Gene expression profiling to characterize sediment toxicity--a pilot study using Caenorhabditis elegans whole genome microarrays

Exposure to nanopolystyrene and its 4 chemically modified derivatives at predicted environmental concentrations causes differently regulatory mechanisms in nematode Caenorhabditis elegans

Nanoplastics represented by nanopolystyrene (NPS) and its chemically modified derivatives are environmentally ecotoxicological hotpots in recent years, but their toxicity and underlying mechanisms have not been fully identified. Here we employed Caenorhabditis elegans as an animal model to systematically compare the toxicity between nanopolystyrene and its 4 chemically modified derivatives (PS-PEG, PS-COOH, PS-SOOOH and PS-NH₂) at predicted environmental concentrations. Our study demonstrated that compared with PS exposed group, PS-NH₂ exposure (15 μg/L) caused a significant decline in lifespan by suppressed DAF-16/insulin signaling and shortened body length by inhibiting DBL-1/TGF β signaling. Different from PS-NH₂ exposed group, PS-SOOOH exposure (15 μg/L) could not cause changes in lifespan, but shortened body length by inhibiting DBL-1/TGF β signaling. In addition, PS-COOH, PS-SOOOH or PS-NH₂ exposure (1 μg/L or 15 μg/L) caused more serious toxicity in reducing locomotion behavior and causing gut barrier deficit. Hence the rank order in toxicity of PS-NH₂＞PS-SOOOH＞PS-COOH＞PS＞PS-PEG was identified. Furthermore, we also presented evidence to support the contention that the observed toxic effects on nematodes were linked to oxide stress and activation of anti-oxidative molecules for reversing the adverse effects induced by nanopolystyrene and its 4 chemically modified derivatives. Our data highlighted nanoplastics may be charge-dependently toxic to environmental organisms, and the screened low toxic modification may support polystyrene nanoparticles continued application for daily consumer goods and biomedicine.

Chironomidae (Midge) Sensitivities to Ammonia Using Multiple Endpoints in China and Australia for the Development of Water Quality Criteria for Freshwater River Systems in China

Deriving water quality criteria (WQC) for aquatic risk assessment requires sufficient toxicity data, which can determine the accuracy of WQC. Given that toxicity data vary between test species and endpoints, there is a great need to compare such data to generate the most suitable data set for WQC derivation. In the present study, a series of 11 ammonia exposure bioassays were conducted on Chironomidae species in either China or Australia, with test species and test endpoints varied (2 Chironomus sp., enzymatic up to lethal endpoints, and no-observed-effect concentration up to median lethal concentration [LC50] as endpoint metrics). There were no statistically significant differences between toxicity results generated from China compared to Australia using Chironomus sp., indicating that published data on native species generated in different countries could be appropriate for inclusion in the development of local Chinese WQC. In addition, the Chironomidae larvae laboratory-based toxicity value (LC50 = 384.6 mg/L) was lower than that of the in situ field-based toxicity value (LC50 ≥ 451.2 mg/L) where sensitive life stages are used, and, specifically for C. riparius, endpoints linked to biochemical and gene expression effects could be as sensitive as or more sensitive than chronic endpoints, both of which were more sensitive than acute endpoints. These findings help in the development of WQC by demonstrating the suitability of inclusion of toxicity data from a range of sources, as well as adding to the overall pool of knowledge regarding sensitivity to ammonia which can be used in aquatic risk assessment. Environ Toxicol Chem  2021;40:2899-2911. © 2021 SETAC.

Testing the low dose mixtures hypothesis from the Halifax project

In 2013, 60 scientists, representing a larger group of 174 scientists from 26 nations, met in Halifax, Nova Scotia to consider whether - using published research - it was logical to anticipate that a mixture of chemicals, each thought to be non-carcinogenic, might act together in that mixture as a virtual carcinogen. The group identified 89 such chemicals, each one affecting one or more Hallmark(s) - collectively covering all Hallmarks of Cancer - confirming the possibility that a chemical mixture could induce all the Hallmarks and function as a virtual carcinogen, thereby supporting the concern that chemical safety research that does not evaluate mixtures, is incomplete. Based on these observations, the Halifax Project developed the Low-Dose Carcinogenesis Hypothesis which posits "…that low-dose exposures to [mixtures of] disruptive chemicals that are not individually carcinogenic may be capable of instigating and/or enabling carcinogenesis." Although testing all possible combinations of over 80,000 chemicals of commerce would be impractical, prudence requires designing a methodology to test whether low-dose chemical mixtures might be carcinogenic. As an initial step toward testing this hypothesis, we conducted a mini review of published empirical observations of biological exposures to chemical mixtures to assess what empirical data exists on which to base future research. We reviewed studies on chemical mixtures with the criteria that the studies reported both different concentrations of chemicals and mixtures composed of different chemicals. We found a paucity of research on this important question. The majority of studies reported hormone related processes and used chemical concentrations selected to facilitate studying how mixtures behave in experiments that were often removed from clinical relevance, i.e., chemicals were not studied at human-relevant concentrations. New research programs must be envisioned to enable study of how mixtures of small doses of chemicals affect human health, starting, when at all possible, from non-malignant specimens when studies are done in vitro. This research should use human relevant concentrations of chemicals, expand research beyond the historic focus on endocrine endpoints and endocrine related cancers, and specifically seek effects that arise uniquely from exposure to chemical mixtures at human-relevant concentrations.

