Oceanographic Processes of Coral Reefs: Physical and Biological Links in the Great Barrier Reef

Cover
Half Title
Title
Copyright
Dedication
Contents
Foreword
About the Editors
Contributors
Section 1 The Key Role of Oceanography and How It Influences Life in the GBR
	Chapter 1 The Emergence of Biophysical Sciences for the Great Barrier Reef
		1.1. Introduction
		1.2. The Growth of Biophysical Science of the GBR
		1.3. GBR Biophysics in This Book
		Acknowledgements
		References
	Chapter 2 The Physical Oceanography of the Great Barrier Reef: A Review
		2.1. Introduction
		2.2. The External Forcing of the Water Circulation in the GBR
			2.2.1. The Tides and the Mean Sea Level
			2.2.2. The Circulation in the Coral Sea
			2.2.3. The Wind
			2.2.4. Waves in the Coral Sea
		2.3. The Rugged Bathymetry Generates a Bioengineered Water Circulation
			2.3.1. Flows Past a Headland in Shallow Coastal Waters
			2.3.2. Flows Past an Island in Shallow Waters
			2.3.3. Flows Past a Linear String of Islands and Reefs
			2.3.4. Flows through a Reef Matrix: The Tidal Friction and Sticky Water Effects
			2.3.5. South Warden Reef Isolating the FNGBR from the NGBR
			2.3.6. Oceanic Inflow in the CGBR
			2.3.7. Topographic Driven Upwelling
			2.3.8. Tidal Jets
			2.3.9. Vertical Stratification on the GBR Continental Shelf
			2.3.10. Wave Breaking
			2.3.11. Boundary Mixing
			2.3.12. Steering of the Tidal Wave by the Reef
			2.3.13. Forcing by the Rivers
		2.4. The Mean Circulation
		2.5. Climate Change
			2.5.1. The Mean Sea Level
			2.5.2. The Wind
			2.5.3. The Temperature
		References
	Chapter 3 Biological and Geological Links on Coral Reef Islands
		3.1. Introduction
			3.1.1. Physical and Biological Linkages between Coral Reefs and Islands
			3.1.2. The Carbonate Factory that Underpins Coral Reef and Island Development
		3.2. The Relationship between Coral Reef Platform Size and Mangrove Colonisation
		3.3. How Does Island Geomorphology Influence Turtle Nesting in the Northern GBR?
			3.3.1. Accessibility of Turtle Nesting Habitat
			3.3.2. Suitability of Turtle Nesting Habitat
			3.3.3. Availability of Turtle Nesting Habitat
		3.4. Human Uses of Islands in the GBR
			3.4.1. Tourism on the Great Barrier Reef
			3.4.2. Coastal Livelihoods in the Central Torres Strait
			3.4.3. Warraber Island: A Central Hub for Maritime Communities
			3.4.4. An Uncertain Future for Reef Islands
		References
	Chapter 4 Currents Modulate the Genetic Character of Marine Populations in the Great Barrier Reef
		4.1. Introduction
		4.2. The Marine World as We Know It
		4.3. The Passage of Genes in the Marine World
		4.4. The Characterization of Marine Populations
		4.5. Modelling the Complex Propagule Movement
		4.6. The Topology of Dispersal Networks
		4.7. Extreme Events
		4.8. Understanding the Mismatch between Hydrodynamics and Population Genetics
		4.9. Conservation Applications
		4.10. Lessons from Afar
		4.11. Future Directions in Seascape Genetics
		References
	Chapter 5 Advances in Understanding Climate Change on the Great Barrier Reef Using Coral-Based Proxies
		5.1. Introduction
		5.2. Coral-Based Palaeoclimate Data Archives
			5.2.1. Advances in Coral Archive Studies
			5.2.2. Palaeothermometry, Palaeosalinity, and pH
			5.2.3. Terrestrial Runoff as a Precipitation Proxy
		5.3. Sublethal Stress Indicators in Corals
			5.3.1. Coral Bleaching
		5.4. Application of Coral-Based Palaeoclimate Proxies in the GBR
		5.5. Conclusions and the Way Forward
		References
	Chapter 6 From the Microscale to the Reef: The Role of Microorganisms in the Chemical Ecology and Gaseous Emissions of the Great Barrier Reef
