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.

Submarine canyons have been recognised as areas of significant ecological and conservation value for their enhanced primary productivity, benthic biomass and biodiversity. In Australia, 753 submarine canyons were mapped on all margins of the continent by the Marine Biodiversity Hub through the Australian Government's National Environmental Research Program. An analysis of canyon geomorphic metrics provided the basis to objectively classify these canyons across a hierarchy of physical characteristics (e.g. volume, depth range, rugosity) separately for shelf-incising and slope-confined canyons (Huang et al., 2014). Here we extend this analysis to include oceanographic variables in presenting a first pass assessment of habitat quality for all canyons on the Australian margin, with a focus on their upper reaches. This study is based on the premise that habitat heterogeneity, productivity and disturbance are the three factors that potentially determine the quality of a canyon habitat. For each factor we derived a range of variables to inform the assessment of habitat quality (see Table). Habitat heterogeneity was measured using a selection of eight geomorphic metrics including canyon volume and rugosity that are considered likely to have a positive relationship with habitat heterogeneity. Canyon productivity was assessed from five variables including: distance to the shelf break as a proxy of nutrient inputs from land and the continental shelf; bottom current speed as an indicator of nutrient supply to benthic epifauna (derived from time-series re-analysis of the BLUElink oceanographic model and in-situ data), and; measures of the probability, frequency and intensity of upwelling (also from BLUElink data). The BLUElink variables have positive relationships with productivity whereas the relationship between distance to shelf and productivity is negative. Benthic disturbance was assessed from the maximum and range of bottom current speeds, and the frequency and intensity of tropical cyclones. According to these relationships, individual canyons were assigned habitat quality scores, first separately for each variable and then aggregated for the three habitat factors. The final scores were obtained by averaging the scores of the three habitat factors. The results show that many submarine canyons on the eastern Australian margin have high habitat quality scores (see Figure). This is interpreted to be mainly due to the influence of the upwelling-favourable East Australian Current which generates high productivity throughout the year. The Albany canyons on the south-western margin also offer high habitat quality for marine species due to complex geometrical and geophysical structures. They also benefit from the upwelling-favourable Flinders Current. In contrast, canyons on the northern and western margins have lower habitat quality. Many of these canyons receive little input from land and continental shelf. In addition, the downwelling- favourable Leeuwin Current, which flows along the western margin of the continent, hampers the supply of deep water nutrients from reaching the upper reaches of canyons, particularly canyon heads that intersect the euphotic zone. Overall, these results provide a framework for targeted studies of canyons aimed at testing and verifying the habitat potential identified here and for establishing monitoring priorities for the ongoing management of canyon ecosystems.

Understanding and predicting the bio-physical relationships between seabed habitats, biological assemblages, and marine biodiversity is critical to managing marine systems. Species distributions and assemblage structure of infauna were examined on the oceanic shelf surrounding Lord Howe Island (LHI) relative to seabed complexity within and adjacent to a newly discovered relict coral reef. High resolution multibeam sonar was used to map the shelf, and identified an extensive relict reef in the middle of the shelf, which separated an inner drowned lagoon from the outer shelf. Shelf sediments and infauna were sampled using a Smith McIntyre grab. The three geomorphic zones (drowned lagoon, relict reef and outer shelf) were strong predictors or surrogates of the physical structure and sediment composition of the LHI shelf and its infaunal assemblage. Infaunal assemblages were highly diverse with many new and endemic species recorded. Each zone supported characteristic assemblages and feeding guilds, with higher abundance and diversity offshore.

This introductory chapter provides an overview of the book's contents and definitions of key concepts including benthic habitat, potential habitat and seafloor geomorphology. The chapter concludes with a summary of commonly used habitat mapping technologies. Benthic (seafloor) habitats are physically distinct areas of seabed that are associated with particular species, communities or assemblages that consistently occur together. Benthic habitat maps are spatial representations of physically distinct areas of seabed that are associated with particular groups of plants and animals. Habitat maps can illustrate the nature, distribution and extent of distinct physical environments present and importantly they can predict the distribution of the associated species and communities.

Three areas in the Torres Strait-Gulf of Papua region were selected for detailed study of sediments and benthic fossil biota. These areas form a transect across the shelf from the Fly River Delta to the shelf edge, near the northern extremity of the Great Barrier Reef. The Torres Strait-Gulf of Papua shelf is a shallow, low-gradient platform, where the shelf edge occurs between 120 and 140 m depth. In the study area, where the sediments range from muddy to gravelly carbonate sands, the sediment deposition rates are low and the relict content of sediment is often high. The three areas show distinct differences in benthic foraminiferal assemblages as indicated by relative abundances at the order level, as well as distribution patterns of individual species; these differences are also reflected in the total microbiotic communities. Given the high relict content in the surface material across these sites, a foraminiferal preservation scale was developed to assess the extent of reworking. Taphonomic features indicate that abrasion is the main factor affecting preservation. Despite poor preservation of the foraminiferal tests, the benthic foraminiferal species have a strong correlation to water depth, indicating that transportation pathways are short. Application of multivariate statistics to analyze the relationship between environmental attributes and the distributions of the microbiota and foraminiferal species indicates the additional importance of factors including percent carbonate mud, percent gravel, organic carbon flux, temperature, salinity and mean grain size. The benthic foraminifera produce a much stronger correlation to the environmental variables than the microbiota, indicating that these organisms can provide a detailed assessment of habitat types.

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. The GA0315_SETasi folder contains video footage; the excel file is the video characterisation data. Underwater video footage represents raw data. Video characterisation dataset include percent cover of substate.

