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Full Description
This landmark publication collates information and studies on the use of estuaries, and specific habitats within them, as nursery, feeding and refuge areas, and migration routes of marine and other fish, many of which are of commercial and conservation importance. The editors and authors of the book have carefully compiled a huge wealth of information from the work of 18 organizations across 11 countries, providing a unique collection of data never before brought together within the covers of one book.
Chapters within this exceptional publication cover habitat use by fishes, recruitment and production in estuaries, links between fish and other trophic levels, endangered and rare species, estuarine development and restoration, environmental quality of estuaries and the management of estuarine fishes. The book notably contains extensive chapters on field methods and data analysis.
Fishes in Estuaries is an essential tool and reference source for fisheries and environmental managers, fish biologists, environmental scientists, aquatic ecologists and conservation biologists. Libraries in all universities and research establishments where biological sciences are studied and taught should have copies of this book on their shelves, as should personnel employed in regulatory and consultant capacities, such as within rivers authorities, environment agencies and fish and wildlife departments.
Comprehensive coverage of commercially exploited species.
Internationally known and respected contributors.
Multi-contributor approach providing very detailed coverage.
Estuaries are a vitally important ecosystem.
Contents
Preface and Acknowledgements xvii
List of Contributors xix
1 Introduction 1
M. Elliott
1.1 Introduction 1
1.2 Objectives 3
1.3 Methodology and scientific background 6
1.4 Final comments 7
1.5 References 7
2 Habitat Use by Fishes in Estuaries and Other Brackish Areas 10
L. Pihl, A. Cattrijsse, I. Codling, S. Mathieson, D.S. McLusky and C. Roberts
2.1 Introduction 10
2.2 Habitat definitions and descriptions (including subhabitats) 11
2.2.1 Tidal freshwater 11
2.2.1.1 Habitat definition 11
2.2.1.2 Habitat description 12
2.2.1.3 Subhabitats 12
2.2.2 Reed beds 12
2.2.2.1 Habitat definition 12
2.2.2.2 Habitat description 12
2.2.2.3 Subhabitats 12
2.2.3 Saltmarsh 13
2.2.3.1 Habitat definition 13
2.2.3.2 Habitat description 13
2.2.3.3 Subhabitats 13
2.2.4 Intertidal soft substratum 13
2.2.4.1 Habitat definition 13
2.2.4.2 Habitat description 13
2.2.4.3 Subhabitats 14
2.2.5 Intertidal hard substratum 14
2.2.5.1 Habitat definition 14
2.2.5.2 Habitat description 14
2.2.5.3 Subhabitats 15
2.2.6 Subtidal soft substratum 15
2.2.6.1 Habitat definition 15
2.2.6.2 Habitat description 15
2.2.6.3 Subhabitats 15
2.2.7 Subtidal hard substratum 16
2.2.7.1 Habitat definition 16
2.2.7.2 Habitat description 16
2.2.7.3 Subhabitats 16
2.2.8 Subtidal seagrass beds 16
2.2.8.1 Habitat definition 16
2.2.8.2 Habitat description 17
2.2.8.3 Subhabitats 17
2.2.9 Biogenic reefs 17
2.2.9.1 Habitat definition 17
2.2.9.2 Habitat description 17
2.2.9.3 Subhabitats 17
2.3 Quantification of fish habitats in selected European estuarine systems 18
2.3.1 Introduction 18
2.3.2 European context of the selected estuarine systems 18
2.3.2.1 Boreal/Atlantic region 18
2.3.2.2 Baltic/Skagerrak region 20
2.3.2.3 Mediterranean region 22
2.3.3 Distribution and extent of fish habitats 24
2.4 Use of habitats by fish in selected European estuarine systems 33
