Zooplankton sampling encompasses a range of methods, but these require specialized equipment, cost, and time. Ship-pumped seawater provides an opportunity to broadly quantify zooplankton abundance and richness during surveys with objectives other than zooplankton characterisation. Here, the effectiveness of sampling ship-pumped seawater for zooplankton was evaluated through the identification of established diurnal and biogeographic patterns as well as comparisons between sampling with surface tows and ship-pumped seawater over the Western Australian margin. Only one species was classed as a fouling organism (unknown Y-shaped polyps), and only one group was excluded from sampling via ship-pumped water (chaetognaths). As expected, we found significant diurnal differences in zooplankton abundance, as well as differences between the Houtman sub-basin (~ 100 km offshore) and the Wallaby (Cuvier) Plateau (~500 km offshore). These results suggest that sampling zooplankton with ship-pumped waters can result in useful broad comparisons of the overall abundance and number of taxa among regions but only when comparisons with surface tows are made. Importantly, sampling via ship-pumped water is not an appropriate method from which to characterize zooplankton communities and in no way replaces or negates the need for more traditional and comprehensive sampling of zooplankton.

Geoscience Australia and the Australian Institute of Marine Science are conducting seabed mapping surveys in northern Australia to generate regional baseline information on seabed environments. The data are being made available to Australia's offshore oil and gas industry to assess the wider significance of planned infrastructure developments designed to bring on regional gas reserves. In 2009 the first of these surveys focused on the Van Diemen Rise, a series of submerged carbonate banks and channels on the tropical, macrotidal northern Australian shelf. Data reveal a relatively complex seabed geomorphology comprising banks, terraces, plains, ridges, and deep/hole/valleys. Banks, terraces and ridges are characterised by partially-cemented coarse carbonate sands supporting species-rich sponge and octacoral communities.The plains and deep/hole/valleys are dominated by muddy fine to medium carbonate sands containing abundant polychaetes and crustaceans. The survey data will be combined with regional datasets to provide a synthesis of seabed environments for the northern Australian shelf. Follow-up surveys are planned for August 2010 and late 2011.

A seabed mapping survey over a series of carbonate banks, intervening channels and surrounding sediment plains on the Van Diemen Rise in the eastern Joseph Bonaparte Gulf was completed under a Memorandum of Understanding between Geoscience Australia and the Australian Institute of Marine Sciences. The survey obtained detailed geological (sedimentological, geochemical, geophysical) and biological data (macro-benthic and infaunal diversity, community structure) for the banks, channels and plains to establish the late-Quaternary evolution of the region and investigate relationships between the physical environment and associated biota for biodiversity prediction. The survey also permits the biodiversity of benthos of the Van Diemen Rise to be put into a biogeographic context of the Arafura-Timor Sea and wider northern Australian marine region. Four study areas were investigated across the outer to inner shelf. Multibeam sonar data provide 100 per cent coverage of the seabed for each study area and are supplemented with geological and biological samples collected from 63 stations. In a novel approach, geochemical data collected at the stations provide an assessment of sediment and water quality for surrogacy research. Oceanographic data collected at four stations on the Van Diemen Rise will provide an understanding of the wave, tide and ocean currents as well as insights into sediment transport. A total of 1,154 square kilometres of multibeam sonar data and 340 line-km of shallow (<100 mbsf) sub-bottom profiles were collected.

