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

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

Abundant box jellyfish, Chironex sp (Cnidaria: Cubozoa: Chirodropidae), discovered at depths of over 50 m on western Australian coastal reefs

Box jellyfish cause human fatalities and have a life cycle and habit associated with shallow waters (<5 m) in mangrove creeks, coastal beaches, embayments. In north-western Australia, tow video and epibenthic sled surveys discovered large numbers (64 in a 1500 m tow or 0.05 m(-2)) of Chironex sp. very near to the benthos (<50 cm) at depths of 39-56 m. This is the first record of a population of box jellyfish closely associated with the benthos at such depths. Chironex were not widespread, occurring only in 2 of 33 tow videos and 3 of 41 epibenthic sleds spread over 2000 km(2). All Chironex filmed or captured were on low to medium relief reefs with rich filter feeder communities. None were on soft sediment habitat despite these habitats comprising 49% of all sites. The importance of the reef habitat to Chironex remains unclear. Being associated with filter feeder communities might represent a hazard, and other studies have shown C. fleckeri avoid habitats which represent a risk of entanglement of their tentacles. Most of our observations were made during the period of lowest tidal current flow in the morning. This may represent a period favourable for active hunting for prey close to the seabed

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

Accelerating Species Recognition and Labelling of Fish From Underwater Video With Machine-Assisted Deep Learning

Machine-assisted object detection and classification of fish species from Baited Remote Underwater Video Station (BRUVS) surveys using deep learning algorithms presents an opportunity for optimising analysis time and rapid reporting of marine ecosystem statuses. Training object detection algorithms for BRUVS analysis presents significant challenges: the model requires training datasets with bounding boxes already applied identifying the location of all fish individuals in a scene, and it requires training datasets identifying species with labels. In both cases, substantial volumes of data are required and this is currently a manual, labour-intensive process, resulting in a paucity of the labelled data currently required for training object detection models for species detection. Here, we present a “machine-assisted” approach for i) a generalised model to automate the application of bounding boxes to any underwater environment containing fish and ii) fish detection and classification to species identification level, up to 12 target species. A catch-all “fish” classification is applied to fish individuals that remain unidentified due to a lack of available training and validation data. Machine-assisted bounding box annotation was shown to detect and label fish on out-of-sample datasets with a recall between 0.70 and 0.89 and automated labelling of 12 targeted species with an F1 score of 0.79. On average, 12% of fish were given a bounding box with species labels and 88% of fish were located and given a fish label and identified for manual labelling. Taking a combined, machine-assisted approach presents a significant advancement towards the applied use of deep learning for fish species detection in fish analysis and workflows and has potential for future fish ecologist uptake if integrated into video analysis software. Manual labelling and classification effort is still required, and a community effort to address the limitation presented by a severe paucity of training data would improve automation accuracy and encourage increased uptake

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

Habitat value of subsea wells and pipelines for fishery target species in Australia

Subsea pipelines and wells installed to support the oil and gas industry represent some of the most extensive and numerous anthropogenic structures throughout global marine ecosystems. There remains a paucity of information on the habitat value of these structures for fishery target species and, as a result, little understanding of how decommissioning should be conducted to minimise impacts to populations of these economically and socially important species. We assess the diversity and abundance of species that are targets of recreational and commercial fisheries on 33 subsea wells and 17 pipelines across the tropical northwest and temperate southeast marine regions of Australia. We examine relationships between fish identity and abundance and a range of environmental (e.g., depth, location), infrastructure-specific (e.g., pipeline position, diameter, age, length of pipeline, height of well, position on well), and biological (% cover of epibiota) variables using video filmed by remotely operated vehicles during their routine offshore inspection and maintenance campaigns. A total of 100 fishery target species were observed across subsea well and pipeline infrastructure, 56 species uniquely observed on pipelines and nine unique to wells. The families Lutjanidae (snapper), Serranidae (rock cods, groupers, perch), and Carangidae (trevallies) were most common and abundant on both wells and pipelines. In the northwest, lutjanids were most abundant around the base of wells, in shallow depths, on shorter wells, and where pipelines spanned the seafloor. A greater number of fishery target species and abundance of ocean perch (Helicolenus spp.) were also associated with pipelines that spanned the seafloor in temperate southeast Australia. The combined biomass of three species of snapper on wells in the northwest was 1,270 kg, with production levels for these species on each well estimated to be 105.2 g m2 year-1. The present study serves as an important reference point for informing decommissioning decisions for pipeline and well infrastructure and demonstrates the utility of industry-held data for science. We suggest that key predictor variables identified here be incorporated into comprehensive before-after-control-impact scientific studies for specific fields/assets to enable the prediction of potential impacts of decommissioning scenarios on marine communities present and quantification of such impacts after the decommissioning activity has occurred

A Field and Video-annotation Guide for Baited Remote Underwater stereo-video Surveys of Demersal Fish Assemblages

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 is annotated. These disparities limit the interoperability of datasets obtained across studies, preventing broadscale 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‐BRUVs 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 standardized protocol that will reduce methodological variation among researchers and encourage the use of Findable, Accessible, Interoperable and Reusable workflows to increase the ability to synthesize global datasets and answer a broad suite of ecological questions