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).

The distribution of metal and petroleum-derived contaminants within sediments around oil and gas infrastructure in the Gippsland Basin, Australia

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.

The Influence of Oil-in-Water Preparations on the Toxicity of Crude Oil to Marine Invertebrates and Fish Following Short-Term Pulse and Continuous Exposures

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.

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.

A Comparison of Short-Term and Continuous Exposures in Toxicity Tests of Produced Waters, Condensate, and Crude Oil to Marine Invertebrates and Fish

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.

Beyond Thresholds: A Holistic Approach to Impact Assessment Is Needed to Enable Accurate Predictions of Environmental Risk from Oil Spills

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.

Baseline characterization of aerobic hydrocarbon degrading microbial communities in deep-sea sediments of the Great Australian Bight, Australia

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.

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.

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.

Photo-induced toxicity following exposure to crude oil and ultraviolet radiation in 2 Australian fishes

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.

The impacts of modern-use pesticides on shrimp aquaculture: An assessment for north eastern Australia

The use of pyrethroid and neonicotinoid insecticides has increased in Australia over the last decade, and as a consequence, increased concentrations of the neonicotinoid insecticide imidacloprid have been measured in Australian rivers. Previous studies have shown that non-target crustaceans, including commercially important species, can be extremely sensitive to these pesticides. Most shrimp farms in Australia are predominantly located adjacent to estuaries so they can obtain their required saline water, which support multiple land uses upstream (e.g. sugar-cane farming, banana farming, beef cattle and urbanisation). Larval and post-larval shrimp may be most susceptible to the impacts of these pesticides because of their high surface area to volume ratio and rapid growth requirements. However, given the uncertainties in the levels of insecticides in farm intake water and regarding the impacts of insecticide exposure on shrimp larvae, the risks that the increased use of new classes of pesticide pose towards survival of post-larval phase shrimp cannot be adequately predicted. To assess the potential for risk, toxicity in 20day past hatch post-larval Black Tiger shrimp (Penaeus monodon) to modern use insecticides, imidacloprid, bifenthin, and fipronil was measured as decreased survival and feeding inhibition. Post-larval phase shrimp were sensitive to fipronil, bifenthrin, and imidacloprid, in that order, at concentrations that were comparable to those that cause mortality other crustaceans. Bifenthrin and imidacloprid exposure reduced the ability of post-larval shrimp to capture live prey at environmentally realistic concentrations. Concentrations of a broad suite of pesticides were also measured in shrimp farm intake waters. Some pesticides were detected in every sample. Most of the pesticides detected were measured below concentrations that are toxic to post-larval shrimp as used in this study, although pesticides exceed guideline values, suggesting the possibility of indirect or mixture-related impacts. However, at two study sites, the concentrations of insecticides were sufficient to cause toxicity in shrimp post larvae, based on the risk assessment undertaken in this study.

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.

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

Most catchments discharging into the Great Barrier Reef lagoon have elevated loads of suspended sediment, nutrients, and pesticides, including photosystem II inhibiting herbicides, associated with upstream agricultural land use. To investigate potential impacts of declining water quality on fish physiology, RNA sequencing (RNASeq) was used to characterize and compare the hepatic transcriptomes of barramundi (Lates calcarifer) captured from 2 of these tropical river catchments in Queensland, Australia. The Daintree and Tully Rivers differ in upstream land uses, as well as sediment, nutrient, and pesticide loads, with the area of agricultural land use and contaminant loads lower in the Daintree. In fish collected from the Tully River, transcripts involved in fatty acid metabolism, amino acid metabolism, and citrate cycling were also more abundant, suggesting elevated circulating cortisol concentrations, whereas transcripts involved in immune responses were less abundant. Fish from the Tully also had an increased abundance of transcripts associated with xenobiotic metabolism. Previous laboratory-based studies observed similar patterns in fish and amphibians exposed to the agricultural herbicide atrazine. If these transcriptomic patterns are manifested at the whole organism level, the differences in water quality between the 2 rivers may alter fish growth and fitness. Environ Toxicol Chem 2017;36:103-112. © 2016 SETAC.

Challenges for using quantitative PCR test batteries as a TIE-type approach to identify metal exposure in benthic invertebrates

The epibenthic amphipod Melita plumulosa shows unique gene expression profiles when exposed to different contaminants. We hypothesized that specific changes in transcript abundance could be used in a battery of quantitative polymerase chain reaction (qPCR) assays as a toxicity identification evaluation (TIE)-like approach to identify the most relevant stressor in field-contaminated sediments. To test this hypothesis, seven candidate transcriptomic markers were selected, and their specificity following metal exposure was confirmed. The performance of these markers across different levels of added metals was verified. The ability of these transcripts to act as markers was tested by exposing amphipods to metal-contaminated field-collected sediments and measuring changes in transcript abundance via qPCR. For two of the three sediments tested, at least some of the transcriptomic patterns matched our predictions, suggesting that they would be effective in helping to identify metal exposure in field sediments. However, following exposure to the third sediment, transcriptomic patterns were unlike our predictions. These results suggest that the seven transcripts may be insufficient to discern individual contaminants from complex mixtures and that microarray or RNA-Seq global gene expression profiles may be more effective for TIE. Changes in transcriptomics based on laboratory exposures to single compounds should be carefully validated before the results are used to analyze mixtures.

Altered levels of endocrine biomarkers in juvenile barramundi (Lates calcarifer; Bloch) following exposure to commercial herbicide and surfactant formulations

Agricultural pesticides that are known endocrine disrupting chemicals have been detected in waters in the Great Barrier Reef catchment and lagoon. Altered transcription levels of liver vitellogenin (vtg) have been documented in wild populations of 2 Great Barrier Reef fisheries species and were strongly associated with pesticide-containing runoff from sugarcane plantations. The present study examined endocrine and physiological biomarkers in juvenile barramundi (Lates calcarifer) exposed to environmentally relevant concentrations of commercial herbicide (ATRADEX(®) WG Herbicide, DIUREX(®) WG Herbicide) and surfactant (ACTIVATOR(®) 90) formulations commonly used on sugarcane in the Great Barrier Reef catchment. Estrogenic biomarkers (namely, liver vtg messenger RNA and plasma 17β-estradiol) increased following exposure to commercial mixtures but not to the analytical grade chemical, suggesting an estrogenic response to the additives. In contrast, brain aromatase (cyp19a1b) transcription levels, plasma testosterone and 11-ketotestosterone concentrations, and gill ventilation rates were not affected by any of the experimental exposures. These findings support the assertion that exposure to pesticide-containing runoff from sugarcane plantations is a potential causative agent of altered liver vtg transcription levels in wild barramundi. Whether exposure patterns in the Great Barrier Reef catchment and lagoon are sufficient to impair fish sexual and reproductive development and ultimately influence fish population dynamics remains to be determined. These findings highlight the need to consider both active and so-called inert ingredients in commercial pesticide formulations for environmental risk assessments.

