Strategic Research Fund for the Marine Environment (SRFME) Interim final report June 2005 Edited by John K. Keesing and John N. Heine CSIRO Marine and Atmospheric Research Strategic Research Fund for the Marine Environment: interim final report, June 2005. Bibliography. ISBN 1 921061 06 5. 1. CSIRO – Appropriations and expenditures. 2. Marine sciences – Research – Western Australia – Finance. 3. Marine resources – Research – Western Australia – Finance. I. Keesing, John K. II. Heine, John N. III. CSIRO. Marine and Atmospheric Research. 354.5709941 CONTENTS EXECUTIVE SUMMARY 6 CHAPTER 1 8 1.1 About SRFME 8 1.1.1 Role and Purpose of SRFME 8 1.1.2 Background to SRFME 8 1.2 Structure and Governance of SRFME 9 1.2.1 SRFME Joint Venture Management Committee 9 1.2.2 SRFME Technical Advisory Committee 10 1.2.3 SRFME Research Director and Project Leaders 10 1.3 The SRFME Framework and Research Portfolio Structure 11 1.3.1 The SRFME Framework 11 1.3.2 SRFME Research Portfolio Structure 12 1.4 Collaborative Linkages Program 13 1.4.1 SRFME PhD Scholarships 13 1.4.2 SRFME Collaborative Research Projects 13 1.4.3 State Linkage Projects 13 1.5 SRFME Core Projects 14 1.5.1 Development of the SRFME Core Projects 14 1.5.2 Biophysical Oceanography Core Project 14 1.5.3 Coastal Ecosystems and Biodiversity Core Project 14 1.5.4 Integrated Modelling Core Project 14 CHAPTER 2 15 2. COLLABORATIVE LINKAGES PROGRAM: PhD PROJECTS 15 2.1 SRFME PhD Scholarship Program 15 2.2 SRFME PhD Projects, Students, and Affi liations 15 2.3 PhD Scholars Reports 16 2.3.1 The Development and Validation of Algorithms for Remotely Sensing Case II Waters 16 2.3.2 Remotely Sensing Seasonal and Interannual Oceanic Primary Production for Western Australian Waters 20 2.3.3 Seagrass Responses to Light Availability: A Mechanistic Approach 25 2.3.4 The Role of Detached Macrophyte Accumulations for Fish Production and Biodiversity in Coastal Ecosystems 29 2.3.5 Ichthyoplankton Assemblage Structure in Coastal, Shelf and Slope Waters off South-western Australia 33 2.3.6 Comparisons Between Benthic Macroinvertebrate Assemblages in Estuarine and Nearshore Marine Habitats 37 2.3.7 Uncertainty Associated with Marine Ecosystem Models 39 2.3.8 Coastal Groundwater Discharge and Nutrient Supply in a Semi-enclosed Marine Basin 42 2.3.9 Biogeochemistry of Seagrass Sediments 47 2.3.10 The Infl uence of Benthic Microalgae on Nitrogen Cycling in Western Australia 51 2.3.11 Ecological and Historical Processes Maintaining Macroalgal Diversity in the Recherche Archipelago, Western Australia 54 2.3.12 Diurnal Fluctuations in Primary Production in Shallow Waters off South-western Australia 58 2.3.13 An Investigation of Spatial and Temporal Variations in the Abundance and Species Composition of Microzooplankton and Their Growth and Grazing Rates off Western Australia 60 SRFME interim final report June 2005 1 CHAPTER 3 64 3. COLLABORATIVE LINKAGES PROGRAM: COLLABORATIVE PROJECTS 64 3.1 SRFME Collaborative Projects 64 3.2 SRFME Collaborative Projects, PI’s, and Affi liations 64 3.3 Collaborative Project Reports 65 3.3.1 Interaction of Coastal Currents, Phytoplankton Dynamics and Trophic Transfer in the Coastal Waters of Western Australia 65 3.3.2 Spatial Patterns in Sessile Benthic Sponge and Ascidian Communities of the Recherche Archipelago 72 3.3.3 Understanding the Natural Variability of Currents Along the Western Australian Coastline 78 3.3.4 Ecological Interactions in Coastal Marine Ecosystems: Trophodynamics 89 3.3.5 Ecological Interactions in Coastal Marine Ecosystems: Rock Lobster 98 3.3.6 Ecophysiology of Benthic Primary Producers 104 3.3.7 Biodiversity of Marine Fauna on the Central West Coast 112 3.3.8 Ecological Interactions in Coastal Marine Ecosystems: The Fish Communities and Main Fish Populations of the Jurien Bay Marine Park 116 CHAPTER 4 122 4. COLLABORATIVE LINKAGES PROGRAM: STATE LINKAGES PROJECTS 122 4.1 SRFME State Linkages Projects 122 4.2 SRFME State Linkages Projects, PI’s, and Affi liations 122 4.3 SRFME State Linkages Projects Reports 123 4.3.1 Twelfth International Marine Biological Workshop: The Marine Flora and Fauna of Esperance, Western Australia 123 4.3.2 Establishing Reference and Monitoring Sites to Assess a Key Indicator of Ecosystem Health (Seagrass Health) on the Central West Coast of Western Australia 125 4.3.3 Baseline Biodiversity Monitoring in the Proposed Jurien Bay Marine Park, Survey 3 129 4.3.4 Assessing the Benefi ts of Closed Fishing Areas for Spawning Aggregations and Egg Production for Coral Trout 133 4.3.5 Providing Marine Algal Taxonomic Expertise to Coastal Ecosystem and Biodiversity in Western Australia, a Core CSIRO Work Priority Area, and Preparation of an Interactive Key to the Seagrass Epiphytes 136 4.3.6 