2.4.1 Fish species habitat use 33
2.4.1.1 Data treatment 33
2.4.1.2 Proportion of known data 35
2.4.2 Species richness and distribution between habitats 39
2.4.2.1 All fish species 39
2.4.2.2 Commercial species 41
2.4.3 Habitat utilisation 42
2.4.4 Habitat importance 43
2.4.5 Ecological guilds 46
2.5 Discussion 48
2.6 References 52
3 Recruitment and Production of Commercial Species in Estuaries 54
M.J. Costa, H.N. Cabral, P. Drake, A.N. Economou, C. Fernandez-Delgado, L. Gordo, J. Marchand and R. Thiel
3.1 Introduction 54
3.2 Distribution and commercial importance 55
3.3 Production 63
3.3.1 Production of estuarine fish communities 66
3.3.2 Production of some of the main species 71
3.3.2.1 Diadromous species 71
3.3.2.2 Marine seasonal migrants as adults 74
3.3.2.3 Marine migrants as juveniles 75
3.3.2.4 Estuarine-resident species 78
3.3.3 Discussion 81
3.4 Recruitment-related strategies of the life-cycles 82
3.4.1 Freshwater spawners 85
3.4.2 Brackish-water spawners 86
3.4.3 Marine spawners 87
3.5 Natural factors affecting recruitment 89
3.5.1 Mortality rates 89
3.5.2 Abiotic factors 90
3.5.2.1 Temperature 91
3.5.2.2 Salinity 92
3.5.2.3 Oxygen depletion 93
3.5.2.4 Hydrodynamics and wind stress 95
3.5.2.5 Other parameters 97
3.5.3 Biotic factors 98
3.5.3.1 Food availability 98
3.5.3.2 Predation and cannibalism 98
3.5.3.3 Competition 100
3.5.3.4 Vegetation and sediment structure 100
3.6 Anthropogenic effects on recruitment 101
3.6.1 Power stations 101
3.6.2 Water quality 102
3.6.2.1 Eutrophication 102
3.6.3 Effects of channelisation and land claim 102
3.6.3.1 Engineering works 102
3.6.3.2 Dams and barrages 103
3.7 References 104
4 Links between Fish and Other Trophic Levels 124
M. Elliott, K.L. Hemingway, M.J. Costello, S. Duhamel, K. Hostens, M. Labropoulou, S. Marshall and H. Winkler
4.1 Introduction and methods for study 124
4.2 Food webs and food chains 126
4.2.1 Estuarine food webs 127
4.2.1.1 Subtidal soft substratum 133
4.2.1.2 Subtidal hard/biogenic reefs 134
4.2.1.3 Seagrasses 135
4.2.1.4 Water column 137
4.2.1.5 Intertidal soft 138
4.2.1.6 Lagoons 139
4.2.2 Fish as prey 141
4.3 Species feeding guild matrix and analysis 146
4.3.1 Introduction 146
4.3.1.1 Prey selectivity and prey importance 147
4.3.1.2 Opportunistic versus specialised feeding 150
4.3.2 Planktonic feeders (including phyto- and zooplanktonic) 153
4.3.3 Herbivores (macrovegetation) 154
4.3.4 Detritivores and scavengers 155
4.3.5 Bed feeders 155
4.3.5.1 Benthophagous (infauna) 155
4.3.6 Demersal feeders 155
4.3.6.1 Hyperbenthos feeding (including mysids) 155
4.3.7 Piscivorous feeders 157
4.3.7.1 Cannibalism 158
4.3.8 Parasites 159
4.4 Factors controlling feeding 161
4.4.1 Environmental (non-biological) factors 161
4.4.1.1 Geographic/climate change 161
4.4.1.2 Hydrographic regime (tidal and other factors) 166
4.4.1.3 Site specificity/substratum 167
4.4.2 Biological factors (within species) 168
4.4.2.1 Life stages, including age and size differences 168
4.4.2.2 Sex 171
4.4.2.3 Ecotrophomorphology 172
4.4.2.4 Behaviour 174
4.4.2.5 Intra- and interspecific competition 179
4.4.2.6 Resource partitioning 182
4.4.2.7 Parasites 185
4.5 Consumption and production 186
4.5.1 Introduction and case studies 186
4.5.2 Energy flow 194
4.6 Discussion 194
4.7 References 195
5 Endangered and Rare Species 217
M. Costello, M. Elliott and R. Thiel
5.1 Introduction 217
5.2 Conservation designations 218
5.3 Available information 219
5.4 Threatened species: published data 219
