Infauna are rarely considered in biodiversity assessments of coral reefs and surrounding areas despite their importance in these ecosystems regarding nutrient cycling, bioerosion, and other ecological processes. We surveyed infaunal assemblages in three areas (Mandu, Point Cloates, Gnaraloo) along the Carnarvon Shelf, Western Australia, a region that supports Ningaloo Reef, a relatively pristine coral reef protected by the Ningaloo Marine Park and new proposed Commonwealth marine reserve. Infauna were sampled with a Smith-McIntyre grab and sieved through 500 µm. Environmental data were collected (depth, seabed reflectance, sediment characteristics (grain-size, carbonate, kurtosis, sorting)) so that abiotic factors associated with infaunal assemblages could be identified. A total of 423 species and 4036 individuals were recorded from 145 grabs, with a large percentage (41.7%) represented by rare species (<2 individuals per species). Assemblages were dominated by arthropods, annelids, and molluscs (92.2% of species, 90.2% individuals) and scavengers, suspension feeders, and deposit feeders (25.3% of species, 51.2% of individuals). Assemblages were significantly different among all three areas, but the most distinct assemblages were recorded from the southernmost area of Gnaraloo. Infauna varied significantly with depth and sediment composition (mud and gravel), although these relationships were weak, possibly due to a combination of the assemblage diversity and the high numbers of rare species. Results from the current study broadly quantify infaunal diversity in the region and identify potential spatial and environmental patterns which will help inform future marine management plans, including providing baseline information about communities that can be used to assess potential future impacts and efficacy of protected areas in soft sediment habitats adjacent to coral reefs.

A growing need to manage marine biodiversity sustainably at local, regional and global scales cannot be met by applying the limited existing biological data. Abiotic surrogates of biodiversity are thus increasingly valuable in filling the gaps in our knowledge of biodiversity patterns, especially identification of hotspots, habitats needed by endangered or commercially valuable species and systems or processes important to the sustained provision of ecosystem services. This review examines the use of abiotic variables as surrogates for patterns in benthic assemblages with particular regard to how variables are tied to processes affecting biodiversity and how easily those variables can be measured at scales relevant to resource management decisions.

This study presents new information on the regional geochemical characteristics of deep-sea floor sediments (1300 - 2423 m water depth) on the Lord Howe Rise (deep-sea plateau) and Gifford Guyot (seamount/tablemount), remote areas off eastern Australia. The aim was to provide a coherent synthesis for a suite of geochemical data that can be used to make habitat inferences and to develop surrogates of biodiversity. Sediment characteristics analysed were mineralogy, organic carbon and nitrogen concentrations and isotopic compositions, and concentrations of major and trace elements. We also measured parameters that convey information about the reactivity of organic matter and on the bio-availability of bioactive trace elements (e.g. chlorin indices and acid-extractable elements). Surface sediments from the region were calcareous oozes that were carbon-lean (0.26±0.1%) and had moderate to high chlorin indices (0.62 - 0.97)..

The Joseph Bonaparte Gulf (JBG) is an offshore area in northern Australia, with active petroleum exploration and infrastructure development. The Van Diemen Rise, an area of raised banks and channels in the northeastern region of the JBG, has been proposed for protection as part of the Oceanic Shoals Commonwealth Marine Reserve. However, baseline information for much of this area is lacking, including spatial and environmental patterns of biological communities. This study uses still imagery of the sea floor in four study areas across the Van Diemen Rise, collected during two seabed mapping surveys conducted by Geoscience Australia and the Australian Institute of Marine Science, in 2009 and 2010. Based on these analyses benthic communities are characterised, and important species and morphological groups are compared with a number of abiotic variables. In so doing, a preliminary assessment is given as to which abiotic variables make the most appropriate surrogates for characterising benthic communities in the region. A number of variables are found to correlate significantly and strongly with some of the biological groups determined in this study. Pheophytin, Si/Al and mud content correlate with the large habitat forming species Mopsella sp., Ianthella sp. and Xestospongia sp. respectively. Backscatter signals from multibeam sonar surveys correlate very strongly with depth and also to some degree with a number of the functional growth forms of sponges. Based on the positive results of this preliminary data investigation, it is recommended that non-linear modelling and robust multivariate analyses be applied to the data set to investigate more complex relationship. This study provides baseline information on the ecology and morphology of key habitat-forming organisms in the northeastern Joseph Bonaparte Gulf which will be facilitate marine monitoring programs for reserve management and environmental impact assessments for industry activity.