Altered transcription levels of endocrine associated genes in two fisheries species collected from the Great Barrier Reef catchment and lagoon

The Great Barrier Reef (GBR) is chronically exposed to agricultural run-off containing pesticides, many of which are known endocrine disrupting chemicals (EDCs). Here, we measure mRNA transcript abundance of two EDC biomarkers in wild populations of barramundi (Lates calcarifer) and coral trout (Plectropomus leopardus and Plectropomus maculatus). Transcription levels of liver vitellogenin (vtg) differed significantly in both species amongst sites with different exposures to agricultural run-off; brain aromatase (cyp19a1b) revealed some differences for barramundi only. Exposure to run-off from sugarcane that contains pesticides is a likely pathway given (i) significant associations between barramundi vtg transcription levels, catchment sugarcane land use, and river pesticide concentrations, and (ii) consistency between patterns of coral trout vtg transcription levels and pesticide distribution in the GBR lagoon. Given the potential consequences of such exposure for reproductive fitness and population dynamics, these results are cause for concern for the sustainability of fisheries resources downstream from agricultural land uses.

Next generation sequence analysis of the transcriptome of Sydney rock oysters (Saccostrea glomerata) exposed to a range of environmental stressors

Sydney rock oysters (Saccostrea glomerata) were exposed to environmental stressors at contaminated field sites or in a controlled laboratory setting. RNA seq transcriptome data were generated for the gill and digestive gland using Roche's 454 pyrosequencing technology. 28,685 contigs were de novo assembled which encoded 11,671 different protein products. The data will act as a reference for future studies in ecology, immunology and environmental toxicology.

454 pyrosequencing-based analysis of gene expression profiles in the amphipod Melita plumulosa: transcriptome assembly and toxicant induced changes

Next generation sequencing using Roche's 454 pyrosequencing platform can be used to generate genomic information for non-model organisms, although there are bioinformatic challenges associated with these studies. These challenges are compounded by a lack of a standardized protocol to either assemble data or to evaluate the quality of a de novo transcriptome. This study presents an assembly of the control and toxicant responsive transcriptome of Melita plumulosa, an Australian amphipod commonly used in ecotoxicological studies. RNA was harvested from control amphipods, juvenile amphipods, and from amphipods exposed to either metal or diesel contaminated sediments. This RNA was used as the basis for a 454 based transcriptome sequencing effort. Sequencing generated 1.3 million reads from control, juvenile, metal-exposed and diesel-exposed amphipods. Different read filtering and assembly protocols were evaluated to generate an assembly that (i) had an optimal number of contigs; (ii) had long contigs; (iii) contained a suitable representation of conserved genes; and (iv) had long ortholog alignment lengths relative to the length of each contig. A final assembly, generated using fixed-length trimming based on the sequence quality scores, followed by assembly using the MIRA algorithm, produced the best results. The 26,625 contigs generated via this approach were annotated using Blast2GO, and the differential expression between treatments and control was determined by mapping with BWA followed by DESeq. Although the mapping generated low coverage, many differentially expressed contigs, including some with known developmental or toxicological function, were identified. This study demonstrated that 454 pyrosequencing is an effective means of generating reference transcriptome information for organisms, such as the amphipod M. plumulosa, that have no genomic information available in databases or in closely related sequenced species. It also demonstrated how optimization of read filtering protocols and assembly approaches changes the utility of results obtained from next generation sequencing studies, and establishes criteria to determine the quality of a de novo assembly in species lacking a reference genome. This new transcriptomic knowledge provides the genomic foundation for the creation of microarray and qPCR assays, serving as a reference transcriptome in future RNAseq studies, and allowing both the biology and ecotoxicology of this organism to be better understood. This approach will allow genomics-based methodology to be applied to a wider range of environmentally relevant species.

The role of biomarkers in the assessment of aquatic ecosystem health

Ensuring the health of aquatic ecosystems and identifying species at risk from the detrimental effects of environmental contaminants can be facilitated by integrating analytical chemical analysis with carefully selected biological endpoints measured in tissues of species of concern. These biological endpoints include molecular, biochemical, and physiological markers (i.e., biomarkers) that when integrated, can clarify issues of contaminant bioavailability, bioaccumulation, and ecological effects while enabling a better understanding of the effects of nonchemical stressors. In the case of contaminant stressors, an understanding of chemical modes of toxicity can be incorporated with diagnostic markers of aquatic animal physiology to help understand the health status of aquatic organisms in the field. Furthermore, new approaches in functional genomics and bioinformatics can help discriminate individual chemicals, or groups of chemicals among complex mixtures that may contribute to adverse biological effects. Although the use of biomarkers is not a new paradigm, such approaches have been underused in the context of ecological risk assessment and natural resource damage assessment. From a regulatory standpoint, these approaches can help better assess the complex effects from coastal development activities to assessing ecosystem integrity pre- and post development or site remediation.

