Ecotoxicogenomics: the challenge of integrating genomics into aquatic and terrestrial ecotoxicology

Temperature rise and its influence on the toxic effects caused by cyanotoxins in a neotropical catfish

Potentially toxic cyanobacterial blooms (cyanoHABs) have become a problem in public water supply reservoirs. Temperature rise caused by climate change can increase the frequency and intensity of blooms, which may influence the cyanotoxins concentration in the environment. This study aimed to evaluate the effect of the temperature on the responses of a Neotropical catfish exposed to a neurotoxin-rich cyanobacterial crude extract (Raphidiopsis raciborskii T3). Juveniles of Rhamdia quelen were exposed to four treatments, based on study data: control at 25 °C (C25), control at 30 °C (C30), crude extract equivalent to 105 cells.mL-l of R. raciborskii at 25 °C (CE25) and 30 °C (CE30). After 96 h of exposure, the fish were anesthetized and blood was taken. After euthanasia, the gill, posterior kidney, brain, muscle, liver and gonad were sampled for hematological, biochemical, genotoxic and histopathological biomarker analysis. Liver was sampled for proteomic analysis for identification of proteins related to energy production. Water samples were collected at the beginning and the end of the experiment for neurotoxins quantification. Different parameters in both males and females were altered at CE25, evidencing the effects of neurotoxins in freshwater fish. At CE30, a water warming scenario, more effects were observed in females than at 25 °C, such as activation of saxitoxin metabolism pathway and genotoxicity. More damage to macromolecules was observed in females at the higher temperature, demonstrating that the increase in temperature can aggravate the toxicity of neurotoxins produced by R. raciborskii T3.

Lipid metabolism in crocodilians: A field with promising applications in the field of ecotoxicology

In the last years, lipid physiology has become an important research target for systems biology applied to the field of ecotoxicology. Lipids are not only essential components of biological membranes, but also participate in extra and intracellular signaling processes and as signal transducers and amplifiers of regulatory cascades. Particularly in sauropsids, lipids are the main source of energy for reproduction, growth, and embryonic development. In nature, organisms are exposed to different stressors, such as parasites, diseases and environmental contaminants, which interact with lipid signaling and metabolic pathways, disrupting lipid homeostasis. The system biology approach applied to ecotoxicological studies is crucial to evaluate metabolic regulation under environmental stress produced by xenobiotics. In this review, we cover information of molecular mechanisms that contribute to lipid metabolism homeostasis in sauropsids, specifically in crocodilian species. We focus on the role of lipid metabolism as a powerful source of energy and its importance during oocyte maturation, which has been increasingly recognized in many species, but information is still scarce in crocodiles. Finally, we highlight priorities for future research on the influence of environmental stressors on lipid metabolism, their potential effect on the reproductive system and thus on the offspring, and their implications on crocodilians conservation.

How does temperature rise affect a freshwater catfish Rhamdia quelen? A proteomic approach

Outside of scientific circles, climate change is a hotly debated topic due to all its consequences. Changes in the temperature can affect aquatic organisms and it is important to understand and to detect earlier signals. This study aimed to analyze how a Neotropical fish species responds to temperature increases, using proteomic analysis as a tool. For this, fish of the species Rhamdia quelen, male and female, were exposed to two temperatures: 25 °C and 30 °C. After 96 h, the animals were anesthetized, euthanized and the liver was collected for proteomic analysis. Using freely available online software and databases (e.g. MetaboAnalyst, Gene Ontology and UniProt), we define the altered proteins in both sexes: 42 in females and 62 in males. Data are available via ProteomeXchange with identifier PXD046475. Differences between the two temperatures were observed mainly in the amino acid metabolic pathways. The cellular process and the immune response was altered, indicating that effects at lower levels of biological organization could serve as a predictor of higher-level effects when temperature rise affects wildlife populations. Thus, we conclude that the increase in temperature is capable of altering important cellular and physiological processes in R. quelen fish, with this response being different for males and females.

Derivation of Transcriptomics-Based Points of Departure for 20 Per- or Polyfluoroalkyl Substances Using a Larval Fathead Minnow (Pimephales promelas) Reduced Transcriptome Assay

Traditional toxicity testing has been unable to keep pace with the introduction of new chemicals into commerce. Consequently, there are limited or no toxicity data for many chemicals to which fish and wildlife may be exposed. Per- and polyfluoroalkyl substances (PFAS) are emblematic of this issue in that ecological hazards of most PFAS remain uncharacterized. The present study employed a high-throughput assay to identify the concentration at which 20 PFAS, with diverse properties, elicited a concerted gene expression response (termed a transcriptomics-based point of departure [tPOD]) in larval fathead minnows (Pimephales promelas; 5-6 days postfertilization) exposed for 24 h. Based on a reduced transcriptome approach that measured whole-body expression of 1832 genes, the median tPOD for the 20 PFAS tested was 10 µM. Longer-chain carboxylic acids (12-13 C-F); an eight-C-F dialcohol, N-alkyl sulfonamide; and telomer sulfonic acid were among the most potent PFAS, eliciting gene expression responses at concentrations <1 µM. With a few exceptions, larval fathead minnow tPODs were concordant with those based on whole-transcriptome response in human cell lines. However, larval fathead minnow tPODs were often greater than those for Daphnia magna exposed to the same PFAS. The tPODs overlapped concentrations at which other sublethal effects have been reported in fish (available for 10 PFAS). Nonetheless, fathead minnow tPODs were orders of magnitude higher than aqueous PFAS concentrations detected in tributaries of the North American Great Lakes, suggesting a substantial margin of safety. Overall, results broadly support the use of a fathead minnow larval transcriptomics assay to derive screening-level potency estimates for use in ecological risk-based prioritization. Environ Toxicol Chem 2024;00:1-16. © 2024 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Reporting and reproducibility: Proteomics of fish models in environmental toxicology and ecotoxicology

Environmental toxicology and ecotoxicology research efforts are employing proteomics with fish models as New Approach Methodologies, along with in silico, in vitro and other omics techniques to elucidate hazards of toxicants and toxins. We performed a critical review of toxicology studies with fish models using proteomics and reported fundamental parameters across experimental design, sample preparation, mass spectrometry, and bioinformatics of fish, which represent alternative vertebrate models in environmental toxicology, and routinely studied animals in ecotoxicology. We observed inconsistencies in reporting and methodologies among experimental designs, sample preparations, data acquisitions and bioinformatics, which can affect reproducibility of experimental results. We identified a distinct need to develop reporting guidelines for proteomics use in environmental toxicology and ecotoxicology, increased QA/QC throughout studies, and method optimization with an emphasis on reducing inconsistencies among studies. Several recommendations are offered as logical steps to advance development and application of this emerging research area to understand chemical hazards to public health and the environment.

Missing Genomic Resources for the Next Generation of Environmental Risk Assessment

Environmental risk assessment traditionally relies on a wide range of in vivo testing to assess the potential hazards of chemicals in the environment. These tests are often time-consuming and costly and can cause test organisms' suffering. Recent developments of reliable low-cost alternatives, both in vivo- and in silico-based, opened the door to reconsider current toxicity assessment. However, many of these new approach methodologies (NAMs) rely on high-quality annotated genomes for surrogate species of regulatory risk assessment. Currently, a lack of genomic information slows the process of NAM development. Here, we present a phylogenetically resolved overview of missing genomic resources for surrogate species within a regulatory ecotoxicological risk assessment. We call for an organized and systematic effort within the (regulatory) ecotoxicological community to provide these missing genomic resources. Further, we discuss the potential of a standardized genomic surrogate species landscape to enable a robust and nonanimal-reliant ecotoxicological risk assessment in the systems ecotoxicology era.

