Fish and Fisheries in Estuaries, 2 Volume Set A Global Perspective

Fish and Fisheries in Estuaries: A Global Perspective brings together the current state of knowledge of estuarine fish in one inclusive work. Featuring contributions by more than fifty internationally-recognized researchers and estuarine ichthyological specialists, this landmark resource covers fish assemblages and functional groups, recruitment and production in estuaries, feeding ecology and trophic dynamics, fisheries and the conservation of estuarine fish, and much more.

Thirteen in-depth chapters and two method appendices examine major aspects of fish and fisheries in estuaries throughout the world. The text describes the biology of estuarine fish and their connections with estuarine and adjacent marine and freshwater ecosystems, as well as examining the ways human industrialization and global events such as climate change are impacting both native and non-native species. Topics include habitat diversity, fish foraging behavior, ecological engineering tools and models, hazards and risks to estuarine fish and fisheries, and estuarine environmental health. Offering detailed information on the biology and ecology of estuarine fish and fisheries, this authoritative reference:

• Explores current approaches and future research directions aimed at achieving a balance between exploitation and conservation of estuarine fishes
• Discusses environmental quality objectives and sustainable management of estuary fisheries
• Addresses the impacts of increased human use of resources such as food, space, and water to estuarine fish and fisheries
• Features numerous international case studies of management of fisheries, threatened species, estuarine rehabilitation, reproduction and ontogeny, and others
• Covers study and sampling methods, field equipment, and data processing, analysis, and interpretation

Fish and Fisheries in Estuaries: A Global Perspective is an indispensable tool and reference point for fish biologists, fisheries scientists, ecologists and environmental scientists, aquatic ecologists, conservation biologists, estuarine managers and advanced students and instructors in fish biology and fisheries programs.

Alan Whitfield, Emeritus Chief Scientist, South African Institute for Aquatic Biodiversity (SAIAB), Grahamstown, Eastern Cape Province, South Africa
Kenneth Able, Professor Emeritus, Marine Field Station, Rutgers University, Tuckerton, New Jersey, USAStephen J. M. Blaber, Senior Research Fellow, CSIRO Marine Research, St Lucia, Queensland, Australia
Mike Elliott, Director, International Estuarine & Coastal Specialists Ltd, and Professor in Estuarine & Coastal Sciences, University of Hull, Hull, UK

