Integrated transcriptomics and metabolomics analyses reveal benzo[a]pyrene enhances the toxicity of mercury to the Manila clam, Ruditapes philippinarum

Integrated transcriptomic and metabolomic approaches reveal molecular response and potential biomarkers of the deep-sea mussel Gigantidas platifrons to copper exposure

Metal pollution caused by deep-sea mining activities has potential detrimental effects on deep-sea ecosystems. However, our knowledge of how deep-sea organisms respond to this pollution is limited, given the challenges of remoteness and technology. To address this, we conducted a toxicity experiment by using deep-sea mussel Gigantidas platifrons as model animals and exposing them to different copper (Cu) concentrations (50 and 500 μg/L) for 7 days. Transcriptomics and LC-MS-based metabolomics methods were employed to characterize the profiles of transcription and metabolism in deep-sea mussels exposed to Cu. Transcriptomic results suggested that Cu toxicity significantly affected the immune response, apoptosis, and signaling processes in G. platifrons. Metabolomic results demonstrated that Cu exposure disrupted its carbohydrate metabolism, anaerobic metabolism and amino acid metabolism. By integrating both sets of results, transcriptomic and metabolomic, we find that Cu exposure significantly disrupts the metabolic pathway of protein digestion and absorption in G. platifrons. Furthermore, several key genes (e.g., heat shock protein 70 and baculoviral IAP repeat-containing protein 2/3) and metabolites (e.g., alanine and succinate) were identified as potential molecular biomarkers for deep-sea mussel's responses to Cu toxicity. This study contributes novel insight for assessing the potential effects of deep-sea mining activities on deep-sea organisms.

Decoding the molecular concerto: Toxicotranscriptomic evaluation of microplastic and nanoplastic impacts on aquatic organisms

The pervasive and steadily increasing presence of microplastics/nanoplastics (MPs/NPs) in aquatic environments has raised significant concerns regarding their potential adverse effects on aquatic organisms and their integration into trophic dynamics. This emerging issue has garnered the attention of (eco)toxicologists, promoting the utilization of toxicotranscriptomics to unravel the responses of aquatic organisms not only to MPs/NPs but also to a wide spectrum of environmental pollutants. This review aims to systematically explore the broad repertoire of predicted molecular responses by aquatic organisms, providing valuable intuitions into complex interactions between plastic pollutants and aquatic biota. By synthesizing the latest literature, present analysis sheds light on transcriptomic signatures like gene expression, interconnected pathways and overall molecular mechanisms influenced by various plasticizers. Harmful effects of these contaminants on key genes/protein transcripts associated with crucial pathways lead to abnormal immune response, metabolic response, neural response, apoptosis and DNA damage, growth, development, reproductive abnormalities, detoxification, and oxidative stress in aquatic organisms. However, unique challenge lies in enhancing the fingerprint of MPs/NPs, presenting complicated enigma that requires decoding their specific impact at molecular levels. The exploration endeavors, not only to consolidate existing knowledge, but also to identify critical gaps in understanding, push forward the frontiers of knowledge about transcriptomic signatures of plastic contaminants. Moreover, this appraisal emphasizes the imperative to monitor and mitigate the contamination of commercially important aquatic species by MPs/NPs, highlighting the pivotal role that regulatory frameworks must play in protecting all aquatic ecosystems. This commitment aligns with the broader goal of ensuring the sustainability of aquatic resources and the resilience of ecosystems facing the growing threat of plastic pollutants.

Insights into tolerance mechanisms of earthworms (Eisenia fetida) in copper-contaminated soils by integrating multi-omics analyses

