The mapping of seabed environments is fundamental to successful fisheries management and environmental monitoring, however, there is an emerging need to better characterise habitats based upon appropriate physical parameters. In this study, relationships between seabed geomorphology and the distribution of benthic habitats were examined using multibeam sonar, underwater video, predicted wave energy, and sediment data for Esperance Bay, part of the Recherche Archipelago. This shallow (<50 m), high energy, biogenic sediment dominated environment is located in temperate southwestern Australia. Exposure to wave energy appears to determine the distribution of unconsolidated substrate, and is the most useful regional scale predictor of rhodolith and seagrass habitats. Although they are intermittently smothered by mobile sediments, limestone reefs provide habitat for a wide range of sessile organisms, even in very high wave exposure environments. The distribution of rhodolith beds is related to poorly sorted sediments that contain high gravel, mud, and CaCO3 percentages. Our results reveal that in the Recherche Archipelago, wave abrasion coupled with localised sediment transport and accumulation play a major role in increasing the diversity of inner shelf benthic habitats. This highlights the value of assessing geomorphic processes in order to better understand the distribution and structure of benthic habitats.

The mapping of seabed environments is fundamental to successful fisheries management and environmental monitoring, however, there is an emerging need to better characterise habitats based upon appropriate physical parameters. In this study, relationships between seabed geomorphology and the distribution of benthic habitats were examined using multibeam sonar, underwater video, predicted wave energy, and sediment data for Esperance Bay, part of the Recherche Archipelago. This shallow (<50 m), high energy, biogenic sediment dominated environment is located in temperate southwestern Australia. Exposure to wave energy appears to determine the distribution of unconsolidated substrate, and is the most useful regional scale predictor of rhodolith and seagrass habitats. Although they are intermittently smothered by mobile sediments, limestone reefs provide habitat for a wide range of sessile organisms, even in very high wave exposure environments. The distribution of rhodolith beds is related to poorly sorted sediments that contain high gravel, mud, and CaCO3 percentages. Our results reveal that in the Recherche Archipelago, wave abrasion coupled with localised sediment transport and accumulation play a major role in increasing the diversity of inner shelf benthic habitats. This highlights the value of assessing geomorphic processes in order to better understand the distribution and structure of benthic habitats.

The mapping of seabed environments is fundamental to successful fisheries management and environmental monitoring, however, there is an emerging need to better characterise habitats based upon appropriate physical parameters. In this study, relationships between seabed geomorphology and the distribution of benthic habitats were examined using multibeam sonar, underwater video, predicted wave energy, and sediment data for Esperance Bay, part of the Recherche Archipelago. This shallow (<50 m), high energy, biogenic sediment dominated environment is located in temperate southwestern Australia. Exposure to wave energy appears to determine the distribution of unconsolidated substrate, and is the most useful regional scale predictor of rhodolith and seagrass habitats. Although they are intermittently smothered by mobile sediments, limestone reefs provide habitat for a wide range of sessile organisms, even in very high wave exposure environments. The distribution of rhodolith beds is related to poorly sorted sediments that contain high gravel, mud, and CaCO3 percentages. Our results reveal that in the Recherche Archipelago, wave abrasion coupled with localised sediment transport and accumulation play a major role in increasing the diversity of inner shelf benthic habitats. This highlights the value of assessing geomorphic processes in order to better understand the distribution and structure of benthic habitats.

The mapping of seabed environments is fundamental to successful fisheries management and environmental monitoring, however, there is an emerging need to better characterise habitats based upon appropriate physical parameters. In this study, relationships between seabed geomorphology and the distribution of benthic habitats were examined using multibeam sonar, underwater video, predicted wave energy, and sediment data for Esperance Bay, part of the Recherche Archipelago. This shallow (<50 m), high energy, biogenic sediment dominated environment is located in temperate southwestern Australia. Exposure to wave energy appears to determine the distribution of unconsolidated substrate, and is the most useful regional scale predictor of rhodolith and seagrass habitats. Although they are intermittently smothered by mobile sediments, limestone reefs provide habitat for a wide range of sessile organisms, even in very high wave exposure environments. The distribution of rhodolith beds is related to poorly sorted sediments that contain high gravel, mud, and CaCO3 percentages. Our results reveal that in the Recherche Archipelago, wave abrasion coupled with localised sediment transport and accumulation play a major role in increasing the diversity of inner shelf benthic habitats. This highlights the value of assessing geomorphic processes in order to better understand the distribution and structure of benthic habitats.

