A series of short field surveys in Jervis Bay, New South Wales, were undertaken by Geoscience Australia staff as part of the Surrogates Program in the Commonwealth Environmental Research Facilities (CERF) Marine Biodiversity Hub. The aim of the Jervis Bay field work was to collect accurately co-located physical and biological data to enable research into the utility of physical parameters as surrogates for patterns of benthic biodiversity in shallow soft-sediment habitats. In this report the survey design and sampling methods are described; selected field datasets are mapped and discussed; initial results of the laboratory analysis of seabed samples are presented; and there is a brief description of the upcoming analysis of covariance of the physical and biological datasets. The major outputs of the survey work to date are: 1. High-resolution multibeam acoustic datasets for priority areas along the open coast of Jervis Bay (Beecroft Head to Drum and Drumsticks), within the Jervis Bay National Park; and within the southern bay around Darling Road, and in the bay entrance. 2. High quality underwater video footage of benthic habitats in the Darling Road study area acquired with Geoscience Australia's shallow-water towed-video system. The video was used to characterise benthic habitat types, relief/bedform types, and biota occurrence. Characterisations were collected in real-time along bi-directional (six offshore and four alongshore) towed video transects, and were subsequently processed and mapped into three ArcGIS map layers. 3. A set of broad-scale (bay-wide) widely-spaced, co-located sediment and biotic (infauna) seabed samples from the bay's soft-sediment habitats (polychaete mounds, drift algal beds, sand flats, and sand ripple and wave habitats); 4. Sediment samples for geochemical, biogeochemical and sedimentological analyses. 5. A new acoustic doppler current profiler was successfully trialed, and is now being used to collect seabed current data in the Darling Road study area. 6. A progress report on the survey work was presented at the annual CERF Marine Biodiversity Hub's Annual Science Workshop in October 2008.

Williams et al. (2009) report on new multibeam sonar bathymetry and underwater video data collected from submarine canyons and seamounts on Australia's southeast continental margin to 'investigate the degree to which geomorphic features act as surrogates for benthic megafaunal biodiversity' (p. 214). The authors describe what they view as deficiencies in the design of the Marine Protected Areas (MPAs) in the southeast region of Australia, in which geomorphology information was employed as a surrogate to infer regional-scale patterns of benthic biodiversity. This comment is designed to support and underscore the importance of evaluating MPA designs and the validity of using abiotic surrogates such as geomorphology to infer biodiversity patterns, and seeks to clarify some of the discrepancies in geomorphic terminologies and approaches used between the original study and the Williams et al. (2009) evaluation. It is our opinion that the MPA design criteria used by the Australian Government are incorrectly reported by Williams et al. (2009). In particular, we emphasise the necessity for consistent terminology and approaches when undertaking comparative analyses of geomorphic features. We show that the MPA selection criteria used by the Australian Government addressed the issues of false homogeneity described by Williams et al. (2009), but that final placement of MPAs was based on additional stakeholder considerations. Finally, we argue that although the Williams et al. (2009) study provides valuable information on biological distributions within seamounts and canyons, the hypothesis that geomorphic features (particularly seamounts and submarine canyons) are surrogates for benthic biodiversity is not tested explicitly by their study.

Disturbances characterise many natural environments - on land, a forest fire that removes a patch of old-growth trees is an example. The trees that first colonise the vacant patch may be a different species to the surrounding old-growth forest and hence, taken together, the disturbed and undisturbed forest has a higher biodiversity than the original undisturbed forest. This simple example demonstrates the intermediate disturbance hypothesis (IDH) that has applications in many natural environments. The application of IDH is significant for managers tasked with managing and conserving the biodiversity that exists in a given area. In this report we have used models of seabed sediment mobilisation to examine IDH for Australia's continental shelf environment. Although other disturbance processes may occur (eg. biological, temperature, salinity, anthropogenic, etc.) our study addresses only the physical disturbance of the seabed by waves and currents. Our study has shown that it is feasible to model the frequency and magnitude of seabed disturbance in relation to the dominant energy source (wave-dominated shelf, tide-dominated shelf or tropical cyclone dominated shelf). We focussed our attention on high-energy, patch-clearing events defined as exceeding the Shields parameter value of 0.25. Based on what is known about rates of ecological succession for different substrate types (gravel, sand, mud) we derive maps predicting the spatial distribution of a dimensionless ecological disturbance index (ED). Only a small portion of the shelf (perhaps ~10%) is characterised by a disturbance regime as defined here. Within these areas, the recurrence interval of disturbance events is comparable to the rate of ecological succession and meets our defined criteria for a disturbance regime. To our knowledge, this is the first time such an analysis has been attempted for any continental shelf on the earth.

