Cover	1
	Title Page	5
	Copyright Page	6
	Contents	9
	Preface	11
	Acknowledgments	12
	List of Contributors	13
	Chapter 1 Introduction to Estuarine Ecology	17
	1.1 Background, Theory, and Issues	17
	1.2 Definitions, Terms, and Objectives	20
	1.2.1 Definitions of Estuary and Ecology, and Difficulties in Applying These Definitions to Estuaries	20
	1.3 Three Views of a Generalized Estuary	22
	1.3.1 Top view	22
	1.3.2 Cross-Section View	23
	1.3.3 Longitudinal Section	24
	1.4 Estuarine Food Webs and Energy Flow	24
	1.5 The Ever-Changing Dynamic Properties of an Estuary	26
	1.6 High Productivity: An Estuarine Focal Point	27
	1.6.1 Reasons for High Estuarine Primary Productivity	27
	1.6.2 Other Important Hypotheses about Estuarine Ecology	28
	1.7 Human Impacts and Management of Estuarine Ecosystems	28
	1.8 The Potential Impacts of Future Trends on Estuarine Ecosystems	29
	1.9 How We Will Proceed Through the Book	30
	Further Reading	30
	References	30
	Chapter 2 Estuarine Geomorphology, Circulation, and Mixing	32
	2.1 Introduction	32
	2.2 Glaciation Cycles	32
	2.3 Definition	33
	2.4 Classification of Estuaries	33
	2.4.1 Geomorphic Classification	33
	2.4.2 Water Balance Classification and Gravitational Circulation	38
	2.4.3 Classification by Salinity Stratification	39
	2.4.4 Classification Based on Dynamics	41
	2.4.5 Characterizing Conditions with Reynolds and Richardson Numbers	42
	2.5 Tidal Circulation	44
	2.6 Wind-Driven Circulation	45
	2.7 Concluding Remarks	46
	Review Questions	48
	References	49
	Chapter 3 Estuarine Chemistry	52
	3.1 Basics in Biogeochemical Cycles and Chemical Principles	52
	3.1.1 Linking Estuarine Chemistry with Estuarine Ecology	52
	3.1.2 Global Biogeochemistry	52
	3.1.3 Thermodynamics and Kinetics	53
	3.1.4 Redox Chemistry	54
	3.2 Mixing and Particle Effects on the Chemistry of Estuarine Waters	54
	3.2.1 Reactivity of Dissolved Constituents	54
	3.2.2 Sources and Mixing of Dissolved Salts in Estuaries	56
	3.2.3 Measurement of Salinity	57
	3.2.4 Dissolved Gases and Atmosphere–Water Exchange	57
	3.2.5 Dissolved CO2 and Carbonate Chemistry	59
	3.2.6 Effects of Suspended Particulates and Chemical Interactions	59
	3.2.7 Estuarine Turbidity Maximum, Benthic Boundary Layer, and Fluid Muds	61
	3.3 Biogeochemistry of Organic Matter	61
	3.3.1 Particulate and Dissolved Organic Matter in Estuaries	61
	3.3.2 Decomposition of Organic Detritus	63
	3.3.3 Early Diagenesis	64
	3.3.4 Characterization of Organic Matter Using Biomarker Techniques	65
	3.4 Macronutrient Cycling	66
	3.4.1 Sources of Nitrogen in Estuaries	66
	3.4.2 Transformations of Inorganic and Organic Nitrogen	68
	3.4.3 Sediment–Water Exchange of Dissolved Nitrogen	70
	3.4.4 Sources of Phosphorus to Estuaries	71
	3.4.5 Phosphorus Fluxes Across the Sediment–Water Interface	72
	3.4.6 Cycling of Inorganic and Organic Phosphorus	73
	3.4.7 Sources of Silica to Estuaries	73
	3.4.8 Cycling of Silica	74
	3.4.9 Sources of Sulfur to Estuaries	74
	3.4.10 Transformations of Inorganic and Organic Sulfur	75
	3.4.11 Sulfur at the Sediment–Water Interface	76
	3.4.12 Carbon Cycling in Estuaries	77
	3.4.13 Transformations and Cycling of Dissolved and Particulate Organic Carbon (DOC and POC)	78
	3.5 Concluding Remarks	80
	Review Questions	81
	References	82
	Chapter 4 Estuarine Phytoplankton	94
	4.1 Introduction	94
	4.2 The Players: Phytoplankton Community Composition and Function	95
	4.2.1 Cyanobacteria	96
	4.2.2 Green Algae	96
	4.2.3 Cryptophytes	97
	4.2.4 Chrysophytes	97
	4.2.5 Diatoms	97
