Coral Reefs: An Ecosystem in Transition

Preface

Contents

Part I:History and Perspective

Coral Research: Past Efforts and Future Horizons

1 Introduction

2 Early Coral Reef Research

3 Present Areas of Research and Future Directions

4 Future Horizons

References

Part II:Geology and Evolution

The Paleoecology of Coral Reefs

1 Introduction

1.1 What Is Paleoecology?

1.2 A Brief History of Reefs

1.3 The Past, The Present, and The Future

2 Constraints and Influences over Coral Reef Development

2.1 Local Controls

2.2 Regional and Global: Secular

2.3 Latitudinal Range Limits

2.4 Biotic Factors

2.5 Autecology of Reef Organisms

3 Reef Paleoproductivity

4 Biotic Interactions

5 Paleo Community Ecology

6 Global Change: Environmental Influences on Species Distribution Patterns

6.1 Reef Growth and Global Change

6.2 Range Expansions/Contractions

7 Diversity Through Time: Evolutionary Ecology and Biotic Turnover

7.1 Cenozoic Patterns

7.2 Deep Time

8 The History of Modern Biogeographic Patterns

9 Reef Paleoecology, Historical Ecology, and Conservation Biology

10 Proxies for Environmental Change

11 Summary

References

Remote Sensing of Coral Reef Processes

1 Introduction

2 Brief History of Coral Reef Remote Sensing

3 Remote Sensing Basics

4 Coral Reef Remote Sensing Considerations

5 Remote Sensing of Optically Shallow Waters

6 Coral Reef Remote Sensing Applications

7 Conclusion

References

Coral Taxonomy and Evolution

1 Taxonomy

1.1 Traditional Concepts of Species

1.2 Classification

1.2.1 Syngameons

2 Variation in Species

2.1 Environmental Variation

2.2 Geographic Variation

2.3 Genetic Links Among Populations

3 Taxonomic Issues

3.1 Taxonomic Certainty and Geographic Range

3.2 Arbitrary Decisions

3.3 Geographic Variation in Synonymies

4 Natural Organization

5 Evolutionary Mechanisms

5.1 Reticulate Evolution

5.2 Ocean Currents and Reticulate Patterns

5.3 Competing Hypotheses

5.3.1 Darwin’s Centers of Origin

5.3.2 Croizat’s Panbiogeography

5.3.3 Vicariance Biogeography

5.3.4 Dispersion and the Founder Principle

5.3.5 Equilibrium Theory

5.3.6 Competing Hypotheses in Summary

5.4 Where Reticulate Evolution and Darwinian Evolution Meet

Acknowledgments

References

The Coral Triangle

1 Introduction

2 Delineating the Coral Triangle

3 Hotspots of Biodiversity and Endemism

4 Characteristics of the Coral Triangle

5 Reasons for Existence of the Coral Triangle

5.1 Geological History

5.2 Dispersion

5.3 Biogeographic Patterns

5.4 Evolution

6 Future Impacts in the Coral Triangle

References

Part III:oral Biology: Symbiosis, Photosynthesisand Calcification

Sexual Reproduction of Scleractinian Corals

1 Introduction

2 Coral Life Cycle and Reproduction

2.1 Asexual Budding and Reproduction

3 Historical Perspectives on Coral Reproduction

4 Recent Advances in Coral Reproduction Research

4.1 Biogeographical Patterns of Coral Reproduction

4.2 Environmental Influences on Coral Reproduction

4.3 Molecular Perspectives on Coral Reproduction

5 Patterns of Sexual Reproduction

6 Sexual Patterns

6.1 Systematic Trends in Sexual Patterns

7 Mode of Development

8 Summary and Conclusions

References

Zooxanthellae: The Yellow Symbionts Inside Animals

1 Introduction

2 Geological History

3 Cellular Anatomy and the Symbiosome

4 Division and Reproduction

5 Taxonomy from Morphology to Molecular Biology, Genus to Genotype

6 Inter- and Intrahost Transmission

7 Host Specificity

8 The Host Factor and the Nature of Translocated Compounds

9 Population Dynamics and Controls

10 Distribution Within Colony and Polyp

11 Photosynthesis

12 Ecology: Geography, Temperature, and Host Effects

References

Light as a Source of Information and Energy in Zooxanthellate Corals

1 Introduction

2 The Underwater Light Field to Which Corals are Exposed

3 Light as an Informational Signal in Corals