Geoscience Australia undertook a marine survey of the Vlaming Sub-basin in March and April 2012 to provide seabed and shallow geological information to support an assessment of the CO2 storage potential of this sedimentary basin. The survey was undertaken under the Australian Government's National CO2 Infrastructure Plan (NCIP) to help identify sites suitable for the long term storage of CO2 within reasonable distances of major sources of CO2 emissions. The Vlaming Sub-basin is located offshore from Perth, Western Australia, and was previously identified by the Carbon Storage Taskforce (2009) as potentially suitable for CO2 storage. The principal aim of the Vlaming Sub-basin marine survey (GA survey number GA0334) was to look for evidence of fault reactivation and of any past or current gas or fluid seepage at the seabed. The survey also mapped seabed habitats and biota in the areas of interest to provide information on communities and biophysical features that may be associated with seepage. This data package brings together the following datasets which describe biophysical aspects of seafloor sediments: GEOCAT#74276. Underwater video footage from the Vlaming Sub-basin (GA0334). GEOCAT#76463. GA0334 Vlaming sub-basin Species identification of worms from grab. GEOCAT#78540. Vlaming Sub-Basin Marine Environmental Survey (GA-0334/S. Supporter GP 1373) (NCIP Program) - High Resolution Bathymetry grids. GEOCAT# 78550. Seabed environments and shallow geology of the Vlaming sub-basin, Western Australia: Chlorin analyses of seabed sediments. GEOCAT#78551. Seabed environments and shallow geology of the Vlaming sub-basin, Western Australia: Inorganic elements of seabed sediments. GEOCAT#78552. Seabed environments and shallow geology of the Vlaming sub-basin, Western Australia: Bulk organic carbon and nitrogen isotopes and concentrations in seabed sediments. GEOCAT#78553. Seabed environments and shallow geology of the Vlaming sub-basin, Western Australia: Sediment oxygen demand of seabed sediments. GEOCAT#78564. Seabed environments and shallow geology of the Vlaming sub-basin, Western Australia: Chlorophyll a, b and c of seabed sediments. GEOCAT#78565. Seabed environments and shallow geology of the Vlaming sub-basin, Western Australia: %carbonate and specific surface area of seabed sediments. GEOCAT#79176. Seabed environments and shallow geology of the Vlaming sub-basin, Western Australia: Grain size and carbonate concentrations of seabed sediments. GEOCAT#79345. Ecology / Infaunal morphospecies identifications from the Vlaming Sub-basin (GA0334). An account of the field operations is published in: GEOCAT 74626. Nicholas, W. A., Borissova, I., Radke, L., Tran, M., Bernardel, G., Jorgensen, D M., Siwabessy, J., Carroll, A. and Whiteway, T., 2012. Seabed Environments and Shallow Geology of the Vlaming Sub-Basin, Western Australia - Marine data for the Investigation of the Geological Storage of CO2. GA0334 Post-Survey Report. Geoscience Australia, Record 2013/09. A preliminary interpretation of seabed data is provided in: GEOCAT 78846. Nicholas, W. A., Howard, F., Carroll, A., Siwabessy, J., Tran, M., Picard, K., Przeslawski, R. and Radke, L. 2014. Seabed Environments and shallow sub-surface geology of the Vlaming Sub-basin, offshore Perth Basin: summary report on observed and potential seepage, and habitats. Geoscience Australia, Record 2014/XXX. Information on the broader study, evaluating the Vlaming Sub-basin CO2 storage potential and providing details of the suitable storage sites, is available in: GEOCAT 79332. Borissova, I, Lech, M.E., Jorgensen, D.C, Southby, C., Wang, L., Bernardel, G., Nicholas, T., Lescinsky, D.L. and Johnston, S. An integrated study of the CO2 storage potential in the offshore Vlaming Sub-basin. Geoscience Australia, Record 2014/XXX.