		6.1. Introduction
		6.2. From the Macro to the Microscale
		6.3. The Marine Environment from the Perspective of a Microorganism
			6.3.1. Molecular Diffusion and Fluid Flow Shape Life at the Microscale
			6.3.2. Cell Density and Encounter Rates at the Microscale
		6.4. Chemical Transformation Mediated by Microbes on the Great Barrier Reef
			6.4.1. Water Column
			6.4.2. Reef Sediments
			6.4.3. Host Association
			6.4.4. Gaseous Emissions
		6.5. The Impact of Gaseous Emissions from the GBR
		6.6. Conclusion: From the Microscale to the Reef
		References
Section 2 Land-Sea Connectivity
	Chapter 7 Great Barrier Reef Ecohydrology
		7.1. Introduction
		7.2. GBR Hydrology: River Discharge and Major Flow Pathways
		7.3. GBR Ecological Connectivity within the Catchment and to the Reef
			7.3.1. Passive Connectivity and Dispersal
			7.3.2. Active Connectivity, Dispersal, and Migration
		7.4. Threats: Barriers to Connectivity and Landscape Modification
			7.4.1. Natural Barriers within the GBR Catchment Area
			7.4.2. Anthropogenic Barriers within the Catchment Area
			7.4.3. Landscape Modification
		7.5. Consequences of Modifications to the GBR Catchment Area
		7.6. Future Connectivity: Development and Management
		7.7. Implications for the GBR and Future Approaches
		Acknowledgements
		References
	Chapter 8 Sediment and Nutrient Flux from Land
		8.1. Introduction
		8.2. History of Research on Understanding Sediment and Nutrient Fluxes to the GBR
		8.3. Sources and Fluxes of Sediment to the GBR
		8.4. Sources and Fluxes of Nitrogen and Phosphorus to the GBR
		8.5. Transformations of Sediment and Nutrients Across the Catchment to Marine Continuum
		8.6. Management Options to Reduce Sediment and Nutrient Loads to the GBR
		8.7. Conclusions
		Acknowledgements
		References
	Chapter 9 Dispersal and Environmental Impacts of Pan-Oceanic Contaminants
		9.1. Introduction
		9.2. Pan-Oceanic Dispersal and Accumulation of Plastic Pollution
		9.3. Pan-Oceanic Pollution by EGCS Washwater and Fuel Oils
		9.4. Conclusions
		References
	Chapter 10 Jellyfish: A Window into Pesticide Distribution and Risks on the Great Barrier Reef
		10.1. General Introduction
		10.2. History of Pesticide Use in Northern Australia
		10.3. Pesticide Inputs to the GBR
		10.4. Measurement of Pesticides on the GBR
		10.5. Jellyfish Life History
		10.6. Cassiopea
		10.7. Challenges and Future Directions
		Bibliography
	Chapter 11 The Influence of the Spatiotemporal Dynamics of Fish Populations on the Outcomes of Land-Sea Connectivity
		11.1. Introduction
		11.2. Sources of Energy and Nutrients
		11.3. Events in Fish Populations that Influence Land-Sea Connectivity
		11.4. Ecological Outcomes of Land-Sea Connectivity for the GBR
			11.4.1. Trophic Outcomes
			11.4.2. The Specific Role of Fish in Nutrient Translocation
			11.4.3. Trophic Importance of Fish beyond Energy Translocation
		11.5. Consequences of Changes to Land-Sea Connectivity for Ecological Functioning
			11.5.1. Major Challenges
		11.6. Ensuring the Future of Fish-Mediated Land-Sea Connectivity
			11.6.1. Problems with the Current Biological Knowledge Base
			11.6.2. Approaches to Support Functionally Robust and Dynamic Fish-Mediated Land-Sea Connectivity
		References
Section 3 Biophysical Oceanography
	Chapter 12 Estimates of Wind Drift Coefficient to Inform Biophysical Models of Seagrass Dispersal in the Great Barrier Reef
		12.1. Introduction
		12.2. Methods
		12.3. Results
		12.4. Discussion
		12.5. Research Gaps
		12.6. Conclusion
		References
	Chapter 13 Interactions between Dugong Biology and the Biophysical Determinants of Their Environment: A Review