4 Fluorescent Proteins

5 Light as an Energy Source

6 The Zooxanthellae–Coral Association

7 Photoacclimation of the Zooxanthellae

8 Energy and Nutrient Fluxes

9 Colony Architecture

10 Conclusions

References

Coral Calcification, Cells to Reefs

1 Introduction

2 The Different Types of Biomineralization and the Coral Calcification

3 The Site of Coral Calcification: The Subcalicoblastic Extracellular Calcifying Medium

3.1 The Skeletogenic Tissue: The Calicoblastic Epithelium

3.2 The Subcalicoblastic Extracellular Calcifying Medium

3.3 ECM: Open or Closed Compartment?

3.4 Physicochemical Characteristics of the Subcalicoblastic Extracellular Calcifying Medium

3.5 Site of the Initial Mineral Deposition

4 Physiology of Coral Calcification

4.1 Coral Calcification: A Chemical Reaction with Four Molecules

4.2 Measurement of Coral Calcification

4.3 Ion Supply or Removal for Calcification: Paracellular and Passive or Transcellular and Active?

4.3.1 Ion Delivery to the Site of Mineralization: Three Possibilities

4.3.2 Energetic Dependence of Ion Transport

4.3.3 Calcium Transport

4.3.4 Dissolved Inorganic Carbon (DIC)

4.3.5 Removal of H+

4.3.6 What About Other Mineralizing Organisms?

4.4 The First Mineral: Amorphous or Crystalline?

4.5 Carbonic Anhydrase: A Key Enzyme

4.6 The Key Role of Organic Matrix

4.6.1 Content in OM

4.6.2 Synthesis of OM

4.6.3 Biochemical Characterization of OM

4.6.4 Role of OM in Calcification

4.6.5 Interaction of OM and Calcium Carbonate

4.6.6 Comparison with OM from Other Invertebrates

4.6.7 Conclusions

4.7 The Cost of Calcification

5 Environmental Control of Calcification

5.1 Light

5.1.1 Background History of LEC

5.1.2 LEC During a Daily Cycle

5.1.3 Controversy on LEC

5.1.4 Hypothesis for LEC

LEC and Inorganic Chemistry

LEC and Inorganic Carbon

LEC and Supply of Ions

LEC and Removal of Phosphates

LEC and Organic Chemistry

LEC and Supply of Precursors for Organic Matrix Synthesis

LEC and Oxygen

LEC and Supply of ATP

LEC and Nitrogen

5.1.5 Paradox of LEC

5.1.6 Conclusion on LEC

5.2 Temperature

6 Unity and Diversity of Coral Skeletons

6.1 The Basic Mechanism: Fibers and Centers of Mineralization

6.2 Concentric Layers: Annual, Diel Patterns

6.3 Nanograins as Units of Mineralization?

7 Conclusions

References

Coral Calcification Under Ocean Acidification and Global Change

1 Introduction

1.1 The Ecological Importance of Coral Calcification

1.2 Global and Local Environmental Changes and Their Effects on Coral Reef Calcification

1.2.1 Global Warming and Bleaching

1.2.2 Eutrophication

1.2.3 Coral Breakage by Tourism, Boating, and Fishing

1.2.4 Ocean Acidification

2 Basics of Coral Calcification Relevant to Ocean Acidification

2.1 Light and Dark Calcification, the Effect of the Symbiotic Algae, and the Classical Calcification Hypothesis of Goreau

2.2 Direct Supply of Seawater to the Biomineralization Site

2.3 Information from Shell Chemistry and Isotopes

3 Sensitivity of Corals and Coral Reefs to Changes in the Carbonate Chemistry of the Water

3.1 Carbonate Chemistry of Seawater and the Use of Variable Experimental Techniques

3.2 The Effects of Ocean Acidification on Individual Corals and the Connection to Cell- and Tissue-Level Processes

3.2.1 Direct Effects on Coral Calcification

3.2.2 Potential Effect on Symbiotic Algae

3.2.3 Direct Effect of CO2

3.2.4 pH-Mediated Effects

3.2.5 Change in the Buffering Capacity

3.2.6 Conclusion: Origins of the Sensitivity of Corals to Ocean Acidification

3.3 Ocean Acidification and Coral Reefs at the Community Level

3.3.1 Community Calcification as a Function of Warag

3.3.2 CaCO3 Dissolution in Coral Reefs

3.4 Implications for the Future Existence of Coral Reefs

4 General Conclusions

References

Simulating and Quantifying the Environmental Influence on Coral Colony Growth and Form

