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

Identifying transcriptomic indicators of tertiary treated municipal effluent in longnose dace (Rhinichthys cataractae) caged under semi-controlled conditions in experimental raceways

To evaluate effects of tertiary treated wastewater treatment plant effluent (MWWE) on transcriptomic responses in longnose dace (Rhinichthys cataractae; LND) we conducted a semi-controlled study in experimental raceways (Advancing Canadian Water Assets facility) imbedded in the Pine Creek treatment plant (Calgary, AB). LND collected from a reference site in the Bow River (REF) were caged in raceways containing either 5 % Pine Creek effluent (PC) or Bow River water (BR; control) over 28 d. Liver transcriptomes were analyzed in males and females sampled on days 7, 14 and 28 from BR and PC, and compared to REF fish on day 0. Concurrent with the caging, selected environmental substances of concern were analyzed in the BR and PC. Significantly different unigenes (SDUs) in females (vs males) within both BR and PC raceways increased over time and compared to REF fish. Moreover, SDUs in females and males within the same treatment (i.e., BR, PC) showed a temporal increase as well as compared to REF fish. Time was the dominant factor affecting SDUs, whereas sex and treatment had less of an impact on the transcriptome profiling. Gene Set Enrichment Analysis of BR vs PC over time revealed effects on genes involved in growth, metabolism of carbohydrates and lipids, and immune system on day 7; however, by day 28, 80-100 % of the transcripts localized to enriched biomarkers were associated with tissue immune responses in both sexes. Exposure to 5 % effluent had significant effects on female liver somatic index but no effects were observed on other phenotypic health indices in either sex. BR was used as the source of reference water, but analyses showed trace amounts of ESOCs. Analyses did not point towards definitive response patterns that could be used in field-based ecotoxicogenomic studies on the impacts of well-treated MWWE but suggested compromised adaptive immune responses.

Exploring within-ecodistrict lake organic matter variability and identifying possible environmental contaminant biomarkers using sedimentomics

Sedimentomics methods offer insight into the physiological parameters that influence freshwater sediment organic matter (sedOM). To date, most sedimentomics studies characterized variations across large spatial and environmental gradients; here we examine whether sedimentomics methods capture subtle sedOM variations within a relatively homogeneous study area in southwestern Nova Scotia, Canada. Additionally, we explore the lake sedimentome for candidate biomarkers related to ongoing carnivorous animal farming in the region. Sediment cores were recovered from seven lakes across a trophic (oligo- to eu- trophic) and anthropogenic land use gradient (carnivorous animal farming in catchment, downstream of farming, no farming nearby). Subsamples that dated prior to 1910 (pre-carnivorous animal farming) and later than 2010 (during carnivorous animal farming) were analyzed using UHPLC-HRMS in both negative (ESI-) and positive (ESI+) electrospray ionization modes. Cluster analysis (k-means) showed replicate samples from a given lake clustered distinctly from one another in both ESI modes, indicating sedOM captured subtle variations between lake systems. PCA combined with multiple linear regression indicated carnivorous animal farming and OM source explained most of the observed variation in lake sedOM. Principal component analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA) of ESI- and ESI+ data sets identified 103 unique candidate biomarkers. Ten strong candidate biomarkers were identified using graphical methods; more research is required for biomarker verification and molecular characterization. Our results indicate sedimentomics could be used in environmentally homogeneous areas, offering insight into the controls of sedOM cycling. Additionally, we identified prospective biomarkers related to carnivorous animal farming that could be used to understand relative contributions of farming to ongoing eutrophication issues in southwestern Nova Scotia.

Fish metabolome from sub-urban lakes of the Paris area (France) and potential influence of noxious metabolites produced by cyanobacteria

The recent democratization of high-throughput molecular phenotyping allows the rapid expansion of promising untargeted multi-dimensional approaches (e.g. epigenomics, transcriptomics, proteomics, and/or metabolomics). Indeed, these emerging omics tools, processed for ecologically relevant species, may present innovative perspectives for environmental assessments, that could provide early warning of eco(toxico)logical impairments. In a previous pilot study (Sotton et al., Chemosphere 2019), we explore by ¹H NMR the bio-indicative potential of metabolomics analyses on the liver of 2 sentinel fish species (Perca fluviatilis and Lepomis gibbosus) collected in 8 water bodies of the peri-urban Paris' area (France). In the present study, we further investigate on the same samples the high potential of high-throughput UHPLC-HRMS/MS analyses. We show that the LC-MS metabolome investigation allows a clear separation of individuals according to the species, but also according to their respective sampling lakes. Interestingly, similar variations of Perca and Lepomis metabolomes occur locally indicating that site-specific environmental constraints drive the metabolome variations which seem to be influenced by the production of noxious molecules by cyanobacterial blooms in certain lakes. Thus, the development of such reliable environmental metabolomics approaches appears to constitute an innovative bio-indicative tool for the assessment of ecological stress, such as toxigenic cyanobacterial blooms, and aim at being further follow up.

