Transcriptomic profiling permits the identification of pollutant sources and effects in ambient water samples

Detecting Local Adaptation between North and South European Atlantic Salmon Populations

Pollution and other anthropogenic effects have driven a decrease in Atlantic salmon (Salmo salar) in the Iberian Peninsula. The restocking effort carried out in the 1980s, with salmon from northern latitudes with the aim of mitigating the decline of native populations, failed, probably due to the deficiency in adaptation of foreign salmon from northern Europe to the warm waters of the Iberian Peninsula. This result would imply that the Iberian populations of Atlantic salmon have experienced local adaptation in their past evolutionary history, as has been described for other populations of this species and other salmonids. Local adaptation can occur by divergent selections between environments, favoring the fixation of alleles that increase the fitness of a population in the environment it inhabits relative to other alleles favored in another population. In this work, we compared the genomes of different populations from the Iberian Peninsula (Atlantic and Cantabric basins) and Scotland in order to provide tentative evidence of candidate SNPs responsible for the adaptive differences between populations, which may explain the failures of restocking carried out during the 1980s. For this purpose, the samples were genotyped with a 220,000 high-density SNP array (Affymetrix) specific to Atlantic salmon. Our results revealed potential evidence of local adaptation for North Spanish and Scottish populations. As expected, most differences concerned the comparison of the Iberian Peninsula with Scotland, although there were also differences between Atlantic and Cantabric populations. A high proportion of the genes identified are related to development and cellular metabolism, DNA transcription and anatomical structure. A particular SNP was identified within the NADP-dependent malic enzyme-2 (_mMEP-2*), previously reported by independent studies as a candidate for local adaptation in salmon from the Iberian Peninsula. Interestingly, the corresponding SNP within the _mMEP-2* region was consistent with a genomic pattern of divergent selection.

Evaluating environmental impact of STP effluents on receiving water in Beijing by the joint use of chemical analysis and biomonitoring

To evaluate the environmental impact of receiving water from the Qinghe River sewage treatment plant (STP) effluents in Beijing, we collected sediments and Bellamya aeruginosa (Up-site, Discharge-site, and Down-site) both in 2017 and 2018 and analyzed the samples via chemical analysis, biological responses and transcriptomics. In two years of data, our biological results showed that AChE activities presented different degrees of influence on B. aeruginosa captured at sampling points of the STP compared to control sites (P < 0.05). Additionally, indicators of the antioxidant system (e.g., SOD, CAT, GST, EROD activity) and MDA content were significantly increased in the whole tissue at the Up-site of the STP. Integration of the assessed biomarkers using the integrated biomarker response (IBR) index ranked the environmental impact at sites as Up-site > Discharge-site > Down-site. In terms of the transcriptome data, B. aeruginosa collected from the Discharge-site of the STP showed greater transcriptomic response than it did from all other sites. KEGG pathway analysis revealed that sewage significantly altered the expression of genes involved in xenobiotics by cytochrome P450, drug metabolism-cytochrome P450, glutathione metabolism, oxidative phosphorylation, citrate (TCA) cycle, glycolysis/gluconeogenesis, apoptotic and Parkinson's disease. The concentrations of 34 organic pollutants (17 PAHs, 10 PAEs, 7 EDCs) were measured. The chemical concentrations of pollutants decreased from Up-site to Down-site and were well correlated with enzyme activity, IBR, and transcriptomic results. Our results demonstrated that the combined use of chemical analysis, biological responses and transcriptome data is necessary to validate the efficacy of a battery of biomarkers chosen to detect environmental stress due to pollution.

A Review of Current and Emerging Approaches for Water Pollution Monitoring

The aquatic ecosystem is continuously threatened by the infiltration and discharge of anthropogenic wastewaters. This issue requires the unending improvement of monitoring systems to become more comprehensive and specific to targeted pollutants. This review intended to elucidate the overall aspects explored by researchers in developing better water pollution monitoring tools in recent years. The discussion is encircled around three main elements that have been extensively used as the basis for the development of monitoring methods, namely the dissolved compounds, bacterial indicator, and nucleic acids. The latest technologies applied in wastewater and surface water mapped from these key players were reviewed and categorized into physicochemical and compound characterizations, biomonitoring, and molecular approaches in taxonomical and functional analyses. Overall, researchers are continuously rallying to enhance the detection of causal source for water pollution through either conventional or mostly advanced approaches focusing on spectrometry, high-throughput sequencing, and flow cytometry technology among others. From this review’s perspective, each pollution evaluation technology has its own advantages and it would be beneficial for several aspects of pollutants assessments to be combined and established as a complementary package for better aquatic environmental management in the long run.

Transcriptomic Profiles in Zebrafish Liver Permit the Discrimination of Surface Water with Pollution Gradient and Different Discharges

The present study aims to evaluate the potential of transcriptomic profiles in evaluating the impacts of complex mixtures of pollutants at environmentally relevant concentrations on aquatic vertebrates. The changes in gene expression were determined using microarray in the liver of male zebrafish (Danio rerio) exposed to surface water collected from selected locations on the Hun River, China. The numbers of differentially expressed genes (DEGs) in each treatment ranged from 728 to 3292, which were positively correlated with chemical oxygen demand (COD). Predominant transcriptomic responses included peroxisome proliferator-activated receptors (PPAR) signaling and steroid biosynthesis. Key pathways in immune system were also affected. Notably, two human diseases related pathways, insulin resistance and Salmonella infection were enriched. Clustering analysis and principle component analysis with DEGs differentiated the upstream and downstream site of Shenyang City, and the mainstream and the tributary sites near the junction. Comparison the gene expression profiles of zebrafish exposed to river surface water with those to individual chemicals found higher similarity of the river water with estradiol than several other organic pollutants and metals. Results suggested that the transcriptomic profiles of zebrafish is promising in differentiating surface water with pollution gradient and different discharges and in providing valuable information to support discharge management.