Effects of atrazine on endocrinology and physiology in juvenile barramundi, Lates calcarifer (Bloch)

Exposure to certain environmental contaminants such as agricultural pesticides can alter normal endocrine and reproductive parameters in wild fish populations. Recent studies have found widespread pesticide contamination across the rivers that discharge into the Great Barrier Reef lagoon. Potential impacts on native fish species exposed to known endocrine disrupting chemicals such as atrazine, simazine, and diuron have not been assessed. In the present study, the authors examined the endocrine and physiological effects of short-term, acute exposure of environmentally relevant concentrations of analytical grade atrazine in juvenile barramundi (Lates calcarifer) in a controlled laboratory experiment. Expression of hepatic vitellogenin was not affected, supporting results of previous studies that showed that atrazine does not have a direct estrogenic effect via mediation of estrogen receptors. The lack of effect on brain cytochrome P19B (CYP19B) expression levels, combined with increases in testosterone (T) and 17β estradiol and a stable T:17β estradiol ratio, does not support the hypothesis that atrazine has an indirect estrogenic effect via modulation of aromatase expression. Gill ventilation rate, a measure of oxidative stress, did not change in contrast to other studies finding enhanced osmoregulatory disturbance and gill histopathology after atrazine exposure. To more closely reflect field conditions, the authors recommend that laboratory studies should focus more on examining the effects of commercial pesticide formulations that contain additional ingredients that have been found to be disruptive to endocrine function.

Dissolved and particulate copper exposure induces differing gene expression profiles and mechanisms of toxicity in the deposit feeding amphipod Melita plumulosa

Uptake of metals via ingestion is an important route of exposure for many invertebrates, and it has been suggested that the toxic response to metals accumulated via food differs from that of metals accumulated via the dissolved phase. To test this hypothesis, the deposit-feeding epibenthic amphipod Melita plumulosa was exposed to nontoxic or reproductively toxic concentrations of copper via the overlying water, via ingestion of sediment, or via a combination of the two. Rates of copper uptake from the two exposure routes were predicted using a biokinetic model. Gene expression profiles were measured via microarray analysis and confirmed via quantitative polymerase chain reaction. Differences in expression profiles were related to the exposure route more than to individual or combined rates of copper uptake. Chitinase and digestive protease transcript expression levels correlated to the copper uptake rate from sediment, rather than from the dissolved phase or combined total uptake rate. Overall, this study supports the hypothesis that metals accumulated via ingestion have a different mode of toxic action than metals taken up from water. Consequently, guidelines that only consider dissolved metal exposure, including equilibrium-partitioning-based guidelines, may underestimate the potential effects from deposited or resuspended metal-contaminated sediments.

Assessing mechanisms of toxicant response in the amphipod Melita plumulosa through transcriptomic profiling

This study describes the function of transcripts with altered abundance in the epibenthic amphipod, Melita plumulosa, following whole-sediment exposure to a series of common environmental contaminants. M. plumulosa were exposed for 48 h to sediments spiked and equilibrated with the following contaminants at concentrations predicted to cause sublethal effects to reproduction: porewater ammonia 30 mg L(-1); bifenthrin at 100 μg kg(-1); fipronil at 50 μg kg(-1); 0.6% diesel; 0.3% crude oil; 250 mg Cu kg(-1); 400 mg Ni kg(-1); and 400 mg Zn kg(-1). RNA was extracted and hybridized against a custom Agilent microarray developed for this species. Although the microarray represented a partial transcriptome and not all features on the array could be annotated, unique transcriptomic profiles were generated for each of the contaminant exposures. Hierarchical clustering grouped the expression profiles together by contaminant class, with copper and zinc, the petroleum products and nickel, and the pesticides each forming a distinct cluster. Many of the transcriptional changes observed were consistent with patterns previously described in other crustaceans. The changes in the transcriptome demonstrated that contaminant exposure caused changes in digestive function, growth and moulting, and the cytoskeleton following metal exposure, whereas exposure to petroleum products caused changes in carbohydrate metabolism, xenobiotic metabolism and hormone cycling. Functional analysis of these gene expression profiles can provide a better understanding of modes of toxic action and permits the prediction of mixture effects within contaminated ecosystems.

Using transcriptomic profiles in the diatom Phaeodactylum tricornutum to identify and prioritize stressors

The transcriptomic profile of the marine diatom, Phaeodactylum tricornutum, exposed to several ecologically relevant stressors, was used to develop toxicity identification evaluation (TIE)-like gene expression assays. Algal growth inhibition was measured by flow cytometry to determine exposure concentrations that elicited a sublethal toxic response. P. tricornutum was exposed to concentrations of copper (2 μg L⁻¹), cadmium (5 μg L⁻¹), silver (20 μg L⁻¹), simazine (75 μg L⁻¹), the water accommodated fraction (WAF) of weathered crude oil (5 mg L⁻¹), 50 μg L⁻¹ ammonia, a decreased salinity treatment (15‰), and a mixture exposure of ammonia, decreased salinity and cadmium (10 μg L⁻¹). Analysis of the gene expression via microarray indicated that unique transcriptomic signals were generated for each of the individual treatments. Transcriptomic profiles of ammonia and the mixture treatment overlapped substantially. Photosynthesis related transcripts were altered in the simazine (herbicide) treatment. A transcript involved in degrading hydrocarbons, dioxygenase, had increased abundance after crude oil exposure. Overall, transcriptomic responses in the different treatments were associated with stress responses, membrane transport, transcription and translation and could be linked to contaminant mode of action. The transcriptomic profiles were used to design real-time (quantitative) polymerase chain reaction (qPCR) assays that would link changes in transcript abundance to a particular stressor in a TIE-based approach. At least one transcript for each contaminant tested (copper, cadmium, silver, salinity and ammonia) responded exclusively to that contaminant. With further development of additional transcriptomic markers for each contaminant, this new approach has potential to enhance traditional toxicology bioassays by providing additional lines of evidence to identify biologically relevant stressors within a contaminated ecosystem based on changes in the transcriptomic profile.