Microplastics elicit an immune-agitative state in coral

Microplastic pollution in the ocean is a major problem, as its pervasiveness elicits concerns the health impacts microplastics may have on marine life (such as reef-building corals). As a primary endpoint, the organismal lipidome can define the weakening of fitness and reveal the physiological context of adverse health effects in organisms. To gain insight into the effects of microplastics on coral health, lipid profiling was performed via an untargeted lipidomic approach on the coral Turbinaria mesenterina exposed to ~10 μm polystyrene microparticles for 10 days. Considerable microplastic accumulation and obvious effects relating with immune activation were observed in the coral treated with a near environmentally relevant concentration of microplastics (10 μg/L); however, these effects were not evident in the high level (100 μg/L) treatment group. In particular, increased levels of membrane lipids with 20:4 and 22:6 fatty acid chains reallocated from the triacylglycerol pool were observed in coral host cells and symbiotic algae, respectively, which could upregulate immune activity and realign symbiotic communication in coral. High levels of polyunsaturation can sensitize the coral cell membrane to lipid peroxidation and increase cell death, which is of greater concern; additionally, the photoprotective capacity of symbiotic algae was compromised. As a result, coral physiological functions were altered. These results show that, realistic levels of microplastic pollution can affect coral health and should be a concern.

Face mask derived micro(nano)plastics and organic compounds potentially induce threat to aquatic ecosystem security revealed by toxicogenomics-based assay

Micro(nano)plastics widely detected in aquatic environments have caused serious threat to water quality security. However, as a potential important source of micro(nano)plastics in surface water during the COVID-19 pandemic, the ecological risks of face mask waste to aquatic environments remain poorly understood. Herein, we comprehensively characterized the micro(nano)plastics and organic compounds released from four daily used face masks in aqueous environments and further evaluated their potential impacts on aquatic ecosystem safety by quantitative genotoxicity assay. Results from spectroscopy and high-resolution mass spectrum showed that plastic microfibers/particles (∼11%-83%) and leachable organic compounds (∼15%-87%) were dominantly emitted pollutants, which were significantly higher than nanoplastics (< ∼5%) based on mass of carbon. Additionally, a toxicogenomics approach using green fluorescence protein-fused whole-cell array revealed that membrane stress was the primary response upon the exposure to micro(nano)plastics, whereas the emitted organic chemicals were mainly responsible for DNA damage involving most of the DNA repair pathways (e.g., base/nucleotide excision repair, mismatch repair, double-strand break repair), implying their severe threat to membrane structure and DNA replication of microorganisms. Therefore, the persistent release of discarded face masks derived pollutants might exacerbate water quality and even adversely affect aquatic microbial functions. These findings would contribute to unraveling the potential effects of face mask waste on aquatic ecosystem security and highlight the necessity for more developed management regulations in face mask disposal.

Genes-to-Pathways Species Conservation Analysis: Enabling the Exploration of Conservation of Biological Pathways and Processes Across Species

The last two decades have witnessed a strong momentum toward integration of cell-based and computational approaches in safety assessments. This is fueling a global regulatory paradigm shift toward reduction and replacement of the use of animals in toxicity tests while promoting the use of new approach methodologies. The understanding of conservation of molecular targets and pathways provides an opportunity to extrapolate effects across species and ultimately to determine the taxonomic applicability domain of assays and biological effects. Despite the wealth of genome-linked data available, there is a compelling need for improved accessibility, while ensuring that it reflects the underpinning biology. We present the novel pipeline Genes-to-Pathways Species Conservation Analysis (G2P-SCAN) to further support understanding on cross-species extrapolation of biological processes. This R package extracts, synthetizes, and structures the data available from different databases, that is, gene orthologs, protein families, entities, and reactions, linked to human genes and respective pathways across six relevant model species. The use of G2P-SCAN enables the overall analysis of orthology and functional families to substantiate the identification of conservation and susceptibility at the pathway level. In the present study we discuss five case studies, demonstrating the validity of the developed pipeline and its potential use as species extrapolation support. We foresee this pipeline will provide valuable biological insights and create space for the use of mechanistically based data to inform potential species susceptibility for research and safety decision purposes. Environ Toxicol Chem 2023;42:1152-1166. © 2023 UNILEVER GLOBAL IP LTD. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Detection of Salmonella dublin using the vitellogenin 2 promoter of Daphnia magna

Salmonella is a well-known bacterium that causes waterborne diseases in humans and primates. The need for test models to detect such pathogens and study the responses of such organisms to induced toxic environments is vital. Daphnia magna has been ubiquitously used in aquatic life monitoring for decades because of outstanding properties, such as facile cultivation, short lifespan, and high reproductive capacity. In this study, the proteomic response of D. magna exposed to four Salmonella strains (Salmonella dublin, Salmonella enteritidis, Salmonella enterica, and Salmonella typhimurium) was characterized. As indicated by two-dimensional gel electrophoresis, vitellogenin fused with superoxide dismutase was completely suppressed under exposure to S. dublin. Thus, we evaluated the feasibility of using the vitellogenin 2 gene as a biomarker for S. dublin detection, particularly in providing rapid, visual detection through fluorescent signals. Accordingly, the applicability of the HeLa cells transfected with pBABE-Vtg2B-H2B-GFP as a biomarker for the detection of S. dublin was evaluated, and it was confirmed that the fluorescence signal decreased only when S. dublin was treated. Therefore, such HeLa cells can be utilized as a novel biomarker for detecting S. dublin.

Gene expression and biochemical patterns in the digestive gland of the mussel Mytilus galloprovincialis (Lamarck, 1819) exposed to 17α-ethinylestradiol

Contaminants of emerging concern (CECs) are a class of chemicals that can spread throughout the environment and may cause adverse biological and ecological effects. While there are many different classes of CECs, one of the most well documented in the aquatic environment are pharmaceutical drugs, such as natural and synthetic estrogens. In particular, the widespread presence of the synthetic estrogen 17 α-Ethinylestradiol (EE2) in water may lead to bioaccumulation in sediment and biota. EE2 is the primary component in contraceptive pills, and is a derivative of the natural hormone estradiol (E2). In this study, the mussel Mytilus galloprovincialis was exposed to EE2 in a semi-static and time-dependent experiment, for a total exposure period of 28 days. Biochemical and transcriptomics analyses were performed on mussel digestive glands after exposure for 14 (T14) and 28 (T28) days. Metabolic and DNA impairments, as well as activation of antioxidant and biotransformation enzymes activation, were detected in T28 exposed mussels. RNA-Seq analysis showed significant differential expression of 160 (T14 compared to controls), 33 (T28 compared to controls) and 79 (T14 compared to T28) genes. Signs of stress after EE2 treatment included up-regulation of gene/proteins involved with immune function, lipid transport, and metabolic and antibacterial properties. This study elucidates the underlying mechanisms of EE2 in a filter feeding organisms to elucidate the effects of this human pharmaceutical on aquatic biota.

Pilot testing and optimization of a larval fathead minnow high throughput transcriptomics assay

Concentrations at which global gene expression profiles in cells or animals exposed to a test substance start to differ significantly from those of controls have been proposed as an alternative point of departure for use in screening level hazard assessment. The present study describes pilot testing of a high throughput compatible transcriptomics assay with larval fathead minnows. One day post hatch fathead minnows were exposed to eleven different concentrations of three metals, three selective serotonin reuptake inhibitors, and four neonicotinoid-like compounds for 24 h and concentration response modeling was applied to whole body gene expression data. Transcriptomics-based points of departure (tPODs) were consistently lower than effect concentrations reported in apical endpoint studies in fish. However, larval fathead minnow-based tPODs were not always lower than concentrations reported to elicit apical toxicity in other aquatic organisms like crustaceans or insects. Random in silico subsampling of data from the pilot assays was used to evaluate various assay design and acceptance considerations such as transcriptome coverage, number of replicate individuals to sequence per treatment, and minimum number of differentially expressed genes to produce a reliable tPOD estimate. Results showed a strong association between the total number of genes for which a concentration response relationship could be derived and the overall variability in the resulting tPOD estimates. We conclude that, for our current assay design and analysis pipeline, tPODs based on fewer than 15 differentially expressed genes are likely to be unreliable for screening and that interindividual variability in gene expression profiles appears to be a more significant driver of tPOD variability than sample size alone. Results represent initial steps toward developing high throughput transcriptomics assays for use in ecological hazard screening.

