Transcriptomic underpinning of toxicant-mediated physiological function alterations in three terrestrial invertebrate taxa: a review

Biomarker and adverse outcome pathway responses of Tubifex tubifex (sludge worm) exposed to environmentally-relevant levels of acenaphthene: insights from behavioral, physiological, and chemical structure-activity analyses

Polycyclic aromatic hydrocarbons (PAHs), including acenaphthene, pose a significant threat to aquatic ecosystems by harming vital organisms such as benthic invertebrates. This study evaluated the impact of environmentally relevant concentrations of acenaphthene on Tubifex tubifex, focusing on sublethal acute toxicity and subchronic biomarker responses. Key biomarkers assessed included histopathological changes and the modulation of antioxidant enzymes: catalase (CAT), superoxide dismutase (SOD), glutathione S-transferase (GST), and malondialdehyde (MDA). Additionally, the study examined structure-activity relationships and species sensitivity distribution (SSD). Concentrations exceeding the solubility threshold of acenaphthene (3.9 mg/L) triggered distinct, concentration-dependent behavioral responses in Tubifex tubifex, such as clumping, mucus secretion, and body wrinkling. Prolonged exposure exacerbated these behavioral dysfunctions, while subchronic exposure resulted in significant histopathological alterations, including epithelial hyperplasia, inflammation, edema, fibrosis, and degenerative changes. The edematic appearance of the body wall suggested a potential immune response to exposure. Furthermore, increased activities of CAT, SOD, and GST indicated oxidative stress in the worms. The study found a 1.5-fold increase in CAT and GST activity, a fivefold increase in SOD, and a striking 100-fold increase in MDA levels compared to controls, signifying an overwhelmed antioxidant defense system and potential cellular disruption. The SSD curve revealed hazard concentrations (HC50 and HC90), indicating that Tubifex tubifex exhibited lower sensitivity to acenaphthene compared to other taxa. In silico analysis and read-across models confirmed the potential of acenaphthene to induce significant oxidative stress upon exposure. The correlation between biomarker responses and structure-activity relationship analysis highlighted the aromatic nature of acenaphthene as a key factor in generating reactive metabolites, inhibiting antioxidant enzymes, and promoting redox cycling, ultimately contributing to adverse outcomes. These findings, coupled with behavioral responses and SSD curve inferences, underscore the importance of the solubility threshold of acenaphthene as a critical benchmark for evaluating its ecological impact in aquatic environments.

Molecular level toxicity effects of As(V) on Folsomia candida: Integrated transcriptomics and metabolomics analyses

Arsenic (As) is a widespread metalloid with well-known toxicity. To date, numerous studies have focused on individual level toxicity (e.g., growth and reproduction) of As to typical invertebrate springtails in soils, however, the molecular level toxicity and mechanism was poorly understood. Here, an integrated transcriptomics and metabolomics approach was used to reveal responses of Folsomia candida exposed to As(V) of 10 and 60 mg kg-1 at which the individual level endpoints were influenced. Transcriptomics identified 5349 and 4020 differentially expressed genes (DEGs) in low and high concentration groups, respectively, and the most DEGs were down-regulated. Enrichment analysis showed that low and high concentrations of As(V) significantly inhibited chromatin/chromosome-related biological processes (chromatin/chromosome organization, nucleosome assembly and organization, etc.) in springtails. At high concentration treatment, structural constituent of cuticle, chitin metabolic process and peptidase activity (serine-type peptidase activity, endopeptidase activity, etc.) were inhibited or disturbed. Moreover, the apoptosis pathway was significantly induced. Metabolomics analysis identified 271 differential changed metabolites (DCMs) in springtails exposed to high concentration of As. Steroid hormone biosynthesis was the most significantly affected pathway. Several DCMs that related to chitin metabolism could further support above transcriptomic results. These findings further extended the knowledge of As toxic mechanisms to soil fauna and offer important information for the environmental risk assessment.

Synergistic effect of pyrene and heavy metals (Zn, Pb, and Cd) on phytoremediation potential of Medicago sativa L. (alfalfa) in multi-contaminated soil

The environment in India is contaminated with polycyclic aromatic hydrocarbons (PAHs) due to the occurrence of large anthropogenic activities, i.e., fuel combustion, mineral roasting, and biomass burning. Hence, 13 toxic PAHs were detected: phenanthrene, anthracene, fluoranthene, pyrene, and benz(a) anthracene, ben-zo; (b) fluoranthene, benzo(k) fluoranthene, benzo(a) pyrene, benzo(ghi)perylene, dibenz (ah) anthracene, indeno1,2,3-(cd) pyrene, coronene and coronene in the environment (i.e., ambient particulate matter, road dust, sludge, and sewage) of the most industrialized area. Pollutants such as heavy metals and polycyclic aromatic hydrocarbons co-contaminate the soil and pose a significant hazard to the ecosystem because these pollutants are harmful to both humans and the environment. Phytoremediation is an economical plant-based natural approach for soil clean-up that has no negative impact on ecosystems. The aim of this study was to investigate the effects of pyrene (500 mg kg-1), Zn (150 mg kg-1), Pb (150 mg kg-1), and Cd (150 mg kg-1) alone and in combination on the phytoextraction efficiency of Medicago sativa growing in contaminated soil. Plant biomass, biochemical activities, translocation factors, accumulation of heavy metals, and pyrene removal were determined. After 60 days of planting, compared with those of the control plants, the growth parameters, biomass, and chlorophyll content of the M. sativa plants were significantly lower, and the reactive oxygen species activity, such as proline and polyphenol content and metallothionein protein content, was markedly greater in the pyrene and heavy metal-polluted soils. Furthermore, the combined toxicity of pyrene and all three metals on M. sativa growth and biochemical parameters was significantly greater than that of pyrene, Zn, Pb, or Cd alone, indicating the synergistic effect of pyrene and heavy metals on cytotoxicity. Pyrene stress increased Cd accumulation in M. sativa. After pyrene exposure alone or in combination with Zn-pyrene, a greater pyrene removal rate (85.5-81.44%) was observed than that in Pb-pyrene, Cd-pyrene, and Zn-Pb-Cd-pyrene polluted soils (62.78-71.27%), indicating that zinc can enhance the removal of pyrene from contaminated soil. The resulting hypotheses demonstrated that Medicago sativa can be used as a promising phytoremediation agent for co-contaminated soil.