Comparison of toxicity and transcriptomic profiles in a diatom exposed to oil, dispersants, dispersed oil

Dispersants are commonly used to mitigate the impact of oil spills, however, the ecological cost associated with their use is uncertain. The toxicity of weathered oil, dispersed weathered oil, and the hydrocarbon-based dispersant Slickgone NS(®), to the diatom Phaeodactylum tricornutum has been examined using standardized toxicity tests. The assumption that most toxicity occurs via narcosis was tested by measuring membrane damage in diatoms after exposure to one of the petroleum products. The mode of toxic action was determined using microarray-based gene expression profiling in diatoms after exposure to one of the petroleum products. The diatoms were found to be much more sensitive to dispersants than to the water accommodated fraction (WAF), and more sensitive to the chemically enhanced WAF (CEWAF) than to either the WAF itself or the dispersants. Exposure to dispersants and CEWAF caused membrane damage, while exposure to WAF did not. The gene expression profiles resulting from exposure to all three petroleum mixtures were highly similar, suggesting a similar mode of action for these compounds. The observed toxicity bore no relationship to PAH concentrations in the water column or to total petroleum hydrocarbon (TPH), suggesting that an undescribed component of the oil was causing toxicity. Taken together, these results suggest that the use of dispersants to clean up oil spills will dramatically increase the oil toxicity to diatoms, and may have implications for ecological processes such as the timing of blooms necessary for recruitment.

Estrogen receptor mRNA expression patterns in the liver and ovary of female rainbow trout over a complete reproductive cycle

Estrogens are critical hormones involved in reproduction and need to bind to estrogen receptors in target organs for biological activity. Fishes have two distinct estrogen receptor subtypes, alpha (α) and beta (β), with variable combinations of additional isoforms of each subtype dependent on the history of genome duplication within a taxon. The comparative expression patterns of estrogen receptor isoforms during the female reproductive cycle will provide important insights into the unique function and importance of each. The purpose of this study was to measure the mRNAs for the four estrogen receptor isoforms (erα1, erα2, erβ1, erβ2) in the liver and ovary of adult, female rainbow trout over the course of an annual reproductive cycle. The expression of estrogen receptor mRNA isoforms was measured by quantitative real-time RT-PCR. Several reproductive indices (gonadosomatic index, maximum oocyte diameter, plasma estradiol-17β, plasma vitellogenin, and ovulation) were also quantified for comparison and used in a correlation analysis to examine any inter-relationships. Of the four isoforms, the expression of erα1 was highest in the liver, and had a significant positive correlation with liver erβ1 expression. Liver expression of erα2 mRNA was the lowest, but showed a significant positive correlation with maximum oocyte diameter in the ovary. The pattern of the erβ isoforms in liver was one of initially elevated mRNA expression followed by a gradual decrease as reproductive development proceeded. In the ovary the erβ1 isoform had the highest mRNA expression of all estrogen receptor isoforms, at the beginning of the reproductive cycle, but then decreased afterward. Both ovarian erβ isoforms had a significant positive correlation with one another. In contrast, erα2 mRNA expression showed a high maximum level in the ovary near the end of the cycle along with a significant positive correlation with plasma estradiol-17β levels; the highest gonadosomatic indices, maximum oocyte diameter, and vitellogenin levels occurred then too.

Relationships between the transcriptome and physiological indicators of reproduction in female rainbow trout over an annual cycle

Normal transcriptomic patterns along the brain-pituitary-gonad-liver (BPGL) axis should be better characterized if endocrine-disrupting compound-induced changes in gene expression are to be understood. Female rainbow trout were studied over a complete year-long reproductive cycle. Tissue samples from pituitary, ovary, and liver were collected for microarray analysis using the 16K Genomic Research on Atlantic Salmon Project (GRASP) microarray and for quantitative polymerase chain reaction measures of estrogen receptor (ER) isoform messenger RNA (mRNA) levels. Plasma was collected to determine levels of circulating estradiol-17β (E2), follicle-stimulating hormone (FSH), and luteinizing hormone (LH). As an a priori hypothesis, changes in gene expression were correlated to either circulating levels of E2, FSH, and LH, or ER mRNAs quantified by quantitative polymerase chain reaction. In the liver, most transcriptomic patterns correlated to levels of either E2, LH, or ERs. Fewer ovarian transcripts could be correlated to levels of E2, ERα, or FSH. No significant associations were obvious in the pituitary. As a post hoc hypothesis, changes in transcript abundance were compared with microarray features with known roles in gonadal maturation. Many altered transcripts in the ovary correlated to transcript levels of estradiol 17-beta-dehydrogenase 8 or 17 B HSD12, or to glycoprotein alpha chain 1 or 2. In the pituitary, genes involved with the growth axis (e.g., growth hormone, insulin-related growth factor binding protein) correlated with the most transcripts. These results suggest that transcriptional networks along the BPGL axis may be regulated by factors other than circulating steroid hormones.

Promise and progress in environmental genomics: a status report on the applications of gene expression-based microarray studies in ecologically relevant fish species

The advent of any new technology is typically met with great excitement. So it was a few years ago, when the combination of advances in sequencing technology and the development of microarray technology made measurements of global gene expression in ecologically relevant species possible. Many of the review papers published around that time promised that these new technologies would revolutionize environmental biology as they had revolutionized medicine and related fields. A few years have passed since these technological advancements have been made, and the use of microarray studies in non-model fish species has been adopted in many laboratories internationally. Has the relatively widespread adoption of this technology really revolutionized the fields of environmental biology, including ecotoxicology, aquaculture and ecology, as promised? Or have these studies merely become a novelty and a potential distraction for scientists addressing environmentally relevant questions? In this review, the promises made in early review papers, in particular about the advances that the use of microarrays would enable, are summarized; these claims are compared to the results of recent studies to determine whether the forecasted changes have materialized. Some applications, as discussed in the paper, have been realized and have led to advances in their field, others are still under development.