		13.1. Introduction
		13.2. Information on the Dugong\'s Morphology, Physiology, and Traditions Relevant to Its Ecology
			13.2.1. Challenges
			13.2.2. Morphological and Sensory Adaptations
			13.2.3. Socially Transmitted Knowledge
		13.3. Interactions between Dugong Biology and the Biophysical Attributes of Their Environment
			13.3.1. Seagrasses
			13.3.2. Water Depth and Bottom Type
			13.3.3. Waves
			13.3.4. Tides
			13.3.5. Currents
			13.3.6. Coastline Features
			13.3.7. Light
			13.3.8. Water Temperature
			13.3.9. Predation Risk
		13.4. How Might These Interactions Be Affected by Climate Change in the GBR?
		13.5. Future Directions
			13.5.1. Modelling
			13.5.2. Anatomical Studies
			13.5.3. Captive Animals
			13.5.4. Field Studies: Seagrasses
			13.5.5. Field Studies: Application of New Technologies to Dugong Studies
		Acknowledgments
		References
	Chapter 14 Biophysical Interactions of Jellyfish on the Great Barrier Reef
		14.1. Introduction
		14.2. Sensory and Nervous Systems
		14.3. Mobility
		14.4. Behaviours and Ecology
			14.4.1. Aggregations
			14.4.2. Visually Guided Behaviours
			14.4.3. Behaviours and Population Structures
		14.5. Future Research Directions
			14.5.1. Polyps
			14.5.2. Medusae
			14.5.3. Biophysical Modelling
		14.6. Conclusions
		References
	Chapter 15 More Intense Severe Tropical Cyclones in Recent Decades Cause Greater Impacts on Mangroves Bordering Australia\'s Great Barrier Reef
		15.1. Introduction
		15.2. Methods
			15.2.1. The GBR Study Area and Data about Cyclones
			15.2.2. Areas of Damaged Mangroves
			15.2.3. Severity of Damage to Mangroves
			15.2.4. Sea Level Data
		15.3. Results
			15.3.1. Number and Intensity of STCs
			15.3.2. Spatial Extent of Damage to Mangrove Communities
			15.3.3. Damage at Specific Landfall Sites of STCs in the GBR Region
			15.3.4. Severity of Canopy Damage and Loss to Mangroves
			15.3.5. Recovery Rates of Impacted Mangroves
		15.4. Discussion
			15.4.1. STCs Making Landfall Were More Intense and More Frequent Over Recent Decades
			15.4.2. Increased Intensity of STCs Making Landfall Influenced the Area of Impacted Mangroves
			15.4.3. The Increased Intensity of STCs Making Landfall Affected the Severity of Mangrove Canopy Loss
			15.4.4. Canopy Recovery Rates Were Dependent on Forest Type
			15.4.5. The Impacts of Successive STCs Making Landfall Were Accumulative
			15.4.6. Cyclone Damage and Recovery of Mangrove Canopies Is an On-Going Natural Process, but Can Recovery Be Sustainable as Impacts Escalate with Global Climate Change?