The genome sequence of the common earthworm, Lumbricus terrestris (Linnaeus, 1758)

We present a genome assembly from an individual Lumbricus terrestris (the common earthworm; Annelida; Clitellata; Haplotaxida; Lumbricidae). The genome sequence is 1,056.5 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.93 kilobases in length.

Multiple insights into lignin-mediated cadmium detoxification in rice (Oryza sativa)

Cadmium (Cd) is readily absorbed by rice and enters the food chain, posing a health risk to humans. A better understanding of the mechanisms of Cd-induced responses in rice will help in developing solutions to reduce Cd uptake in rice. Therefore, this research attempted to reveal the detoxification mechanisms of rice in response to Cd through physiological, transcriptomic and molecular approaches. The results showed that Cd stress restricted rice growth, led to Cd accumulation and H2O2 production, and resulted cell death. Transcriptomic sequencing revealed glutathione and phenylpropanoid were the major metabolic pathways under Cd stress. Physiological studies showed that antioxidant enzyme activities, glutathione and lignin contents were significantly increased under Cd stress. In response to Cd stress, q-PCR results showed that genes related to lignin and glutathione biosynthesis were upregulated, whereas metal transporter genes were downregulated. Further pot experiment with rice cultivars with increased and decreased lignin content confirmed the causal relationship between increased lignin and reduced Cd in rice. This study provides a comprehensive understanding of lignin-mediated detoxification mechanism in rice under Cd stress and explains the function of lignin in production of low-Cd rice to ensure human health and food safety.

Adaptation of a marine diatom to ocean acidification increases its sensitivity to toxic metal exposure

Most previous studies investigating the interplay of ocean acidification (OA) and heavy metal on marine phytoplankton were only conducted in short-term, which may provide conservative estimates of the adaptive capacity of them. Here, we examined the physiological responses of long-term (~900 generations) OA-adapted and non-adapted populations of the diatom Phaeodactylum tricornutum to different concentrations of the two heavy metals Cd and Cu. Our results showed that long-term OA selected populations exhibited significantly lower growth and reduced photosynthetic activity than ambient CO₂ selected populations at relatively high heavy metal levels. Those findings suggest that the adaptations to high CO₂ results in an increased sensitivity of the marine diatom to toxic metal exposure. This study provides evidence for the costs and the cascading consequences associated with the adaptation of phytoplankton to elevated CO₂ conditions, and improves our understanding of the complex interactions of future OA and heavy metal pollution in marine waters.

Nrf2/Keap1 pathway in countering arsenic-induced oxidative stress in mice after chronic exposure at environmentally-relevant concentrations

Contamination of drinking water by carcinogen arsenic (As) is of worldwide concern as its exposure poses potential threat to human health. As such, it is important to understand the mechanisms associated with As-induced toxicity to humans. The Nrf2/Keap1 signal pathway is one of the most important defense mechanisms in cells to counter oxidative stress; however, limited information is available regarding its role in countering As-induced stress in model animal mouse. In this study, we assessed the responses of Nrf2/keap1 pathway in mice after chronic exposure to As at environmentally-relevant concentrations of 10-200 μg L^-1 for 30 days via drinking water. Our results indicate that chronic As exposure had limited effect on mouse growth. However, As induced oxidative stress to mice as indicated by increased content of malondialdehyde (MDA; 52-90%), an index of lipid peroxidation. Further, arsenic exposure reduced the activity of superoxide dismutase (SOD; 14-18%), an indication of reduced anti-oxidative activity. Besides, arsenic exposure increased MnSOD mRNA transcription by 25-66%, and decreased the mRNA transcriptions of Cu/ZnSOD by 72-83% and metallothionein by 16-75%, a cysteine-rich protein involved in metal detoxification. To counter arsenic toxicity, the expression of transcription factor for Nrf2 and Keap1 was increased by 2.8-8.9 and 0.2-8.1 fold in mice. To effectively reduce As-induced oxidative stress, the Nrf2/Keap1 transcription factor upregulated several downstream anti-oxidative genes, including heme oxygenase-1 (0.9-2.5 fold), glutamate-cysteine ligase catalytic subunit (0.6-1.7 fold), and NADH quinone dehydrogenase 1 (2.1-4.8 fold). This study shows the importance of Nrf2/Keap1 signaling pathway and associated anti-oxidative enzymes in countering As-toxicity in mice, possibly having implication for human health.

Gene Expression Profiles in Two Razor Clam Populations: Discerning Drivers of Population Status

With rapidly changing marine ecosystems, shifts in abundance and distribution are being documented for a variety of intertidal species. We examined two adjacent populations of Pacific razor clams (Siliqua patula) in lower Cook Inlet, Alaska. One population (east) supported a sport and personal use fishery, but this has been closed since 2015 due to declines in abundance, and the second population (west) continues to support commercial and sport fisheries. We used gene expression to investigate potential causes of the east side decline, comparing razor clam physiological responses between east and west Cook Inlet. The target gene profile used was developed for razor clam populations in Alaska based on physiological responses to environmental stressors. In this study, we identified no differences of gene expression between east and west populations, leading to two potential conclusions: (1) differences in factors capable of influencing physiology exist between the east and west and are sufficient to influence razor clam populations but are not detected by the genes in our panel, or (2) physiological processes do not account for the differences in abundance, and other factors such as predation or changes in habitat may be impacting the east Cook Inlet population.

