The planktobenthos is an important area with unique environmental conditions and represents the immediate link between the benthos and the water column. Despite its close links with the seafloor, the planktobenthos has never been deliberately sampled concurrently with the benthos. We have developed a new method for planktobenthic sampling which allows concurrent collection of benthic and suprabenthic specimens. The Mounted Assembly for Planktobenthic Sampling (MAPS) uses a novel tri-layered net with a seafloor-triggered opening and closing mechanism attached to an epibenthic sled. The MAPS was deployed on the Carnarvon Shelf in Western Australia and was successful at separately sampling both benthic and planktobenthic fauna. A wide variety of epibenthic and infaunal animals were collected from the sled while planktobenthic animals such as mysids were identified from all three nets. The tri-layered net was particularly effective at collecting a broad range of planktobenthic organisms, including smaller fragile larvae and adults which may have otherwise been destroyed during collection in a single net. The number of species in planktobenthic and benthic samples was correlated, although the strength and significance of this relationship varied among taxonomic groups. Importantly, the MAPS can be modified for use on a wide variety of benthic sleds to target a range of organisms. The concurrent collection of planktobenthic and benthic biota will contribute to a range of research areas, including larval ecology, nutrient cycling, biogeography and surrogacy research.

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.

Reliable marine benthic habitat maps at regional and national scales are needed to enable the move towards the sustainable management of marine environmental resources. The most effective means of developing broad-scale benthic habitat maps is to use commonly available marine physical data due to the paucity of adequate biological data and the prohibitive cost of directly sampling benthic biota over large areas. A new robust method of mapping marine benthic habitats at this scale was developed based on a stratified approach to habitat classification. This approach explicitly uses knowledge of marine benthic ecology to determine an appropriate number of stratification levels, to choose the most suitable environmental variables for each level, and to select ecologically significant boundary conditions (i.e. threshold values) for each variable. Three stratification levels, with nine environmental variables, were created using a spatial segmentation approach. Each level represents major environmental processes and characteristics of the Australian marine benthic environment. The finest scale of benthic habitat is represented by seafloor physical properties of topography, sediment grain size and seabed shear stress. Water-column nutrient parameters and bottom water temperature depicted the intermediate scale, while the broadest scale was defined by seabed insolation parameters derived from depth data. The classifications of the three stratified levels were implemented using an object-based fuzzy classification technique that recognises that habitats are largely homogenous spatial regions, and transitions between habitats are often gradual. Classification reliability was indicated in confidence maps. Physical habitat diversity was evaluated for the final benthic habitat map that combines the three classifications. The final benthic habitat map identifies the structurally complex continental shelf break as an area of relatively high habitat diversity. Continental Shelf Research

Physical sedimentological processes such as the mobilisation and transport of shelf sediments during extreme storm events give rise to disturbances that characterise many shelf ecosystems. The intermediate disturbance hypothesis predicts that biodiversity is controlled by the frequency of disturbance events, their spatial extent and the amount of time required for ecological succession. A review of available literature suggests that periods of ecological succession in shelf environments range from 1 to over 10 years. Physical sedimentological processes operating on continental shelves having this same return frequency include synoptic storms, eddies shed from intruding ocean currents and extreme storm events (cyclones, typhoons and hurricanes). Modelling studies that characterise the Australian continental shelf in terms of bed stress due to tides, waves and ocean currents were used here to create a map of ecological disturbance, defined as occurring when the Shield's parameter exceeds a threshold of 0.25. We also define a dimensionless ecological disturbance ratio (ED) as the rate of ecological succession divided by the recurrence interval of disturbance events. The results illustrate that on the outer part of Australia's southern, wave-dominated shelf the mean number of days between threshold events that the Shield's parameter exceeds 0.25 is several hundred days.

