Coupling caging and proteomics on the European flounder (Platichthys flesus) to assess the estuarine water quality at micro scale

Proteomic profiling of the serological response to a chemically-inactivated nodavirus vaccine in European sea bass Dicentrarchus labrax

The analysis of animal responses to immunization is fundamental to vaccine development, enabling the evaluation of immune responses and the elucidation of key mechanisms underlying protective immunity. Such insights are essential for advancing vaccines through clinical trial stages and regulatory approval. Furthermore, understanding the molecular signatures of approved vaccines not only deepens our knowledge of their function but also guides the rational design and improvement of future vaccines. This study aims to elucidate alterations in protein abundance patterns in the sera of European sea bass, D. labrax, following immunization with a chemically-inactivated nodavirus vaccine. The shotgun proteome comparison revealed that in vaccinated animals, compared to controls, there is a modulation of the redox balance favouring reactive oxygen species (ROS), an intricate interaction between coagulation and the immune system resulting in the lower abundance of hematopoiesis-related FLT3, and indications of functional adaptive immunity demonstrated by the lower abundance of pentraxin fusion protein-like and the over-representation of myosins. To the best of our knowledge, this study represents the inaugural investigation of the immune response in fish using a proteomics approach, employing D. labrax as the host and nodavirus as the pathogen used for vaccination and challenge.

Environmental signatures and fish proteomics: A multidisciplinary study to identify the major stressors in estuaries located in French agricultural watersheds

Watersheds and estuaries are impacted by multiple anthropogenic stressors that affect their biodiversity and functioning. Assessing their ecological quality has consequently remained challenging for scientists and stakeholders. In this paper, we propose a multidisciplinary approach to identify the stressors in seven small French estuaries located in agricultural watersheds. We collected data from landscape (geography, hydrobiology) to estuary (pollutant chemistry) and fish individual scales (environmental signatures, proteomics). This integrative approach focused on the whole hydrosystems, from river basins to estuaries. To characterize each watershed, we attempted to determine the land use considering geographic indicators (agricultural and urbanised surfaces) and landscape patterns (hedges density and riparian vegetation). Juveniles of European flounder (Platichthys flesus) were captured in September, after an average residence of five summer months in the estuary. Analyses of water, sediments and biota allowed to determine the concentrations of dissolved inorganic nitrogen species, pesticides and trace elements in the systems. Environmental signatures were also measured in flounder tissues. These environmental parameters were used to establish a typology of the watersheds. Furthermore, data from proteomics on fish liver were combined with environmental signatures to determine the responses of fish to stressors in their environments. Differential protein abundances highlighted a dysregulation related to the detoxification of xenobiotics (mainly pesticides) in agricultural watersheds, characterized by intensive cereal and vegetable crops and high livestock. Omics also revealed a dysregulation of proteins associated with the response to hypoxia and heat stress in some estuaries. Furthermore, we highlighted a dysregulation of proteins involved in urea cycle, immunity and metabolism of fatty acids in several systems. Finally, the combination of environmental and molecular signatures appears to be a relevant method to identify the major stressors operating within hydrosystems.

Advancing environmental monitoring across the water continuum combining biomarker analysis in multiple sentinel species: A case study in the Seine-Normandie Basin (France)

Nowadays, biomarkers are recognized as valuable tools to complement chemical and ecological assessments in biomonitoring programs. They provide insights into the effects of contaminant exposures on individuals and establish connections between environmental pressure and biological response at higher levels. In the last decade, strong improvements in the design of experimental protocols and the result interpretation facilitated the use of biomarker across wide geographical areas, including aquatic continua. Notably, the statistical establishment of reference values and thresholds enabled the discrimination of contamination effects in environmental conditions, allowed interspecies comparisons, and eliminated the need of a reference site. The aim of this work was to study freshwater-estuarine-coastal water continua by applying biomarker measurements in multi-species caged organisms. During two campaigns, eight sentinel species, encompassing fish, mollusks, and crustaceans, were deployed to cover 25 sites from rivers to the sea. As much as possible, a common methodology was employed for biomarker measurements (DNA damage and phagocytosis efficiency) and data interpretation based on guidelines established using reference values and induction/inhibition thresholds (establishment of three effect levels). The methodology was successfully implemented and allowed us to assess the environmental quality. Employing multiple species per site enhances confidence in observed trends. The results highlight the feasibility of integrating biomarker-based environmental monitoring programs across a continuum scale. Biomarker results align with Water Framework Directive indicators in cases of poor site quality. Additionally, when discrepancies arise between chemical and ecological statuses, biomarker findings offer a comprehensive perspective to elucidate the disparities. Presented as a pilot project, this work contributes to gain insights into current biomonitoring needs, providing new questions and perspectives.