Heavy metal detoxification mechanisms by microalgae: Insights from transcriptomics analysis

Heavy metal pollution in ecosystem is a global threat. The associated toxicity and carcinogenic nature of heavy metals/metalloids such as mercury, cadmium, lead, and arsenic are imposing a severe risk to both ecological diversity and human lives. Harnessing the adaptive feature of microalgae for remediating toxic heavy metal has reached a milestone in past few decades. Transcriptomics analyses have provided mechanistic insights to map the dynamics of cellular events under heavy metal stress, thus deciphering the strategic responses of microalgae. Here, the present review comprehensively addresses the elicited molecular responses of microalgae to detoxify the heavy metal stress. The review highlights the intricate role of biochemical components and signaling networks mediating stress responsive transitions of microalgae at physiological level. Furthermore, the differential gene expression signifying the transporters involved in uptake, distribution/sequestration, and efflux of heavy metal has also been reviewed. In a nutshell, this study provided a comprehensive understanding of the molecular mechanisms adopted by microalgae at transcriptome level to nullify the oxidative stress while detoxifying the heavy metals.

Application of in situ bioremediation strategies in soils amended with sewage sludges

Increasing soil loss and the scarcity of useful land requires new reusing strategies. Thus, recovery of polluted soils recovery offers a chance for economic and social regeneration. With this objective, different soil cleaning technologies have been developed during the last few decades. On one hand, classical physical and/or chemical technologies can be found which are efficient, but have high costs and impacts upon ecosystems. On the other hand, biological methods (such as phytoremediation, bioremediation and vermiremediation) are relatively cost effective and eco-friendly, but also more time-consuming. These biological methods and their yields have been widely studied but little is known about the interaction between different soil cleaning methods. The combination of different biological strategies could lead to an improvement in remediation performance. Hence, in the present work, different micro-, vermi- and phyto-remediation combinations are applied in a sewage sludge polluted landfill in Gernika-Lumo (Basque Country) which was used as a disposal point for decades, in search of the treatment (single) or combination (dual or triple) of treatments with best remediation yields. Eight experimental groups were applied (n=3) placing earthworms (E), bacteria (B), plants (P), bacteria+earthworms (B+E), bacteria+plants (B+P), plants+earthworms (P+E) plants+bacteria+earthworms (P+B+E) and a non-treated (N.T.) group in the experimental plot (Landfill 17), for 12 months. In order to assess the efficiency of each treatment, a complete characterization (chemical and ecotoxicological) was carried out before and after remediation. Results showed high removal rates for dieldrin (between 50% and 78%) in all the experimental groups. In contrast, removal rates around 20-25% were achieved for heavy metals (Cd 15%-35%; Ni 24%-37%; Pb 15%-33%; Cr 7%-39%) and benzo(a)pyrene (19.5%-28%). The highest reductions were observed in dual (P+E, B+E) and triple (P+B+E) treatments. The best elimination yields were obtained after P+B+E treatment, as highlighted by the battery of ecotoxicological tests and bioassays performed with earthworms, plants and bacteria.

Study on molecular level toxicity of Sb(V) to soil springtails: using a combination of transcriptomics and metabolomics

To date, numerous studies have focused on the toxicity of antimony (Sb) to soil-dwelling organisms at the individual level. However, little is known about Sb-caused molecular level toxicity. Here, an integrated transcriptomics and metabolomics approach was used to better reveal toxicity of Sb(V) to springtails Folsomia candida considering environmentally relevant speciation of Sb. No significant effects of Sb(V) on survival, reproduction and growth of springtails were observed using the ISO standard test. Transcriptomics analysis identified 1015 and 3367 differentially expressed genes (DEGs) after 2 and 7 d of exposure, indicating an increasing transcriptomal changes with time. Significantly enriched top GO (Gene Ontology) terms (chitin metabolic process, chitin binding and extracellular region) were shared between the two time exposure groups. However, no enriched KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway was shared, with fatty acid metabolism and apoptosis-fly being the most significant pathway, respectively. Metabolomics analysis identified 155 differential changed metabolites (DCMs) in springtails after 7 d of exposure. Antifolate resistance was the most significantly enriched pathway, in which dihydrofolic acid was up-regulated and three purine nucleotides (adenosine 5'-monophosphate, inosine 5'-monophosphate, guanosine 5'-monophosphate) were down-regulated. This indicated obvious repression of DNA replication, which was also observed by transcriptomics. Additionally, metabolites level related to chitin, oxidative stress, and protein metabolism significantly changed, and these metabolites could also support and confirm main transcriptomic results. Thus, the combination of multiomics facilitated better understanding of the molecular level of toxicity of Sb(V) in Collembola.

High-throughput toxicogenomic screening of chemicals in the environment using metabolically competent hepatic cell cultures

The ToxCast in vitro screening program has provided concentration-response bioactivity data across more than a thousand assay endpoints for thousands of chemicals found in our environment and commerce. However, most ToxCast screening assays have evaluated individual biological targets in cancer cell lines lacking integrated physiological functionality (such as receptor signaling, metabolism). We evaluated differentiated HepaRGTM cells, a human liver-derived cell model understood to effectively model physiologically relevant hepatic signaling. Expression of 93 gene transcripts was measured by quantitative polymerase chain reaction using Fluidigm 96.96 dynamic arrays in response to 1060 chemicals tested in eight-point concentration-response. A Bayesian framework quantitatively modeled chemical-induced changes in gene expression via six transcription factors including: aryl hydrocarbon receptor, constitutive androstane receptor, pregnane X receptor, farnesoid X receptor, androgen receptor, and peroxisome proliferator-activated receptor alpha. For these chemicals the network model translates transcriptomic data into Bayesian inferences about molecular targets known to activate toxicological adverse outcome pathways. These data also provide new insights into the molecular signaling network of HepaRGTM cell cultures.

Insights into the mechanisms underlying the remediation potential of earthworms in contaminated soil: A critical review of research progress and prospects

In recent years, soil pollution is a major global concern drawing worldwide attention. Earthworms can resist high concentrations of soil pollutants and play a vital role in removing them effectively. Vermiremediation, using earthworms to remove contaminants from soil or help to degrade non-recyclable chemicals, is proved to be an alternative, low-cost technology for treating contaminated soil. However, knowledge about the mechanisms and framework of the vermiremediation various organic and inorganic contaminants is still limited. Therefore, we reviewed the research progress of effects of soil contaminants on earthworms and potential of earthworm used for remediation soil contaminated with heavy metals, polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), polycyclic aromatic hydrocarbons (PAHs), pesticides, as well as crude oil. Especially, the possible processes, mechanisms, advantages and limitations, and how to boost the efficiency of vermiremediation are well addressed in this review. Finally, future prospects of vermiremediation soil contamination are listed to promote further studies and application of vermiremediation in contaminated soils.

