Andrew J. Boulton, University of New England, Armidale, Australia

Margaret A. Brock, University of Tasmania, Tasmania, Australia

Belinda J. Robson, Murdoch University, Murdoch, Australia

Darren S. Ryder, University of New England, Armidale, Australia

Jane M. Chambers, Murdoch University, Murdoch, Australia

Jenny A. Davis, University of Canberra, Canberra, Australia

About the companion website, xii

PART I: PROCESSES IN AQUATIC ECOSYSTEMS, 1

1 Australian waters: diverse, variable and valuable, 3

1.1 The challenge for aquatic ecologists, 3

1.2 Defi ning some common terms, 6

1.3 Australian inland waters: their diversity and distribution, 6

1.4 The water regime: ‘where, when and to what extent water is present’, 7

1.4.1 Water budgets, scale issues and human influences on water regimes, 7

1.4.2 Components of the water regime, 8

1.4.3 Water regime variability, 9

1.5 Linkages in aquatic ecosystems: from molecular bonds to global exchanges, 11

1.5.1 Wonderful water and its molecular linkages, 11

1.5.2 Linkages at the catchment scale, 12

1.5.3 Linkages at the global scale: the hydrological cycle, 13

1.5.4 Continental linkages and surface waters in Australia, 15

1.5.5 Continental linkages and groundwaters in Australia, 19

1.6 The structure of this book, 20

2 Physical processes in standing waters, 21

2.1 Depth and physical processes, 21

2.2 Let there be light ..., 21

2.2.1 Light reaching the water surface, 21

2.2.2 Light below the water surface, 22

2.2.3 Seeing through water: Secchi discs and quantum sensors, 24

2.3 The euphotic zone, 24

2.4 Light and life, 25

2.5 Temperature and stratification, 25

2.5.1 Causes of stratifi cation, 26

2.6 Using circulation patterns to classify standing waters, 27

2.7 Ecological implications of the different types of stratifi cation and mixing, 29

2.8 Deep versus shallow standing waters: depth matters, 31

2.8.1 How deep standing waters form, 32

2.8.2 How shallow standing waters form, 32

2.9 Synthesis, 35

3 Chemical processes in standing waters, 37

3.1 ‘There’s a certain chemistry ...’, 37

3.2 Dissolved gases, 37

3.2.1 Oxygen, 38

3.2.2 Carbon dioxide, 41

3.2.3 Hydrogen, 42

3.2.4 Methane, 43

3.3 Sources of ions, 45

3.4 Ionic composition of Australian standing waters, 45

3.5 Conductivity, salinity and total dissolved solids, 45

3.6 Ionic composition and trophic state, 47

3.6.1 Some common anions, 47

3.6.2 Some common cations, 48

3.7 Redox reactions and redox potential, 50

3.8 Redox reactions and some common metals, 51

3.9 Nutrients, nutrient limitation and ecological stoichiometry, 52

3.9.1 Phosphorus, 53

3.9.2 Nitrogen, 55

3.9.3 Carbon, 58

3.10 Water regime, drying and water chemistry, 60

3.10.1 What happens to water chemistry during a wetting-drying cycle?, 60

3.11 Synthesis, 62

4 Biological processes in standing waters, 63

4.1 Biological players on a physical and chemical stage, 63

4.2 Major ecological zones and habitats, 64

4.3 Blurred boundaries and mobile assemblages, 66

4.4 Trophic groups and sources of energy, 66

4.5 Producers, 69

4.5.1 An ecological classification of producers, 72

4.5.2 Microscopic aquatic plants, 72

4.5.3 Macroscopic aquatic plants, 74

4.5.4 Plants living in water: benefits and constraints, 76

4.5.5 Alternative states: changes in plant dominance in shallow waterbodies, 77

4.6 Consumers, 80

4.6.1 Decomposers: the importance of microbes and fungi, 80

4.6.2 Invertebrate detritivores, 81

4.6.3 Invertebrate herbivores, 82

4.6.4 Invertebrate carnivores, 83

4.6.5 Vertebrate herbivores, 84

4.6.6 Vertebrate carnivores, 85

4.6.7 Predation and trophic cascades, 86

4.6.8 Trophic cascades and biomanipulation, 87

4.6.9 How vertebrates use waterbodies: linkages and subsidies, 87

4.7 Biological processes in temporary standing waters, 90

4.8 Biological processes in saline standing waters, 94

4.9 Synthesis, 95

5 Physical processes in running waters, 97

5.1 Flow and the diversity of running waters, 97

5.2 Scale, ecological hierarchies and networks, 97

5.3 A hierarchical classification of physical features, 99

5.3.1 Physical features and channel flows, 101

5.4 Hydrology and stream flow, 103

