Characterisation of Scott Reef Lagoon Biota - Fish and Benthic Macrobenthos Report. Scott Reef Biological Survey Expedition December 1999.

Baited remote underwater video stations (BRUVS (TM)) were deployed to census deep water fish communities (30-70 m) at 19 sites in South Scott Reef lagoon in November and December 1999. The sites were selected to cover nominally representative habitat types and depth contours across 6 regions of South Scott Reef lagoon. These regions, were East Hook Entrance, East Hook, East Lagoon, Central Lagoon, South Lagoon and West Lagoon. A total of 112 deployments were made along three transects running outward from the centre of South Scott Reef lagoon to both East Hook and West Hook and to the southern shallow region, as well as along the drop-off at the entrance to the lagoon. Six BRUVS (TM) were deployed at each site, at similar depths, separated by intervals of approximately 150 m. A GPS fix was taken for all BRUVS (TM) deployed. Each BRUVS (TM) was lowered to the seafloor, with an attached rope and surface float marking its position, enabling recovery later in the day. Normal daily operations were to deploy all six units in one site during the morning, followed by a second deployment at a new site in the afternoon. As a test, on one occasion, two BRUVS (TM) were deployed at night with underwater torches attached for illumination. Each BRUVS (TM) recorded onto a 90 minute Hi-8 video tape until the tape was full. The deployed units were recovered after the maximum recording time and generally within 4 hours of deployment. Tapes were scanned on a Sony Trinitron 14 inch Monitor using a Sony Video Hi-8 Cassette Recorder with a Sony Control Unit editing deck. This allowed fast-forward, play-back, zoom X2 and freeze to enable definitive species identifications, and to speed data collection. Data collected from each tape included a brief description of the seabed topography and benthic community, a species name, the time (hr:min:sec) of first sighting of the individual species, the species activities/behaviours (in 6 categories) in the field of view, the time that an individual species began to feed at the bait canister and/or the time at which the most number of individuals was active in the field of view, and the maximum number of each species sighted simultaneously in any one field of view. These data were initially entered into a Microsoft Excel spreadsheet. This study was undertaken to determine species richness and diversity of fishes, sharks, rays and sea snakes below the limits of safe SCUBA diving in South Scott Reef lagoon, using baited remote underwater video stations (BRUVS (TM)).BRUVS (TM) data was used in combination with benthic community data derived from surveys with television recordings from a remotely operated vehicle (ROV) to provide;1. a statistical clustering by similar fish communities of the different habitats and regions in the South Scott Reef lagoon and2. a measure of association between fish communities and broad habitat classifications. This study was part of a more extensive survey of North Scott Reef lagoon and South Scott Reef lagoon, "Characterisation of Scott Reef lagoon biota - fish and macrobenthos" carried out during November and December, 1999. Work in North Scott Reef lagoon focused on shallow water benthic communities, which were sampled by the divers using hand-held underwater video cameras. Sampling in South Scott Reef lagoon used more diverse methods and focused on not only the benthic communities but the demersal fish communities as well. In South Scott Reef lagoon the benthic communities were sampled using divers, ROVs and grabs, while fish communities were sampled using deployed baited remote underwater video stations (BRUVS (TM)).

In September/October 1993, fish communities at North Scott Reef, South Scott Reef, Seringapatam Reef and the Rowley Shoals (Mermaid Reef, Clerke Reef and Imperieuse Reef) were surveyed. Fish population censuses for a number of reef fish families (Chaetodontidae, Pomacentridae, Acanthuridae, Scaridae, Labridae, Caesionidae, Siganidae, Pomacanthidae and Zanclidae) were carried out by trained divers at a number of outer reef slope and lagoon sites at each reef. The log5 abundance of fish species was recorded during 45-minute SCUBA swims in which the observer swam a zig-zag course along an approximately 250m long section of the reef within a depth range of 0-12m.Absolute counts of snappers, emperors, cods and butterfly fish (Lutjanidae, Lethrinidae, Serranidae and Chaetodontidae) were also made at outer reef slope and lagoon sites.Additional fish counts of Labridae and Pomacentridae were made at 3 sites at South Scott Reef using standardised counting methods developed for long-term monitoring of fish populations on the Great Barrier Reef. This technique involved counting fish along 5 replicate 50m x 2m transects per site at a depth of approximately 6m.In addition to the quantitative counts of the groups mentioned above, lists of all species of fish observed at each site were compiled. This study was initiated to quantitatively characterise the fish communities on the major offshore reef systems of north west Australia (Scott Reefs, Seringapatam Reef and the Rowley Shoals) and to compare their composition and structure to fish communities at similar latitudes in the Great Barrier Reef and the Coral Sea.