Hyperaccumulation of cadmium by scallop Chlamys farreri revealed by comparative transcriptome analysis

Cadmium (Cd) is a hazardous environmental contaminant, which has a serious effect on the ecosystem, food safety and human health. Scallop could accumulate high concentration of Cd from the environment and has been regarded as a Cd hyper-accumulator. In this work, we investigated the antioxidative defense, detoxification and transport of Cd in the kidneys of scallops by transcriptome analysis. A total of 598 differentially expressed genes including 387 up-regulated and 211 down-regulated ones were obtained during Cd exposure, and 46 up-regulated and 260 down-regulated ones were obtained during depuration. Cadmium exposure could cause oxidative stress in the kidneys, which was particularly shown in the pathways involved in proteasome and oxidative phosphorylation. The mRNA expression of 5 metallothionein (MT) genes were overexpressed under Cd exposure and significantly decreased during Cd depuration, which played a vital role in Cd chelation and detoxification. The expression of divalent metal transporter (DMT) genes were down-regulated insignificantly during accumulation and depuration of Cd, which suggested that the DMT played little roles in Cd transport in scallops. A positive relationship in the expression of the zinc transporter (ZIP6 and ZIP1) genes with Cd exposure and depuration was observed, which confirmed its important role for Cd uptake in the kidneys of scallops. 26S proteasome activities and MT expression were Cd-dependent. This study supplied the important reference on the hyperaccumulation of Cd by scallops and identified some effective bioindicators for the environmental risk assessment.

Epigenetic effects of (nano)materials in environmental species - Cu case study in Enchytraeus crypticus

Chemical stressors can induce epigenomic changes, i.e., changes that are transferred to the next generation, even when the stressor is removed. Literature on chemical induced epigenetic effects in environmental species is scarce. We here provide the first results on epigenetic effects caused by nanomaterials with an environmental OECD standard soil model species Enchytraeus crypticus species. We assessed the epigenetic potential in terms of global DNA methylation, gene-specific methylation via bisulfite sequencing and MS-HRM (Methylation Sensitive - High Resolution Melting), and gene expression qPCR for genes involved in DNA methylation, histone modifications, non-coding RNA and stress response mechanisms). We have exposed E. crypticus in a multigenerational (MG) test design to Cu (copper oxide nanomaterials (CuO NMs) and copper salt (CuCl₂)). To link possible epigenetic effects to population changes, we used exposure concentrations (ECx) that caused a 10% and 50% reduction in the reproductive output (10% and 50% are the standards for regulatory Risk Assessment), the organisms were exposed for five consecutive generations (F1-F5) plus two generations after transferring to clean media (F5-F7), 7 generations in a total of 224 days. Results showed that MG exposure to Cu increased global DNA methylation and corresponded with phenotypic effects (reproduction). Gene expression analyses showed changes in the epigenetic, stress and detoxification gene targets, depending on the generation and Cu form, also occurring in post-exposure generations, hence indicative of transgenerational effects. There were in general clear differences between organisms exposed to different Cu-forms, hence indicate nanoparticulate-specific effects.

Bioaccumulation of decabromodiphenyl ether affects the antioxidant system in the clam Mactra veneriformis

Antioxidant enzymes play vital roles against oxidative stress induced by decabromodiphenyl ether (BDE-209), being widespread in marine environment. However, the effect of BDE-209 on antioxidant enzymes remains poorly understood in marine bivalves. In this study, the clams Mactra veneriformis were exposed to 0.1, 1, and 10 μg/L BDE-209 for 7 days and then maintained in clean seawater for 3 days as the depuration. The bioaccumulation of BDE-209 and the effects on superoxide dismutase, catalase, and glutathione peroxidase were investigated. BDE-209 accumulation was concentration-dependent and decreased by 36%-52% after recovery. Malondialdehyde contents increased in a time- and dose-dependent manner. mRNA expression and activity of antioxidant enzymes changed with different patterns and recovered after depuration. These results suggested that antioxidant systems were triggered to protect the clams from oxidative damage caused by BDE-209. Thus, this research is helpful in elucidating the effect of BDE-209 on antioxidant system in marine bivalves.

Protective role of metallothionein during regeneration in Eisenia andrei exposed to cadmium

Lumbricid earthworms are often exposed to simultaneous action of various environmental stressors like soil contamination, temperature fluctuation or predators' attacks, which may induce extrusion of coelomocyte-containing coelomic fluid or loss of tail segments. If the injuries are not lethal, renewal of the immune-competent cells and soluble components of coelomic fluid and/or the regeneration of tail segments occurs. The aim of our investigations was to test the hypothesis that exposure of adult earthworms Eisenia andrei to cadmium-polluted soil at room temperature (RT) and/or low temperature (6°C) have adverse effects on restoration of experimentally depleted coelomocytes or on regeneration of amputated posterior segments. Intact control earthworms and their experimental counterparts subjected to electrostimulation-induced coelomocyte depletion or surgical amputation of posterior segments were maintained either in control soil or in soil spiked with cadmium chloride (500mg/kg air-dried soil) at RT or 6°C. Four weeks after the beginning of experiments, cadmium accumulation in earthworm bodies was significantly lower at 6°C than at room temperature. The numbers of restored cells and fluorophore contents were hardly affected by temperature or cadmium. However, cocoon production was reduced by cadmium and completely abolished at 6°C and regeneration of amputated posterior segments was inhibited in cold but was enhanced by cadmium exposure at RT. Independently on the temperature, the 4-week cadmium exposure of adult earthworms was connected with significantly upregulated expression of Cd-metallothionein (but not of catalase, lysenin and phytochelatin) in coelomocytes.

