Mesophotic fish communities of the ancient coastline in Western Australia

Marine diversity across the Australian continental shelf is shaped by characteristic benthic habitats which are determined by geomorphic features such as paleoshorelines. In north-western Australia there has been little attention on the fish communities that inhabit an ancient coastline at ~125 m depth (the designated AC125), which is specified as a key ecological feature (KEF) of the region and is thought to comprise hard substrate and support enhanced diversity. We investigated drivers of fish species richness and assemblage composition spanning six degrees of latitude along sections of the ancient coastline, categorised as ‘on’ and ‘off’ the AC125 based on depth, across a range of habitats and seafloor complexity (~60–180 m depth). While some surveyed sections of the AC125 had hard bottom substrate and supported enhanced fish diversity, including over half of the total species observed, species richness and abundance overall were not greater on the AC125 than immediately adjacent to the AC125. Instead, depth, seafloor complexity and habitat type explained patterns in richness and abundance, and structured fish assemblages at both local and broad spatial scales. Fewer fishes were associated with deep sites characterized by negligible complexity and soft-bottom habitats, in contrast to shallower depths that featured benthic biota and pockets of complex substrate. Drivers of abundance of common species were species-specific and primarily related to sampling Areas, depth and substrate. Fishes of the ancient coastline and adjacent habitats are representative of mesophotic fish communities of the region, included species important to fisheries and conservation, and several species were observed deeper than their currently known distribution. This study provides the first assessment of fish biodiversity associated with an ancient coastline feature, improving our understanding of the function it plays in regional spatial patterns in abundance of mesophotic fishes. Management decisions that incorporate the broader variety of depths and habitats surrounding the designated AC125 could enhance the ecological role of this KEF, contributing to effective conservation of fish biodiversity on Australia’s north west shelf

Generalised deep learning model for semi-automated length measurement of fish in stereo-BRUVS

Assessing the health of fish populations relies on determining the length of fish in sample species subsets, in conjunction with other key ecosystem markers; thereby, inferring overall health of communities. Despite attempts to use artificial intelligence (AI) to measure fish, most measurement remains a manual process, often necessitating fish being removed from the water. Overcoming this limitation and potentially harmful intervention by measuring fish without disturbance in their natural habitat would greatly enhance and expedite the process. Stereo baited remote underwater video systems (stereo-BRUVS) are widely used as a non-invasive, stressless method for manually counting and measuring fish in aquaculture, fisheries and conservation management. However, the application of deep learning (DL) to stereo-BRUVS image processing is showing encouraging progress towards replacing the manual and labour-intensive task of precisely locating the heads and tails of fish with computer-vision-based algorithms. Here, we present a generalised, semi-automated method for measuring the length of fish using DL with near-human accuracy for numerous species of fish. Additionally, we combine the DL method with a highly precise stereo-BRUVS calibration method, which uses calibration cubes to ensure precision within a few millimetres in calculated lengths. In a human versus DL comparison of accuracy, we show that, although DL commonly slightly over-estimates or under-estimates length, with enough repeated measurements, the two values average and converge to the same length, demonstrated by a Pearson correlation coefficient (r) of 0.99 for n=3954 measurement in ‘out-of-sample’ test data. We demonstrate, through the inclusion of visual examples of stereo-BRUVS scenes, the accuracy of this approach. The head-to-tail measurement method presented here builds on, and advances, previously published object detection for stereo-BRUVS. Furthermore, by replacing the manual process of four careful mouse clicks on the screen to precisely locate the head and tail of a fish in two images, with two fast clicks anywhere on that fish in those two images, a significant reduction in image processing and analysis time is expected. By reducing analysis times, more images can be processed; thereby, increasing the amount of data available for environmental reporting and decision making

A large-scale experiment finds no evidence that a seismic survey impacts a demersal fish fauna

