Global transcriptomic profiling in barramundi (Lates calcarifer) from rivers impacted by differing agricultural land uses

Multi-omic responses of fish exposed to complex chemical mixtures in the Shenandoah River watershed

To evaluate relationships between different anthropogenic impacts, contaminant occurrence, and fish health, we conducted in situ fish exposures across the Shenandoah River watershed at five sites with different land use. Exposure water was analyzed for over 500 chemical constituents, and organismal, metabolomic, and transcriptomic endpoints were measured in fathead minnows. Adverse reproductive outcomes were observed in fish exposed in the upper watershed at both wastewater treatment plant (WWTP) effluent- and agriculture-impacted sites, including decreased gonadosomatic index and altered secondary sex characteristics. This was accompanied with increased mortality at the site most impacted by agricultural activities. Molecular biomarkers of estrogen exposure were unchanged and consistent with low or non-detectable concentrations of common estrogens, indicating that alternative mechanisms were involved in organismal adverse outcomes. Hepatic metabolomic and transcriptomic profiles were altered in a site-specific manner, consistent with variation in land use and contaminant profiles. Integrated biomarker response data were useful for evaluating mechanistic linkages between contaminants and adverse outcomes, suggesting that reproductive endocrine disruption, altered lipid processes, and immunosuppression may have been involved in these organismal impacts. This study demonstrated linkages between human-impact, contaminant occurrence, and exposure effects in the Shenandoah River watershed and showed increased risk of adverse outcomes in fathead minnows exposed to complex mixtures at sites impacted by municipal wastewater discharges and agricultural practices.

Pesticides in the Great Barrier Reef catchment area: Plausible risks to fish populations

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;00:1-24. © 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).

Transcriptomic and Histological Analysis of the Greentail Prawn (Metapenaeus bennettae) Following Light Crude Oil Exposure

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.

Monitoring of emerging contaminants of concern in the aquatic environment: a review of studies showing the application of effect-based measures

Water scarcity is increasingly a global cause of concern mainly due to widespread changes in climate conditions and increased consumptive water use driven by the exponential increase in population growth. In addition, increased pollution of fresh water sources due to rising production and consumption of pharmaceuticals and organic chemicals will further exacerbate this concern. Although surface water contamination by individual chemicals is often at very low concentration, pharmaceuticals for instance are designed to be efficacious at low concentrations, creating genuine concern for their presence in freshwater sources. Furthermore, the additive impact of multiple compounds may result in toxic or other biological effects that otherwise will not be induced by individual chemicals. Globally, different legislative frameworks have led to pre-emptive efforts which aim to ensure good water ecological status. Reports detailing the use and types of effect-based measures covering specific bioassay batteries that can identify specific mode of actions of chemical pollutants in the aquatic ecosystem to evaluate the real threat of pollutants to aquatic lives and ultimately human lives have recently emerged from monitoring networks such as the NORMAN network. In this review, we critically evaluate some studies within the last decade that have implemented effect-based monitoring of pharmaceuticals and organic chemicals in aquatic fauna, evaluating the occurrence of different chemical pollutants and the impact of these pollutants on aquatic fauna with special focus on pollutants that are contaminants of emerging concern (CEC) in urban wastewater. A critical discussion on studies that have used effect-based measures to assess biological impact of pharmaceutical/organic compound in the aquatic ecosystem and the endpoints measurements employed is presented. The application of effect-based monitoring of chemicals other than assessment of water quality status is also discussed.

A bioassay on tissue cholinesterase activity of Rutilus kutum (Kamensky, 1901) exposed to some common pesticides in Iran

The toxicological effects of three commonly used pesticides in Iran on the fries of Caspian kutum (Rutilus kutum, Kamensky, 1901) were investigated through determining 50.00% lethal concentration (LC₅₀) 96hr and cholinesterase (ChE) inhibition. The LC₅₀ 96-hr of carbaryl, glyphosate, and malathion were equal to 11.69, 6.64, and 0.97 mg L^-1, respectively, that were considered as harmful (10.00 - 100 mg L^-1), toxic (1.00 - 10.00 mg L^-1) and very toxic (< 1.00 mg L^-1) compounds for this species. The exposure of fries to sub-lethal concentrations of the pesticides over 15 days indicated that the average of ChE activity in the head and trunk were 1086.89 ± 124.34 and 627.36 ± 99.60 mU min^-1 per mg protein, respectively, with a significant difference relative to each other. There was a significant difference between fry exposed to all three pesticides and the control group in cholinesterase inhibition. The fries exposed to carbaryl (890.12 ± 28.08 mU min^-1 per mg protein) and glyphosate (891.77 ± 31.61 mU min^-1 per mg protein) showed lower ChE inhibition than those exposed to malathion (790.00 ± 58.14 mU min^-1 per mg protein).