Metabolomics: A New Approach in the Evaluation of Effects in Human Beings and Wildlife Associated with Environmental Exposition to POPs

Human beings and wild organisms are exposed daily to a broad range of environmental stressors. Among them are the persistent organic pollutants that can trigger adverse effects on these organisms due to their toxicity properties. There is evidence that metabolomics can be used to identify biomarkers of effect by altering the profiles of endogenous metabolites in biological fluids or tissues. This approach is relatively new and has been used in vitro studies mainly. Therefore, this review addresses those that have used metabolomics as a key tool to identify metabolites associated with environmental exposure to POPs in wildlife and human populations and that can be used as biomarkers of effect. The published results suggest that the metabolic pathways that produce energy, fatty acids, and amino acids are commonly affected by POPs. Furthermore, these pathways can be promoters of additional effects. In the future, metabolomics combined with other omics will improve understanding of the origin, development, and progression of the effects caused by environmental exposure.

Potential neurotoxicity, immunotoxicity, and carcinogenicity induced by metribuzin and tebuconazole exposure in earthworms (Eisenia fetida) revealed by transcriptome analysis

Metribuzin and tebuconazole have been widely used in agriculture for several decades. Apart from endocrine disruption, little is known about their toxicological effects on organisms without thyroid organs, at the transcriptional level. To explore this toxicity, model earthworm species Eisenia fetida, hatched from the same cocoon and cultured under identical environmental conditions, were independently exposed to the two chemicals at non-lethal concentrations in OECD artificial soil for 48 h after exposure. RNA-seq technology was used to analyze and compare the gene expression profiles of earthworms exposed to metribuzin and tebuconazole. The functions of differentially expressed genes and their standard response patterns of upregulated and downregulated expression for both pesticides were verified. The findings demonstrated that metribuzin and tebuconazole are both potentially toxic to earthworms. Toxicological effects mainly involved the nervous system, immune system, and tumors, at the transcriptional level, as well as the induction of cytochrome P450-dependent detoxification and oxidative stress. In addition, the mitogen-activated protein kinase kinase kinase gene was identified as a biomarker, and the mitogen-activated protein kinase signaling pathway was verified to be a part of the adverse outcome pathway of metribuzin and tebuconazole and their structural analogs.

Sea Anemones Responding to Sex Hormones, Oxybenzone, and Benzyl Butyl Phthalate: Transcriptional Profiling and in Silico Modelling Provide Clues to Decipher Endocrine Disruption in Cnidarians

Endocrine disruption is suspected in cnidarians, but questions remain how occurs. Steroid sex hormones are detected in corals and sea anemones even though these animals do not have estrogen receptors and their repertoire of steroidogenic enzymes appears to be incomplete. Pathways associated with sex hormone biosynthesis and sterol signaling are an understudied area in cnidarian biology. The objective of this study was to identify a suite of genes that can be linked to exposure of endocrine disruptors. Exaiptasia diaphana were exposed to nominal 20ppb concentrations of estradiol (E2), testosterone (T), cholesterol, oxybenzone (BP-3), or benzyl butyl phthalate (BBP) for 4 h. Eleven genes of interest (GOIs) were chosen from a previously generated EST library. The GOIs are 17β-hydroxysteroid dehydrogenases type 14 (17β HSD14) and type 12 (17β HSD12), Niemann-Pick C type 2 (NPC2), Equistatin (EI), Complement component C3 (C3), Cathepsin L (CTSL), Patched domain-containing protein 3 (PTCH3), Smoothened (SMO), Desert Hedgehog (DHH), Zinc finger protein GLI2 (GLI2), and Vitellogenin (VTG). These GOIs were selected because of functional associations with steroid hormone biosynthesis; cholesterol binding/transport; immunity; phagocytosis; or Hedgehog signaling. Quantitative Real-Time PCR quantified expression of GOIs. In silico modelling utilized protein structures from Protein Data Bank as well as creating protein structures with SWISS-MODEL. Results show transcription of steroidogenic enzymes, and cholesterol binding/transport proteins have similar transcription profiles for E2, T, and cholesterol treatments, but different profiles when BP-3 or BBP is present. C3 expression can differentiate between exposures to BP-3 versus BBP as well as exposure to cholesterol versus sex hormones. In silico modelling revealed all ligands (E2, T, cholesterol, BBP, and BP-3) have favorable binding affinities with 17β HSD14, 17β HSD12, NPC2, SMO, and PTCH proteins. VTG expression was down-regulated in the sterol treatments but up-regulated in BP-3 and BBP treatments. In summary, these eleven GOIs collectively generate unique transcriptional profiles capable of discriminating between the five chemical exposures used in this investigation. This suite of GOIs are candidate biomarkers for detecting transcriptional changes in steroidogenesis, gametogenesis, sterol transport, and Hedgehog signaling. Detection of disruptions in these pathways offers new insight into endocrine disruption in cnidarians.

De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins

The aim of this study was to generate and analyze the atlas of the loggerhead turtle blood transcriptome by RNA-seq, as well as identify and characterize thioredoxin (Tnxs) and peroxiredoxin (Prdxs) antioxidant enzymes of the greatest interest in the control of peroxide levels and other biological functions. The transcriptome of loggerhead turtle was sequenced using the Illumina Hiseq 2000 platform and de novo assembly was performed using the Trinity pipeline. The assembly comprised 515,597 contigs with an N50 of 2,631 bp. Contigs were analyzed with CD-Hit obtaining 374,545 unigenes, of which 165,676 had ORFs encoding putative proteins longer than 100 amino acids. A total of 52,147 (31.5%) of these transcripts had significant homology matches in at least one of the five databases used. From the enrichment of GO terms, 180 proteins with antioxidant activity were identified, among these 28 Prdxs and 50 putative Tnxs. The putative proteins of loggerhead turtles encoded by the genes Prdx1, Prdx3, Prdx5, Prdx6, Txn and Txnip were predicted and characterized in silico. When comparing Prdxs and Txns of loggerhead turtle with homologous human proteins, they showed 18 (9%), 52 (18%) 94 (43%), 36 (16%), 35 (33%) and 74 (19%) amino acid mutations respectively. However, they showed high conservation in active sites and structural motifs (98%), with few specific modifications. Of these, Prdx1, Prdx3, Prdx5, Prdx6, Txn and Txnip presented 0, 25, 18, three, six and two deleterious changes. This study provides a high quality blood transcriptome and functional annotation of loggerhead sea turtles.

Gene Expression Changes in Epinephelus marginatus (Teleostei, Serranidae) Liver as Molecular Biomarker of Iron Ore Contamination

The aim of this study was to determine selected molecular biomarkers of iron ore contamination in Epinephelus marginatus. Molecular biomarkers were tested by checking the relative expression of genes involved in oxidative stress, trace element regulation, and cellular damage, by RT-qPCR. Iron ore exposure caused the downregulation of ferroportin (FP) gene expression and a significant upregulation in superoxide dismutase (SOD) and cytochrome P450 1A (CYP1A) genes. Iron ore affects gene expression in E. marginatus liver, indicating that it can potentially induce toxic effects in fish. Moreover, this altered gene expression pattern may be applied in monitoring iron ore contamination in marine environments.

Susceptibility of the Non-Targeted Crustacean Eurytemora affinis to the Endocrine Disruptor Tebufenozide: A Transcriptomic Approach

Copepods are zooplanktonic crustaceans ubiquitously widespread in aquatic systems. Although they are not the target, copepods are exposed to a wide variety of pollutants such as insect growth regulators (IGRs). The aim of this study was to investigate the molecular response of a non-targeted organism, the copepod Eurytemora affinis, to an IGR. Adult males and females were exposed to two sub-lethal concentrations of tebufenozide (TEB). Our results indicate a sex-specific response with a higher sensitivity in males, potentially due to a differential activation of stress response pathways. In both sexes, exposure to TEB triggered similar pathways to those found in targeted species by modulating the transcription of early and late ecdysone responsive genes. Among them were genes involved in cuticle metabolism, muscle contraction, neurotransmission, and gametogenesis, whose mis-regulation could lead to moult, locomotor, and reproductive impairments. Furthermore, genes involved in epigenetic processes were found in both sexes, which highlights the potential impact of exposure to TEB on future generations. This work allows identification of (i) potential biomarkers of ecdysone agonists and (ii) further assessment of putative physiological responses to characterize the effects of TEB at higher biological levels. The present study reinforces the suitability of using E. affinis as an ecotoxicological model.