In NW Australia a range of emergent reefs bound the western margin of the Oceanic Shoals bioregion, but with the major feature being numerous submerged shoals lying along and across the shelf edge. Scott Reef, the largest emergent reef system, has a diverse shallow water coral reef ecosystem that has demonstrated impressive resilience to cyclone and coral bleaching disturbances over the last 15 years (Gilmour et al, 2013). The adjacent deeper lagoon of South Scott Reef covers approximately 300 km2 in depths of 30-?70m. This deeper lagoon has areas of very high live coral cover and represents the largest example of a mesophotic reef system in the region. The slightly deeper distribution of these habitats appears to have ameliorated those impacts such as thermal stress and cyclones, which have caused significant disturbance to the adjacent shallow areas. A spatial model using multibeam and seabed surveys with towed video and AUV in 2009 and 2011 has been developed by AIMS to describe and predict the distribution of the key mesophotic habitats. While this model is the most advanced of its type for such a reef system, additional research suggests that fine?scale water movement, including turbulence and upwelling driven by internal waves, may be a key driver of these habitat patterns. We used the RV Falkor’s time at Scott Reef to characterise these detailed oceanographic processes with the goal of integrating the physical and biological data to further develop the spatial model, then extend this approach to other reefs and shoals in the region. The fine scale hydrodynamics and their relationship to patterns of seabed biodiversity was explored from RV Falkor with intensive oceanographic measurements of the water column across these features and detailed imaging transects of the seabed habitats using the SOI DDROV and other camera gear.

This report is preliminary and produced by the Western Australian Museum's Marine Survey Team from a shallow water (0-20 metres depth) survey of Mermaid, Scott and Seringapatam Reefs. The purpose of the study is to ascertain the status of the biodiversity (an overview census) of selected marine phyla. The sites chosen are a combination of new sites, those previously visited by the Museum in 1986 and a number of sites currently being monitored by the Australian Institute of Marine Science.

The coral and communities at the AIMS Long Term Monitoring (LTM) sites at Scott Reef, Seringapatam and Rowley Shoals were re-surveyed, following periodic surveys since 1994. In addition to the Proposed Field Program, the following work was completed: Benthic LTM surveys at three additional sites at Scott Reef. Coral species diversity surveys at four additional sites at Scott Reef. Benthic LTM surveys of coral communities at 13 sites in the deep lagoon (20-60m) at South Reef using ROV. Colony size-frequency surveys at six sites at Scott Reef. Genetic samples of surviving Seriatopora hystrix from 7 sites at Scott Reef. Additional temperature loggers and current metres deployed at Rowley Shoals. Video and photographic documentation of the Rowley Shoals, in water and from air using drones This project is a co-investment between Woodside Energy Ltd (WEL) and AIMS, in order to build scientific knowledge at Scott Reef, Seringapatam and Rowley Shoals and was undertaken between 4th – 25th November 2017.