5.4.1 Measuring discharge, 103

5.4.2 Measuring current velocity, 104

5.5 Hydrographs, catchment characteristics and groundwater interactions, 106

5.6 Flow variability and its implications, 108

5.7 The physical process of transport, 110

5.7.1 The sources of sediment, 111

5.7.2 Sediment particle size and distribution, 112

5.7.3 Current velocity, erosion and transport, 113

5.7.4 Sediment dynamics and channel form, 114

5.7.5 Floodplain sedimentation and billabong formation, 115

5.8 River profi les and longitudinal changes in physical features, 118

5.9 Synthesis, 119

6 Chemical processes in running waters, 120

6.1 The complex web of factors, 120

6.2 Dissolved gases, 120

6.3 Ionic composition of Australian rivers, 123

6.4 Sources of ions, 124

6.5 Nutrients and nutrient spiralling, 126

6.5.1 Transport and retention of nutrients, 128

6.6 Carbon and organic matter, 129

6.6.1 Dissolved organic matter in rivers, 130

6.6.2 Solute processes: dissolved substances in running waters, 132

6.7 Longitudinal changes in chemical features, 133

6.8 Synthesis, 135

7 Biological processes in running waters, 136

7.1 Factors affecting biological processes at various scales, 136

7.2 Zones and habitats: parallels and contrasts with standing waters, 136

7.3 Living with flow, 138

7.4 Sources of energy in running waters, 142

7.4.1 Producers, 142

7.4.2 The distribution of different life-forms of producers, 143

7.4.3 Open-water producers in large rivers, 146

7.4.4 Classifying consumers in running waters, 146

7.4.5 Invertebrate herbivores, 147

7.4.6 Invertebrate carnivores, 149

7.4.7 Vertebrate herbivores, 150

7.4.8 Vertebrate carnivores, 151

7.4.9 Decomposers, 154

7.4.10 Functional feeding groups, 157

7.5 The fate of a dead eucalypt leaf that falls into a stream ..., 158

7.6 Conceptual models of running-water ecosystems, 160

7.7 The role of disturbance, 163

7.7.1 Post-disturbance recolonization processes, 164

7.7.2 Recolonization, dispersal and biogeography in Australian running waters, 168

7.7.3 Setting the biogeographic scene: ancient rocks, variable climates, 170

7.7.4 Some biogeographic patterns in Australian inland waters, 170

7.8 Synthesis, 173

8 Groundwater processes and management, 174

8.1 Out of sight, out of mind?, 174

8.2 An integrated definition of groundwaters, 174

8.3 Physical processes in groundwaters, 176

8.3.1 Groundwater discharge, permeability, porosity and Darcy’s Law, 178

8.3.2 Physical processes between groundwaters and surface waters, 180

8.3.3 Groundwater temperature, 183

8.4 Chemical processes in groundwaters, 184

8.4.1 Principal chemical processes in groundwater, 184

8.4.2 Chemical processes along gradients of dissolved oxygen, 186

8.5 Biological processes in groundwaters, 187

8.5.1 Groundwater microbiology, 188

8.5.2 Buried treasures in Australia: groundwater invertebrates and fishes, 190

8.5.3 Biodiversity and ecology of Australian groundwater fauna, 191

8.5.4 Physical, chemical and biological drivers of groundwater ecological processes, 193

8.5.5 Groundwater-dependent ecosystems (GDEs), 195

8.6 Management issues in Australian groundwaters, 197

8.7 Ecosystem services and conservation of Australian groundwaters, 201

8.8 Synthesis, 202

PART II: MANAGEMENT OF AQUATIC ECOSYSTEMS, 205

9 Management issues: water regime, 207

9.1 ‘When the well is dry ...’, 207

9.2 Changes to water regimes by humans in Australia: a brief history, 207

9.2.1 Changing water regime, changing processes, 210

9.3 Diverse impoundments with diverse effects, 211

9.3.1 Impoundments as ecological barriers, 214

9.3.2 Impoundments and estuaries, 215

9.4 Ecological effects of water extraction, 216

9.4.1 Ecological effects of drainage and irrigation, 218

9.4.2 Ecological effects of inter-basin transfers, 219

9.4.3 Ecological effects of urbanization, 220

9.5 Water regimes and environmental watering, 221

9.5.1 Environmental watering: ecological objectives and outcomes, 223

9.5.2 Environmental watering: risks and tactics, 225

9.6 ‘Breaking down the barriers’: fishways and dam removal, 226

9.7 Synthesis, 227

10 Management issues: physical features, 229

