Marine Animal Forests. The Ecology of Benthic Biodiversity Hotspots

bfm-978-3-319-21012-4%2F1
	Marine Animal Forests: Foreword
	Acknowledgments
	Contents
	About the Editors
	Contributors
Binder1
	1
		1 Animal Forests of the World: An Overview
			1 What Is a Marine Animal Forest?
			2 Marine Animal Forests Through Depths and Latitudes
			3 The Main Components of the Marine Animal Forests
				3.1 Sponges
				3.2 Cnidarians
				3.3 Bryozoans, Ascidians, Polychaetes, and Bivalves
			4 Ecosystem Functions and Effects of Anthropogenic Impacts on the Animal Forests
			5 Perspectives and Challenges of Future Research
				5.1 Distribution of the Animal Forests of the World
				5.2 Benthic-Pelagic Coupling Processes
				5.3 Photobiology and the Limits of Symbiosis
				5.4 Metabolism and Biochemical Pathways: The Use of Energy
				5.5 Reproduction
				5.6 Connectivity and Resilience
				5.7 Growth and Carbon Sink
				5.8 Scientific Outreach
			6 Conclusion
			References
	2 (1)
		2 Caribbean Coral Reefs: Past, Present, and Insights into the Future
			1 Introduction
			2 Caribbean Coral Reefs in the Past
			3 Caribbean Coral Reefs in the Present
			4 Current Threats Affecting Caribbean Coral Reefs
			5 General Conclusion
			References
	3
		3 Brazilian Marine Animal Forests: A New World to Discover in the Southwestern Atlantic
			1 Introduction
			2 Tropical Coast of Brazil: Environmental Characteristics and Benthic Habitats
			3 Benthic Ecology and Diversity: Eco-Engineers in BRAF
				3.1 Porifera
				3.2 Cnidarians
				3.3 Mollusca
				3.4 Bryozoa
				3.5 Ascidiacea
			4 Threats to BRAF
				4.1 Urbanization
				4.2 Aquaculture
				4.3 Invasive Species
				4.4 Fishing and Bottom Trawling
				4.5 Climate Change
				4.6 Mining (Petroleum, Gas, and Minerals)
			5 Mesophotic and Deep-Sea Ecosystems Along the Brazilian Coast: A Lack of Knowledge and Clear Legal Framework for Management
			6 Conclusions and Future Directions
			7 Cross-References
			References
	4 (1)
		4 Diversity and Evolution of Octocoral Animal Forests at Both Sides of Tropical America
			1 Introduction
			2 Octocoral Animal Forests Assemblages and Diversity
			3 Caribbean Octocoral Communities
			4 Eastern Pacific Octocoral Communities
			5 Symbiosis
				5.1 Microorganisms
				5.2 Invertebrates
				5.3 Reef Fish
			6 Gorgonian Animal Forests Demography
				6.1 Growth
				6.2 Reproduction
			7 Animal Forests in a Changing Ocean
				7.1 Effects of Storms
				7.2 Global Warming
				7.3 Invasive Species
				7.4 Ocean Acidification
			8 Evolutionary Biology
			9 Conclusions
			10 Future Directions
			References
	5
		5 Sponge Grounds as Key Marine Habitats: A Synthetic Review of Types, Structure, Functional Roles, and Conservation Concerns
			1 Introduction
			2 Coral Reef Sponge Aggregations
			3 Mangrove Sponge Aggregations
			4 Deep-Sea Astrophorid and Hexactinellid Grounds
			5 Glass Sponge Reefs
			6 Lithistid Aggregations
			7 Carnivorous Sponge Grounds
			8 Antarctic Aggregations
			9 Conservation Concerns for Sponge Aggregations
			10 Conclusions and Future Directions
			11 Cross-References
			References
	6 (1)
