Multifactorial Analysis of Environmental Metabolomic Data in Ecotoxicology: Wild Marine Mussel Exposed to WWTP Effluent as a Case Study

Mixture effects of pharmaceuticals carbamazepine, diclofenac and venlafaxine on Mytilus galloprovincialis mussel probed by metabolomics and proteogenomics combined approach

Exposure to single molecules under laboratory conditions has led to a better understanding of the mechanisms of action (MeOAs) and effects of pharmaceutical active compounds (PhACs) on non-target organisms. However, not taking the co-occurrence of contaminants in the environment and their possible interactions into account may lead to underestimation of their impacts. In this study, we combined untargeted metabolomics and proteogenomics approaches to assess the mixture effects of diclofenac, carbamazepine and venlafaxine on marine mussels (Mytilus galloprovincialis). Our multi-omics approach and data fusion strategy highlighted how such xenobiotic cocktails induce important cellular changes that can be harmful to marine bivalves. This response is mainly characterized by energy metabolism disruption, fatty acid degradation, protein synthesis and degradation, and the induction of endoplasmic reticulum stress and oxidative stress. The known MeOAs and molecular signatures of PhACs were taken into consideration to gain insight into the mixture effects, thereby revealing a potential additive effect. Multi-omics approaches on mussels as sentinels offer a comprehensive overview of molecular and cellular responses triggered by exposure to contaminant mixtures, even at environmental concentrations.

Insights on the Organ-Dependent, Molecular Sexual Dimorphism in the Zebra Mussel, Dreissena polymorpha, Revealed by Ultra-High-Performance Liquid Chromatography-Tandem Mass Spectrometry Metabolomics

The zebra mussel, Dreissena polymorpha, is extensively used as a sentinel species for biosurveys of environmental contaminants in freshwater ecosystems and for ecotoxicological studies. However, its metabolome remains poorly understood, particularly in light of the potential molecular sexual dimorphism between its different tissues. From an ecotoxicological point of view, inter-sex and inter-organ differences in the metabolome suggest variability in responsiveness, which can influence the analysis and interpretation of data, particularly in the case where males and females would be analyzed indifferently. This study aimed to assess the extent to which the molecular fingerprints of functionally diverse tissues like the digestive glands, gonads, gills, and mantle of D. polymorpha can reveal tissue-specific molecular sexual dimorphism. We employed a non-targeted metabolomic approach using liquid chromatography high-resolution mass spectrometry and revealed a significant sexual molecular dimorphism in the gonads, and to a lesser extent in the digestive glands, of D. polymorpha. Our results highlight the critical need to consider inter-sex differences in the metabolome of D. polymorpha to avoid confounding factors, particularly when investigating environmental effects on molecular regulation in the gonads, and to a lesser extent in the digestive glands.

Targeted metabolomics characterizes metabolite occurrence and variability in stable freshwater mussel populations

Freshwater mussels (order Unionida) play a key role in freshwater systems as ecosystem engineers and indicators of aquatic ecosystem health. The fauna is globally imperilled due to a diversity of suspected factors; however, causes for many population declines and mortality events remain unconfirmed due partly to limited health assessment tools. Mussel-monitoring activities often rely on population-level measurements, such as abundance and age structure, which reflect delayed responses to environmental conditions. Measures of organismal health would enable preemptive detection of declining condition before population-level effects manifest. Metabolomic analysis can identify shifts in biochemical pathways in response to stressors and changing environmental conditions; however, interpretation of the results requires information on inherent variability of metabolite concentrations in mussel populations. We targeted metabolites in the haemolymph of two common mussels, Lampsilis cardium and Lampsilis siliquoidea, from three Indiana streams (USA) using ultra-high-performance liquid chromatography combined with quadrupole time-of-flight mass spectroscopy. The influence of species, stream and sex on metabolite variability was examined with distance-based redundancy analysis. Metabolite variability was most influenced by species, followed by site and sex. Inter- and intraspecies metabolite variability among sexes was less distinct than differences among locations. We further categorized metabolites by occurrence and variability in mussel populations. Metabolites with high occurrence (Categories 1 and 2) included those indicative of energy status (catabolism versus anabolism; arginine, proline, carnitine, nicotinic acid, pantothenic acid), oxidative stress (proline, glutamine, glutamate) and protein metabolism (thymidine, cytidine, inosine). Metabolites with lower occurrence (Category 3) are constituents of assorted metabolic pathways and can be important biomarkers with additional temporal sampling to characterize their variability. These data provide a reference for future temporal (before/after) monitoring and for studies of stressor-metabolite linkages in freshwater mussels.

