Bringing fish life back to Noosa: restoring lost oyster reef habitats in the Noosa Biosphere Final Report Dr Ben Gilby, Prof. Thomas Schlacher, Dr Andrew Olds, Prof. Rod Connolly, Dr Christopher Henderson, Miss Cassandra Duncan, Mr Nicholas Ortodossi, Mr Thomas Brook, Ms Felicity Hardcastle, and Mr Ashley Rummell. School of Science and Engineering University of the Sunshine Coast QLD, 4556, Australia 1 Table of Contents Acknowledgement to project partners and contributors ……..….…………………………………..…………..……. 3 Summary ………………………………………………………………………………………………………………….…..…………..……. 4 Chapter 1: Introduction and background to the Noosa River Oyster Reef Restoration Trail …………….. 9 Chapter 2: Spatial restoration ecology: placing restoration in a landscape context ………....……..….… 29 Chapter 3: Maximising the benefits of oyster reef restoration for finfish and their fisheries ..…………51 Chapter 4: Seascape context modifies how fish respond to restored oyster reef structures …….……79 Chapter 5: Landscape context modifies the rate and distribution of predation around habitat restoration sites …………………………………………………………………………………………………………………….….……99 Chapter 6: Effects of oyster reef restoration extend across coastal seascapes…………………………...…119 Chapter 7: Identifying restoration hotspots to maximise outcomes for multiple restoration benefits ………………………………………………………………………………………………………………………………………………….…..135 References …………………………….………………………………………………………………………………….…….…….…….160 Appendix: Monitoring of the Noosa River Oyster Reefs; November 2017 - November 2018: Report to Noosa Council, and Queensland Department of Agriculture and Fisheries ……….………..……………..…190 2 Acknowledgement to project partners and contributors The authors acknowledge Noosa Council, Noosa Biosphere Reserve Foundation, The Thomas Foundation, Noosa Parks Association and the University of the Sunshine Coast for providing funding for this research and for championing oyster reef restoration efforts in the Noosa River. The authors particularly acknowledge the generous contributions of Chris Gillies (The Nature Conservancy, Australia), Cherie O’Sullivan (Noosa Council), Michael Gloster (NPA) and Simon Walker (Ecological Service Professionals) to the restoration efforts in Noosa. The authors acknowledge the contribution of our co-authors Charles Peterson (University of North Carolina), Christine Voss (University of North Carolina), Melanie Bishop (Macquarie University), Michael Elliot (University of Hull) and Jonathan Grabowski (Northeastern University) towards the concepts and ideas discussed in chapter three. Finally, the authors acknowledge the efforts of Nicholas Yabsley, Hayden Borland, Sarah Thackwray, Ellen Bingham, Jarren Collins, Tyson Jones and Lucy Goodridge Gaines and countless other student volunteers from University of the Sunshine Coast towards field work and the processing of data. 3 Summary Ecological restoration facilitates the recovery of ecosystems and can augment or re-establish animal populations both at restoration sites and across landscapes more broadly. With increasing recognition of the damage that human activities have on ecosystems, ecological restoration activities are increasing in both prevalence and scale across marine, freshwater and terrestrial ecosystems globally, and often have specific goals around enhancing both lost or degraded ecosystems, and the animal populations that those ecosystems support. Despite this, there has been relatively few studies that have quantified the effects of ecological restoration on multiple attributes of restored ecosystems, and then used this information to optimise the design and placement of subsequent efforts. Oyster reefs, a biogenic coastal ecosystem providing habitat for a diversity of estuarine species, are significantly threatened by human activities. Globally, up to 85% of oyster reefs have been lost, and some regions have experienced up to 96% loss due to the combined effects of disease, declining water quality, and overharvesting. This loss of structurally complex oyster reefs from coastal and estuarine ecosystems has been hypothesised as a significant contributor towards fish diversity and fisheries declines in many coastal systems. Consequently, oyster reef restoration has increased in prevalence globally. Whilst these efforts have increasingly focused on enhancing the abundance and diversity of fish and fisheries at restoration sites, few studies have quantified the effects of oyster restoration on fish in regions outside of North America, on the ecological functions that fish provide around restored reefs, or the degree to which the benefits of oyster restoration expand across entire estuaries. Consequently, this sort of information has rarely been used to optimise oyster reef restoration plans and monitoring