Zebrafish CYP1A expression in transgenic Caenorhabditis elegans protects from exposures to benzo[a]pyrene and a complex polycyclic aromatic hydrocarbon mixture

Polycyclic aromatic hydrocarbons (PAHs) are environmental toxicants primarily produced during incomplete combustion; some are carcinogens. PAHs can be safely metabolized or, paradoxically, bioactivated via specific cytochrome P450 (CYP) enzymes to more reactive metabolites, some of which can damage DNA and proteins. Among the CYP isoforms implicated in PAH metabolism, CYP1A enzymes have been reported to both sensitize and protect from PAH toxicity. To clarify the role of CYP1A in PAH toxicity, we generated transgenic Caenorhabditis elegans that express CYP1A at a basal (but not inducible) level. Because this species does not normally express any CYP1 family enzyme, this approach permitted a test of the role of basally expressed CYP1A in PAH toxicity. We exposed C. elegans at different life stages to either the PAH benzo[a]pyrene (BaP) alone, or a real-world mixture dominated by PAHs extracted from the sediment of a highly contaminated site on the Elizabeth River (VA, USA). This site, the former Atlantic Wood Industries, was declared a Superfund site due to coal tar creosote contamination that caused very high levels (in the [mg/mL] range) of high molecular weight PAHs within the sediments. We demonstrate that CYP1A protects against BaP-induced growth delay, reproductive toxicity, and reduction of steady state ATP levels. Lack of sensitivity of a DNA repair (Nucleotide Excision Repair)-deficient strain suggested that CYP1A did not produce significant levels of DNA-reactive metabolites from BaP. The protective effects of CYP1A in Elizabeth River sediment extract (ERSE)-exposed nematodes were less pronounced than those seen in BaP-exposed nematodes; CYP1A expression protected against ERSE-induced reduction of steady-state ATP levels, but not other outcomes of exposure to sediment extracts. Overall, we find that in C. elegans, a basal level of CYP1A activity is protective against the examined PAH exposures.

Toxicity of nonylphenol and nonylphenol ethoxylate on Caenorhabditis elegans

Among the most used chemicals in the world are nonionic surfactants. One of these environmental pollutants is nonylphenol ethoxylate (NP-9), also known as Tergitol, and its degradation product, nonylphenol (NP). The objective of this work was to determine the toxicity of NP and NP-9 in Caenorhabditis elegans. Wild-type L4 larvae were exposed to different concentrations of the surfactants to measure functional endpoints. Mutant strains were employed to promote the activation of toxicity signaling pathways related to mtl-2, gst-1, gpx-4, gpx-6, sod-4, hsp-70 and hsp-4. Additionally, stress response was also assessed using a daf-16::GFP transgenic strain. The lethality was concentration dependent, with 24-h LC₅₀ of 122 μM and 3215 μM for NP and NP-9, respectively. Both compounds inhibited nematode growth, although NP was more potent; and at non-lethal concentrations, nematode locomotion was reduced. The increase in the expression of tested genes was significant at 10 μM for NP-9 and 0.001 μM for NP, implying a likely role for the activation of oxidative and cellular stress, as well as metabolism pathways. With the exception of glutathione peroxidase, which has a bimodal concentration-response curve for NP, typical of endocrine disruption, the other curves for this xenobiotic in the strains evaluated were almost flat for most concentrations, until reaching 50-100 μM, where the effect peaked. NP and NP-9 induced the activation and nuclear translocation of DAF-16, suggesting that transcription of stress-response genes may be mediated by the insulin/IGF-1 signaling pathway. In contrast, NP-9 induced a concentration-dependent response for the sod-4 and hsp-4 mutants, with greater fluorescence induction than NP at similar levels. In short, NP and NP-9 affect the physiology of C. elegans and modulate gene expression related to ROS production, cellular stress and metabolism of xenobiotics.

Quantification of microplastics along the Caribbean Coastline of Colombia: Pollution profile and biological effects on Caenorhabditis elegans

The Caribbean Coast of Colombia has a flourishing plastic industry with weak and insufficient waste management policies and practices, leading to plastic pollution along its touristic beaches. In this work, primary and secondary microplastics (MPs) were surveyed at four different locations along the Colombian Caribbean Coast. Primary microplastics, specifically white new plastic pellets, represented the largest amount of MPs found, with densities decreasing in the order Cartagena > Coveñas > Puerto Colombia > Riohacha. This distribution was connected to the vicinity of MPs sources, marine currents and wind direction. The presence of secondary MPs was associated with urban centers and proximity to river mouths. The FTIR characterization showed polyethylene as the predominant resin type, with different degrees of surface oxidation. Aqueous extracts from sampled MPs were tested on Caenorhabditis elegans. Secondary MPs elicited greater toxicological responses than pellets, especially those from Cartagena Bay, suggesting MPs act as carriers for biologically-active pollutants.

Research Progress on Toxic Effects and Water Quality Criteria of Triclosan

Triclosan (TCS) is an effective broad-spectrum antimicrobial agent that is widely used in personal care products. It has been detected in different environmental media, and poses high potential ecological risk. In this article, we carried out a literature review of recent studies on the toxic effects of TCS from different aspects at the molecular, cell, tissue, organ, and individual level. TCS can exhibit acute toxicity to aquatic organisms, affect the normal expression and physiological function of enzymes and genes, and produce cytotoxicity. Many studies have demonstrated that TCS exerts significant endocrine-disrupting effects on organisms, interfering the normal physiological functions of the reproductive, thyroid, and nervous systems via related signaling pathways. Moreover, we reported current research on the water quality criteria of TCS and discuss possible future research directions.

Caenorhabditis elegans as a tool for environmental risk assessment: emerging and promising applications for a "nobelized worm"

Caenorhabditis elegans has been an invaluable model organism in research fields such as developmental biology and neurobiology. Neurotoxicity is one of the subfields greatly profiting from the C. elegans model within biomedical context, while the corresponding potential of the organism applied to environmental studies is relevant but has been largely underexplored. Within the biomedical scope, the implication of metals and organic chemicals with pesticide activity (hereinafter designated as pesticides) in the etiology of several neurodegenerative diseases has been extensively investigated using this nematode as a primary model organism. Additionally, as a well-known experimental model bearing high sensitivity to different contaminants and representing important functional levels in soil and aquatic ecosystems, C. elegans has high potential to be extensively integrated within Environmental Risk Assessment (ERA) routines. In spite of the recognition of some regulatory agencies, this actual step has yet to be made. The purpose of this review is to discuss the major advantages supporting the inclusion of C. elegans in lower tiers of ERA. Special emphasis was given to its sensitivity to metals and pesticides, which is similar to that of other model organisms commonly used in ERA (e.g. Daphnia magna and Eisenia sp.), and to the large array of endpoints that can be tested with the species, both concerning the aquatic and the soil compartments. The inclusion of C. elegans testing may hence represent a relevant advance in ERA, providing ecologically relevant insights toward improvement of the regulatory capacity for establishing appropriate environmental protection benchmarks.