In vitro infection of sheep lice (Bovicola ovis Schrank) by Steinernematid and Heterorhabditid nematodes

Control of sheep lice with conventional pesticides can be compromised by difficulty in contacting lice in the dense water repellent fleeces of sheep, particularly when sheep have not been recently shorn. Entomopathogenic nematodes (ENs) are motile and are able to actively seek out insect hosts. They have particular advantages for the control of pests in cryptic habitats, such as the fleeces of sheep and avoid many of the problems frequently associated with chemical controls. This study investigated whether ENs were able infect and kill Bovicola ovis and compared the effectiveness of different species at different temperatures and when applied to wool. Four species of nematodes, Steinernema carpocapsae, Steinernema riobrave, Steinernema feltiae and Heterorhabditis bacteriophora were tested. All were shown to infect and kill lice in Petri dish assays at 30°C. At 35°C, the percent infection for S. carpocapsae and S. riobrave was significantly higher than for the other two species and percent infection by S. feltiae was significantly greater than for H. bacteriophora (P<0.05). At 37°C the percent mortality induced by S. riobrave was significantly greater than for S. carpocapsae (P<0.05). All species were able to locate and infect lice in wool when formulated in water with 8% Tween 80. In wool assays the percent lice infected with nematodes was significantly greater for S. riobrave than H. bacteriophora at 25°C, but there were no other differences between species (P=0.05). S. carpocapsae, S. riobrave and S. feltiae caused significantly higher lice mortality than H. bacteriophora at both 25 and 35°C in wool assays, but mortality induced by the three steinernematid species did not differ significantly (P>0.05). It is concluded that of the ENs studied S. riobrave is likely to be most effective against B. ovis when applied to live sheep because of its greater tolerance to high temperatures and 'cruiser' foraging strategy.

Differential regulation of components of the apoptotic and ubiquitin-mediated proteolytic pathway in slow- and fast- twitch muscle type in lambs receiving increasing amounts of dietary non-structural carbohydrate

Non-fibre carbohydrate (NFC) rich diets are commonly fed in ruminant production systems. The objective was to determine whether NFC challenge affects proteasome activity, or messenger ribonucleic acid (mRNA) expression of proteasome subunits or apoptotic Bcl-2 proteins, in slow- or fast- twitch muscle of sheep. For 12 d prior to slaughter, lambs (n = 8) received either a control diet (28.4% of dry matter as grain), or a diet of increasing amounts of grain up to 79.1% of dry matter. A decrease in urinary pH (P = 0.01), base excess of blood and extracellular fluid (P = 0.01), bicarbonate (P = 0.03) and total carbon dioxide (P = 0.04), and an increase in anion gap (P = 0.07) in NFC lambs are indicative of metabolic acidosis. NFC lambs had significantly lower mRNA expression of the 20S -β subunit (P = 0.05), and a tendency toward lower mRNA expression of the 20S-α subunit (P = 0.11) and the 19S isoform (P = 0.15) in soleus, but not to the same extent in extensor digitorum longus (EDL) muscle. Downregulation of Bad mRNA expression occurred in both soleus (P = 0.10) and EDL (P = 0.08) muscle as a result of NFC challenge. These results indicate that NFC challenge does affect mRNA expression of genes related to the proteasome and apoptosis in a muscle specific manner. Key words: Ubiquitin-mediated proteolytic pathway, non-fibre carbohydrate, apoptosis, sheep

Hepatic gene expression in rainbow trout (Oncorhynchus mykiss) exposed to different hydrocarbon mixtures

Traditional biomarkers for hydrocarbon exposure are not induced by all petroleum substances. The objective of this study was to determine if exposure to a crude oil and different refined oils would generate a common hydrocarbon-specific response in gene expression profiles that could be used as generic biomarkers of hydrocarbon exposure. Juvenile rainbow trout (Oncorhynchus mykiss) were exposed to the water accommodated fraction (WAF) of either kerosene, gas oil, heavy fuel oil, or crude oil for 96 h. Tissue was collected for RNA extraction and microarray analysis. Exposure to each WAF resulted in a different list of differentially regulated genes, with few genes in common across treatments. Exposure to crude oil WAF changed the expression of genes including cytochrome P4501A (CYP1A) and glutathione-S-transferase (GST) with known roles in detoxification pathways. These gene expression profiles were compared to others from previous experiments that used a diverse suite of toxicants. Clustering algorithms successfully identified gene expression profiles resulting from hydrocarbon exposure. These preliminary analyses highlight the difficulties of using single genes as diagnostic of petroleum hydrocarbon exposures. Further work is needed to determine if multivariate transcriptomic-based biomarkers may be a more effective tool than single gene studies for exposure monitoring of different oils.

Temporal patterns in the transcriptomic response of rainbow trout, Oncorhynchus mykiss, to crude oil

Time is often not characterized as a variable in ecotoxicogenomic studies. In this study, temporal changes in gene expression were determined during exposure to crude oil and a subsequent recovery period. Juvenile rainbow trout, Oncorhynchus mykiss, were exposed for 96 h to the water accommodated fractions of 0.4, 2 or 10 mgl(-1) crude oil loadings. Following 96 h of exposure, fish were transferred to recovery tanks. Gill and liver samples were collected after 24 and 96 h of exposure, and after 96 h of recovery for RNA extraction and microarray analysis. Fluorescently labeled cDNA was hybridized against matched controls, using salmonid cDNA arrays. Each exposure scenario generated unique patterns of altered gene expression. More genes responded to crude oil in the gill than in the liver. In the gill, 1137 genes had altered expression at 24 h, 2003 genes had altered expression levels at 96 h of exposure, yet by 96 h of recovery, no genes were significantly altered in expression. In the liver at 10 mgl(-1), only five genes were changed at 24 h, yet 192 genes had altered expression after 96 h recovery. At 2 mgl(-1) in the liver, many genes had altered regulation at all three time points. The 0.4 mgl(-1) loading also showed 289 genes upregulated at 24 h after exposure. The Gene Ontology terms associated with altered expression in the liver suggested that the processes of protein synthesis, xenobiotic metabolism, and oxidoreductase activity were altered. The concentration-responsive expression profile of cytochrome P450 1A, a biomarker for oil exposure, did not predict the majority of gene expression profiles in any tissue or dose, since direct relationships with dose were not observed for most genes. While the genes and their associated functions agree with known modes of toxic action for crude oil, the gene lists obtained do not match our previously published work, presumably due to array analysis procedures. These results demonstrate that changes in gene expression with time and dose may be complicated, and should be characterized in controlled laboratory settings before attempts are made to interpret responses in field-collected organisms. Further, processes for analyzing microarray data need to be developed such that standardized gene lists are developed, or that analysis does not rely on lists of significantly altered genes before arrays can be further evaluated as a monitoring tool.