		Acknowledgements
		Supplementary Data File
		References
	Chapter 16 Dispersal and Connectivity of Marine Turtles in the Great Barrier Reef and Links to the South Pacific Ocean
		16.1. Introduction
		16.2. Beach Dispersal
			16.2.1. Case Study 1: Nearshore Dispersal
			16.2.2. Case Study 2: Pelagic Dispersal from the Southern GBR
			16.2.3. Case Study 3: Hawksbill and Green Turtle Dispersal from the Northern GBR
		16.3. Partitioning of Foraging Habitats
		16.4. Key Research Pathways for Oceanography
		References
	Chapter 17 Interactions between Oceanography and the Behaviour of Larval Reef Fish
		17.1. Introduction
			17.1.1. Dispersal Distances of Passive Larvae
		17.2. Swimming and Sensory Abilities of Larvae
			17.2.1. Swimming Ability of Larvae
			17.2.2. Sensory Abilities and Orientation of Larvae
			17.2.3. Longer-Distance Orientation Capabilities
		17.3. Sensory Fields
			17.3.1. Spatial Scale of Cues
			17.3.2. The Time Larvae Spend in Near Reef Waters
		17.4. Biophysical Modelling
			17.4.1. Biophysical Modelling and Determining Relevant Timeframes for Dispersal?
			17.4.2. Topography Influences Dispersal Trajectories
		17.5. Currents Influence Dispersal and Population Genetics
		17.6. Biophysical Modelling: Where to Go from Here?
		References
	Chapter 18 Incorporating Biophysical Larval Dispersal Simulations into Coral Reef Conservation Decision-Making
		18.1. Introduction
		18.2. Biophysical Larval Dispersal Simulation Models
		18.3. Incorporating Larval Dispersal into Conservation Decisions
			18.3.1. Example 1: Designing Adequate Networks of No-Take Marine Protected Areas
			18.3.2. Example 2: Spatial Planning of Coral Reef Restoration Actions
			18.3.3. Example 3: Controlling Crown-of-Thorns Populations
			18.3.4. Limitations of Existing Methods
		18.4. Optimal Control Strategy for Crown-of-Thorns Starfish Control
			18.4.1. Notation
			18.4.2. Objective Function
			18.4.3. Constraints
			18.4.4. Model Parameterisation
			18.4.5. Identifying the Optimal Control Strategy
			18.4.6. Comparison with a Network Theory Approach
		18.5. Discussion
		References
	Chapter 19 A Historical Perspective on Thermal- and Heatwave-Induced Bleaching on the Great Barrier Reef
		19.1. Background
			19.1.1. Thermally Induced Coral Bleaching
		19.2. Great Barrier Reef Bleaching
			19.2.1. Recent Bleaching and Heatwaves (Post-1970s)
			19.2.2. Approaches to Obtaining Pre-1970s Bleaching Records
			19.2.3. Pre-1970s Bleaching Events—The 1929 GBR (Low Isles) Observational Record
			19.2.4. Pre-1970s Bleaching Events—Global and GBR Proxy-Based Record
		19.3. Moving Bleaching Baselines
			19.3.1. Great Barrier Reef Bleaching Thresholds over Time
		19.4. Conclusions
		References
	Chapter 20 Biophysical Processes Involved in the Initiation and Spread of Population Irruptions of Crown-of-Thorns Starfish on the Great Barrier Reef
		20.1. Introduction
		20.2. Crown-of-Thorns Starfish and the Great Barrier Reef
			20.2.1. Documented History of Population Irruptions
			20.2.2. The \"Initiation Box\"
			20.2.3. Current Status of Population Irruptions
		20.3. Putative Causes of Population Irruptions
		20.4. Biophysical Processes Affecting Population Irruptions of Crown-of-Thorns Starfish
			20.4.1. Ocean Currents
		20.5. Managing Population Irruptions of Crown-of-Thorns Starfish
			20.5.1. Large-Scale Management Interventions
			20.5.2. Local-Scale Management Interventions
		20.6. Key Knowledge Gaps and Research Priorities
			20.6.1. Measuring Settlement Rates
