Many rock oysters have evolved to thrive in the intertidal environment where they experience intense desiccation pressure and wide temperature fluctuations. The tropical natal rock oyster, Saccostrea cucullata, and the black-lip rock oyster, Saccostrea echinata, have higher reported thermal optima and tolerances than the better studied temperate species. However, the genetic basis of their thermotolerance, important for understanding their potential for climate adaptation, has not been characterised. We generated contig-level genome assemblies for two tropical rock oysters, Saccostrea cucullata and S. echinata. The final S. cucullata assembly was 1.2 Gb and comprised 23,868 contigs (contig N50 0.115 Mb), whereas the S. echinata assembly was 0.923 Gb and comprised 424 contigs (contig N50 19.7 Mb). BUSCO analysis (mollusca_odb10, n = 5295) indicated high gene-space completeness for both genomes (S. cucullata: 93.4% complete; S. echinata: 99.0% complete). K-mer-based genome size estimates indicated that both assemblies exceeded the inferred haploid genome size, consistent with partial retention of alternative haplotypes in highly heterozygous bivalve genomes. Both oyster genomes showed increased orthologues of heat shock proteins and histones compared to temperate species, suggesting potential mechanisms for thermal tolerance and environmental adaptability. In S. cucullata, many of the heat shock proteins were expressed following air exposure, which would include a mild heat stress among other stressors, further reinforcing their role in temperature tolerance. These results suggest both species are likely to be resilient to near term climate stress as well as having the potential to adapt to changing environments, and thus there is potential expansion for rock oyster aquaculture beyond the commonly-farmed Magallana gigas or Saccostrea glomerata species and the further development of a tropical rock oyster industry.

Citizen science is increasingly popular but requires training and modifications to sampling procedures so that volunteer-collected environmental DNA (eDNA) samples can be included in biodiversity surveys. In this study, we optimised methodology for a citizen science project targeting fish taxa; ensuring simple, safe and effective eDNA sampling. We compared species richness and composition of fish eDNA data obtained from a single type of passive sampler with that obtained from Longmire's preserved water samples at three waterways in north Queensland, Australia. The results showed substantial differences in richness and species composition between the two sampling approaches assessed using cytochrome c oxidase subunit I (COI) and mitochondrial 16S assays. Longmire's preserved water samples resulted in higher read abundances and greater richness for both assays. The fish composition differed between the two sampling approaches, despite identical sampling locations and times. This study demonstrates how two different sampling and preservation approaches can lead to different fish detection results in tropical aquatic systems.

Marine heatwaves can lead to mass mortality events, affecting bivalves. The saucer scallop (Ylistrum balloti) is an important commercial species found in Western Australia (WA) and central Queensland. The largest fishery for this species in WA is at Shark Bay, on the central WA coastline. The fishery has been impacted by heatwaves in the recent past and has yet to fully recover. Whether thermal pressures are influencing the fishery's recovery is uncertain, as other factors, including larval advection, could also influence recovery. A functional genomics approach was used to address this uncertainty. Scallops were collected from multiple locations in Shark Bay with different water temperatures and from a small, more southerly fishery adjacent to Perth. A full genome was assembled. The genome contains comparatively few gene copies of heat shock protein 70, an important indicator of thermal stress, particularly from class 12, which has been highly duplicated in other heat tolerant bivalves. Transcriptomic profiles in scallops collected from the different locations were compared, with the greatest differences observed in scallops collected from an area of Shark Bay with the warmest water temperatures. Some transcripts with altered abundance encoded heat shock proteins, proteins involved in macromolecule repair, and those with a primary metabolism role. Although this study is a snapshot of a few individuals at a single time point, it adds to the weight of evidence that extreme heatwave events and climate change impacts the recruitment of this commercially important species.

Changing ocean temperatures are already causing declines in populations of marine organisms. Predicting the capacity of organisms to adjust to the pressures posed by climate change is a topic of much current research effort, particularly for species we farm or harvest. To explore one measure of phenotypic plasticity, the physiological compensations in response to heat stress as might be experienced in a marine heatwave, we exposed Yellowtail Kingfish (Seriola lalandi) to sublethal heat stress, and used the transcriptome in gill and muscle, benchmarked against heat shock proteins and oxidative stress indicators, to characterise the acute heat stress response (6 h after the initiation of stress), and the physiological compensation to that response (24 and 72 h after the initiation of stress). The heat stress experiments induced elevations in heat shock proteins, as measured in blood, demonstrating the sublethal stress level. The initial response (6 h) to heat stress included the expected cellular stress response. Exposure of 24 h or more led to altered transcriptomic patterns for protein degradation, membrane transporters, and primary metabolism. In the muscle, numerous transcripts with mitochondrial function had altered abundance. There was a profound change to the regulation of transcription, as well as numerous transcripts with differential exon usage, suggesting that this may be a mechanism for conferring physiological resilience to heat stress. These results demonstrate the processes involved in acclimation to heat stress in this species, and the utility of using the transcriptome to assess plasticity. It also showed that differential exon usage may be an important mechanism for conferring plasticity. Future work should investigate the role of genome regulation, and alternative splicing in particular, on conferring resilience to temperature changes.