Relevance of flounder caging and proteomics to explore the impact of a major industrial accident caused by fire on the Seine estuarine water quality

On September 26th 2019, a major fire occurred in the Lubrizol factory located near the Seine estuary, in Rouen-France. Juvenile flounders were captured in the Canche estuary (a reference system) and caged one month in the Canche and in the Seine downstream the accident site. No significant increases of PAHs, PCBs and PFAS was detected in Seine vs Canche sediments after the accident, but a significant increase of dioxins and furans was observed in water and sewage sludge in the Rouen wastewater treatment plant. The proteomics approach highlighted a dysregulation of proteins associated with cholesterol synthesis and lipid metabolism, in fish caged in the Seine. The overall results suggested that the fire produced air borne dioxins and furans that got deposited on soil and subsequently entered in the Seine estuarine waters via runoff; thus contaminating fish preys and caged flounders in the Seine estuary.

Multi-level assessment of the origin, feeding area and organohalogen contamination on salmon from the Baltic Sea

The Atlantic salmon (Salmo salar) population in the Baltic Sea consists of wild and hatchery-reared fish that have been released into the sea to support salmon stocks. During feeding migration, salmon migrate to different parts of the Baltic Sea and are exposed to various biotic and abiotic stressors, such as organohalogen compounds (OHCs). The effects of salmon origin (wild or hatchery-reared), feeding area (Baltic Main Basin, Bothnian Sea, and Gulf of Finland), and OHC concentration on the differences in hepatic proteome of salmon were investigated. Multi-level analysis of the OHC concentration, transcriptome, proteome, and oxidative stress biomarkers measured from the same salmon individuals were performed to find the key variables (origin, feeding area, OHC concentrations, and oxidative stress) that best account for the differences in the transcriptome and proteome between the salmon groups. When comparing wild and hatchery-reared salmon, differences were found in xenobiotic and amino acid metabolism-related pathways. When comparing salmon from different feeding areas, the amino acid and carbohydrate metabolic pathways were notably different. Several proteins found in these pathways are correlated with the concentrations of polychlorinated biphenyls (PCBs). The multi-level analysis also revealed amino acid metabolic pathways in connection with PCBs and oxidative stress variables related to glutathione metabolism. Other pathways found in the multi-level analysis included genetic information processes related to ribosomes, signaling and cellular processes related to the cytoskeleton, and the immune system, which were connected mainly to the concentrations of Polychlorinated biphenyls and Dichlorodiphenyltrichloroethane and their metabolites. These results suggest that the hepatic proteome of salmon in the Baltic Sea, together with the transcriptome, is more affected by the OHC concentrations and oxidative stress of the feeding area than the origin of the salmon.

Integration of environmental signatures and omics-based approaches on the European flounder to assist with health assessment of estuarine ecosystems in Brittany, France

This study aimed to develop a multidisciplinary approach to assess the ecological status of six moderate-sized French estuaries. For each estuary, we gathered geographical information, hydrobiological data, chemistry of pollutants and fish biology, including integration of proteomics and transcriptomics data. This integrative study covered the entire hydrological system studied, from the watershed to the estuary, and considered all the anthropogenic factors that can impact this environment. To reach this goal, European flounder (Platichthys flesus) were collected from six estuaries in September, which ensures a minimum residence time of five months within an estuary. Geographical metrics are used to characterize land use in each watershed. The concentrations of nitrite, nitrate, organic pollutants, and trace elements were measured in water, sediments and biota. All of these environmental parameters allowed to set up a typology of estuaries. Classical fish biomarkers, coupled with molecular data from transcriptomics and shotgun proteomics, highlighted the flounder's responses to stressors in its environment. We analysed the protein abundances and gene expression levels in the liver of fish from the different estuaries. We showed clear positive deregulation of proteins associated with xenobiotic detoxification in a system characterized by a large population density and industrial activity, as well as in a predominantly agricultural catchment area (mostly cultures of vegetables and pig breeding) mainly impacted by pesticides. Fish from the latter estuary also displayed strong deregulation of the urea cycle, most probably related to high nitrogen load. Proteomic and transcriptomic data also revealed a deregulation of proteins and genes related to the response to hypoxia, and a probable endocrine disruption in some estuaries. Coupling these data allowed the precise identification of the main stressors interacting within each hydrosystem.