		6 Mesophotic Coral Ecosystems
			1 Introduction
			2 Habitat-Forming Megabenthos
				2.1 Phototrophic Taxa
				2.2 Symbiont Biodiversity
				2.3 Benthic Macroalgae
				2.4 Azooxanthellate Benthic Taxa
			3 Coral Reef Fishes
			4 Ongoing MCE Exploration and Implications for Biodiversity
			5 Cross-References
			References
	7
		7 Animal Forests in Deep Coastal Bottoms and Continental Shelves of the Mediterranean Sea
			1 Exploration of Hard Bottoms at Intermediate Depths in the Mediterranean Sea
			2 Animal Forests at 40-200 m Depth in the Mediterranean Sea
				2.1 Deep Coastal Assemblages
				2.2 Continental Shelf Assemblages
				2.3 Shelf Edge and Upper Slope Assemblages
				2.4 Assemblages in Offshore Banks and Seamounts
			3 Case Studies in the Mediterranean Sea
				3.1 Cap de Creus
				3.2 Menorca Channel
				3.3 Gulf of St. Eufemia
				3.4 Carloforte Shoal
			4 What Do We Know About the Ecology of These Animal Forests?
				4.1 Population Structure
				4.2 Trophic Ecology
				4.3 Sexual Reproduction
				4.4 Associated Fauna
			5 Treats
				5.1 Fishing Impact
				5.2 Deep Mass Mortalities
				5.3 Other Sources of Impact
			6 Future Research and Actions
			References
	8
		8 Global Biodiversity in Cold-Water Coral Reef Ecosystems
			1 Global Distribution of Cold-Water Coral Reefs
				1.1 Introduction
			2 Biodiversity Associated with CWC Reefs
				2.1 Fauna Associated with Coral Biofilm, Including Meiofauna
				2.2 Macrobenthic Grazers, Deposit Feeders, and Predators
				2.3 Suspension and Filter Feeders
				2.4 Demersal Fish Communities
			3 Emerging Ecological Paradigms
				3.1 Species (α) Diversity
				3.2 Community (beta) Diversity
				3.3 Regional (gamma) Diversity
			4 Knowledge Gaps and Technical Limitations
				4.1 Baseline Information in Key Regions
				4.2 Habitat Use by Migratory Animals
				4.3 Regional Biogeography
				4.4 Cryptic Diversity
			5 Frontiers in Technology
				5.1 Landers and Observatories
				5.2 Robotics and Engineering
				5.3 Genomics
			6 Conclusion and Future Directions
			References
	9
		9 Coexistence in Cold Waters: Animal Forests in Seaweed-Dominated Habitats in Southern High-Latitudes
			1 Introduction
				1.1 Animal Forest in Cold-Water Ecosystems
				1.2 Theoretical Gaps and Challenges in the Framework of AFs
			2 Coexistence of Animal and Macroalgal Forests
				2.1 Animal and Macroalgal Forests Under a Morpho-Functional Approach
				2.2 Epilithic Animal Forests Among Macroalgal Forests in Punta Santa Ana: A Case Study in the Strait of Magellan Coast
					2.2.1 Distribution of Animal and Macroalgal Forests Influenced by the Topography of the Rocky Reef from Punta Santa Ana
						Inclined Surfaces
						Vertical Surfaces
						Overhanging Surfaces
			3 Ecological Patterns of Animal Forests on the Southern Tip of South America and Antarctic Continental Shelves
				3.1 Abundance Patterns of Gregarious and Clonal Animal Forests
				3.2 Distribution Pattern of Gregarious and Clonal Animal Forests: Is There a Pattern Along a Latitudinal Gradient Between Mage...
					3.2.1 A Hypothesis
			4 Highlights and Outlook
			5 Cross-References
			References
	10
		10 Animal Forests in the Chilean Fjords: Discoveries, Perspectives, and Threats in Shallow and Deep Waters
			1 Introduction
			2 Animal Forests of Chilean Patagonia: Latitudinal, Longitudinal, and Bathymetric Distribution
				2.1 Marine Animal Forests Conformed by Animals with Massive Calcified Skeletons
					2.1.1 Animal Forests Conformed by Calcifying Bioengineers Presenting a Massive Exoskeleton
						Mussel Banks
						Brachiopod Banks
						Barnacle Aggregations
					2.1.2 Animal Forests Conformed by Calcifying Bioengineers Presenting a Massive Endoskeleton
						Cold-Water Stony Coral Forests
						Cold-Water Hydrocoral Forests
						Ectoprocta Aggregations
				2.2 Animal Forests Consisting of Calcifying Bioengineers Presenting Scattered Calcified Structures
				2.3 Marine Non-Calcifying Animal Forests
			3 Threats and Observed Impacts
				3.1 Indirect Anthropogenic Impacts on Animal Forests of the Chilean Patagonian Fjord Region
				3.2 Direct Anthropogenic Impacts on Animal Forests of the Chilean Patagonian Fjord Region
				3.3 Aquaculture
				3.4 Natural Hazards, Which Threaten Animal Forests of the Chilean Patagonian Fjord Region
				3.5 Effects and Impacts of Anthropogenic Activities and Natural Hazards on the Animal Forests of the Chilean Patagonian Fjord ...