The impact of nanoparticles zero-valent iron (nZVI) and rhizosphere microorganisms on the phytoremediation ability of white willow and its response

Soil contaminated with heavy metals (HMs) is a serious problem throughout the world that threatens all living organisms in the soil. Therefore, large-scale remediation is necessary. This study investigated a new combination of remediation techniques on heavy metal contaminated soil, phytoremediation, and soil amendment with nano-sized zero-valent iron (nZVI) and rhizosphere microorganisms. White willow (Salix alba L.) was grown for 160 days in pots containing Pb, Cu, and Cd and amended with 0, 150, and 300 (mg kg^-1) of nZVI and rhizosphere microorganisms, including the arbuscular mycorrhizal fungus (AMF), Rhizophagus irregularis, and the plant growth promoting rhizobacteria (PGPR), Pseudomonas fluorescens. The results showed that inoculation with PGPR and AMF, particularly dual inoculation, improved plant growth as well as the physiological and biochemical parameters of white willow, and increased the bioconcentration factor (BCF) of Pb, Cu, and Cd. The low dose of nZVI significantly increased the root length and the leaf area of the seedlings and increased the BCF of Cd. In contrast, the high dose of nZVI had negative effects on the seedlings growth and the BCF of Pb and Cu, about - 32% and - 63%, respectively. Our results demonstrate that nZVI at low doses can improve plant performance in a phytoremediation context and that the use of beneficial rhizosphere microorganisms can minimize nZVI stress in plants and make them less susceptible to stress even under high dose conditions.

Ecotoxicological impacts of surface water and wastewater from conventional and advanced treatment technologies on brood size, larval length, and cytochrome P450 (35A3) expression in Caenorhabditis elegans

Anthropogenic micropollutants and transformation products (TPs) negatively affect aquatic ecosystems and water resources. Wastewater treatment plants (WWTP) represent major point sources for (micro)pollutants and TPs in urban water cycles. The aim of the current study was to assess the removal of micropollutants and toxicity during conventional and advanced wastewater treatment. Using wild-type and transgenic Caenorhabditis elegans, the endpoint reproduction, growth, and cytochrome P450 (CYP) 35A3 induction (via cyp-35A3::GFP) were assessed. Samples were collected at four WWTPs and a receiving surface water. One WWTP included the advanced treatments: ozonation followed by granular activated carbon (GAC) or biological filtration (BF), respectively. Relevant micropollutants and WWTP parameters (n = 111) were included. Significant reproductive toxicity was detected for one WWTP effluent (31-83% reduced brood size). Three of four effluents significantly promoted the growth of C. elegans larvae (49-55% increased lengths). This effect was also observed for the GAC (34-41%) and BF (30%) post-treatments. Markedly, significant cyp-35A3::GFP induction was detected for one effluent before and after ozonation, being more pronounced for the ozonated samples (5- and 7.4-fold above controls). While the advanced treatments decreased the concentrations of most micropollutants, the observed effects may be attributed to effects of residual target compounds and/or compounds not included in the target chemical analysis. This highlights the need for an integrated assessment of (advanced) wastewater treatment covering both biological and chemical parameters.

Transcriptional changes measured in rice roots after exposure to arsenite-contaminated sediments

Transcriptional analyses are discussed to provide a deeper understanding of the molecular mechanisms underlying toxic effects. Thus, they can complement classic ecotoxicological test methods and potentially allow the identification of biomarkers associated to the exposure of chemical stressors and or adverse biological effects. This feasibility study intended to identify a set of potential gene expression biomarkers for arsenite-exposure in rice roots that could complement the informative value of an existing sediment-contact test with rice. A sediment-contact test with Oryza sativa with the parameters inhibition of root and shoot elongation as phenotypic endpoints was used as basis. Rice plants were exposed to arsenite-spiked sediments. Transcriptomic changes in response to arsenite were observed by means of cDNA-microarray analysis regarding the whole-transcriptome at two sublethal arsenite concentrations. In order to identify candidate biomarker genes, differentially expressed genes were identified. Arsenite-induced differentially expressed genes were significantly associated with gene ontology (GO)-terms that indicated a general stress response. Of the differentially expressed genes, five genes were selected and their expression was measured at seven arsenite concentrations by means of qPCR in order to obtain their expression profiles. Three candidate biomarker genes showed a dose-dependent upregulation, while two showed no clear dose-dependent expression. The expression of all candidate biomarkers was also assessed in rice plants grown on two arsenic-contaminated natural sediments, but only one biomarker gene showed the expected upregulation.

Toxicity profile of organic extracts from Magdalena River sediments

The Magdalena River, the main river of Colombia, receives contaminated effluents from different anthropogenic activities along its path. However, the Magdalena River is used as drinking water source for approximately 30 million inhabitants, as well as a major source of fish for human consumption. Only a few studies have been conducted to evaluate the environmental and toxicological quality of the Magdalena River. To evaluate sediment toxicity, wild-type and GFP transgenic Caenorhabditis elegans were exposed to methanolic extracts, and effects on lethality, locomotion, growth, and gene expression were determined based on fluorescence spectroscopy. These biological and biochemical parameters were correlated with measured pollutant concentrations (PAHs and trace elements), identifying patterns of toxicity along the course of the river. Effects on lethality, growth, and locomotion were observed in areas influenced by industrial, gold mining, and petrochemical activities. Changes in gene expression were evident for cyp-34A9, especially in the sampling site located near an oil refinery, and at the seaport, in Barranquilla City. Body bend movements were moderately correlated with Cr and As concentrations. The expression of mtl-1, mtl-2, hsp-6, and hsp-70 were significantly associated with Pb/U, Pb, Sr, and As/Sr/Pb/U, respectively. Interestingly, toxicity of methanolic as well as aqueous extracts were more prone to be dependent on Cd, Zn, and Th. In general, ecological risk assessment showed sediments display low environmental impact in terms of evaluated metals and PAHs. Different types of waste disposal on the Magdalena River, as a result of mining, domestic, agricultural, and industrial activities, incorporate toxic pollutants in sediments, which are capable of generating a toxic response in C. elegans.

