Transcriptional and physiological response of fathead minnows (Pimephales promelas) exposed to urban waters entering into wildlife protected areas

Transcriptome analyses in juvenile yellow perch (Perca flavescens) exposed in vivo to clothianidin and chlorantraniliprole: Possible sampling bias

The St. Lawrence River is an important North American waterway that is subject to anthropogenic pressures including intensive urbanization, and agricultural development. Pesticides are widely used for agricultural activities in fields surrounding the yellow perch (Perca flavescens) habitat in Lake St. Pierre (Quebec, Canada), a fluvial lake of the river where the perch population has collapsed. Clothianidin and chlorantraniliprole were two of the most detected insecticides in surface waters near perch spawning areas. The objectives of the present study were to evaluate the transcriptional and biochemical effects of these two pesticides on juvenile yellow perch exposed for 28d to environmental doses of each compound alone and in a mixture under laboratory/aquaria conditions. Hepatic mRNA-sequencing revealed an effect of chlorantraniliprole alone (37 genes) and combined with clothianidin (251 genes), but no effects of clothianidin alone were observed in perch. Dysregulated genes were mostly related to circadian rhythms and to Ca2+ signaling, the latter effect has been previously associated with chlorantraniliprole mode of action in insects. Moreover, chronic exposure to clothianidin increased the activity of acetylcholinesterase in the brain of exposed fish, suggesting a potential non-target effect of this insecticide. Further analyses of three clock genes by qRT-PCR suggested that part of the observed effects of chlorantraniliprole on the circadian gene regulation of juvenile perch could be the result of time-of-day of sacrifice. These results provide insight into biological effects of insecticides in juvenile perch and highlight the importance of considering the circadian rhythm in experimental design and results analyses.

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.

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.

EcoToxModules: Custom Gene Sets to Organize and Analyze Toxicogenomics Data from Ecological Species

Traditional results from toxicogenomics studies are complex lists of significantly impacted genes or gene sets, which are challenging to synthesize down to actionable results with a clear interpretation. Here, we defined two sets of 21 custom gene sets, called the functional and statistical EcoToxModules, in fathead minnow (Pimephales promelas) to (1) re-cast predefined molecular pathways into a toxicological framework and (2) provide a data-driven, unsupervised grouping of genes impacted by exposure to environmental contaminants. The functional EcoToxModules were identified by re-organizing KEGG pathways into biological processes that are more relevant to ecotoxicology based on the input from expert scientists and regulators. The statistical EcoToxModules were identified using co-expression analysis of publicly available microarray data (n = 303 profiles) measured in livers of fathead minnows after exposure to 38 different conditions. Potential applications of the EcoToxModules were demonstrated with two case studies that represent exposure to a pure chemical and to environmental wastewater samples. In comparisons to differential expression and gene set analysis, we found that EcoToxModule responses were consistent with these traditional results. Additionally, they were easier to visualize and quantitatively compare across different conditions, which facilitated drawing conclusions about the relative toxicity of the exposures within each case study.

A Self-Organizing Map of the Fathead Minnow Liver Transcriptome to Identify Consistent Toxicogenomic Patterns across Chemical Fingerprints

Lack of consistent findings in different experimental settings remains a major challenge in toxicogenomics. The present study investigated whether consistency between findings of different microarray experiments can be improved when the analysis is based on a common reference frame ("toxicogenomic universe"), which can be generated using the machine learning algorithm of the self-organizing map (SOM). This algorithm arranges and clusters genes on a 2-dimensional grid according to their similarity in expression across all considered data. In the present study, 19 data sets, comprising of 54 different adult fathead minnow liver exposure experiments, were retrieved from Gene Expression Omnibus and used to train a SOM. The resulting toxicogenomic universe aggregates 58 872 probes to 2500 nodes and was used to project, visualize, and compare the fingerprints of these 54 different experiments. For example, we could identify a common pattern, with 14% of significantly regulated nodes in common, in the data sets of an interlaboratory study of ethinylestradiol exposures. Consistency could be improved compared with the 5% total overlap in regulated genes reported before. Furthermore, we could determine a specific and consistent estrogen-related pattern of differentially expressed nodes and clusters in the toxicogenomic universe by applying additional clustering steps and comparing all obtained fingerprints. Our study shows that the SOM-based approach is useful for generating comparable toxicogenomic fingerprints and improving consistency between results of different experiments. Environ Toxicol Chem 2020;39:526-537. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.