1 Introduction

2 Three-Dimensional Images of Coral Colonies Obtained Using Computer Tomography Scanning

3 Morphometrics of Three-Dimensional Complex-Shaped Branching Colonies

4 The Accretive Growth Model

5 Comparison Between Coral Colony Morphologies and Simulated Forms

References

Physiological Adaptation to Symbiosis in Cnidarians

1 The Coral/Zooxanthella Holobiont: A Chimera?

2 First Adaptation: A Marine Microalgae Living in an Intracellular Medium

3 Second Adaptation: The Need of a Permanent Supply of CO2 for Symbiont Photosynthesis

4 Third Adaptation: Withstand Hyperoxia

4.1 High Diversity of Enzymatic Antioxidative Defense is a Consequence of Symbiosis

4.2 Nonenzymatic Antioxidative Mechanisms

5 Fourth Adaptation: Withstand Solar Radiations

5.1 Ultraviolet Screens

5.2 Host and Symbiont Pigments

6 Conclusion

References

Part IV:The Coral Reef Ecosystem: Bacteria, Zooplankton,Algae, Invertebrates, Fishes and Model

Biogeochemistry of Nutrients

1 Introduction

2 Summary of Reviews

3 Nutrient Pool Sizes

4 Productivity

5 Mass Transfer

6 Implications of Mass Transfer and Questions Revisited

7 Summary: A Mass Transfer Interpretation of Coral Reef Biogeochemistry

References

The Role of Dissolved Organic Nitrogen (DON) in Coral Biology and Reef Ecology

1 Significance and Newly Raised Questions Regarding DON

2 Concentration and Distribution of DON, DIN, and PON in Coral Reef Water

3 Behavior of DON in Coral Reef Water

4 Nitrogen Compounds in DON

4.1 Urea

4.2 Dissolved Free Amino Acids (DFAA)

4.3 Dissolved Combined Amino Acids (DCAA)

4.4 Humic Acid and Fulvic Substances

4.5 Nitrogen Fixation

5 Role of DON in the Coral Reef Ecosystem

References

The Role of Plankton in Coral Trophodynamics

1 Introduction

2 Effect of Heterotrophy on Coral Physiology

2.1 Effect of Heterotrophy on Tissue Growth

2.1.1 Animal Tissue Fraction

2.1.2 Algal Fraction

2.2 Effect of Heterotrophy on Rates of Photosynthesis

2.3 Effect of Heterotrophy on Skeletal Growth

3 Energetic Inputs from Heterotrophy

4 Perspectives and Directions for Future Research

5 Conclusions

References

Fish or Germs? Microbial Dynamics Associated with Changing Trophic Structures on Coral Reefs