Seismic surveys are used to locate oil and gas reserves below the seabed and can be a major source of noise in marine environments. Their effects on commercial fisheries are a subject of debate, with experimental studies often producing results that are difficult to interpret. We overcame these issues in a large-scale experiment that quantified the impacts of exposure to a commercial seismic source on an assemblage of tropical demersal fishes targeted by commercial fisheries on the North West Shelf of Western Australia. We show that there were no short-term (days) or long-term (months) effects of exposure on the composition, abundance, size structure, behavior, or movement of this fauna. These multiple lines of evidence suggest that seismic surveys have little impact on demersal fishes in this environment

A field and video-annotation guide for baited remote underwater stereo-video surveys of demersal fish assemblages

Researchers TL, BG, JW, NB and JM were supported by the Marine Biodiversity Hub through funding from the Australian Government's National Environmental Science Program. Data validation scripts and GlobalArchive.org were supported by the Australian Research Data Commons, the Gorgon-Barrow Island Gorgon Barrow Island Net Conservation Benefits Fund, administered by the Government of Western Australia and the BHP/UWA Biodiversity and Societal Benefits of Restricted Access Areas collaboration.1. Baited remote underwater stereo-video systems (stereo-BRUVs) are a popular tool to sample demersal fish assemblages and gather data on their relative abundance and body-size structure in a robust, cost-effective, and non-invasive manner. Given the rapid uptake of the method, subtle differences have emerged in the way stereo-BRUVs are deployed and how the resulting imagery are annotated. These disparities limit the interoperability of datasets obtained across studies, preventing broad-scale insights into the dynamics of ecological systems. 2. We provide the first globally accepted guide for using stereo-BRUVs to survey demersal fish assemblages and associated benthic habitats. 3. Information on stereo-BRUV design, camera settings, field operations, and image annotation are outlined. Additionally, we provide links to protocols for data validation, archiving, and sharing. 4. Globally, the use of stereo-BRUVs is spreading rapidly. We provide a standardised protocol that will reduce methodological variation among researchers and encourage the use of Findable, Accessible, Interoperable, and Reproducible (FAIR) workflows to increase the ability to synthesise global datasets and answer a broad suite of ecological questions.Publisher PDFPeer reviewe

Fish-habitat associations in the region offshore from James price point - a rapid assessment using baited remote underwater video stations (BRUVS)

A "snapshot" of the fish-habitat associations in the vicinity of James Price Point was obtained during a single expedition in October 2009, when Baited Remote Underwater Video Stations (BRUVS) were deployed in coastal waters to survey the demersal and semi-demersal ichthyofauna. A total of 7108 individuals from 116 species of fishes, sharks, rays and sea snakes were recorded from 154 sites. Bony fishes were represented by 8 orders, and cartilaginous fishes were well represented by the Carcharhiniformes, Rajiformes and Orectolobiformes. There were 2 species of hydrophiid sea snakes. Multivariate analysis showed that species responded to the amount of epibenthic cover in the study area and that there was an interaction between depth and sediment composition, as well as depth and epibenthic cover, in defining four fish assemblages to the north and south of James Price Point. Diversity appeared to increase with depth amongst these assemblages. The sandy seabed offshore from James Price Point was inhabited by a "deep sandy" fish assemblage, which intruded inshore across the study area, and was characterised by the presence of ponyfish (Leiognathus), threadfin bream (Nemipterus) and queenfish (Scomberoides). On either side were shallow, northern and deeper, southern, assemblages inhabiting "gardens" of macroalgae, filter-feeders and some seagrass beds. These epibenthic habitats at the northern and southern ends of the survey area were clearly important to many species, but in general there appeared to be little association of particular vertebrate species or biotic habitat types with the James Price Point area itself. The study area was notable for the diversity and abundance of the fauna, given the shallow depth, lack of rugose seafloor topography and lack of sub-tidal coral reefs in the area sampled. Coarse comparison with the fauna at similar distance to shore in similar latitudes in the Great Barrier Reef Marine Park, the Burrup Peninsula and the Kimberley indicated that the study area had more small pelagic planktivores and more large semi-demersal predators. There was also an absence of some species normally associated with muddy seafloors and fringing coral reefs that are common on BRUVS set elsewhere in regions with less extreme tidal ranges. © Royal Society of Western Australia 2011

