Fishes in Estuaries

Dr Mike Elliott and Krystal L. Hemingway are both based at the Institute of Estuarine and Coastal Studies, University of Hull, U. K.

"This book is impressive because it is so comprehensive and yet usable... Fishes in Estuaries should be the first book to be consulted by anyone, including fishers, scientists and managers, seeking information about estuarine fishes, and should be on all their bookshelves!" Fish and Fisheries "It is anticipated that the findings of this book could be used to provide ecologically based guidelines for the preservation, restoration, and management of fish populations... this book would be a useful addition to the bookshelf of anyone interested in estuarine fishes."Copeia "This book provides a highly practical and valuable synthesis on fishes in esturies... It provides the reader with a good starting point to the wealth of divers information on the subject. Its logical layout means that the book is easy to dip onto to find the desired pointers. As such, it is an excellent standard text and will be widely used."Journal of Fish Biology

• Preface and Acknowledgements xviiList of Contributors xix1 Introduction 1M. Elliott1.1 Introduction 11.2 Objectives 31.3 Methodology and scientific background 61.4 Final comments 71.5 References 72 Habitat Use by Fishes in Estuaries and Other Brackish Areas 10L. Pihl, A. Cattrijsse, I. Codling, S. Mathieson, D.S. McLusky and C. Roberts2.1 Introduction 102.2 Habitat definitions and descriptions (including subhabitats) 112.2.1 Tidal freshwater 112.2.1.1 Habitat definition 112.2.1.2 Habitat description 122.2.1.3 Subhabitats 122.2.2 Reed beds 122.2.2.1 Habitat definition 122.2.2.2 Habitat description 122.2.2.3 Subhabitats 122.2.3 Saltmarsh 132.2.3.1 Habitat definition 132.2.3.2 Habitat description 132.2.3.3 Subhabitats 132.2.4 Intertidal soft substratum 132.2.4.1 Habitat definition 132.2.4.2 Habitat description 132.2.4.3 Subhabitats 142.2.5 Intertidal hard substratum 142.2.5.1 Habitat definition 142.2.5.2 Habitat description 142.2.5.3 Subhabitats 152.2.6 Subtidal soft substratum 152.2.6.1 Habitat definition 152.2.6.2 Habitat description 152.2.6.3 Subhabitats 152.2.7 Subtidal hard substratum 162.2.7.1 Habitat definition 162.2.7.2 Habitat description 162.2.7.3 Subhabitats 162.2.8 Subtidal seagrass beds 162.2.8.1 Habitat definition 162.2.8.2 Habitat description 172.2.8.3 Subhabitats 172.2.9 Biogenic reefs 172.2.9.1 Habitat definition 172.2.9.2 Habitat description 172.2.9.3 Subhabitats 172.3 Quantification of fish habitats in selected European estuarine systems 182.3.1 Introduction 182.3.2 European context of the selected estuarine systems 182.3.2.1 Boreal/Atlantic region 182.3.2.2 Baltic/Skagerrak region 202.3.2.3 Mediterranean region 222.3.3 Distribution and extent of fish habitats 242.4 Use of habitats by fish in selected European estuarine systems 332.4.1 Fish species habitat use 332.4.1.1 Data treatment 332.4.1.2 Proportion of known data 352.4.2 Species richness and distribution between habitats 392.4.2.1 All fish species 392.4.2.2 Commercial species 412.4.3 Habitat utilisation 422.4.4 Habitat importance 432.4.5 Ecological guilds 462.5 Discussion 482.6 References 523 Recruitment and Production of Commercial Species in Estuaries 54M.J. Costa, H.N. Cabral, P. Drake, A.N. Economou, C. Fernandez-Delgado, L. Gordo, J. Marchand and R. Thiel3.1 Introduction 543.2 Distribution and commercial importance 553.3 Production 633.3.1 Production of estuarine fish communities 663.3.2 Production of some of the main species 713.3.2.1 Diadromous species 713.3.2.2 Marine seasonal migrants as adults 743.3.2.3 Marine migrants as juveniles 753.3.2.4 Estuarine-resident species 783.3.3 Discussion 813.4 Recruitment-related strategies of the life-cycles 823.4.1 Freshwater spawners 853.4.2 Brackish-water spawners 863.4.3 Marine spawners 873.5 Natural factors affecting recruitment 893.5.1 Mortality rates 893.5.2 Abiotic factors 903.5.2.1 Temperature 913.5.2.2 Salinity 923.5.2.3 Oxygen depletion 933.5.2.4 Hydrodynamics and wind stress 953.5.2.5 Other parameters 973.5.3 Biotic factors 983.5.3.1 Food availability 983.5.3.2 