The threatened status of shellfish reefs has been well established globally (e.g Beck et al 2011) however the ecological consequences of these losses is still largely unknown. In Australia, shellfish reefs are one of the most imperilled marine habitat types (Gillies et al 2018), due to historical overharvest and widespread eutrophication of coastal waters through the use of fertilizers, livestock and human waste. Marine bivalves are important ecosystem engineers providing habitat, shelter and a food source for other species in benthic soft-sediment environments. In addition, filter-feeding bivalves link benthic and pelagic components of ecosystems through filtration and excretion. Through their filter feeding, they produce large amounts of faeces (digested seston) and pseudofaeces (rejected particles bound up in mucus) which are deposited on the benthos. This process brings energy and nutrients from the pelagic system to the benthic system (bentho-pelagic coupling). The removal of large quantities of seston can serve an important ecosystem function by improving water quality and clarity. The filtration of water performed by bivalves has been demonstrated to reduce water turbidity, improving light penetration and thereby enhancing growing conditions for seagrasses (Wall et al 2008). In systems where healthy populations of bivalves remain, they can filter a volume equivalent or larger than the entire estuary volume within the residence time of the water (zu Ermgassen et al 2013). While such densities of oysters are rare today, this highlights the critical ecosystem services that are lost when oyster reefs decline. Furthermore, it demonstrates the potential functions that can be regained through oyster reef restoration. Given the increasing awareness of the decline of these ecosystems, interest in restoration efforts to restore critical ecosystem functions has been growing. However, conservation and restoration decision making is underpinned by reliable quantification of relevant ecosystem services (zu Ermgassen et al 2016). For example, there are plans to restore some of the natural oyster reefs of Sydney Rock Oyster (Saccostrea glomerata) in Port Stephens, New South Wales. One of the main drivers motivating this restoration project is restoring lost ecosystem services. The filtration rates of Australian oysters has been demonstrated in aquarium studies using filtered water augmented with algae, yet little is known about filtration and biodeposition rates of oysters using raw seawater. In this study, we provide the first evaluation of the filtration and biodeposition rate of four species of bivalves using raw seawater, providing a proxy for natural biodeposition rates. As such, this study provides a first indication of the filtration/nutrient cycling function that may be restored following oyster restoration efforts.

This record provides an overview of the scope and research output of the NESP Marine Biodiversity Hub project "Improving our understanding of pressures on the marine environment". For specific data outputs from this project, please see child records associated with this metadata. -------------------- The marine environment in Australia is influenced by a wide range of different pressures that impact on different parts of the marine ecosystem in different ways. This project aims to assist DoE, and other research users, to improve understanding of the potential impacts of anthropogenic disturbance to marine conservation values by providing up-to-date data and analyses on the spatial distribution of pressures and trends. The research is designed to inform decision making under the EPBC Act (acceptability of proposed activities, evaluation of effectiveness of mitigation measures) on NMES (including Key Ecological Features), implementation of multiple strategies in four Marine Bioregional Plans (i.e. strategies B, C, D and F), management of Commonwealth Marine Reserves (e.g. strategies 1 and 2 in the South-east Commonwealth Marine Reserve Network Management Plan 2013-23) and State of the Environment reporting. The project will involve a re-examination of the pressure analyses undertaken through the marine bioregional planning program and the 2011 SOE Report (marine chapter) and determine where pressure mapping can be improved to enhance those analyses (for instance for those pressures for which data deficiency was identified). It will also examine the strengths and weaknesses of the different pressure assessment methodologies used by both the MBP process and the SOE 2011 process and propose a methodology that can support both initiatives into the future. The project will provide pressures profiles for CMRs and will assist Parks Australia in understanding how pressures interact with the values they identify in CMRs. The project will also consider relative impact, and how spatial mapping can assist in understanding both relative and cumulative impact. As an adjunct to the cumulative impact investigation, the project will also investigate how changes in socio-economic valuing of conservation values may influence the degree of investment in understanding and management of cumulative impact. This particular work will further the risk-based approach to cumulative impact that was investigated under the NERP Hub. Planned Outputs • Produce description of summary of changes and trends in pressures on the commonwealth marine environment in the offshore marine environment from 1991 to 2010. • Production of inshore and offshore pressure summaries to inform SOE reporting (2011-2015) • Produce description of trends in pressures acting on the commonwealth marine environment (onshore & offshore) between 1991 & 2015, with refined summaries for all KEFs and CMRs. • Distribute pressure data and pressure data summaries through NPEI compliant data infrastructure. • Produce analysis and description of the likely future states (for example, climate (interannual and decadal), shipping, modification of fisheries activity, coastal eutrophication) • Re-evaluation of the pressure assessments published in the 2012 Marine Bioregional Plans , ensuring consistency of output, updating the profiles for all KEFs • Report on the changing socio-economic valuing of conservation values to the concept of acceptable impact, or acceptable risk of impact • Report on a risk based framework to manage the uncertainty information bases for different decision making requirements with example case

The Marine Futures Project was designed to benchmark the current status of key Western Australian marine ecosystems, based on an improved understanding of the relationship between marine habitats, biodiversity and our use of these values. Approximately 1,500 km2 of seafloor were mapped using hydroacoustics (Reson 8101 Multibeam), and expected benthic habitats "ground-truthed" using towed video transects and baited remote underwater video systems. Both sources of information were then combined in a spatial predictive modelling framework to produce fine-scale habitat maps showing the extent of substrate types, biotic formations, etc. Surveys took place across 9 study areas, including Broke Inlet, a relatively remote area 400km south of Perth, between the towns of Augusta and Albany. The nearest major town, Manjimup, is situated 100km north and the small coastal settlement Windy Harbour approximately 30km west of Broke Inlet. The Inlet is entirely surrounded by the D’Entrecasteaux National Park, which is accessible via a sealed road and attracts limited ‘through-traffic’ to the area. The marine environment off Broke is one fairly untouched by major tourism pressures and thus this location was selected due to its relative inaccessibility.