			4 Conclusions and Future Directions
			References
	11
		11 Antarctic Marine Animal Forests: Three-Dimensional Communities in Southern Ocean Ecosystems
			1 Introduction
			2 Definitions and Perspectives
			3 Areal Coverage
			4 Distribution, Limitations, and Species Richness
			5 System Architecture
			6 Ecosystem Engineering, Associated Fauna, and Secondary Habitat Formation
			7 Interactions Between Soil/Sediment and Their Inhabitants
			8 Energy Flow and Other Ecological Processes
			9 Air and Water, the Surrounding Environments
			10 Ecosystem Response to Disturbance
			11 Climate Change and Direct Human Impacts
			12 Conservation Issues
			13 Future Directions
				13.1 Mapping Structural and Functional Diversity of Biotic Communities
				13.2 Understanding Ecosystem Function
				13.3 Research Strategies
				13.4 Cross-System Comparisons
			14 Cross-References
			References
	12
		12 Drawing the Line at Neglected Marine Ecosystems: Ecology of Vermetid Reefs in a Changing Ocean
			1 Introduction
				1.1 A Reef Constructed by Gastropod Snails and Encrusting Coralline Algae: The Mediterranean Vermetid Reef
				1.2 The Peculiar Biology and Ecology of the Mediterranean Vermetid Reefs
			2 Importance of Vermetid Reefs in Providing Valuable Ecosystem Services
				2.1 Supporting High Biodiversity Levels
				2.2 Preventing Coastal Erosion, Regulating Sediment Transport, and Providing Carbon Sequestration
			3 Potential Threats to Vermetid Reefs´ Persistence Within the Mediterranean Sea
				3.1 Biological and Chemical Pollution
				3.2 Sea Level Rise, Ocean Warming and Acidification
				3.3 Recreational Uses and Related Human Impacts
			4 Conclusion and Future Directions
			References
	13
		13 Where Seaweed Forests Meet Animal Forests: The Examples of Macroalgae in Coral Reefs and the Mediterranean Coralligenous Ec...
			1 Introduction
			2 The Mediterranean Coralligenous Ecosystem
				2.1 Community Structure and Ecosystem Functioning
				2.2 Macroalgae
				2.3 Seaweed Forests Versus Animal Forests
			3 The Coral Reef Ecosystem Complex
				3.1 Community Structure and Ecosystem Functioning
				3.2 Macroalgae
				3.3 Seaweed Forests Versus Animal Forests
			4 Discussion, Conclusions, and Future Directions
			References
	14
		14 Hydroids (Cnidaria, Hydrozoa): A Neglected Component of Animal Forests
			1 Introduction
			2 Deciduous Hydroid Forests
			3 Perennial Hydroid Forests
			4 Interactions with Other Organisms
			5 Trophic Ecology, Feeding Behavior, and Reproductive Strategies
			6 Emerging Threats for Hydroid Forests
			7 Conclusions
			References
	15
		15 Evolution of the Marine Animal Forest: EvoDevo of Corals, Sea Anemones, and Jellyfishes
			1 Introduction
			2 An Ancient Origin for the Basic Body Plan of Cnidarians
			3 Genetic Pathways in the Cnidarian Toolkit
			4 Cnidarian Gastrulation and the Organizer
			5 Cnidarians Axis Patterning
			6 Cnidarian Hox Genes
			7 Future Directions
			References
	16
		16 Metabarcoding Techniques for Assessing Biodiversity of Marine Animal Forests
			1 Introduction
			2 DNA-Barcoding and Metabarcoding
			3 Specific Challenges of Marine Hard-Bottom Communities
			4 Sampling and Preservation
			5 Sample Preprocessing and DNA Extraction
			6 Primer Design, Sample Multiplexing and PCR Protocols
			7 High-Throughput Sequencing
			8 Bioinformatic Analyses
				8.1 Quality Control and Demultiplexing
				8.2 Clustering Methods for Delimiting MOTUs
				8.3 Methods for Taxonomic Assignment
				8.4 Refining of the Final Matrix
			9 Summary of Pipelines for Eukaryotic Metabarcoding
			10 Reporting the Results
			11 Future Perspectives
			References
	17
		17 Deep-Sea Suprabenthic Communities: The Forgotten Biodiversity
			1 Introduction
			2 Sampling the Deep-Sea Suprabenthos
			3 Suprabenthos in Deep-Sea Areas of the World
			4 Atlantic Ocean
			5 Mediterranean Sea
			6 Southern Ocean
			7 Pacific Ocean
			8 Deep-Sea Suprabenthos Distribution Patterns
			9 Suprabenthos in the Deep-Sea Animal Forests
			10 Conclusions
			11 Cross-References
			References
	18
		18 Living in the Canopy of the Animal Forest: Physical and Biogeochemical Aspects
			1 Introduction
			2 The Hydrodynamics Inside and Above the Marine Animal Forest
				2.1 Structure of the Turbulent Boundary Layer Over Flat Beds in Steady Flows
				2.2 Structure of the Turbulent Boundary Layer Over Large Obstacles in Steady Flows: The Canopy Effect
				2.3 Inherent Similarities of Canopy Steady Flows
				2.4 Variation of a Steady Flow with Canopy Density
				2.5 Variation of a Steady Flow with Canopy Flexibility
				2.6 Structure of the Canopy Boundary Layer in Oscillatory Flows
			3 The Biogeochemistry Inside and Above the Canopy of the Animal Forest
				3.1 Bulk Mass Transfer Rates Across Canopy Boundaries
				3.2 Uptake Inside the Canopy
				3.3 Relating Bulk Mass Transfer Across the Canopy to Local Mass Transfer Limitations
			4 Living in the Canopy of the Animal Forest
				4.1 Living in a Sparse Animal Forest
				4.2 Living in a Moderately Populated Animal Forest
				4.3 Living in a Dense Animal Forest
			5 Conclusions and Future Directions
			References
	19
		19 Demography of Animal Forests: The Example of Mediterranean Gorgonians
			1 Gorgonians: The Mediterranean Miniature Animal Forests
			2 Recovery After Drastic Mortality Event: The Study Case of a Paramuricea clavata Population in the Gulf of La Spezia (Liguria...