A key component of marine bioregional planning is to map the spatial patterns of marine biodiversity, often measured as species richness, total abundance or abundance/presence of key taxa. In this study, predictive modelling approaches were used to map soft bottom benthic biodiversity on the Carnarvon Shelf, Western Australia, using a range of physical surrogates. This surrogacy approach could also explicitly link physical environmental attributes to the marine biodiversity patterns. The statistical results show that between 20% and 37% of variances on the two biodiversity measures (Species Richness and Total Abundance) were explained by the Random Forest Decision Tree models. The best statistical validation performance was found at the Point Cloates area. This was followed by the Gnaraloo area, then by the Mandu Creek area. The models identified different individual physical surrogates for the three study areas and the two biodiversity measures. However, it was found that the infaunal biodiversity at the three study areas of the Carnarvon Shelf were driven by similar ecological process. Sediment properties were the most important physical surrogates for the infaunal biodiversity. Coarser and heterogeneous sediments favour higher infaunal species richness and total abundance. The prediction maps indicate the highest infaunal biodiversity at deeper water of the Point Cloates area. In contrast, the majority of the Mandu creek area has low infaunal biodiversity. This may be due to the much narrower shelf width (e.g., ~6 km) in this part of Carnarvon Shelf than the Point Cloates and Gnaraloo areas. The narrow shelf would limit the space for oceanographic processes to work on the sediment and develop heterogeneous sediment properties that support diverse and productive infaunal species.

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.

High-precision measurements of N2 in benthic chamber waters indicated that denitrification occurs within the major sedimentary facies in Port Phillip Bay. The integrated fluxes of biogenic N2 , ammonia, nitrate and nitrite showed that the stoichiometric relationship between organic C and N in the muddy sediments, occupying about 70% of the seafloor, was 5.7, this being similar to the Redfield ratio of 6.6. High denitrifying efficiencies (75-85%; denitrification rates ~1.3 mmol N2 m-2 day-1) at organic carbon loadings of ~15-25 mmol m-2 day-1 indicate that most N processed through the sediments was returned to the overlying waters as biologically (generally) unavailable N2. At sites of high organic carbon loadings to the sediments (>100 mmol m-2 day-1) denitrification rates and denitrifying efficiencies were near zero and most N is returned to the Bay waters as biologically available ammonium. In chambers 'spiked' with 15NO3 , denitrifyers used nitrate produced in the sediments in situ, rather than the exogenous nitrate in overlying waters. The sedimentary microbial processes of ammonification, nitrification and denitrification are therefore tightly coupled.

Flythrough movie showing the bathymetry of the continental shelf within the Oceanic Shoals Commonwealth Marine Reserve (Timor Sea), highlighting carbonate banks and pinnacles as benthic habitats. The bathymetric image is derived from multibeam sonar collected in 2012 using a 300 kHz Simrad EM3002 system on RV Solander and gridded at 2 m resolution. The Oceanic Shoals Reserve is a study site for the Marine Biodiversity Research Hub, funded through the National Environmental Research Program. Survey work was carried out as a collaboration between Geoscience Australia, the Australian Institute of Marine Science and University of Western Australia. Further information is provided in GA Record 2013/38.

Geoscience Australia carried out a marine survey on Lord Howe Island shelf (NSW) in 2008 (SS06-2008) to map seabed bathymetry and characterise benthic environments through co-located sampling of surface sediments and infauna, rock coring, observation of benthic habitats using underwater towed video, and measurement of ocean tides and wave-generated currents. Sub-bottom profile data was also collected to map sediment thickness and shelf stratigraphy. Data and samples were acquired using the National Facility Research Vessel Southern Surveyor. Bathymetric data from this survey was merged with other pre-existing bathymetric data (including LADS) to generate a grid covering 1034 sq km. As part of a separate Geoscience Australia survey in 2007 (TAN0713), an oceanographic mooring was deployed on the northern edge of Lord Howe Island shelf. The mooring was recovered during the 2008 survey following a 6 month deployment. This folder contains the images derived from benthic samples taken on cruise SS06_2008 aboard Southern Surveyor. The main folder houses all images taken while processing samples at the microscope. These images formed the first point of reference in identifying subsequent specimens to save wear and tear on the specimens put aside as reference material. Three additonal folders exist within the main folder. Amphipoda contains repeats of the amphipod taxa, SS062008Biota contains images of live organisms taken as soon as the sample was recovered to the ship and Tanaidacea contains repeats of the tanaid taxa.

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.