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. This 81 sample dataset comprises acidextractable concentrations of trace elements (Fe, Mn, Co, Ni, Cu, Zn, Ge, As, Cd and Pb) in surface seabed sediments (~0 to 2 cm) from Jervis Bay.

Publicly available bathymetry and geophysical data can be used to map geomorphic features of the Antarctic continental margin and adjoining ocean basins at scales of 1:1-5 million. These data can also be used to map likely locations for some Vulnerable Marine Ecosystems. Seamounts over a certain size are readily identified and submarine canyons and mid ocean ridge central valleys which harbour hydrothermal vents can be located. Geomorphic features and their properties can be related to major habitat characteristics such as sea floor type (hard versus soft), ice keel scouring, sediment deposition or erosion and current regimes. Where more detailed data are available, shelf geomorphology can be shown to provide a guide to the distribution in the area of the shelf benthic communities recognised by Gutt (2007). The geomorphic mapping method presented here provides a layer to add to benthic bioregionalistion using readily available data.

The Oceanic Shoals Commonwealth Marine Reserve (CMR) (>71,000 km2) is located in the Timor Sea and is part of the National Representative System of Marine Protected Areas of Australia. The Reserve incorporates extensive areas of carbonate banks and terraces that are recognised in the North and North West Marine Region Management Plans as Key Ecological Features (KEFs). Although poorly studied, these features have been identified as potential biodiversity hotspots for the Australian tropical north. As part of the National Environment Research Program (NERP), Geoscience Australia (GA) in collaboration with the Australian Institute of Marine Sciences (AIMS) undertook a marine biodiversity survey in 2012 to improve the knowledge of this area and better understand the importance of these KEFs. Amongst the many activities undertaken, continuous high-resolution multibeam mapping, video and still camera observations, and physical seabed sampling of four areas covering 510 km2 within the western side of the CMR was completed. Multibeam imagery reveals a high geomorphic diversity in the Oceanic Shoals CMR, with numerous banks and terraces, elevated 30 to 65 m above the generally flat seabed (~105 m water depth), that provide hard substrate for benthic communities. The surrounding plains are characterised by fields of depressions (pockmarks) formed in soft silty sediments that are generally barren of any epibenthos. A distinctive feature of many pockmarks is a linear scour mark that extends several tens of metres (up to 150 m) from pockmark depressions. Previous numerical and flume tank simulations have shown that scouring of pockmarks occurs in the direction of the dominant near-seabed flow. These geomorphic features may therefore serve as a proxy for local-scale bottom currents, which may in turn inform on sediment processes operating in these areas and contribute to the understanding of the distribution of biodiversity. This study focused on characterising these seabed scoured depressions and investigating their potential as an environmental proxy for habitat studies. The study used ArcGIS spatial analyst tools to quantify the features and explored their potential relationships with other variables (e.g. multibeam backscatter, regional modelled bottom stress, biological abundance and presence/absence) to provide insight into their development, and contribute to a better understanding of the environment surrounding carbonate banks. Preliminary results show a relationship between pockmark types, i.e. with or without scour mark, and backscatter strength. This relationship suggests some additional shallow sub-surface control, mainly related to the presence of buried carbonate bank. In addition, the results suggest that tidal flows are redirected by the banks, leading to locally varied flow directions and 'shadowing' in the lee of the larger banks. This in turn is likely to have an influence on the observed density and abundance of benthic assemblages.

The identification of marine habitats based on physical parameters is increasingly important for marine reserve design, allowing characterisation of habitat types over much wider areas than is possible from often patchy biological data. Marine management zones often contain a wide array of physical environments, which may not be captured in the biological sampling effort. The mismatch between biological and physical information leads to uncertainty in the application of bio-physical relationships at the broader management scale. In this study, a case study from northern Australia is used to demonstrate a methodology for defining uncertainties which result from the extrapolation of bio-physical associations across areas where detailed biological data is absent. In addition, uncertainties relating to the interpolation of physical data sets and that resulting from the cluster analysis applied to the physical data are calculated and mapped, providing marine managers with greater robustness in their analysis of habitat distributions.