Earthworms can resist high levels of soil copper (Cu) contamination and play an essential role in absorbing them effectively. However, the molecular mechanisms underlying Cu tolerance in earthworms are poorly understood. To address this research gap, we studied alterations of Eisenia fetida in antioxidant enzymes, gut microbiota, metabolites, and genes under varying levels of Cu exposure soils (0, 67.58, 168.96, 337.92 mg/kg). Our results revealed a reduction in antioxidant enzyme activities across all treatment groups, indicating an adaptive response to alleviate Cu-induced oxidative stress. Analysis of gut microbiota revealed a significant increase in the abundance of bacteria associated with nutrient uptake and Cu2+ excretion under Cu stress. Furthermore, metabolomic analysis discovered an increase in certain metabolites associated with energy metabolism, such as pyruvic acid, L-malic acid, and fumaric acid, as Cu concentration escalated. These results suggested that enhanced energy supply contributes to the elevated tolerance of E. fetida towards Cu. Additionally, transcriptome analysis not only identified crucial detoxification genes (Hsp70, CTSL, GST, CHAC, and GCLC), but also confirmed the critical role of glutathione metabolism as a key pathway in E. fetida Cu detoxification processes. These findings provide a new perspective on the molecular mechanisms of Cu tolerance in earthworms.

Construction of protein-protein interaction network in sulfate-reducing bacteria: Unveiling of global response to Hg

Sulfate-reducing bacteria (SRB) play pivotal roles in the biotransformation of mercury (Hg). However, unrevealed global responses of SRB to Hg have restricted our understanding of details of Hg biotransformation processes. The absence of protein-protein interaction (PPI) network under Hg stimuli has been a bottleneck of proteomic analysis for molecular mechanisms of Hg transformation. This study constructed the first comprehensive PPI network of SRB in response to Hg, encompassing 67 connected nodes, 26 independent nodes, and 121 edges, covering 93% of differentially expressed proteins from both previous studies and this study. The network suggested that proteomic changes of SRB in response to Hg occurred globally, including microbial metabolism in diverse environments, carbon metabolism, nucleic acid metabolism and translation, nucleic acid repair, transport systems, nitrogen metabolism, and methyltransferase activity, partial of which could cover the known knowledge. Antibiotic resistance was the original response revealed by this network, providing insights into of Hg biotransformation mechanisms. This study firstly provided the foundational network for a comprehensive understanding of SRB's responses to Hg, convenient for exploration of potential targets for Hg biotransformation. Furthermore, the network indicated that Hg enhances the metabolic activities and modification pathways of SRB to maintain cellular activities, shedding light on the influences of Hg on the carbon, nitrogen, and sulfur cycles at the cellular level.

Bioconcentration, biotransformation, and transcriptomic impact of the UV-filter 4-MBC in the manila clam Ruditapes philippinarum

Ultraviolet filters (UV-filters) are compounds extensively used in personal care products. These compounds are produced at increasing rates and discharged into marine ecosystems in unknown quantities and with no regulation, making them emerging contaminants. Among those, the UV-filter 4-Methylbenzylidene camphor (4-MBC) is used in a variety of personal care products such as sunscreens, soaps, or lipsticks. This high consumption has resulted in its presence in various environmental matrices at in concentrations ranging from ng to μg L-1. Very little is known, however, about the possible adverse effects in exposed non-target organisms. Our study presents novel data on the bioconcentration, toxicokinetics, and molecular effects of 4-MBC in a marine bivalve species of commercial interest, Ruditapes philippinarum (Manila clam). Organisms were exposed at two different concentrations (1.34 and 10.79 μg L-1) of 4-MBC for 7 days, followed by a 3-day depuration period (clean sea waters). Bioconcentration factors (BCF) were 3562 and 2229 L kg-1 for the low and high exposure concentrations, respectively, making this pollutant bioaccumulative according to REACH criteria. Up to six 4-MBC biotransformation products (BTPs)were identified, 2 of them for the first time. Transcriptomic analysis revealed between 658 and 1310 differently expressed genes (DEGs) after 4-MBC exposure. Functional and enrichment analysis of the DEGs showed the activation of the detoxification pathway to metabolize and excrete the bioconcentrated 4-MBC, which also involved energy depletion and caused an impact on the metabolism of carbohydrates and lipids and in the oxidative phosphorylation pathways. Oxidative stress and immune response were also evidenced through the activation of cathepsins and the complement system. Such elucidation of the mode of action of a ubiquitous pollutant such as 4-MBC at the molecular level is valuable both from an environmental point of view and for the sustainable production of Manila clam, one of the most cultivated mollusk species worldwide.