In August/September 1993, surveys of coral community composition and structure were carried out at Scott Reefs (North Scott Reef and South Scott Reef) and two reefs in the Rowley Shoals group (Mermaid Reef and Clerke Reef).Coral communities were surveyed at a total of 94 sites, using a semi-quantitative visual survey method and a subset of these sites were surveyed using a video belt transect technique. Sites were areas of around 100-300 m², arranged along cross-reef profiles on the reef flats in a depth range of 0.5-2 m and on the slopes or adjacent reef floor at 4-6 m and 8-12 m. Aerial photography was used to assist in selection of study areas.During each visual survey a detailed list of coral species was made and the relative abundance of each taxa, as a percentage of total macro-benthos, was estimated. The site descriptors recorded were maximum and minimum depth (measured); and subjective estimates of the following: slope; percentage cover of hard substrate; percentage cover of major benthic groups (hard coral, soft coral, macro algae and sponge); percentage cover of substratum categories (platform; large blocks; small blocks; rubble; gravel; sand). An additional 4 sites were surveyed, without recording detailed species lists.A Sony Hi 8 video camera was used to film five replicate 20 m long belt transects about 40 cm wide, within each of the 3 depth ranges, in a sub-set of the sites used for visual surveys. Estimates of percent cover of hard coral, soft coral, algae and bare substratum were made using point sampling of the video tape. At 25 regularly spaced pauses along each video tape, the identity of each item under five points marked on the screen of the TV monitor (one near each corner and one in the centre) was recorded. Percent cover estimates were used to estimate the heterogeneity of the bottom cover as a basis for designing an appropriate sample protocol for a future monitoring program. The visual surveys were carried out to determine whether recognisable, taxonomically consistent assemblages of coral species occurred at the shallow water study sites and to determine the approximate spatial extent of these corals. The surveys were also used to provide detailed taxonomic descriptions of the coral communities at the sites where the video transects were recorded. These surveys were the first quantitative assessments of coral community structure on northwest Australian offshore reefs, previous coral surveys being largely concerned with taxonomic and biogeographic problems.The information collected during this survey formed the basis of of site selection for the subsequent long-term monitoring project.

Ten current meter moorings, a weather station, two tide gauges and 45 temperature loggers were deployed at Scott Reef, prior to the coral spawning event in March, 2003 and recovered in June, 2003. In addition to moored instruments, surface drifters were deployed to map surface circulation. CTD casts were also made. Arrays of instruments were deployed to quantify patterns of water circulation and stratification in the vicinity of Scott Reef. Surface drifters were deployed to observe both the local fine scale circulation in the immediate vicinity of Scott Reef, and to better understand the potential connectivity between reef systems along this region of the West Australian North West Shelf and possible transport of spawned material. The goal was to elucidate key physical oceanographic mechanisms influencing observed temporal and spatial variability of coral recruitment and coral bleaching at Scott Reef.As part of this study a preliminary depth-averaged hydrodynamic model was developed and applied to describe in broad detail the major features of depth averaged tidal circulation. This research is the "Physical Environment" sub-project of the project "Biological and Physical Environment at Scott Reef 2003"

Towed Video transects + Digital StillsSloVid Digital StillsCTDBRUVSSBRUVSEcho SounderSediment Samples (CSIRO) ARP7 Reefs Trip 6578To characterise the status of and natural temporal variability in sessile benthic biota and associated fish communities, across the plateau areas around Browse Island and its deeper waters. The project will provide a reference dataset, updated seasonally for two years, for the status of key biodiversity indicator habitats around Browse Island.

We undertook a biological data acquisition program as part of the transit of the R.V. Southern Surveyor between Darwin and Cairns 15-24 October 2012. The overarching aim of this program was to use an ROV and benthic sled to collect benthic marine information and specimens for biodiversity and biodiscovery research in areas previously mapped by Geoscience Australia during survey GA-276, including a bank (Area I) and terrace/hole feature within the proposed Wessel Islands CMR (Area II). This study focuses on sessile invertebrates such as sponges and octocorals due to their ecological importance as habitat providers and their chemical importance as sources of marine natural products and medicines. In less than 24 hours of sampling effort, survey SS2012/t07 resulted in 261 voucher specimens which will be used for biodiversity and natural products research. A total of 49 samples are to be lodged at the ABL, and samples with weights larger than 300 g will be sent to the NCI for screening of active compounds against cancer and HIV. Sponges were the most abundant group collected based on both biomass (~ 139 kg) and number of voucher specimens (93), followed by cnidarians (30 kg, 73 vouchers), particularly hard corals (23 kg, 11 vouchers). As expected the top of the bank in Area I had a seemingly diverse and abundant sessile invertebrate community, with consistent patchy occurrence of sponges, octocorals, and hard corals. The terrace at in Area II supports moderate densities of sponges and octocorals, while the adjacent deep hole at ~ 100 m seems to be covered with muddy gravel and supports scattered mobile and sedentary invertebrates, of which crinoids dominate, as well as skates and numerous small demersal fish.