Evaluation of biomarkers for ecotoxicity assessment by dose-response dynamic models: Effects of nitrofurazone on antioxidant enzymes in the model ciliated protozoan Euplotes vannus

Understanding dose-responses is crucial for determining the utility of biomarkers in ecotoxicity assessment. Nitrofurazone is a broad-spectrum antibiotic that is widely used in the aquaculture industry in China despite its detrimental effects on ecosystems. Potential dose-response models were examined for the effect of nitrofurazone on two antioxidant enzymes, superoxide dismutase (SOD) and glutathione peroxidase (GPx), in the ciliated protozoan Euplotes vannus. This was achieved by measuring enzyme activity and gene expression profiling of SOD and GPx in ciliate cells exposed to nitrofurazone at doses ranging from 0 to 180mgl^-1 for 6h, 12h, 18h and 24h. Dose-response dynamics were characterized by mathematical models. Results showed that: 1) dose-response patterns differed significantly among the tested endpoints, nitrofurazone concentrations and durations of exposure; 2) GPx activity was the best candidate biomarker because of its linear dose-response relationship; 3) SOD activity and mRNA relative expression levels of GPx and SOD are also candidate biomarkers but their dose-responses were non-linear and therefore more difficult to interpret; 4) partitioning the dose-response dynamic model by piecewise function can help to clarify the relationships between biological endpoints. This study demonstrates the utility of dynamic model analysis and the potential of antioxidant enzymes, in particular GPx activity, as a candidate biomarkers for environmental monitoring and risk assessment of nitrofurazone in the aquaculture industry.

1H NMR Metabolic Profiling of Earthworm (Eisenia fetida) Coelomic Fluid, Coelomocytes, and Tissue: Identification of a New Metabolite-Malylglutamate

Earthworm metabolism is recognized as a useful tool for monitoring environmental insults and measuring ecotoxicity, yet extensive earthworm metabolic profiling using ¹H nuclear magnetic resonance (NMR) spectroscopy has been limited in scope. This study aims to expand the embedded metabolic material in earthworm coelomic fluid, coelomocytes, and tissue to aid systems toxicology research. Fifty-nine metabolites within Eisenia fetida were identified, with 47 detected in coelomic fluid, 41 in coelomocytes, and 54 in whole-worm samples and tissue extracts. The newly detected but known metabolites 2-aminobutyrate, nicotinurate, Nδ,Nδ,Nδ-trimethylornithine, and trigonelline are reported along with a novel compound, malylglutamate, elucidated using 2D NMR and high-resolution MS/MS. We postulate that malylglutamate acts as a glutamate/malate store, chelator, and anionic osmolyte and helps to provide electrolyte balance.

Antioxidant and gene expression responses of Eisenia fetida following repeated exposure to BDE209 and Pb in a soil-earthworm system

This study first adopted repeated treatment model to investigate stress responses in earthworms (Eisenia fetida) following exposure to decabromodiphenyl ether (BDE209) and lead (Pb), which are the mainly co-existed contaminants at e-waste recycling sites. We evaluated the impacts of BDE209-Pb on antioxidative enzyme (superoxide dismutase, SOD; catalase, CAT) activities, malondialdehyde (MDA) contents and transcriptional levels of three target genes (SOD, CAT and Hsp70), and further explored the relationships among these biomarkers. Results demonstrated that almost all the parameters were generally induced and the responses followed certain dose-effect relationships. Compared to the controls, a significant (P<0.05) up-regulation trend of expression levels of the three genes could be clearly observed after 14days incubation. Additionally, there existed good correlations between target genes expression levels and antioxidant enzyme activities (R>0.64). The observations could provide important information of ecotoxicological effects of BDE209-Pb in a soil-earthworm system as well as the mechanism of antioxidant defense.

Gene expression profile changes in Eisenia fetida chronically exposed to PFOA

Eisenia fetida is a terrestrial organism, which can be used to diagnose sub-lethal concentrations of PFOA by using molecular biomarkers. In order to identify potential molecular biomarkers, we have exposed E. fetida to 10 mg/kg of PFOA in soil for 8 months. The mRNA isolation, sequencing, transcriptome assembly followed by differential gene expression studies have revealed that genes that are involved in apoptotic process, reproduction, calcium signalling, neuronal development and lipid metabolism are predominantly affected. Highly specific genes that are altered by PFOA can be further validated and used as biomarker to detect sub-lethal concentrations of PFOA in the soil.

Responses of growth inhibition and antioxidant gene expression in earthworms (Eisenia fetida) exposed to tetrabromobisphenol A, hexabromocyclododecane and decabromodiphenyl ether

Tetrabromobisphenol A (TBBPA), hexabromocyclododecane (HBCD) and decabromodiphenyl ether (BDE 209), suspected ubiquitous contaminants, account for the largest volume of brominated flame retardants (BFRs) since penta-BDE and octa-BDE have been phased out globally. In this paper, the growth inhibition and gene transcript levels of antioxidant enzymes (superoxide dismutase (SOD), catalase (CAT)) and the stress-response gene involved in the prevention of oxidative stress (Hsp70) of earthworms (Eisenia fetida) exposed to TBBPA, HBCD and BDE 209 were measured to identify the toxicity effects of selected BFRs on earthworms. The growth of earthworms treated by TBBPA at 200 and 400 mg/kg dw were inhibited at rate of 13.7% and 22.0% respectively, while there was no significant growth inhibition by HBCD and BDE 209. A significant (P<0.01) up-regulation of SOD expression level was observed in earthworms exposed to TBBPA at 50 mg/kg dw (1.77-fold) and to HBCD at 400 mg/kg dw (2.06-fold). The transcript level of Hsp70 gene was significantly up-regulated (P<0.01) when earthworms exposed to TBBPA at concentration of 50-200 mg/kg (2.16-2.19-fold) and HBCD at 400 mg/kg (2.61-fold). No significant variation of CAT gene expression in all the BFRs treatments was observed, neither does all the target gene expression level exposed to BDE 209. Assessed by growth inhibition and the changes at mRNA levels of encoding genes in earthworms, TBBPA showed the greatest toxicity, followed by HBCD and BDE 209, consistent with trends in molecular properties. The results help to understand the molecular mechanism of antioxidant defense.

Abiotic stressors and stress responses: What commonalities appear between species across biological organization levels?