As part of Geoscience Australia's commitment towards the National Environmental Programme's Marine Biodiversity Hub, we have developed a fully four-dimensional (3D x time) biophysical dispersal model to simulate the movement of marine larvae over large, topographically complex areas. The model uses parallel processing on Australia's national supercomputer to handle large numbers of simulated larvae (on the order of several billion), and saves positional information as points within a relational database management system RDBMS). The model was used to study Australia's northwest marine region, with specific attention given to connectivity patterns among Australia's north-western Commonwealth Marine Reserves and Key Ecological Features (KEFs). These KEFs include carbonate terraces, banks and reefs on the shelf that support diverse benthic assemblages of sponges and corals, and canyons that extend from the shelf edge to the continental slope and are potential biodiversity hotspots. We will show animations of larval movement near canyons within the Gascoyne CMR; larval dispersal probability clouds partitioned by depth and time; as well as matrices of connectivity values among features of interest. We demonstrate how the data can be used to identify connectivity corridors in marine environments, and how the matrices can be analysed to identify key connections within the network. Information from the model can be used to inform priorities for monitoring the performance of reserves through examining net contributions of different reserves (i.e. are they sources or sinks), and studying changes in connectivity structure through adding and removing reserve areas.

This report provides a description of the activities completed during the Outer Darwin Harbour Mapping Survey, from 28 May and 23 June 2015 on the RV Solander (Survey GA0351/SOL6187). This survey was a collaboration between Geoscience Australia (GA), the Australian Institute of Marine Science (AIMS) and Department of Land Resource Management (Northern Territory Government) and the first of four surveys in the Darwin Harbour Seabed Habitat Mapping Program. This 4 year program (2014-2018) aims to improve knowledge of the marine environments in the Darwin and Bynoe Harbour regions by collating and collecting baseline information and developing thematic habitat maps that will underpin future marine resource management decisions. The program was made possible through funds provided by the INPEX-led Ichthys LNG Project to Northern Territory Government Department of Land Resource Management, and co-investment from Geoscience Australia and Australian Institute of Marine Science. The specific objectives of the Outer Darwin Harbour Marine Survey GA0351/SOL6187 were to: 1. Obtain high resolution geophysical (bathymetry) data for outer Darwin Harbour, including Shoal Bay; 2. Characterise substrates (acoustic backscatter properties, grainsize, sediment chemistry) for outer Darwin Harbour, including Shoal Bay; and 3. Collect tidal data for the survey area. Data acquired during the survey included: 720 km2 multibeam sonar bathymetry and acoustic backscatter; 96 sampling stations collecting seabed sediments, underwater photography and video imagery and oceanographic information including tidal data and 54 sound velocity profiles.