Acquiring an evolutionary perspective in marine ecotoxicology to tackle emerging concerns in a rapidly changing ocean

Tens of thousands of anthropogenic chemicals and wastes enter the marine environment each year as a consequence of the ever-increasing anthropogenic activities and demographic growth of the human population, which is majorly concentrated along coastal areas. Marine ecotoxicology has had a crucial role in helping shed light on the fate of chemicals in the environment, and improving our understanding of how they can affect natural ecosystems. However, chemical contamination is not occurring in isolation, but rather against a rapidly changing environmental horizon. Most environmental studies have been focusing on short-term within-generation responses of single life stages of single species to single stressors. As a consequence, one-dimensional ecotoxicology cannot enable us to appreciate the degree and magnitude of future impacts of chemicals on marine ecosystems. Current approaches that lack an evolutionary perspective within the context of ongoing and future local and global stressors will likely lead us to under or over estimations of the impacts that chemicals will exert on marine organisms. It is therefore urgent to define whether marine organisms can acclimate, i.e. adjust their phenotypes through transgenerational plasticity, or rapidly adapt, i.e. realign the population phenotypic performances to maximize fitness, to the new chemical environment within a selective horizon defined by global changes. To foster a significant advancement in this research area, we review briefly the history of ecotoxicology, synthesis our current understanding of the fate and impact of contaminants under global changes, and critically discuss the benefits and challenges of integrative approaches toward developing an evolutionary perspective in marine ecotoxicology: particularly through a multigenerational approach. The inclusion of multigenerational studies in Ecological Risk Assessment framework (ERA) would provide significant and more accurately information to help predict the risks of pollution in a rapidly changing ocean.

The Era of Nanomaterials: A Safe Solution or a Risk for Marine Environmental Pollution?

In recent years, the application of engineered nanomaterials (ENMs) in environmental remediation gained increasing attention. Due to their large surface area and high reactivity, ENMs offer the potential for the efficient removal of pollutants from environmental matrices with better performances compared to conventional techniques. However, their fate and safety upon environmental application, which can be associated with their release into the environment, are largely unknown. It is essential to develop systems that can predict ENM interactions with biological systems, their overall environmental and human health impact. Until now, Life-Cycle Assessment (LCA) tools have been employed to investigate ENMs potential environmental impact, from raw material production, design and to their final disposal. However, LCA studies focused on the environmental impact of the production phase lacking information on their environmental impact deriving from in situ employment. A recently developed eco-design framework aimed to fill this knowledge gap by using ecotoxicological tools that allow the assessment of potential hazards posed by ENMs to natural ecosystems and wildlife. In the present review, we illustrate the development of the eco-design framework and review the application of ecotoxicology as a valuable strategy to develop ecosafe ENMs for environmental remediation. Furthermore, we critically describe the currently available ENMs for marine environment remediation and discuss their pros and cons in safe environmental applications together with the need to balance benefits and risks promoting an environmentally safe nanoremediation (ecosafe) for the future.

Ecotoxicology of persistent organic pollutants in birds

Considering the explosive growth of the list of persistent organic pollutants (POPs), the scientific community is combatting increasing challenges to protect humans and wildlife from the potentially negative consequences of POPs. Herein, we characterize the main aspects and progress in the ecotoxicology of POPs in avian species since 2000. The majority of previous efforts has revealed the global occurrence of high levels of various POPs in birds. Laboratory research and epidemiological studies imply that POPs exert a broad-spectrum of side-effects on birds by interfering with their endocrine, immune and neural system, reproduction, and development, and growth. However, inconsistent results suggest that the potential effects of POP exposure on the physiological parameters in birds are multifactorial, involving a multitude of biological processes, species-specific differences, gender, age and types of compounds. Great progress has been achieved in identifying the species-specific sensitivity to dioxin-like compounds, which is attributed to different amino acid residues in the ligand-binding domain of the aryl hydrocarbon receptor. Besides the conventional concentration additivity, several studies have suggested that different classes of POPs possibly act synergistically or antagonistically based on their concentration. However, ecotoxicology information is still recorded in a scattered and inadequate manner, including lack of enough avian species, limited number of POPs investigated, and insufficient geographical representation, and thus our understanding of the effects of POPs on birds remains rudimentary, although mechanistic understanding of their mode of action is progressing. Particularly, research on what happens to wild bird populations and their ecosystems under POP stress is still unavailable. Thus, our aim is to predict and trace the effects POPs at different biological organization levels, especially from the molecular, cellular and individual levels to the population, community and ecosystem levels because of the limited and scattered information, as mentioned above.

Cross-species extrapolation of chemical sensitivity

Ecosystems are usually populated by many species. Each of these species carries the potential to show a different sensitivity towards all of the numerous chemical compounds that can be present in their environment. Since experimentally testing all possible species-chemical combinations is impossible, the ecological risk assessment of chemicals largely depends on cross-species extrapolation approaches. This review overviews currently existing cross-species extrapolation methodologies, and discusses i) how species sensitivity could be described, ii) which predictors might be useful for explaining differences in species sensitivity, and iii) which statistical considerations are important. We argue that risk assessment can benefit most from modelling approaches when sensitivity is described based on ecologically relevant and robust effects. Additionally, specific attention should be paid to heterogeneity of the training data (e.g. exposure duration, pH, temperature), since this strongly influences the reliability of the resulting models. Regarding which predictors are useful for explaining differences in species sensitivity, we review interspecies-correlation, relatedness-based, traits-based, and genomic-based extrapolation methods, describing the amount of mechanistic information the predictors contain, the amount of input data the models require, and the extent to which the different methods provide protection for ecological entities. We develop a conceptual framework, incorporating the strengths of each of the methods described. Finally, the discussion of statistical considerations reveals that regardless of the method used, statistically significant models can be found, although the usefulness, applicability, and understanding of these models varies considerably. We therefore recommend publication of scientific code along with scientific studies to simultaneously clarify modelling choices and enable elaboration on existing work. In general, this review specifies the data requirements of different cross-species extrapolation methods, aiming to make regulators and publishers more aware that access to raw- and meta-data needs to be improved to make future cross-species extrapolation efforts successful, enabling their integration into the regulatory environment.

Differential gene expression profile of male and female copepods in response to cadmium exposure

In this study, the whole transcriptome and sex-specific differential gene expression of the copepod Pseudodiaptomus annandalei exposed to cadmium (Cd) were investigated. P. annandalei were exposed to 40 μg/L Cd from the naupliar stage to male and female adults. High-throughput transcriptome sequencing (RNA-seq) was performed with copepod samples using an Illumina Hiseq™ 2000 platform. TransDecoder analysis found 32,625 putative open reading frame contigs. At p-values of <0.001, a total of 4756 differentially expressed genes (DEGs) (2216 up-regulated and 2540 down-regulated genes) were found in male copepods. Whereas a total of 2879 DEGs (2007 up-regulated and 872 down-regulated genes) were found in female copepods. A few selected cellular stress response genes, involved in xenobiotic metabolism, energy metabolism, growth, and development as a result of Cd exposure in the copepods were discussed. The study showed that most of these processes were changed in a sex-specific manner, accounting for the different sensitivities of male and female copepods. Results suggest and reinforce that sex is an important factor to be considered in ecotoxicogenomics.

