Williams et al. (2009) report on new multibeam sonar bathymetry and underwater video data collected from submarine canyons and seamounts on Australia's southeast continental margin to 'investigate the degree to which geomorphic features act as surrogates for benthic megafaunal biodiversity' (p. 214). The authors describe what they view as deficiencies in the design of the Marine Protected Areas (MPAs) in the southeast region of Australia, in which geomorphology information was employed as a surrogate to infer regional-scale patterns of benthic biodiversity. This comment is designed to support and underscore the importance of evaluating MPA designs and the validity of using abiotic surrogates such as geomorphology to infer biodiversity patterns, and seeks to clarify some of the discrepancies in geomorphic terminologies and approaches used between the original study and the Williams et al. (2009) evaluation. It is our opinion that the MPA design criteria used by the Australian Government are incorrectly reported by Williams et al. (2009). In particular, we emphasise the necessity for consistent terminology and approaches when undertaking comparative analyses of geomorphic features. We show that the MPA selection criteria used by the Australian Government addressed the issues of false homogeneity described by Williams et al. (2009), but that final placement of MPAs was based on additional stakeholder considerations. Finally, we argue that although the Williams et al. (2009) study provides valuable information on biological distributions within seamounts and canyons, the hypothesis that geomorphic features (particularly seamounts and submarine canyons) are surrogates for benthic biodiversity is not tested explicitly by their study.

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.

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.

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 & 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 42 sample data set comprises the mineraology of surface seabed sediment (~0-2 cm) in Jervis Bay. More information: Radke, L.C., Huang, Z., Przeslawski, R., Webster, I.T., McArthur, M.A., Anderson, T.J., P.J. Siwabessy, Brooke, B. 2011. Including biogeochemical factors and a temporal component in benthic habitat maps: influences on infaunal diversity in a temperate embayment. Marine and Freshwater Research 62 (12): 1432 - 1448. Huang, Z., McArthur, M., Radke, L., Anderson, T., Nichol, S., Siwabessy, J. and Brooke, B. 2012. Developing physical surrogates for benthic biodiversity using co-located samples and regression tree models: a conceptual synthesis for a sandy temperature embayment. International Journal of Geographical Information Science DOI:10.1080/13658816.2012.658808.

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 & 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. More Information: Radke, L.C., Huang, Z., Przeslawski, R., Webster, I.T., McArthur, M.A., Anderson, T.J., P.J. Siwabessy, Brooke, B. 2011. Including biogeochemical factors and a temporal component in benthic habitat maps: influences on infaunal diversity in a temperate embayment. Marine and Freshwater Research 62 (12): 1432 - 1448. Huang, Z., McArthur, M., Radke, L., Anderson, T., Nichol, S., Siwabessy, J. and Brooke, B. 2012. Developing physical surrogates for benthic biodiversity using co-located samples and regression tree models: a conceptual synthesis for a sandy temperature embayment. International Journal of Geographical Information Science DOI:10.1080/13658816.2012.658808.

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.

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 126 sample dataset comprises chlorophyll a and pheophytin a measurements on surface seabed sediments (~0 to 2 cm) from Jervis Bay.

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 126 sample data set comprises TCO2 flux and pool data for surface seabed sediments (~0 to 2 cm).

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 110 sample data-set comprises salinity, dissolved oxygen, water temperature and light attenuation (KD) measurements from Jervis Bay.

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 18 sample data set comprises %TOC, %TN, TOC/TN ratios, carbon and nitrogen isotopic ratios and major and trace element concnetrations of plant and algae tissues from Jervis Bay. The red algae likely belong to the genera Gracilaria edulis and Acrosorium venulosum which are abundant in the Bay, and are often observed to washup on the beaches.