In November 2012, the Australian Government finalised a national network of Commonwealth Marine Reserves (CMR) covering 3.1 million km2 and representing the full range of large scale benthic habitats known to exist around mainland Australia. This network was designed using the best available regional-scale information, including maps of seabed geomorphic features and associated Key Ecological Features. To support the management objectives of the marine reserves, new site-specific information is required to improve our understanding of biodiversity patterns and ecosystem processes across a range of spatial scales. In this context, the Marine Biodiversity Hub (funded through the National Environmental Research Program) recently completed a collaborative 'voyage of discovery' to the Oceanic Shoals CMR in the Timor Sea. This area was chosen because it hosts globally significant levels of biodiversity (including endemic sponge and coral taxa), faces rapidly increasing pressures from human activities (offshore energy industry, fishing) yet is recognised as one of the most poorly known regions of Northern Australia. Undertaken in September 2012 on board RV Solander, the survey acquired biophysical data on the shallow seabed environments for targeted areas within the Oceanic Shoals CMR, with a focus on the carbonate banks that characterise this tropical shelf and are recognised as a Key Ecological Feature. Data collected included 500 km2 of high resolution (300 kHz) multibeam sonar bathymetry and acoustic backscatter across four grids, plus seabed sediment samples, underwater tow-video transects (~1 km length), pelagic and demersal baited underwater video, epifaunal and infaunal samples and water column profiles at pre-determined stations. Station locations were designed to provide a random but spatially balanced distribution of sample sites, with weighting toward the banks. This design also facilitated observations of patterns of benthic biodiversity at local to feature-scale and transitions associated with depth-gradients and exposure to tidal currents. Results reveal the banks are broadly circular to elliptical with steep sides, mantled by muddy sand and gravel with areas of hard ground. Rising to water depths of 50-70 m, the banks support benthic assemblages of sponges and corals (including hard corals at shallower sites) which in turn support other marine invertebrates. In strong contrast, the surrounding seabed is characterised by barren, mud-dominated sediments in 70-100 m water depth, although infaunal samples reveal diverse biological communities beneath the seafloor. While the bank assemblages are locally isolated, the potential exists for connectivity between shoals via tide-driven larval dispersal. Ongoing work is aimed at identifying species to determine overlap between bank communities, as well as modelling the sources, pathways and sinks for larvae as a proxy for understanding the physical processes controlling the patterns of biodiversity across the Oceanic Shoals CMR at multiple scales.

Geoscience Australia's GEOMACS model was utilised to produce hindcast hourly time series of continental shelf (~20 - 300 m depth) bed shear stress (unit of measure: Pascal, Pa) on a 0.1 degree grid covering the period March 1997 to February 2008 (inclusive). The hindcast data represents the combined contribution to the bed shear stress by waves, tides, wind and densitydriven circulation. Ecological data collected from Torres Strait suggests that bed shear stresses exceeding 0.4 Pa are important in determining the species present (Long, Bode, & Pitcher 1997). Although this data may not be representative of other regions or benthic communities, it has been utilised to calculate two parameters for determining the relationship between shear bed stress and the benthic community. One of the parameters, which is denoted by , and is calculated using; represents the stress in excess of 0.4 Pa integrated over time as a proportion of the total stress integrated over time, and is intended to represent the proportion of the total integrated stress that has some control on the benthic community (Hughes & Harris 2008).

Submerged relict reef systems and modern coral communities discovered around the Balls Pyramid shelf are presented as new evidence of extensive carbonate production at the boundary of reef-forming seas. Balls Pyramid is the southernmost island in a chain of island-reefs in the southwest Pacific Ocean, 24 km south of the southernmost known coral reef in the Pacific Ocean at Lord Howe Island. This paper explores the detailed geomorphic structure of the shelf through the production of a high resolution bathymetric model from multibeam echosounder data and depth estimates from satellite imagery. Key seafloor features identified include a large, mid shelf reef dominating the shelf landscape in 20 - 60 m water depth, mid shelf basins and channels, and shelf margin terrace sequences in 50 - 100 m depth. Sub-bottom profiles, backscatter, drill core and vibro-core data are used to investigate the seafloor composition. Drill cores extracted from the submerged reef surface confirm coral, coralline algae and cemented sands composition, and vibro-core material extracted from unconsolidated areas demonstrate substantial accumulation of carbonates shed from the reef surface. Underwater video imagery reveals abundant modern mesophotic reef communities, including hard corals, colonising the relict reef surface. This paper reveals prolific past reef growth and abundant modern coral growth on what was previously considered to be a planated volcanic shelf outside of reef-forming seas, thus extending understanding of reef evolution at, and beyond, the limits of growth.

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 wavegenerated 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. jb_s1 is an ArcINFO grid of southern part of Jervis Bay survey area (south1 is part of Darling RD grid) produced from the processed EM3002 bathymetry data using the CARIS HIPS and SIPS software

This dataset contains sediment and geochemistry information for the Oceanic Shoals Commonwealth Marine Reserve (CMR) in the Timor Sea collected by Geoscience Australia during September and October 2012 on RV Solander (survey GA0339/SOL5650). Further information on the survey is available in the post-survey report published as Geoscience Australia Record 2013/38: Nichol, S.L., Howard, F.J.F., Kool, J., Stowar, M., Bouchet, P., Radke, L., Siwabessy, J., Przeslawski, R., Picard, K., Alvarez de Glasby, B., Colquhoun, J., Letessier, T. & Heyward, A. 2013. Oceanic Shoals Commonwealth Marine Reserve (Timor Sea) Biodiversity Survey: GA0339/SOL5650 - Post Survey Report. Record 2013/38. Geoscience Australia: Canberra. (GEOCAT #76658).