Analysis of pesticide mixtures discharged to the lagoon of the Great Barrier Reef, Australia

Organisms and ecosystems are generally exposed to mixtures of chemicals rather than to individual chemicals, but there have been relatively few detailed analyses of the mixtures of pesticides that occur in surface waters. This study examined over 2600 water samples, analysed for between 21 and 47 pesticides, from 15 waterways that discharge to the lagoon of the Great Barrier Reef in Queensland, Australia between July 1, 2011 and June 30, 2015. Essentially all the samples (99.8%) contained detectable concentrations (>limit of detection) of pesticides and pesticide mixtures. Approximately, 10% of the samples contained no quantifiable (>limit of reporting) pesticides, 10% contained one quantifiable pesticide and 80% contained quantifiable mixtures of 2-20 pesticides. Approximately 82% of samples that contained quantifiable mixtures had more than two modes of action (MoAs), but only approximately 6% had five or more MoAs. The mode, average and median number of quantifiable pesticides in all the samples were 2, 5.1 and 4, respectively. The most commonly detected compounds both individually and in mixtures were the pesticides atrazine, diuron, imidacloprid, hexazinone, 2,4-D, and the degradation product desethylatrazine. The number of pesticides and modes of action of pesticides in mixtures differed spatially and were affected by land use. Waterways draining catchments where sugar cane was a major land use had mixtures with the most pesticides.

Adequate supply of dietary taurine stimulates expression of molecular markers of growth and protein turnover in juvenile barramundi (Lates calcarifer)

A trial was conducted to investigate the effect of dietary taurine (Tau) supply on the plasma amino acid composition and hepatic expression of several genes in juvenile barramundi (Lates calcarifer) after feeding. Triplicate tanks of fish (average weight, 89.3 g) were fed diets containing either a deficient (1 g kg^-1), adequate (8 g kg^-1) or excessive (19 g kg^-1) level of dietary Tau. Liver tissues collected before feeding, and at 2- and 4-h post-feeding, were analysed for expression of genes involved in pathways of sulphur amino acid turnover, Tau biosynthesis and transport, target of rapamycin (TOR) signalling, the somatotropic axis and protein turnover. The treatment had no significant effect on the profiles of any amino acid in plasma collected over time after feeding, other than Tau and glycine. The expression profile of cystine and Tau synthetic genes suggested an effect of Tau excess on the metabolism of cystine. Markers of two pathways of Tau biosynthesis appear to be active in this species, providing proof that this species possesses the ability to synthesise Tau from SAA precursors. A marker for the regulation of Tau transport and homeostasis was shown to be directly regulated by Tau availability, whilst a link between adequate supply of Tau and TOR pathway-mediated growth stimulation was also apparent. An observed depression in expression of genes of the somatotropic axis, coupled with upregulation of the proteolytic and TOR-suppressing genes, in response to excessive Tau supply in the diet, signalled that excessive Tau may not be conducive to optimal growth in this species.

RNA-sequencing to assess the health of wild yellow perch (Perca flavescens) populations from the St. Lawrence River, Canada

This study aimed to better understand in situ cumulative effects of anthropogenic stressors on the health of St. Lawrence River (QC, Canada) yellow perch populations using high-throughput transcriptomics and a multi-biological level approach. Fish were collected in the upstream fluvial Lake Saint-François (LSF) with low degree of environmental perturbations; Lake Saint-Louis (LSL) considered having a moderate degree of anthropogenic stressors, and Lake Saint-Pierre (LSP) a sector where the perch population has been severely declining. Morphometric results indicated that fish from the downstream LSP showed lower body condition compared to LSF and LSL. Liver transcriptomic responses were assessed by RNA-sequencing. Two hundred and eighty genes were over-transcribed in LSP perch while 200 genes were under-transcribed compared to LSF and LSL. In LSP fish, genes transcripts related to reproduction, retinol, iron, thyroid hormones, oxidative stress, lipid metabolism and immune functions were among the most abundant suggesting that multiple metabolic and physiological pathways were impacted by environmental stressors at this site. Inhibition of liver superoxide dismutase, catalase and glutathione S-transferase activities were also observed at the cellular level. Overall, identified impacted biological pathways in perch from LSP may help understand the precarious state of this population and identify the factors inhibiting its recovery.