Dedication

Preface

Author Details

Acknowledgements

Chapter 1: Introduction

1.1 Scope of the book

1.2 Reasons why this synthesis is important

1.3 Estuary definition and types

1.4 Chapter descriptions

1.5 Conclusions

1.6 References

Chapter 2: Fish Assemblages and Functional Groups

2.1 Introduction

2.2 Zoogeography and estuarine fish assemblages

2.3 Estuarine typology and fish assemblages

2.4 Fish guilds and functional groups

2.4.1 Estuarine Use Functional Group (EUFG)

2.4.2 Feeding Mode Functional Group (FMFG)

2.4.3 Reproductive Mode Functional Group (RMFG)

2.5 Do functional groups drive fish assemblage structure?

2.6 Fish functional groups and guild analyses

2.7 Acknowledgements

2.8 References

Chapter 3: Reproduction, Ontogeny and Recruitment

3.1 Introduction

Scope of the Chapter

3.2 Estuarine support of reproduction and recruitment

3.2.1 Replenishment: modes and patterns

3.2.1.1 Modes of reproduction

3.2.1.2 Early life stages and nurseries

3.2.2 Sources of variability in reproductive success and recruitment

3.2.2.1 Habitat and water quality

3.2.2.2 Hydrography and physics

3.2.2.3 Foods of early life stages

3.2.2.4 Predators

3.2.2.5 Weather, climate and estuarine change

3.3 Early-life stages and recruitment dynamics

3.3.1 Dispersal, transport and retention

3.3.1.1 Offshore to estuary transport processes

3.3.1.2 Swimming as a transport mechanism

3.3.1.3 Near- and within-estuary transport processes

3.3.1.4 Retention: estuarine features and processes

3.3.2 Settlement

3.3.3 Larval and juvenile production processes

3.3.3.1 Larval feeding

Ontogenetic shifts and feeding success

Nutritional considerations

3.3.4 Larval and juvenile production: growth and mortality

3.3.4.1 Rates and variability

Stage durations

3.3.4.2 Predation

3.3.4.3 Environmental factors

3.4 Adults and recruitment

3.4.1 Adult stock

3.4.1.1 Stock structure, contingents and cohorts

3.4.1.2 Maternal effects

3.4.2 Scales and patterns of variability in reproductive success

3.4.2.1 Recruitment levels and variability

3.4.2.2 Adult stock and recruitment

3.4.2.3 Predicting and forecasting recruitment

3.4.3 Recruitment: an integrated, evolved process

3.5 Threats to reproduction and recruitment in estuaries

3.5.1 Excessive fishing: depletion of adults and bycatch of juveniles

3.5.2 Habitat destruction and degradation

3.5.3 Impoundments and flow regulation

3.5.4 Power plants

3.5.5 Estuary contaminants, water quality degradation

3.5.6 Eutrophication

3.5.7 Climate change

3.5.8 Catastrophic events

3.6 Case Studies

3.6.1 Pleuronectiformes

3.6.2 Sciaenidae

3.6.3 Anchoa mitchilli (Engraulidae)

3.6.4 Brevoortia tyrannus and Brevoortia spp. (Clupeidae)

3.6.5 Morone saxatilis (Moronidae)

3.6.6 Gadidae and Clupeidae (Baltic Sea)

3.6.7 Lateolabrax japonicus (Lateolabracidae)

3.6.8 Fundulus heteroclitus (Fundulidae)

3.7 Summary and conclusions

3.8 Acknowledgements

3.9 References

Chapter 4: Habitat Use and Connectivity

4.1 Introduction

4.2 Habitat diversity

4.2.1 Water column habitat

4.2.2 Unstructured shallow habitats

4.2.3 Structured benthic habitats

4.2.3.1 Salt marshes

4.2.3.2 Submerged aquatic vegetation

4.2.3.3 Mangroves

4.2.3.4 Shellfish beds

4.2.3.5 Woody debris

4.2.3.6 Rocky and gravel bottoms

4.3 Geomorphological and hydrological variables

4.4. Physico-chemical variables

4.5 Dynamics of juvenile habitat use

4.5.1 Temperature effects

4.5.2 Salinity effects

4.5.3 Diadromy

4.5.4 Settlement habitats

4.5.5 Connectivity among habitats

4.5.6 Alien species

4.6 Adult habitat

4.7 Habitat fidelity and juvenile and adult fishes

4.8 Ecological context