				2.1 Study Site, Sampling, and Model Parameterization
				2.2 Mortality and Recovery Dynamics
					2.2.1 Density
					2.2.2 Recruitment
					2.2.3 Size Structure
			3 The Mediterranean Red Coral Corallium rubrum (L. 1758): An Exemplary Case Study of an Overexploited Gorgonian
				3.1 Shallow Populations
				3.2 Deep Populations
				3.3 Demography of Corallium rubrum
					3.3.1 Growth Rates
					3.3.2 Recruitment
					3.3.3 Reproductive Features
					3.3.4 Population Trends
			4 Recovery Dynamics of the Studied Populations
				4.1 Paramuricea clavata
				4.2 Corallium rubrum Recovery Dynamics
			5 Conclusive Remarks
			References
	20
		20 Importance of Recruitment Processes in the Dynamics and Resilience of Coral Reef Assemblages
			1 Introduction
				1.1 The ``Coral Reef Crisis´´
				1.2 The Importance of Recruitment Processes
				1.3 Complexities of the Coral Life Cycle
				1.4 Objectives of This Chapter
			2 Spatiotemporal Patterns of Recruitment and Major Controlling Factors
				2.1 Spatial Patterns
				2.2 Temporal Changes
				2.3 Perspectives
			3 Post-settlement Events, Regulation Processes, and Life Strategies
				3.1 Post-settlement Events and Regulation Processes
				3.2 Supply-Side Ecology
				3.3 Life Strategies
				3.4 Perspectives
			4 Recruitment, Recovery, and Resilience
				4.1 Recruitment Rate as Indicator of Resilience
				4.2 The Importance of Recruitment for Recovery
				4.3 How Much Recruitment for Persistence?
				4.4 Perspectives
			5 Conclusions
			6 Cross-References
			References
	21
		21 Reproductive Strategies in Marine Invertebrates and the Structuring of Marine Animal Forests
			1 Introduction
			2 Negative and Positive Interactions as Drivers of Habitat Complexity and Biodiversity
			3 The Diversity of Invertebrate Reproductive Strategies
				3.1 Asexual Reproduction
				3.2 Sexual Reproduction
				3.3 Diversity in Life Cycles, Distribution of Resources, and Habitat Stability
				3.4 Pelagic Larval Development
				3.5 Dispersal of Brooding Species
			4 Reproductive Ecology of Different Types of Animal Forests
				4.1 Tropical Coral Reefs
				4.2 Temperate Shallow Communities
				4.3 Cold-Water Corals
				4.4 Antarctic Benthic Ecosystems
			5 Structuring of Animal Forests at Small Scales
			6 What Genes Can Tell: Gene Flow, Connectivity, and Clonality
			7 Persistence of Animal Forests in Time
				7.1 Recolonization and Recovery
				7.2 Resilience and Vulnerability of Reproductive Cycles
			References
	22
		22 Growth Patterns in Long-Lived Coral Species
			1 Growth in Modular Organisms
			2 Methodologies for the Study of Growth in Corals
			3 Growth in Scleractinian Corals: Cold-Water Corals as a Case Study
			4 Growth in Octocorals: The Mediterranean Red Coral (Corallium rubrum) Case Study
				4.1 Colony Age Assessment
				4.2 Colony Growth Rate
			5 Growth in Antipatharia: The Millennial Black Corals of the Genus Leiopathes Case Study
			6 Modeling Coral Growth
				6.1 Organism and Population Growth Models
				6.2 Growth Indeterminacy, Trophic Shading, and Bioenergetic Implications of Shape
				6.3 Growth of Calcified Structures and Skeletal Ring Formation
				6.4 An Application of a Growth Model to the Case Study of Corallium rubrum
				6.5 Morphogenesis Models
			7 Conclusions and Perspectives
			8 Cross-References
			Glossary
			References
	23
		23 The Builders of the Oceans - Part I: Coral Architecture from the Tropics to the Poles, from the Shallow to the Deep
			1 A Journey Across the Marine Animal Forest
				1.1 Animal Trees and Bushes of the Seascape over the World
				1.2 Life in the Coral Animal Forest