Prediction of adverse effects of effluents containing phenolic compounds in the Ba River on the ovary of fish (Hemiculter leucisculus) using transcriptomic and metabolomic analyses

The aim of this work was to evaluate the endocrine disrupting effects on the ovarian development of sharpbelly (Hemiculter leucisculus) caused by effluents containing phenolic compounds. This was achieved using integrated transcriptomic and metabolomic analyses, along with histopathological examinations. Sharpbelly, an indigenous freshwater fish widely distributed in East Asia, were collected by pole fishing from three sampling sites in the Ba River. These sampling sites include a mid-stream site near a wastewater outfall and a reference site located upstream and a far field comparison site located downstream. In sharpbelly collected near the wastewater discharge, the oocyte development was activated, compared to the other two sites. Histopathological alterations in the fish ovaries were likely due to the upregulated steroid hormone biosynthesis process, as suggested by the differentially expressed genes (e.g., hsd3b, hsd17b1) and differentially accumulated metabolites (e.g., pregnenolone). Additionally, under the stress of effluents containing phenolic compounds, genes related to the signaling pathways for oxidative phosphorylation and leukocyte transendothelial migration were dysregulated, suggesting the potential induction of inflammation and several ovarian diseases. Overall, these findings suggest that effluents containing phenolic compounds influence ovary development and reproductive function of female sharpbelly. Whether there is any resulting dysfunction of folliculogenesis, abnormality of ovulation, production of premature eggs and/or potential induction of ovarian cancers remains to be determined by further studies, for a better evaluation on effluents containing phenolic compounds to the fish fertility and the health of their offspring, and even the stability of the wild fish population. Notably, the integration of transcriptomics and metabolomics can complement the routine chemical analysis to comprehensively monitor the effects of wastewater treatment plant effluents on the health of wild fish.

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.

Disentangling of the ecotoxicological signal using "omics" analyses, a lesson from the survey of the impact of cyanobacterial proliferations on fishes

Omics technologies offer unprecedented perspectives for the rational investigation of complex biological systems. Indeed, omics present the ability of offering an extensive perception of the biochemistry and physiology of the cell and of any perturbing consequences of contaminants through the joint investigation of thousands of molecular responses simultaneously; then it has recently conducted to a fervent attention by research ecotoxicologists. Beyond the presentation of latest advances, exemplified here by omics investigation of cyanobacterial deleterious effects on various fishes (at various experimental and biological scales and with various analytical tools and pipeline), the present review paper re-explores the promising perspectives and also the pitfalls of such holistic investigations of the ecotoxicological response of organisms for environmental assessment.

De novo transcriptomic analysis predicts the effects of phenolic compounds in Ba River on the liver of female sharpbelly (Hemiculter lucidus)

This work aimed at predicting the toxic effects of phenolic compounds in Ba River on the health of female sharpbelly (Hemiculter lucidus) by the de novo transcriptomic analysis of the liver. Sharpbelly, a native fish living in freshwater ecosystem of East Asia, were sampled upstream, near, and downstream of a wastewater discharge to the Ba river. Based on the occurrence of bisphenol A (BPA), nonylphenol (NP), and 4-tert-octylphenol (4-t-OP) in the water and fish sampled from each site, up-, mid-, and down-stream were interpreted as control, high, and low treatment groups, respectively. In the mid-stream group the Fulton's condition factor (CF) and body weight were remarkably increased by approximate 20%; the gonado-somatic index (GSI) and hepatosomatic index (HSI) in mid-stream fish showed a similar increasing trend but lacking of statistical difference. Exposure to wastewater effluent caused 160 and 162 differentially expressed genes (DEGs) in up-mid and down-mid stream groups, respectively. Two sets of DEGs were primarily enriched in the signaling pathways of drug metabolism, endocrine system, cellular process, and lipid metabolism in the mid-stream sharpbelly, which may alter the fish behavior, disrupt the reproductive function, and lead to hypothyroidism, hepatic steatosis, etc. Taken together, our results linked the disrupted signaling pathways with activities of phenolic compounds to predict the potential effects of wastewater effluent on the health of wild fish.

Morphometric and proteomic responses of early-life stage rainbow trout (Oncorhynchus mykiss) to the aquatic herbicide diquat dibromide