This study presents compelling evidence for a diverse and abundant seabed community which has developed over the course of the Holocene beneath the Amery Ice Shelf in East Antarctica. Fossil analysis of a 47 cm long sediment core reveals a rich modern fauna, dominated by filter feeders (sponges and bryozoans), with an abundant infauna predominantly of polychaetes. The down-core assemblage reveals a succession in the colonisation of this site. The lower portion of the core (prior to ~9600 yr BP) is completely devoid of preserved fauna. The first colonisers of the site after this time were the mobile benthic organisms. Their occurrence in the core is matched by the first appearance of planktonic taxa, indicating a retreat of the ice shelf following the last glaciation to within sufficient distance to advect planktonic particles via bottom currents. The benthic infauna and filter feeders emerged during the peak abundance of the planktonic organisms, indicating their dependence on this advected food supply which is brought via bottom currents flowing from the open shelf waters of Prydz Bay. Understanding patterns of species succession in this environment has important implications for determining the potential significance of future global change. The collapse of Antarctic ice shelves, as has happened in recent times, would significantly change the organic supply regime, and therefore the nature of these sub-ice shelf benthic communities.

This is a compilation of all the processed multibeam bathymetry data that Geoscience Australia holds in its database for the Cato, West and Birds Island (Coral Sea) in the northeastern coast of Queensland. The compilation and the processing of GA's bathymetric data in the Coral Sea was produced following a request by an external client in July 2013.

Geoscience Australia is investigating the suitability of offshore sedimentary basins as potential CO2 storage sites. In May 2012 a seabed survey (GA0335/SOL5463) was undertaken in collaboration with the Australian Institute of Marine Science to acquire baseline marine data in the Petrel Sub-basin, Joseph Bonaparte Gulf. The aim was to collect information on possible connections (faults and fluid pathways) between the seabed and key basin units, and to characterise seabed habitats and biota. Two areas were surveyed (Area 1: 471 km2, depth ~ 80-100 m; Area 2: 181 km2, depth ~ 30-70 m), chosen to investigate the seabed over the potential supercritical CO2 boundary (Area 1) and the basin margin (Area 2), with Area 2 located around Flat Top 1 Well. Data analysed include multibeam sonar bathymetry and backscatter, seabed samples and their geochemical and biological properties, video footage and still images of seabed habitats and biota, and acoustic sub-bottom profiles. Pockmarks, providing evidence for fluid release, are present at the seabed, and are particularly numerous in Area 1. Area 1 is part of a sediment-starved, low-relief section of shelf characterised by seabed plains, relict estuarine paleochannels, and low-lying ridges. Facies analysis and radiocarbon dating of relict coastal plain sediment indicates Area 1 was a mangrove-rich environment around 15,500 years ago, transgressed near the end of the Last Glacial period (Meltwater Pulse 1A). Modern seabed habitats have developed on these relict geomorphic features, which have been little modified by recent seabed processes. Seabed habitats include areas of barren and bioturbated sediments, and mixed patches of sponges and octocorals on hardgrounds. In the sub-surface, stacked sequences of northwest-dipping to flat-lying, well-stratified sediments, variably incised by palaeochannels characterise the shallow geology of Area 1. Some shallow faulting through these deposits was noted, but direct linkages between seabed features and deep-seated faults were not observed. Area 2 is dominated by carbonate banks and ridges. Low-lying ridges, terraces and plains are commonly overlain by hummocky sediment of uncertain origin. Pockmarks are present on the margins of banks, and on and adjacent to ridges. Despite the co-location of banks and ridges with major faults at depth, there is a lack of direct evidence for structural connectivity, particularly because of significant acoustic masking in the sub-surface profiles of Area 2. While no direct structural relationship was observed in the acoustic sub-bottom profiles between these banks, ridges and faults visible in the basin seismic profiles, some faults extend through the upper basin units towards the seabed on the margin of Area 2. No evidence was detected at the seabed for the presence of thermogenic hydrocarbons or other fluids sourced from the basin, including beneath the CO2 supercritical boundary. The source of fluids driving pockmark formation in Area 1 is most likely decomposing mangrove-rich organic matter within late Pleistocene estuarine sediments. The gas generated is dominated by CO2. Additional fluids are potentially derived from sediment compaction and dewatering. Conceptual models derived from this are being used to inform regional-scale assessments of CO2 storage prospectivity in the Petrel Sub-basin.

In order to protect the diversity of marine life in Australia's Exclusive Economic Zone (EEZ), the federal parliament has passed the Environmental Protection and Biodiversity Conservation (EPBC) Act 1999. The Act is being implemented through the design of a national representative system of marine protected areas (MPAs) that will place under protection a representative portion of Australia's EEZ by 2012. A total of 13 MPAs have already been nominated for the southeast region in 2006. Limited biological data in Australia's EEZ has resulted in biophysical information compiled by Geoscience Australia being used as a proxy for seabed biodiversity in support of marine conservation planning. Information we use to characterise the seabed includes bathymetry, geomorphology, acoustic properties, sediment properties, slope and sediment mobilisation due to waves and tides. To better characterise habitats on the Australian continental shelf, Geoscience Australia is creating 'seascape' maps (similar to geological facies maps) that integrate these multiple layers of spatial data, and are useful for the prediction of the distribution of biodiversity in Australia's EEZ. This information provides 100% spatial coverage based on objective, multivariate statistical methods and offers certainty for managers and stakeholders including the oil and gas industry, who are involved with designing Australia's national MPA system. Certainty for industries operating in the EEZ is enhanced by a reproducible, science-based approach for identifying conservation priorities and the classification of seafloor types within multiple use areas.