Permeable, sandy sediments cover most of the continental shelf. The important role of pore-water advective flow on biogeochemical processes in these sediments has been highlighted in recent studies. Such flow can be driven by wave-action, water-density and interactions between topography and bottom currents, in addition to biological activity, and can create spatially complex and highly dynamic benthic environments in which processes vary on timescales ranging from minutes to months. It is well known that the patchiness of soft sediment (organic matter/bacteria, particle diversity, redox) is likely to be a major determinant of species diversity, but previous studies have not specifically defined patches based on a range of biologically-relevant physico-chemical variables, nor observed how patches change across time. This study, as part of the Surrogates Program in the Commonwealth Environmental Research Facilities Marine Biodiversity Hub, investigated temporal changes in the geochemistry, physical sediments and infauna of sandy sediments in Jervis Bay at two times.

The aim of the study was to explore different approaches of feature selection, extraction and reduction from backscatter angular response curves for a relatively complex seabed. The study area is located at Point Cloates along the coast of central Western Australia where water depths range from 6 to 200 m and is characterised by extensive sandy bedforms, flat sandy seabed and numerous reefs. A Simrad EM3002 300 kHz sonar system was used to collect multibeam data across an area of 281 km2 in 2008. A series of radiometric and geometric corrections were applied to the backscatter data. The angular response curves were derived separately for port and starboard by averaging 100 pings along the ship track. Seabed sediment texture was characterised from 90 samples that were analysed for grain size properties (gravel, sand, mud%) and classified into six sediment classes. Co-located towed-video transects from the survey were used to identify areas of rocky seabed. Four approaches of processing the angular response curves have been explored. The first approach used all effective beam angles (4o to 51o) with a manual feature selection method in the modelling process. The second approach used principal component analysis to condense the 48 variables into four (explained 99% data variance). The third approach extracted nine parameters from two domains of the angular response curves including slope, intercept, orthogonal distance and mean. The fourth approach derived continuum-removed angular response curves. Probability Neural Network was used as the classifier. The classification results show that the continuum removal approach performed the best with an overall accuracy of 73% when classifying the seven seabed classes (Figure 1).When merging the six sediment classes into four, which results in five seabed classes, the performance was improved for all approaches.

The Carnarvon Shelf Survey (SOL4769, GA survey #0308) was conducted on the R.V. Solander in collaboration with the Australian Institute of Marine Science between 12 August and 15 September 2008. The survey was operated as part of the Surrogates Program of the CERF Marine Biodiversity Hub. The survey was completed under a Memorandum of Understanding between GA and the AIMS and represents the first of three surveys planned under this agreement. The objective was to collect high-quality, accurately co-located data to enable the robust testing of a range of physical parameters as surrogates of patterns of benthic biodiversity. Underwater video footage and still images were collected from 122 stations from water depths of 13-125 m, although video quality varies among transects and some still images were not of suitable quality for analysis. Images from the still camera can be found in 'Image Library', and images from towed video screen captures can be found in 'Tow Video Stills'. Image files from screen captures are named according to area (1 = Mandu, 2 = Point Cloates, 3 = Gnarloo) followed by the station number and video identifier (TVA1). For example, 2_032TVA1 would represent a towed video transect from Station 32 at Point Cloates. See GA Record 2009/02 (Geocat #68525) for further details. Video footage was recorded to mini DV tapes, and copied to digital format. The original mini DV tapes are archived at AIMS-WA.

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.

Geoscience Australia carried out a marine survey on Carnarvon shelf (WA) in 2008 (SOL4769) to map seabed bathymetry and characterise benthic environments through co-located 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. TheGA0308_Carnarvon_SOL4976 folder contains video footage and still images. The MS databse, the Excel files are video characterisation datasets: Carnarvon_video data (export).mdb; all_substrata_tx.xls (transect level); all_substrata_patch.xls (patch level); all_benthos_tx.xls (transect level); all_benthos_patch.xls (patch level); Carnarvon_QAQC_VIDEOlog.doc (QAQC document); Attribute_metadata.xls (attribute definition). Underwater towed-video footage abd still images represent the raw data. Video characterisation datasets include percent cover of substrata and benthic taxa characterised at two spatial scales: transect scale (mean values per transect) and patch scale (mean values for each patch type within a transect).

The dataset contains three grids. Each of the ArcINFO grids is an output of a finescale hydrodynamic model, the Simulating WAves Nearshore (SWAN) model (Booij et al., 1999; Ris et al., 1999).The grids describe the modelled maximum orbital velocity (m/s) which can be used as estimation of seabed exposure in Jervis Bay.

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.

Anthropogenic threats to benthic habitats do not pose an equal risk, nor are they uniformly distributed over the broad depth range of marine habitats. Deep sea benthic environments have, by and large, not been heavily exploited and most are in relatively good condition. In contrast, shelf and coastal habitats, and deep ocean pelagic fisheries, have been exploited extensively and human impacts here are locally severe. A critical point is that anthropogenic threats do not act in isolation; rather, they are cumulative and the impacts are compounded for every affected habitat. In general, the impacts of humans on benthic habitats is poorly understood. Habitat mapping provides condition assessments and establishes baselines against which changes can be measured. GeoHab scientists ranked the impacts on benthic habitats from fishing as the greatest threat, followed by pollution and litter, aggregate mining, oil and gas, coastal development, tourism, cables, shipping, invasive species, climate change and construction of wind farms. The majority of authors (84%) reported that monitoring changes in habitat condition over time was a planned or likely outcome of the work carried out. In this chapter the main anthropogenic threats to benthic habitats are reviewed in relation to their potential impacts on benthic environments.

Geoscience Australia carried out a marine survey on Lord Howe Island shelf (NSW) in 2008 (SS062008) to map seabed bathymetry and characterise benthic environments through colocated sampling of surface sediments and infauna, rock coring, observation of benthic habitats using underwater towed video, and measurement of ocean tides and wavegenerated currents. Subbottom 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 preexisting 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. lh_back_8m is a backscatter grid of the Lord Howe survey area produced from the processed EM300 backscatter data of the survey area using the CMST-GA MB Process.

The term 'surrogacy' is used in habitat mapping with reference to the biophysical variables that can be mapped with a quantifiable correspondence to the occurrence of benthic species and communities. Surrogacy research can be defined as an empirical method of determining which easily measured characteristics best describe the species assemblage in a particular space and at a particular time. These characteristics act as predictors (with some known probability and uncertainty) for the occurrence of species assemblages in unexplored areas. Abiotic variables are, in general, more easily and less expensively obtained than biological observations, which is a key driver for surrogacy research. However, the suite of abiotic factors that exert control over the occurrence of species (its niche) is also a scientifically interesting aspect of ecology that provides important insights into a species evolution and biogeography. This chapter provides a review of surrogates used by case study authors and of the methods used to quantify relationships between variables.