Trace metals exposure in three different coastal compartments show specific morphological and reproductive traits across generations in a sentinel copepod

The effect of exposure from several compartments of the environment at the level of individuals was rarely investigated. This study reports the effect of contaminants from varied compartments like sediment resuspension, elutriation from resuspended sediment (extract) and seawater spiked trace metal mixtures (TM) on morphological and reproductive traits of the pelagic bioindicator copepod Eurytemora affinis. At the population level of E. affinis, lowest survival was observed in dissolved exposures (TM and extract) in the first generation (G1), showing some adaptation in the second generation (G2). An opposite trend for resuspended sediment showed higher sensitivity in survival at G2. At the individual level, prosome length and volume proved to be sensitive parameters for resuspended sediments, whereas clutch size and egg diameter were more sensitive to TM and extract. Although the generation of decontamination (G3, no exposure), showed a significant recovery at the population level (survival % along with clutch size) of E. affinis exposed to resuspended sediment, morphological characteristics like prosome length and volume showed no such recovery (lower than control, p < 0.05). To the contrary, dissolved exposure showed no significant recovery from G1 to G3 on neither survival %, clutch size, egg diameter, prosome volume, but an increase of prosome length (p < 0.05). Such tradeoffs in combatting the stress from varied sources of toxicity were observed in all exposures, from G1 to G3. The number of lipid droplets inside the body cavity of E. affinis showed a significant positive correlation with trace metal bioaccumulation (p < 0.01) along with a negative correlation (p < 0.05) with survival and clutch size in each treatment. This confirms the inability of copepods to utilize lipids under stressful conditions. Our study tenders certain morphological and reproductive markers that show specificity to different compartments of exposure, promising an advantage in risk assessment and fish feed studies.

Decoupling carry-over effects from environment in fish nursery grounds

Life-history trait expression not only depends on the current environmental constraints, but also on the past ones that shaped traits expressed earlier in life. Such an effect, named carry-over, can occur in fish nursery grounds when juvenile performances after settlement are influenced by their larval traits in combination with conditions experienced in nurseries. To date, the impacts of environmental and human stressors on post-settlement traits have been assessed, but independently from larval traits, so that the contributions of environmental versus carry-over constraints remain unquantified. Here, we used a reconstructive approach based on otolith microstructure to investigate how carry-over and environment affect life-history traits of the European seabass, Dicentrarchus labrax. In the northeast Atlantic Ocean, seabass juveniles were collected in six French estuarine nursery areas with contrasted environmental conditions (water temperature, salinity, food availability, and anthropogenic impacts), and five of their life-history traits across ontogenetic stages were measured (pelagic growth, larval duration, size at settlement, post-settlement growth and body condition). Piecewise structural equation model emphasized the strong co-variation of larval traits in response to food availability and temperature in the pelagic environment, stressing that fast growing larvae are characterized by shorter pelagic larval duration, but larger size at recruitment. However, the magnitude of carry-over effects greatly varied between traits, revealing that larval trait impacts on post-settlement traits remained minor as compared to the nursery environment. In estuarine nurseries, our findings suggest that resource allocation results from a trade-off between somatic growth and energy storage. Fish juveniles exposed to anthropogenic stress or risk of food limitation tended to predominantly invest in storage, whereas individuals in favourable conditions allocated their resources in somatic growth. These findings highlight the importance of heterogeneity in pelagic and nursery environments in understanding trait variations and population dynamic of estuarine dependent fish.

