
4.1 Equilibrial Dynamics 502
4.2 Disturbance Dynamics 503
5 Hysteresis in Reef Dynamics and the Urgency for Reef Management 504
6 Ecological Feedbacks Drive Hysteresis 504
7 Managing the Resilience of Reefs 506
7.1 Management of PreventableDisturbances 506
7.2 Management of Unpreventable Disturbances 507
References 508
Index 510