Transcriptomic analysis of zebrafish (Danio rerio) embryos to assess integrated biotoxicity of Xitiaoxi River waters

Assessing the toxicity posed by mixtures of unknown chemicals to aquatic organisms is challenging. In this study, water samples from six cross-sections along the Xitiaoxi River Basin (XRB) were monthly or bimonthly collected in 2014. The year-period physiochemical parameters as well as one-month-water sample based acute biotoxicity tests showed that the river water quality of the year was generally in a good status. High performance liquid chromatography (HPLC) screening based on one-month-water samples suggested that the organic pollutants might be non-to-moderately-polar chemicals in very low concentrations. One-month-water sample based RNA-seq was performed to measure the mRNA differential expression profile of zebrafish larvae to furtherly explore the potential bioeffect and the spatial water quality change of the river. Result indicated that the number of deferentially expressed genes (DEGs) tended to increase along the downstream direction of the river. Gene ontology (GO) enrichment analysis implied that the key pollutants might mainly be the function disruptors of biological processes. Principle components analysis (PCA) combining with transcripts and one-month-water sample based physiochemical parameters indicated that the pollution might be similar at TP, DP and CTB sites while pollution homology existed on some extent between YBQ and JW sites. Although the water quality of the river had a complex time-space alternation during the year, and the one-month-data based RNA-seq could not reflex the whole year-water quality of a watershed, the gene expression profile via RNA-seq provided an alternative way for assessing integrated biotoxicity of surface water, and it was relatively fit for early-warning of water quality of a watershed with unobservable acute toxicity. However, the identification of detail toxicants and the links between DEGs and pollution level as well as physiological-biochemical toxicity needed further investigation.

Monitoring sublethal changes in fish physiology following exposure to a light, unweathered crude oil

Biomarkers are frequently used to determine the exposure of fish to petroleum hydrocarbons following an oil spill. These biomarkers must be chosen carefully if they are to be used to determine sublethal toxic impacts as well as oil exposure. Many commonly used biomarkers relate to the metabolism of high molecular weight, typically pyrogenic, polycyclic aromatic hydrocarbons (PAHs), which are not abundant in unweathered crude oil. The goal of this study was to compare the efficacy of different biomarkers, including histological examination and transcriptomic profiling, in showing exposure to oil and the potential for sublethal toxic impacts. To achieve these goals, subadults/adults of the spotted dragonet (Repomucenus calcaratus) were exposed to a representative light, unweathered Australian oil for 96 h, so that the physiological changes that occur with exposure could be documented. Fish were then transferred to clean sediment for 90 h to quantify recovery. Biomarker changes, including PAH metabolites, 7-ethoxyresorufin O-deethylase (EROD), and histopathology, are presented in this work. In addition, a de novo transcriptome for the spotted dragonet was assembled, and differential transcript abundance was determined for the gill and liver of petroleum-exposed fish relative to a control. Increased levels of some biliary phenanthrene metabolites were seen throughout the exposure period. EROD levels showed modest, but not significant, increases. Transcriptomic differences were noted in the abundances of transcripts with a role in inflammation, primary metabolism and cardiac function. The patterns of transcript abundance in the gill and the liver changed in a manner that reflected exposure and recovery. The histology showed elevated prevalence of lesions, most notably vacuolization in liver and heart tissue, multi-organ necrosis, and lamellar epithelial lifting and telangiectasia in the gill. These findings suggest that short-term exposures to low molecular weight PAHs could elicit changes in the health of fish that are well predicted by the transcriptome. Furthermore, when light oil is released into the environment, exposure and subsequent risk would be better estimated using phenanthrene metabolite levels rather than EROD. This study also adds to the weight of evidence that exposure to low molecular weight PAHs may cause cardiac problems in fish. Further study is needed to determine the impact of these changes on reproductive capacity, long-term survival, and other population specific parameters.