Characterization of imidacloprid-induced hepatotoxicity and its mechanisms based on a metabolomic approach in Xenopus laevis

The toxic effects of imidacloprid are attracting increased concern because of its widespread use in agriculture and its persistence in the aquatic environment. Imidacloprid bioaccumulates and triggers various morphological and behavioral responses in amphibians, but the toxic effects and mechanism of imidacloprid in amphibians remain uncertain. In this study, the acute toxicity and chronic effects of imidacloprid on Xenopus laevis were studied. Acute toxicity for 96 h revealed that imidacloprid had an LC₅₀ value of 74.18 mg/L. After exposure for 28 d under 1/10 and 1/100 LC_50, liver samples from X. laevis were employed for biochemical analyses, pathological studies, and nontargeted metabolomics to systematically assess the toxic effects and mechanisms of imidacloprid. The results showed that oxidative stress and hepatic tissue morphology changes were observed in treated X. laevis liver. Twelve metabolites involved in metabolic pathway were altered between the control and high exposure groups and twenty-one metabolites were altered between the control and low exposure group. Eight metabolic pathways exposed to high levels and nine metabolic pathways exposed to low level of imidacloprid were disturbed. These pathways were primarily related to amino acid metabolism, lipid metabolism, and nucleotide metabolism. Our research provides essential information to evaluate the potential toxicity of imidacloprid to nontarget aquatic organisms.

Liquid chromatography-mass spectrometry based metabolomics investigation of different tissues of Mytilus galloprovincialis

The Mediterranean mussel (Mytilus galloprovincialis) is widely used in monitoring programs and in ecotoxicological studies to examine the biological effects of physicochemical parameter changes and the impact of chemical pollutants. Metabolomics has recently demonstrated high potential to gain further insight into the molecular effects of chemical exposure and the success of its application is dependent on the extent of prior metabolomics knowledge available on the target organism. Therefore, the purpose of this study was the investigation of the metabolites of five different functional tissues of male and female Mediterranean mussels (digestive gland, foot, gill and gonad tissues and in the remaining soft tissues) accessible to the analysis using the most common sample preparation recommended for tissue analysis (i.e. Bligh & Dyer). Metabolic fingerprints were acquired via liquid chromatography high-resolution mass spectrometry and the identification was based on an internal database developed in the laboratory. It led to the identification of 110 metabolites, among which amino acids, carboxylic acids, purine and pyrimidine metabolites were often the most abundant. The metabolic contents of the five tissues quantitatively and qualitatively differed, with a clear distinction between male and female contents observed in the gonads and digestive glands. These results underline the importance of selecting the most suitable tissue and sex to study the impact of contamination on metabolism and the need for further research to deeper characterize the metabolome of this organism.

Tissue-Specific Toxicokinetics of Aqueous Radium-226 in an Estuarine Mussel, Geukensia demissa

Radiological contamination of coastal habitats poses potential risk for native fauna, but the bioavailability of aqueous radium (Ra) and other dissolved metals to marine bivalves remains unclear. This study was the first to examine the tissue-specific disposition of aqueous ²²⁶Ra in a coastal mussel, specifically the Atlantic ribbed mussel Geukensia demissa. Most organ groups reached steady-state concentrations within 7 days during experimental exposure, with an average uptake rate constant of 0.0013 mL g^-1 d^-1. When moved to Ra-free synthetic seawater, mussels rapidly eliminated aqueous ²²⁶Ra (average elimination rate constant 1.56 d^-1). The biological half-life for aqueous ²²⁶Ra ranged from 8.9 h for the gills and labial palps to 15.4 h for the muscle. Although previous field studies have demonstrated notable ²²⁶Ra accumulation in the soft tissues of marine mussels and that, for freshwater mussels, tissue-incorporated ²²⁶Ra derives primarily from the aqueous phase, our tissue-specific bioconcentration factors (BCFs) were on the order of (8.3 ± 1.5) × 10^-4 indicating low accumulation potential of aqueous ²²⁶Ra in estuarine mussels. This suggests marine and estuarine mussels obtain ²²⁶Ra from an alternate route, such as particulate-sorbed Ra ingested during filter-feeding or from a contaminated food source.