Resistance to insect growth regulator insecticides in populations of sheep lice as assessed by a moulting disruption assay

Low-volume, backline applications with the benzoylphenyl urea insecticides triflumuron and diflubenzuron represent in excess of 70% of treatments for the control of sheep lice, Bovicola ovis (Schrank) (Phthiraptera: Trichodectidae), in Australia. Reports of reduced effectiveness from 2003 and subsequent controlled treatment trials suggested the emergence of resistance to these compounds in B. ovis populations. A laboratory assay based on the measurement of moulting success in nymphs was developed and used to assess susceptibility to diflubenzuron and triflumuron in louse populations collected from sheep where a control failure had occurred. These tests confirmed the development of resistance to triflumuron and diflubenzuron in at least two instances, with estimated resistance ratios of 67-94X at LC(50).

Long-term effects of feeding monensin on methane production in lactating dairy cows

The objective of this study was to determine the long-term effects of feeding monensin on methane (CH4) production in lactating dairy cows. Twenty-four lactating Holstein dairy cows (1.46 +/- 0.17 parity; 620 +/- 5.9 kg of live weight; 92.5 +/- 2.62 d in milk) housed in a tie-stall facility were used in the study. The study was conducted as paired comparisons in a completely randomized design with repeated measurements in a color-coded, double-blind experiment. The cows were paired by parity and days in milk and allocated to 1 of 2 treatments: 1) the regular milking cow total mixed ration (TMR) with a forage-to-concentrate ratio of 60:40 (control TMR; placebo premix) vs. a medicated TMR (monensin TMR; regular TMR + 24 mg of Rumensin Premix/kg of dry matter) fed ad libitum. The animals were fed and milked twice daily (feeding at 0830 and 1300 h; milking at 0500 and 1500 h) and CH4 production was measured prior to introducing the treatments and monthly thereafter for 6 mo using an open-circuit indirect calorimetry system. Monensin reduced CH4 production by 7% (expressed as grams per day) and by 9% (expressed as grams per kilogram of body weight), which were sustained for 6 mo (mean, 458.7 vs. 428.7 +/- 7.75 g/d and 0.738 vs. 0.675 +/- 0.0141, control vs. monensin, respectively). Monensin reduced milk fat percentage by 9% (3.90 vs. 3.53 +/- 0.098%, control vs. monensin, respectively) and reduced milk protein by 4% (3.37 vs. 3.23 +/- 0.031%, control vs. monensin, respectively). Monensin did not affect the dry matter intake or milk yield of the cows. These results suggest that medicating a 60:40 forage-to-concentrate TMR with 24 mg of Rumensin Premix/kg of dry matter is a viable strategy for reducing CH4 production in lactating Holstein dairy cows.

Gene expression profiles in rainbow trout, Onchorynchus mykiss, exposed to a simple chemical mixture

Among proposed uses for microarrays in environmental toxiciology is the identification of key contributors to toxicity within a mixture. However, it remains uncertain whether the transcriptomic profiles resulting from exposure to a mixture have patterns of altered gene expression that contain identifiable contributions from each toxicant component. We exposed isogenic rainbow trout Onchorynchus mykiss, to sublethal levels of ethynylestradiol, 2,2,4,4-tetrabromodiphenyl ether, and chromium VI or to a mixture of all three toxicants Fluorescently labeled complementary DNA (cDNA) were generated and hybridized against a commercially available Salmonid array spotted with 16,000 cDNAs. Data were analyzed using analysis of variance (p<0.05) with a Benjamani-Hochberg multiple test correction (Genespring [Agilent] software package) to identify up and downregulated genes. Gene clustering patterns that can be used as "expression signatures" were determined using hierarchical cluster analysis. The gene ontology terms associated with significantly altered genes were also used to identify functional groups that were associated with toxicant exposure. Cross-ontological analytics approach was used to assign functional annotations to genes with "unknown" function. Our analysis indicates that transcriptomic profiles resulting from the mixture exposure resemble those of the individual contaminant exposures, but are not a simple additive list. However, patterns of altered genes representative of each component of the mixture are clearly discernible, and the functional classes of genes altered represent the individual components of the mixture. These findings indicate that the use of microarrays to identify transcriptomic profiles may aid in the identification of key stressors within a chemical mixture, ultimately improving environmental assessment.

Temporal changes in gene expression in rainbow trout exposed to ethynyl estradiol

We examined changes in the genomic response during continuous exposure to the xenoestrogen ethynyl estradiol. Isogenic rainbow trout Oncorhynchus mykiss were exposed to nominal concentrations of 100 ng/L ethynyl estradiol (EE2) for a period of 3 weeks. At fixed time points within the exposure, fish were euthanized, livers harvested and RNA extracted. Fluorescently labeled cDNA were generated and hybridized against a commercially available Salmonid array (GRASP project, University of Victoria, Canada) spotted with 16,000 cDNAs. The slides were scanned to measure abundance of a given transcript in each sample relative to controls. Data were analyzed via Genespring (Silicon Genetics) to identify a list of up and down regulated genes, and to determine gene clustering patterns that can be used as "expression signatures". Gene ontology was determined using the annotation available from the GRASP website. Our analysis indicates each exposure time period generated specific gene expression profiles. Changes in gene expression were best understood by grouping genes by their gene expression profiles rather than examining fold change at a particular time point. Many of the genes commonly used as biomarkers of exposure to xenoestrogens were not induced initially and did not have gene expression profiles typical of the majority of genes with altered expression.