Environmental exposure to a major urban wastewater effluent: Effects on the energy metabolism of northern pike

Municipal wastewater effluents (MWWEs) consist of dynamic and complex mixtures of chemical and biological compounds that can alter the health of exposed aquatic organisms. Disturbance of energy metabolism has been reported in fish exposed to MWWEs. However, there is a scarcity of knowledge on the physiological events leading to perturbation of energy balance and thyroid regulation, and associated lipid metabolism. The objective of the present study was to use a set of biomarkers, from gene transcription to body condition, to investigate the effects of a chronic environmental exposure to a major primary MWWE on fatty acid metabolism and thyroid hormone levels in northern pike (Esox lucius) collected from the St. Lawrence River near Montreal (QC, Canada). The exposure of pike to MWWE was examined through determination of a suite of persistent and bioaccumulative halogenated flame retardants in liver as this effluent is a known regional source for these chemicals. Greater hepatic concentrations of polybrominated diphenyl ethers (PBDEs, range: 29.6-465ng/g w.w. and 88.8-823ng/g w.w. in females and males, respectively) and other halogenated flame retardants (e.g., dechlorane-related compounds) were determined in fish collected downstream of the MWWE's point of discharge relative to the upstream site. This exposure in male pike was associated with decreased acyl-coA oxidase (acox1) and fatty acid synthase (fasn) mRNA levels as well as a decreased acyl-coA oxidase (ACOX) activity in liver. In female pike, MWWE exposure was associated with lower circulating free and total triiodothyronine (T₃) levels and a tendency for greater total lipid percentages in liver. Present findings provide evidence that chronic exposure of a top predator fish to MWWE can be related to gender-specific effects on fatty acid metabolism and thyroid hormone homeostasis, and highlight the need for further investigation.

How Does Reference Site Selection Influence Interpretation of Omics Data?: Evaluating Liver Transcriptome Responses in Male Rainbow Darter (Etheostoma caeruleum) across an Urban Environment

Studies quantifying the influence of reference site selection on transcriptomic profiles in aquatic organisms exposed to complex mixtures are lacking in the literature, despite the significant implications of such research for the interpretation of omics data sets. We measured hepatic transcriptomic responses in fish across an urban environment in the central Grand River watershed (Ontario, Canada). Adult male rainbow darter (RBD) (Etheostoma caeruleum) were collected from nine sites at varying distances from two major municipal wastewater treatment plants (MWWTPs) (Waterloo, Kitchener), including three upstream reference sites. The transcriptomic response in RBD was independently compared with that of fish from each of the three reference sites. Data collected in fish downstream of the Waterloo MWWTP (poorest effluent quality) suggested that ∼15.5% of the transcriptome response was influenced by reference site selection. In contrast, at sites where the impact of MWWTPs was less-pronounced and fish showed less of a transcriptome response, reference site selection had a greater influence (i.e., ∼56.9% of transcripts were different depending on the site used). This study highlights the importance of conducting transcriptomics studies that leverage more than one reference site, and it broadens our understanding of the molecular responses in fish in dynamic natural environments.

Application of cDNA-AFLP to biomarker exploration in a non-model species Grandidierella japonica

Biomarkers of exposure can be used to identify specific contaminants that are adversely affecting aquatic organisms. However, it remains prohibitively costly to investigate multiple novel biomarkers of exposure in a non-model species, despite the development of next-generation sequencing technology. In this study, we focused on the use of cDNA-amplified fragment length polymorphism (AFLP) as a cost-effective biomarker discovery tool to test whether it could identify biomarkers of exposure in the non-model amphipod species Grandidierella japonica. Loci were identified that were differentially expressed in amphipods exposed to reference chemicals (Cu, Zn, and nicotine) and to an environmental sample (road dust) at sublethal concentrations. Eight loci were shown to respond consistently to nicotine at different concentrations, but not to Cu or Zn. Some of the loci also responded to an environmental road dust sample containing nicotine. These findings suggest that loci identified using cDNA-AFLP could be used as biomarkers of nicotine exposure in environmental samples with complex matrices. Further studies with other organisms and toxicants are needed, but we have demonstrated that the use of cDNA-AFLP to identify biomarkers for ecotoxicological studies of non-model species is at least feasible.

Defining the role of omics in assessing ecosystem health: Perspectives from the Canadian environmental monitoring program

Scientific reviews and studies continue to describe omics technologies as the next generation of tools for environmental monitoring, while cautioning that there are limitations and obstacles to overcome. However, omics has not yet transitioned into national environmental monitoring programs designed to assess ecosystem health. Using the example of the Canadian Environmental Effects Monitoring (EEM) program, the authors describe the steps that would be required for omics technologies to be included in such an established program. These steps include baseline collection of omics endpoints across different species and sites to generate a range of what is biologically normal within a particular ecosystem. Natural individual variability in the omes is not adequately characterized and is often not measured in the field, but is a key component to an environmental monitoring program, to determine the critical effect size or action threshold for management. Omics endpoints must develop a level of standardization, consistency, and rigor that will allow interpretation of the relevance of changes across broader scales. To date, population-level consequences of routinely measured endpoints such as reduced gonad size or intersex in fish is not entirely clear, and the significance of genome-wide molecular, proteome, or metabolic changes on organism or population health is further removed from the levels of ecological change traditionally managed. The present review is not intended to dismiss the idea that omics will play a future role in large-scale environmental monitoring studies, but rather outlines the necessary actions for its inclusion in regulatory monitoring programs focused on assessing ecosystem health.