See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/45256642 A Review and Synthesis of Australian Fisheries Habitat Research, Major Threats, Issues and Gaps in Knowledge of Coastal and Marine Fisheries Habitats - A Prospectus of Opportunitie... Article · January 1998 Source: OAI CITATIONS READS 24 244 4 authors, including: Daniel M. Alongi Norman C Duke Tropical Coastal & Mangrove Consultants James Cook University 217 PUBLICATIONS 15,835 CITATIONS 265 PUBLICATIONS 14,165 CITATIONS SEE PROFILE SEE PROFILE Some of the authors of this publication are also working on these related projects: MangroveWatch - community science in action View project Large-scale dieback of mangroves in Australia's Gulf of Carpentaria: a severe ecosystem response, coincidental with an unusually extreme weather event View project All content following this page was uploaded by Norman C Duke on 14 December 2013. The user has requested enhancement of the downloaded file. A REVIEW AND SYNTHESIS OF AUSTRALIAN FISHERIES HABITAT RESEARCH MAJOR THREATS, ISSUES AND GAPS IN KNOWLEDGE OF COASTAL AND MARINE FISHERIES HABITATS - A PROSPECTUS OF OPPORTUNITIES FOR THE FRDC “ECOSYSTEM PROTECTION PROGRAM” VOLUME 2: SCOPING REVIEW Mike Cappo, Daniel M. Alongi, David McB. Williams and Norman Duke PRODUCED AT THE REQUEST OF THE FISHERIES RESEARCH & DEVELOPMENT CORPORATION FRDC 95/055 AUSTRALIAN INSTITUTE OF MARINE SCIENCE FEBRUARY 1998 Contents ISSUE 1: NATURAL DYNAMICS IN FISHERIES HABITATS AND ENVIRONMENTAL VARIABILITY 13 1.1 Overview and FRDC role 13 1.1.1 The issues 13 1.1.2 The literature 19 1.1.3 FRDC action 28 1.2 Major forcings shape habitat dynamics - currents, tides, geomorphology and climate 34 1.2.1 Effects of the environment on fisheries 44 1.2.2 The nature of disturbance 53 1.2.3 Fisheries ecosystem management, bioregionalisations and the National Representative System of Marine Protected Areas 53 1.3 Fisheries-habitat links 69 1.3.1 Key issues 69 1.3.2 Lack of regional overviews of pattern and process in fisheries production 71 1.3.3 The use of production figures in assessing the state of fisheries habitats 81 1.3.4 Lack of knowledge of links between life-histories and habitats 86 1.3.5 The concepts of “estuarine dependence”, “estuarine opportunism” and “critical habitats” 95 1.4 An overview of processes, connectivity and production in the major fisheries habitats 100 1.4.1 Coastal freshwater 101 1.4.1.1 Fishery-habitat links 104 1.4.2 Saltmarsh (and saltpan) 106 1.4.3 Mangroves 109 1.4.3.1 Fishery-habitat links 119 1.4.4 Seagrasses 121 1.4.4.1 Fishery-habitat links 132 1.4.5 Sheltered coasts and estuaries 138 1.4.5.1 Fishery-habitat links 142 3 FRDC 95/055: A Review and Synthesis of Australian Fisheries Habitat Research 1.4.6 Open coasts - sandy shores 160 1.4.6.1 Fishery-habitat links 163 1.4.7 Open coasts - hard substrata 166 1.4.7.1 Fishery-habitat links 167 1.4.8 Coral reefs 170 1.4.9 Continental shelves 172 1.4.9.1 Fishery-habitat links 174 ISSUE 2: CHANGES TO DRAINAGE AND HABITAT ALTERATION 177 2.1 Overview and FRDC role 177 2.1.1 The issues 177 2.1.2 The literature 181 2.1.3 FRDC action 185 2.2 Coastal floodplains and wetlands - most vulnerable habitats? 195 2.2.1 The acid sulfate soil problem 196 2.2.2 Wetland loss 200 2.3 Estuarine “Environmental Flows” of freshwater 206 2.3.1 Barriers and alienation of habitat 209 2.3.2 The need for FISHWAYS 215 2.4 Saline intrusion and salinisation of estuaries 216 2.5 Training walls and channel modifications alter tidal and wave forcing 218 2.5.1 Lagoon opening regimes - foregone fisheries production due to opening or closure 219 2.6 Canal estates 221 2.7 Sediment instability, seagrass dieback and “narrow-banding” 222 2.8 Habitat rehabilitation, restoration and creation 225 ISSUE 3: NUTRIENT AND CONTAMINANT INPUTS 241 3.1 Overview and FRDC role 241 3.1.1 The issues 241 3.1.2 The literature 246 3.1.3 FRDC action 253 3.2 Effects on ecosystems - seagrass dieback, algal blooms and the need for biomonitors 260 3.2.1 Regional variability 266 3.2.2 Biomonitors and the symptoms of eutrophication - the need for innovation 268 4 Contents 3.3 Effects on ecosystems - de-nitrification cycles and phytoplankton blooms 271 3.3.1 Mangroves as nutrient scrubbers 272 3.3.2 Key uncertainties 272 3.3.3 Toxic and nuisance phytoplankton blooms 274 3.4 Contaminants and pathogens 278 3.4.1 Hydrocarbons 278 3.4.2 Metal contamination 279 3.4.3 Organochlorines and organometals 281 3.4.4 Sewage plumes 282 ISSUE 4: EFFECTS OF HARVESTING ON BIODIVERSITY AND ECOSYSTEMS 285 4.1 Overview and FRDC role 285 4.1.1 The issues 285 4.1.2 The