4.9 Connectivity between estuarine, freshwater and marine ecosystems

4.9.1 Migrations into estuaries

4.9.2 Migrations out of estuaries

4.9.3 Migrations between estuaries

4.10 Conclusions

4.11 Acknowledgements

4.12 References

*Chapter 5: Feeding Ecology and Trophic Dynamics

5.1 Introduction

5.2 Fish foraging behaviour and food intake

5.2.1 Prey detection

5.2.2 Feeding periodicity

5.2.3 Food intake

5.2.4 Feeding movements and migrations

5.3 Factors influencing feeding ecology

5.3.1 Environmental factors

5.3.1.1 Water temperature, salinity and dissolved oxygen

5.3.1.2 Tidal regime and substratum composition

5.3.2 Biological factors

5.3.2.1 Body size

5.3.2.2 Ontogenetic changes in fish diets

5.3.3 Foraging specializations

5.3.4 Opportunistic versus specialised feeding

5.4 Ecotrophomorphology

5.5 Trophic categorization

5.5.1 Herbivorous species

5.5.2 Detritivorous species

5.5.3 Zoobenthivorous species

5.5.4 Zooplanktivorous species

5.5.5 Piscivorous species

5.5.5.1 Cannabilism

5.6 Competition, resource partitioning, energy flow and connectivity

5.6.1 Intraspecific and interspecific competition

5.6.2 Resource portioning

5.6.3 Energy flow and connectivity

5.7 Fishbase approach to Functional Feeding Groups

5.7.1 Example of a FFG analysis

5.8 Fish food sources in estuaries

5.8.1 Submerged macrophyte habitats

5.8.2 Emergent macrophyte habitats

5.9 Food web complexity

5.9.1 Vertical and horizontal feeding patterns by fishes

5.10 Predators of fish in estuaries

5.10.1 Invertebrates

5.10.2 Birds

5.10.3 Reptiles

5.10.4 Mammals

5.11 Effects of natural and anthropogenic perturbations on food webs

5.12 Acknowledgements

5.13 References

Chapter 6: Fishes and Estuarine Environmental Health

6.1 Estuarine environmental health: concepts, definitions and assessment

6.2 Anthropogenic pressures impacting estuarine fish assemblages

6.2.1 Habitat loss and physical degradation

6.2.2 Pollution

6.2.3 River flow regulation

6.2.4 Fisheries and aquaculture

6.2.5 Non-indigenous species

6.2.6 Climate change

6.2.7 Integration of human pressures: the global change context

6.3 Fishes biomarkers responding to human pressures

6.3.1 Fish biomarkers and biomagnification

6.3.2 Biomarkers of exposure

6.4 Fishes as biological indicators

6.5 Main methodological approaches to assess estuarine health using fish as indicators

6.5.1 Historical data and reference conditions

6.5.2 Experimental approaches

6.5.3 Environmental impact assessment and other risk assessment methods

6.5.4 Qualitative methods

6.5.5 Quantitative indicators

6.5.6 Models

6.6 Environmental health fish-based indices

6.7 Disentangling fish responses in the multi-stress context of global changes

6.7.1 Univariate approaches

6.7.2 Multivariate approaches

6.8 Future research directions

6.9 References

Chapter 7: Climate Change and Fishes in Estuaries

7.1 Introduction

7.2 Global, regional and local patterns

7.2.1 Predictors of fish taxonomic diversity at global and regional scales

7.2.2 Predictors of fish taxonomic diversity at local scales

7.2.3 Predictors of fish functional diversity at global, regional and local scales

7.3 Potential impacts of environmental/climate stressors on estuarine fish

7.3.1 Salinity and freshwater flow impacts

7.3.2 Temperature impacts

7.3.3 Dissolved oxygen impacts

7.3.4 Impacts of elevated CO2

7.3.5 Sea level rise

7.3.6 Estuary entrance channel openings and fish access

7.3.7 Disease

7.4 Climate change and fisheries in estuaries

7.4.1 Links to fisheries catches

7.4.2 Socio-economic effects and management implications

7.5 Case studies

7.5.1 Arctic

7.5.2 Temperate northern Atlantic