Contaminants of emerging concern in the Maumee River and their effects on freshwater mussel physiology

Contaminants of emerging concern pose a serious hazard to aquatic wildlife, especially freshwater mussels. The growing number of contaminants in aquatic systems requires scientists and managers to prioritize contaminants that are most likely to elicit a biological response for further monitoring and toxicological testing. The objectives of this study were to identify a sub-category of contaminants most likely to affect Pyganodon grandis and to describe alterations in metabolites and gene expression between various sites. Mussels were deployed in cages for two weeks at four sites along the Maumee River Basin, Ohio, USA. Water samples were analyzed for the presence of 220 contaminants. Hemolymph samples were collected for metabolomics and analyzed using mass spectrometry. Contaminants that significantly covaried with metabolites were identified using partial least-squares (PLS) regression. Tissue samples were collected for transcriptomics, RNA was sequenced using an Illumina HiSeq 2500, and differential expression analysis was performed on assembled transcripts. Of the 220 targeted contaminants, 69 were detected in at least one water sample. Of the 186 metabolites detected in mussel hemolymph, 43 showed significant differences between the four sites. The PLS model identified 44 contaminants that significantly covaried with changes in metabolites. A total of 296 transcripts were differentially expressed between two or more sites, 107 received BLAST hits, and 52 were annotated and assigned to one or more Gene Ontology domains. Our analyses reveal the contaminants that significantly covaried with changes in metabolites and are most likely to negatively impact freshwater mussel health and contribute to ongoing population declines in this group of highly endangered animals. Our integration of "omics" technologies provides a broad and in-depth assessment of the short-term effects of contaminants on organismal physiology. Our findings highlight which contaminants are most likely to be causing these changes and should be prioritized for more extensive toxicological testing.

Transcriptomic and metabolomic integration to assess the response of gilthead sea bream (Sparus aurata) exposed to the most used insect repellent: DEET

DEET is one of the most frequently detected insect repellents in the environment reaching concentrations of several μg L^-1 in surface water. There is scarce information available regarding its mode of action in non-target organisms. Here, we have used an integrated metabolomic and transcriptomic approach to elucidate the possible adverse effects of DEET exposure in the marine fish gilthead sea bream (Sparus aurata). Individuals were exposed at an environmentally relevant concentration of DEET (10 μg L^-1) for 22 days in a continuous flow-through system. Transcriptomic analysis revealed 250 differentially expressed genes in liver, while metabolomic analysis identified 190 differentially modulated features in liver and 98 in plasma. Multi-omic data integration and visualization allowed elucidation of the modes of action of DEET exposure, including: energy depletion through the disruption of carbohydrate and amino acids metabolisms, oxidative stress leading to DNA damage, lipid peroxidation, and damage to cell membrane and apoptosis. Activation of xenobiotic pathway as well as the inmune-inflammatory reaction was evidenced in the present work.

Untargeted Metabolomics Reveals Antidepressant Effects in a Marine Photosynthetic Organism: The Diatom Phaeodactylum tricornutum as a Case Study

The increased use of antidepressants, along with their increased occurrence in aquatic environments, is of concern for marine organisms. Although these pharmaceutical compounds have been shown to negatively affect marine diatoms, their mode of action in these non-target, single-cell phototrophic organisms is yet unknown. Using a Fourier-transform ion cyclotron-resonance mass spectrometer (FT-ICR-MS) we evaluated the effects of fluoxetine in the metabolomics of the model diatom Phaeodactylum tricornutum, as well as the potential use of the identified metabolites as exposure biomarkers. Diatom growth was severely impaired after fluoxetine exposure, particularly in the highest dose tested, along with a down-regulation of photosynthetic and carbohydrate metabolisms. Notably, several mechanisms that are normally down-regulated by fluoxetine in mammal organisms were also down-regulated in diatoms (e.g., glycerolipid metabolism, phosphatidylinositol signalling pathway, vitamin metabolism, terpenoid backbone biosynthesis and serotonin remobilization metabolism). Additionally, the present work also identified a set of potential biomarkers of fluoxetine exposure that were up-regulated with increasing fluoxetine exposure concentration and are of high metabolic significance following the disclosed mode of action, reinforcing the use of metabolomics approaches in ecotoxicology.