literature 286 4.1.3 FRDC action 291 4.2 Bycatch and incidental take 296 4.2.1 Gillnetting - interactions with “charismatic megafauna” and bycatch issues 297 4.2.2 Trawling and scallop dredging 300 4.2.3 Bycatch in other fisheries -- estuarine angling, trawling and pocket- netting -- bycatch of juveniles of important species 307 4.2.4 Shoreline harvesting 309 4.2.5 Bycatch in other fisheries - longlining 310 4.3 Habitat damage 311 4.4 Secondary effects of discards 315 4.5 Indirect effects of the reduction of target species and habitat damage 316 4.5.1 Species shifts on reefs 316 4.5.2 Indirect effects of the reduction of target species and habitat damage -- species shifts on trawl grounds 319 4.5.3 Indirect effects of the reduction of target species - competition with predators for food fishes 322 4.6 Changes in demography under fishing pressure 323 4.7 Generation of litter and the environmental consequences 324 4.8 Reducing the effects of fishing 325 4.9 Assessing the effects of fishing 328 5 FRDC 95/055: A Review and Synthesis of Australian Fisheries Habitat Research ISSUE 5: INTRODUCED AND TRANSLOCATED PESTS AND DISEASES 333 5.1 Overview and FRDC role 333 5.1.1 The issues 333 5.1.2 The literature 340 5.1.3 FRDC action 343 5.2 Ballast water and hull-fouling organisms -- ship-vectored threats to mariculture and temperate fisheries habitats 346 5.2.1 Toxic and nuisance dinoflagellate blooms - a threat to mariculture 347 5.2.2 Marine pests that alter ecosystem structure 348 5.2.3 Disease 354 5.3 Translocated fishes and introduced pests in lower catchments 357 5.3.1 The role of habitat disturbance 357 5.3.2 Translocated fishes 360 5.3.3 Noxious aquatic macrophytes, woody weeds and pasture grasses 361 GLOSSARY OF ACRONYMS 369 APPENDICES Appendix 1: Standing Committee on Fisheries and Aquaculture - Fisheries Environment and Health Committee Terms of Reference (Hamdorf 1994) 373 Appendix 2: Fisheries Environment and Health Committee Research Priorities Draft (June 1996) see Hamdorf (1994) 374 Appendix 3: A Collation of Investment by THE FRDC in Projects with some Focus on Issues covered in this Review 377 Appendix 4: Summary of results of fisheries-habitat studies in inshore bays and estuaries, by Region, location, habitat type, fisheries taxa, life-history stage and source 393 Appendix 5: Summary of results of fisheries-habitat studies on rocky coasts and reefs, by region, location, habitat type, fisheries taxa, life-history stage and source. 418 Appendix 6 :Summary of results of fisheries-habitat studies on continental shelves, by region, location, habitat type, fisheries taxa, life-history stage and source. 431 6 Tables, Figures and Boxes Table 1.1.1 Breakdown of literature from the entire bibliography by number of papers containing specific information on natural dynamics and fisheries links. 20 Table 1.1.2 Breakdown of literature from the entire bibliography by number of papers containing specific information on natural dynamics and threats. 20 Table 1.1.3(a) Selected references documenting or invoking major sources of variation in fisheries-habitat links by habitat type. 25 Table 1.1.3(b) Selected references documenting or invoking major sources of variation in fisheries-habitat links by habitat type. 27 Table 1.1.4 Summary of Major Opportunities for FRDC investment in addressing R&D Gaps in knowledge of “Natural Dynamics”. 31 Table 1.2.1 Distribution of estuarine wetlands in tropical and subtropical Australia with extreme tide range. 35 Table 1.2.3.1 Descriptions for IMCRA regions. 61 Table 1.2.3.2 Examples of the detailed attribute data for IMCRA regions. 66 Table 1.3.2.1 Similarity in composition of major target families in nearshore fin- fisheries of Australia. 73 Table 1.3.2.2 Comparison of rank occurrence in numerical terms of taxa in studies done in estuarine and marine embayments at similar latitudes in southern Australia. 76 Table 1.3.2.3 Comparison of commercial and recreational catch (t yr-1) and production (kg Ha-1 yr-1) from Victorian, NSW and WA bays, inlets and estuaries. 79 7 FRDC 95/055: A Review and Synthesis of Australian Fisheries Habitat Research Table 1.3.2.4 Differences in area of habitat and estimated total (commercial + recreational) finfish production (tonnes) from the Clarence and Richmond Rivers. 80 Table 1.3.2.5 Comparison of biomass estimates (grams metre-2) from habitats within estuaries in the tropics and sub-tropics, using a variety of gears (see Appendix 4). 81 Table 1.3.4.1 Variation amongst species within genera, and within species amongst regions in requirements for nursery habitats.