Preface ........................................................ xi
Acknowledgments and Dedication ................................. xv
CHAPTER 1 Introduction
The Origin of Life: Microcosm Earth ............................. 2
Microcosms and Mesocosms of Aquatic Ecosystems .................. 5
Restoration of Damaged Ecological Systems ....................... 8
Summary ......................................................... 8
Taxonomic Notes ................................................. 8
References ...................................................... 9
PART I PHYSICAL ENVIRONMENT
CHAPTER 2 The Envelope: Physical Parameters and Energy
State
Temperature .................................................... 17
Water Motion ................................................... 23
Tides: Simulating the Effects of Sun and Moon .................. 35
References ..................................................... 41
CHAPTER 3 Substrate: The Active Role of Rock, Mud, and Sand
The Solid Earth and Life ....................................... 44
Chemical Relationships Between Rocks, Sea Water, and
Organisms ................................................... 48
The Solid Earth, Rock, and Model Ecosystems .................... 50
Sediments and Model Ecosystems ................................. 51
Geological Storage ............................................. 59
References ..................................................... 60
CHAPTER 4 Water Composition: Management of Salinity,
Hardness, and Evaporation
Water Structure and Characteristics ............................ 62
Ocean Salinity ................................................. 63
Hardness of Fresh Waters ....................................... 67
Water and Model Ecosystems ..................................... 71
Algal Scrubbing and Water Composition .......................... 71
Marine Microcosms and Aquaria .................................. 72
Quality of Top-up Water ........................................ 73
References ..................................................... 73
CHAPTER 5 The Input of Solar Energy: Lighting Requirements
Photosynthesis and Its Origin .................................. 75
Solar Radiation and Water ...................................... 79
Light Absorption by Water Plants ............................... 82
Light Intensity and Plants ..................................... 82
Photorespiration ............................................... 88
Light and Model Ecosystems ..................................... 89
Light and Physiological Considerations Summary ................. 91
References ..................................................... 92
CHAPTER 6 The Input of Organic Energy: Particulates and
Feeding
Particulates, Energy Supply, and Aquatic Ecosystems ............ 93
Inorganic Particulates ......................................... 95
Organic Particulates ........................................... 95
Humic Substance ................................................ 97
Particulates and Aquatic Models ................................ 97
Biofilms ....................................................... 98
Particulate Import in Aquatic Models .......................... 100
Aquatic Ecosystem Restoration ................................. 100
References .................................................... 100
PART II BIOCHEMICAL ENVIRONMENT
CHAPTER 7 Metabolism: Respiration, Photosynthesis, and
Biological Loading
Metabolism .................................................... 105
Respiration ................................................... 106
Bacterial Metabolism .......................................... 110
Photosynthesis ................................................ 112
Biological Loading ............................................ 114
References .................................................... 115
CHAPTER 8 Organisms and Gas Exchange: Oxygen, Carbon
Dioxide, pH, and Alkalinity
Oxygen Exchange ............................................... 118
Oxygen, Model Ecosystems, and Ecosystem Restoration ........... 120
Carbon Dioxide Exchange ....................................... 121
Carbon Dioxide and Global Aquatic Restoration ................. 122
Managing Carbon Dioxide and pH in Microcosms and Mesocosms .... 124
Gas Exchange and Selected Model Ecosystems .................... 125
References .................................................... 128
CHAPTER 9 The Primary Nutrients - Nitrogen, Phosphorus,
and Silica: Limitation and Eutrophication
Nutrients in Natural Waters ................................... 131
Eutrophication and Hypereutrophication of Natural Waters ...... 134
Nutrients and Model Ecosystems ................................ 136
Summary ....................................................... 139
References .................................................... 140
CHAPTER 10 Biomineralization and Calcification: A Key to
Biosphere and Ecosystem Function
The Process of Biomineralization .............................. 143
The Carbonate System and the Formation of Calcite and
Aragonite ..................................................... 143
Halimeda: Photosynthesis-Induced Calcification ................ 145
Calcification in Stony Corals ................................. 146
Calcification, Stony Corals, Coral Reefs, and Global
Warming .................................................... 148
Calcification in Mesocosms and Aquaria ........................ 150
Coral Reef Aquaria and Stony Coral Calcification .............. 151
References .................................................... 154
CHAPTER 11 Control of the Biochemical Environment: Filters,
Bacteria, and the Algal Turf Scrubber
Sterilization Methods ......................................... 156
Bacteriological Filtration .................................... 156
Reef Systems .................................................. 157
Denitrification ............................................... 157
Foam Fractionation (Protein Skimming) Photosynthetic
Methods .................................................... 158
Algal Turfs ................................................... 159
The Algal Turf Scrubber (ATSTM) ............................... 161
Algal Scrubbers and the Modeling of Ecosystems ................ 165
Summary ....................................................... 168
References .................................................... 169
Part III BIOLOGICAL STRUCTURE
CHAPTER 12 Community Structure: Biodiversity in Model
Ecosystems
The Framework of Biodiversity ................................. 173
The Community ................................................. 175
The Biome ..................................................... 175
Features of Communities ....................................... 181
The Magnitude of Biodiversity ................................. 183
Community Structure and Ecological Models Scaling and
Reproduction .................................................. 186
Model Diversity ............................................... 187
Summary ....................................................... 189
References .................................................... 189
CHAPTER 13 Trophic Structure: Ecosystems and the Dynamics
of Food Chains
Energy Capture and Flow ....................................... 192
Food Webs ..................................................... 193
Food Webs in Model Ecosystems ................................. 195
Establishment of Food Webs .................................... 196