	4.2.6 Prymnesiophytes	98
	4.2.7 Dinoflagellates	98
	4.2.8 Assessing Phytoplankton Communities	99
	4.3 Spatial and Temporal Patterns of Phytoplankton Biomass and Productivity	101
	4.4 Factors Controlling Phytoplankton Productivity and Community Composition	104
	4.4.1 Light	104
	4.4.2 Nutrients	105
	4.4.3 Temperature	107
	4.4.4 “Top Down” Control: Herbivory	107
	4.5 Human and Climatic Impacts on Coastal Phytoplankton Dynamics	108
	4.5.1 Effects of Nutrient Over-Enrichment on Estuarine Phytoplankton	108
	4.5.2 The Roles of Climatic Variability in Eutrophication Dynamics	108
	4.6 Harmful Algal Blooms (HABs)	111
	4.7 Nutrient Management of Phytoplankton Production and Composition	111
	Acknowledgments	115
	Review Questions	115
	References	116
	Chapter 5 Estuarine Seagrasses	122
	5.1 Introduction	122
	5.2 Diversity and Global Distribution	123
	5.3 Biomass and Productivity	124
	5.4 Factors Controlling Productivity and Community Composition	126
	5.4.1 Light	127
	5.4.2 Temperature	127
	5.4.3 Salinity	128
	5.4.4 Nutrients	128
	5.4.5 Inorganic Carbon	129
	5.4.6 Oxygen and Sulfide Dynamics	129
	5.5 Ecosystem Benefits	130
	5.5.1 Consequences of Physical Effects on Water Movement	130
	5.5.2 Biogeochemical Effects	131
	5.5.3 Submersed Plants as Food and Habitat	132
	5.5.4 Ecosystem Services	133
	5.6 Human Impacts and Management	134
	Review Questions	136
	References	137
	Chapter 6 Coastal Marshes	142
	6.1 Introduction	142
	6.2 Diversity, Zonation, and Global Distribution	142
	6.2.1 General Features and Typology of Coastal Marshes	142
	6.2.2 Distribution and Zonation of Coastal Marshes	144
	6.3 Patterns and Processes Controlling Structure, Biomass, and Productivity	148
	6.3.1 The Effect of Measurement Method on Productivity Results	150
	6.3.2 Factors Affecting Marsh Productivity	150
	6.3.3 Top-down Control of Marsh Vegetation	153
	6.3.4 Factors Affecting Marsh Accretion and Habitat Change	155
	6.4 Carbon Dynamics and Greenhouse Gas Emissions in Coastal Marshes	156
	6.4.1 Decomposition of Organic Matter in Coastal Marshes	157
	6.4.2 Greenhouse Gas Emissions	157
	6.5 Human Impacts, Management, and Assessment of Coastal Marshes	158
	6.5.1 Upstream Alterations	159
	6.5.2 Functions and Values of Coastal Marshes	160
	6.5.3 Indicators of Coastal Marsh Stability and Productivity	160
	Study Questions	162
	References	163
	Chapter 7 Mangrove Wetlands	169
	7.1 Introduction	169
	7.2 Biogeography	170
	7.2.1 Diversity	170
	7.2.2 Global Patterns	170
	7.3 Ecogeomorphology and Ecosystem Processes	172
	7.3.1 Hierarchy of Ecosystem Patterns	173
	7.3.2 Biomass and Productivity	174
	7.3.3 Litter Dynamics and Export	177
	7.3.4 Mangrove Food Webs	178
	7.3.5 Net Ecosystem Productivity and Nutrient Biogeochemistry	178
	7.4 Factors Controlling Productivity and Distribution	181
	7.4.1 Hydroperiod and Waterlogged Soils	181
	7.4.2 Resources and Regulators	182
	7.4.3 Vivipary	184
	7.5 Human Impacts, Conservation, and Carbon Sequestration	185
	7.5.1 Human Exploitation	185
	7.5.2 Biodiversity	187
	7.5.3 Mangroves as Invasive Species	187
	7.5.4 Sea Level Rise	187
	7.5.5 Mangroves as Blue Carbon Ecosystems	188
	Study Questions	189
	References	191
	Chapter 8 Estuarine Benthic Algae	197
	8.1 Introduction	197
	8.2 Taxonomy	197
	8.3 Functional Forms	199
	8.4 Habitats	201
	8.4.1 Soft-bottom: Mud/Sandflats, Seagrass Beds, and Marshes	201
	8.4.2 Hard-bottom: Rocky Intertidal, Shallow Subtidal	201
	8.4.3 Coral Reefs	202
	8.5 Spatial Patterns of Biomass and Productivity	202