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 wavegenerated 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. jb_s4 is an ArcINFO grid of southern part of Jervis Bay survey area (south4 is part of Darling RD grid) produced from the processed EM3002 bathymetry data using the CARIS HIPS and SIPS software

Northern Australia has been the focus of recent marine biodiversity research to support resource management for both industry and conservation. Much of this research has targeted habitat-forming sessile invertebrates and charismatic megafauna, but smaller macrofauna and infauna must also be considered due to their important roles in ecosystem functions. In this study, a Smith-McIntyre grab was used during two surveys in 2009 and 2010 to the Joseph Bonaparte Gulf to collect sediment samples which were then elutriated over a 500µm sieve. The associated polychaetes were identified to species-level. A total of 2224 individual polychaetes were collected from 133 grabs and represent 43 families, including several new species, at least one new genus (Pilargidae) and many new distribution records. Biodiversity patterns were also analysed according to environmental and spatial factors (grain-size, carbonate, total organic content, depth, distance offshore) in order to inform predictive models and further our understanding of ecosystem processes in the region. These patterns differ from those of larger epifauna collected on the same surveys, highlighting the need to consider small macrofauna in biodiversity research and associated marine management.

Marine benthic biodiversity can be quantified using a range of sampling methods, including benthic sleds or trawls, grabs, and imaging systems, each of which targets a particular community or habitat. Research studies often incorporate only one of these sampling methods in published results, and the generality of marine biodiversity patterns identified among different sampling methods remains unknown. In this study we use three biological collections obtained during a collaborative survey between Geoscience Australian and the Australian Institute of Marine Science to the Van Diemen Rise in northern Australia: 1) Infauna sampled from a Smith-McIntyre grab, 2) Epifauna sampled from a benthic sled, and 3) Biological communities identified from video. For each dataset, we investigated potential patterns of species richness and community structure in relation to depth, geomorphology, and study area, as well as the relationships between datasets. No gear type yielded data that was strongly correlated with depth, but different patterns were evident among gear types based on study area and geomorphology. Comparisons among datasets indicate that species richness from sleds and grabs are more strongly correlated with each other than with richness from video. Further research is planned to incorporate datasets from other regions and habitats in order to provide a general assessment of sampling methods used in the quantification of benthic marine biodiversity in Australasia.

Submarine canyons are recognised as having an influence on oceanographic processes, sediment transport, productivity and benthic biodiversity from the shelf to the slope. However, not all canyons are the same and the relative importance of an individual canyon will, in part, be determined by its form, shape and position on the continental margin. Here we present an analysis of these parameters using an updated national dataset of 713 submarine canyons for the margin of mainland Australia. Attribute data for each canyon is used to classify them into canyon types across a hierarchy of canyon physical characteristics for shelf-incised and slope-confined (blind) canyons. At each level on the hierarchy, large groupings of canyons are identified that represent common sets of characteristics. The spatial distribution of canyons on the Australian margin is not regular, with clusters located in the east, southeast, west and southwest. The northern margin has the lowest concentration of canyons. We also assess the potential productivity associated with the various canyon types using chlorophyll-a data derived from satellite (MODIS) images. Shelf-incised canyons are associated with significantly higher and more temporally variable chlorophyll-a concentrations, consistent with their function as conduits for upwelling. Australian submarine canyons are well represented in the national network of marine protected areas, with 36 percent of the mapped canyon population intersecting (whole or in part) a Commonwealth Marine Reserve. This information is relevant to setting priorities for the management of these reserves. Results from this study provide a framework for further analysis of the relative importance of canyons on the Australian margin.

Baseline information on biodiversity and habitats is required to manage Australia's northern tropical marine estate. This study aims to develop an improved understanding of seafloor environments of the Timor Sea. Clustering methods were applied to a large dataset comprising physical and geochemical variables which describe organic matter (OM) reactivity/quantity/source and geochemical processes. Infauna data were used to assess different groupings. Clusters based on physical/geochemical data discriminated infauna better than geomorphic features. Major variations amongst clusters included grainsize and a cross-shelf transition in from authigenic-Mn /As enrichments (inner shelf) to authigenic-P enrichment (outer shelf). Groups comprising raised features had the highest reactive OM concentrations (e.g. low chlorin indices and C:N-ratios, and high k) and benthic algal '13C signatures. Surface area normalised OM concentrations higher than continental shelf norms were observed in association with: (i) low -15N, inferring Trichodesmium input; and (ii) pockmarks, which impart bottom-up controls on seabed chemistry and cause inconsistencies between bulk and pigment OM pools. Low Shannon-Wiener diversity occurred in association with low redox and porewater pH and evidence for high energy. Highest beta-diversity was observed at euphotic depths. Geochemical data and clustering methods used here provide insight into ecosystem processes influencing biodiversity patterns in the region.