Transcriptomic alterations in the brain of painted turtles (Chrysemys picta) developmentally exposed to bisphenol A or ethinyl estradiol

Developmental exposure of turtles and other reptiles to endocrine-disrupting chemicals (EDCs), including bisphenol A (BPA) and ethinyl estradiol (EE), can stimulate partial to full gonadal sex-reversal in males. We have also recently shown that in ovo exposure to either EDC can induce similar sex-dependent behavioral changes typified by improved spatial learning and memory or possibly feminized brain responses. Observed behavioral changes are presumed to be due to BPA- and EE-induced brain transcriptomic alterations during development. To test this hypothesis, we treated painted turtles (Chrysemys picta) at developmental stage 17, incubated at 26°C (male-inducing temperature), with 1) BPA (1 ng/µl), 2) EE (4 ng/µl), or 3) vehicle ethanol (control group). Ten months after hatching and completion of the behavioral tests, juvenile turtles were euthanized, brains were collected and frozen in liquid nitrogen, and RNA was isolated for RNA-Seq analysis. Turtles exposed to BPA clustered separately from EE-exposed and control individuals. More transcripts and gene pathways were altered in BPA vs. EE individuals. The one transcript upregulated in both BPA- and EE-exposed individuals was the mitochondrial-associated gene, ND5, which is involved in oxidative phosphorylation. Early exposure of turtles to BPA increases transcripts linked with ribosomal and mitochondrial functions, especially bioenergetics, which has been previously linked with improved cognitive performance. In summary, even though both BPA and EE resulted in similar behavioral alterations, they diverge in the pattern of neural transcript alterations with early BPA significantly upregulating several genes involved in oxidative phosphorylation, mitochondrial activity, and ribosomal function, which could enhance cognitive performance.

Distinct transcriptomic responses of Caenorhabditis elegans to pristine and sulfidized silver nanoparticles

Manufactured nanoparticles (MNP) rapidly undergo aging processes once released from products. Silver sulfide (Ag2S) is the major transformation product formed during the wastewater treatment process for Ag-MNP. We examined toxicogenomic responses of pristine Ag-MNP, sulfidized Ag-MNP (sAg-MNP), and AgNO3 to a model soil organism, Caenorhabditis elegans. Transcriptomic profiling of nematodes which were exposed at the EC30 for reproduction for AgNO3, Ag-MNP, and sAg-MNP resulted in 571 differentially expressed genes. We independently verified expression of 4 genes (numr-1, rol-8, col-158, and grl-20) using qRT-PCR. Only 11% of differentially expressed genes were common among the three treatments. Gene ontology enrichment analysis also revealed that Ag-MNP and sAg-MNP had distinct toxicity mechanisms and did not share any of the biological processes. The processes most affected by Ag-MNP relate to metabolism, while those processes most affected by sAg-MNP relate to molting and the cuticle, and the most impacted processes for AgNO3 exposed nematodes was stress related. Additionally, as observed from qRT-PCR and mutant experiments, the responses to sAg-MNP were distinct from AgNO3 while some of the effects of pristine MNP were similar to AgNO3, suggesting that effects from Ag-MNP is partially due to dissolved silver ions.

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.

Global gene expression profiling using heterologous DNA microarrays to analyze alterations in the transcriptome of Mus spretus mice living in a heavily polluted environment

Microarray platforms are a good approach for assessing biological responses to pollution as they enable the simultaneous analyses of changes in the expression of thousands of genes. As an omic and non-targeted methodology, this technique is open to unforeseen responses under particular environmental conditions. In this study, we successfully apply a commercial oligonucleotide microarray containing Mus musculus whole-genome probes to compare and assess the biological effects of living in a heavily polluted settlement, the Domingo Rubio stream (DRS), at the Huelva Estuary (SW Spain), on inhabitant free-living Mus spretus mice. Our microarray results show that mice living in DRS suffer dramatic changes in gene and protein expression compared with reference specimens. DRS mice showed alteration in the oxidative status of hepatocytes, with activation of both the innate and the acquired immune responses and the induction of chronic inflammation, accompanied by metabolic alterations that imply the accumulation of lipids in the liver (hepatic steatosis). The identified deregulated genes may be useful as biomarkers of environmental pollution.

Challenges for using quantitative PCR test batteries as a TIE-type approach to identify metal exposure in benthic invertebrates

The epibenthic amphipod Melita plumulosa shows unique gene expression profiles when exposed to different contaminants. We hypothesized that specific changes in transcript abundance could be used in a battery of quantitative polymerase chain reaction (qPCR) assays as a toxicity identification evaluation (TIE)-like approach to identify the most relevant stressor in field-contaminated sediments. To test this hypothesis, seven candidate transcriptomic markers were selected, and their specificity following metal exposure was confirmed. The performance of these markers across different levels of added metals was verified. The ability of these transcripts to act as markers was tested by exposing amphipods to metal-contaminated field-collected sediments and measuring changes in transcript abundance via qPCR. For two of the three sediments tested, at least some of the transcriptomic patterns matched our predictions, suggesting that they would be effective in helping to identify metal exposure in field sediments. However, following exposure to the third sediment, transcriptomic patterns were unlike our predictions. These results suggest that the seven transcripts may be insufficient to discern individual contaminants from complex mixtures and that microarray or RNA-Seq global gene expression profiles may be more effective for TIE. Changes in transcriptomics based on laboratory exposures to single compounds should be carefully validated before the results are used to analyze mixtures.

Adsorbable organic bromine compounds (AOBr) in aquatic samples: a nematode-based toxicogenomic assessment of the exposure hazard

Elevated levels of adsorbable organic bromine compounds (AOBr) have been detected in German lakes, and cyanobacteria like Microcystis, which are known for the synthesis of microcystins, are one of the main producers of natural organobromines. However, very little is known about how environmental realistic concentrations of organobromines impact invertebrates. Here, the nematode Caenorhabditis elegans was exposed to AOBr-containing surface water samples and to a Microcystis aeruginosa-enriched batch culture (MC-BA) and compared to single organobromines and microcystin-LR exposures. Stimulatory effects were observed in certain life trait variables, which were particularly pronounced in nematodes exposed to MC-BA. A whole genome DNA-microarray revealed that MC-BA led to the differential expression of more than 2000 genes, many of which are known to be involved in metabolic, neurologic, and morphologic processes. Moreover, the upregulation of cyp- and the downregulation of abu-genes suggested the presence of chronic stress. However, the nematodes were not marked by negative phenotypic responses. The observed difference in MC-BA and microcystin-LR (which impacted lifespan, growth, and reproduction) exposed nematodes was hypothesized to be likely due to other compounds within the batch culture. Most likely, the exposure to low concentrations of organobromines appears to buffer the effects of toxic substances, like microcystin-LR.