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. This 128 sample data set comprises major, minor and trace elements derived from x-ray fluorescence analysis of surface seabed sediments (~0-2 cm). Sediment surface area data are also presented.

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. Seabed sediment samples were collected by a Smith McIntyre grab at a total of 36 locations (see Brooke et al. 2010). The full sample set represents 16 sampling stations, with multiple (2 or 3) samples taken at 10 of these stations.

Geoscience Australia carried out marine surveys in south-east Tasmania in 2008 and 2009 (GA0315) to map seabed bathymetry and characterise benthic environments through observation of habitats using underwater towed video. Data was acquired using the Tasmania Aquaculture and Fisheries Institute (TAFI) Research Vessel Challenger. Bathymetric mapping was undertaken in seven survey areas, including: Freycinet Pensinula (83 sq km, east coast and shelf); Tasman Peninsula (117 sq km, east coast and shelf); Port Arthur and adjacent open coast (17 sq km); The Friars (41 sq km, south of Bruny Island); lower Huon River estuary (39 sq km); D Entrecastreaux Channel (7 sq km, at Tinderbox north of Bruny Island), and; Maria Island (3 sq km, western side). Video characterisations of the seabed concentrated on areas of bedrock reef and adjacent seabed in all mapped areas, except for D Entrecastreaux Channel and Maria Island. Seabed sediment samples were collected by TAFI in August 2010 in a targeted area to the east of Tasman Peninsula. Samples were collected at 25 stations using a Van Veen grab, from which a 50 - 100 g sub-sample was taken and submitted to Geoscience Australia for analysis.

A number of terms used in this book are derived from the fields of biogeography and benthic ecology and these are defined in the glossary; the reader is also referred to the works cited at the end of this chapter for further information. Many of the case studies presented in this book refer to habitat classification schemes that have been developed based on principles of biogeography and ecology. For these reasons a brief overview is provided here to explain the concepts of biodiversity, biogeography and benthic ecology that are most relevant to habitat mapping and classification. Of particular relevance is that these concepts underpin classification schemes employed by GeoHab scientists in mapping habitats and other bioregions. A selection of published schemes, from both deep and shallow water environments, are reviewed and their similarities and differences are examined.

The characterisation of benthic habitats based on their abiotic (physical and chemical) attributes remains poorly defined in the marine environment, but is becoming increasingly central in the development of marine management plans in Australia and elsewhere in the world. The current study tested this link between physical and biological datasets for the southern Gulf of Carpentaria, Australia. The results presented were based on a range of physical factors, including the sediment composition (grain size and carbonate content), sediment mobility, water depth and organic carbon flux, and their relationship to the distribution and diversity of benthic macrofauna was tested. The results reveal the importance of process-based indices, such as sediment mobility, in addition to other environmental factors in defining the distribution of the benthic macrofauna. The distribution of the benthic macrofauna changes gradationally across the south-eastern Gulf, associated with changes in the per cent mud and gravel, the seabed exposure and the water depth. Patterns of diversity also reveal the importance of physical processes such as sediment mobility in defining benthic habitats. The species' environment relationships observed at the small scale of the current study are consistent with broader associations observed for other organisms within the Gulf.

The Carnarvon shelf at Point Cloates, Western Australia, is characterised by a series of prominent ridges and hundreds of mounds that provide hardground habitat for coral and sponge gardens. The largest ridge is 20 m high, extends 15 km alongshore in 60 m water depth and is interpreted as a drowned fringing reef. To landward, smaller ridges up to 1.5 km long and 16 m high are aligned to the north-northeast and are interpreted as relict aeolian dunes. Mounds are less than 5 m high and may also have a sub-aerial origin. In contrast, the surrounding seafloor is sandy with relatively low densities of epibenthic organisms. The dune ridges are estimated to be Late Pleistocene in age and their preservation is attributed to cementation of calcareous sands to form aeolianite, prior to the postglacial marine transgression. On the outer shelf, sponges grow on isolated low profile ridges at ~85 m and 105 m depth and are also interpreted as partially preserved relict shorelines.