Abiotic and past climatic conditions drive protein abundance variation among natural populations of the caddisfly Crunoecia irrorata

Deducing impacts of environmental change on species and the populations they form in nature is an important goal in contemporary ecology. Achieving this goal is hampered by our limited understanding of the influence of naturally occurring environmental variation on the molecular systems of ecologically relevant species, as the pathways underlying fitness-affecting plastic responses have primarily been studied in model organisms and under controlled laboratory conditions. Here, to test the hypothesis that proteome variation systematically relates to variation in abiotic conditions, we establish such relationships by profiling the proteomes of 24 natural populations of the spring-dwelling caddisfly Crunoecia irrorata. We identified protein networks whose abundances correlated with environmental (abiotic) gradients such as in situ pH, oxygen- and nitrate concentrations but also climatic data such as past thermal minima and temperature seasonality. Our analyses suggest that variations in abiotic conditions induce discrete proteome responses such as the differential abundance of proteins associated with cytoskeletal function, heat-shock proteins and proteins related to post-translational modification. Identifying these drivers of proteome divergence characterizes molecular "noise", and positions it as a background against which molecular signatures of species' adaptive responses to stressful conditions can be identified.

Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure

BACKGROUND

Despite being one of the primary mechanisms of gene expression regulation in eukaryotes, alternative splicing is often overlooked in ecotoxicogenomic studies. The process of alternative splicing facilitates the production of multiple mRNA isoforms from a single gene thereby greatly increasing the diversity of the transcriptome and proteome. This process can be important in enabling the organism to cope with stressful conditions. Accurate identification of splice sites using RNA sequencing requires alignment to independent exonic positions within the genome, presenting bioinformatic challenges, particularly when using short read data. Although technological advances allow for the detection of splicing patterns on a genome-wide scale, very little is known about the extent of intraspecies variation in splicing patterns, particularly in response to environmental stressors. In this study, we used RNA-sequencing to study the molecular responses to acute copper exposure in three lineages of Daphnia pulex by focusing on the contribution of alternative splicing in addition to gene expression responses.

RESULTS

By comparing the overall gene expression and splicing patterns among all 15 copper-exposed samples and 6 controls, we identified 588 differentially expressed (DE) genes and 16 differentially spliced (DS) genes. Most of the DS genes (13) were not found to be DE, suggesting unique transcriptional regulation in response to copper that went unnoticed with conventional DE analysis. To understand the influence of genetic background on gene expression and alternative splicing responses to Cu, each of the three lineages was analyzed separately. In contrast to the overall analysis, each lineage had a higher proportion of unique DS genes than DE genes suggesting that genetic background has a larger influence on DS than on DE. Gene Ontology analysis revealed that some pathways involved in stress response were jointly regulated by DS and DE genes while others were regulated by only transcription or only splicing.

CONCLUSIONS

Our findings suggest an important role for alternative splicing in shaping transcriptome diversity in response to metal exposure in Daphnia, highlighting the importance of integrating splicing analyses with gene expression surveys to characterize molecular pathways in evolutionary and environmental studies.

Environmental lipidomics: understanding the response of organisms and ecosystems to a changing world

BACKGROUND

Understanding the interaction between organisms and the environment is important for predicting and mitigating the effects of global phenomena such as climate change, and the fate, transport, and health effects of anthropogenic pollutants. By understanding organism and ecosystem responses to environmental stressors at the molecular level, mechanisms of toxicity and adaptation can be determined. This information has important implications in human and environmental health, engineering biotechnologies, and understanding the interaction between anthropogenic induced changes and the biosphere. One class of molecules with unique promise for environmental science are lipids; lipids are highly abundant and ubiquitous across nearly all organisms, and lipid profiles often change drastically in response to external stimuli. These changes allow organisms to maintain essential biological functions, for example, membrane fluidity, as they adapt to a changing climate and chemical environment. Lipidomics can help scientists understand the historical and present biofeedback processes in climate change and the biogeochemical processes affecting nutrient cycles. Lipids can also be used to understand how ecosystems respond to historical environmental changes with lipid signatures dating back to hundreds of millions of years, which can help predict similar changes in the future. In addition, lipids are direct targets of environmental stressors, for example, lipids are easily prone to oxidative damage, which occurs during exposure to most toxins.

AIM OF REVIEW

This is the first review to summarize the current efforts to comprehensively measure lipids to better understand the interaction between organisms and their environment. This review focuses on lipidomic applications in the arenas of environmental toxicology and exposure assessment, xenobiotic exposures and health (e.g., obesity), global climate change, and nutrient cycles. Moreover, this review summarizes the use of and the potential for lipidomics in engineering biotechnologies for the remediation of persistent compounds and biofuel production.

KEY SCIENTIFIC CONCEPT

With the preservation of certain lipids across millions of years and our ever-increasing understanding of their diverse biological roles, lipidomic-based approaches provide a unique utility to increase our understanding of the contemporary and historical interactions between organisms, ecosystems, and anthropogenically-induced environmental changes.

Inorganic Mercury and Methyl-Mercury Uptake and Effects in the Aquatic Plant Elodea nuttallii: A Review of Multi-Omic Data in the Field and in Controlled Conditions

(1) Background: Mercury is a threat for the aquatic environment. Nonetheless, the entrance of Hg into food webs is not fully understood. Macrophytes are both central for Hg entry in food webs and are seen as good candidates for biomonitoring and bioremediation; (2) Methods: We review the knowledge gained on the uptake and effects of inorganic Hg (IHg) and methyl-Hg (MMHg) in the macrophyte Elodea nuttallii found in temperate freshwaters; (3) Results: E. nuttallii bioaccumulates IHg and MMHg, but IHg shows a higher affinity to cell walls. At the individual level, IHg reduced chlorophyll, while MMHg increased anthocyanin. Transcriptomics and metabolomics in shoots revealed that MMHg regulated a higher number of genes than IHg. Proteomics and metabolomics in cytosol revealed that IHg had more effect than MMHg; (4) Conclusions: MMHg and IHg show different cellular toxicity pathways. MMHg’s main impact appears on the non-soluble compartment, while IHg’s main impact happens on the soluble compartment. This is congruent with the higher affinity of IHg with dissolved OM (DOM) or cell walls. E. nuttallii is promising for biomonitoring, as its uptake and molecular responses reflect exposure to IHg and MMHg. More generally, multi-omics approaches identify cellular toxicity pathways and the early impact of sublethal pollution.

A sub-individual multilevel approach for an integrative assessment of CuO nanoparticle effects on Corbicula fluminea

Because they are widely used, copper oxide nanoparticles (CuO NPs) are likely to enter the aquatic environment and then reach the sediment. We have examined the effect of CuO NPs in the freshwater endobenthic bivalve Corbicula fluminea. Some previous studies have investigated effects at biochemical and physiological levels, but molecular endpoints are still poorly studied despite they are sensitive in early detection of NPs effect. In the present study, we have investigated short-term effects (96 h) of CuO NP (12, 30 nm; 0, 20 and 100 μg/L) using molecular endpoints as well as more conventional biochemical and physiological markers. The expression of antioxidant (CuZnSOD, MnSOD, Cat, Se-GPx, Trxr) and antitoxic (GST-Pi, HSP70, MT, Pgp, MRP1) related genes was measured at the mRNA level while antioxidant (SOD, TAC) and antitoxic (GST, ACP) defenses, energetic reserves and metabolism (ETS, Tri, LDH), and cellular damages (LPO) were assessed using a biochemical approach. The filtration rate measured at 96 h provided information at the physiological scale. Gene expression and filtration rate were responsive to CuO NPs but the effects differed according to the NP size. The results suggest that defense mechanisms may have been set up following 30 nm-NP exposure. The response to 12 nm-NP was lower but still showed that exposure to 12 nm-NP led to activation of cellular elimination mechanisms. The lowering of the filtration rate may have protected the organisms from the contamination. However, this raised the question of further repercussions on organism biology. Together, the results (i) indicate that CuO NP may exert effects at different levels even after a short-term exposure and (ii) point out the precocity of molecular response.