1 Introduction

2 Trophic Structure on Coral Reefs

3 Herbivores

4 Dissolved Inorganic Nitrogen and Soluble Reactive Phosphorus

5 Dissolved Organic Carbon and Coral Reef Microbes

6 Microbes and the Coral Holobiont

7 Local Connections Between Coral Disease, Fishing, and Fleshy Algae

8 Large-Scale Connections Between Coral Disease, Fishing, Fleshy Algae, and Eutrophication

9 The DDAMed Model

10 The Future

References

Coral Reef Algae

1 Importance of Coral Reef Algae

2 Diversity

3 Distribution and Abundance

4 Ecological Processes Controlling Algal Populations and Communities

4.1 Factors Limiting Settlement and Growth: Suitable Substrate

4.2 Factors Limiting Settlement and Growth: Light

4.3 Factors Limiting Settlement and Growth: Nutrients

4.3.1 Allochthonous Versus Autochthonous Sources of Nutrients

4.3.2 N Versus P Limitation of Coral Reef Algae

4.3.3 Efficient Nutrient Uptake by Coral Reef Algae

4.3.4 Nutrient Storage and Retention by Coral Reef Algae

4.3.5 Recycling of Nutrients by Coral Reef Algae: Turnover Rates

4.4 Factors Causing Removal: The Importance of Herbivory in Limiting Algal Proliferation

4.5 Factors Causing Removal: Chemical Defenses and Interactions

4.6 Benthic-Community-Level Interactions: Nutrient Supply Shapes Community Structure

4.7 Benthic-Community-Level Interactions: Positive Algal Cues for Coral Larvae

4.8 Benthic-Community-Level Interactions: Negative Algal Cues for Coral Larvae

4.9 Benthic-Community-Level Interactions: Algal/Coral Competition

4.10 Benthic-Community-Level Interactions: Invasive Species

4.11 Climate Change

5 Phase Shifts, Alternative Stable States, and the Stability of Algal-Dominated Tropical Reefs

5.1 The Nature of Transitions to Algal Domination of Tropical Reefs: Phase Shifts Versus Alternative Stable States

References

Invertebrates and Their Roles in Coral Reef Ecosystems

1 Introduction

2 Historical Overview

3 Overview of Major Invertebrate Taxa

3.1 Major Taxa

3.2 Minor Taxa

3.2.1 Epibenthic Consumers

3.2.2 Infaunal Consumers

3.2.3 Parasites

3.2.4 Microphagous Microbenthos and Meiofauna

4 Invertebrate Reef Habitats

4.1 The Cryptic Reef Habitat

4.1.1 Classification

4.1.2 Cryptic Environment

4.2 Habitat Providers

4.2.1 Porifera

4.2.2 Scleractinia

4.2.3 Alcyoniina (Gorgonacea)

4.2.4 Actiniaria

4.2.5 Antipatharia

4.2.6 Millepora

4.2.7 Polychaeta

4.2.8 Crinoidea

4.2.9 Ascidiacea

4.2.10 Motile Taxa

4.3 Bioerosion

4.4 Framework Consolidation

4.5 Growth Form Modification

5 Biotic Interactions

5.1 Predation

5.1.1 Corallivores

5.1.2 Other Kinds of Predators

5.2 Herbivory

5.3 Other Consumers

5.4 Symbiosis

5.4.1 Mutualisms and commensalisms

5.4.2 Parasitism

5.5 Competition

5.6 Indirect Effects

6 Trophic Interactions

6.1 Guilds and Reef Invertebrates

6.2 Food Webs

6.3 Quantitative Modeling

6.4 Prey for Fishes

7 Outlook and Implications

7.1 Major Recent Developments

7.2 Likely Future Research Foci

References

Coral Reef Fishes: Opportunities, Challenges and Concerns

1 Introduction

2 Biases in Knowledge of Coral Reef Fishes

3 The Human Element in Study and Exploitation of Coral Reef Fishes

4 Complexity in the Early Life History of Coral Reef Fishes

4.1 Eggs

4.2 Pelagic Larvae

4.3 Post-Settlement Larvae and Juveniles

5 Topics in the Lives of Adult Coral Reef Fishes

5.1 Trophic Links on Coral Reefs

5.2 Coral Reef Fishes as Habitats

6 Crises in Management and Conservation of Coral Reef Fishes

7 Perspectives

References

Competition Among Sessile Organisms on Coral Reefs

1 Introduction

2 Methods of Studying Competition Among Sessile Organisms on Reefs

2.1 Field Surveys at a Single Point in Time

2.2 Long-Term Field Monitoring

2.3 Field Experiments

2.4 Laboratory Experiments

2.5 Mathematical Modeling

3 Mechanisms of Competition

3.1 Cnidarians

3.2 Other Sessile Invertebrates

3.3 Macroalgae

4 Factors That Alter Competition Among Sessile Reef Organisms

5 Effects of Competition Among Sessile Organisms

5.1 Effects on Individuals

5.2 Effects on Populations and Communities

6 Conclusions and Directions for Future Research

References

Scaling Up Models of the Dynamics of Coral Reef Ecosystems:An Approach for Science-Based Management of Global Change

1 Introduction

1.1 The Coral Reef Crisis

1.2 The Rise of Modeling

1.3 The Challenges of Complexityand Complicatedness

2 Modeling Local-Scale Dynamics

2.1 The Need for Local Models to IncludePhase Shifts

3 Connecting Processes at Localand Regional Scales

4 Coupling of Ecological and Social Systems

5 Ecosystem-Based Models

5.1 Bottom-Up Effects on Ecosystem Function

5.2 Top-Down Effects on Ecosystem Function

6 Conclusions and Outlook

7 Summary

References

Part V:Disturbances

The Impact of Climate Change on Coral Reef Ecosystems

1 Introduction

2 The Coral Reef Environment

3 The Influence of Rising Atmospheric Carbon Dioxide and Other Greenhouse Gases

4 Changes to Tropical/Sub-tropical Oceans

5 Impacts on Coral Reefs

5.1 Impacts of Thermal Stress

5.2 Impacts of Ocean Acidification

5.3 Other Factors Associated with Climate Change

5.4 Ecosystem Responses and Outcomes

6 The Role of Acclimation and Adaptation in Altering Projections of the State of Coral Reefs Under Climate Change

7 Prospects for Coral Reefs and Dependent Societies in the Coming Decades and Century

8 Conclusions and Future Directions

References

Coral Bleaching: Causes and Mechanisms

1 Introduction

2 Causes of Coral Bleaching

3 Mechanisms of Coral Bleaching

4 Acclimatization/Adaptation of Host and Zooxanthellae

5 Conclusions and Future Directions

References

The Potential for Temperature Acclimatisation of Reef Corals in the Face of Climate Change