Predation and cannibalism 983.5.3.3 Competition 1003.5.3.4 Vegetation and sediment structure 1003.6 Anthropogenic effects on recruitment 1013.6.1 Power stations 1013.6.2 Water quality 1023.6.2.1 Eutrophication 1023.6.3 Effects of channelisation and land claim 1023.6.3.1 Engineering works 1023.6.3.2 Dams and barrages 1033.7 References 1044 Links between Fish and Other Trophic Levels 124M. Elliott, K.L. Hemingway, M.J. Costello, S. Duhamel, K. Hostens, M. Labropoulou, S. Marshall and H. Winkler4.1 Introduction and methods for study 1244.2 Food webs and food chains 1264.2.1 Estuarine food webs 1274.2.1.1 Subtidal soft substratum 1334.2.1.2 Subtidal hard/biogenic reefs 1344.2.1.3 Seagrasses 1354.2.1.4 Water column 1374.2.1.5 Intertidal soft 1384.2.1.6 Lagoons 1394.2.2 Fish as prey 1414.3 Species feeding guild matrix and analysis 1464.3.1 Introduction 1464.3.1.1 Prey selectivity and prey importance 1474.3.1.2 Opportunistic versus specialised feeding 1504.3.2 Planktonic feeders (including phyto- and zooplanktonic) 1534.3.3 Herbivores (macrovegetation) 1544.3.4 Detritivores and scavengers 1554.3.5 Bed feeders 1554.3.5.1 Benthophagous (infauna) 1554.3.6 Demersal feeders 1554.3.6.1 Hyperbenthos feeding (including mysids) 1554.3.7 Piscivorous feeders 1574.3.7.1 Cannibalism 1584.3.8 Parasites 1594.4 Factors controlling feeding 1614.4.1 Environmental (non-biological) factors 1614.4.1.1 Geographic/climate change 1614.4.1.2 Hydrographic regime (tidal and other factors) 1664.4.1.3 Site specificity/substratum 1674.4.2 Biological factors (within species) 1684.4.2.1 Life stages, including age and size differences 1684.4.2.2 Sex 1714.4.2.3 Ecotrophomorphology 1724.4.2.4 Behaviour 1744.4.2.5 Intra- and interspecific competition 1794.4.2.6 Resource partitioning 1824.4.2.7 Parasites 1854.5 Consumption and production 1864.5.1 Introduction and case studies 1864.5.2 Energy flow 1944.6 Discussion 1944.7 References 1955 Endangered and Rare Species 217M. Costello, M. Elliott and R. Thiel5.1 Introduction 2175.2 Conservation designations 2185.3 Available information 2195.4 Threatened species: published data 2195.4.1 Status of marine and estuarine species 2195.4.2 Case study: Spanish data – comparison of data sources 2335.5 Threatened species: European expert assessment 2335.6 Case studies 2505.6.1 Protection of marine and estuarine fishes 2505.6.2 Species according to the European Habitat Directive: the Elbe estuary 2515.6.3 Effects of temperature change on endangered, threatened or fragile European marine and estuarine species 2525.7 Generic guidelines for the protection of endangered species. Case study: allis shad, Alosa alosa and twaite shad, Alosa fallax fallax 2535.7.1 Status 2535.7.2 Population size and structure 2545.7.3 Habitat requirements 2555.7.4 Management and protection 2555.8 Rehabilitation and management of endangered species 2575.8.1 The categorisation of endangered species. Case study: the Elbe estuary, Germany 2575.8.2 The improvement of habitat diversity. Case study: artificially built backwaters in the Elbe estuary, Germany 2575.9 Rehabilitation and management of an endangered estuarine species: case study of the smelt Osmerus eperlanus in the Forth (UK) and Elbe (Germany) estuaries 2595.10 Discussion 2605.11 References 2626 Estuarine Development/Habitat Restoration and Re-creation and their Role in Estuarine Management for the Benefit of Aquatic Resources 266A. Cattrijsse, I. Codling, A. Conides, S. Duhamel, R.N. Gibson, K. Hostens, S. Mathieson and D.S. McLusky6.1 Historical loss of estuarine habitats 2666.2 Mechanisms of wetland loss 2676.2.1 Natural changes in geomorphology 2696.2.2 Poldering and land-claim 2756.2.3 Channel management 2776.2.4 Port and transport infrastructure and other artificial structures 2786.2.4.1 Channel stabilisation with dykes 2796.2.4.2 Embanked roads and bridges in the intertidal zone 2806.2.4.3 Docks, wharves and jetties 2806.2.4.4 Aquaculture structures 2816.2.5 Power stations and water abstraction 2816.2.6 Barrages 2826.2.7 Fisheries 2836.2.8 Others 2866.3 Effects of the different mechanisms 2866.3.1 Natural changes in geomorphology 