	8.5.1 Broad Geographic Scale—Latitudinal Differences	202
	8.5.2 Depth Distribution	203
	8.5.3 Energy Regime	203
	8.5.4 Diel Cycle	204
	8.5.5 Seasonal Cycle	204
	8.6 Methods for Determining Productivity	206
	8.7 Factors Regulating Productivity and Community Composition	208
	8.7.1 Light	208
	8.7.2 Nutrients	208
	8.7.3 Grazing	210
	8.8 Energy Flow	211
	8.8.1 Recycling of Nutrients	211
	8.8.2 Carbon Storage	211
	8.8.3 Herbivory	212
	8.8.4 Detrital Pathway	212
	8.8.5 Dissolved Organic Carbon	212
	8.8.6 Export of Carbon	212
	8.9 Feedbacks and Interactions	213
	8.9.1 Feedbacks on Biogeochemical Cycling in Soft Sediment Estuaries	213
	8.9.2 Feedbacks on Sediment Stabilization	214
	8.9.3 Effects on Faunal Biomass, Diversity, and Abundance	214
	8.9.4 Facilitation by Fauna	214
	8.9.5 Competition Between Benthic Algal Primary Producers	215
	8.9.6 Interactions with Marine Diseases	216
	8.10 Human Impacts	216
	8.10.1 Eutrophication	216
	8.10.2 Invasions	217
	8.10.3 Climate Change	219
	Study Questions	220
	References	221
	Chapter 9 Estuarine Microbial Ecology	229
	9.1 Introduction	229
	9.2 Diversity and Global Distribution in Estuaries	229
	9.2.1 Bacteria and Archaea	231
	9.2.2 Protists	233
	9.2.3 Fungi	233
	9.2.4 Viruses	234
	9.3 Factors Controlling Productivity and Community Composition	234
	9.3.1 Microbial Food Webs	234
	9.3.2 Organic Carbon Decomposition and Trophic Dynamics	235
	9.3.3 Microbes and Productivity	237
	9.3.4 Environmental Factors Affecting Microbial Communities	237
	9.4 Metabolic Diversity and Element Cycling	238
	9.4.1 Carbon Fixation and Mineralization	239
	9.4.2 Nitrogen Cycling	240
	9.4.3 Sulfur Cycling	241
	9.4.4 Iron and Manganese Cycling	243
	9.4.5 Phosphorous Cycling	243
	9.5 Summary	244
	Review Questions	244
	References	246
	Chapter 10 Estuarine Zooplankton	251
	10.1 Introduction	251
	10.1.1 Why Is this Important	251
	10.1.2 Key Concepts and Definitions	251
	10.1.3 Brief Description of Tools and Approaches (Nets, Acoustics & Optics, Models)	253
	10.2 Diversity and Global Distribution in Estuaries	254
	10.3 Spatial and Temporal Patterns of Biomass and Productivity	256
	10.3.1 Spatial Patterns of Biomass	256
	10.3.2 Temporal Patterns in Biomass and Production	257
	10.4 Factors Controlling Productivity and Community Composition	257
	10.4.1 Physiological Challenges for Zooplankton in Estuaries	257
	10.4.2 Trophic Interactions	259
	10.5 Special Topics Unique to Zooplankton	262
	10.5.1 Recruitment	262
	10.5.2 Introduced Species	263
	10.5.3 Eutrophication and Deoxygenation	264
	10.5.4 Pollutants	264
	10.5.5 Freshwater Diversions and Dams	265
	Questions	265
	Further Reading	266
	References	266
	Chapter 11 Estuarine Benthos	269
	11.1 Introduction	269
	11.1.1 Sampling	271
	11.2 Diversity and Global Distribution in Estuaries	273
	11.3 Spatial and Temporal Patterns of Abundance, Biomass, and Productivity	274
	11.4 Factors Controlling Productivity and Community Composition	276
	11.4.1 Salinity	276
	11.4.2 Effects of Oxygen	277
	11.4.3 Substrate–Benthos Relationships	279
	11.4.4 Plant–Benthos Interactions	279
	11.4.5 Recruitment and Planktonic Dispersal	280
	11.4.6 Density-Dependent Controls and Population Cycles	281
	11.4.7 Top-Down and Bottom-Up Controls	282
	11.5 Special Topics for Estuarine Benthos	283
	11.5.1 Human Impacts on Estuarine Benthos	283
	11.5.2 Invasive Species	286
	Study Questions	287
	References	288
	Chapter 12 Estuarine Nekton	290
	12.1 Introduction	290
	12.2 Diversity and Global Distribution in Estuaries	291