Dynamics of 17alpha-ethynylestradiol exposure in rainbow trout (Oncorhynchus mykiss): absorption, tissue distribution, and hepatic gene expression pattern

17alpha-Ethynylestradiol (EE2) is a synthetic estrogen identified in sewage effluents. To understand better the absorption kinetics of EE2 and the induction of vitellogenin (VTG) and estrogen receptor alpha (ERalpha) mRNA, we subjected male rainbow trout (Onchorynchus mykiss) to continuous water exposures of 125 ng/L of EE2 for up to 61 d. Trout were either repetitively sampled for blood plasma or serially killed at selected time intervals. Vitellogenin, ERalpha mRNA, and EE2 were measured using enzyme-linked immunosorbent assay and using quantitative polymerase chain reaction and gas chromatography-mass spectrometry, respectively. In separate experiments, trout were exposed to EE2 for 7 d, and hepatic gene expression was assessed using a low- and high-density cDNA microarray. The EE2 was rapidly absorbed by the trout, with an apparent equilibrium at 16 h in plasma and liver. The ERalpha mRNA levels also increased rapidly, reaching near-peak levels by 48 h. In contrast, plasma levels of VTG continuously increased for 19 d. After 61 d, tissues with the highest levels of VTG were the liver, kidney, and testes. Microarray-based gene expression studies provided unexpected results. In some cases, known estrogen-responsive genes (e.g., ERalpha) were unresponsive, whereas many of the genes that have no apparent link to estrogen function or EE2 toxicity were significantly altered in expression. Of the two microarray approaches tested in the present study, the high-density array appeared to be superior because of the improved quality of the hybridization signal and the robustness of the response in terms of the number of genes identified as being EE2 responsive.

Dose-response relationships in gene expression profiles in rainbow trout, Oncorhyncus mykiss, exposed to ethynylestradiol

Determining how gene expression profiles change with toxicant dose will improve the utility of arrays in identifying biomarkers and modes of toxic action. Isogenic rainbow trout, Oncorhyncus mykiss,were exposed to 10, 50 or 100 ng/L ethynylestradiol (a xeno-estrogen) for 7 days. Following exposure hepatic RNA was extracted. Fluorescently labeled cDNA were generated and hybridized against a commercially available Atlantic Salmon/Trout array (GRASP project, University of Victoria) spotted with 16,000 cDNAs. Transcript expression in treated vs control fish was analyzed via Genespring (Silicon Genetics) to identify genes with altered expression, as well as to determine gene clustering patterns that can be used as "expression signatures". Array results were confirmed via qRT PCR. Our analysis indicates that gene expression profiles varied somewhat with dose. Established biomarkers of exposure to estrogenic chemicals, such as vitellogenin, vitelline envelope proteins, and the estrogen receptor alpha, were induced at every dose. Other genes were dose specific, suggesting that different doses induce distinct physiological responses. These findings demonstrate that cDNA microarrays could be used to identify both toxicant class and relative dose.

Gene expression patterns in rainbow trout, Oncorhynchus mykiss, exposed to a suite of model toxicants

The increased availability and use of DNA microarrays has allowed the characterization of gene expression patterns associated with exposure to different toxicants. An important question is whether toxicant induced changes in gene expression in fish are sufficiently diverse to allow for identification of specific modes of action and/or specific contaminants. In theory, each class of toxicant may generate a gene expression profile unique to its mode of toxic action. In this study, isogenic (cloned) rainbow trout Oncorhynchus mykiss were exposed to sublethal levels of a series of model toxicants with varying modes of action, including ethynylestradiol (xeno-estrogen), 2,2,4,4'-tetrabromodiphenyl ether (BDE-47, thyroid active), diquat (oxidant stressor), chromium VI, and benzo[a]pyrene (BaP) for a period of 1-3 weeks. An additional experiment measured trenbolone (anabolic steroid; model androgen) induced gene expression changes in sexually mature female trout. Following exposure, fish were euthanized, livers removed and RNA extracted. Fluorescently labeled cDNA were generated and hybridized against a commercially available Atlantic Salmon/Trout array (GRASP project, University of Victoria) spotted with 16,000 cDNA's. The slides were scanned to measure abundance of a given transcript in each sample relative to controls. Data were analyzed via Genespring (Silicon Genetics) to identify a list of up- and downregulated genes, as well as to determine gene clustering patterns that can be used as "expression signatures". The results indicate each toxicant exposure caused between 64 and 222 genes to be significantly altered in expression. Most genes exhibiting altered expression responded to only one of the toxicants and relatively few were co-expressed in multiple treatments. For example, BaP and Diquat, both of which exert toxicity via oxidative stress, upregulated 28 of the same genes, of over 100 genes altered by either treatment. Other genes associated with steroidogenesis, p450 and estrogen responsive genes appear to be useful for selectively identifying toxicant mode of action in fish, suggesting a link between gene expression profile and mode of toxicity. Our array results showed good agreement with quantitative real time polymerase chain reaction (qRT PCR), which demonstrates that the arrays are an accurate measure of gene expression. The specificity of the gene expression profile in response to a model toxicant, the link between genes with altered expression and mode of toxic action, and the consistency between array and qRT PCR results all suggest that cDNA microarrays have the potential to screen environmental contaminants for biomarkers and mode of toxic action.

Oral exposure of PBDE-47 in fish: toxicokinetics and reproductive effects in Japanese Medaka (Oryzias latipes) and fathead minnows (Pimephales promelas)

The toxicokinetics of 2,2,4,4-tetrabromodiphenyl ether (PBDE-47) was studied in the Japanese Medaka (Oryzias latipes) after a single oral exposure followed by termination at specific time points. The effects of repeated oral exposure to PBDE-47 on reproductive performance was assessed using a pair breeding experimental design with fathead minnows (Pimephales promelas) given daily PBDE-47 exposures for 25 days, during which fecundity was measured as an indicator of reproductive performance. Medaka and fathead minnows were orally exposed to PBDE-47 by bioencapsulation in brine shrimp, Artemia sp. In the medaka studies, measurable levels of PBDE-47 were detected in the carcass within 0.25 h with peak levels occurring at 8 h. The body levels of PBDE-47 slowly declined and were still 25% of peak levels at 624 h after dosing. Assimilation of the bioencapsulated dose was at least 80% and may well approach 100%. The PBDE-47 concentration-time profile was fitted to a one-compartment clearance-volume toxicokinetic model and the model-predicted value for elimination half-life was determined to be 281 h and the first-order absorption rate constant was Ka = 0.26 hr(-1). In the fathead minnow study, egg laying in the PBDE-treated breeding pairs stopped after 10 days. The condition factor of PBDE-treated males was significantly reduced (P <0.011) compared with control males, whereas no significant difference was observed in females. Histological examination revealed a greater than 50% reduction in mature sperm in PBDE-47 exposed minnows compared to controls. Collectively, these results suggest PBDE-47 is selectively toxic to sexually mature male fathead minnows.