Much of the deep sea comprises soft-sediment habitats dominated by low abundances of small infauna, and traditional methods of biological sampling may therefore fail to sufficiently quantify biodiversity. During feeding and burrowing, many deep sea animals bioturbate the sediment, leaving signs of their activities called lebensspuren ('life traces'). In this study, we use three criteria to assess whether the quantification of lebensspuren from high resolution still images is an appropriate technique to broadly quantify biological activity in the deep sea: 1) The ability to differentiate biological assemblages between geographic regions; 2) the ability to reveal known biological patterns across environmental gradients; and 3) correlation with other methods of biological characterisation often used in the deep sea (e.g. video). Lebensspuren were quantified using a univariate measure of track richness and a multivariate measure of lebensspuren assemblages from the eastern (1712 images, 13 stations) and western (949 images, 11 stations) Australian margins. A total of 46 lebensspuren types were identified, including those matching named trace fossils. Assemblages were significantly different between the two regions, with five lebensspuren types accounting for over 95% of the differentiation (ovoid pinnate trace, crater row, spider feature, matchstick feature, mesh feature). Track richness in the combined margins dataset was correlated to depth, chlorin index (i.e. organic freshness), and possibly mud, although the strength of the relationships varied according to the dataset used. There was no relationship to total organic carbon. Lebensspuren richness from still images was significantly related to lebensspuren from video but not to occurrence of epifauna. Based on these results, the quantification of lebensspuren from still images seems an appropriate measure to broadly characterise biological activity in deep sea soft sediment ecosystems.

This dataset contains species identifications of molluscs collected during survey SOL5117 (R.V. Solander, 30 July - 27 August, 2010). Animals were collected from the Joseph Bonaparte Gulf with a benthic sled (SL) and Smith McIntyre grab (GR). Specimens were lodged at Northern Territory Museum on the 27 August 2010. Species-level identifications were undertaken by Richard Willan at the Northern Territory Museum and were delivered to Geoscience Australia on the December 2010 (for large samples) and 26 June 2012 (for smaller molluscs from grabs). See GA Record 2011/08 for further details on survey methods and specimen acquisition. Data is presented here exactly as delivered by the taxonomist, and Geoscience Australia is unable to verify the accuracy of the taxonomic identifications. Comments: The following comments relate to live-taken specimens only: 1. The SOL5117 molluscan samples contain at least one new species (Talabrica sp.), one new record for Australia (Oliva rufofulgurata), and five new records for Commonwealth waters north of the Northern Territory (Strombus hickeyi, Trigonostoma textilis, Dentalium formosum, Phyllidiopsis shireeenae, Ceratosoma trilobatum). 2. Many of the molluscan species in the SOL5117 grab samples, both live individuals and dead shells, are represented only by tiny juveniles, so identification to species level is not possible because the shell characters change considerably as the species reaches maturity. 3. Clearly the majority of molluscs in the SOL5117 samples are represented by dead shells only. 4. Species richness is far higher than suggested by these samples. Judging from the range of species present in the SOL4934 and SOL5117 samples plus the accumulation of species through the samples, the molluscan biodiversity in this area would be between 400 and 500 species, the great majority micromolluscs (i.e., < 5 mm in greatest dimension). 5. The SOL5117 molluscan samples are not as comprehensive as the earlier SOL4934 samples taken in the same areas(s). 6. The SOL5117 molluscan samples provide us with hardly any picture of the composition or abundance of molluscs within or between the sites. 7. The SOL5117 molluscan samples should not be used to assess the conservation status of the submarine communities in the area(s) sampled. 8. More targeted and intensive sampling is required to appropriately measure molluscan diversity, abundance and communities in this region. ~ R Willan

This resource contains geochemistry data 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). This dataset comprises bulk organic carbon and nitrogen concentrations (and isotopes) from the upper 2 cm of seabed sediment. The Oceanic Shoals Commonwealth Marine Reserve survey was undertaken as an activity within the Australian Government's National Environmental Research Program Marine Biodiversity Hub and was the key component of Research Theme 4 - Regional Biodiversity Discovery to Support Marine Bioregional Plans. Hub partners involved in the survey included the Australian Institute of Marine Science, Geoscience Australia, the University of Western Australia, Museum Victoria and the Museum and Art Gallery of the Northern Territory. Data acquired during the survey included: multibeam sonar bathymetry and acoustic backscatter; sub-bottom acoustic profiles; physical samples of seabed sediments, infauna and epibenthic biota; towed underwater video and still camera observations of seabed habitats; baited video observations of demersal and pelagic fish, and; oceanographic measurements of the water column from CTD (conductivity, temperature, depth) casts and from deployment of sea surface drifters. 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).