				1.3 A Journey Through the Coral Animal Forest of the Underwater World
			2 Cross-References
			References
	24
		24 The Builders of the Oceans – Part II: Corals from the Past to the Present (The Stone from the Sea)
			1 Historical Coral
			2 Since the Beginning
			3 The Eye of the Idol and the Arrow of the Dead
			4 A Prayer Made of Coral
			5 Pass the Coral, I Mean the Hammer
			6 Give Me a Coral and I Will Builda City
			7 Do I Drink You or Should I Wear You?
				7.1 Take Two Corals and Call Me in the Morning
				7.2 The Metamorphic Coral
			8 The Transitional Origins of Coral
			9 Concluding Remarks
			10 Epilogue
			References
	25
		25 Framework-Forming Scleractinian Cold-Water Corals Through Space and Time: A Late Quaternary North Atlantic Perspective
			1 Framework-Forming Scleractinian Cold-Water Corals: A Brief Introduction
			2 Modern North Atlantic-Wide Distribution
			3 Environmental Controls
				3.1 Species-Specific Requirements
			4 Coral Habitats
				4.1 Corals as Habitat Provider
					4.1.1 Seamounts
					4.1.2 Canyons
					4.1.3 Mud Volcanoes
				4.2 Corals as Seafloor Modifier
				4.3 Coral Mounds
					4.3.1 Mound Formation
					4.3.2 Topographic Variety of Coral Mounds
					4.3.3 Geographical Distribution of Coral Mounds in the North Atlantic
					4.3.4 Environmental Controls of Mound Aggradation
			5 Dating Cold-Water Corals: A Key to the Past, But How to Read It?
				5.1 Data Inventory
				5.2 Spatiotemporal Distribution Pattern of North Atlantic Corals and Coral Mounds During the Last 71,000 Years
			6 Future Directions
			7 Cross-References
			References
	26
		26 Seston Quality and Available Food: Importance in the Benthic Biogeochemical Cycles
			1 Introduction
			2 What Is Seston?
			3 Where Is Seston Produced?
			4 What Can Change Seston Quality or Quantity?
				4.1 Biological Factors
				4.2 Physical Factors
				4.3 Seasonality
			5 How Do We Evaluate Seston Nutritional Quality?
				5.1 Sample Collection
				5.2 Biochemical Parameters for Seston´s Quality Evaluation
					5.2.1 Bulk Biochemical Parameters
						Bulk Organic Matter
						Carbon
						Nitrogen
					5.2.2 Specific Biochemical Parameters
						Amino Acids
						Proteins
						Carbohydrates
						Lipids
					5.2.3 Indices to Measure Seston Quality
						The C/N Index
						The Food Index
						The EHAA/THAA Index
			6 What Changes in Seston Quality Affect Communities and How?
				6.1 Changes in Activity
				6.2 Changes in Organisms Composition or Storage
			7 Conclusions and Future Perspective
			References
	27
		27 Activity Rhythm Measurement in Suspension Feeders
			1 Introduction
				1.1 Suspension-Feeding Dynamics
			2 Measuring Descriptors of Individual or Colony Activity
				2.1 Automated Analysis Systems Using Image Analysis
					2.1.1 Measuring Patches of Individuals: The Case of the Red Coral, Corallium rubrum
					2.1.2 The Case of Connected Individuals with Parazoanthus axinellae
					2.1.3 Accessing Individual Filtration Events: The Case of a Serpulid Worm Ditrupa arietina
					2.1.4 Switching of the Feeding Mode: The Case of Individual Activity of the Bivalve Abra
					2.1.5 Measuring Filtration Rates of Individuals or Patches of Mytilus with Image Analysis
					2.1.6 The Case of Individual Filtration in Mytilus galloprovincialis
				2.2 Measures with High-Speed Valvometric Sensors: Long-Term Activity Estimates Using High-Frequency Noninvasive (HFNI) Valvome...
				2.3 Measures with Mixture of Sensors
					2.3.1 Analysis Using Combined Sensors and Different Species: Case Study of the Impact of Hydroid Activity on Serpulid Recruitm...