Organisms are regularly subjected to abiotic stressors related to increasing anthropogenic activities, including chemicals and climatic changes that induce major stresses. Based on various key taxa involved in ecosystem functioning (photosynthetic microorganisms, plants, invertebrates), we review how organisms respond and adapt to chemical- and temperature-induced stresses from molecular to population level. Using field-realistic studies, our integrative analysis aims to compare i) how molecular and physiological mechanisms related to protection, repair and energy allocation can impact life history traits of stressed organisms, and ii) to what extent trait responses influence individual and population responses. Common response mechanisms are evident at molecular and cellular scales but become rather difficult to define at higher levels due to evolutionary distance and environmental complexity. We provide new insights into the understanding of the impact of molecular and cellular responses on individual and population dynamics and assess the potential related effects on communities and ecosystem functioning.

Dermal exposure of Eisenia andrei earthworms: Effects of heavy metals on metallothionein and phytochelatin synthase gene expressions in coelomocytes

Parameters such as total number of coelomocytes, riboflavin content in coelomocytes, expression of genes implied in metal homeostasis, and detoxification mechanisms can be used as biomarkers to assess the impact of metals on annelids. Defense biomarkers (detoxification gene expressions and coelomocyte parameters) were investigated in the ecotoxicologically important species Eisenia andrei following in vivo exposure to 5 different metals (zinc, copper, nickel, lead, and cadmium) at known concentrations. Coelomocyte numbers and riboflavin content were not affected by metallic exposure, but metal-specific gene expression variations were evidenced.

Transcriptomic response to estrogen exposure in the male Zhikong scallop, Chlamys farreri

The transcriptomes of Zhikong scallop exposed to 17β-estradiol were determined using the Roche/454. A total of 51,997 unigenes, representing 45,030 contigs and 6967 singlets were obtained. And 14,028, 19,798 and 14,981 of these unigenes were annotated from the non-redundant nucleic acid database, non-redundant protein database and Swiss protein database, respectively. A total of 10,699 unigenes were further annotated to biological processes (9080), molecular functions (8692) and cellular components (7829) using the GO, and 8945 unigenes were mapped to biological pathways including the metabolism (2862) and genetic information processing (2263). Most importantly, 16,692 unigenes and 18,686 unigenes in testis, and 10,492 unigenes and 13,186 unigenes in digestive gland were up-regulated significantly after exposure to 50 and 500 ng E2/L; while 10,212 unigenes and 9409 unigenes in testis and 10,629 unigenes and 9463 unigenes in digestive gland were down-regulated. These valuable information provides insights into the mechanisms in invertebrate exposure to EDCs.

Chronic PFOS exposure alters the expression of neuronal development-related human homologues in Eisenia fetida

PFOS is a toxic, persistent environmental pollutant which is widespread worldwide. PFOS contamination has entered the food chain and is interfering with normal development in man and is neurotoxic, hepatotoxic and tumorigenic. The earthworm, Eisenia fetida is one of the organisms which can help to diagnose soil health and contamination at lower levels in the food chain. Studying the chronic effects of sub-lethal PFOS exposure in such an organism is therefore appropriate. As PFOS bioaccumulates and is not easily biodegraded, it is biomagnified up the food chain. Gene expression studies will give us information to develop biomarkers for early diagnosis of soil contamination, well before this contaminant passes up the food chain. We have carried out mRNA sequencing of control and chronically PFOS exposed E. fetida and reconstructed the transcripts in silico and identified the differentially expressed genes. Our findings suggest that PFOS up/down regulates neurodegenerative-related human homologues and can cause neuronal damage in E. fetida. This information will help to understand the links between neurodegenerative disorders and environmental pollutants such as PFOS. Furthermore, these up/down regulated genes can be used as biomarkers to detect a sub-lethal presence of PFOS in soil. Neuronal calcium sensor-2, nucleoside diphosphate kinase, polyadenylate-binding protein-1 and mitochondrial Pyruvate dehydrogenase protein-X component, could be potential biomarkers for sub lethal concentrations of PFOS.

Effects of zinc on CarE activities and its gene transcript level in the English grain aphid, Sitobion avenae

As a selective stress, heavy metals play an important role in inducing the adaptive adjustments of insects to changing environments. Carboxylesterase (CarE) is one kind of biomarker that could help us to explore the adaptation mechanism of aphids to heavy metal stress. In this study, CarE activity and gene expression level were investigated in English grain aphids, Sitobion avenae (F.) (Hemiptera: Aphididae), exposed to Zn2+ at concentrations of 0, 400, and 1600 mg/kg for 5, 15, 25, and 30 generations. The results showed that the CarE activity was significantly different between different Zn2+ concentrations and different generations. The CarE activity significantly decreased with increasing generations. In the higher generations, the CarE activity was strongly inhibited by the 1600 mg/kg of Zn2+. Realtime quantitative PCR revealed that the CarE gene expression pattern in S. avenae was up-regulated under the condition of 400 mg/kg and 1600 mg/kg of Zn2+, but a significant difference was not found after long-term exposure to high concentrations of Zn2+. It was concluded that CarE could be the sensitive biomarker for S. avenae response to the presence of Zn2+. In order to adapt to heavy metal Zn2+ stress, S. avenae had particular patterns of gene expression under long-term stress.

Using biomarkers in an evolutionary context: lessons from the analysis of biological responses of oligochaete annelids to metal exposure

Anthropogenic activities may lead to the accumulation of inorganic and organic compounds in topsoils. Biota living in close contact with contaminated soils may experience stress at different levels of biological organization throughout the continuum from molecular to community level. Biological responses observed at the individual or infra-individual level of biological organization led to the development of biomarkers. The development of biomarkers consists often in evidencing biological modifications following a contaminant stress in laboratory conditions, using naïve organisms and it is sometime proposed to use the biological state of individuals from sentinel species collected in the field to evaluate the level of environmental exposure. However, considering the possibility of local adaptation following long-term exposure, organisms response sampled in the field may substantially differ from laboratory specimens. In this review, we discuss this point focusing on the definition and validity of molecular biomarkers of metal pollution using earthworms of the Lumbricidae family.