Ecotoxicity of nanomaterials in amphibians: A critical review

Nanomaterials (NMs) have been used in a growing number of commercial products, and their rapid expansion could lead to their release into the aquatic environments. However, there is limited knowledge about the impact of NMs in the biota, especially the amphibians. The present study revised the historical use of amphibian species as a model system for nanoecotoxicological studies and summarized the data available in the scientific literature about the genotoxic, mutagenic, histopathological, embryotoxic and reproductive effects of NMs in different groups of amphibians. The interaction, bioaccumulation, mode of action (MoA) and ecotoxicity of NMs on amphibians were also revised. The nanoecotoxicological studies were conducted with 11 amphibian species, being eight species of the order Anura and three species of the order Caudata. Xenopus laevis was the most studied species. The studies were conducted mainly with inorganic NMs (72%) compared to organic ones. The nanoecotoxicity depends on NM behavior and transformation in the environment, as well as the developmental stages of amphibians. The known effects of NMs in amphibians were mainly reported with reactive oxygen species (ROS) production, oxidative stress, and genotoxic effects. Results emphasize the need for further studies testing the ecotoxicity of different NMs, concentrations and exposure periods at environmentally relevant approaches. Furthermore, standard protocols for nanoecotoxicological tests using amphibians are required. Revised data showed that amphibians are suitable organisms to assess the environmental impact of NMs and indicated significant research gaps concerning the ecotoxicity of NMs on freshwater ecosystems and recommendations for future researches.

Season influences the transcriptomic effects of dietary exposure to PVP/PEI coated Ag nanoparticles on mussels Mytilus galloprovincialis

Toxicity of AgNPs has been widely studied in waterborne exposed aquatic organisms. However, toxic effects caused by AgNPs ingested through the diet and depending on the season are still unexplored. The first cell response after exposure to xenobiotics occurs at gene transcription level. Thus, the aim of this study was to assess transcription level effects in the digestive gland of female mussels after dietary exposure to AgNPs both in autumn and in spring. Mussels were fed daily for 21 days with Isochrysis galbana microalgae previously exposed for 24 h to a dose close to environmentally relevant concentrations of 1 μg Ag/L PVP/PEI coated 5 nm AgNPs (in spring) and to a higher dose of 10 μg Ag/L of the same AgNPs both in autumn and in spring. After 1 and 21 days, mussels RNA was hybridized in a custom microarray containing 7806 annotated genes. Mussels were more responsive to the high dose compared to the low dose of AgNPs and a higher number of probes were altered in autumn than in spring. In both seasons, significantly regulated genes were involved in the cytoskeleton and lipid transport and metabolism COG categories, among others, while genes involved in carbohydrate transport and metabolism were specifically altered in autumn. Overall, transcription patterns were differently altered depending on the exposure time and season, indicating that season should be considered in ecotoxicological studies of metal nanoparticles in mussels.

Map and model-moving from observation to prediction in toxicogenomics

BACKGROUND

Chemicals induce compound-specific changes in the transcriptome of an organism (toxicogenomic fingerprints). This provides potential insights about the cellular or physiological responses to chemical exposure and adverse effects, which is needed in assessment of chemical-related hazards or environmental health. In this regard, comparison or connection of different experiments becomes important when interpreting toxicogenomic experiments. Owing to lack of capturing response dynamics, comparability is often limited. In this study, we aim to overcome these constraints.

RESULTS

We developed an experimental design and bioinformatic analysis strategy to infer time- and concentration-resolved toxicogenomic fingerprints. We projected the fingerprints to a universal coordinate system (toxicogenomic universe) based on a self-organizing map of toxicogenomic data retrieved from public databases. Genes clustering together in regions of the map indicate functional relation due to co-expression under chemical exposure. To allow for quantitative description and extrapolation of the gene expression responses we developed a time- and concentration-dependent regression model. We applied the analysis strategy in a microarray case study exposing zebrafish embryos to 3 selected model compounds including 2 cyclooxygenase inhibitors. After identification of key responses in the transcriptome we could compare and characterize their association to developmental, toxicokinetic, and toxicodynamic processes using the parameter estimates for affected gene clusters. Furthermore, we discuss an association of toxicogenomic effects with measured internal concentrations.

CONCLUSIONS

The design and analysis pipeline described here could serve as a blueprint for creating comparable toxicogenomic fingerprints of chemicals. It integrates, aggregates, and models time- and concentration-resolved toxicogenomic data.

Investigating a transcriptomic approach on marine mussel hemocytes exposed to carbon nanofibers: An in vitro/in vivo comparison

Manufactured nanomaterials are an ideal test case of the precautionary principle due to their novelty and potential environmental release. In the context of regulation, it is difficult to implement for manufactured nanomaterials as current testing paradigms identify risk late into the production process, slowing down innovation and increasing costs. One proposed concept, namely safe(r)-by-design, is to incorporate risk and hazard assessment into the design process of novel manufactured nanomaterials by identifying risks early. When investigating the manufacturing process for nanomaterials, differences between products will be very similar along key physicochemical properties and biological endpoints at the individual level may not be sensitive enough to detect differences whereas lower levels of biological organization may be able to detect these variations. In this sense, the present study used a transcriptomic approach on Mytilus edulis hemocytes following an in vitro and in vivo exposure to three carbon nanofibers created using different production methods. Integrative modeling was used to identify if gene expression could be in linked to physicochemical features. The results suggested that gene expression was more strongly associated with the carbon structure of the nanofibers than chemical purity. With respect to the in vitro/in vivo relationship, results suggested an inverse relationship in how the physicochemical impact gene expression.

Towards the development of a high throughput screening approach for Mytilus edulis hemocytes: A case study on silicon-based nanomaterials

To have an understanding of potential mechanistic effects, sublethal endpoints able to discriminate between nanomaterials with similar physical and chemical features need to be used. In this sense, quantitative PCR was used to measure a battery of genes linked to a wide array of different cellular processes. Gene expression was measured in Mytilus edulis hemocytes following an in vitro and in vivo exposure to pure silicon (40 nm) and carbon-coated silicon (40 and 75 nm) after 24 h. Partial least squares discriminant analysis and correlation analysis were used to develop an integrative model, describing the relationship between genes, to identify which genes were important in describing responses to engineered nanomaterial exposure. The results suggested that some discriminations could be made based on the presence of a carbon coating or the alteration of size which could inform industrial patterns on ways to reduce the ecotoxicological impact of their product. The results also indicate that HTS on Mytilus hemocytes may be integrated into a safer-by-design approach but additional characterization of nanomaterial behavior in media is required to determine if it is a suitable alternative to in vivo testing.

Molecular Effects of Inorganic and Methyl Mercury in Aquatic Primary Producers: Comparing Impact to A Macrophyte and A Green Microalga in Controlled Conditions

Mercury (Hg) remains hazardous in aquatic environments, because of its toxicity and high biomagnification in food webs. In phytoplankton and macrophytes, Hg compounds at high concentration have been reported to affect the growth, photosynthesis, and nutrient metabolism, as well as to induce oxidative stress and damage. Here, we reviewed the recent knowledge gained on cellular toxicity of inorganic and methyl Hg (IHg; MeHg) in aquatic primary producers at more relevant environmental concentrations, with a particular focus on omics data. In addition, we compared a case study conducted with transcriptomic on the green microalga Chlamydomonas reinhardtii and the macrophyte Elodea nuttallii. At lower concentrations, IHg and MeHg influenced similar gene categories, including energy metabolism, cell structure, and nutrition. In addition, genes involved in the cell motility in the microalgae, and in hormone metabolism in the macrophyte were regulated. At equivalent intracellular concentration, MeHg regulated more genes than IHg supporting a higher molecular impact of the former. At the organism level in C. reinhardtii, MeHg increased reactive oxygen species, while both IHg and MeHg increased photosynthesis efficiency, whereas in E. nuttallii MeHg induced anti-oxidant responses and IHg reduced chlorophyll content. Data showed differences, according to species and characteristics of life cycle, in responses at the gene and cellular levels, but evidenced a higher molecular impact of MeHg than IHg and different cellular toxicity pathways in aquatic primary producers.