7.5.3 Temperate northern Pacific

7.5.4 Tropical Atlantic

7.5.5 Indo-Pacific

7.5.6 Temperate South America

7.5.7 Temperate southern Africa

7.5.8 Temperate Australia

7.6 Gaps in knowledge and future research directions

7.7 Acknowledgements

7.8 References

Chapter 8: Estuarine Degradation and Rehabilitation

8.1 Introduction

8.1.1 Hazards and risks to estuarine fish and fisheries and their habitats

8.1.2 Effects of climate change on estuarine fish and fisheries

8.1.3 Effects of estuarine degradation on ecosystem services

8.1.4 Effects of estuarine degradation on water quality and impacts on fish

8.1.5 Heavy metals

8.1.6 Organic pollutants

8.1.7 Pharmaceutical and personal care products

8.1.8 Nutrients

8.1.9 Effects on water quantity, hydropeak and flow alteration on fish

8.1.10 Effects on fishing

8.2 Estuarine restoration and habitat creation

8.3 Current practices

8.4 Ecological engineering

8.5 Contribution of modelling tools to more process-based restoration objectives

8.5.1 Introduction

8..5.2 Framework

8.5.2.1 Towards a more process-orientated approach

8.5.2.2 Towards integrated objectives

8.6 Why modelling processes?

8.6.1 Physical phenomena

8.6.2 Species use of the estuarine environment and compartmental interactions

8.6.3 Overview

8.7 Modelling tools

8.7.1 Biogeochemical modelling

8.7.2 Hydromorphological-sedimentary modelling

8.8 Life cycle modelling

8.8.1 ‘Static’ approaches: statistical habitat suitability

8.8.2 Dynamic approach: the probability to attaining suitable habitats

8.9 Food web modelling

8.10 The way forward

8.11 From theory to practice

8.11.1 A case study of restoration in the Schelde Estuary

8.11.2 Ecological restoration by opportunity: an example from the Gironde Estuary

8.11.2.1 Gironde restoration summary

8.11.3 Case study – restoration of former salt hay farms

8.11.4 Case study – habitat alteration and restoration linked to a common reed invasion

8.11.5 Restoration of whole estuaries and wetland systems

8.12 Concluding comments

8.13 Acknowledgements

8.14 References

Chapter 9: Estuarine Fisheries

9.1 Introduction

9.2 Estuarine fishery sectors

9.3 Problems and issues in fisheries

9.4 Fishery yields

9.5 Estuarine fisheries: a selection of case studies

9.5.1 Asian fisheries

9.5.1.1 The Hilsa Fishery, South Asia

9.5.1.2 The Lake Chilika Fishery, India

9.5.1.3 The Pichavaram Fishery, India

9.5.1.4 The Larut-Matang Fishery, Indonesia

9.5.2 African fisheries

9.5.2.1 The Kosi Bay Lakes Fishery, South Africa

9.5.2.2 The Sundays Estuary Fishery, South Africa

9.5.2.3 The Ébrié Lagoon Fishery, Ivory Coast

9.5.3 South and Central American fisheries

9.5.3.1 The Gulf of Nicoya Fishery, Costa Rica

9.5.3.2 The Cienaga Grande de Santa Marta Fishery, Columbia

9.5.3.3 The fisheries of Lake Maracaibo, Venezuela

9.5.3.4 The Valenca Delta Fishery, Brazil

9.5.4 Australasian fisheries

9.5.4.1 Lates calcarifer fisheries of Australia and Papua New Guinea

9.5.5 European and North American fisheries

9.6 The main fishery species in Europe and North America

9.6.1 Diadromous species

9.6.2 Marine seasonal migrants as adults

9.6.3 Marine migrants as juveniles

9.6.4 Estuarine-resident species

9.7 Connectivity

9.8 Concluding remarks

9.9 Acknowledgements

9.10 References

Chapter 10: Conservation of Estuarine Fishes

10.1 Introduction

10.2 Analysis of threats to estuarine fish conservation

10.2.1 Fisheries

10.2.2 Habitat alteration/loss

10.2.3 Water quality and quantity alterations

10.2.4 Climate change

10.2.5 Non-native species

10.3 Conservation interventions and instruments

10.3.1 Legislative frameworks

10.3.1.1 International initiatives