SSH gene expression profile of Eisenia andrei exposed in situ to a naturally contaminated soil from an abandoned uranium mine

The effects of the exposure of earthworms (Eisenia andrei) to contaminated soil from an abandoned uranium mine, were assessed through gene expression profile evaluation by Suppression Subtractive Hybridization (SSH). Organisms were exposed in situ for 56 days, in containers placed both in a contaminated and in a non-contaminated site (reference). Organisms were sampled after 14 and 56 days of exposure. Results showed that the main physiological functions affected by the exposure to metals and radionuclides were: metabolism, oxireductase activity, redox homeostasis and response to chemical stimulus and stress. The relative expression of NADH dehydrogenase subunit 1 and elongation factor 1 alpha was also affected, since the genes encoding these enzymes were significantly up and down-regulated, after 14 and 56 days of exposure, respectively. Also, an EST with homology for SET oncogene was found to be up-regulated. To the best of our knowledge, this is the first time that this gene was identified in earthworms and thus, further studies are required, to clarify its involvement in the toxicity of metals and radionuclides. Considering the results herein presented, gene expression profiling proved to be a very useful tool to detect earthworms underlying responses to metals and radionuclides exposure, pointing out for the detection and development of potential new biomarkers.

Metal bioaccumulation, genotoxicity and gene expression in the European wood mouse (Apodemus sylvaticus) inhabiting an abandoned uranium mining area

Genotoxic effects caused by the exposure to wastes containing metals and radionuclides were investigated in the European wood mice (Apodemus sylvaticus). The animals were captured in the surroundings of an abandoned uranium mining site. DNA damage was assessed by comet assay; gene expression and single nucleotide polymorphisms (SNPs) were assessed, respectively, by Real-Time PCR and melt curve analysis. The bioaccumulation of metals in the liver, kidney and bones was also determined to help clarify cause-effect relationships. Results confirmed the bioaccumulation of cadmium and uranium in organisms exposed to uranium mining wastes. P53 gene was found to be significantly up-regulated in the liver of those organisms and SNPs in the Rb gene were also detected in the kidney. Our results showed that uranium mining wastes caused serious DNA damage resulting in genomic instability, disclosed by the significant increase in DNA strand breaks and P53 gene expression disturbance. These effects can have severe consequences, since they may contribute for the emergence of serious genetic diseases. The fact that mice are often used as bioindicator species for the evaluation of risks of environmental exposure to humans, raises concerns on the risks for human populations living near uranium mining areas.

Genetic variation in parthenogenetic collembolans is associated with differences in fitness and cadmium-induced transcriptome responses

Ecotoxicological tests may be biased by the use of laboratory strains that usually contain very limited genetic diversity. It is therefore essential to study how genetic variation influences stress tolerance relevant for toxicity outcomes. To that end we studied sensitivity to cadmium in two distinct genotypes of the parthogenetic soil ecotoxicological model organism Folsomia candida. Clonal lines of both genotypes (TO1 and TO2) showed divergent fitness responses to cadmium exposure; TO2 reproduction was 20% less affected by cadmium. Statistical analyses revealed significant differences between the cadmium-affected transcriptomes: i) the number of genes affected by cadmium in TO2 was only minor (~22%) compared to TO1; ii) 97 genes showed a genotype × cadmium interaction and their response to cadmium showed globally larger fold changes in TO1 when compared to TO2; iii) the interaction genes showed a concerted manner of expression in TO1, while a less coordinated pattern was observed in TO2. We conclude that (1) there is genetic variation in parthenogenetic populations of F. candida, and (2) this variation affects life-history and molecular end points relative to cadmium toxicity. This sheds new light on the sources of biological variability in test results, even when the test organisms are thought to be genetically homogeneous because of their parthenogenetic reproduction.

Transcriptional responses in Enchytraeus albidus (Oligochaeta): comparison between cadmium and zinc exposure and linkage to reproduction effects

Metal ecotoxicity to soil organisms (for example, in enchytraeids) has been addressed mainly by assessing effects on survival and reproduction, but very little is known about the underlying molecular mechanisms of responses. The main purpose of the present study was to assess and compare the transcriptional responses of Enchytraeus albidus to an essential (Zn) and a nonessential (Cd) metal. Exposure was performed with two concentrations with a known effect on reproduction (effective concentration for 50% [EC50] and 90% [EC90]) at three time points (2, 4, and 8 d). Results showed that transcriptional responses were influenced by exposure duration but, independently of that, the mechanisms of response to Cd and Zn were consistently different. Both metals affected pathways related to the regulation of gene expression, calcium homeostasis, and cellular respiration. Mechanisms of toxicity that were exclusively associated with Cd exposures were the inhibition of DNA repair and the impairment of ubiquitin-mediated proteolysis. The microarray for E. albidus was a useful tool for detecting molecular pathways affected by metal exposures. Transcriptional responses strongly correlated with known mechanisms of Cd and Zn responses in other organisms, suggesting cross-species conserved mechanisms of action. It should be highlighted not only that the authors could retrieve mechanistic information but also that genes responded within 2 to 8 d of exposure. This represents an additional advantage of using such molecular endpoints as a complement to the traditional, more time-consuming endpoints.

Biomarker measurements in Trifolium repens and Eisenia fetida to assess the toxicity of soil contaminated with landfill leachate: a microcosm study

To assess the toxicity of a soil contaminated with landfill leachate, biomarker measurements in two species living in close contact with the soil, i.e. a plant species Trifolium repens and an animal species Eisenia fetida, were conducted. Briefly, both species were studied after simultaneous exposure conducted in microcosms. The organisms were exposed to soil supplemented with pure leachate, leachate diluted to 50%; leachate diluted to 25% and without leachate. After a 10 weeks exposure period, we observed an increase in the Olive Trail Moment in T. repens, compared to the reference, for 50% and pure leachate. The response observed appears to be dose-dependent and linear in our experimental conditions. Addition of the leachate to the reference soil induced an increase in Cd-Metallothionein-coding mRNA quantity in E. fetida. In addition, expression level of another gene implied in detoxification and coding Phytochelatin synthase was significantly induced in worms exposed to the reference soil spiked with the leachate, regardless presence of T. repens. Thus, T. repens and E. fetida can be used in a complementary manner to assess soil quality. Sensitivities of the test species yield sensitive bioassays as both species responded at low doses despite the buffering effect of the soil.