Metabolism of the aquatic pollutant diclofenac in the Lymnaea stagnalis freshwater gastropod

The metabolism of organic contaminants in Lymnaea stagnalis freshwater gastropod remains unknown. Yet, pharmaceuticals-like the NSAID diclofenac-are continuously released in the aquatic environment, thereby representing a risk to aquatic organisms. In addition, lower invertebrates may be affected by this pollution since they are likely to bioaccumulate contaminants. The metabolism of pharmaceuticals in L. stagnalis requires further investigation to understand their detoxification mechanisms and characterized the risk posed by contaminant exposure in this species. In this study, a non-targeted strategy using liquid chromatography combined with high-resolution mass spectrometry was applied to highlight metabolites formed in L. stagnalis freshwater snails exposed to 300 µg/L diclofenac for 3 and 7 days. Nineteen metabolites were revealed by this approach, 12 of which were observed for the first time in an aquatic organism exposed to diclofenac. Phase I metabolism involved hydroxylation, with detection of 3'-, 4'-, and 5-hydroxydiclofenac and three dihydroxylated metabolites, as well as cyclization, oxidative decarboxylation, and dehydrogenation, while phase II metabolism consisted of glucose and sulfate conjugation. Among these reactions, the two main DCF detoxification pathways detected in L. stagnalis were hydroxylation (phase I) and glucosidation (phase II).

Effects of WS2 Nanosheets on N2-fixing Cyanobacteria: ROS overproduction, cell membrane damage, and cell metabolic reprogramming

The ecotoxicity of tungsten disulfide (WS₂) nanomaterials remains unclear so far. Here, the toxicity of WS₂ nanosheets on N₂-fixing cyanobacteria (Nostoc sphaeroides) was evaluated. Specifically, Nostoc were cultivated in media spiked with different concentrations of WS₂ nanosheets (0, 0.05, 0.1 and 0.5 mg/L) for 96 h. Relative to unexposed cells, WS₂ nanosheets at 0.5 mg/L significantly decreased cell density, content of total sugar and protein by 10.9 %, 0.43 %, and 6.1 %, respectively. Gas chromatography-mass spectrometry (GC-MS)-based metabolomics revealed that WS₂ nanosheets exposure altered the metabolite profile of Nostoc in a dose-dependent manner. Energy metabolism related pathways, including the Calvin-Benson-Bassham (CBB) cycle and tricarboxylic acid (TCA) cycle, were significantly inhibited. In addition, WS₂ nanosheets exposure resulted in downregulation (20-40 %) of S-containing amino acids (cystine, methionine, and cysteine) and sulfuric acid. Additionally, fatty acids and antioxidant-related compounds (formononetin, catechin, epigallocatechin, dehydroascorbic acid, and alpha-tocopherol) in Nostoc were drastically decreased by 4-50 % upon exposure to WS₂ nanosheets, which implies oxidative stress induced by the nanomaterials. Biochemical assays for reactive oxygen species (ROS) and malondialdehyde (MDA) confirmed that WS₂ nanosheets triggered ROS overproduction and induced lipid peroxidation. Taken together, WS₂ exposure perturbed carbon (C), nitrogen (N), and sulfate (S) metabolism of Nostoc, which may influence C, N, and S cycling, given the important roles of cyanobacteria in these processes. These results highlight the need for caution in the application and environmental release of WS₂ nanomaterials to prevent unintended environmental impacts due to their potential ecotoxicity.