					2.3.2 Measuring with Combined Sensors: Shell Movements in Cerastoderma edule
			3 Future Directions
			4 Cross-References
			References
	28
		28 Filter-Feeding Zoobenthos and Hydrodynamics
			1 Introduction
			2 Grazing Potential of Filter-Feeding Zoobenthos and Actual Impact
			3 Biomixing in Stagnant Water
			4 Filter Feeding and Biomixing in the Benthic Boundary Layer
			5 Filter Feeding in the Viscous Sublayer
			6 Case Study: Grazing Impact in Odense Fjord (Denmark)
			7 Conclusions
			8 Cross-References
			References
	29
		29 Energetics, Particle Capture, and Growth Dynamics of Benthic Suspension Feeders
			1 Introduction
			2 The Diversity of Suspension Feeders
				2.1 Capture Mechanisms and Structures
				2.2 The Prey Resource for Suspension Feeders
				2.3 The Role of Water Movement
			3 Energy Intake and Feeding Surface Area
				3.1 Energetic Costs for Suspension Feeders
				3.2 Competition and Energetics
			4 Energetics and Growth Models for Suspension Feeders
			5 Dynamic Energy Budget Models
				5.1 Why DEB Is an Improvement
				5.2 DEB Model: The Upper Part
				5.3 DEB Model: The Middle Part
				5.4 DEB Model: The Lower Part
				5.5 How to Account the Role of Temperature?
				5.6 The Main Model Outputs
			6 Detailed Examples of Energetics for Suspension Feeders
				6.1 Cnidaria
					6.1.1 Energy Intake
					6.1.2 Energetic Costs
					6.1.3 Symbiosis with Primary Producers
					6.1.4 The Size of Feeding Units
				6.2 Bivalve Mollusks
					6.2.1 Energy Intake
					6.2.2 Energetics Costs and Energy Budget
					6.2.3 Putting It All Together: An Example Using the DEB Approach in Modeling Mussel Distribution
				6.3 Cirripede Crustaceans
					6.3.1 Energy Intake
					6.3.2 Energetics Costs
					6.3.3 Energy Budgets and Growth
			References
	30
		30 Benthic-Pelagic Coupling: New Perspectives in the Animal Forests
			1 Introduction
			2 Epibenthic Water Layer and the Quality of Available Food
			3 Seasonality in Benthic-Pelagic Coupling Processes
			4 The Importance of the Short-Time Approach and the Activity of Benthic Organisms: Food Pulses
			5 The Return to the System
			6 Long-Term Integration of the Animal Forest Trophic Ecology: Biomarkers
			7 New Approach for C Sinks Estimation: Combining Seascape Ecology and Experimental Design
			8 Conclusion
			9 Cross-References
			References
	31
		31 Symbiotic Versus Nonsymbiotic Octocorals: Physiological and Ecological Implications
			1 Introduction
			2 Distribution of Symbiotic and Nonsymbiotic Octocorals
			3 Symbiont Acquisition and Specificity
			4 Octocoral Physiology
				4.1 Effect of Polyp Morphology and Behavior on Metabolic and Feeding Rates
				4.2 Autotrophic and Heterotrophic Contributions to the Energetic Budget
			5 Octocorals Under Climate Change
			6 Future Directions
			7 Cross-References
			References
	32
		32 Trophic Ecology and Habitat Provision in Cold-Water Coral Ecosystems
			1 Introduction
				1.1 Types of CWC Animal Forests
			2 Trophic Ecology
				2.1 Framing Environment
				2.2 Food Transport by Near-Bottom Currents
				2.3 Feeding in Cold-Water Coral Forests
			3 Cold-Water Corals as Habitat Providers and Biodiversity Hot Spots
				3.1 Sea Pen Stands
				3.2 Hard-Bottom Coral Gardens
					3.2.1 Paragorgia
					3.2.2 Primnoa Resedaeformis
						Habitat 1: Young and Live Substrate
						Habitat 2: Old and Dead Substrate
			4 Cold-Water Coral Reefs
				4.1 Habitat 1: Live Coral Zone
				4.2 Habitat 2: Dead Coral Zone
				4.3 Habitat 3: Rubble Zone
			5 Cold-Water Coral Forests as Feeding Place and Nurseries for Fish
			6 The Role of Symbionts
			7 Coral Associates in Cold Versus Warm Waters
			8 Conclusion
			9 Cross-References
			References
	33
		33 Animal Forests Through Time: Historical Data to Understand Present Changes in Marine Ecosystems
			1 Introduction
			2 Using Historical Data to Understand the Past
			3 Using Historical Data to Set Restoration Goals
			4 Using Historical Ecology to Plan for the Future
			5 Limitations of Historical Ecology
			6 Conclusion
			7 Cross-References
			References
	34
		34 Ecosystem-Based Management: Opportunities and Challenges for Application in the Ocean Forest
			1 Introduction
			2 The Ecosystem Approach in Practice: Case Histories from Australia
				2.1 Place-Based Protection: Great Barrier Reef
				2.2 Threat-Based Protection: Ecosystem Approach to Fisheries Management
				2.3 Overarching Policy Approach to Protection: Australia´s Oceans Policy
				2.4 Contrasting the Experiences