Bioaccumulation of trace metal elements and biomarker responses in caged juvenile flounder at a polluted site: Effects of fish density and time exposure

This study investigates the effect of fish density and exposure duration on trace metal elements (TME) bioaccumulation and several biomarkers response. Juvenile flounders were caged at low, medium and high densities and exposed during 15 or 30 days in the Seine estuary. The concentrations of the TME measured in the muscle of the caged fish were all in agreement with their bioavailability percentage in the sediments. Higher concentrations of TME were found in flounders' muscle exposed for 15 days compared with those caged for 30 days. For the same exposure time, the density of fish had no effect on the accumulation of the TME in the flounders' muscle. Biomarkers responses varied according to density and duration of exposure. Special care should be taken in their interpretation. We underline that for an optimal assessment of TME pollution in the field, 15 days with low densities of fish per cage are sufficient.

Integrative multi-biomarker approach on caged rainbow trout: A biomonitoring tool for wastewater treatment plant effluents toxicity assessment

The complex mixtures of contaminants released in wastewater treatment plant (WWTP) effluents are a major source of pollution for aquatic ecosystems. The present work aimed to assess the environmental risk posed by WWTP effluents by applying a multi-biomarker approach on caged rainbow trout (Oncorhynchus mykiss) juveniles. Fish were caged upstream and downstream of a WWTP for 21 days. To evaluate fish health, biomarkers representing immune, reproductive, nervous, detoxification, and antioxidant functions were assayed. Biomarker responses were then synthesized using an Integrated Biomarker Response (IBR) index. The IBR highlighted similar response patterns for the upstream and downstream sites. Caged juvenile females showed increased activities of innate immune parameters (lysozyme and complement), histological lesions and reduced glycogen content in the hepatic tissue, and higher muscle cholinergic metabolism. However, the intensity of the observed effects was more severe downstream of the WWTP. The present results suggest that the constitutive pollution level of the Meuse River measured upstream from the studied WWTP can have deleterious effects on fish health condition, which are exacerbated by the exposure to WWTP effluents. Our results infer that the application of IBR index is a promising tool to apply with active biomonitoring approaches as it provides comprehensive information about the biological effects caused by point source pollution such as WWTP, but also by the constitutive pollutions levels encountered in the receiving environment.

Responses of the copepod Eurytemora affinis to trace metal exposure: A candidate for sentinel to marine sediment resuspension effects

Our study reports the ability of Eurytemora affinis to indicate certain responses in 96 h when exposed to resuspended sediment from a polluted site (PS, Seine estuary, France), less polluted site (LPS, Canche estuary, France) and dissolved trace metals. Mortality from dissolved trace metal was highest (57.5 %) followed by PS (38.59 %) > LPS (24.04 %). The exposure to PS sediment resulted in significantly lower no. of early larval stage (nauplii < 2), sex-ratio (39.24 % of males) and higher ovigerous female (>10). Eurytemora affinis bioaccumulated high concentrations of copper (27.3 mg/kg), nickel (12.8 mg/kg), lead (21.8 mg/kg) and arsenic (13.7 mg/kg) from PS exposure with significantly lower bioaccumulation of metals from LPS. The bioconcentration factor (BCF) was highest from dissolved toxicity (>2000) followed by PS that showed significantly higher BCF for Nickel and Copper, compared to LPS. The responses of E. affinis to different matrices exemplify its role as a sentinel.

Time-dependent biological responses of juvenile yellow perch (Perca flavescens) exposed in situ to a major urban effluent