			20.6.2. Improved Understanding of Larval Retention and Dispersal
			20.6.3. Environmental Change
		References
	Chapter 21 The Biophysics of Sharks and Rays on the Great Barrier Reef
		21.1. Introduction
		21.2. Linkages between GBR Physical Habitats and Sharks and Rays
			21.2.1. Shark and Ray Diversity and Ecological Groupings
			21.2.2. Biophysical Relationships Shape Shark and Ray Behaviour and Community Composition
			21.2.3. Sharks and Rays as Habitat Engineers
		21.3. Trophodynamics of GBR Sharks and Rays
		21.4. Effects of Biophysical Factors on Shark and Ray Movement and Distribution
			21.4.1. Biophysical Drivers of Movement
			21.4.2. Influence of Extreme Weather Events
		21.5. The Physiological Linkages between Sharks and Rays and Their Environment
		21.6. Conclusions and Future Directions
		Acknowledgements
		References
Section 4 Consequences: Impact on GBR Water and Remediation
	Chapter 22 Impacts of Climate Change Stressors on the Great Barrier Reef
		22.1. Introduction
		22.2. Climate Change Stressors
			22.2.1. Chemical Processes in a Changing Ocean—Warming and Acidification
			22.2.2. Physical Processes in a Changing Ocean—Storms and Sea Level Rise
		22.3. Conclusion
		Acknowledgments
		References
	Chapter 23 Selective Breeding and Promotion of Naturally Heat-Tolerant Coral Reef Species
		23.1. Introduction
		23.2. Great Barrier Reef Oceanography and Dispersal (and How Differences Impact Species)
		23.3. Selective Breeding and Promotion of Natural Heat Tolerance
		23.4. Influence of Oceanic Processes for Selective Breeding in Coral Reef-Associated Species
			23.4.1. A. Corals
			23.4.2. B. Fish
		23.5. Synthesis and Comparison of the Two Case Studies within an Eco/Evo Framework
		References
	Chapter 24 Coastal Wetland Restoration: Case Studies from Great Barrier Reef Catchments
		24.1. Introduction
		24.2. Values-Based Framework
		24.3. Case Studies
			24.3.1. Case Study: Tidal Bund Wall Removal and Tidal Ingress at Mungalla Station
			24.3.2. Case Study: Mechanical Weed Removal in Irrigation Channels and Lagoons on the Burdekin Floodplain
			24.3.3. Case Study: Feral Pig Exclusion Fencing for Wetland Protection and Restoration
		24.4. Lessons Learned and Future Opportunities
		24.5. Conclusion
		References
	Chapter 25 Pathways to Improved Water Quality in the GBR Lagoon—Exploring Opportunities for Broadscale Application of Low-Risk Practices in the Lower Burdekin Irrigated Agriculture Areas
		25.1. Introduction
		25.2. Water Quality Pollutants and Their Function
			25.2.1. Pollutant Effects on GBR Ecosystems
			25.2.2. Land-Based Delivery of DIN to the GBR
		25.3. Land Based Activity and Managing DIN Export in the Lower Burdekin
			25.3.1. Irrigation Systems and DIN Pathways
			25.3.2. Irrigation and Rising Water Table
		25.4. Managing DIN Export from the Field
			25.4.1. Optimising Fertiliser Management
			25.4.2. Optimising Furrow Irrigation Management
		25.5. Programs for DIN Reduction for the GBR and the Lower Burdekin
			25.5.1. Valuing the GBR
			25.5.2. Setting Targets for DIN Reduction
			25.5.3. Progress towards DIN Reduction Targets
			25.5.4. Factors Affecting the Rate of Uptake of Low-Risk Practices
			25.5.5. Reframing the WQIPs for Social Inclusion
		25.6. Transformative Approaches to Achieving Water Quality
		25.7. Conclusion
		Acknowledgements
		References
	Chapter 26 Raine Island Recovery Project—Intervening at One of the Most Significant Sites on the Great Barrier Reef
