The Lord Howe Island survey SS06-2008 in April 2008 aboard the RV Southern Surveyor was a collaboration between the University of Wollongong and Geoscience Australia. The survey was also an activity of the Commonwealth Environment Research Facilities' (CERF) Marine Biodiversity Hub, of which Geoscience Australia is a partner, and will contribute to the revised Plan of Management for the Lord Howe Marine Parks. The objectives of the survey were to map the morphology and benthic environments of the shallow shelf that surrounds Lord Howe Island as well as the deeper flanks of this largely submarine volcano. Of particular interest was the apparent drowned reef structure on the shelf and the spatial distribution of seabed habitats and infauna. The data collected are required to better understand the history of reef growth at Lord Howe Island, which sits at the southernmost limit of reef formation, and links between the physical environment and ecological processes that control the spatial distribution of biodiversity on the shelf. The morphology of the flanks of the submarine volcano was also examined to reveal whether they provide evidence of major erosional and depositional processes acting on the volcano. This report provides a description of the survey activities and the results of the processing and initial analysis of the data and samples collected.

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 Plans as Key Ecological Features (KEFs). Although poorly studied, these banks and terraces have been identified as potential biodiversity hotspots for the Australian tropical north. As part of the National Environment Research Program Marine Biodiversity Hub, Geoscience Australia in collaboration with the Australian Institute of Marine Science 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 up to 1 m deep (pockmarks) formed in soft silty sediments that are generally barren of any epibenthos (Fig .1). 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. We used ArcGIS spatial analyst tools to quantify the features and explored their potential relationships with other variables (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 banks. 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.

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. Sample diversity indices calculated in PRIMER (version 6) using the species level data from JBinfauna_species (25Oct10).xls.

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.

A seabed mapping survey over a series of carbonate banks, intervening channels and surrounding sediment plains on the Van Diemen Rise in the eastern Joseph Bonaparte Gulf was completed under a Memorandum of Understanding between Geoscience Australia and the Australian Institute of Marine Sciences. The survey obtained detailed geological (sedimentological, geochemical, geophysical) and biological data (macro-benthic and infaunal diversity, community structure) for the banks, channels and plains to establish the late-Quaternary evolution of the region and investigate relationships between the physical environment and associated biota for biodiversity prediction. The survey also permits the biodiversity of benthos of the Van Diemen Rise to be put into a biogeographic context of the Arafura-Timor Sea and wider northern Australian marine region. Four study areas were investigated across the outer to inner shelf. Multibeam sonar data provide 100 per cent coverage of the seabed for each study area and are supplemented with geological and biological samples collected from 63 stations. In a novel approach, geochemical data collected at the stations provide an assessment of sediment and water quality for surrogacy research. Oceanographic data collected at four stations on the Van Diemen Rise will provide an understanding of the wave, tide and ocean currents as well as insights into sediment transport. A total of 1,154 square kilometres of multibeam sonar data and 340 line-km of shallow (<100 mbsf) sub-bottom profiles were collected.

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.

Zooplankton sampling encompasses a range of methods, but these require specialized equipment, cost, and time. Ship-pumped seawater provides an opportunity to broadly quantify zooplankton abundance and richness during surveys with objectives other than zooplankton characterisation. Here, the effectiveness of sampling ship-pumped seawater for zooplankton was evaluated through the identification of established diurnal and biogeographic patterns as well as comparisons between sampling with surface tows and ship-pumped seawater over the Western Australian margin. Only one species was classed as a fouling organism (unknown Y-shaped polyps), and only one group was excluded from sampling via ship-pumped water (chaetognaths). As expected, we found significant diurnal differences in zooplankton abundance, as well as differences between the Houtman sub-basin (~ 100 km offshore) and the Wallaby (Cuvier) Plateau (~500 km offshore). These results suggest that sampling zooplankton with ship-pumped waters can result in useful broad comparisons of the overall abundance and number of taxa among regions but only when comparisons with surface tows are made. Importantly, sampling via ship-pumped water is not an appropriate method from which to characterize zooplankton communities and in no way replaces or negates the need for more traditional and comprehensive sampling of zooplankton.

Climate change is threatening tropical reefs across the world, with most scientists agreeing that the current changes in climate conditions are occurring at a much faster rate than in the past and are potentially beyond the capacity of reefs to adapt and recover. Current research in tropical ecosystems focuses largely on corals and fishes, although other benthic marine invertebrates provide crucial services to reef systems, with roles in nutrient cycling, water quality regulation, and herbivory. We review available information on the effects of environmental conditions associated with climate change on noncoral tropical benthic invertebrates, including inferences from modern and fossil records. Increasing sea surface temperatures may decrease survivorship and increase the developmental rate, as well as alter the timing of gonad development, spawning, and food availability. Environmental changes associated with climate change are linked to larger ecological processes, including changes in larval dispersal and recruitment success, shifts in community structure and range extensions, and the establishment and spread of invasive species. Loss of some species will trigger economic losses and negative effects on ecosystem function. Our review is intended to create a framework with which to predict the vulnerability of benthic invertebrates to the stressors associated with climate change, as well as their adaptive capacity. We anticipate that this review will assist scientists, managers, and policy-makers to better develop and implement regional research and management strategies, based on observed and predicted changes in environmental conditions.

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. This is a folder of the images derived from benthic samples taken on cruise Sol4769 aboard RV Solander. Subfolders house images of Echinodermata, Mollusca, Polychaete, images taken of fresh material during cruise, and various categories of Crustacea, denoted by a C_ prefix in the folder name. Images of fresh material were made using a Canon EOS 40D camera on a rostrum in the wet lab of the ship. Images of preserved material were made using a Nikon Coolpix camera mounted on a Macroscope in the benthic lab at GA. These images formed the first point of reference in identifying subsequent specimens to save wear and tear on the specimens put aside as reference material.

An international effort is underway to establish a representative system of marine protected areas (MPAs) in the Southern Ocean to help provide for the long-term conservation of marine biodiversity in the region. Critical to this undertaking is understanding the distribution of benthic assemblages. Our aim is to identify the areas where benthic marine assemblages are likely to differ in the Southern Ocean including near-shore Antarctica. We achieve this by using a hierarchical spatial classification of ecoregions, bathomes and environmental types. Ecoregions are defined according to available data on biogeographic patterns and environmental drivers on dispersal. Bathomes are identified according to depth strata defined by known species distributions. Environmental types are uniquely classified according to the geomorphic features found within the bathomes in each ecoregion. We identified 23 ecoregions and nine bathomes. From a set of 30 types of geomorphic features of the seabed, 846 unique environmental types were classified for the Southern Ocean. We applied the environmental types as surrogates of different assemblages of biodiversity to assess the representativeness of MPAs. We found that for existing MPAs no ecoregion has their full range of environmental types represented and 12 ecoregions have no MPAs. Current MPA planning processes, if implemented, will substantially increase the representation of environmental types particularly within 7 ecoregions. To meet internationally agreed conservation goals, additional MPAs will be needed. To assist with this process, we identified 119 locations with spatially restricted environmental types, which should be considered for inclusion in future MPAs.