			3 Sustainable Forestry and the Ecosystem Approach
				3.1 The Socioecological Context of Uses of the Forests
				3.2 Sustainable Forestry and the Ecosystem Approach
			4 Syntheses of Case Histories and EA Principles
			5 Discussion
			6 Cross-References
			References
	35
		35 The Impact of Anthropogenic Activity on Cold-Water Corals
			1 Introduction
				1.1 Cold-Water Corals as Animal Forests
				1.2 Economic Activities with Potential to Impact Cold-Water Corals
			2 Human Activities with Potential Impacts on Cold-Water Coral Habitats
				2.1 Bottom Trawling
				2.2 Bottom-Set Longlines
				2.3 Bottom-Set Gillnets
				2.4 Pots and Traps
				2.5 Deep-Sea Mineral Mining and Disposal of Tailings from Land-Based Mines
				2.6 Oil Exploration and Production
				2.7 Litter
				2.8 Submarine Cables
				2.9 Radioactive Waste
				2.10 Elevated Carbon Dioxide in the Atmosphere and Oceans
			3 Discussion
				3.1 Spatial Extent of Human Activities
				3.2 Magnitude of Human Impacts
				3.3 Measuring Spatial Distribution of Cold-Water Coral Habitats
				3.4 Evaluating Sensitivity to Human Activities
				3.5 Cumulative Impacts
				3.6 Mitigating Human Impacts on Cold-Water Coral Habitats
				3.7 Final Remarks
			4 Cross-References
			References
	36
		36 Harvesting and Collection of Animal Forest Species
			1 Introduction
			2 The Issue of Sustainability for a Growing Marine Aquarium Trade
			3 A Shift in the Marine Aquarium Trade
			4 Case Studies of Aquarium Harvest Damage to Reefs
			5 Past Attempts at Improved Sustainability of the Marine Aquarium Trade
			6 Lack of Data Availability and Quality: A Challenge for Managers and Fishers
			7 Successes in Improving Management of Coral Harvest Fisheries
			8 Coral Fishery Management in Developed Countries
			9 Coral Fishery Management in Developing Countries
			10 Coral Aquaculture: A Sustainable Future for Coral Fisheries?
			11 Conclusion and Future Directions
			References
	37
		37 Impact of Bottom Fishing on Animal Forests: Science, Conservation, and Fisheries Management
			1 Introduction
			2 Fishing Impacts Studies: Their Strength and Limitations
			3 Fishing Impacts on ``Animal Forests´´
				3.1 Direct Impacts
				3.2 Indirect Impacts
			4 Fishing Impacts, Scaling Up the Problem
			5 Direct Management Implications from Fishing Impact Studies on ``Animal Forests´´
			6 Trawling and the Comparison to Forest Clear-Cutting: Should Trawling Be Banned ``Outright´´?
			7 Leaving the Blame Game: The Importance of Stakeholder Engagement
			8 Conclusion and Further Direction
			References
	38
		38 Genetic Connectivity and Conservation of Temperate and Cold-Water Habitat-Forming Corals
			1 Introduction
				1.1 Larval Ecology: From Dispersal to Connectivity
				1.2 Genetic Connectivity as a Conservation and Management Tool
					1.2.1 Population Genetics and Its Quantitative Descriptors
					1.2.2 Genetic Connectivity
			2 Genetic Connectivity in Temperate and Cold-Water Habitat-Forming Corals
				2.1 Population Structure and Connectivity in Scleractinian Corals
				2.2 Population Structure and Connectivity in Gorgonian Corals
			3 Genetic Connectivity in Invertebrates Associated to Temperate Biogenic Reefs
			4 Case Studies
				4.1 The Deep Cold-Water Coral Desmophyllum dianthus
				4.2 The Precious Coral Corallium rubrum
			5 Conservation and Management Applications
			6 Conclusion
			7 Future Directions
			8 Cross-References
			References
	39
		39 Contrasting Effects of Ocean Acidification on Coral Reef ``Animal Forests´´ Versus Seaweed ``Kelp Forests´´
			1 Introduction
			2 Summary of the Effects of Ocean Acidification
				2.1 Effects of Ocean Acidification on Seaweed ``Kelp Forests´´
				2.2 Effects of Ocean Acidification on Coral Reef ``Animal Forests´´
			3 Effects of Ocean Acidification on Photosynthesis and Calcification
				3.1 DIC Uptake via CCMs
				3.2 Calcification
					3.2.1 Calcification in Corals
					3.2.2 Calcification in Coralline Algae
			4 Mediating Role of the Environment: Temperature, Water Motion, Nutrients, pH Variability, and Light
				4.1 Temperature and Ocean Acidification
				4.2 Nutrients and Ocean Acidification
				4.3 Light and Ocean Acidification
				4.4 Water Motion and Ocean Acidification
				4.5 pH Variability and Ocean Acidification
			5 Conclusions and Future Directions
			6 Cross-References
			References
	40
		40 Octocoral Diseases in a Changing Ocean
			1 Introduction
			2 Historical Perspective
			3 Major Octocoral Diseases