programs. The Noosa River oyster reef restoration trial is the first shellfish restoration project installed in Queensland, Australia. The project sought to restore the structurally complex oyster reefs that were once abundant in the Noosa River, thereby enhancing habitat availability and complexity for fish species of commercial and recreational significance, and subsequently the important ecological functions that these species perform. We installed and surveyed 14 oyster reef restoration sites in the Noosa River estuary, that were placed to encompass differences in seascape connectivity and proximity to nearby mangroves, seagrasses, urban structures and the estuary mouth. These reefs therefore provide the optimal study design to test for the effects of spatial placement and design of oyster restoration actions on fish, fisheries and ecological functions. This report has six key aims. We set the global context for the oyster reef restoration project in Noosa by (1) identifying the degree to 4 which landscape context is considered in the selection of restoration sites across all environmental realms globally; and (2) identifying gaps in the global understanding of the effectiveness of oyster restoration fin fish, and synthesise current research to optimise future outcomes. We then used the oyster restoration sites in the Noosa River estuary to; (3) identify whether the seascape context of restored oyster reefs (especially seascape connectivity with seagrasses and mangroves) modifies the degree to which they augment fish abundance and diversity; (4) determine the effects of oyster reef restoration on the rate and distribution of the key ecological function of predation at and around the restored oyster reefs; (5) quantify how restored oyster reefs influence the distribution and abundance of fish across the estuary (i.e. beyond the reefs themselves) ; and (6) use spatial modelling techniques to optimise the placement of subsequent oyster reef restoration efforts in the river for oyster growth, fish, fisheries and ecological functioning by incorporating all information gathered in chapters 3, 4 and 5, and our 2018 annual monitoring report. To identify the degree to which landscape context (i.e. the size, shape, and spatial arrangement of ecosystems) is considered when selecting restoration sites globally (see Chapter 2), we reviewed restoration projects from the global primary literature. Fewer than one in eight restoration projects considered landscape context in the selection of restoration sites (11% of 472 projects). This figure was remarkably similar across terrestrial (10% of 243 projects), marine (13% of 89) and freshwater (13% of 164) ecosystems. Of the 54 restoration projects that considered landscape context in site selection, just over half (56%) reported that animal populations were larger or more diverse than in control areas. These results indicate that more tightly integrating concepts from spatial ecology and systematic conservation planning into restoration practice, such as the consideration of the landscape context, could improve the design, optimise placement and enhance the ecological effectiveness of restoration projects in all ecosystems. To identify gaps in the global understanding of the effectiveness of oyster restoration for finfish and synthesise current research to optimise future outcomes (see Chapter 3), we reviewed the global literature of oyster reef restoration for finfish. Global declines in oyster reefs have resulted in reduced habitat heterogeneity, extent, and quality for some coastal finfish, potentially reducing fish populations and catches. Although, it is well established that habitat restoration results in higher finfish biomass and diversity where oyster reefs replace bare sand or mud substrates, the principles of habitat quality, ecological connectivity and broader ecosystem management are poorly integrated within oyster reef restoration ecology. The inclusion of such principles could be instructive in enhancing the benefits of projects on fish populations throughout estuarine seascapes and increase 5 stakeholder engagement and cost-effectiveness. This review presents a framework for projects seeking to restore both oyster reef habitat and finfish communities. To identify whether the seascape context of individual reefs modifies the degree to which they augment fish abundance and diversity (see Chapter 4), we used baited remote underwater video stations (BRUVS) to survey fish assemblages at the 14-oyster reef and at control sites. The seascape context of coastal ecosystems plays a pivotal role in shaping patterns in fish recruitment, abundance and diversity, however, there is a paucity of information regarding the trajectories in which these relationships follow whilst