Rice husks and their hydrochars cause unexpected stress response in the nematode Caenorhabditis elegans: reduced transcription of stress-related genes

Currently, char substrates gain a lot of interest since soils amended with such substrates are being discussed to increase in fertility and productivity, water retention, and mitigation of greenhouse gases. Char substrates can be produced by carbonization of organic matter. Among different process conditions, temperature is the main factor controlling the occurrence of organic and inorganic contaminants such as phenols and furfurals, which may affect target and non-target organisms. The hydrochar produced at 200 °C contained both furfural and phenol with concentrations of 282 and 324 mg kg(-1) in contrast to the 300 °C hydrochar, which contained only phenol with a concentration of 666 mg kg(-1). By washing with acetone and water, these concentrations were significantly reduced. In this study, the potential toxic effects of hydrochars on the free-living nematode Caenorhabditis elegans were investigated via gene transcription studies using the following four matrices: (i) raw rice husk, (ii) unwashed rice char, (iii) acetone/water washed rice char, and (iv) the wash water of the two rice chars produced at 200 and 300 °C via hydrothermal carbonization (HTC). Furthermore, genetically modified strains, where the green fluorescent protein (GFP) gene sequence is linked to a reporter gene central in specific anti-stress regulations, were also exposed to these matrices. Transgenic worms exposed to hydrochars showed very weak, if any, fluorescence, and expression of the associated RNAs related to stress response and biotransformation genes was surprisingly downregulated. Similar patterns were also found for the raw rice husk. It is hypothesized that an unidentified chemical trigger exists in the rice husk, which is not destroyed during the HTC process. Therefore, the use of GFP transgenic nematode strains cannot be recommended as a general rapid monitoring tool for farmers treating their fields with artificial char. However, it is hypothesized that the observed reduced transcriptional response with the subsequent lack of energy-consuming stress response is an energy-saving mechanism in the exposed nematodes. If this holds true in future studies, this finding opens the window to an innovative new field of stress ecology.

Experimental studies with nematodes in ecotoxicology: an overview

With respect to their high abundances, their role as intermediaries between microorganisms and higher trophic levels, and their ubiquitous occurrence in all habitats, nematodes are of strong potential interest as environmental indicators. Ecotoxicological methods to evaluate the risk of anthropogenic pollutants on ecosystems require both in vitro and in vivo toxicity tests to investigate either mechanisms or pathways of toxicity and to set accurate toxicity thresholds. For this, the interest in nematodes as model organisms in ecotoxicology increased over the past few decades and existing appropriate experimental methods are reviewed in this manuscript. An overview of the various existing ecotoxicological tools for nematodes, ranging from molecular laboratory methods to experimental model ecosystem approaches, and their role as indicator organisms is given. The reviewed studies, approaches that range from species-based to community-based methods, reveal exciting possibilities for the future use of nematodes in ecotoxicological studies. Suitable ecotoxicological tools and ecological indices for nematodes should be integrated in weight-of-evidence approaches for assessing the ecological risk of contamination.

Cytotoxic and genotoxic responses of the RTgill-W1 fish cells in combination with the yeast oestrogen screen to determine the sediment quality of Lagos lagoon, Nigeria

Economic advancements in developing countries have seen an increase in urbanisation and industrialisation with a rise in the levels of discharge of effluents and municipal waste into aquatic ecosystems. Unfortunately, aquatic environmental regulations in these countries are often rudimentary and the development of environmental monitoring programmes will help identify ecological risks. As an example, the current study assesses the pollution status of 11 sampling sites in Lagos lagoon, Nigeria. The organic solvent sediment extracts were assessed for cytotoxicity and genotoxicity in rainbow trout gill-W1 cells. The induction of oestrogenic activities using the yeast oestrogen screen was also determined. The sediments were analysed for polycyclic aromatic hydrocarbons (PAHs) and other contaminants (polychlorinated biphenyls, organochlorine and organophosphate pesticides). Only sediments from three sites were cytotoxic at both 25 and 12.5mg eQsed/ml using the Alamar Blue cell viability assay. The alkaline Comet assay showed that all sites caused significant DNA damage at 7 mg eQsed/ml; the extent of the damage was site specific. The measure of oxidative damage to DNA via the formamidopyrimidine DNA-glycosylase-modified Comet assay revealed similar results. Toxicity to yeast cells was observed in extracts from six sites; of the remaining sites, only two exhibited oestrogenic activity. There was no strong consistent relationship between sediment PAH concentrations and the cell toxicity endpoints. The dynamic nature of Lagos lagoon with its tides and freshwater inputs are suggested as factors that make it difficult to link the sources of pollution observed at each site with PAH levels and toxic endpoints. The study has demonstrated that the Comet assay is a sensitive endpoint to identify sediments that possess genotoxic contaminants, and this in vitro bioassay has the potential to be incorporated into an environmental monitoring framework for Lagos lagoon.

Impacts of different exposure scenarios on transcript abundances in Danio rerio embryos when investigating the toxicological burden of riverine sediments

Purpose

Recently, a proof-of-concept study revealed the suitability of transcriptome analyses to obtain and assess changes in the abundance of transcripts in zebrafish (Danio rerio) embryos after exposure to organic sediment extracts. The present study investigated changes in the transcript abundance in zebrafish embryos exposed to whole sediment samples and corresponding organic extracts in order to identify the impact of different exposure pathways on sediment toxicity.

Materials and Methods

Danio rerio embryos were exposed to sublethal concentrations of three sediment samples from the Danube River, Germany. The sediment samples were investigated both as freeze-dried samples and as organic extracts. Silica dust and a process control of the extraction procedure were used as references. After exposure, mRNA was isolated and changes in profiles of gene expression levels were examined by an oligonucleotide microarray. The microarray results were compared with bioassays, chemical analysis of the sediments and profiles of gene expression levels induced by several single substances.