Mechanisms of Gills Response to Cadmium Exposure in Greenfin Horse-Faced Filefish (Thamnaconus septentrionalis): Oxidative Stress, Immune Response, and Energy Metabolism

Cadmium (Cd) pollution has become a global issue due to industrial and agricultural developments. However, the molecular mechanism of Cd-induced detrimental effects and relevant signal transduction/metabolic networks are largely unknown in marine fishes. Here, greenfin horse-faced filefish (Thamnaconus septentrionalis) were exposed to 5.0 mg/L Cd up to 7 days. We applied both biochemical methods and multi-omics techniques to investigate how the gills respond to Cd exposure. Our findings revealed that Cd exposure caused the formation of reactive oxygen species (ROS), which in turn activated the MAPK and apoptotic pathways to alleviate oxidative stress and cell damage. Glycolysis, protein degradation, as well as fatty acid metabolism might assist to meet the requirements of nutrition and energy under Cd stress. We also found that long-term (7 days, "long-term" means compared to 12 and 48 h) Cd exposure caused the accumulation of succinate, which would in turn trigger an inflammatory response and start an immunological process. Moreover, ferroptosis might induce inflammation. Overall, Cd exposure caused oxidative stress, energy metabolism disturbance, and immune response in greenfin horse-faced filefish. Our conclusions can be used as references for safety risk assessment of Cd to marine economic fishes.

Integrated transcriptomic and biochemical characterization of the mechanisms governing stress responses in soil-dwelling invertebrate (Folsomia candida) upon exposure to dibutyl phthalate

Dibutyl phthalate (DBP) is one of the most commonly utilized plasticizers and a frequently detected phthalic acid ester (PAE) compound in soil samples. However, the toxicological effects of DBP on soil-dwelling organisms remain poorly understood. This study employed a multi-biomarker approach to investigate the impact of DBP exposure on Folsomia candida's survival, reproduction, enzyme activity levels, and transcriptional profiles. Analyses of antioxidant biomarkers, including catalase (CAT) and glutathione S-transferase (GST), as well as detoxifying enzymes such as acetylcholinesterase (AChE), Cytochrome P450 (CYP450), and lipid peroxidation (LPO), revealed significant increases in CAT activity, GST levels, and CYP450 expression following treatment with various doses of DBP for 2, 4, 7, or 14 days. Additionally, LPO induction was observed along with significant AChE inhibition. In total, 3175 differentially expressed genes (DEGs) were identified following DBP treatment that were enriched in six Gene Ontology (GO) terms and 144 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including 85 upregulated and 59 downregulated primarily associated with lipid metabolism, signal transduction, DNA repair, and cell growth and death. Overall these results provide foundational insights for further research into the molecular mechanisms underlying responses of soil invertebrates to DBP exposure.

The combined effects of polyethylene microplastics and benzoanthracene on Manila clam Ruditapes philippinarum

Microplastic (MP) toxicity has recently been explored in various marine species. Along with the toxicity of plastics polymer itself, additional substances or pollutants that are absorbed onto it may also be harmful. In the present study, we investigated the combined impacts of polyethylene microplastics (PE MPs) and an organic pollutant (Benzo(a)anthracene, BaA) on Manila clam Ruditapes philippinarum during a one-week exposure. Two PE MPs concentrations (26 μg L^-1 and 260 μg L^-1) and one BaA concentration (3 μg L^-1) were tested. The clams were exposed to BaA and PE MPs either alone or in combination. BaA and PE MPs were incubated before the combined exposure. The biological effects of PE MPs and BaA on the clams were evaluated by considering several assays such as feeding rate, anti-oxidant enzyme activities, and the expression levels of stress-related genes. The feeding rate significantly decreased in individual PE MPs and individual BaA groups while it remained unchanged in combined groups. Superoxide dismutase (SOD) was the most affected among the biochemical parameters. Malondialdehyde (MDA), and glutathione peroxidase (GPx) activities were slightly affected, whereas no changes were observed in glutathione s-transferase (GST) activities. CYP1A1, CYP3A4, and HSP70 gene expressions displayed slightly significant changes. Considering all stressor groups, high PE MPs exposure (260 μg L^-1 PE MPs) more effectively altered the biological parameters in the clams compared to individual low PE MPs and BaA exposure, and their combination. The results also indicated the negligible vector role of PE MPs to transport BaA into the clam tissues.