	12.2.1 Physiological Adaptations to Environmental Conditions	291
	12.2.2 Behavioral Adaptations to Environmental Conditions	293
	12.2.3 Physiological Feeding Adaptations	294
	12.2.4 Behavioral Feeding Adaptations	294
	12.2.5 Nekton Diets and Food Webs	295
	12.3 Spatial and Temporal Patterns of Biomass and Productivity	297
	12.3.1 Habitat Usage	297
	12.3.2 Habitat-Specific Use: Functional Relationships	298
	12.3.3 Life History Strategies	299
	12.4 Factors Controlling Productivity and Community Composition	301
	12.4.1 Year Class Success	301
	12.4.2 Survival and Growth	302
	12.4.3 Biotic and Abiotic Factors	303
	Review Questions	305
	References	306
	Chapter 13 Estuarine Wildlife	308
	13.1 Introduction	308
	13.2 Patterns of Diversity	309
	13.2.1 The Players	309
	13.2.2 Diversity	311
	13.2.3 Endemism and Specialization	312
	13.3 Temporal and Spatial Patterns in Biomass and Productivity	314
	13.3.1 Time	314
	13.3.2 Space	316
	13.4 Species Interactions Affecting Productivity and Community Composition	316
	13.4.1 Herbivory	317
	13.4.2 Predation	318
	13.4.3 Competition	319
	13.4.4 Disease	320
	13.5 Human Effects on Estuarine Wildlife	321
	13.5.1 Sea Level Rise and Climate Change	321
	13.5.2 Habitat Conversion and Fragmentation	321
	13.5.3 Invasive Species	322
	13.5.4 Pollution	323
	13.5.5 Hunting and Disturbance	323
	13.5.6 Management of Estuaries for Wildlife	324
	Acknowledgments	324
	Study Questions	325
	References	326
	Chapter 14 Estuarine Ecosystem Metabolism	329
	14.1 Introduction	329
	14.2 Basic Definitions and Concepts	330
	14.3 Approaches for Estimating Ecosystem Metabolism	333
	14.3.1 Measuring Components of Ecosystem Metabolism	333
	14.3.2 Direct Air-Ecosystem Gas Exchange	336
	14.3.3 Open Water Measurements	339
	14.3.4 Input-Output Budgets	340
	14.3.5 Transport-Transformation Models	340
	14.4 Regulating Factors and Spatial and Temporal Patterns	340
	14.4.1 Light and Water Clarity	341
	14.4.2 Temperature	342
	14.4.3 Inorganic Nutrient and Organic Matter Inputs and Toxic Contaminants	342
	14.4.4 Exchanges of Organic Matter within Ecosystems	344
	14.4.5 River Flow, Flushing, and Wind	344
	14.4.6 Water Depth	345
	14.5 Ecosystem Metabolism Applications and Case Studies	347
	14.5.1 Tomales Bay	347
	14.5.2 Parker River-Plum Island Sound	347
	14.5.3 Chesapeake Bay System	352
	14.5.4 Scheldt Estuary	354
	14.6 Cross-Ecosystem Comparisons	356
	14.6.1 Trophic State and Dominant Controls	356
	14.6.2 Eutrophication Effects on Metabolism	356
	14.6.3 Coastal Ecosystems and Global Carbon Balance	357
	14.6.4 Estuaries and Blue Carbon Sequestration	358
	14.7 Metabolic Responses to Climate Change and Variability	361
	14.8 Summary and Conclusions	361
	Acknowledgements	362
	Study Questions	362
	References	363
	Chapter 15 Estuarine Food Webs	369
	15.1 Introduction	369
	15.1.1 Food Chains and Food Webs	370
	15.1.2 Functional Groups and Trophic Guilds	371
	15.1.3 Trophic Efficiencies	372
	15.1.4 Food Chain Length	373
	15.2 Portraying Food Webs	374
	15.2.1 Ecological Pyramids	374
	15.2.2 Projecting Food Webs to Food Chains	374
	15.2.3 Trophic Spectra	375
	15.2.4 Biomass Body-Size Spectra	375
	15.3 Trophic Theory	377
	15.3.1 Direct Trophic Interactions	377
	15.3.2 Indirect Trophic Interactions	377
	15.3.3 Trophic Cascades	378
	15.4 Attributes of Estuarine Food Webs	379
	15.4.1 Spatial Mosaic of Coastal Habitats	379
	15.4.2 The Importance of Detritus	379
	15.5 Constructing Food Web Models	380
	15.5.1 Choosing the Appropriate Scale and Currency	381