2866.3.1.1 Effects on the physical habitat with reference to benthos 2866.3.1.2 Effects on fishes 2876.3.2 Poldering and land-claim 2876.3.2.1 Effects on the physical habitat with reference to benthos 2876.3.2.2 Effects on fishes 2886.3.3 Channel management 2896.3.3.1 Effects on the physical habitat with reference to benthos 2896.3.3.2 Effects on fishes 2916.3.4 Port and transport infrastructure and other artificial structures 2916.3.4.1 Effects of the physical habitat with reference to benthos 2916.3.4.2 Effects on fishes 2926.3.5 Power stations and water abstraction 2936.3.5.1 Effects on the physical habitat with reference to benthos 2936.3.5.2 Effects on fishes 2946.3.6 Dams and barrages 2976.3.6.1 Effects on the physical habitat with reference to benthos 2976.3.7 Fisheries 3016.3.7.1 Effects on the physical habitat with reference to benthos 3016.4 Restoration of estuarine habitats 3026.4.1 Mitigation and compensation 3036.4.2 Decreased risk of flooding 3046.4.3 Conservation purposes 3066.4.4 Fisheries 3066.4.5 Deliberate non-interference 3076.5 Good and bad practice for the management of fish populations in estuaries 3076.5.1 Impact studies 3076.5.2 Habitat creation 3086.5.3 Cost–benefit analysis 3096.6 References 3107 Environmental Quality of Estuaries 322J. Marchand, I. Codling, P. Drake, M. Elliott, L. Pihl and J. Rebelo7.1 Introduction 3227.2 Metal pollution 3237.2.1 Sources of pollution 3237.2.2 Levels of pollution 3237.2.2.1 Spatial extent 3257.2.2.2 Frequency, duration and trends 3257.2.3 Effects of pollution 3267.2.3.1 Environmental effects 3277.2.3.2 Effects on fishes and/or macrocrustaceans 3277.2.4 Assessment of pollution levels 3367.3 Oils and petrochemicals 3387.3.1 Sources of pollution 3397.3.2 Levels of pollution 3407.3.2.1 Spatial extent 3407.3.2.2 Frequency, duration and trends 3407.3.3 Effects of pollution 3417.3.3.1 Environmental effects 3417.3.3.2 Effects on fishes and/or macrocrustaceans 3427.4 Persistent and synthetic organic chemicals 3437.4.1 Sources of pollution 3447.4.2 Levels of pollution 3457.4.2.1 Spatial extent 3457.4.2.2 Frequency, duration and trends 3467.4.3 Effects of pollution 3467.4.3.1 Environmental effects 3467.4.3.2 Effects on fishes and/or macrocrustaceans 3477.5 Nutrients and organic matter 3487.5.1 Sources and levels of pollution 3487.5.2 Levels of pollution 3497.5.2.1 Spatial extent 3497.5.2.2 Frequency, duration and trends 3507.5.3 Effects of pollution 3517.6 Physical disturbances 3547.6.1 Cause and degree of disturbance 3557.6.1.1 Dredging and dredged-material disposal 3557.6.1.2 Physical inputs 3567.6.1.3 Fishing disturbances 3577.6.2 Effects of disturbance 3587.6.2.1 Environmental effects 3587.6.2.2 Effects on fishes and/or macrocrustaceans 3617.7 Energy and thermal pollution 3637.7.1 Sources of pollution 3637.7.2 Levels of pollution 3647.7.2.1 Spatial extent 3647.7.2.2 Frequency, duration and trends 3667.7.3 Effects of pollution 3677.7.3.1 Environmental effects 3677.7.3.2 Effects on fishes and/or macrocrustaceans 3677.8 Radioactivity 3687.8.1 Sources of pollution 3687.8.2 Levels and spatial extent of pollution 3697.8.2.1 Frequency, duration and trends 3727.8.3 Effects of pollution 3737.8.3.1 Environmental effects 3737.8.3.2 Effects on fishes and/or macrocrustaceans 3747.9 Biological pollutants: invading, introduced and nuisance species 3747.9.1 Indirect effects of introduced species on fish and macrocrustaceans 3757.9.1.1 Predation and competition 3757.9.1.2 Spawning and nursery grounds 3777.9.2 Direct effects on fish and shellfish 3787.9.2.1 Case study of Anguillicola crassus, parasite of Anguilla anguilla 3807.9.3 Summary 3827.10 Biological pollutants: pathogens 3837.10.1 Sources of pollution 3837.10.2 Spatial extent and degree of pollution 3847.10.3 Environmental effects of pollution 3847.11 Management aspects of environmental quality 3857.11.1 Management aims and philosophies 3857.11.2 Management issues in detecting pollution responses at several levels of biological organisation 3877.11.3 The derivation and use of ecological and environmental quality objectives and standards 3897.11.4 Estuarine classification