Application of multi-omics combined with bioinformatics techniques to assess salinity stress response and tolerance mechanisms of Pacific oyster (Crassostrea gigas) during depuration

Depuration is a vital stage to ensure the safety of oyster consumption, and salinity had a great impact on the environmental adaptability of oysters, but the underlying molecular mechanism was poorly understood during depuration stage. Here, Crassostrea gigas was depurated for 72 h at different salinity (26, 29, 32, 35, 38 g/L, corresponding to ±20%, ±10% salinity fluctuation away from oyster's production area) and then analyzed by using transcriptome, proteome, and metabolome combined with bioinformatics techniques. The transcriptome showed that the salinity stress led to 3185 differentially expressed genes and mainly enriched in amino acid metabolism, carbohydrate metabolism, lipid metabolism, etc. A total of 464 differentially expressed proteins were screened by the proteome, and the number of up-regulated expression proteins was less than the down-regulated, indicating that the salinity stress would affect the regulation of metabolism and immunity in oysters. 248 metabolites significantly changed in response to depuration salinity stress in oysters, including phosphate organic acids and their derivatives, lipids, etc. The results of integrated omics analysis indicated that the depuration salinity stress induced abnormal metabolism of the citrate cycle (TCA cycle), lipid metabolism, glycolysis, nucleotide metabolism, ribosome, ATP-binding cassette (ABC) transport pathway, etc. By contrast with Pro-depuration, more radical responses were observed in the S38 group. Based on the results, we suggested that the 10% salinity fluctuation was suitable for oyster depuration and the combination of multi-omics analysis could provide a new perspective for the analysis of the mechanism changes.

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.

Immunotoxicity of pentachlorophenol to a marine bivalve species and potential toxification mechanisms underpinning

The ubiquitous presence of pentachlorophenol (PCP) in ocean environments threatens marine organisms. However, its effects on immunity of marine invertebrates at environmentally realistic levels are still largely unknown. In this study, the immunotoxicity of PCP to a representative bivalve species was evaluated. In addition, its impacts on metabolism, energy supply, detoxification, and oxidative stress status were also analysed by physiological examination as well as comparative transcriptomic and metabolomic analyses to reveal potential mechanisms underpinning. Results illustrated that the immunity of blood clams was evidently hampered upon PCP exposure. Additionally, significant alterations in energy metabolism were detected in PCP-exposed clams. Meanwhile, the expressions of key detoxification genes and the in vivo contents (or activity) of key detoxification enzymes were markedly altered. Exposure to PCP also triggered significant elevations in intracellular ROS and MDA whereas evident suppression of haemocyte viability. The abovementioned findings were further supported by transcriptomic and metabolomic analyses. Our results suggest that PCP may hamper the immunity of the blood clam by (i) constraining the cellular energy supply through disrupting metabolism; and (ii) damaging haemocytes through inducing oxidative stress. Considering the high similarity of immunity among species, many marine invertebrates may be threatened by PCP, which deserves more attention.

Histology study and transcriptome analysis of the testis of Loach(Misgurnus anguillicaudatus) in response to phenanthrene exposure