Early Biological Modulations Resulting from 1-Week Venlafaxine Exposure of Marine Mussels Mytilus galloprovincialis Determined by a Metabolomic Approach

There is growing evidence of the presence of pharmaceuticals in natural waters and their accumulation in aquatic organisms. While their mode of action on non-target organisms is still not clearly understood, their effects warrant assessment. The present study assessed the metabolome of the Mediterranean mussel (Mytilus galloprovincialis) exposed to a 10 µg/L nominal concentration of the antidepressant venlafaxine (VLF) at 3 time-points (1, 3, and 7 days). Over the exposure period, we observed up- or down-modulations of 113 metabolites, belonging to several metabolisms, e.g., amino acids (phenylalanine, tyrosine, tryptophan, etc.), purine and pyrimidine metabolisms (adenosine, cyclic AMP, thymidine, etc.), and several other metabolites involved in diverse functions. Serotonin showed the same time-course modulation pattern in both male and female mussels, which was consistent with its mode of action in humans, i.e., after a slight decrease on the first day of exposure, its levels increased at day 7 in exposed mussels. We found that the modulation pattern of impacted metabolites was not constant over time and it was gender-specific, as male and female mussels responded differently to VLF exposure.

Environmental Metabolomics Promises and Achievements in the Field of Aquatic Ecotoxicology: Viewed through the Pharmaceutical Lens

Scientists often set ambitious targets using environmental metabolomics to address challenging ecotoxicological issues. This promising approach has a high potential to elucidate the mechanisms of action (MeOAs) of contaminants (in hazard assessments) and to develop biomarkers (in environmental biomonitoring). However, metabolomics fingerprints often involve a complex mixture of molecular effects that are hard to link to a specific MeOA (if detected in the analytical conditions used). Given these promises and limitations, here we propose an updated review on the achievements of this approach. Metabolomics-based studies conducted on the effects of pharmaceutical active compounds in aquatic organisms provide a relevant means to review the achievements of this approach, as prior knowledge about the MeOA of these molecules could help overcome some shortcomings. This review highlighted that current metabolomics advances have enabled more accurate MeOA assessment, especially when combined with other omics approaches. The combination of metabolomics with other measured biological endpoints has also turned out to be an efficient way to link molecular effects to (sub)-individual adverse outcomes, thereby paving the way to the construction of adverse outcome pathways (AOPs). Here, we also discuss the importance of determining MeOA as a key strategy in the identification of MeOA-specific biomarkers for biomonitoring. We have put forward some recommendations to take full advantage of environmental metabolomics and thus help fulfil these promises.

Multi-omic approach to evaluate the response of gilt-head sea bream (Sparus aurata) exposed to the UV filter sulisobenzone

Sulisobenzone (BP-4) is one of the benzophenone type UV filters most frequently detected in aquatic ecosystems. As a suspected endocrine disrupting compound, scarce information is available yet about other molecular effects and its mechanism of action. Here, we used an integrated transcriptomic and metabolomic approach to improve the current understanding on the toxicity of BP-4 towards aquatic species. Gilt-head sea bream individuals were exposed at environmentally relevant concentrations (10 μg L^-1) for 22 days. Transcriptomic analysis revealed 371 differentially expressed genes in liver while metabolomic analysis identified 123 differentially modulated features in plasma and 118 in liver. Integration of transcriptomic and metabolomic data showed disruption of the energy metabolism (>10 pathways related to the metabolism of amino acids and carbohydrates were impacted) and lipid metabolism (5 glycerophospholipids and the expression of 3 enzymes were affected), suggesting oxidative stress. We also observed, for the first time in vivo and at environmental relevant concentrations, the disruption of several enzymes involved in the steroid and thyroid hormones biosynthesis. DNA and RNA synthesis was also impacted by changes in the purine and pyrimidine metabolisms. Overall, the multiomic workflow presented here increases the evidence on suspected effects of BP-4 exposure and identifies additional modes of action of the compounds that could have been overlooked by using single omic approaches.