Results and Discussion

The microarray approach elucidated significant changes in the abundance of transcripts in exposed zebrafish embryos compared to the references. Generally, results could be related to Ah-receptor-mediated effects as confirmed by bioassays and chemical analysis of dioxin-like contaminants, as well as to exposure to stress-inducing compounds. Furthermore, the results indicated that mixtures of chemicals, as present in sediment and extract samples, result in complex changes of gene expression level profiles difficult to compare with profiles induced by single chemical substances. Specifically, patterns of transcript abundances were less influenced by the chemical composition at the sampling site compared t the method of exposure (sediment/extract). This effect might be related to different bioavailability of chemicals.

Conclusions

The apparent difference between the exposure scenarios is an important aspect that needs to be addressed when conducting analyses of alterations in the expression level of mRNA.

Changes in the expression of cyp35a family genes in the soil nematode Caenorhabditis elegans under controlled exposure to chlorpyrifos using passive dosing

In order to use sensitive molecular-level biomarkers for the evaluation of environmental risks, it is necessary to establish a quantitative dose-response relationship. Passive dosing is regarded as a promising new technique for maintaining a constant exposure condition of hydrophobic chemicals in the assay medium. The main goals of the present study were (1) to quantitatively compare gene expression results obtained using the passive dosing method and the conventional spiking method and (2) to investigate changes in gene expression with respect to the free concentration and exposure duration using passive dosing. Chlorpyrifos (CP), which is oxidized by the cytochrome P450 monooxygenases, was selected as a model chemical, and the expression of cytochrome P450 subfamily protein 35A gene series (cyp-35a1-5) was analyzed by quantitative real-time PCR on soil nematode Caenorhabditis elegans. Whereas the free concentration of CP rapidly decreased and the expression of cyp genes varied with the volume of exposure medium and the test duration when the spiking method was used, the free concentration in the assay medium was stable throughout the experiment when the passive dosing method was used. In addition, the level of gene expression increased with exposure time up to 8 h and with increasing CP concentration. The observed increased gene expression could be explained by increasing body residue concentration of CP with exposure time. In conclusion, quantitative dose-response relationships for gene expression biomarkers could be obtained for highly hydrophobic chemicals when the constant exposure condition is provided and the free concentration is used as the dose-metric.

Neurotoxic evaluation of two organobromine model compounds and natural AOBr-containing surface water samples by a Caenorhabditis elegans test

Brominated organic compounds are known as disinfection byproducts. Very recently, however, even natural brominated organic compounds (analyzed as adsorbable organic bromine; AOBr) have been found in decaying freshwater cyanobacteria blooms. Among the identified compounds was dibromoacetic acid (DBAA), which has proven to be neurotoxic at rather high concentrations in mammalian assays. Currently it is open how single compounds as well as complex mixtures impact organisms at environmentally realistic concentrations. Furthermore, it is also unclear how natural organic matter, mainly humic substances (HS), which are present in all freshwater systems, modulates the toxic impact of AOBr. Therefore, two AOBr compounds (DBAA and tetrabromobisphenol-A; TBBP-A) and AOBr-containing water samples were tested using a Caenorhabditis elegans neurotoxicity assay that measured autonomic and sensory functions. TBBP-A had an impact on three response variables of C. elegans and can be classified neurotoxic. In contrast to our expectations, DBAA led to neurostimulation of two autonomic functions, but had a temporary impact on the defecation interval. All surface water samples contained measurable amounts of AOBr. Exposure of C. elegans to concentrated water samples - one in particular - increased three of the four locomotion traits and left defecation activity and both sensory variables unchanged. This stimulation might be due to unidentified compounds in the samples or to a hormetic effect of the AOBr compounds. Thermotactic behavior was characterized by a temporary preference for the colder environment, indicating a temporary mild neurotoxicity. Overall, the set of relative simple phenotypic tests used in the current study revealed a meaningful neurotoxic or neurostimulative profile in response to chemical compounds or natural samples. Furthermore, it shows that the resulting response to natural AOBr compounds at environmentally realistic concentrations was not necessarily adverse, but instead, that the mixtures of natural AOBr were neurostimulatory.

A cross-omics toxicological evaluation of drinking water treated with different processes

Cross-omics profiling and phenotypic analysis were conducted to comprehensively assess the toxicities of source of drinking water (SDW), effluent of conventional treatment (ECT) and effluent of advanced treatment (EAT) in a water treatment plant. SDW feeding increased body weight, and relative liver and kidney weights of mice. Hepatic histopathological damages and serum biochemical alterations were observed in the mice fed with SDW and ECT, but EAT feeding showed no obvious effects. Transcriptomic analysis demonstrated that exposure to water samples caused differential expression of hundreds of genes in livers. Cluster analysis of the differentially expressed genes which generated by both microarrays and digital gene expression showed similar grouping patterns. Proteomic and metabolomics analyses indicated that drinking SDW, ECT and EAT generated 59, 145 and 41 significantly altered proteins in livers and 8, 2 and 0 altered metabolites in serum, respectively. SDW was found to affect several metabolic pathways including metabolism of xenobiotics by cytochrome P450 and fatty acid metabolism. SDW and ECT might induce molecular toxicities to mice, but the advanced treatment process can reduce the potential health risk by effectively removing toxic chemicals in drinking water.

Integrating transcriptomics into triad-based soil-quality assessment

The present study examined how transcriptomics tools can be included in a triad-based soil-quality assessment to assess the toxicity of soils from riverbanks polluted by metals. To that end, the authors measured chemical soil properties and used the International Organization for Standardization guideline for ecotoxicological tests and a newly developed microarray for gene expression in the indicator soil arthropod Folsomia candida. Microarray analysis revealed that the oxidative stress response pathway was significantly affected in all soils except one. The data indicate that changes in cell redox homeostasis are a significant signature of metal stress. Finally, 32 genes showed significant dose-dependent expression with metal concentrations. They are promising genetic markers providing an early indication of the need for higher-tier testing of soil quality. During the bioassay, the toxicity of the least polluted soils could be removed by sterilization. The gene expression profile for this soil did not show a metal-related signature, confirming that a factor other than metals (most likely of biological origin) caused the toxicity. The present study demonstrates the feasibility and advantages of integrating transcriptomics into triad-based soil-quality assessment. Combining molecular and organismal life-history trait stress responses helps to identify causes of adverse effects in bioassays. Further validation is needed for verifying the set of genes with dose-dependent expression patterns linked with toxic stress.