5.4.1 Status of marine and estuarine species 219
5.4.2 Case study: Spanish data - comparison of data sources 233
5.5 Threatened species: European expert assessment 233
5.6 Case studies 250
5.6.1 Protection of marine and estuarine fishes 250
5.6.2 Species according to the European Habitat Directive: the Elbe estuary 251
5.6.3 Effects of temperature change on endangered, threatened or fragile European marine and estuarine species 252
5.7 Generic guidelines for the protection of endangered species. Case study: allis shad, Alosa alosa and twaite shad, Alosa fallax fallax 253
5.7.1 Status 253
5.7.2 Population size and structure 254
5.7.3 Habitat requirements 255
5.7.4 Management and protection 255
5.8 Rehabilitation and management of endangered species 257
5.8.1 The categorisation of endangered species. Case study: the Elbe estuary, Germany 257
5.8.2 The improvement of habitat diversity. Case study: artificially built backwaters in the Elbe estuary, Germany 257
5.9 Rehabilitation and management of an endangered estuarine species: case study of the smelt Osmerus eperlanus in the Forth (UK) and Elbe (Germany) estuaries 259
5.10 Discussion 260
5.11 References 262
6 Estuarine Development/Habitat Restoration and Re-creation and their Role in Estuarine Management for the Benefit of Aquatic Resources 266
A. Cattrijsse, I. Codling, A. Conides, S. Duhamel, R.N. Gibson, K. Hostens, S. Mathieson and D.S. McLusky
6.1 Historical loss of estuarine habitats 266
6.2 Mechanisms of wetland loss 267
6.2.1 Natural changes in geomorphology 269
6.2.2 Poldering and land-claim 275
6.2.3 Channel management 277
6.2.4 Port and transport infrastructure and other artificial structures 278
6.2.4.1 Channel stabilisation with dykes 279
6.2.4.2 Embanked roads and bridges in the intertidal zone 280
6.2.4.3 Docks, wharves and jetties 280
6.2.4.4 Aquaculture structures 281
6.2.5 Power stations and water abstraction 281
6.2.6 Barrages 282
6.2.7 Fisheries 283
6.2.8 Others 286
6.3 Effects of the different mechanisms 286
6.3.1 Natural changes in geomorphology 286
6.3.1.1 Effects on the physical habitat with reference to benthos 286
6.3.1.2 Effects on fishes 287
6.3.2 Poldering and land-claim 287
6.3.2.1 Effects on the physical habitat with reference to benthos 287
6.3.2.2 Effects on fishes 288
6.3.3 Channel management 289
6.3.3.1 Effects on the physical habitat with reference to benthos 289
6.3.3.2 Effects on fishes 291
6.3.4 Port and transport infrastructure and other artificial structures 291
6.3.4.1 Effects of the physical habitat with reference to benthos 291
6.3.4.2 Effects on fishes 292
6.3.5 Power stations and water abstraction 293
6.3.5.1 Effects on the physical habitat with reference to benthos 293
6.3.5.2 Effects on fishes 294
6.3.6 Dams and barrages 297
6.3.6.1 Effects on the physical habitat with reference to benthos 297
6.3.7 Fisheries 301
6.3.7.1 Effects on the physical habitat with reference to benthos 301
6.4 Restoration of estuarine habitats 302
6.4.1 Mitigation and compensation 303
6.4.2 Decreased risk of flooding 304
6.4.3 Conservation purposes 306
6.4.4 Fisheries 306
6.4.5 Deliberate non-interference 307
6.5 Good and bad practice for the management of fish populations in estuaries 307
6.5.1 Impact studies 307
6.5.2 Habitat creation 308
6.5.3 Cost-benefit analysis 309
6.6 References 310
7 Environmental Quality of Estuaries 322
J. Marchand, I. Codling, P. Drake, M. Elliott, L. Pihl and J. Rebelo
7.1 Introduction 322
7.2 Metal pollution 323
7.2.1 Sources of pollution 323
7.2.2 Levels of pollution 323