Rapid development and deployment of marine carbon dioxide removal (mCDR) approaches will be required to prevent the worst consequences of climate change and meet national treaty obligations under the Paris agreement. However, approaches to monitor the efficacy and environmental safety of mCDR are not being developed with the same intensity as the technology. Verification will be required to convince a sceptical public and regulatory community of the overall benefit of mCDR as well as provide the regulatory community a basis for risk assessments that will be required for at scale deployments. In this perspective, we posit that genomics-based approaches can be used to assess the efficacy of carbon sequestration and monitor for the possibility of unintended consequences. By adopting these approaches, it will be feasible to develop the evidence portfolio necessary to underpin assessments of the risks, benefits and trade-offs involved in responsible deployment of mCDR.

Waterways that drain the Great Barrier Reef catchment area (GBRCA) transport pollutants to marine habitats, provide a critical corridor between freshwater and marine habitats for migratory fish species, and are of high socioecological value. Some of these waterways contain concentrations of pesticide active ingredients (PAIs) that exceed Australian ecotoxicity threshold values (ETVs) for ecosystem protection. In this article, we use a "pathway to harm" model with five key criteria to assess whether the available information supports the hypothesis that PAIs are or could have harmful effects on fish and arthropod populations. Strong evidence of the first three criteria and circumstantial weaker evidence of the fourth and fifth criteria are presented. Specifically, we demonstrate that exceedances of Australian and New Zealand ETVs for ecosystem protection are widespread in the GBRCA, that the PAI contaminated water occurs (spatially and temporally) in important habitats for fisheries, and that there are clear direct and indirect mechanisms by which PAIs could cause harmful effects. The evidence of individuals and populations of fish and arthropods being adversely affected species is more circumstantial but consistent with PAIs causing harmful effects in the freshwater ecosystems of Great Barrier Reef waterways. We advocate strengthening the links between PAI concentrations and fish health because of the cultural values placed on the freshwater ecosystems by relevant stakeholders and Traditional Owners, with the aim that stronger links between elevated PAI concentrations and changes in recreationally and culturally important fish species will inspire improvements in water quality. Integr Environ Assess Manag 2024;20:1256-1279. © 2023 Commonwealth of Australia and The Commonwealth Scientific and Industrial Research Organisation. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Oil spills remain a persistent threat to marine life, but their long-term effects across different taxonomic groups are poorly understood. Few ecosystem models can predict the long-term effects of oil spills in marine systems due to data gaps and complexity of both marine systems and oil as a contaminant mixture. To support the development of regional ecosystem models, we reviewed the available data on the effects of oil spills on the marine ecosystem, and present and apply a process for selecting and assessing data on contaminant stressors. Our region of interest is the Salish Sea, a marginal sea in the Pacific Ocean, spanning the USA and Canada. We collate and present the data currently available on the impacts of polycyclic aromatic hydrocarbons (PAHs), oil-derived persistent organic pollutants, across multiple ecological groups within the Salish Sea. We then apply a scoring system to gauge the usefulness of those data for modelling the ecosystem impacts of these contaminant stressors. Within the available data on ecological processes and impacts of PAH, we identify data gaps in PAH uptake rates and metabolism across most biological groups, and in the overall effects of contaminants on marine mammals, sharks, and seabirds. These data gaps highlight research priorities that can enhance long-term risk assessments of oil-related contaminants on the marine ecosystem, and support broader modelling efforts and environmental management efforts in the Salish Sea and beyond.