Unravelling the mechanisms of PFOS toxicity by combining morphological and transcriptomic analyses in zebrafish embryos

Exposure to PFOS (perfluorooctanesulfonate) has been related to toxic effects on lipid metabolism, immunological response, and different endocrine systems. We present here a transcriptomic analysis of zebrafish embryos exposed to different concentrations of PFOS (0.03-1.0 mg/L) from 48 to 120 hpf. No major survival or morphological alterations (swimming bladder inflation, kyphosis, eye separation and size…) were observed below the 1.0 mg/L mark. Conversely, we observed significant increase in transcripts related to lipid transport and metabolism even at the lowest used concentration. In addition, we observed a general decrease on transcripts related to natural immunity and defense again infections, which adds to the recent concerns about PFOS as immunotoxicant, particularly in humans. Derived PoD (Point of Departure) values for transcriptional changes (0.011 mg/L) were about 200-fold lower than the corresponding PoD values for morphometric effects (2.53 mg/L), and close to levels observed in human blood serum or bird eggs. Our data suggest that currently applicable tolerable levels of PFOS in commercial goods should be re-evaluated, taking into account its potential effects on lipid metabolism and the immune system.

Blood Transcriptomics Analysis of Fish Exposed to Perfluoro Alkyls Substances: Assessment of a Non-Lethal Sampling Technique for Advancing Aquatic Toxicology Research

In contrast to mammals, the blood from other vertebrates such as fish contains nucleated red cells. Using a fathead minnow ( Pimephales promelas) oligonucleotide microarray, we compared altered transcripts in the liver and whole blood after exposure to environmentally relevant concentrations of perfluorooctanesulfonic acid (PFOS) and a mixture of seven types of perfluoro alkyl substances (PFAS), including perfluorooctanoic acid (PFOA). We used quantitative polymerase chain reactions and cell-based assays to confirm the main effects and found that blood responded with a greater number of altered genes than the liver. The exposure to PFAS altered similar genes with central roles in a cellular pathway in both tissues, including estrogen receptor α and peroxisome proliferator activator β and γ, indicating that the genes previously associated with PFAS exposure are differentially expressed in blood and liver. The altered transcripts are involved with cholesterol metabolism and mitochondrial function. Our data confirmed that PFAS are weak xenoestrogens and exert effects on DNA integrity. Gene expression profiling from blood samples not related with the immune system, including very-low-density lipoprotein, vitellogenin, estrogen receptor, and thyroid hormone receptor, demonstrated that blood is a useful tissue for assessing endocrine disruption in non-mammalian vertebrates. We conclude that the use of blood for non-lethal sampling in genomics studies is informative and particularly useful for assessing the effects of pollution in endangered species. Further, using blood will reduce animal use and widen the experimental design options for studying the effects of contaminant exposure on wildlife.

Latin American protected areas: Protected from chemical pollution?

Protected areas (PAs) are critically important means to preserve species and maintain natural ecosystems. However, the potential impacts of chemical pollution on PAs are seldom mentioned in the scientific literature. Research on the extent of the occurrence of chemical pollution inside PAs and in-depth assessments of how chemical contaminants may adversely affect the maintenance of species abundance, species survival, and ecosystem functions are scarce to nonexistent. We investigated 1) the occurrence of chemical contaminants inside 119 PAs in Latin America from publically available databases, and 2) reviewed case studies of chemical contaminants and pollution in 4 Latin American PAs. Cases of chemical pollution and contamination inside Latin American PAs mostly originated from sources such as mining, oil, and gas extraction. To date, the focus of the research on chemical pollution research inside Latin American PAs has been primarily on the detection of contamination, typically limited to trace metals. Where management actions have occurred, they have been reactive rather than proactive. Protected areas established in wetlands are the most affected by chemical pollution. Based on the information from the pollution and/or contamination occurrence and the case studies analyzed, Latin American PAs are not well safeguarded from chemical pollution, resulting in both challenges and opportunities to conserve biodiversity and ecosystems. Integr Environ Assess Manag 2017;13:360-370. © 2016 SETAC.