The Marine Biodiversity Hub was funded by the Australian Government Commonwealth Environmental Research Facilities (CERF) between 2007 and 2010. The Hub was developed to improve the scientific knowledge available to support marine bioregional planning and addressed two fundamental questions: 1. How can we predict the distribution of marine biodiversity; and 2. How can we use this improved capability to conserve and manage biodiversity in a multiple-use environment? This talk focuses on the Surrogates Program, one of four research programs in the Hub. The Surrogates Program addressed the above questions by testing and developing physical variables as surrogates of marine biodiversity, with a focus on seabed environments. In the program, we employed a range of marine survey technologies to collect high-quality and co-located benthic physical and biological data at four selected areas in temperate and tropical waters. We also developed advanced spatial and statistical approaches to test the degree of covariance between the physical and biological data, identify ecological processes, and generate prediction maps. During a number of field campaigns, we deployed a range of instruments to collect data including multibeam sonar, sediment grabs, benthic sleds, towed-video/still images and Autonomous Underwater Vehicles. GIS, machine-learning models and the SWAN hydrodynamic model were used to derive and predict a large number of physical variables as potential surrogates. The effectiveness of the surrogacy approaches were examined using multivariate analyses and spatial modelling techniques. In general, we found that using physical surrogates to predict marine biodiversity is a cost-effective approach. The new knowledge of surrogates and seabed ecological processes directly supports the management of the Australian marine estate. Other major outputs of the Surrogates Program include: - Thirty-seven new and updated national-scale marine physical environmental datasets; - High resolution bathymetry of targeted areas, covering almost 2000 km2, plus 171 km of underwater video transects, 402 sediment grab samples and 232 epifauna samples; - New seabed exposure and fetch models/datasets; and - Peer-reviewed reports and papers in scientific journals. The success of the Marine Biodiversity Hub has enabled the Hub to be refunded for a further four years through the new National Environmental Research Program. In this, Geoscience Australia (GA) is collaborating with the University of Tasmania, CSIRO Marine & Atmospheric Research, Australian Institute of Marine Science, Museum of Victoria, University of Western Australia and Charles Darwin University; GA is also leading Theme 3 Project 1 which focuses on identifying the functions and processes of shelf and canyon ecosystems. The project is expected to further advance marine biodiversity research in Australia by investigating the role of large-scale physical features on the shelf in influencing patterns of marine biodiversity.

The Tasmanian Shelf survey was conducted on the Challenger in collaboration with the Tasmanian Aquaculture and Fisheries Institute between the 13-16th June, 2008 and 23rd February to the 14th March, 2009 (GA survey #0315). The survey was operated as part of the Surrogates Program of the CERF Marine Biodiversity Hub. The objective was to collect co-located physical and biological data to enable the robust testing of a range of physical parameters as surrogates of benthic biodiversity patterns. A total of 55 video transects were surveyed from five study areas (Tasman Peninsula, Freycinet Peninsula, The Friars, Huon river, and Port Arthur channel) in water depths ranging from 15-110 m. Video was recorded to mini DV tapes, and copied to digital format. For further information on this survey please refer to the post-survey report (GA Record 2009/043 - Geocat #69755).

Geoscience Australia carried out marine surveys in Jervis Bay (NSW) in 2007, 2008 and 2009 (GA303, GA305, GA309, GA312) to map seabed bathymetry and characterise benthic environments through co-located sampling of surface sediments (for textural and biogeochemical analysis) and infauna, observation of benthic habitats using underwater towed video and stills photography, and measurement of ocean tides and wave-generated currents. Data and samples were acquired using the Defence Science and Technology Organisation (DSTO) Research Vessel Kimbla. Bathymetric mapping, sampling and tide/wave measurement were concentrated in a 3x5 km survey grid (named Darling Road Grid, DRG) within the southern part of the Jervis Bay, incorporating the bay entrance. Additional sampling and stills photography plus bathymetric mapping along transits was undertaken at representative habitat types outside the DRG. The GA0309_0312_JervisBay2008 folder contains video footage; the GA0326_JervisBay2009 folder contains still images; and the files are the video characterisation datasets. Underwater towed-video footage and still images represent the raw data. Video characterisation datasets include substrata types and the presence/absence of benthic taxa.

