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.

This resource contains multibeam sonar backscatter data for the continental shelf area of Flinders Commonwealth Marine Reserve, northeast Tasmania. Multibeam data were collected by Geoscience Australia and University of Tasmania in May 2011 (survey GA0331) and June-July 2012 (survey GA0337) on RV Challenger. The survey used a Kongsberg EM3002 300 kHz multibeam sonar system mounted in single head configuration to broadly classify the seabed into hard (bedrock reef), soft (sedimentary) and mixed substrate types at select locations across the shelf. The 2011 survey involved reconnaissance mapping along a series of cross-shelf transects, covering a total of 767 line km. For the 2012 survey, multibeam data (bathymetry and backscatter) were collected at 40 pre-determined stations, each covering an area approximately 200 x 200 m. The location of stations was selected using a Generalised Random Tessellation Stratified (GRTS) sampling design that ensured an even spatial distribution of sites. Multibeam data was also collected along transits between GRTS stations (410 line km) and across a 30 km2 area of the outer shelf, incorporating areas of low profile reef, sandy shelf and three shelf-incising canyon heads. Backscatter data are gridded to 2 m spatial resolution. The 2012 survey also included seabed observations at the 40 GRTS stations using a drop camera and collection of sediment samples at 31 stations using a Shipek grab. The Flinders CMR survey was a pilot study undertaken in 2012 as part of the National Marine Biodiversity Hub's National Monitoring Evaluation and Reporting Theme. The aim of this theme is to develop a blueprint for the sustained monitoring of the South-east Commonwealth Marine Reserve Network, specifically; 1) to contribute to an inventory of demersal and epibenthic conservation values in the reserve and 2) to test methodologies and deployment strategies in order to inform future survey design efforts. Several gear types were deployed; including multibeam sonar, shallow-water (less than 150m) Baited Remote Underwater Video Systems (BRUVS), deep- water BRUVS (to 600 m), towed video and digital stereo stills. Embargo statement: Resource embargoed pending completion of NERP research. Release date 31 December 2014. Attribution statement: Data was sourced from the NERP Marine Biodiversity Hub. The Marine Biodiversity Hub is supported through funding from the Australian Government's National Environmental Research Program (NERP), administered by the Department of Sustainability, Environment, Water, Population and Communities (DSEWPAC). Dataset name: National Environmental Research Program (NERP) Marine Biodiversity Hub, 2012, Flinders Commonwealth Marine Reserve Shelf Backscatter

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_s2 is an ArcINFO grid of southern part of Jervis Bay survey area (south2 is part of Darling RD grid) produced from the processed EM3002 bathymetry data using the CARIS HIPS and SIPS software

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. Included in the parameters that represent the magnitude of the bulk of the data are the quartiles of the distribution; Q25, Q50 and Q75 (i.e. the values for which 25, 50 and 75 percent of the observations fall below). Q50, or the 0.50 Quartile of the Geomacs output, represents the values for which 50% of the observations fall below (Hughes & Harris 2008).

Although marine reserves are becoming increasingly important as anthropogenic impacts on the marine environment continue to increase, we have little baseline information for most marine environments. In this study, we focus on the Oceanic Shoals Commonwealth Marine Reserve (CMR) in northern Australia, particularly the carbonate banks and terraces of the Sahul Shelf and Van Diemen Rise which have been designated a Key Ecological Feature (KEF). We use a species-level inventory compiled from three marine surveys to the CMR to address several questions relevant to marine management: 1) Are carbonate banks and other raised geomorphic features associated with biodiversity hotspots? 2) Are there environmental or biogeographic variables that can help explain local and regional differences in community structure? 3) How do sponge communities differ between individual raised geomorphic features? Approximately 750 sponge specimens were collected in the Oceanic Shoals CMR and assigned to 348 species, of which only 18% included taxonomically described species. Between the eastern and western CMR, there was no difference between sponge species richness or assemblages on raised geomorphic features. Within individual raised geomorphic features, sponge assemblages were significantly different (ANOSIM: Global R = 0.328, p < 0.001), but species richness was not. There were no environmental factors related to sponge species richness, although sponge assemblages were weakly but significantly related to several environmental variables (mean depth, mean backscatter, mean slope). These patterns of sponge diversity are considered in the context of marine reserve management in order to explore how such information may help support the future management of this region.