Risk assessment of pesticides in estuaries: a review addressing the persistence of an old problem in complex environments

Estuaries, coastal lagoons and other transition ecosystems tend to become the ultimate reservoirs of pollutants transported by continental runoff, among which pesticides constitute the class of most concern. High amounts of dissolved and particulated organic matter greatly contribute to the accumulation of pesticides that eventually become trapped in sediments or find their way along food chains. Perhaps not so surprisingly, it is common to find elevated levels of pesticides in estuarine sediments decades after their embargo. Still, it remains challenging to address ecotoxicity in circumstances that invariably imply mixtures of contaminants and multiple factors affecting bioavailability. Despite advances in methods for detecting pesticides in waters, sediments and organisms, chemical data alone are insufficient to predict risk. Many researchers have been opting for ex situ bioassays that mimic the concentrations of pesticides in estuarine waters and sediments using a range of ecologically relevant model organisms, with emphasis on fish, molluscs and crustaceans. These experimental procedures unravelled novel risk factors and important insights on toxicological mechanisms, albeit with some prejudice of ecological relevance. On the other hand, in situ bioassays, translocation experiments and passive biomonitoring strive to spot causality through an intricate mesh of confounding factors and cocktails of pollutants. Seemingly, the most informative works are integrative approaches that combine different assessment strategies, multiple endpoints and advanced computational and geographical models to determine risk. State-of-art System Biology approaches combining high-content screening approaches involving "omics" and bioinformatics, can assist discovering and predicting novel Adverse Outcome Pathways that better reflect the cumulative risk of persisting and emerging pesticides among the wide range of stressors that affect estuaries.

Transcriptomic, lipid, and histological profiles suggest changes in health in fish from a pesticide hot spot

Barramundi (Lates calcarifer) were collected at the beginning (1st sampling) and end (2nd sampling) of the wet season from Sandy Creek, an agriculturally impacted catchment in the Mackay Whitsundays region of the Great Barrier Reef catchment area, and from Repulse Creek, located approximately 100 km north in Conway National Park, to assess the impacts of pesticide exposure. Gill and liver histology, lipid class composition in muscle, and the hepatic transcriptome were examined. The first sample of Repulse Creek fish showed little tissue damage and low transcript levels of xenobiotic metabolism enzymes. Sandy Creek fish showed altered transcriptomic patterns, including those that regulate lipid metabolism, xenobiotic metabolism, and immune response; gross histological alterations including lipidosis; and differences in some lipid classes. The second sampling of Repulse Creek fish showed similar alterations in hepatic transcriptome and tissue structure as fish from Sandy Creek. These changes may indicate a decrease in health of pesticide exposed fish.

Evaluation of mercury in a freshwater environment impacted by an organomercury fungicide using diffusive gradient in thin films

The use of pesticides to manage pest problems for crop protection is common practice around the world, and their accumulation in soils and contamination of water bodies is a global environmental problem. In Australia, an organomercury (Hg)-based fungicide is the most popular for control of pineapple disease of sugarcane. However, the presence of Hg is of great concern because of potential adverse effects in the environment. The purpose of this work was to evaluate the residual levels of Hg in soils of sugarcane cultivation from a catchment in North Queensland (Australia). Mercury was surveyed in soils close to the Tully River at 3 different depths (100, 200 and 300mm). Additionally, total Hg (THg) and the labile fraction of Hg in water (measured by the diffusive gradient in thin film technique) were determined in the Tully River. A pristine site, the Tully Gorge National Park upstream of sugarcane fields, was selected for background Hg concentration estimation. In soils, Hg levels ranged from 18 to 264μgkg^-1, with one of the soil samples being almost 10 times higher than at other sites at the surface level (199μgkg^-1). Total and labile concentrations of Hg in water increased from the Hg-elevated soil sampling sites (0.085μgL^-1 and 0.061μgL^-1) to downstream sites (0.082μgL^-1 and 0.066μgL^-1), which is likely due to agricultural runoff. Indeed, except for the upstream control site, the THg concentration in water is over the limit permitted by the Australian freshwater quality guideline for protection of 99% species (0.06μgL^-1). These findings point to the need to perform further research to reveal the mechanisms for release of Hg from soil and whether this might be causing important adverse effects to the Great Barrier Reef located in front of this river catchment.

Omics and cytokine discovery in fish: Presenting the Yellowtail kingfish (Seriola lalandi) as a case study

A continued programme of research is essential to overcome production bottlenecks in any aquacultured fish species. Since the introduction of genetic and molecular techniques, the quality of immune research undertaken in fish has greatly improved. Thousands of species specific cytokine genes have been discovered, which can be used to conduct more sensitive studies to understand how fish physiology is affected by aquaculture environments or disease. Newly available transcriptomic technologies, make it increasingly easier to study the immunogenetics of farmed species for which little data exists. This paper reviews how the application of transcriptomic procedures such as RNA Sequencing (RNA-Seq) can advance fish research. As a case study, we present some preliminary findings using RNA-Seq to identify cytokine related genes in Seriola lalandi. These will allow in-depth investigations to understand the immune responses of these fish in response to environmental change or disease and help in the development of therapeutic approaches.