Providing accurate maps of coral reefs where the spatial scale and labels of the mapped features correspond to map units appropriate for examining biological and geomorphic structures and processes is a major challenge for remote sensing. The objective of this work is to assess the accuracy and relevance of the process used to derive geomorphic zone and benthic community zone maps for three western Pacific coral reefs produced from multi-scale, object-based image analysis (OBIA) of high-spatial-resolution multi-spectral images, guided by field survey data. Three Quickbird-2 multi-spectral data sets from reefs in Australia, Palau and Fiji and georeferenced field photographs were used in a multi-scale segmentation and object-based image classification to map geomorphic zones and benthic community zones. A per-pixel approach was also tested for mapping benthic community zones. Validation of the maps and comparison to past approaches indicated the multi-scale OBIA process enabled field data, operator field experience and a conceptual hierarchical model of the coral reef environment to be linked to provide output maps at geomorphic zone and benthic community scales on coral reefs. The OBIA mapping accuracies were comparable with previously published work using other methods; however, the classes mapped were matched to a predetermined set of features on the reef.

Standard deviation of depth was calculated from the bathymetry surface for each cell using the ArcGIS Spatial Analyst Focal Statistics "STD" parameter. Standard deviation of depth represents the dispersion of depth values (in meters) around the mean depth within a square 3x3 cell window. The 2x2 meter resolution standard deviation of depth GeoTIFF was exported and added as a new map layer to aid in benthic habitat classification. Acoustic imagery was acquired for the VICRNM on two separate missions onboard the NOAA ship, Nancy Foster. The first mission took place from 2/18/04 to 3/5/04. The second mission took place from 2/1/05 to 2/12/05. On both missions, seafloor depths between 14 to 55 m were mapped using a RESON SeaBat 8101 ER (240 kHz) MBES sensor. This pole-mounted system measured water depths across a 150 degree swath consisting of 101 individual 1.5 degree x 1.5 degree beams. The beams to the port and starboard of nadir (i.e., directly underneath the ship) overlapped adjacent survey lines by approximately 10 m. The vessel survey speed was between 5 and 8 kn. In 2004, the ship's location was determined by a Trimble DSM 132 DGPS system, which provided a RTCM differential data stream from the U.S. Coast Guard Continually Operating Reference Station (CORS) at Port Isabel, Puerto Rico. Gyro, heave, pitch and roll correctors were acquired using an Ixsea Octans gyrocompass. In 2005, the ship's positioning and orientation were determined by the Applanix POS/MV 320 V4, which is a GPS aided Inertial Motion Unit (IMU) providing measurements of roll, pitch and heading. The POS/MV obtained its positions from two dual frequency Trimble Zephyr GPS antennae. An auxiliary Trimble DSM 132 DGPS system provided a RTCM differential data stream from the U.S. Coast Guard CORS at Port Isabel, Puerto Rico. For both years, CTD (conductivity, temperature and depth) measurements were taken approximately every 4 hours using a Seabird Electronics SBE-19 to correct for the changing sound velocities in the water column. In 2004, raw data were logged in .xtf (extended triton format) using Triton ISIS software 6.2. In 2005, raw data were logged in .gsf (generic sensor format) using SAIC ISS 2000 software. Data from 2004 were referenced to the WGS84 UTM 20 N horizontal coordinate system, and data from 2005 were referenced to the NAD83 UTM 20 N horizontal coordinate system. Data from both projects were referenced to the Mean Lower Low Water (MLLW) vertical tidal coordinate system. The 2004 and 2005 MBES bathymetric data were both corrected for sensor offsets, latency, roll, pitch, yaw, static draft, the changing speed of sound in the water column and the influence of tides in CARIS Hips & Sips 5.3 and 5.4, respectively. The 2004 data was then binned to create a 1 x 1 m raster surface, and the 2005 data was binned to a create 2 x 2 m raster surface. After these final surfaces were created, the datum for the 2004 bathymetric surfaces was transformed from WGS84 to NAD83 using the "Project Raster" function in ArcGIS 9.1. The 2004 surface was transformed so that it would have the same datum as the 2005 surface. The 2004 bathymetric surface was then down sampled from 1 x 1 to 2 x 2 m using the "Resample" function in ArcGIS 9.1. The 2004 surface was resampled so it would have the same spatial resolution as the 2005 surface. Having the same coordinate systems and spatial resolutions, the final 2004 and 2005 bathymetry rasters were then merged using the Raster Calculator function "Merge" in ArcGIS's Spatial Analyst Extension to create a seamless bathymetry surface for the entire VICRNM area south of St. John. For a complete description of the data acquisition and processing parameters, please see the data acquisition and processing reports (DAPRs) for projects: NF-04-06-VI and NF-05-05-VI (Monaco & Rooney, 2004; Battista & Lazar, 2005).