10.3.1.2 Regional initiatives

10.3.1.3 National initiatives

10.3.1.4 Environmental non-governmental organisations

10.3.2 Role of protected areas

10.3.3 Rehabilitation and habitat restoration

10.3.4 Catchment conservation

10.3.5 Captive breeding and stocking

10.4 Threatened species and extinction risk: some case studies

10.4.1 Estuarine pipefish Syngnathus watermeyeri

10.4.2 Ganges shark Glyphis gangeticus

10.4.3 Totoaba Totoaba macdonaldi

10.4.4 European eel Anguilla anguilla

10.4.5 Cape stumpnose Rhabdosargus holubi

10.5 Current and future challenges

10.6 Conclusions

10.7 Acknowledgements and dedication

10.8 References

Chapter 11: Non-native Species in Estuaries

11.1 Introduction

11.2 What conditions favor non-native species in estuaries?

11.2.1 Overview

11.2.2 San Francisco Estuary

11.2.3 Baltic Sea

11.2.4 Chesapeake Bay

11.2.5 Tagus Estuary

11.2.6 South African estuaries

11.2.7 Overview

11.3 What are the characteristics of successful non-native estuarine fishes?

11.3.1 General characteristics

11.3.2 Taxonomy

11.3.3 Mode of introduction

11.4 Do non-native species become integrated into the biota of estuaries?

11.4.1 Alternatives to species invasions

11.4.2 Novel species, novel ecosystems

11.4.3 Overview

11.5 How should non-native species in estuaries be managed?

11.6 How do non-native fishes fit into estuarine ecosystems?

11.7 Conclusions

11.8 Acknowledgements

11.9 References

Chapter 12: Management of Fishes and Fisheries in Estuaries

12.1 Introduction

12.2 Management background, aims and philosophies

12.2.1 Background and basis for management

12.2.2 Environmental Quality Objectives and sustainable management

  12.2.2.1 Indicators and monitoring as tools in management

 12.2.3 Information for estuarine management

12.2.3.1 Information needs and communicating management issues

12.2.3.2 Information and data production, use and dissemination

12.2.4 Case studies of priority issues for management

12.2.4.1 Australia

12.2.4.2 Humber (UK)

12.2.4.3 United States of America

12.3 Management of activities and habitats, monitoring and surveillance

12.3.1 Estuarine environmental management

12.3.2 Monitoring of activities for management

12.3.3 Licencing of plans and projects

12.3.4 Cumulative effects assessment

12.3.5 Management of recreational fishing

12.3.6 Management of habitats

12.3.6.1 Management of loss and gain in estuarine habitats

12.4 Management approaches at whole catchment and estuary level

12.4.1 Management of catchments

12.4.2 Whole estuary management approaches

12.4.3 Determining if estuarine management is successful

12.4.4 Estuarine management: holistic case studies

12.4.4.1 New Zealand

12.4.4.2 Japan

12.4.4.3 South Africa

12.4.4.4 Eastern United States of America

12.4.4.5 Western United States of America

12.5 Management of species and stocks/fisheries

12.5.1 Background

12.5.2 Management of species and stocks case studies

12.5.2.1 United Kingdom

12.5.2.2 Baltic Sea

12.5.2.3 Australia

12.5.2.4 United States of America

12.6 Administrative and legal aspects of managing estuarine fish ecology and fisheries

12.6.1 Governance background

12.6.2 European legislation

12.6.2.1 The Water Framework Directive

12.6.2.2 Habitat and Species Directive

12.6.3 Administrative bodies

12.6.3.1 Management authorities: the Humber Estuary, UK example

12.6.3.2 Laws and administration: the USA example

12.7 Main messages and recommendations for management

12.8 Future research into management methods

12.9 Acknowledgements

12.10 References

Chapter 13: Fish and Fisheries in Estuaries: Global Synthesis and Future Research Directions