10.1 Changing physical features, changing processes, 229

10.2 Human activities and the physical environment, 230

10.2.1 Human changes to catchments, 230

10.2.2 Human changes to basins and channels, 232

10.3 Sedimentation: a physical process with negative fallout, 235

10.3.1 Human activities and sedimentation, 236

10.3.2 Ecological effects of sedimentation, 238

10.3.3 Management of sedimentation, 239

10.4 Physical processes and land-water interfaces, 241

10.4.1 Ecological roles of fringing and riparian zones, 241

10.4.2 Threats to land-water interfaces, 243

10.4.3 Management of land-water interfaces, 245

10.5 Recovering natural physical complexity, 248

10.6 Synthesis, 249

11 Management issues: water quality, 250

11.1 What is water quality?, 250

11.2 Managing water quality, 250

11.3 Eutrophication, 253

11.3.1 Natural and anthropogenic eutrophication, 253

11.3.2 Drivers, stressors and processes of eutrophication, 253

11.3.3 Ecological impacts and effects on ecosystem services, 256

11.3.4 Management of eutrophication, 258

11.4 Salinization, 259

11.4.1 Natural and anthropogenic salinization, 259

11.4.2 Drivers, stressors and processes of salinization, 259

11.4.3 Ecological impacts and effects on ecosystem services, 261

11.4.4 Management of salinization, 262

11.5 Acidifi cation, 264

11.5.1 Natural and anthropogenic acidifi cation, 264

11.5.2 Drivers, stressors and processes of acidification, 264

11.5.3 Ecological impacts and effects on ecosystem services, 267

11.5.4 Management of acidification, 268

11.6 Pollution, 269

11.6.1 Drivers, stressors and processes of pollution, 269

11.6.2 Ecological impacts and effects on ecosystem services, 271

11.6.3 Management of pollution, 273

11.7 Water quality guidelines, 274

11.8 Monitoring and assessing water quality, 275

11.8.1 Condition monitoring, 275

11.8.2 Detecting environmental impacts, 277

11.9 Multiple stressors and models of ecosystem change, 277

11.10 Synthesis, 279

12 Management issues: biodiversity conservation and climate change, 281

12.1 What is biodiversity and why does it need conservation?, 281

12.1.1 Setting priorities in biodiversity conservation, 281

12.2 Aquatic landscapes: networks and mosaics of habitats, 283

12.3 Protected areas for conserving freshwater communities, 284

12.4 Having good connections: dispersal and connectivity in conservation, 286

12.5 Protecting refuges to conserve aquatic communities, 287

12.6 Conserving aquatic species and populations, 288

12.6.1 The special challenge of conserving species with complex life histories, 288

12.6.2 The spatial extent of populations and metapopulations, 289

12.6.3 What are ‘Evolutionarily Significant Units’?, 289

12.6.4 Hidden biodiversity: cryptic species, 290

12.6.5 Endemic species and relictual faunas, 290

12.7 Threatened communities and species, 291

12.8 In the wrong place: ‘exotic aquatics’ and invasive species, 293

12.8.1 Invasive predators and competitors, 294

12.8.2 Domestic and hybridizing invasive aquatic species, 294

12.8.3 Invasive ‘ecosystem engineers’, 297

12.8.4 Potential effects of climate change on aquatic invasive species, 298

12.9 Climate change and Australian aquatic ecosystems, 299

12.9.1 Effects of increased water temperature, 300

12.9.2 Effects of changes to the hydrological cycle and water regimes, 300

12.9.3 Effects of sea-level rise, 301

12.9.4 Effects of changes to atmospheric conditions, 302

12.9.5 Effects of reduced snow cover and alpine warming, 302

12.9.6 How do these climatic changes affect freshwater species and ecosystems?, 302

12.9.7 Planned adaptation to climate change in aquatic ecosystems, 305

12.10 Synthesis, 307

13 Integrating ecology and management: a synthesis, 308

13.1 The ‘big picture’: integrating ecology and management, 308

13.2 The ‘bigger picture’: integrating social, economic and political goals, 309

13.3 Strategic adaptive management in aquatic ecology, 311

13.4 Resolving conflicts in freshwater management: a role for aquatic ecologists?, 313

13.5 Future challenges and opportunities: where to from here?, 315

13.6 Synthesis, 319

References, 321

Index, 347

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