Interactive effects of UV, benzo[alpha] pyrene, and cadmium on DNA damage and repair in embryos of the grass shrimp Paleomonetes pugio

We examined the link between DNA strand breaks and hatching rates in grass shrimp, (Paleomonetes pugio), embryos exposed to 0.2 microM benzo[alpha] pyrene (BP), 5 microM cadmium (Cd) and 330 kJ/m(2) UV light, either alone or together. After exposure, embryos were transferred to clean seawater with or without 5 microM Cd. Hatching rates and DNA strand breaks (Comet Assay) were determined. DNA lesions caused by exposure to BP, UV light, or BP/cadmium were rapidly repaired and were not associated with any effects on hatching. Exposure to Cd after exposure to BP or UV did not affect embryological development or DNA repair. Exposure to BP/UV resulted in a high level of DNA lesions which were slowly repaired. Exposure to cadmium following BP/UV exposure inhibited hatching and DNA repair. Adducts formed during exposure to BP/UV exposure may be difficult to excise or may saturate the nucleotide excision repair system.

Genotoxicant induced DNA damage and repair in early and late developmental stages of the grass shrimp Paleomonetes pugio embryo as measured by the comet assay

In this study, data are presented which link frequency of DNA strand breaks and repair capability to developmental stage. Stages 4 and 7 embryos of the grass shrimp (Palaemonetes pugio) were exposed to various concentrations of benzo[alpha]pyrene (BalphaP), Cr(VI) and hydrogen peroxide. Following exposure, responses were measured as changes in hatching rates and DNA strand breaks (using the comet assay). The comet assay was modified by treatment of isolated nuclei with endonucleases which cleave DNA at oxidative lesions in DNA prior to electrophoresis. DNA repair was followed by transfer of toxicant exposed embryos to clean water and periodic determination of strand breaks. DNA strand breaks were higher in stage 7 embryos than in stage 4 embryos after exposure to the same concentration of different genotoxicants. However, when samples were treated with endonucleases to measure oxidative lesions, the total amount of DNA damage between stages 4 and 7 were similar. After toxicant exposure and transfer to clean water, DNA strand breaks in stage 7 embryos returned to background levels more rapidly than in stage 4 embryos. Similarly, samples treated with endonucleases during DNA repair studies showed that oxidative lesions were repaired more rapidly in stage 7 than in stage 4. These findings suggest that because of rapid DNA repair in late embryo stages that early embryo stages are more likely to have developmental effects after genotoxicant exposure.

Toxicology tests with aquatic animals need to consider the trophic transfer of metals

Water quality criteria for metals have largely been based on toxicity tests in which organisms are exposed to dissolved metals, often at concentrations that exceed by several orders of magnitude those which are found even in contaminated waters; these tests assume that ecological impacts can be extrapolated from acute toxicity assessments. We have shown that when marine copepods are exposed to metals (Ag, Cd, Hg, Se, Zn) through their diet the reproductive capacity decreases by up to 75% because fewer eggs are produced and the hatching success of the eggs which are produced is diminished. These sublethal effects occur at metal concentrations that are 2-3 orders of magnitude below acutely toxic concentrations. Metals accumulated in copepods by trophic transfer deposit in internal tissues, and only modest increases above background levels can depress reproductive capability. Metals accumulated from the dissolved phase deposit primarily on external surfaces, where they have negligible effects at environmentally realistic concentrations. Toxicity tests must consider the bioaccumulation of metals from dietary exposure in order to account for sublethal effects at metal concentrations that are comparable to those in contaminated waters.

Relating the reproductive toxicity of five ingested metals in calanoid copepods with sulfur affinity

The sublethal toxicity of dietary Ag, Cd, Hg, Mn, and Zn to marine copepods, measured as depressed egg production, was evaluated as a function of ambient metal concentrations and metal concentrations in copepod tissues. All metals were toxic following 4-h feedings on metal-contaminated phytoplankton food, but there was a four order of magnitude difference between the inhibitory concentration in copepod tissues of the most toxic (2.4 nmol g(-1) dry wt. for Hg) and least toxic (13.4 micromol g(-1) dry wt. for Mn) metals. Metal concentrations in copepods that elicited a toxic response were about 3 times higher than background concentrations for Ag and 9 times higher for Hg, about 2 times higher for Cd, two orders of magnitude higher for Mn, and only 5% higher for Zn. Copepods exposed to lower concentrations of Zn for longer periods (1 week), resulting in tissue Zn concentrations similar to those in the short-term exposures, were not affected, suggesting that copepods were capable of adjusting to slowly increasing Zn by sequestration of this metal. Toxic metal concentrations in copepod tissues were directly proportional (r2 = 0.85) to the affinity of the metals for sulfur, as indicated by the solubility products of the metal sulfides. This relationship, together with protein analysis of eggs, published recently, suggests that metals affect egg production by binding to enzymes involved with vitellogenesis.

Sublethal effects of silver in zooplankton: importance of exposure pathways and implications for toxicity testing

In aquatic environments, organisms are exposed to contaminants via direct uptake from water and by trophic transfer. However, most toxicity tests only examine uptake via the dissolved phase. We compared the response of marine and freshwater crustacean zooplankton to silver following dissolved and food exposure. Silver, like other metals, concentrates in aquatic food chains and may exert toxicity. In standard solute exposure toxicity tests, Ag is toxic to zooplankton at concentrations of 400 nM for marine copepods and 100 nM for freshwater cladocerans, concentrations far greater than those in most waters. However, if Ag is accumulated from algal food, reproductive success decreases by >50% when algae are exposed to only 1 nM Ag in copepods and 0.5 nM Ag in cladocerans. These concentrations are within an order of magnitude of those found in contaminated estuaries. Following dietary exposure, decreased egg production and viability occur when tissue Ag concentrations increase three- to fourfold to 0.3 ppm in cladocerans and 0.5 ppm in copepods. Assimilated Ag depresses egg production by reducing yolk protein deposition and ovarian development. Our results indicate that ecologically relevant toxicity tests should consider sublethal effects of contaminants obtained from food since these effects cannot be predicted from exposures to only dissolved contaminants.