Trophic Structure in Aquaria .................................. 201
The Organisms ................................................. 202
References .................................................... 202
CHAPTER 14 Primary Producers: Plants That Grow on the Bottom
Benthic Algae ................................................. 203
Algae in Model Ecosystems ..................................... 219
Submerged Aquatic Vegetation .................................. 222
Marine SAV and Model Ecosystems ............................... 229
Freshwater SAV and Model Ecosystems ........................... 231
Emergent Aquatic Vegetation ................................... 234
EAV and Model Ecosystems ...................................... 242
Plant Communities and the Restoration of Wild Ecosystems ...... 250
References .................................................... 251
CHAPTER 15 Herbivores: Predators of Plants and Omnivores,
Predators of Plants and Animals
Types of Herbivores ........................................... 254
Plant Defenses ................................................ 256
Modifications of Marine and Freshwater Herbivores ............. 257
Herbivores and Model Ecosystems ............................... 263
References .................................................... 265
CHAPTER 16 Carnivores: Predators of Animals
The Carnivore Predator ........................................ 267
The Prey ...................................................... 268
The Dynamics of Predation ..................................... 269
Marine and Freshwater Predators ............................... 269
Predators and Synthetic Ecosystems ............................ 275
References .................................................... 279
CHAPTER 17 Plankton and Planktivores: Floating Plants and
Animals and Their Predators
Plankton Size and Composition ................................. 282
The Bacteria .................................................. 282
Phytoplankton ................................................. 282
The Planktonic Food Web ....................................... 286
Mechanisms of Filter Feeding .................................. 288
Plankton, Particulates, and Model Ecosystems .................. 293
Wild Ecosystem Restoration .................................... 300
References .................................................... 302
CHAPTER 18 Detritus and Detritivores: The Dynamics of Muddy
Bottoms
The Deep Ocean ................................................ 307
Bacteria ...................................................... 307
Fungi ......................................................... 307
Protozoa ...................................................... 309
Meiobenthos: Protozoans ....................................... 309
Meiofauna: The Multicellular Invertebrates .................... 311
Macrobenthos .................................................. 313
Deposit Feeding in Saltwater Soft Bottoms ..................... 317
Deposit Feeding in Freshwater Soft Bottoms .................... 319
Carnivores and the Detritivore Community ...................... 321
Detritus and Its Role in Model Ecosystems ..................... 321
References .................................................... 327
CHAPTER 19 Symbionts and Other Feeders
Zooxanthellae and Their Animal Hosts .......................... 329
Biology and Ecology of Corals ................................. 332
The Positive Feedback Loop between Photosynthesis and
Calcification ................................................. 334
Anthozoans and Microcosms, Mesocosms, and Aquaria ............. 335
Parasitism .................................................... 336
Environment, General Health, and Disease ...................... 337
Biodiversity .................................................. 337
Quarantine (Prevention of Transmission) ....................... 337
Disease Treatment in Model Ecosystems ......................... 338
References .................................................... 339
Part IV ECOLOGICAL SYSTEMS IN MICROCOSMS, MESOCOSMS,
AND AQUARIA
CHAPTER 20 Models of Coral Reef Ecosystems
Modeling Coral Reef Ecosystems ................................ 344
Caribbean Coral Reef Microcosm at the Museum of Natural
History ....................................................... 345
Coral Reef Microcosm at the Smithsonian Marine Station ........ 353
Great Barrier Reef Mesocosm ................................... 353
A 130-Gallon Reef Microcosm ................................... 356
Summary ....................................................... 368
References .................................................... 368
CHAPTER 21 A Subarctic/Boreal Microcosm: Test of
a Biogeographic Model The Rocky, Embayed Coast of
the Northwestern
Atlantic Geological History ................................... 371
The Gulf of Maine ............................................. 376
The Core Subarctic ............................................ 387
Core Subarctic vs Mixed Subarctic/Boreal ...................... 393
A Maine Shore Microcosm ....................................... 395
An Opportunity to Test Biogeographic Theory ................... 403
References .................................................... 404
CHAPTER 22 Estuaries: Ecosystem Modeling and Restoration
Where Fresh and Salt Waters Interact .......................... 405
Chesapeake Bay in Mesocosm .................................... 406
A Florida Estuary in Mesocosm ................................. 416
Nutrient Dynamics in Estuarine Models ......................... 439
Estuarine Restoration ......................................... 439
References .................................................... 441
CHAPTER 23 Freshwater Ecosystem Models
A Florida Everglades Stream and Wetland ....................... 443
A Blackwater Home Aquarium .................................... 450
Restoration of Freshwater Ecosystems .......................... 452
References .................................................... 452
PART V THE ENVIRONMENT AND ECOLOGICAL ENGINEERING
CHAPTER 24 Organisms and Natural Products: Commercial
Ecosystem Culture
The Aquarium World ............................................ 458
Pharmaceutical Culture ........................................ 462
References .................................................... 463
Nutrient Removal from Agricultural Wastewaters (Nonpoint
Source) ....................................................... 474
Nutrient Removal from Rivers .................................. 479
Bioenergy and Solar Energy Recovery Using ATS Systems ......... 480
Aquacultural Wastewaters ...................................... 481
Industrial Wastewaters and ATS Systems ........................ 484
References .................................................... 489
CHAPTER 25 Large Scale: Water Quality Management with Solar
Energy Capture
The Quality of US Surface and Ground Waters ................... 467
Nutrient Removal from Domestic Wastewaters .................... 468
PART VI SUMMARY
CHAPTER 26 Microcosms, Mesocosms, and Macrocosms: Building
and Restoring Ecosystems, a Synthesis
Principles of Ecological Modeling ............................. 494
Ecosystems in Home Aquaria .................................... 498
Applied Model Ecosystems ...................................... 499
References .................................................... 499
Index ......................................................... 501
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