Assistance for the Publication of The Marine Flora and Fauna of Esperance, Western Australia 137 2 SRFME interim final report June 2005 CHAPTER 5 143 5. SRFME CORE PROJECT ONE 143 5.1 Biophysical Oceanography off Western Australia: Dynamics across the Continental Shelf and Slope 143 5.2 Investigators 143 5.3 Executive summary 143 5.4 Introduction 145 5.4.1 Background 145 5.4.2 Objectives 146 5.4.3 Field program 147 5.5 Major fi ndings 149 5.5.1 Oceanography and meteorology 150 5.5.1.1 Introduction 150 5.5.1.2 Large-scale perspective 150 5.5.1.3 Meteorology 151 5.5.1.4 The Leeuwin Current and shelf currents 154 5.5.1.5 Oceanographic transects: water properties 158 5.5.2 Phytoplankton dynamics 169 5.5.2.1 Biomass and primary production – methodological considerations 170 5.5.2.2 Results and discussion 177 5.5.3 Mesozooplankton dynamics 187 5.5.3.1 Mesozooplankton communities: abundance and biomass 187 5.5.3.2 Mesozooplankton: estimation of secondary production 192 5.5.3.3 Mesozooplankton grazing 196 5.5.4 Bioacoustics 200 5.5.4.1 Introduction 200 5.5.4.2 Low frequency bioacoustics 200 5.5.4.3 High frequency bioacoustics 204 5.4.4.4 Summary and conclusion 208 5.6 Acknowledgements 208 5.7 References 209 5.8 Conference attendance and presentations 212 5.9 Publications and/or outcomes to date 213 SRFME interim final report June 2005 3 CHAPTER 6 215 6. SRFME CORE PROJECT TWO 215 6.1 Coastal Ecosystems and Biodiversity 215 6.2 Investigators 215 6.3 Executive summary 215 6.4 Introduction 217 6.5 Coastal Project 218 6.6 Spatial patterns in invertebrate communities 238 6.7 Spatial patterns in Jurien Bay fi sh communities 244 6.8 Depth-related variation in nutrient availability on temperate reefs: Use of C:N ratios to assess the nutrient status of macroalgae growing at different depths in the Esperance region, Western Australia 249 6.9 Nitrogen and phosphorous concentrations in seagrasses 257 6.10 Ecological interactions 265 6.11 Spatial subsidies: trophic linkages among habitats at local and cross-shelf scales 277 6.12 Biogeochemistry: Pelagic nutrient supply and cycling 282 6.13 Remote Sensing of coastal ocean colour 291 6.13.1 Overview 291 6.13.1.1 Remote sensing data processing 291 6.13.1.2 Validation 294 6.13.1.3 Modelling and algorithm development 295 6.13.2 Remote Sensing data processing 295 6.13.2.1 Digital Time-series 296 6.13.2.2 SST and chlorophyll images 297 6.13.3 Remote sensing validation 304 6.13.3.1 Sample collection and methods 304 6.13.3.2 Sample location 305 6.13.3.3 Results and Discussion 305 6.13.3.4 Summary 318 6.13.3.5 SST validation 318 6.13.4 Modelling and algorithm development 320 6.13.4.1 Modelling and validation 320 6.13.4.2 Hyperspectral Remote Sensing of Coastal Waters 323 APPENDIX 1 331 APPENDIX 2 332 APPENDIX 3 334 4 SRFME interim final report June 2005 CHAPTER 7 335 7. SRFME CORE PROJECT THREE 335 7.1 Integrated Modelling 335 7.2 Introduction 335 7.3 Investigators 335 7.4 Large-scale ocean processes 337 7.5 Hydrodynamics 344 7.6 Sediment dynamics 354 7.7 Biogeochemical modelling 359 7.8 Benthic habitat modelling 367 7.9 Management Assessment 372 7.10 Visualisation and data delivery 373 7.11 Conference attendance and presentations 379 7.12 Publications and/or outcomes to date 381 7.13 References 382 CHAPTER 8 8. Acknowledgements 385 SRFME interim final report June 2005 5 EXECUTIVE SUMMARY The Strategic Research Fund for the Marine Environment (SRFME) is a 6-year (2001-2006), $20 million joint venture between CSIRO and the Western Australia Government. SRFME has the following as its mission: SRFME will enhance Western Australia’s marine research capability and capacity, deliver strategic research outcomes of benefi t to Western Australia and enhance collaboration among marine researchers in Western Australia. SRFME was established with the following high-level goals: • Build capability and capacity in marine science in Western Australia • Facilitate strong collaboration among the Western Australian marine science community • Conduct fundamental and strategic research that is of benefi t to Western Australia and Australia With these goals and focus in mind, SRFME has invested in strategic research on the Western Australian marine environment in a way which enhances capability and capacity for marine science, encourages collaboration amongst the Western Australian research community and delivers strategic research outcomes which will have long-term benefi ts to the state. This report completed in June 2005 is an interim report aimed at presenting SRFME’s achievements to date to its members, stakeholders and collaborators. Much of the work presented here is still in progress and will be completed over the coming year with a fi nal report for SRFME anticipated in June 2006.