Mapping of benthic habitats seldom considers biogeochemical variables or changes across time. We aimed to: (i) develop winter and summer benthic habitat maps for a sandy embayment; and (ii) compare the effectiveness of various maps for differentiating infauna. Patch-types (internally homogeneous areas of seafloor) were constructed using combinations of abiotic parameters, and are presented in sediment-based, biogeochemistry-based and combined sediment/biogeochemistry-based habitat maps. August and February surveys were undertaken in Jervis Bay, Australia, to collect samples for physical (%mud, sorting, %carbonate), biogeochemical (chlorophyll a, sulfur, sediment metabolism, bio-available elements) and infaunal analyses. Boosted Decision Tree and cokriging models generated spatially continuous data-layers. Habitat maps were made from classified layers using GIS overlays, and were interpreted from a biophysical-process perspective. Biogeochemistry and %mud varied spatially and temporally, even in visually homogeneous sediments. Species turnover across patch-types was important for diversity, and the utility of habitat maps for differentiating biological communities varied across months. Diversity patterns were broadly related to reactive carbon and redox which varied temporally. Inclusion of biogeochemical factors and time in habitat maps provides a better framework for differentiating species and interpreting biodiversity patterns than once-off studies based solely on sedimentology or video-analysis.

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 colocated 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. 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. Feeding guild counts per sample. Aggregated from species level data in LHI_Infauna_species (27Oct10).csv using the information in LHI_taxa_info.xls

Understanding marine biodiversity has received much attention from an ecological and conservation management perspectives. The Australian Government's Department of the Environment, Water, Heritage and the Arts has initiated the Commonwealth Environment Research Facilities (CERF) initiative to enhance the understanding of Australia's natural environment for policy making. One part of the CERF initiative through the marine biodiversity hub was to predict biodivesity from expansive physical variables. This talk presents some of the work arising from this area.

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 50 sample data set comprises %TOC, %TN, TOC/TN ratios, and carbon and nitrogen isotopic ratios for surface (0.0 to 2.0 cm) sediments from Jervis Bay.

This chapter presents a broad synthesis and overview based on the 57 case studies included in Part 2 of this book, and on questionnaires completed by the authors. The case studies covered areas of seafloor ranging from 0.15 to over 1,000,000 km2 (average of 26,600 km2) and a broad range of geomorphic feature types. The mean depths of the study areas ranged from 8 to 2,375 m, with about half of the studies on the shelf (depth <120 m) and half on the slope and at greater depths. Mapping resolution ranged from 0.1 to 170 m (mean of 13 m). There is a relatively equal distribution of studies among the four naturalness categories: near-pristine (n=17), largely unmodified (n = 16), modified (n=13) and extensively modified (n=10). In terms of threats to habitats, most authors identified fishing (n=46) as the most significant threat, followed by pollution (n=12), oil and gas development (n=7) and aggregate mining (n=7). Anthropogenic climate change was viewed as an immediate threat to benthic habitats by only three authors (n=3). Water depth was found to be the most useful surrogate for benthic communities in the most studies (n=17), followed by substrate/sediment type (n=14), acoustic backscatter (n=12), wave-current exposure (n=10), grain size (n=10), seabed rugosity (n=9) and BPI/TPI (n=8). Water properties (temperature, salinity) and seabed slope are less useful surrogates. A range of analytical methods were used to identify surrogates, with ARC GIS being by far the most popular method (23 out of 44 studies that specified a methodology).

This report provides a description of the CERF Marine Biodiversity Hub's survey of the Carnarvon Shelf, Western Australia, in August and September, 2008. The survey was a collaboration between the Australian Institute of Marine Science (AIMS) and Geoscience Australia (GA) aboard RV Solander, as part of the Hub's Surrogates Program. The purpose of field surveys in the Surrogates Program is 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 in strategically selected, spatially discrete areas that are representative of much broader benthic environments. The report describes the methods employed in the survey and the datasets collected. Additional processing of most of the physical data (wave and current measurements, multibeam sonar bathymetry and backscatter, sediment grab samples, acoustic sediment profiles) and biological data (towed underwater video and stills photography, bottom sediment samples, near-bottom plankton samples) collected is required before comparative analysis between the data sets can commence. However, a number of initial interpretations of the physical data have been made and examples of the types of biota encountered in the towed video and stills photography and initial interpretations of the benthic communities encountered, are provided. The survey was focussed on three strategically selected study areas on the southern Carnarvon Shelf at Mandu, Point Cloates and Gnaraloo. A small additional area was also examined near the Muiron Islands, in the mouth of Exmouth Gulf, at the end of the survey.