As oil and gas infrastructure comes to the end of its working life, a decommissioning decision must be made: should the infrastructure be abandoned in situ, repurposed, partially removed, or fully removed? Environmental contaminants around oil and gas infrastructure could influence these decisions because contaminants in sediments could degrade the value of the infrastructure as habitat, enter the seafood supply if the area is re-opened for commercial and/or recreational fishing, or be made biologically available as sediment is resuspended when the structures are moved. An initial risk hypothesis, however, may postulate that these concerns are only relevant if contaminant concentrations are above screening values that predict the possibility of environmental harm or contaminant bioaccumulation. To determine whether a substantive contaminants-based risk assessment is needed for infrastructure in the Gippsland Basin (South-eastern Australia), we measured the concentration of metals and polycyclic aromatic hydrocarbons (PAHs) in benthic sediments collected around eight platforms earmarked for decommissioning. The measurements were compared to preset screening values and to background contaminant concentrations in reference sites. Lead (Pb), zinc (Zn), PAHs and other contaminants were occasionally measured at concentrations that exceeded reference values, most often within 150 m of the platforms. The exceedance of a few screening values by contaminants at some platforms indicates that these platforms require further analysis to determine the contaminant risks associated with any decommissioning option.

Following an oil spill, accurate assessments of the ecological risks of exposure to compounds within petroleum are required, as is knowledge regarding how those risks may change with the use of chemical dispersants. Laboratory toxicity tests are frequently used to assess these risks, but differences in the methods for preparation of oil-in-water solutions may confound interpretation, as may differences in exposure time to those solutions. In the present study, we used recently developed modifications of standardized ecotoxicity tests with copepods (Acartia sinjiensis), sea urchins (Heliocidaris tuberculata), and fish embryos (Seriola lalandi) to assess their response to crude oil solutions and assessed whether the oil-in-water preparation method changed the results. We created a water-accommodated fraction, a chemically enhanced water-accommodated fraction, and a high-energy water-accommodated fraction (HEWAF) using standard approaches using two different dispersants, Corexit 9500 and Slickgone NS. We found that toxicity was best related to total polycyclic aromatic hydrocarbon (TPAH) concentrations in solution, regardless of the preparation method used, and that the HEWAF was the most toxic because it dispersed the highest quantity of oil into solution. The TPAH composition in water did not vary appreciably with different preparation methods. For copepods and sea urchins, we also found that at least some of the toxic response could be attributed to the chemical oil dispersant. We did not observe the characteristic cardiac deformities that have been previously reported in fish embryos, most likely due to the use of unweathered oil, and, as a consequence, the high proportion of naphthalenes relative to cardiotoxic polycyclic aromatic hydrocarbon in the overall composition. The present study highlights the need to characterize both the TPAH composition and concentration in test solutions when assessing oil toxicity. Environ Toxicol Chem 2022;41:2580-2594. © 2022 SETAC.

Oil spills pose a significant threat to marine biodiversity. Crude oil can partition into sediments where it may be persistent, placing benthic species such as decapods at particular risk of exposure. Transcriptomic and histological tools are often used to investigate the effects of hydrocarbon exposure on marine organisms following oil spill events, allowing for the identification of metabolic pathways impacted by oil exposure. However, there is limited information available for decapod crustaceans, many of which carry significant economic value. In the present study, we assess the sublethal impacts of crude oil exposure in the commercially important Australian greentail prawn (Metapenaeus bennettae) using transcriptomic and histological analyses. Prawns exposed to light, unweathered crude oil “spiked” sediments for 90 h were transferred to clean sediments for a further 72 h to assess recovery. Chemical analyses indicated that polycyclic aromatic hydrocarbons increased by approximately 65% and 91% in prawn muscle following 24 and 90 h of exposure, respectively, and significantly decreased during 24‐ and 72‐h recovery periods. Transcriptomic responses followed an exposure and recovery pattern with innate immunity and nutrient metabolism transcripts significantly lowered in abundance after 24 h of exposure and were higher in abundance after 72 h of recovery. In addition, transcription/translation, cellular responses, and DNA repair pathways were significantly impacted after 24 h of exposure and recovered after 72 h of recovery. However, histological alterations such as tubule atrophy indicated an increase in severity after 24 and 72 h of recovery. The present study provides new insights into the sublethal impacts of crude oil exposure in greentail prawns and identifies molecular pathways altered by exposure. We expect these findings to inform future management associated with oil extraction activity and spills. Environ Toxicol Chem 2022;41:2162–2180. © 2022 John Wiley & Sons Ltd. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Phytoplankton activity underpins marine food webs, yet we have struggled to elucidate their diverse metabolism and physiology using traditional methods. Transcriptomics offers the ability to view the immediate cellular response of algae and algal communities to varying environmental conditions, as well as an alternative to sequencing the genome of protists, which can be challenging. Here, we review insights from transcriptomics into the ecology, evolution, and physiology of freshwater and marine phytoplankton, and offer best practices for the implementation of future transcriptomic projects on phytoplankton.