Hepatic transcriptomic profiles from barramundi, Lates calcarifer, as a means of assessing organism health and identifying stressors in rivers in northern Queensland

Resource managers need to differentiate between sites with and without contaminants and those where contaminants cause impacts. Potentially, transcriptomes could be used to evaluate sites where contaminant-induced effects may occur, to identify causative stressors of effects and potential adverse outcomes. To test this hypothesis, the hepatic transcriptomes in Barramundi, a perciforme teleost fish, (Lates calcarifer) from two reference sites, two agriculturally impacted sites sampled during the dry season, and an impacted site sampled during the wet season were compared. The hepatic transcriptome was profiled using RNA-Seq. Multivariate analysis showed that transcriptomes were clustered based on site and by inference water quality, but not sampling time. The largest differences in transcriptomic profile were between reference sites and a site sampled during high run-off, showing that impacted sites can be identified via RNA-Seq. Transcripts with altered abundance were linked to xenobiotic metabolism, peroxisome proliferation and stress responses, indicating putative stressors with the potential for adverse outcomes in barramundi.

Differential metabolic profiles associated to movement behaviour of stream-resident brown trout (Salmo trutta)

The mechanisms that can contribute in the fish movement strategies and the associated behaviour can be complex and related to the physiology, genetic and ecology of each species. In the case of the brown trout (Salmo trutta), in recent research works, individual differences in mobility have been observed in a population living in a high mountain river reach (Pyrenees, NE Spain). The population is mostly sedentary but a small percentage of individuals exhibit a mobile behavior, mainly upstream movements. Metabolomics can reflect changes in the physiological process and can determine different profiles depending on behaviour. Here, a non-targeted metabolomics approach was used to find possible changes in the blood metabolomic profile of S. trutta related to its movement behaviour, using a minimally invasive sampling. Results showed a differentiation in the metabolomic profiles of the trouts and different level concentrations of some metabolites (e.g. cortisol) according to the home range classification (pattern of movements: sedentary or mobile). The change in metabolomic profiles can generally occur during the upstream movement and probably reflects the changes in metabolite profile from the non-mobile season to mobile season. This study reveals the contribution of the metabolomic analyses to better understand the behaviour of organisms.

A protocol for identifying suitable biomarkers to assess fish health: A systematic review

Background

Biomarkers have been used extensively to provide the connection between external levels of contaminant exposure, internal levels of tissue contamination, and early adverse effects in organisms.

Objectives

To present a three-step protocol for identifying suitable biomarkers to assess fish health in coastal and marine ecosystems, using Gladstone Harbour (Australia) as a case study.

Methods

Prior to applying our protocol, clear working definitions for biomarkers were developed to ensure consistency with the global literature on fish health assessment. First, contaminants of concern were identified based on the presence of point and diffuse sources of pollution and available monitoring data for the ecosystem of interest. Second, suitable fish species were identified using fisheries dependent and independent data, and prioritised based on potential pathways of exposure to the contaminants of concern. Finally, a systematic and critical literature review was conducted on the use of biomarkers to assess the health of fish exposed to the contaminants of concern.

Results/Discussion

We present clear working definitions for bioaccumulation markers, biomarkers of exposure, biomarkers of effect and biomarkers of susceptibility. Based on emission and concentration information, seven metals were identified as contaminants of concern for Gladstone Harbour. Twenty out of 232 fish species were abundant enough to be potentially suitable for biomarker studies; five of these were prioritised based on potential pathways of exposure and susceptibility to metals. The literature search on biomarkers yielded 5,035 articles, of which 151met the inclusion criteria. Based on our review, the most suitable biomarkers include bioaccumulation markers, biomarkers of exposure (CYP1A, EROD, SOD, LPOX, HSP, MT, DNA strand breaks, micronuclei, apoptosis), and biomarkers of effect (histopathology, TAG:ST).

Conclusion

Our protocol outlines a clear pathway to identify suitable biomarkers to assess fish health in coastal and marine ecosystems, which can be applied to biomarker studies in aquatic ecosystems around the world.