7.2.2.1 Spatial extent 325
7.2.2.2 Frequency, duration and trends 325
7.2.3 Effects of pollution 326
7.2.3.1 Environmental effects 327
7.2.3.2 Effects on fishes and/or macrocrustaceans 327
7.2.4 Assessment of pollution levels 336
7.3 Oils and petrochemicals 338
7.3.1 Sources of pollution 339
7.3.2 Levels of pollution 340
7.3.2.1 Spatial extent 340
7.3.2.2 Frequency, duration and trends 340
7.3.3 Effects of pollution 341
7.3.3.1 Environmental effects 341
7.3.3.2 Effects on fishes and/or macrocrustaceans 342
7.4 Persistent and synthetic organic chemicals 343
7.4.1 Sources of pollution 344
7.4.2 Levels of pollution 345
7.4.2.1 Spatial extent 345
7.4.2.2 Frequency, duration and trends 346
7.4.3 Effects of pollution 346
7.4.3.1 Environmental effects 346
7.4.3.2 Effects on fishes and/or macrocrustaceans 347
7.5 Nutrients and organic matter 348
7.5.1 Sources and levels of pollution 348
7.5.2 Levels of pollution 349
7.5.2.1 Spatial extent 349
7.5.2.2 Frequency, duration and trends 350
7.5.3 Effects of pollution 351
7.6 Physical disturbances 354
7.6.1 Cause and degree of disturbance 355
7.6.1.1 Dredging and dredged-material disposal 355
7.6.1.2 Physical inputs 356
7.6.1.3 Fishing disturbances 357
7.6.2 Effects of disturbance 358
7.6.2.1 Environmental effects 358
7.6.2.2 Effects on fishes and/or macrocrustaceans 361
7.7 Energy and thermal pollution 363
7.7.1 Sources of pollution 363
7.7.2 Levels of pollution 364
7.7.2.1 Spatial extent 364
7.7.2.2 Frequency, duration and trends 366
7.7.3 Effects of pollution 367
7.7.3.1 Environmental effects 367
7.7.3.2 Effects on fishes and/or macrocrustaceans 367
7.8 Radioactivity 368
7.8.1 Sources of pollution 368
7.8.2 Levels and spatial extent of pollution 369
7.8.2.1 Frequency, duration and trends 372
7.8.3 Effects of pollution 373
7.8.3.1 Environmental effects 373
7.8.3.2 Effects on fishes and/or macrocrustaceans 374
7.9 Biological pollutants: invading, introduced and nuisance species 374
7.9.1 Indirect effects of introduced species on fish and macrocrustaceans 375
7.9.1.1 Predation and competition 375
7.9.1.2 Spawning and nursery grounds 377
7.9.2 Direct effects on fish and shellfish 378
7.9.2.1 Case study of Anguillicola crassus, parasite of Anguilla anguilla 380
7.9.3 Summary 382
7.10 Biological pollutants: pathogens 383
7.10.1 Sources of pollution 383
7.10.2 Spatial extent and degree of pollution 384
7.10.3 Environmental effects of pollution 384
7.11 Management aspects of environmental quality 385
7.11.1 Management aims and philosophies 385
7.11.2 Management issues in detecting pollution responses at several levels of biological organisation 387
7.11.3 The derivation and use of ecological and environmental quality objectives and standards 389
7.11.4 Estuarine classification schemes 392
7.12 Discussion (including cost-benefit analysis) 392
7.13 References 394
8 Field Methods 410
K.L. Hemingway and M. Elliott
8.1 Introduction 410
8.1.1 Strategies of field sampling 410
8.1.2 Hypotheses generation 412
8.1.3 Case studies of field strategies 412
8.2 Field methods and features of use 414
8.2.1 Description of terms used within the fishing methods matrix 414
8.2.2 Methods 424
8.2.2.1 Plankton nets 424
8.2.2.2 Encircling and vertical nets 428
8.2.2.3 Trawl nets 432
8.2.2.4 Dredges and sledges 441
8.2.2.5 Fixed and drift nets 445
8.2.2.6 Traps 451
8.2.2.7 Lines 454
8.2.2.8 Pumping 455
8.2.2.9 Hand-gathering methods 458
8.2.2.10 Observation techniques 460
8.2.2.11 Other techniques 464
8.3 Gear choice and efficiency limitations 465