Phenanthrene (PHE) is one of the most abundant polycyclic aromatic hydrocarbon compounds (PAHs) in the aquatic environment. The loaches were exposed at concentrations of 0.30、1.00、3.00 mg L^-1 for 60 days. The effects of PHE on the testis development were evaluated by calculating the survival rate, observing the structure of testis and analyzing transcriptome. Firstly, PHE markedly decreased the survival rate in a dose-dependent manner. Then, the number and density of spermatogonia, primary spermatocytes, secondary spermatocytes and spermatids were substantially reduced under PHE exposure. The space in the seminiferous tubule obviously increased in the high PHE concentration group. Meanwhile, transcriptome comparative analysis identified 5329 differentially expressed genes (DEGs) including 2928 up-regulated and 2401 down-regulated in the testis of loach exposed PHE for 60 days. Meiotic cell cycle, arganelle fission, ATPase activity and adenylate nucleotide binding were significantly differences by GO (Gene Ontology) enrichment. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis revealed that TNF (Tumor Necrosis Factor) signaling pathway, CAMs (Cell Adhesion Molecules), cytochrome P450 and lipid metabolism were markedly regulated. In addition, eight DEGs were randomly selected from the testis transcriptomics results for qPCR verification, the results were consistent with RNA-Seq. Finally, related genes (piwil2, dmc1, vasa, ubr2, dnd, rnf17, plcb2, c-fos, gpx4) of testis development were further confirmed and they were differentially regulated after PHE exposure. In summary, a survey of the mechanism of loach testis response to PHE was performed, and a large number of gene expression levels regarding metabolism, spermatogenesis and immunity genes were acquired from RNA-seq. This study provide informations for elucidating the molecular mechanism of PHE affected the testis development of loach.

Metabolomics as a valid analytical technique in environmental exposure research: application and progress

BACKGROUND

In recent years, studies have shown that exposure to environmental pollutants (e.g., radiation, heavy metal substances, air pollutants, organic pollutants) is a leading cause of human non-communicable diseases. The key to disease prevention is to clarify the harmful mechanisms and toxic effects of environmental pollutants on the body. Metabolomics is a high-sensitivity, high-throughput omics technology that can obtain detailed metabolite information of an organism. It is a crucial tool for gaining a comprehensive understanding of the pathway network regulation mechanism of the organism. Its application is widespread in many research fields such as environmental exposure assessment, medicine, systems biology, and biomarker discovery.

AIM OF REVIEW

Recent findings show that metabolomics can be used to obtain molecular snapshots of organisms after environmental exposure, to help understand the interaction between environmental exposure and organisms, and to identify potential biomarkers and biological mechanisms.

KEY SCIENTIFIC CONCEPTS OF REVIEW

This review focuses on the application of metabolomics to understand the biological effects of radiation, heavy metals, air pollution, and persistent organic pollutants exposure, and examines some potential biomarkers and toxicity mechanisms.

Microplastics influence physiological processes, growth and reproduction in the Manila clam, Ruditapes philippinarum

Microplastics (<5 mm) are widely distributed in marine environments and pose a serious threat to bivalves. Here, the ingestion and accumulation of polystyrene microplastics (PS microplastics, diameters 5 and 10 μm) by the Manila clam, Ruditapes philippinarum, and their impacts on physiological processes, growth and reproduction were studied. The results showed that both PS microplastics were ingested by the Manila clam and accumulated in their gills, hepatopancreases and intestines. Furthermore, the accumulation of 5 and 10 μm PS microplastics significantly increased the rates of respiration and excretion while significantly decreasing feeding and absorption efficiency (AE), leading to a dramatically reduced amount of energy available for growth (SfG) and ultimately led to slower growth. The dynamic energy budget (DEB) model predicts that PS microplastic exposure for 200 days would cause lower shell/flesh growth rates and reproductive potentiality. Transcriptomic profiles support these results, as carbon and protein metabolism and oxytocin and insulin-related signaling pathways were significantly altered in clams in response to PS microplastics. This study provides evidence that microplastics strongly affect the physiological activities, energy allocation, growth and reproduction of filter-feeding bivalves.

Study on toxicity effects of environmental pollutants based on metabolomics: A review

In the past few decades, the toxic effects of environmental pollutants on non-target organisms have received more and more attention. As a new omics technology, metabolomics can clarify the metabolic homeostasis of the organism at the overall level by studying the changes in the relative contents of endogenous metabolites in the organism. Recently, a large number of studies have used metabolomics technology to study the toxic effects of environmental pollutants on organisms. In this review, we reviewed the analysis processes and data processes of metabolomics and its application in the study of the toxic effects of environmental pollutants including heavy metals, pesticides, polychlorinated biphenyls, polycyclic aromatic hydrocarbons, polybrominated diphenyl ethers and microplastics. In addition, we emphasized that the combination of metabolomics and other omics technologies will help to explore the toxic mechanism of environmental pollutants and provide new research ideas for the toxicological evaluation of environmental pollutants.