The abundance and distribution of benthic organisms and communities at both broad and fine scales were surveyed at Montgomery Reef in March and July 2009. Due to the logistical constraints placed on sampling techniques by the macrotidal changes around Montgomery Reef, three sampling techniques were employed to obtain imagery of the benthic environment between the depths of 0 and 53 metres.Reef Walks:With much of the reef edge exposed at low tide, the shallowest sections of the reef (0 to ~6 metres) could be sampled whilst walking across the exposed reef. Digital cameras (Ricoh GX100) were held at 1~1.2 metres above the reef with 1 photograph taken approximately every 2 metres. Teams of researchers walked in parallel, with 3-4 camera deployed simultaneously at a site. Each camera was synchronised with a GPS providing accurate positional information (2 - 5 metres) from which each image could later be georeferenced. Reef walks were conducted to the northeast, southeast, northwest and southwest. Tripod Camera:A simple tripod camera system developed by A. Heyward was trialled to sample the turbid shallow waters between 2 and 16 metres. Each system consisted of a camera tripod with a downward facing digital camera (Ricoh GX100) attached 600mm above the ground and set to photograph every 5 seconds. Each camera was synchronised with a GPS providing accurate positional information from which individual images could later be georeferenced. The tripod systems were attached to 20 metres of rope and lowered off the side of a tender to the bottom and held for a minimum of 5 seconds to allow the camera to complete at least one image while the tripod was located firmly on the substrate. It was noted that using underwater strobes generally reduced image quality. As a result the strobes were turned off and only natural light was relied on for photography. During retrieval the tender was allowed to drift with prevailing wind and tide, with images of the benthos effectively taken every 2 to 5 metres. The start of each transect position allowed the length of each drift to be monitored, so that transects of a nominal length, often around 200m, could be completed before moving the tender to a new location. The advantage of the technique is that even in very turbid water, high resolution digital stills are obtained with the stability afforded by the tripod allowing for cameras to be set with a longer exposure letting in maximum light.Towed Video:The AIMS towed video system was used to survey the deeper water (between 10 and 53 metres) to the north and south of the reef. The system was flown at approximately 1 metre above the sea floor with real time analysis of the video footage (AIMS Towvid) used to examine the broad scale distribution of dominant benthic biota. In addition to video footage, a downward facing digital still camera was attached to the bottom of the towed body. The camera was set to photograph the benthos approximately every 5 metres. The high resolution images allowed for a more detailed assessment of the benthic community. The objectives of the research were three-fold:1. to provide a broad- and fine-scale characterisation the benthic communities and substratum at Montgomery Reef2. to identify similarities and differences in the benthic communities examined and3. to undertake a detailed spatial analysis to examine and map the distribution of these benthic organisms and communities.This research was the first detailed quantitative survey of the benthic communities of Montgomery Reef. Univariate, multivariate and spatial statistics are employed to examine both the similarities and differences in the distribution and relative abundance of these benthic communities. This study is part of a broader regional survey of the Kimberley fringing reefs initiated by AIMS in 2009.

The characterisation of benthic habitats based on their abiotic (physical and chemical) attributes remains poorly defined in the marine environment, but is becoming increasingly central in the development of marine management plans in Australia and elsewhere in the world. The current study tested this link between physical and biological datasets for the southern Gulf of Carpentaria, Australia. The results presented were based on a range of physical factors, including the sediment composition (grain size and carbonate content), sediment mobility, water depth and organic carbon flux, and their relationship to the distribution and diversity of benthic macrofauna was tested. The results reveal the importance of process-based indices, such as sediment mobility, in addition to other environmental factors in defining the distribution of the benthic macrofauna. The distribution of the benthic macrofauna changes gradationally across the south-eastern Gulf, associated with changes in the per cent mud and gravel, the seabed exposure and the water depth. Patterns of diversity also reveal the importance of physical processes such as sediment mobility in defining benthic habitats. The species' environment relationships observed at the small scale of the current study are consistent with broader associations observed for other organisms within the Gulf.

The characterisation of benthic habitats based on their abiotic (physical and chemical) attributes remains poorly defined in the marine environment, but is becoming increasingly central in the development of marine management plans in Australia and elsewhere in the world. The current study tested this link between physical and biological datasets for the southern Gulf of Carpentaria, Australia. The results presented were based on a range of physical factors, including the sediment composition (grain size and carbonate content), sediment mobility, water depth and organic carbon flux, and their relationship to the distribution and diversity of benthic macrofauna was tested. The results reveal the importance of process-based indices, such as sediment mobility, in addition to other environmental factors in defining the distribution of the benthic macrofauna. The distribution of the benthic macrofauna changes gradationally across the south-eastern Gulf, associated with changes in the per cent mud and gravel, the seabed exposure and the water depth. Patterns of diversity also reveal the importance of physical processes such as sediment mobility in defining benthic habitats. The species' environment relationships observed at the small scale of the current study are consistent with broader associations observed for other organisms within the Gulf.