Municipal wastewater treatment plant (WWTP) effluents are significant sources of organic and inorganic pollutants to aquatic ecosystems. Several studies have shown that the health of aquatic organisms can be adversely impacted following exposure to these complex chemical mixtures. The objective of this study was to examine the effects of in situ exposure in the St. Lawrence River (QC, Canada) of juvenile yellow perch (Perca flavescens) to a major WWTP effluent. Perch were caged at a reference site in the St. Lawrence River and downstream of a WWTP effluent-influenced site for one, three, and six weeks. Fish kept in controlled laboratory setting were also examined at the beginning of the experiment to evaluate the potential effect of caging on fish. Liver metabolites and gill oxidative stress biomarkers as well as body condition of perch were investigated at four time points (zero, one, three, and six weeks). Nitrogen (δ¹⁵N) and carbon (δ¹³C) stable isotopes as well as tissue concentrations of halogenated flame retardants and trace metals were also analyzed. Results indicated that body condition of perch caged in the effluent increased after three and six weeks of exposure compared to that of reference fish. Perch caged at the WWTP effluent-influenced site also had higher muscle δ¹³C and slightly depleted muscle δ¹⁵N after three and six weeks of exposure, suggesting differences in sewage-derived nutrient assimilation between sites. Concentrations of Σ₃₄ polybrominated diphenyl ether (PBDE) were 2-fold greater in perch exposed downstream of the WWTP compared to those caged at the reference site. Metal concentrations in kidney of perch after three weeks of exposure were significantly lower at the effluent-influenced site. Kidney concentrations of Cd, Cu, Se, As, Zn and Fe were, however, higher after six weeks of exposure, supporting that metal accumulation is time- and element-specific. The metabolomes of perch from the effluent-influenced and reference sites were similar, but were distinct from the laboratory control fish, suggesting a caging effect on fish. Seven liver metabolites (glucose, malate, fumarate, glutamate, creatinine, histamine, and oxypurinol) were significantly more abundant in perch from cages than in the laboratory control perch. The combination of metabolomics and physiological variables provides a powerful tool to improve our understanding of the mechanisms of action of complex environmental pollutant mixtures in wild fish.

Can proteomics contribute to biomonitoring of aquatic pollution? A critical review

Aquatic pollution is one of the greatest environmental problems, and therefore its control represents one of the major challenges in this century. In recent years, proteomics has emerged as a powerful tool for searching protein biomarkers in the field of pollution biomonitoring. For biomonitoring marine contamination, there is a consensus that bivalves are preferred organisms to assess organic and inorganic pollutants. Thus, the bivalve proteome was intensively studied, particularly the mussel. It is well documented that heavy metal pollution and organic chemicals altered the structural proteins causing degradation of tissues of molluscs. Also, it is well known that proteins involved in stress oxidative such as glutathione and enzymes as catalase, superoxide dismutase or peroxisomes are overexpressed in response to contaminants. Additionally, using bivalves, other groups of proteins proposed as pollution biomarkers are the metabolic proteins. Even though other marine species are used to monitor the pollution, the presence of proteomic tools in these studies is scarce. Concerning freshwater pollution field, a great variety of animal species (fish and crustaceans) are used as biomonitors in proteomics studies compared to plants that are scarcely analysed. In fish species, proteins involved in stress oxidative such as heat shock family or proteins from lipid and carbohydrate metabolism were proposed as candidate biomarkers. On the contrary, for crustaceans there is a lack of proteomic studies individually assessing the contaminants. Novel scenarios, including emerging contaminants and new threats, will require proteomic technology for a systematic search of protein biomarkers and a greater knowledge at molecular level of those cellular pathways induced by contamination.

Are we forgetting the "proteomics" in multi-omics ecotoxicology?

Proteomics plays a significant role in discerning the effects of chemical exposures in animal taxa. Multi-omics applications have become more pervasive in toxicology, however questions remain about whether proteomics is being utilized by the community to its full potential - are we placing too much stock in transcriptomics and other omics approaches for developing adverse outcome pathways? Proteins are more relevant than transcripts because they are direct mediators of the resulting phenotype. There is also rarely perfect stoichiometry between transcript and protein abundance and transcript abundance may not accurately predict physiologic response. Proteins direct all levels of phenotype: structural proteins dictate physical form, enzymes catalyze biochemical reactions, and proteins act as signaling proteins, antibodies, transporters, ion pumps, and transcription factors to control gene expression. Molecular initiating events (MIEs) of AOPs predominantly occur at the level of the protein (e.g. ligand-receptor binding) and proteomics can elucidate novel MIEs and mapping KEs in AOPs. This critical review highlights the need for proteomics in multi-omics studies in environmental toxicology and outlines steps required for inclusion and wider acceptance in chemical risk assessment. We also present case studies of multi-omics approaches that utilize proteomics and discuss some of the challenges and opportunities for proteomics in comparative ecotoxicology. Our intention is not to minimize the importance of other omics technologies, as each has strengths and limitations, but rather to encourage researchers to consider proteomics-based methods in multi-omics studies and AOP development.