Dissolved and particulate copper exposure induces differing gene expression profiles and mechanisms of toxicity in the deposit feeding amphipod Melita plumulosa

Uptake of metals via ingestion is an important route of exposure for many invertebrates, and it has been suggested that the toxic response to metals accumulated via food differs from that of metals accumulated via the dissolved phase. To test this hypothesis, the deposit-feeding epibenthic amphipod Melita plumulosa was exposed to nontoxic or reproductively toxic concentrations of copper via the overlying water, via ingestion of sediment, or via a combination of the two. Rates of copper uptake from the two exposure routes were predicted using a biokinetic model. Gene expression profiles were measured via microarray analysis and confirmed via quantitative polymerase chain reaction. Differences in expression profiles were related to the exposure route more than to individual or combined rates of copper uptake. Chitinase and digestive protease transcript expression levels correlated to the copper uptake rate from sediment, rather than from the dissolved phase or combined total uptake rate. Overall, this study supports the hypothesis that metals accumulated via ingestion have a different mode of toxic action than metals taken up from water. Consequently, guidelines that only consider dissolved metal exposure, including equilibrium-partitioning-based guidelines, may underestimate the potential effects from deposited or resuspended metal-contaminated sediments.

Omics technologies and their applications to evaluate metal toxicity in mice M. spretus as a bioindicator

Metals are important components of living organisms since many biological functions critically depend on their interaction with some metal in the cell. However, human activities have increased toxic metal levels in the terrestrial and aquatic ecosystems affecting living organisms. The impact of metals on cellular metabolism and global homeostasis has been traditionally assessed in free-living organisms by using conventional biomarkers; however, to obtain a global vision of metal toxicity mechanisms and the responses that metals elicit in the organisms, new analytical methodologies are needed. We review the use of omics approaches to assess the response of living organisms under metal stress illustrating the possibilities of different methodologies on the basis of our previous results. Most of this research has been based on free-living mice Mus spretus, a conventional bioindicator used to monitor metal pollution in Doñana National Park (DNP) (SW Spain), which is an important European biological reserve for migrating birds affected by agricultural, mining and industrial activities. The benefits of using omic techniques such as heterologous microarrays, proteomics methodologies (2-DE, iTRAQ®), metallomics, ionomics or metabolomics has been remarked; however, the complexity of these areas requires the integration of omics to achieve a comprehensive assessment of their environmental status. This article is part of a Special Issue entitled: Environmental and structural proteomics.

BIOLOGICAL SIGNIFICANCE

This work presents new contributions in the study of environmental metal pollution in terrestrial ecosystems using Mus spretus mice as bioindicator in Doñana National Park (SW Spain) and surroundings. In addition, it has been demonstrated that the integration of omics multi-analytical approaches provides a very suitable approach for the study of the biological response and metal interactions in exposed and free-living mice (Mus musculus and Mus spretus, respectively) under metal pollution.

Assessing mechanisms of toxicant response in the amphipod Melita plumulosa through transcriptomic profiling

This study describes the function of transcripts with altered abundance in the epibenthic amphipod, Melita plumulosa, following whole-sediment exposure to a series of common environmental contaminants. M. plumulosa were exposed for 48 h to sediments spiked and equilibrated with the following contaminants at concentrations predicted to cause sublethal effects to reproduction: porewater ammonia 30 mg L(-1); bifenthrin at 100 μg kg(-1); fipronil at 50 μg kg(-1); 0.6% diesel; 0.3% crude oil; 250 mg Cu kg(-1); 400 mg Ni kg(-1); and 400 mg Zn kg(-1). RNA was extracted and hybridized against a custom Agilent microarray developed for this species. Although the microarray represented a partial transcriptome and not all features on the array could be annotated, unique transcriptomic profiles were generated for each of the contaminant exposures. Hierarchical clustering grouped the expression profiles together by contaminant class, with copper and zinc, the petroleum products and nickel, and the pesticides each forming a distinct cluster. Many of the transcriptional changes observed were consistent with patterns previously described in other crustaceans. The changes in the transcriptome demonstrated that contaminant exposure caused changes in digestive function, growth and moulting, and the cytoskeleton following metal exposure, whereas exposure to petroleum products caused changes in carbohydrate metabolism, xenobiotic metabolism and hormone cycling. Functional analysis of these gene expression profiles can provide a better understanding of modes of toxic action and permits the prediction of mixture effects within contaminated ecosystems.

Gene-environment and protein-degradation signatures characterize genomic and phenotypic diversity in wild Caenorhabditis elegans populations

Background

Analyzing and understanding the relationship between genotypes and phenotypes is at the heart of genetics. Research on the nematode Caenorhabditis elegans has been instrumental for unraveling genotype-phenotype relations, and has important implications for understanding the biology of mammals, but almost all studies, including forward and reverse genetic screens, are limited by investigations in only one canonical genotype. This hampers the detection and functional analysis of allelic variants, which play a key role in controlling many complex traits. It is therefore essential to explore the full potential of the natural genetic variation and evolutionary context of the genotype-phenotype map in wild C. elegans populations.

Results

We used multiple wild C. elegans populations freshly isolated from local sites to investigate gene sequence polymorphisms and a multitude of phenotypes including the transcriptome, fitness, and behavioral traits. The genotype, transcriptome, and a number of fitness traits showed a direct link with the original site of the strains. The separation between the isolation sites was prevalent on all chromosomes, but chromosome V was the largest contributor to this variation. These results were supported by a differential food preference of the wild isolates for naturally co-existing bacterial species. Comparing polymorphic genes between the populations with a set of genes extracted from 19 different studies on gene expression in C. elegans exposed to biotic and abiotic factors, such as bacteria, osmotic pressure, and temperature, revealed a significant enrichment for genes involved in gene-environment interactions and protein degradation.