13.1 Introduction – Changing estuarine landscapes: habitats, research and society

13.2 What fishes are in estuaries and why?

13.3 Estuarine fish recruitment and habitats – connectivity across space and time

13.3.1 Gaps in knowledge and future research directions

13.4 How much do we really understand about the role of fish in an estuarine food web?

13.4.1 Background

13.4.2 Fish food resources in estuaries

13.4.3 Factors influencing feeding movements, foraging ecology and migrations

13.4.4 Trophic categorization

13.4.5 Resource partitioning, energy flow and food web complexity

13.4.6 Gaps in knowledge and future research directions

13.5 Fishes – good indicators of environmental change?

13.5.1 Background to the integration of human pressures

13.5.2 Fishes as biological indicators

13.5.3 Environmental health fish-based indices

13.5.4 Disentangling fish responses in the multi-stress context of global changes

13.5.5 Gaps in knowledge and future research directions

13.6 Climate change and habitat degradation – a double whammy for fish in estuaries?

13.6.1 Background

13.6.2 Climate change

13.6.3 Habitat degradation

13.6.4 Gaps in knowledge and future research directions

13.7 Estuarine species are invading and shifting their distributions

13.7.1 Invasions of non-native species

13.7.2 The ebb and flow: geographical expansion and contraction of species

13.7.3 Gaps in knowledge and future research directions

13.8 The importance and future of fisheries in estuaries – societal goods and benefits?

13.8.1 Fisheries management in the future

13.9 Estuarine fish conservation for the future

13.9.1 Gaps in knowledge and future research directions

13.10 Restoring and managing estuaries for fish, fisheries and habitats

13.10.1 Management actions for restoring and rehabilitating estuaries

13.10.2 Gaps in knowledge and future research directions

13.11 Science-for-policy and policy-for-science – role of estuarine ichthyologists?

13.12 Fish and fisheries research in estuaries – the way forward

13.13 Acknowledgements

13.14 References

Appendix 1: Study Methods I - Field Equipment, Sampling and Methods

A1.1 Introduction

A1.2 Sampling methods

A1.2.1 ‘Traditional’ sampling (nets and traps)

A1.2.1.1 Trawl nets

Beam trawl

Otter trawl

Pelagic trawl

Other trawls

A1.2.1.2 Seine nets

Beach seine

Other seine nets

A1.2.1.3 Fixed nets and traps

Fyke net

Fixed net/trap (e.g. salmon and eel traps)

Stow net

Entangling nets (gill and trammel nets)

Drop net and drop traps

Pop net and pull-up traps

Other fixed nets and traps

A1.2.1.4 Fishing lines

Long lines

Hand line

A1.2.1.5 Ichthyoplankton samplers

Vertical and horizontal plankton nets

Bongo net

Gulf sampler

Larval light traps

A1.2.1.6 Power station screens

A1.2.1.7 Hand gathering methods

Glass eel tow net and elver dip net

Push net

Kick sampling

A1.2.2 Visual and acoustic methods

A1.2.2.1 Visual detection

Diving

Underwater video

A1.2.2.2 Acoustic detection

Hydroacoustics

Acoustic cameras

Acoustic telemetry

A1.2.2.3 Other observation techniques

A1.2.3 Environmental DNA methods

A1.2.3.1 DNA analysis

DNA and eDNA methods

Targeted PCR methods

High-throughput sequencing

A1.2.3.2 Strengths and disadvantages of DNA-based methods

Feasibility and costs

eDNA and the possible presence of an organism in that environment

Can eDNA provide quantitative information?

DNA techniques for environmental monitoring

A1.3 Factors influencing the design of fish monitoring programmes

A1.3.1 Monitoring techniques

A1.3.2 Spatial considerations

A1.3.3 Temporal considerations

A1.3.4 A decision tree for monitoring, surveillance and survey design

A1.3.4.1 Decision level 1: definition of main questions and hypotheses

A1.3.4.2 Decision level 2: monitoring definition

A1.3.4.3 Decision level 3: types of survey required/desired

A1.3.4.4 Decision level 4: associated parameters/integrated monitoring

A1.3.4.5 Decision level 5: methods to be used in monitoring

A1.4 Acknowledgements

A1.5 References

Appendix 2: Study Methods II - Data Processing, Analysis and Interpretation

A2.1 Introduction

A2.2 Individual level

A2.2.1 Size

A2.2.2 Age/growth determination (otoliths/scales)

A2.2.3 Diet and stomach analyses

A2.2.3.1 Prey selectivity and prey importance

A2.2.4 Sex/gonad development (Gonadosomatic Index)

A2.2.5 External bodies abnormalities and fish health

A2.2.6 Toxins and bioaccumulation

A2.3 Population level

A2.3.1 Abundance

A2.3.2 Biomass

A2.3.3 Condition, disease, parasitism, and liver somatic index

A2.3.4 Genetic structure

A2.3.5 Cohort analysis

A2.3.6 Growth, mortality rates and models

A2.3.7 Production

A2.3.7.1 Biological production

A2.3.7.2 Fisheries production

A2.3.8 Yield models

A2.3.9 Use of fishery statistics

A2.4 Community level

A2.4.1 Community structure

A2.4.2 Multi-metric fish-based indices

A2.5 General analysis methods and the role of models

A2.5.1 The types and roles of numerical models

A2.6 Precision versus accuracy – Analytical Quality Control/Quality Assurance

A2.7 Concluding comments

A2.8 Acknowledgements

A2.9 References

Fish Species Index

Geographical Index

General Index

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