8.3.1 Gear choice 465
8.3.2 Gear efficiency and selectivity 467
8.4 Associated parameters 475
8.4.1 Case examples 476
8.5 Analytical Quality Control (AQC) and Quality Assurance (QA) 477
8.5.1 Adequacy of standardisation and validation of data produced 478
8.5.2 Variation, precision and accuracy in methods 479
8.5.3 Best practice 480
8.5.3.1 Sampling and survey design 480
8.5.3.2 Replication and subsampling 482
8.5.3.3 Frequency of sampling 483
8.5.3.4 Statistical power 484
8.5.3.5 Seasonal and temporal sampling 484
8.5.3.6 Ethical and legislative aspects 486
8.6 Field recording 487
8.6.1 Fish and macrocrustacean data 487
8.6.1.1 Absolute versus relative abundance 487
8.6.1.2 Species and community parameters 487
8.6.1.3 Size and dimensions 488
8.6.1.4 External examination for anomalies 488
8.6.1.5 Population structure 488
8.6.1.6 Behaviour - for direct observation 489
8.6.1.7 Feeding - for direct observation 490
8.6.1.8 By-catch details 490
8.6.1.9 Prey availability 490
8.6.1.10 Preservation 491
8.6.2 Environmental factors and variables 492
8.6.2.1 Factors affecting gear 492
8.6.2.2 Environmental master factors affecting interpretation of fish/shellfish data 492
8.7 Discussion 493
8.8 References 495
9 Data Quality Analysis and Interpretation 510
M. Elliott, K.L. Hemingway, S. Marshall and S. Duhamel
9.1 Introduction 510
9.2 Individual level 511
9.2.1 Size 511
9.2.2 Growth/age determination (otoliths/scales) 512
9.2.3 Diet and stomach analysis 514
9.2.3.1 Prey selectivity and prey importance 515
9.2.4 Sex/gonad development/GSI (Gonad Somatic Index) 520
9.2.5 Health/external body condition 520
9.2.6 Toxics and bioaccumulation 521
9.3 Population level 525
9.3.1 Biomass 525
9.3.2 Condition/disease/parasitism/LSI (liver somatic index) 526
9.3.3 Genetic structure 527
9.3.4 Cohort analysis 529
9.3.5 Growth, mortality rates and models 529
9.3.6 Production 531
9.3.6.1 Biological production 531
9.3.6.2 Fisheries production 532
9.3.7 Yield models 533
9.3.8 Use of fishery statistics 534
9.4 Community level 535
9.4.1 Community structure 535
9.5 General sampling statistics (time series, multivariate methods) 538
9.6 Suggested protocols for monitoring, surveillance and survey design 540
9.6.1 Decision level 1: definition of main questions and hypotheses 540
9.6.2 Decision level 2: monitoring definition 541
9.6.3 Decision level 3: types of survey required/desired 541
9.6.4 Decision level 4: associated parameters/integrated monitoring 542
9.6.5 Decision level 5: methods to be used in monitoring 542
9.7 Discussion 542
9.8 References 544
10 An Overview of the Status, Study and Management of Fishes in Estuaries 555
M. Elliott
10.1 Overview 555
10.2 Field methods and data analysis 557
10.3 Functioning of estuarine systems 559
10.3.1 Habitat description and use 559
10.3.2 Production ecology (trophic relationships, recruitment, production and yield) 560
10.3.3 Endangered and rare species 562
10.3.4 The impacts and effects of human activities 564
10.3.4.1 Overfishing and ecosystem effects of fisheries 566
10.3.4.2 Habitat loss and modification, including repercussions of climate changes 566
10.3.4.3 Repercussions of polluting inputs, including biological, physical and chemical additions to the system 567
10.4 Monitoring and surveillance of estuarine fish communities for management 571
10.5 The development of management procedures 572
10.6 Acknowledgements 573
10.7 References 574
Appendices 577
Taxonomic Index 615
Geographical Index 623
Subject Index 627