Biochemical and molecular responses in oysters Crassostrea brasiliana collected from estuarine aquaculture areas in Southern Brazil

Biochemical and molecular responses were evaluated in oysters Crassostrea brasiliana collected from three oyster farms, at Guaratuba Bay, southern Brazil, forming a pollutant gradient: Farm 1 (reference site - farther from the urban area), Farm 2 (intermediate site) and Farm 3 (nearest to the urban area). Oxidative stress markers, DNA damage and transcript levels of CYP2AU1, CYP2-like1, CYP2-like2, SULT-like, GPx-like, SOD-like, CAT-like, GSTmicrosomal-like, GSTomega-like, FABP-like and ALAd-like genes were analyzed in the gills. The levels of polycyclic aromatic hydrocarbons, linear alkylbenzenes and polychlorinated biphenyls were also evaluated in the soft tissues of the oysters and in the sediment of the Farms. Higher GSTomega-like, CYP2AU1 and FABP-like transcript levels, GR and G6PDH activities and lipid peroxidation levels were observed in oysters from Farms 2 and 3, suggesting pollutant effects on oysters. Alterations in oxidative stress markers also suggest a response against a prooxidant condition in C. brasiliana due to pollutant effects.

Copper toxicity and date palm (Phoenix dactylifera) seedling tolerance: Monitoring of related biomarkers

Date palm (Phoenix dactylifera) seeds were exposed to different copper (Cu) solutions to examine plant stress responses. Low Cu concentrations (0.02 and 0.2 mM) caused an increase of seed germination, whereas higher Cu amounts (2 mM) significantly inhibited seed germination, delayed hypocotyl elongation, increased seedling mortality, and reduced the germination index by more than 90%. Metal-related toxicity symptoms appeared after 15 d of 2 mM of Cu exposure. Biochemical activities such as amylase activity and redox balance elements were examined to study the relationship between external Cu amount and internal plant response. The present study showed that amylolytic activity was dose- and time-dependent. Likewise, H₂ O₂ production increased after exposure to Cu, which was correlated with thiobarbituric acid reactive substance (TBARS) accumulation. Furthermore at low Cu concentrations, superoxide dismutase (SOD) and catalase (CAT) activities increased, suggesting that date palm seed stimulated its metal homeostasis networks. However, the highest cupric ion amounts increased cell oxidant accumulation and reduced enzyme production. Gene expression level measures of P. dactylifera phytochelatin synthase (Pdpcs) and P. dactylifera metallothionein (Pdmt) encoding genes have been carried out to investigate the implication of PdPCS and PdMT proteins in Cu homeostasis and/or its sequestration. Phoenix dactylifera metallothionein induction reached a peak after 30 d of exposure to 0.2 mM of Cu. However, it was down-regulated in plants exposed to higher Cu concentrations. In the same conditions, Pdpcs was overexpressed during 1 mo of exposure before it decreased thereafter. These observations provide a new insight into date palm cell response to Cu, a metal that can be toxic but that is also an essential element. Environ Toxicol Chem 2018;37:797-806. © 2017 SETAC.

Phenotypic responses in Caenorhabditis elegans following chronic low-level exposures to inorganic and organic compounds

Responses of organisms to sublethal exposure of environmental stressors can be difficult to detect. We investigated phenotypic changes in the tissue of Caenorhabditis elegans via Raman spectroscopy, as well as survival and reproductive output when exposed to chronic low doses of metals (copper, zinc, or silver), an herbicide (diuron), and a pesticide (imidacloprid). Raman spectroscopy measures changes in phenotype by providing information about the molecular composition and relative abundance of biomolecules. Multivariate analysis was used to evaluate the significance of treatment phenotype segregation plots compared with controls. Dose-dependent responses were observed for copper, zinc, silver, and diuron, whereas imidacloprid exposure resulted in a small response over the tested concentrations. Concentration-dependent shifts in nematode biomolecular phenotype were observed for copper. Despite having a dose-dependent reproductive response, silver, diuron, and imidacloprid produced inconsistent biological phenotype patterns. In contrast, there was a clear stepwise change between low concentrations (0.00625-0.5 mg/L) and higher concentration (1-2 mg/L) of ionic zinc. The findings demonstrate that measuring phenotypic responses via Raman spectroscopy can provide insights into the biomolecular mechanisms of toxicity. Despite the lack of consistency between survival and Raman-measured phenotypic changes, the results support the effectiveness of Raman spectroscopy and multivariate analysis to detect sublethal responses of chemicals in whole organisms and to identify toxic effect thresholds. Environ Toxicol Chem 2018;37:920-930. © 2017 SETAC.

Fishing for contaminants: identification of three mechanism specific transcriptome signatures using Danio rerio embryos

In ecotoxicology, transcriptomics is an effective way to detect gene expression changes in response to environmental pollutants. Such changes can be used to identify contaminants or contaminant classes and can be applied as early warning signals for pollution. To do so, it is important to distinguish contaminant-specific transcriptomic changes from genetic alterations due to general stress. Here we present a first step in the identification of contaminant class-specific transcriptome signatures. Embryos of zebrafish (Danio rerio) were exposed to three substances (methylmercury, chlorpyrifos and Aroclor 1254, each from 24 to 48 hpf exposed) representing sediment typical contaminant classes. We analyzed the altered transcriptome to detect discriminative genes significantly regulated in reaction to the three applied contaminants. By comparison of the results of the three contaminants, we identified transcriptome signatures and biologically important pathways (using Cytoscape/ClueGO software) that react significantly to the contaminant classes. This approach increases the chance of finding genes that play an important role in contaminant class-specific pathways rather than more general processes.

Omics tools: New challenges in aquatic nanotoxicology?

In recent years, the implication of genomics into ecotoxicological studies has been studied closely to allow a better understanding of organism's responses to environmental contaminants including engineering nanomaterials (ENMs). ENMs are increasingly produced for various applications including cosmetics, electronics, sports equipment, biomedicine and agriculture. Because of their small size, ENMs possess chemical or physical characteristics improved compared to the corresponding macro-sized material. As their application expend, the release of manufactured ENMs into the environment is likely to increase and concern over impacts for the aquatic ecosystem is growing. Several studies reported deleterious effect of ENMs to aquatic organisms, but there is little information about the molecular mechanisms of toxicity. The development of ecotoxicogenomic approaches will improve the characterization of cellular and molecular modes of action of ENMs to aquatic organisms and allow a better prediction of contaminants toxicity. This paper presents an overview of transciptomic/proteomic studies in freshwater and marine organisms exposed to ENMs. Overall, induction of gene expression in relations to defense mechanisms, immune responses, growth and reproduction were measured after ENMs exposures of organisms, but with different patterns depending on exposure duration and concentrations used. In addition, some studies reported a positive correlation between gene expression and cellular modifications, but not at the individual level.

Differential gene expression of Australian Cricotopus draysoni (Diptera: Chironomidae) populations reveals seasonal association in detoxification gene regulation

Understanding the molecular mechanisms of organismal response to human-derived ecosystem change is recognised as a critical tool in monitoring and managing impacts, especially in freshwater systems. Fundamental to this approach is to determine the genes involved in responding to ecosystem change and detect modifications to their expression and activity in natural populations. Potential targets for this approach include well-known detoxification genes that are upregulated in response to stress. Here, we tested whether expression of such genes varied in association with differences in ecosystem health and could be detected in the field. We sampled populations of the freshwater midge, Cricotopus draysoni, from two geographically proximate sites in southeast Queensland, Australia, which differed in their ecosystem health, at multiple time points. We assessed transcriptome-level differential gene expression and predicted greatest differential expression between sites, associated with organismal responses to local physico-chemical factors. In contrast, we observed a clear and dramatic difference in gene expression – including of known detoxification genes – between time points, specifically between periods at the start and end of the austral summer rainfall when in-stream water levels are most different. These data suggest that these waterways experience greatest pollution load when water levels are high following rainfall events.