Australia is increasingly recognised as a global hotspot for sponge biodiversity, with sponges playing key roles in habitat provision, water quality, bioerosion, and biodiscovery. Despite the intense focus on marine resource management in northern Australia, there is a large knowledge gap about sponge communities in this region. This study focuses on shelf environments of the Timor Sea, in particular the Van Diemen Rise and Londonderry Rise which are characterised by extensive carbonate terraces, banks and reefs, separated by soft sediment plains and deeply incised valleys. These carbonate terraces and banks are recognised as a Key Ecological Feature (KEF) in the marine region plans for northern Australia (North and Northwest Marine Regions) and are in part incorporated into the Oceanic Shoals Commonwealth Marine Reserve. To support the management of this marine reserve and its associated KEF, we use new datasets to investigate regional patterns in sponge assemblages and their relationships to seabed geomorphology. To do this, we use sponge assemblage data and multibeam-derived variables (depth, backscatter, slope, geomorphic feature) from seven survey areas located on the Van Diemen Rise (four sites) and Londonderry Rise (three sites), spanning approximately 320 km in an east-west direction. The dataset was collected during three collaborative surveys undertaken in 2009, 2010 and 2012 by Geoscience Australia, the Australian Institute of Marine Science and the Museum and Art Gallery of the Northern Territory as part of the Australian Government's Offshore Energy Security Initiative and the National Environmental Research Program Marine Biodiversity Hub. All surveys returned geophysical, biological, geochemical, and sedimentological data. Benthic biota were collected with a benthic sled across a range of geomorphic features (bank, terrace, ridge, plain, valley) identified from high-resolution multibeam sonar. Sponges were then taxonomically identified to 350 species, with the species accumulation curve indicating there may be over 900 sponge species in the region. Sponge assemblages were different between the Van Diemen Rise and Londonderry Rise, as well as between individual banks in the same area, indicating that different suites of species occurred at regional (east-west) and local (between banks) scales. Relationships between sponges and other multibeam-derived variables are more complex and warrant further research. The current study will help: i) facilitate integrated marine management by providing a baseline species inventory; ii) support the listing of carbonate banks of the Timor Sea shelf as a Key Ecological Feature, and; iii) inform future monitoring of marine protected area performance, particularly for areas of complex seabed geomorphology.

This report provides detailed descriptions (metadata) of 45 Australian marine environmental datasets that have been generated and collated by the Marine Biodiversity Hub as part of Theme 3 - National Ecosystems Knowledge, Project 1 - Shelf and Canyon Ecosystems Functions and Processes. The report also includes a map for each dataset to illustrate coverage and general spatial structure. The datasets contain both marine environmental and biological variables from diverse data sources and include both new and updated information. Among them, the national bathymetry grid and derived products, seabed sediment grids, seabed exposure (GEOMACS) parameters, water quality data, the national canyon dataset and connectivity layers were produced by Geoscience Australia. Other environmental and biological datasets are the outputs of oceanographic models and collections of various governmental and research organisations. These datasets are important for the success of marine biodiversity research in Theme 3 Project 1 in that they describe key aspects of Australian marine physical, geochemical and biological environments. The physical and geochemical datasets not only characterise the static seabed features but also capture the temporal variation and three-dimensional interactions within marine ecosystems. The biological datasets represent a unique collection of fish and megafauna data available at the national scale. Together, these marine environmental datasets enhance our understanding of large-scale ecological processes driving marine biodiversity patterns. However, we should be aware of the uncertainties and potential errors exist in these datasets due to limitations of data collection and processing methods. Data quality issues of individual datasets have been documented in this report where possible.

Marine visual imaging has become a major assessment tool in the science, policy and public understanding of our seas and oceans. The technology to acquire and process this imagery has significantly evolved in recent years through the development of new camera platforms, camera types, lighting systems and analytical software. These advances have led to new challenges in imaging, including storage and management of `big data, manipulation of digital photos, and the extraction of biological and ecological data. The need to address these challenges, within and beyond the scientific community, is set to substantially increase in the near future, as imaging is increasingly used in the designation and evaluation of marine conservation areas, and for the assessment of environmental baselines and impact monitoring for maritime industry. We review the state of the theory, techniques and technologies associated with each of the steps of marine imaging for observation and research, and to provide an outlook on the future from this active scientific and engineering community that develops and uses it.