Measuring and communicating effects of MPAs on deep "shoal" fisheries

Counts by divers have shown a rapid rise in coral trout populations on shallow reefs of the Great Barrier Reef Marine Park closed to fishing in 2004, but the deeper line-fishing grounds (>20m) have been inaccessible to fish biologists until the development of baited remote underwater video stations (BRUVS™). Here we summarise pair-wise comparisons of inter-reef "shoal grounds", closed and open to line-fishing, in terms of abundance and lengths of prized sportfish, bycatch and unfished species. The results of paired "fished-unfished" contrasts all depended on the context of microhabitat type, proximity to fishing ports and species vulnerability to line-fishing. On diffuse, low-relief grounds off Townsville prized target species were actually less abundant in zones closed to fishing. On discrete sunken banks of the Capricorn plateau closed to fishing there were about twice as many prized species, and they were larger than conspecifics on fished banks. A positive effect of closure to fishing around the deep bases of reefs in the Pompeys, Swains and Capricorn- Bunkers was visible only in coral-dominated microhabitats. Reef sharks were consistently more abundant in zones closed to fishing. These differences have been communicated with novel point-and-click, map-based BRUVS footage and data summaries on the "e-Atlas", using Google “Earth” and YouTube. This allows the public to make independent conclusions about the local effects of marine protected areas

Comparing the effects of different coloured artificial illumination on diurnal fish assemblages in the lower mesophotic zone

Artificial illumination is required when sampling with baited remote underwater video systems (BRUVS) in the lower mesophotic zone beyond ~ 90 m depth, yet little is known of how the choice of lighting influences fish assemblages and affects survey results in this zone. Here we use BRUVS equipped with the commonly used GoPro action camera to compare the composition and abundance of diurnal fish assemblages sampled under artificial Royal blue (~ 450 nm), Deep red (~ 660 nm) and natural day white light (~ 5600 K) in the lower mesophotic zone of the north-west shelf of Australia (19° 14.724′S 117° 20.286′E). No significant differences were detected in the fish assemblage composition or the number of species when surveyed using blue, red or white light at our study location. A greater mean total abundance of fish was observed using red light compared with white and blue light, however, individual species showed varied responses to the different light colours. When using consumer-grade action cameras such as GoPros, white light was shown to be far superior in image quality (and therefore ease of fish identification) compared to red and blue light. We recommend sampling diurnal mesophotic fish assemblages using a wavelength of light based on the survey objectives and the capabilities of the camera selected

AIMS 2013 Biodiversity Survey of Glomar Shoal and Rankin Bank

Rankin Bank and Glomar Shoal shoals are situated 147 km North West and 93km North, respectively, of the Dampier Archipelago in North Western Australia. They are the only large, complex bathymetrical features on the outer western shelf of the West Pilbara. Rankin Bank rises steeply from 120m depth along its north eastern margin and in all other quadrants it rises above the surrounding continental shelf from approximately 80m depth. The main body of the shoal takes the form of several highly complex and rugose peaks and plateaus, reaching 20-40m below the sea surface. In comparison, the much larger Glomar Shoal riseson all sides from 80m depth and, as a whole, shallows more gradually to include a plateau region lying within 40m of the surface. At the 60m depth contour Glomar Shoal covers an area of 14699.6 hectares, which is approximately 8.5 times larger than Rankin Bank which covers an area of 1721.5 hectares.The shoals were surveyed from the Australian Institute of Marine Science (AIMS) Research Vessel, RV Solander, using multibeam equipment and technicians provided by Fugro Survey Pty Ltd, during August - September 2013. For both shoals, continuous coverage bathymetry, rugosity digital elevation and terrain models were produced. These data were then used to ensure key areas of depth, aspect and slope were sampled during the subsequent biodiversity sampling cruise in September 2013. Data on biota was collected using underwater towed cameras for benthic habitat assessment and stereo baited remote underwater video stations (SBRUVS) to sample fish. In addition, seabed surface sediments were collected around each shoal, using a grab sampler, and analysed for grain size and chemical composition