When offshore oil and gas infrastructure is no longer needed, it is either removed, partially removed, left in place, or left in place but repurposed. These processes are collectively referred to as decommissioning. Australian legislation requires oil and gas companies to develop acceptable plans for the safe removal of all offshore infrastructure at the end of a project’s life. Over the next 50 years, the liability for this decommissioning in Australia is expected to exceed US$45 billion. Unlike countries such as Norway, the United Kingdom and the Netherlands, Australian decommissioning activities are in their infancy, with only three cases (to date) in Commonwealth waters where infrastructure has been left in place or partially removed as part of decommissioning. Differences between the Australian marine environment and that of other regions around the world where decommissioning-related research is better progressed include very low sedimentation rates, both tropical and temperate habitats, different species composition, low primary production, and frequent tropical cyclones, as well as unique sociodemographic and cultural characteristics. Accordingly, the outcomes of the decision support tools used in other regions to identify preferred decommissioning options may not be equally applicable in Australia. Here we describe research to support risk and impact assessment for offshore decommissioning in Australia, where full removal of infrastructure is the “base case” regulatory default, but other options including partial removal and/or repurposing might provide similar or better outcomes when environmental, social, economic and seafood safety aspects are considered. Based on our review we propose an integrated framework for research needs to meet legislative requirements for decommissioning and identify research gaps that need to be addressed to inform decision-making for decommissioning in the Australian context.

Aquaculture releases nitrogen to the marine environment, potentially changing dynamics of local plankton populations and causing adverse impacts. Metatranscriptomics have been used to study planktonic nutrient cycles and community dynamics. We hypothesised that the metatranscriptome could be used to monitor changing phytoplankton physiology near leases. To test this hypothesis, opportunistic samples were collected from one oceanic location in winter and one estuarine location in spring and analysed via RNASeq. Transcriptomes from different locations were found to have little overlap, due to different community compositions in the oceanic and estuarine locations. Transcript function was similar at each location. Proximity to the salmon pen had little influence over the transcriptome at the estuarine location. In the oceanic environment, diatom-based activity decreased near pens and dinoflagellate-based activity increased as demonstrated through the abundance of carbon fixation and nitrogen-acquisition-related transcripts. Our initial results suggest that the use of the metatranscriptome in monitoring is promising.

Petroleum hydrocarbons can be discharged into the marine environment during offshore oil and gas production or as a result of oil spills, with potential impacts on marine organisms. Ecotoxicological assay durations (typically 24-96 h) used to characterize risks to exposed organisms may not always reflect realistic environmental exposure durations in a high-energy offshore environment where hydrocarbons are mixed and diluted rapidly in the water column. To investigate this, we adapted 3 sensitive toxicity tests to incorporate a short-term pulse exposure to 3 petroleum-based products: a produced water, the water-accommodated fraction (WAF) of a condensate, and a crude oil WAF. We measured 48-h mobility of the copepod Acartia sinjiensis, 72-h larval development of the sea urchin Heliocidaris tuberculata, and 48-h embryo survival and deformities of yellowtail kingfish Seriola lalandi, after exposure to a dilution series of each of the 3 products for 2, 4 to 12, and 24 h and for the standard duration of each toxicity test (continuous exposure). Effects on copepod survival and sea urchin larval development were significantly reduced in short-term exposures to produced water and WAFs compared to continuous exposures. Fish embryos, however, showed an increased frequency of deformities at elevated concentrations regardless of exposure duration, although there was a trend toward increased severity of deformities with continuous exposure. The results demonstrate how exposure duration alters toxic response and how incorporating relevant exposure duration to contaminants into toxicity testing may aid interpretation of more realistic effects (and hence an additional line of evidence in risk assessment) in the receiving environment. Environ Toxicol Chem 2021;40:2587-2600. © 2021 CSIRO. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Abstract The risk assessment for the environmental impact of oil spills in Australia is often conducted in part using a combination of spill mapping and toxicological thresholds derived from laboratory studies. While this process is useful in planning operational responses, such as where to position equipment stockpiles and whether to disperse oil, and can be used to identify areas near the spill site where impacts are likely to occur, it cannot accurately predict the environmental consequences of an oil spill or the ecosystem recovery times. Evidence of this disconnect between model predictions and observed impacts is the lack of a profound effect of the Deepwater Horizon wellhead blowout on recruitment to fisheries in the northern Gulf of Mexico, contrary to the predictions made in the Natural Resources Damage Assessment and despite the occurrence of impacts of the spill on marine mammals, marshes, and deep water ecosystems. The incongruity between predictions made with the current approach using threshold monitoring and impacts measured in the field results from some of the assumptions included in the oil spill models. The incorrect assumptions include that toxicity is acute, results from dissolved phase exposure, and would be readily reversible. The toxicity tests from which threshold models are derived use members of the ecosystem that are easily studied in the lab but may not represent the ecosystem as a whole. The test species are typically highly abundant plankton or planktonic life stages, and they have life histories that account for rapid changes in environmental conditions. As a consequence, these organisms recover quickly from an oil spill. The interdependence of ecosystem components, including the reliance of organisms on their microbiomes, is often overlooked. Additional research to assess these data gaps conducted using economically and ecologically relevant species, especially in Australia and other understudied areas of the world, and the use of population dynamic models, will improve the accuracy of environmental risk assessment for oil spills. Integr Environ Assess Manag 2020;16:813–830. © 2020 SETAC