schemes 3927.12 Discussion (including cost–benefit analysis) 3927.13 References 3948 Field Methods 410K.L. Hemingway and M. Elliott8.1 Introduction 4108.1.1 Strategies of field sampling 4108.1.2 Hypotheses generation 4128.1.3 Case studies of field strategies 4128.2 Field methods and features of use 4148.2.1 Description of terms used within the fishing methods matrix 4148.2.2 Methods 4248.2.2.1 Plankton nets 4248.2.2.2 Encircling and vertical nets 4288.2.2.3 Trawl nets 4328.2.2.4 Dredges and sledges 4418.2.2.5 Fixed and drift nets 4458.2.2.6 Traps 4518.2.2.7 Lines 4548.2.2.8 Pumping 4558.2.2.9 Hand-gathering methods 4588.2.2.10 Observation techniques 4608.2.2.11 Other techniques 4648.3 Gear choice and efficiency limitations 4658.3.1 Gear choice 4658.3.2 Gear efficiency and selectivity 4678.4 Associated parameters 4758.4.1 Case examples 4768.5 Analytical Quality Control (AQC) and Quality Assurance (QA) 4778.5.1 Adequacy of standardisation and validation of data produced 4788.5.2 Variation, precision and accuracy in methods 4798.5.3 Best practice 4808.5.3.1 Sampling and survey design 4808.5.3.2 Replication and subsampling 4828.5.3.3 Frequency of sampling 4838.5.3.4 Statistical power 4848.5.3.5 Seasonal and temporal sampling 4848.5.3.6 Ethical and legislative aspects 4868.6 Field recording 4878.6.1 Fish and macrocrustacean data 4878.6.1.1 Absolute versus relative abundance 4878.6.1.2 Species and community parameters 4878.6.1.3 Size and dimensions 4888.6.1.4 External examination for anomalies 4888.6.1.5 Population structure 4888.6.1.6 Behaviour – for direct observation 4898.6.1.7 Feeding – for direct observation 4908.6.1.8 By-catch details 4908.6.1.9 Prey availability 4908.6.1.10 Preservation 4918.6.2 Environmental factors and variables 4928.6.2.1 Factors affecting gear 4928.6.2.2 Environmental master factors affecting interpretation of fish/shellfish data 4928.7 Discussion 4938.8 References 4959 Data Quality Analysis and Interpretation 510M. Elliott, K.L. Hemingway, S. Marshall and S. Duhamel9.1 Introduction 5109.2 Individual level 5119.2.1 Size 5119.2.2 Growth/age determination (otoliths/scales) 5129.2.3 Diet and stomach analysis 5149.2.3.1 Prey selectivity and prey importance 5159.2.4 Sex/gonad development/GSI (Gonad Somatic Index) 5209.2.5 Health/external body condition 5209.2.6 Toxics and bioaccumulation 5219.3 Population level 5259.3.1 Biomass 5259.3.2 Condition/disease/parasitism/LSI (liver somatic index) 5269.3.3 Genetic structure 5279.3.4 Cohort analysis 5299.3.5 Growth, mortality rates and models 5299.3.6 Production 5319.3.6.1 Biological production 5319.3.6.2 Fisheries production 5329.3.7 Yield models 5339.3.8 Use of fishery statistics 5349.4 Community level 5359.4.1 Community structure 5359.5 General sampling statistics (time series, multivariate methods) 5389.6 Suggested protocols for monitoring, surveillance and survey design 5409.6.1 Decision level 1: definition of main questions and hypotheses 5409.6.2 Decision level 2: monitoring definition 5419.6.3 Decision level 3: types of survey required/desired 5419.6.4 Decision level 4: associated parameters/integrated monitoring 5429.6.5 Decision level 5: methods to be used in monitoring 5429.7 Discussion 5429.8 References 54410 An Overview of the Status, Study and Management of Fishes in Estuaries 555M. Elliott10.1 Overview 55510.2 Field methods and data analysis 55710.3 Functioning of estuarine systems 55910.3.1 Habitat description and use 55910.3.2 Production ecology (trophic relationships, recruitment, production and yield) 56010.3.3 Endangered and rare species 56210.3.4 The impacts and effects of human activities 56410.3.4.1 Overfishing and ecosystem effects of fisheries 56610.3.4.2 Habitat loss and modification, including repercussions of climate changes 56610.3.4.3 Repercussions of polluting inputs, including biological, physical and chemical additions to the system 56710.4 Monitoring and surveillance of estuarine fish communities for management 57110.5 The development of management procedures 57210.6 Acknowledgements 57310.7 References 574Appendices 577Taxonomic Index 615Geographical Index 623Subject Index 627