Geoscience Australia carried out marine surveys in Jervis Bay (NSW) in 2007, 2008 and 2009 (GA303, GA305, GA309, GA312) to map seabed bathymetry and characterise benthic environments through co-located sampling of surface sediments (for textural and biogeochemical analysis) and infauna, observation of benthic habitats using underwater towed video and stills photography, and measurement of ocean tides and wave-generated currents. Data and samples were acquired using the Defence Science and Technology Organisation (DSTO) Research Vessel Kimbla. Bathymetric mapping, sampling and tide/wave measurement were concentrated in a 3x5 km survey grid (named Darling Road Grid, DRG) within the southern part of the Jervis Bay, incorporating the bay entrance. Additional sampling and stills photography plus bathymetric mapping along transits was undertaken at representative habitat types outside the DRG. Sample/species matrix of infaunal taxa derived from Van Veen grab samples taken on the HMS Kimbla surveys GA0312 and GA0315 in Jervis Bay.

Geoscience Australia carried out a marine survey on Carnarvon shelf (WA) in 2008 (SOL4769) to map seabed bathymetry and characterise benthic environments through colocated sampling of surface sediments and infauna, observation of benthic habitats using underwater towed video and stills photography, and measurement of ocean tides and wave generated currents. Data and samples were acquired using the Australian Institute of Marine Science (AIMS) Research Vessel Solander. Bathymetric mapping, sampling and video transects were completed in three survey areas that extended seaward from Ningaloo Reef to the shelf edge, including: Mandu Creek (80 sq km); Point Cloates (281 sq km), and; Gnaraloo (321 sq km). Additional bathymetric mapping (but no sampling or video) was completed between Mandu creek and Point Cloates, covering 277 sq km and north of Mandu Creek, covering 79 sq km. Two oceanographic moorings were deployed in the Point Cloates survey area. The survey also mapped and sampled an area to the northeast of the Muiron Islands covering 52 sq km. Sample/species matrix of infaunal taxa derived from Carnarvon Shelf grab samples taken on the RV Solander cruise Sol4769.

Geoscience Australia carried out a marine survey on Carnarvon shelf (WA) in 2008 (SOL4769) to map seabed bathymetry and characterise benthic environments through colocated sampling of surface sediments and infauna, observation of benthic habitats using underwater towed video and stills photography, and measurement of ocean tides and wave generated currents. Data and samples were acquired using the Australian Institute of Marine Science (AIMS) Research Vessel Solander. Bathymetric mapping, sampling and video transects were completed in three survey areas that extended seaward from Ningaloo Reef to the shelf edge, including: Mandu Creek (80 sq km); Point Cloates (281 sq km), and; Gnaraloo (321 sq km). Additional bathymetric mapping (but no sampling or video) was completed between Mandu creek and Point Cloates, covering 277 sq km and north of Mandu Creek, covering 79 sq km. Two oceanographic moorings were deployed in the Point Cloates survey area. The survey also mapped and sampled an area to the northeast of the Muiron Islands covering 52 sq km. Sample diversity indices calculated in PRIMER (version 6) using the species level data from Carnarvon_infauna(26_Oct_2010).xls

Geoscience Australia carried out marine surveys in Jervis Bay (NSW) in 2007, 2008 and 2009 (GA303, GA305, GA309, GA312) to map seabed bathymetry and characterise benthic environments through colocated sampling of surface sediments (for textural and biogeochemical analysis) and infauna, observation of benthic habitats using underwater towed video and stills photography, and measurement of ocean tides and wave generated currents. Data and samples were acquired using the Defence Science and Technology Organisation (DSTO) Research Vessel Kimbla. Bathymetric mapping, sampling and tide/wave measurement were concentrated in a 3x5 km survey grid (named Darling Road Grid, DRG) within the southern part of the Jervis Bay, incorporating the bay entrance. Additional sampling and stills photography plus bathymetric mapping along transits was undertaken at representative habitat types outside the DRG. Family per sample matrix generated by aggregating species level data in JBinfauna_species (25Oct10).xls using the information in JBinfauna_Taxa_info (25Oct10).xls.