	15.5.2 Composition of the Food Web (Nodes)	381
	15.5.3 Organism Abundance and Biomass	382
	15.5.4 Bioenergetic Rates	382
	15.5.5 Food Habits	382
	15.5.6 Stable Isotopes in Estuarine Food Webs	383
	15.6 Quantitative Analysis of Food Web Network Models	386
	15.6.1 Mass Balance in Food Web Networks	387
	15.6.2 Total System Properties	387
	15.6.3 Trophic Structure	388
	15.6.4 Indirect Interactions	388
	15.6.5 Dynamic Simulation of Food Webs	389
	15.7 Estuarine Food Webs in a Changing Climate	389
	15.8 Summary	390
	Review Questions	391
	References	391
	Chapter 16 Estuarine Ecological Modeling	396
	16.1 Introduction	396
	16.2 Classes of Models	397
	16.3 Developing and Using Mechanistic models	398
	16.3.1 Step 1: Defining the Question	399
	16.3.2 Step 2: Conceptualization	400
	16.3.3 Step 3: Formalization	400
	16.3.4 Step 4: Implementation	400
	16.3.5 Step 5: Parameterization	401
	16.3.6 Step 6: Validation	401
	16.3.7 Step 7: Analysis	403
	16.3.8 Going Through the Steps	403
	16.4 Example 1: Gulf of Mexico Hypoxia	403
	16.4.1 Defining the Question	403
	16.4.2 Simple Two-layer Hypoxia Model	404
	16.4.3 Complex 3D-CoupledHydrodynamic–BiogeochemicalModel	407
	16.4.4 Conclusions from Both Models	410
	16.5 Example 2: Marsh Habitat and Brown Shrimp Production	412
	16.5.1 Defining the Question	412
	16.5.2 Conceptualization	413
	16.5.3 Formalization and Implementation	413
	16.5.4 Parametrization and Validation	416
	16.5.5 Analysis	417
	16.5.6 Conclusions	418
	16.6 Example 3: Coastal Habitat Under Sea Level Rise	418
	16.6.1 Defining the Question	418
	16.6.2 Conceptualization	418
	16.6.3 Formalization and Implementation	420
	16.6.4 Parameterization and Validation	421
	16.6.5 Analysis	421
	16.6.6 Conclusions	423
	16.7 Some Important Concepts from the Examples	424
	16.8 The Future	425
	16.9 Further Reading: Getting Started	425
	Review Questions	426
	References	426
	Chapter 17 Estuarine Fisheries and Aquaculture	430
	17.1 Introduction	430
	17.2 Estuarine Yield	431
	17.2.1 Global Patterns	432
	17.2.2 Physical, Biological, and Evolutionary Drivers	432
	17.3 Fish Population Dynamics and Its Four Factors	433
	17.3.1 Russell’s Axiom	434
	17.3.2 Growth of Fishes	434
	17.3.3 Natural Mortality	436
	17.3.4 Fishing Mortality and Catch-per-unit-effort	437
	17.3.5 Recruitment	439
	17.4 Management of Estuarine Fisheries and Aquaculture	441
	17.4.1 Fisheries Management	441
	17.4.2 Aquaculture Management	444
	17.4.3 Future Challenges	446
	17.5 Summary	447
	Review Questions	447
	References	449
	Chapter 18 Global Climate Change and Estuarine Systems	455
	18.1 Introduction	455
	18.2 Climate Change: Historic Patterns and Projections	457
	18.2.1 Historic Patterns and Projections	457
	18.2.2 Temperature	458
	18.2.3 Sea Level Rise (Eustatic and Relative)	458
	18.2.4 Changes in Storm Frequency and Intensity	459
	18.2.5 Freshwater Input, Sediment Transport, and Nutrient Delivery	460
	18.3 Effects of Climate Change on Estuarine Ecosystems	460
	18.3.1 Temperature	460
	18.3.2 Accelerated Sea Level Rise	461
	18.3.3 Modeling the Effects of Sea Level Rise on Estuarine Marshes	463
	18.3.4 Impacts of Changes in Freshwater Input on Coastal Ecosystems	464
	18.3.5 Storms and Extreme Weather Events	465
	18.3.6 Ocean Acidification	465
	18.4 Human Activity and Coastal Management Implications	465
	18.5 Coastal Wetlands for Climate Change Mitigation: Blue Carbon	467
	18.6 Summary	468
	Study Questions	469
	References	470
	Appendix 1 Multiple Choice Question Answers	474
	Index	475
	EULA	483