		26.1. Introduction
		26.2. Site Description
			26.2.1. What Is Beach Reprofiling?
		26.3. Results
			26.3.1. How Was Beach Reprofiling Implemented?
			26.3.2. A Success Story
			26.3.3. Future Projections
		26.4. Conclusion
		References
	Chapter 27 An Overview of Environmental Engineering Methods for Reducing Coral Bleaching Stress
		27.1. Introduction
		27.2. The Role of Light and Temperature
		27.3. Intervention by Environmental Engineering
		27.4. Cooling
			27.4.1. Mixing and Pumping: A Description
			27.4.2. Undersea Berms
			27.4.3. Underwater Impellors
			27.4.4. Pumping
			27.4.5. Feasibility of Mixing and Pumping
			27.4.6. Risks of Mixing and Pumping
		27.5. Shading
			27.5.1. Surface Films
			27.5.2. Ocean Microbubbles
			27.5.3. Misting and Fogging: A Description
			27.5.4. Smoke Fogging
			27.5.5. Seawater Fogging
			27.5.6. Risks of Local Shading
		27.6. Regional Cooling and Shading
			27.6.1. Marine Cloud Brightening
			27.6.2. Risks of Regional Shading Techniques
		27.7. Where to Next?
		Acknowledgement
		References
	Chapter 28 Sexual Reproduction of Reef Corals and Application to Coral Restoration
		28.1. Introduction
		28.2. Coral Reproduction: Sexual Patterns, Spawning and Planulation, Environmental Influences, and Regional Patterns of Reproduction
			28.2.1. Sexual Patterns
			28.2.2. Mode of Larval Development
			28.2.3. Reproductive Cycles
			28.2.4. Fecundity and Stress
			28.2.5. Environmental Regulation of Reproduction and Synchrony
			28.2.6. Spawning Synchrony and Regional Patterns
			28.2.7. Coral Reproduction on the GBR
			28.2.8. Other Regional Patterns of Coral Reproduction and Varying Synchrony
		28.3. Advances in Coral Restoration and Breeding for Larval-Based Propagation
			28.3.1. Asexual Restoration Methods
			28.3.2. Sexual Reproduction and Larval Production for Restoration
			28.3.3. Flexibility and Limitations of Coral Restoration
		28.4. Conclusions
		Acknowledgements
		References
	Chapter 29 Great Barrier Reef Biophysics: A Synthesis of Challenges and Opportunities
		29.1. Introduction
		29.2. The Present GBR as a Point in Time
			29.2.1. Past Physical Patterns Generated the Present Genetic Character of Populations
			29.2.2. Reef Island Geomorphology
			29.2.3. Many Points in Time and Space Are Revealed by Coral Cores
			29.2.4. The History of Severe Tropical Cyclones
			29.2.5. The History of Coral Bleaching
			29.2.6. The Irruptions of Crown-of-Thorns Starfish
			29.2.7. The Cumulative Impact of Climate Change Stressors
		29.3. The Present GBR in Space
			29.3.1. Pan-Oceanic Pollutants
			29.3.2. Animal Migration
		29.4. Biophysical Oceanography of the Present GBR
			29.4.1. The GBR Physical Oceanography
			29.4.2. Micro-Scale Processes Also Modulate the Large Scales
			29.4.3. The GBR Ecohydrology
			29.4.4. The Human Impact Through Land Use
			29.4.5. Pesticides: The Proposed Jellyfish Watch
			29.4.6. Connectivity for Fish
			29.4.7. Limited Connectivity for Seagrass
			29.4.8. Dugong Biophysics
			29.4.9. Jellyfish Biophysics
			29.4.10. Turtle Biophysics
			29.4.11. The Biophysics of Reef Fish Larvae
			29.4.12. Crown-of-Thorns Starfish Biophysics Modelling
			29.4.13. The Biophysics of Sharks and Rays
		29.5. Remediation Measures
			29.5.1. Selective Breeding of Coral and Fish
			29.5.2. Restoring Wetlands
			29.5.3. Remediation for Irrigated Agriculture and Fertiliser Practices
			29.5.4. Remediation of Beaches for Sea Turtles
			29.5.5. Environmental Engineering to Reduce Coral Bleaching
			29.5.6. Sexual Reproduction of Reef Corals and Application to Coral Restoration
		29.6. Conclusions
			29.6.1. The Importance of small-Scale Physical Processes in Generating Connectivity
			29.6.2. The Importance of the Mesoscale Turbulence in the Coral Sea
			29.6.3. The Importance of Animal Behaviour
			29.6.4. Remediation
		29.7. Key Messages from Authors
		References
Index