Integrated spatial health assessment of yellow perch (Perca flavescens) populations from the St. Lawrence River (QC, Canada), part B: cellular and transcriptomic effects

Multi-biological level assessments have become great tools to evaluate the health of aquatic ecosystems. Using this approach, a complementary study was designed to evaluate the health of yellow perch (Perca flavescens) populations in the St. Lawrence River (Quebec, Canada). In the present study, stress responses were compared at the transcriptomic, cellular, and tissue levels in yellow perch collected at six sites along the river: Lake St. François, Lake St. Louis (north and south), Beauregard Island and Lake St. Pierre (north and south). These results complement the physiological and chemical parameters as well as pathogen infection investigated in a companion paper published in the present issue. Thiobarbituric acid reactive substance (TBARS) analyses indicated the presence of oxidative stress in fish collected in the southern part of Lake St. Louis and at the downstream sites of Lake St. Pierre. High lipid peroxidation levels were found in the muscle of yellow perch caught at Beauregard Island, located downstream of the Montreal's wastewater treatment plant, suggesting an impact of the municipal effluent on redox homeostasis. Transcriptomic results indicated the down-regulation of genes related to lipid, glucose, and retinoid in southern Lake St. Pierre as well as a decrease in retinoid storage. Overall, biochemical and molecular markers indicated that the health status of yellow perch followed a decreasing gradient from upstream to downstream of the St. Lawrence River. This gradient is representative of the cumulative negative impacts of human activities on water and habitat quality along the river.

Footprints of Urban Micro-Pollution in Protected Areas: Investigating the Longitudinal Distribution of Perfluoroalkyl Acids in Wildlife Preserves

Current approaches to protect biodiversity by establishing protected areas usually gloss over water pollution as a threat. Our objective was to determine the longitudinal and seasonal distribution of perfluoroalkyl acids (PFAAs) in water column and sediments from a wastewater dominated stream that enters preservation areas. Water samples were collected along the longitudinal section (six sites, 1000 m away from each other) of the stream during the dry and wet seasons. Sediments were collected from three sites along the stream from three depths. Water and sediments were analyzed for PFAAs using high performance liquid chromatography-tandem mass spectrometry. Eleven PFAAs with 5 to 14 carbon atoms were detected in the water column at all sampling points, with a minor reduction at the last point suggesting a dilution effect. The most detected PFAAs was PFOS, followed by perfluorooctanoic acid (PFOA), and perfluorohexanoic acid (PFHxA). Seasonal differences in PFAAs concentrations suggested contribution of stormwater runoff during the wet season. All analyzed PFAAs in sediments were under the limit of quantification, likely due to the high proportion of sand and low organic matter. However, high concentrations of PFAAs were detected in the water column inside the protected areas, which includes PFOS in concentrations considered not safe for avian wildlife. Water samples appear to be more relevant than sediments to determine PFAAs micro-pollution in water bodies with sandy sediments. Inclusion of a management plans on micro-pollution research, monitoring, and mitigation is recommended for protected areas.

Fish connectivity mapping: linking chemical stressors by their mechanisms of action-driven transcriptomic profiles

Background

A very large and rapidly growing collection of transcriptomic profiles in public repositories is potentially of great value to developing data-driven bioinformatics applications for toxicology/ecotoxicology. Modeled on human connectivity mapping (Cmap) in biomedical research, this study was undertaken to investigate the utility of an analogous Cmap approach in ecotoxicology. Over 3500 zebrafish (Danio rerio) and fathead minnow (Pimephales promelas) transcriptomic profiles, each associated with one of several dozen chemical treatment conditions, were compiled into three distinct collections of rank-ordered gene lists (ROGLs) by species and microarray platforms. Individual query signatures, each consisting of multiple gene probes differentially expressed in a chemical condition, were used to interrogate the reference ROGLs.

Results

Informative connections were established at high success rates within species when, as defined by their mechanisms of action (MOAs), both query signatures and ROGLs were associated with the same or similar chemicals. Thus, a simple query signature functioned effectively as an exposure biomarker without need for a time-consuming process of development and validation. More importantly, a large reference database of ROGLs also enabled a query signature to cross-interrogate other chemical conditions with overlapping MOAs, leading to novel groupings and subgroupings of seemingly unrelated chemicals at a finer resolution. This approach confirmed the identities of several estrogenic chemicals, as well as a polycyclic aromatic hydrocarbon and a neuro-toxin, in the largely uncharacterized water samples near several waste water treatment plants, and thus demonstrates its future potential utility in real world applications.

Conclusions

The power of Cmap should grow as chemical coverages of ROGLs increase, making it a framework easily scalable in the future. The feasibility of toxicity extrapolation across fish species using Cmap needs more study, however, as more gene expression profiles linked to chemical conditions common to multiple fish species are needed.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2406-y) contains supplementary material, which is available to authorized users.