The objective of this study was to examine the acute toxicity and sub-lethal effects of the commercial formulation of diquat dibromide, Reward® Landscape and Aquatic Herbicide, on multiple life stages of rainbow trout. The continuous exposure 96 h LC₅₀ derived for juvenile feeding fry aged 85 d post-hatch was 9.8 mg/L. Rainbow trout eyed embryos and juvenile feeding fry were also exposed to concentrations of Reward® ranging from 0.12 to 10 mg/L during two 24 h pulse exposures separated by 14 d of rearing in fresh water to mimic the manufacturers instructions for direct applications to water bodies. Decreased survival and body morphometrics were evident at 9.3 mg/L during the embryo/alevin exposures, but not in feeding juveniles, indicating a higher sensitivity of the early life stage fish. Quantitative proteomics and subnetwork enrichment analyses were conducted in the livers for both life stages to evaluate protein profiles after exposure to 0.37 mg/L diquat via Reward® exposure. Unique protein profiles were revealed for pre-feeding swim-up fry and for feeding juvenile fish, reflecting differences between the two life stages in sub-cellular responses after diquat dibromide exposure. Hepatic proteome effects were more dramatic in the pre-feeding swim-up fry with 315 proteins differentially expressed between the control and exposed fish while in the later life stage feeding fry, only 84 proteins were different after Reward® exposure. Exposure to Reward® significantly increased RNA/mRNA processes, induced activation of Atk/mTOR and caspase activity, and altered energy homeostasis. Proteomic alterations are associated with reduced growth observed in embryo/alevin at higher exposure concentrations, offering insight into key events underlying growth impairment within the adverse outcome pathway framework. This study is the first to report the sub-cellular and whole organism level effects of diquat dibromide in a commercial formulation and demonstrates that concentrations based on aquatic application rates alter the hepatic proteome.

Cumulative effects of municipal effluent and parasite infection in yellow perch: A field study using high-throughput RNA-sequencing

Multiple metabolic, immune and reproductive effects have been reported in fish residing in effluent-impacted sites. Natural stressors such as parasites also have been shown to impact the responses of organisms to chronic exposure to municipal effluent in the St. Lawrence River (Quebec, Canada). In order to comprehensively evaluate the cumulative impacts of anthropogenic and natural stressors on the health of yellow perch, differential mRNA transcription profiles were examined in juvenile females collected from effluent-impacted and upstream sites with low or high infection levels of the larval trematode Apophallus brevis. Transcriptomics was used to identify biological pathways associated with environmental exposure. In total, 3463 isoforms were differentially transcribed between sites. Patterns reflecting the combined effects of stressors were numerically dominant, with a majority of downregulated transcripts (68%). The differentially expressed transcripts were associated with 27 molecular and cellular functions ranging from cellular development to xenobiotic metabolism and were involved in the development and function of 13 organ systems including hematological, hepatic, nervous, reproductive and endocrine systems. Based on RNA-seq results, sixteen genes were measured by qPCR. Significant differences were observed for six genes in fish exposed to both stressors combined, whereas parasites and effluent individually impacted the transcription of one gene. Lysozyme activity, lipid peroxidation, retinol-binding protein and glucose-6-phosphate dehydrogenase were selected as potential biomarkers of effects to study specific pathways of interest. Lipid peroxidation in perch liver was different between sites, parasite loads, and for combined stressors. Overall, results indicated that juvenile yellow perch responded strongly to combined parasite and effluent exposure, suggesting cumulative effects on immune responses, inflammation and lipid metabolism mediated by retinoid receptors. The present study highlight the importance of using a comprehensive approach combining transcriptomics and endpoints measured at higher levels of biological organization to better understand cumulative risks of contaminants and pathogens in aquatic ecosystems.

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

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

Are we closer to the vision? A proposed framework for incorporating omics into environmental assessments

Environmental science has benefited a great deal from omics-based technologies. High-throughput toxicology has defined adverse outcome pathways (AOPs), prioritized chemicals of concern, and identified novel actions of environmental chemicals. While many of these approaches are conducted under rigorous laboratory conditions, a significant challenge has been the interpretation of omics data in "real-world" exposure scenarios. Clarity in the interpretation of these data limits their use in environmental monitoring programs. In recent years, one overarching objective of many has been to address fundamental questions concerning experimental design and the robustness of data collected under the broad umbrella of environmental genomics. These questions include: (1) the likelihood that molecular profiles return to a predefined baseline level following remediation efforts, (2) how reference site selection in an urban environment influences interpretation of omics data and (3) what is the most appropriate species to monitor in the environment from an omics point of view. In addition, inter-genomics studies have been conducted to assess transcriptome reproducibility in toxicology studies. One lesson learned from inter-genomics studies is that there are core molecular networks that can be identified by multiple laboratories using the same platform. This supports the idea that "omics-networks" defined a priori may be a viable approach moving forward for evaluating environmental impacts over time. Both spatial and temporal variability in ecosystem structure is expected to influence molecular responses to environmental stressors, and it is important to recognize how these variables, as well as individual factor (i.e. sex, age, maturation), may confound interpretation of network responses to chemicals. This mini-review synthesizes the progress made towards adopting these tools into environmental monitoring and identifies future challenges to be addressed, as we move into the next era of high throughput sequencing. A conceptual framework for validating and incorporating molecular networks into environmental monitoring programs is proposed. As AOPs become more defined and their potential in environmental monitoring assessments becomes more recognized, the AOP framework may prove to be the conduit between omics and penultimate ecological responses for environmental risk assessments.