Submarine canyons have been recognised as areas of significant ecological and conservation value for their enhanced primary productivity, benthic biomass and biodiversity. In Australia, 753 submarine canyons were mapped on all margins of the continent by the Marine Biodiversity Hub through the Australian Government's National Environmental Research Program. An analysis of canyon geomorphic metrics provided the basis to objectively classify these canyons across a hierarchy of physical characteristics (e.g. volume, depth range, rugosity) separately for shelf-incising and slope-confined canyons (Huang et al., 2014). Here we extend this analysis to include oceanographic variables in presenting a first pass assessment of habitat quality for all canyons on the Australian margin, with a focus on their upper reaches. This study is based on the premise that habitat heterogeneity, productivity and disturbance are the three factors that potentially determine the quality of a canyon habitat. For each factor we derived a range of variables to inform the assessment of habitat quality (see Table). Habitat heterogeneity was measured using a selection of eight geomorphic metrics including canyon volume and rugosity that are considered likely to have a positive relationship with habitat heterogeneity. Canyon productivity was assessed from five variables including: distance to the shelf break as a proxy of nutrient inputs from land and the continental shelf; bottom current speed as an indicator of nutrient supply to benthic epifauna (derived from time-series re-analysis of the BLUElink oceanographic model and in-situ data), and; measures of the probability, frequency and intensity of upwelling (also from BLUElink data). The BLUElink variables have positive relationships with productivity whereas the relationship between distance to shelf and productivity is negative. Benthic disturbance was assessed from the maximum and range of bottom current speeds, and the frequency and intensity of tropical cyclones. According to these relationships, individual canyons were assigned habitat quality scores, first separately for each variable and then aggregated for the three habitat factors. The final scores were obtained by averaging the scores of the three habitat factors. The results show that many submarine canyons on the eastern Australian margin have high habitat quality scores (see Figure). This is interpreted to be mainly due to the influence of the upwelling-favourable East Australian Current which generates high productivity throughout the year. The Albany canyons on the south-western margin also offer high habitat quality for marine species due to complex geometrical and geophysical structures. They also benefit from the upwelling-favourable Flinders Current. In contrast, canyons on the northern and western margins have lower habitat quality. Many of these canyons receive little input from land and continental shelf. In addition, the downwelling- favourable Leeuwin Current, which flows along the western margin of the continent, hampers the supply of deep water nutrients from reaching the upper reaches of canyons, particularly canyon heads that intersect the euphotic zone. Overall, these results provide a framework for targeted studies of canyons aimed at testing and verifying the habitat potential identified here and for establishing monitoring priorities for the ongoing management of canyon ecosystems.

Imagery collected by still and video cameras is an increasingly important tool for minimal impact, repeatable observations in the marine environment. Data collection from imagery is based on identification, annotation and enumeration of biological subjects and environmental features within an image. For such annotation data to be long-lived and useful beyond their project specific initial purpose, they need to be widely understood. A standardized annotation vocabulary is needed in order to generate regional, national or even global data sets from multiple sources to address broad-scale conservation and ecosystem-based management questions, and also for the development of computer algorithms to automate annotation. This need was addressed, within the Australian context, through the Collaborative and Automated Tools for Analysis of Marine Imagery (CATAMI) project (www.catami.org). The CATAMI classification scheme (CCS) is designed to annotate benthic substrates and biota in marine imagery. It is the first nationally standardised classification based on combinations of coarse-level taxonomy and morphology. The CCS is a flexible, hierarchical classification that bridges the gap between habitat or biotope classifications and taxonomic classifications, allowing for limitations in identifying biological taxa specific to imagery. The CCS is well described, documented, and maintained through web-based data-bases (www.catami.org and http://www.cmar.csiro.au/caab/), and it can be applied across benthic image collection methods, annotation platforms and scoring methods. The CCS was released in 2013 and has already been taken up by on-going Australian marine monitoring programs and by industry environmental consultants. Its incorporation into newly developed on-line image annotation tools further strengthens its continued use and development.