Functional traits of soil invertebrates as indicators for exposure to soil disturbance

We tested a trait-based approach to link a soil disturbance to changes in invertebrate communities. Soils and macro-invertebrates were sampled in sandy soils contaminated by long-term wastewater irrigation, adding notably organic matter and trace metals (TM). We hypothesized that functional traits of invertebrates depict ways of exposure and that exposure routes relate to specific TM pools. Geophages and soft-body invertebrates were chosen to inform on exposure by ingestion or contact, respectively. Trait-based indices depicted more accurately effects of pollution than community density and diversity did. Exposure by ingestion had more deleterious effects than by contact. Both types of exposed invertebrates were influenced by TM, but geophages mainly responded to changes in soil organic matter contents. The trait-based approach requires to be applied in various conditions to uncorrelate specific TM impacts from those of other environmental factors.

Gene expression analysis of 4 biomarker candidates in Eisenia fetida exposed to an environmental metallic trace elements gradient: a microcosm study

Past activities of 2 smelters (Metaleurop Nord and Nyrstar) led to the accumulation of high amounts of Metal Trace Elements (TEs) in top soils of the Noyelles-Godault/Auby area, Northern France. Earthworms were exposed to polluted soils collected in this area to study and better understand the physiological changes, the mechanisms of acclimation, and detoxification resulting from TE exposure. Previously we have cloned and transcriptionally characterized potential biomarkers from immune cells of the ecotoxicologically important earthworm species Eisenia fetida exposed in vivo to TE-spiked standard soils. In the present study, analysis of expression kinetics of four candidate indicator genes (Cadmium-metallothionein, coactosin like protein, phytochelatin synthase and lysenin) was performed in E. fetida after microcosm exposures to natural soils exhibiting an environmental cadmium (Cd) gradient in a kinetic manner. TE body burdens were also measured. This microcosm study provided insights into: (1) the ability of the 4 tested genes to serve as expression biomarkers, (2) detoxification processes through the expression analysis of selected genes, and (3) influence of land uses on the response of potential biomarkers (gene expression or TE uptake).

Multilevel ecotoxicity assessment of polycyclic musk in the earthworm Eisenia fetida using traditional and molecular endpoints

The ecotoxicity assessment of galaxolide (HHCB) and tonalide (AHTN) was investigated in the earthworm Eisenia fetida using traditional and novel molecular endpoints. The median lethal concentration (LC(50)) for 7-day and 14-day exposures was 573.2 and 436.3 μg g(-1) for AHTN, and 489.0 and 392.4 μg g(-1) for HHCB, respectively. There was no observed significant effect on the growth rate of E. fetida after a 28-day exposure except that at the highest concentration (100 μg g(-1)) of AHTN and HHCB, whereas a significant decrease of cocoon production was found in earthworms exposed to 50 and 100 μg g(-1). To assess molecular-level effect, the expression of encoding antioxidant enzymes and stress protein genes were investigated upon sublethal exposures using the quantitative real time PCR assay. The expression level of SOD, CAT and calreticulin genes was up-regulated significantly, while the level of annetocin (ANN) and Hsp70 gene expression was down-regulated in E. fetida. Importantly, the level of ANN expression had a significant positive correlation with the reproduction rate of earthworms. Furthermore, the lowest observed effect concentration (LOECs) of ANN expression level was 3 μg g(-1) for AHTN and 10 μg g(-1) for HHCB, suggesting that ANN gene expression can serve as a more sensitive indicator of exposure to AHTN and HHCB than traditional endpoints such as cocoon production. The transcriptional responses of these genes may provide early warning molecular biomarkers for identifying contaminant exposure, and the data obtained from this study will contribute to better understand the toxicological effect of AHTN and HHCB.

High throughput nano-liter RT-qPCR to classify soil contamination using a soil arthropod

Background

To incorporate genomics data into environmental assessments a mechanistic perspective of interactions between chemicals and induced biological processes needs to be developed. Since chemical compounds with structural similarity often induce comparable biological responses in exposed animals, gene expression signatures can serve as a starting point for the assessment of chemicals and their toxicity, but only when relevant and stable gene panels are available. To design such a panel, we isolated differentially expressed gene fragments from the soil arthropod Folsomia candida, a species often used for ecotoxicological testing. Animals were exposed to two chemically distinct compounds, being a metal (cadmium) and a polycyclic aromatic hydrocarbon (phenanthrene). We investigated the affected molecular responses resulting from either treatment and developed and validated 44 qPCR assays for their responses using a high throughput nano-liter RT-qPCR platform for the analysis of the samples.

Results

Suppressive subtractive hybridization (SSH) was used to retrieve stress-related gene fragments. SSH libraries revealed pathways involved in mitochondrial dysfunction and protein degradation for cadmium and biotransformation for phenanthrene to be overrepresented. Amongst a small cluster of SSH-derived cadmium responsive markers were an inflammatory response protein and an endo-glucanase. Conversely, cytochrome P450 family 6 or 9 was specifically induced by phenanthrene. Differential expressions of these candidate biomarkers were also highly significant in the independently generated test sample set. Toxicity levels in different training samples were not reflected by any of the markers' intensity of expressions. Though, a model based on partial least squares differential analysis (PLS-DA) (with RMSEPs between 9 and 22% and R²s between 0.82 and 0.97) using gene expressions of 25 important qPCR assays correctly predicted the nature of exposures of test samples.

Conclusions

For the application of molecular bio-indication in environmental assessments, multivariate analyses obviously have an added value over univariate methods. Our results suggest that compound discrimination can be achieved by PLS-DA, based on a hard classification of the within-class rankings of samples from a test set. This study clearly shows that the use of high throughput RT-qPCR could be a valuable tool in ecotoxicology combining high throughput with analytical sensitivity.