				3.1 Temperature-Induced Bleaching (BLE)
				3.2 Aspergillosis (ASP)
				3.3 Growth Anomalies (GAN)
				3.4 Black Band Disease (BBD) and Red Band Disease (RBD)
				3.5 Fungal-Protozoan Syndrome (FPS) and Octocoral Vibrio Syndrome (OVS)
				3.6 Black Necrotic Syndrome (BNS)
				3.7 Gorgonian Labyrinthulomycosis (LAB) and Multifocal Purple Spots (MFPS)
				3.8 Octocoral Wasting Syndromes
					3.8.1 Briareum Bleaching Necrosis (BBN) and Briareum Wasting Syndrome (BWS)
					3.8.2 Erythropodium Wasting Syndrome (EWS)
					3.8.3 Gorgonia Wasting Syndrome (GWS)
					3.8.4 Phyllogorgia Wasting Syndrome (PWS)
				3.9 Other Octocoral Disease Conditions (OTH)
			4 Biological Stressors: Predation and Competition
			5 Immunity in Octocorals
			6 Management Perspectives
			References
	41
		41 Conservation and Management of Vulnerable Marine Benthic Ecosystems
			1 Introduction: Animal Forests Under Threat
			2 Protection of Key Habitat-Forming Species and Areas
			3 International Legislation to Protect Animal Forests
				3.1 Environmental Legislation
				3.2 Fisheries Legislation and Vulnerable Marine Ecosystems
			4 Broader Legal Tools for the Protection of Animal Forests
			5 Vulnerable Habitats and Animal Forests
				5.1 Not only Corals and Sponges
			6 Biodiversity, Animal Forests, and Fisheries
			7 Other Animal Forests: Dynamic and Mobile Habitats, not only Sessile Species
			8 Habitat Mapping and Management
			9 Economics and Conservation
			10 Looking to the Future
			11 Cross-References
			Annex
				Examples of national and international laws and frameworks for the protection of animal forests, as referred to in the text
			References
	42
		42 The Animal Forest and Its Socio-Ecological Connections to Land and Coastal Ecosystems
			1 Introduction
				1.1 Connectivity in Tropical Seascapes
				1.2 Global Climate Change Impacts on Animal Forests
			2 Linkages and Complexities of Social and Ecological Systems
				2.1 Transformations of the Yucatan Peninsula
					2.1.1 Conceptual Model of the Yucatn Peninsula
					2.1.2 Geological Formations Influence the Tropical Seascape
			3 Human-Derived Fluxes and Animal Forest Habitat Change
				3.1 Chemical Fluxes
					3.1.1 Water Quality and Nutrient Inputs
				3.2 Biological Fluxes
					3.2.1 Phase Shifts
					3.2.2 Loss of Tropical Wetlands
				3.3 Physical Fluxes
					3.3.1 Coastline Modifications
			4 Management and Conservation of the Animal Forest and Tropical Seascapes
				4.1 Social Inclusion in the Management of Marine Protected Areas
				4.2 Current and Future Management Tools
				4.3 Governance to Improve the Management of Seascape Connectivity
			5 Conclusions
			6 Cross-References
			References
	43
		43 Resilience of the Marine Animal Forest: Lessons from Maldivian Coral Reefs After the Mass Mortality of 1998
			1 Introduction
			2 Recruitment
			3 Colony Density and Size
			4 Colony Health
			5 Cover
			6 Diversity
			7 Community Composition
			8 Trophic Organization
			9 Structural Complexity
			10 Constructional Capacity
			11 Seascape
			12 Final Remarks and Recommendations
			13 Cross-References
			References
	44
		44 Ecosystem Functions and Services of the Marine Animal Forests
			1 Introduction
			2 From Natural Capital to Well-Being: A Pathway From Nature to Humans
			3 Functions of Animal Forests
				3.1 Regulation Functions
				3.2 Habitat Functions
				3.3 Production Functions
				3.4 Information Functions
			4 From Functions to Ecosystem Services and Well-Being
			5 Services From Animal Forests
				5.1 Regulating Services
				5.2 Provisioning Services
				5.3 Habitat Services
				5.4 Information Services
			6 The Measure of Ecosystem Services
				6.1 The Concept of Value
			7 Classical Methods for Ecosystem Services Valuation: A Brief Review
			8 System Methodologies for Ecological Valuation
			9 Emergy and Ecosystem Services Valuation
			10 The Economic Value of Animal Forests
			11 Conclusions and Future Directions
			References
	45
		45 Restoration of the Animal Forests: Harnessing Silviculture Biodiversity Concepts for Coral Transplantation
			1 Introduction
			2 Farmed Coral Transplantation: Aims and Recent Advances
			3 Addressing Biodiversity Concerns in Coral Transplantation: A Take-Home Lesson from Silviculture
				3.1 Genetic Diversity
				3.2 Species Diversity
				3.3 Ecosystem Diversity: Structural Complexity and Habitat Diversity
			4 The Reefs of Tomorrow: Successful Restoration in an Uncertain Future
			5 Cross-References
			References