Respiration disruption and detoxification at the protein expression levels in the Pacific oyster (Crassostrea gigas) under zinc exposure

The Pacific oyster (Crassostrea gigas) can accumulate high levels of zinc (Zn) without obvious toxicity, but the related molecular mechanisms are largely unknown. In the present study, C. gigas were exposed to excess Zn for 9days and the differentially expressed proteins (DEPs) were examined using the isobaric tags for relative and absolute quantitation (iTRAQ) method. In total, 2667 proteins containing at least two peptides and detected in both replicates were used for proteomic analysis. Among these DEPs, 332 were up-regulated and 282 were down-regulated. KEGG enrichment analysis of DEPs revealed that Zn exposure mainly distrubed 'tricarboxylic acid (TCA) cycle', 'electron transport chain (ETC)' and 'glutathione (GSH) metabolism' processes in oysters. Further key protein expressions enriched in these metabolism pathways were analyzed. In TCA cycle, Zn inhibited the Fe-containing protein expressions, which may lead to the accumulation of succinate and induce anaerobiosis. In ETC metabolism process, Zn inhibited ETC complex protein expressions, including complex I-IV, which may affect the electron transport process. Furthermore, Zn induced phytochelatin (PC) and glutathione peroxidase (GPX) expression in GSH catabolism. The proteins play important roles in Zn detoxification and ROS elimination process. The transcriptional expressions of genes encoding these proteins were observed using real-time PCR analysis, and there was good consistency between these two datasets. Overall, we provide direct evidence for Zn toxicity and detoxification mechanisms at protein level.

Returning to normal? Assessing transcriptome recovery over time in male rainbow darter (Etheostoma caeruleum) liver in response to wastewater-treatment plant upgrades

The present study measured hepatic transcriptome responses in male rainbow darter (Etheostoma caeruleum) exposed to 2 municipal wastewater-treatment plants (MWWTPs; Kitchener and Waterloo) over 4 fall seasons (2011-2014) in the Grand River (Ontario, Canada). The overall goal was to determine if upgrades at the Kitchener MWWTP (in 2012) resulted in transcriptome responses indicative of improved effluent quality. The number of differentially expressed probes in fish downstream of the Kitchener outfall (904-1223) remained comparable to that downstream of Waterloo (767-3867). Noteworthy was that year and the interaction of year and site explained variability in more than twice the number of transcripts than site alone, suggesting that year and the interaction of year and site had a greater effect on the transcriptome than site alone. Gene set enrichment analysis revealed a gradual reduction in the number of gene ontologies over time at exposure sites, which corresponded with lower contaminant load. Subnetwork enrichment analysis revealed that there were noticeable shifts in the cell pathways differently expressed in the liver preupgrade and postupgrade. The dominant pathways altered preupgrade were related to genetic modifications and cell division, whereas postupgrade they were associated with the immune system, reproduction, and biochemical responses. Molecular pathways were dynamic over time, and following the upgrades, there was little evidence that gene expression profiles in fish collected from high-impact sites postupgrade were more similar to those in fish collected from reference site. Environ Toxicol Chem 2017;36:2108-2122. © 2017 SETAC.

The role of high-throughput screening in ecotoxicology and engineered nanomaterials

The field of environmental toxicology developed as a result of growing concerns about anthropogenic influences on the environment and how to ameliorate ecological impact. Many governmental bodies are beginning to emphasize prevention rather than mitigation when addressing novel products, leading to more of a focus on identifying potential toxicity prior to release. With the exponential advances in their development and sale, novel metamaterials and biotechnology are set to dramatically outpace the capabilities of current testing strategies. To address the need for a fast, cost-effective means of testing chemicals, high-throughput screening (HTS) is currently being used in toxicology and being adapted to ecotoxicology in projects such as ToxCast and Tox21. Despite the growth of research using HTS platforms, its role in ecotoxicology is still uncertain, particularly in how it should be applied in regulation. The aim of the present review is to discuss common test strategies used in designing HTS platforms, the current potential applications for ecotoxicological research, its role in regulatory policies, and its ability to address growing concerns such as engineered nanomaterials. Environ Toxicol Chem 2017;36:1704-1714. © 2017 SETAC.

Validation of reference genes for RT-qPCR in marine bivalve ecotoxicology: Systematic review and case study using copper treated primary Ruditapes philippinarum hemocytes

The appropriate selection of reference genes for the normalization of non-biological variance in reverse transcription real-time quantitative PCR (RT-qPCR) is essential for the accurate interpretation of the collected data. The use of multiple validated reference genes has been shown to substantially increase the robustness of the normalization. It is therefore considered good practice to validate putative genes under specific conditions, determine the optimal number of genes to be employed, and report the method or methods used. Under this premise, we assessed the current state of reference gene based normalization in RT-qPCR bivalve ecotoxicology studies (post 2011), employing a systematic quantitative literature review. A total of 52 papers met our criteria and were analysed for genes used, the use of multiple reference genes, as well as the validation method employed. We further critically discuss methods for reference gene validation based on a case study using copper exposed primary hemocytes from the marine bivalve Ruditapes philippinarum; including the established algorithms geNorm, NormFinder and BestKeeper, as well as the popular online tool RefFinder. We identified that RT-qPCR normalization is largely performed using single reference genes, while less than 40% of the studies attempted to experimentally validate the expression stability of the genes used. 18s rRNA and β-Actin were the most popular genes, yet their un-validated use did introduce artefactual variance that altered the interpretation of the resulting data. Our findings further suggest that combining the results from multiple individual algorithms and calculating the overall best-ranked gene, as computed by the RefFinder tool, does not by default lead to the identification of the most suitable reference genes.

The Demographic Success of Marsilea Quadrifolia L. in a Man-Made Water Body from Danube Delta Biosphere Reservation

Marsilea quadrifolia L. (water clover) is a unique species from Romanian flora that belongs to the Marsileaceae family and is one of the most vulnerable plants in Europe due to the loss of its habitats. In this paper, the demographic evolution of a new M. quadrifolia population in the Danube Delta Biosphere Reserve and its natural and anthropic threats are reported. The aquatic fern, M. quadrifolia, has colonized a suitable man-made water body. After a decade of monitoring, the demographic trend is positive but the support capacity of habitat for the water clover remains limited in the long term. The population is vulnerable due to succession of vegetation and its vicinity with a human settlement. The establishment of a micro-reserve represents a suitable method to protect and maintain this threatened M. quadrifolia population.

Potential of the small cyclopoid copepod Paracyclopina nana as an invertebrate model for ecotoxicity testing

Aquatic invertebrates contribute significantly to environmental impact assessment of contaminants in aquatic ecosystems. Much effort has been made to identify viable and ecologically relevant invertebrate test organisms to meet rigorous regulatory requirements. Copepods, which are ecologically important and widely distributed in aquatic organisms, offer a huge opportunity as test organisms for aquatic toxicity testing. They have a major role not only in the transfer of energy in aquatic food chains, but also as a medium of transfer of aquatic pollutants across the tropic levels. In this regard, a supratidal and benthic harpacticoid copepod Tigriopus japonicus Mori (order Harpacticoida) has shown promising characteristics as a test organism in the field of ecotoxicology. Because there is a need to standardize a battery of test organisms from species in different phylogenetic and critical ecosystem positions, it is important to identify another unrelated planktonic species for wider application and comparison. In this regard, the cyclopoid copepod Paracyclopina nana Smirnov (order Cyclopoida) has emerged as a potential test organism to meet such requirements. Like T. japonicus, it has a number of features that make it a candidate worth consideration in such efforts. Recently, the genomics of P. nana has been unraveled. Data on biochemical and molecular responses of P. nana against exposure to environmental chemicals and other stressors have been collected. Recently, sequences and expression profiles of a number of genes in P. nana encoding for heat shock proteins, xenobiotic-metabolizing enzymes, and antioxidants have been reported. These genes serve as potential biomarkers in biomonitoring of environmental pollutants. Moreover, the application of gene expression techniques and the use of its whole transcriptome have allowed evaluation of transcriptional changes in P. nana with the ultimate aim of understanding the mechanisms of action of environmental stressors. Whole-animal bioassays and gene expression studies indicate that P. nana may serve as an excellent tool to evaluate the impact of diverse disturbances in the marine environment. With a better understanding of toxicological mechanisms, ecotoxicologists will be able to understand defense mechanisms against toxicants in copepods. In this review, we illustrate the potential of P. nana as an alternative as well as a complementary invertebrate model organism for risk assessment of aquatic pollutants.