An integrated metabolomics and proteogenomics approach reveals molecular alterations following carbamazepine exposure in the male mussel Mytilus galloprovincialis

Carbamazepine is one of the most abundant pharmaceutical active compounds detected in aquatic systems. Based on laboratory exposures, carbamazepine has been proven to adversely affect aquatic organisms. However, the underlying molecular events remain poorly understood. This study aims to investigate the molecular mechanisms potentially associated with toxicological effects of carbamazepine on the mussel Mytilus galloprovincialis exposed for 3 days at realistic concentrations encountered in coastal environments (80 ng/L and 8 μg/L). An integrated metabolomics and proteogenomics approach, including data fusion strategy, was applied to gain more insight in molecular events and cellular processes triggered by carbamazepine exposure. Consistent metabolic and protein signatures revealed a metabolic rewiring and cellular stress at both concentrations (e.g. intensification of protein synthesis, transport and catabolism processes, disruption of lipid and amino acid metabolisms). These highlighted molecular signatures point to the induction of autophagy, closely related with carbamazepine mechanism of action, as well as a destabilization of the lysosomal membranes and an enzymatic overactivity of the peroxisomes. Induction of programmed cell death was highlighted by the modulation of apoptotic cognate proteins. The proposed integrative omics data analysis was shown to be highly relevant to identify the modulations of the two molecular levels, i.e. metabolites and proteins. Multi-omics approach is able to explain the resulting complex biological system, and document stronger toxicological pieces of evidence on pharmaceutical active compounds at environmental concentrations in sentinel organisms.

Metabolomic Studies for the Evaluation of Toxicity Induced by Environmental Toxicants on Model Organisms

Environmental pollution causes significant toxicity to ecosystems. Thus, acquiring a deeper understanding of the concentration of environmental pollutants in ecosystems and, clarifying their potential toxicities is of great significance. Environmental metabolomics is a powerful technique in investigating the effects of pollutants on living organisms in the environment. In this review, we cover the different aspects of the environmental metabolomics approach, which allows the acquisition of reliable data. A step-by-step procedure from sample preparation to data interpretation is also discussed. Additionally, other factors, including model organisms and various types of emerging environmental toxicants are discussed. Moreover, we cover the considerations for successful environmental metabolomics as well as the identification of toxic effects based on data interpretation in combination with phenotype assays. Finally, the effects induced by various types of environmental toxicants in model organisms based on the application of environmental metabolomics are also discussed.

Are bio-based and biodegradable microplastics impacting for blue mussel (Mytilus edulis)?

The substitution of petrochemical plastics by bio-based and biodegradable plastics are in need of an evaluation for the potential toxic impacts that they can have on marine wildlife. This study aims to assess the toxicological effects of polylactic acid microparticles at two concentrations, 10 and 100 μg/L, during 8 days on the blue mussel, Mytilus edulis. No significant oxidative stress (catalase, glutathione-S-transferase and superoxide dismutase activities), neurotoxicity (acetylcholinesterase), or immunotoxicity (lysosomal membrane stability and acid phosphatase activity) were detectable. The multivariate analysis of metabolomic data allowed us to differentiate the individuals according to the exposure. From the loading plot of OPLS-DA, 48 ions down-regulated in the individuals exposed to microplastics. They were identified based on HRMS data as glycerophospholipids.

Neurotoxicity in Marine Invertebrates: An Update

Invertebrates represent about 95% of existing species, and most of them belong to aquatic ecosystems. Marine invertebrates are found at intermediate levels of the food chain and, therefore, they play a central role in the biodiversity of ecosystems. Furthermore, these organisms have a short life cycle, easy laboratory manipulation, and high sensitivity to marine pollution and, therefore, they are considered to be optimal bioindicators for assessing detrimental chemical agents that are related to the marine environment and with potential toxicity to human health, including neurotoxicity. In general, albeit simple, the nervous system of marine invertebrates is composed of neuronal and glial cells, and it exhibits biochemical and functional similarities with the vertebrate nervous system, including humans. In recent decades, new genetic and transcriptomic technologies have made the identification of many neural genes and transcription factors homologous to those in humans possible. Neuroinflammation, oxidative stress, and altered levels of neurotransmitters are some of the aspects of neurotoxic effects that can also occur in marine invertebrate organisms. The purpose of this review is to provide an overview of major marine pollutants, such as heavy metals, pesticides, and micro and nano-plastics, with a focus on their neurotoxic effects in marine invertebrate organisms. This review could be a stimulus to bio-research towards the use of invertebrate model systems other than traditional, ethically questionable, time-consuming, and highly expensive mammalian models.