Box 1 – Terms and Concepts Usedin Considering ResistanceAdaptations of Corals

Terminology

Resistance Adaptations

Measuring Thermal Resistance

1 Historical Perspectives on Coral Acclimatisation and Acclimation

2 Organisms Living Close to their Lethal Limits are more Vulnerable to the Effects of Climate Change

3 Has Coral Bleaching Increased in Intensity and Frequency in Recent Years?

4 Recent Work on Phenotypic Resistance Adaptations to Thermal/Irradiance Stresses in Reef Corals

5 Genomics Approaches to Stress Responses in Corals

6 Epigenetics and Its Significance for Coral Acclimatisation to Elevated Temperature

7 Summary and Conclusions

References

Reef Bioerosion: Agents and Processes

1 Introduction

2 Agents of Bioerosion

2.1 Internal Agents

2.1.1 Microborers

2.1.2 Macroborers

2.2 External Agents

3 Geological History

4 Interactions and Ecological Impact of Bioeroding Agents on Coral Reefs

5 Effects of Anthropogenic and Climatic Changes on Bioerosion Processes

5.1 Direct Effects

5.2 Indirect Effects

6 Perspectives

References

Microbial Diseases of Corals: Pathology and Ecology

1 Introduction

2 The Bacterial Bleaching Disease

2.1 Vibrio shiloi

2.2 Infection of O. patagonica by V. shiloi

2.3 Development of Resistance ofO. patagonica to V. shiloi

2.4 Vibrio coralliilyticus

2.5 Mass Bleaching

3 Black Band Disease

3.1 Environmental Factors

3.2 What is the Causative Agent(S) of BBD?

4 Aspergillosis of Gorgonians

4.1 Disease Signs

4.2 Identification of the Pathogen

4.3 Source of the Pathogen

5 White Plague Diseases

6 White Band Diseases

7 White Pox Disease

8 Yellow Band Disease

9 Brown Band Disease

10 Porites Trematodiasis

11 Skeletal Eroding Band

12 Coral Resistance to Disease

12.1 The Surface Mucus Layer as a Barrierto Infection

12.2 Coral Production of Antibacterials

12.3 Circulating Amoebocytes

12.4 Production of Free Radicalsand Antibacterial Biochemicals

12.5 Bacteriophages (Phages)

References

Coral Reef Diseases in the Atlantic-Caribbean

1 Introduction

2 Historical Perspective

2.1 Black Band Disease

2.2 White Plague Diseases

2.3 White Band Disease and Diadema

2.4 White Patches and Octocoral Mortalities

2.5 Dark Spots Disease

2.6 Caribbean Yellow Band Disease

2.7 Caribbean Ciliate Infection

2.8 Aspergillosis and Purple Spots

2.9 Other Diseases

3 Current Status of Coral Diseases

3.1 Pathogenesis

3.2 Geographic Distribution

3.3 Depth Distribution

3.4 Prevalence, Incidence, and Virulence

3.5 Host Ranges

3.6 Vectors and Reservoirs

4 Environmental Drivers

5 Consequences and Management Implications

6 Summary

References

Factors Determining the Resilience of Coral Reefs to Eutrophication: A Review and Conceptual Model

1 Introduction

2 Responses of Reef Organisms to Eutrophication

2.1 Hard Corals

2.2 Coral Recruitment

2.3 Crustose Coralline Algae

2.4 Macroalgae

2.5 Crown-of-Thorns Starfish (Acanthaster planci)

2.6 Filter-Feeders, Macrobioeroders, and Suspension Feeders

2.6.1 Fishes

3 Factors Influencing the Susceptibility of Reefs to Eutrophication

4 The Conceptual Model

5 Discussion

References

Part VI:Conservation and Management

The Resilience of Coral Reefs and Its Implications for Reef Management

1 Introduction

2 The Concept of Resilience: Definitionsand History

3 Resistance and Recovery

4 Calculating Resilience by Combining Disturbance and Recovery into a Single Framework

4.1 Equilibrial Dynamics

4.2 Disturbance Dynamics

5 Hysteresis in Reef Dynamics and the Urgency for Reef Management

6 Ecological Feedbacks Drive Hysteresis

7 Managing the Resilience of Reefs

7.1 Management of PreventableDisturbances

7.2 Management of Unpreventable Disturbances

References

Index