Crude oil is a key contaminant in aquatic environments entering via natural and anthropogenic sources, causing toxicity in marine organisms. Traditionally, biomarkers have been utilised to determine crude oil exposure and effects in aquatic organisms, however advances in genomic technologies has led to increased adoption of transcriptomic approaches for identifying response and detoxification pathways following contaminant exposure. This study presents the first transcriptome for the greentail prawn (Metapenaeus bennettae), a commercially targeted benthic decapod crustacean from eastern and south-eastern Australia. The Trinity generated de novo assembly, after redundancy clustering, resulted in 86,401 contigs, of these 22,252 displayed strong homology to transcripts in the NCBI's non-redundant protein, Swiss-Prot and TrEMBL databases. Furthermore, Gene Ontology was assigned to 15,079 annotated contigs and KEGG Orthology was identified for 1318 annotated contigs. Transcripts encoding common biomarkers utilised to determine crude oil exposure were identified, including those for detoxification phase I and II enzymes; with 40 transcripts encoding for members of the cytochrome P450 gene family and 8 transcripts encoding glutathione S-Transferases (GSTs). Transcripts encoding oxidative stress enzymes including superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) and metallothionein (MT) were identified, as well as stress induced proteins including crustacean hyperglycemic hormone (CHH) and heat shock proteins (Hsps). The annotated transcriptome of the greentail prawn and the identification of detoxification and stress response transcripts, provides a necessary resource for future studies geared toward characterising differential transcriptomic patterns and molecular pathways after exposure to crude oil in this and other crustacean species of environmental and commercial importance.

Summary Exploratory drilling for deep‐sea oil and gas resources is planned for the Great Australian Bight (GAB). There is scant knowledge of the region's benthic ecosystems and no baseline information of the region's indigenous oil degrading bacteria. To address this knowledge gap, we used next generation sequencing (NGS) of three marker genes ( alkB , c23o and pmoA ) to detect and characterize the microbial communities capable of aerobic hydrocarbon degradation. Unique, highly novel microbial communities capable of degrading hydrocarbons occur in surface sediments at depths between 200 and 2800 m. Clustering at 97% demonstrated differences in community structure with depth, changing most markedly between 400 and 1000 m depth on the continental slope, and identified putative functional ‘ecotypes’ related to depth. Observed differences in community structure showed strong correlations with temperature, other physicochemical properties of the overlying water column and are further modulated by differences in sediment grain size. This study provides important baseline data on hydrocarbon degrading microbial communities prior to the start of petroleum resource extraction. Our data will inform future ecological monitoring of the GAB deep‐sea ecosystem.

Some polycyclic aromatic hydrocarbons (PAHs), components of crude oil, are known to cause increased toxicity when organisms are co‐exposed with ultraviolet radiation, resulting in photo‐induced toxicity. The photodynamic characteristics of some PAHs are of particular concern to places like Australia with high ultraviolet radiation levels. The objective of the present study was to characterize the photo‐induced toxicity of an Australian North West Shelf oil to early life stage yellowtail kingfish (Seriola lalandi) and black bream (Acanthopagrus butcheri). The fish were exposed to high‐energy water accommodated fractions for 24 to 36 h. During the exposure, the fish were either co‐exposed to full‐intensity or filtered natural sunlight and then transferred to clean water. At 48 h, survival, cardiac effects, and spinal deformities were assessed. Yellowtail kingfish embryos co‐exposed to oil and full‐spectrum sunlight exhibited decreased hatching success and a higher incidence of cardiac arrhythmias, compared with filtered sunlight. A significant increase in the incidence of pericardial edema occurred in black bream embryos co‐exposed to full‐spectrum sunlight. These results highlight the need for more studies investigating the effects of PAHs and photo‐induced toxicity under environmental conditions relevant to Australia. Environ Toxicol Chem 2018;37:1359–1366. © 2018 SETAC