The Marine Futures Project was designed to benchmark the current status of key Western Australian marine ecosystems, based on an improved understanding of the relationship between marine habitats, biodiversity and our use of these values. Approximately 1,500 km2 of seafloor were mapped using hydroacoustics (Reson 8101 Multibeam), and expected benthic habitats "ground-truthed" using towed video transects and baited remote underwater video systems. Both sources of information were then combined in a spatial predictive modelling framework to produce fine-scale habitat maps showing the extent of substrate types, biotic formations, etc. Surveys took place across 9 study areas, including the Abrolhos Islands, a group of 122 limestone outcrops surrounded by fringing reed ca. 60km west from the city of Geraldton. The Abrolhos research location is the most northerly of the Marine Futures sampling sites, selected due to the unique mixture of tropical coral reef habitats, and temperate reef and seagrass communities.The hydroacoustics data were processed to construct full coverage maps of bathymetry and textural information.

This record provides an overview of the scope and research output of the NESP Marine Biodiversity Hub project "Analysis and elicitation to support State of the Environment reporting for the full spectrum of data availability". No data outputs were generated by this project. -------------------- The availability and quality of observation data that may be used to support State of the Environment reporting lies on a spectrum from: (i) high quality (e.g. Reef Life Survey, Long term reef monitoring programme, Temperate Reef Monitoring programme, state-based MPA monitoring programmes); (ii) moderate quality (e.g. continuous plankton recorder, occasional by catch surveys); (iii) low quality (anecdotal information) to (iv) expert beliefs but no empirical observations. We currently lack a principled process for utilising and merging data of varying quality and from different sources to form a national perspective to support State of the Environment reporting. The key unifying principle to support such a process is the extent to which the available data is representative of the environmental asset in question. As the extent to which the empirical observations accurately represent the state of the asset in both space and time diminishes, so the reliance on expert opinion increases, to the limit where the only available information is expert opinion. This project will provide an over-arching framework to consider these issues, develop practical protocols for blending different data streams with or without experts’ judgement as appropriate, and thereby provide a foundation for improving State of Environment reporting for all types of data sources, from high to low quality. It will do this by developing and applying protocols to support development of the marine chapter of SoE 2106. This currently being developed within a separate CSIRO funded project. The project will use the experience of developing this chapter to make recommendations about appropriate methodologies for future environmental reporting. Importantly the statistical approach and analysis principles will be consistent regardless of the amount or quality of the information available. As a result the framework and analysis methods will remain relevant, even as the quality and quantity of environmental data at the department’s disposal changes. This will provide the consistency of analysis and reporting that is essential to SoE. Expected Outcomes • The provision of two or three examples that demonstrate a unified approach to the use of expert opinion in SoE reporting. These examples will be identified in close collaboration with the Department and will be developed in time to support the marine chapter of 2016 State of the Environment report, contingent on the availability of resources in the second year of the project and timely interaction with the department. • Assessments of the status and trends of environmental assets in the State of the Environment report will be based on a principled and statistically defensible process that can merges and utilises data from all sources including expert opinion.

Between 2009-2012, Geoscience Australia conducted three surveys to Joseph Bonaparte Gulf and the Timor Sea on the R.V. Solander, in collaboration with the Australian Institute of Science and the Museum and Art Gallery of the Northern Territory. The study areas overlapped the Oceanic Shoals Commonwealth Marine Reserve and the carbonate banks and terraces within it. The surveys were conducted as part of the Australian Government's Energy Security Program (2007-2011) and the National Environment Research Program (2011-2015). On the surveys, a benthic sled was deployed to collect biological samples from the seafloor. Samples were sorted onboard according to phylum, photographed and then sent to taxonomists for species-level identifications. This catalogue includes all onboard photographs taken from identified samples. Sponges were the only group of which all samples were identified, but they include high proportions of unnamed or undescribed species. The catalogue also includes taxonomic identification sheets so that users can cross-reference the species names and images with location and depth.

This record provides an overview of the scope and research output of the NESP Marine Biodiversity Hub project "Road testing decision support tools via case study applications". No data outputs were generated by this project. -------------------- This project will deploy advances in decision-support to assist Commonwealth Marine Reserve managers progress the implementation of evidence-based adaptive management throughout the reserve estate. Two case studies will treat selected decision problems in detail. Specifically: • The identification of decision thresholds that may trigger a change in management, framed within Parks Australia’s performance monitoring template. • The prioritisation of information acquisition through research and monitoring. The two case studies involve coherent integration of ecological models, social and organisational value judgements, and economic analysis. Planned Outputs • Progress reports describing interim outcomes of the (a) decision thresholds and (b) research and monitoring prioritisation case studies. • At least two publications in high impact peer-reviewed journals. • Two final reports describing outcomes of the (a) decision thresholds and (b) research and monitoring prioritisation case studies. • At least two publications in high impact peer-reviewed journals. • Training and associated materials

Point data collected from video drops identifying benthic habitats such as seagrass, macroalgae and reef, collected during field work in 2007 to 2011. Used to support the Benthic Habitat Mapping project undertaken by DENR to map the nearshore benthic habitats of South Australia