Conclusions

We found that wild C. elegans populations are characterized by gene-environment signatures, and we have unlocked a wealth of genotype-phenotype relations for the first time. Studying natural isolates provides a treasure trove of evidence compared with that unearthed by the current research in C. elegans, which covers only a diminutive part of the myriad of genotype-phenotype relations that are present in the wild.

Using transcriptomic profiles in the diatom Phaeodactylum tricornutum to identify and prioritize stressors

The transcriptomic profile of the marine diatom, Phaeodactylum tricornutum, exposed to several ecologically relevant stressors, was used to develop toxicity identification evaluation (TIE)-like gene expression assays. Algal growth inhibition was measured by flow cytometry to determine exposure concentrations that elicited a sublethal toxic response. P. tricornutum was exposed to concentrations of copper (2 μg L⁻¹), cadmium (5 μg L⁻¹), silver (20 μg L⁻¹), simazine (75 μg L⁻¹), the water accommodated fraction (WAF) of weathered crude oil (5 mg L⁻¹), 50 μg L⁻¹ ammonia, a decreased salinity treatment (15‰), and a mixture exposure of ammonia, decreased salinity and cadmium (10 μg L⁻¹). Analysis of the gene expression via microarray indicated that unique transcriptomic signals were generated for each of the individual treatments. Transcriptomic profiles of ammonia and the mixture treatment overlapped substantially. Photosynthesis related transcripts were altered in the simazine (herbicide) treatment. A transcript involved in degrading hydrocarbons, dioxygenase, had increased abundance after crude oil exposure. Overall, transcriptomic responses in the different treatments were associated with stress responses, membrane transport, transcription and translation and could be linked to contaminant mode of action. The transcriptomic profiles were used to design real-time (quantitative) polymerase chain reaction (qPCR) assays that would link changes in transcript abundance to a particular stressor in a TIE-based approach. At least one transcript for each contaminant tested (copper, cadmium, silver, salinity and ammonia) responded exclusively to that contaminant. With further development of additional transcriptomic markers for each contaminant, this new approach has potential to enhance traditional toxicology bioassays by providing additional lines of evidence to identify biologically relevant stressors within a contaminated ecosystem based on changes in the transcriptomic profile.

A new medium for Caenorhabditis elegans toxicology and nanotoxicology studies designed to better reflect natural soil solution conditions

A new toxicity test medium for Caenorhabditis elegans is presented. The test solution is designed to provide a better representation of natural soil pore water conditions than currently available test media. The medium has a composition that can readily be modified to allow for studies of the influences of a range of environmentally relevant parameters on nematode biology and toxicology. Tests conducted in the new medium confirmed that nematodes' reproduction was possible at a range of solution pH levels, offering the potential to conduct toxicity studies under a variety of conditions. A test to establish silver nanoparticle and dissolved silver nitrate toxicity, a study type not feasible in M9 or agar media due to precipitation and nanoparticle agglomeration, indicated lower silver nanoparticle (median effective concentration [EC50] of 6.5 mg Ag/L) than silver nitrate (EC50 0.28 mg Ag/L) toxicity. Characterization identified stable nanoparticle behavior in the new test medium.

Genomic analysis of stress response against arsenic in Caenorhabditis elegans

Arsenic, a known human carcinogen, is widely distributed around the world and found in particularly high concentrations in certain regions including Southwestern US, Eastern Europe, India, China, Taiwan and Mexico. Chronic arsenic poisoning affects millions of people worldwide and is associated with increased risk of many diseases including arthrosclerosis, diabetes and cancer. In this study, we explored genome level global responses to high and low levels of arsenic exposure in Caenorhabditis elegans using Affymetrix expression microarrays. This experimental design allows us to do microarray analysis of dose-response relationships of global gene expression patterns. High dose (0.03%) exposure caused stronger global gene expression changes in comparison with low dose (0.003%) exposure, suggesting a positive dose-response correlation. Biological processes such as oxidative stress, and iron metabolism, which were previously reported to be involved in arsenic toxicity studies using cultured cells, experimental animals, and humans, were found to be affected in C. elegans. We performed genome-wide gene expression comparisons between our microarray data and publicly available C. elegans microarray datasets of cadmium, and sediment exposure samples of German rivers Rhine and Elbe. Bioinformatics analysis of arsenic-responsive regulatory networks were done using FastMEDUSA program. FastMEDUSA analysis identified cancer-related genes, particularly genes associated with leukemia, such as dnj-11, which encodes a protein orthologous to the mammalian ZRF1/MIDA1/MPP11/DNAJC2 family of ribosome-associated molecular chaperones. We analyzed the protective functions of several of the identified genes using RNAi. Our study indicates that C. elegans could be a substitute model to study the mechanism of metal toxicity using high-throughput expression data and bioinformatics tools such as FastMEDUSA.

Transcription profiling in environmental diagnostics: health assessments in Columbia River basin steelhead (Oncorhynchus mykiss)

The health condition of out-migrating juvenile salmonids can influence migration success. Physical damage, pathogenic infection, contaminant exposure, and immune system status can affect survival probability. The present study is part of a wider investigation of out-migration success in juvenile steelhead (Oncorhynchus mykiss) and focuses on the application of molecular profiling to assess sublethal effects of environmental stressors in field-collected fish. We used a suite of genes in O. mykiss to specifically assess responses that could be directly related to steelhead health condition during out-migration. These biomarkers were used on juvenile steelhead captured in the Snake River, a tributary of the Columbia River, in Washington, USA, and were applied on gill and anterior head kidney tissue to assess immune system responses, pathogen-defense (NRAMP, Mx, CXC), general stress (HSP70), metal-binding (metallothionein-A), and xenobiotic metabolism (Cyp1a1) utilizing quantitative polymerase chain reaction (PCR) technology. Upon capture, fish were ranked according to visual external physical conditions into good, fair, poor, and bad categories; gills and kidney tissues were then dissected and preserved for gene analyses. Transcription responses were tissue-specific for gill and anterior head kidney with less significant responses in gill tissue than in kidney. Significant differences between the condition ranks were attributed to NRAMP, MX, CXC, and Cyp1a1 responses. Gene profiling correlated gene expression with pathogen presence, and results indicated that gene profiling can be a useful tool for identifying specific pathogen types responsible for disease. Principal component analysis (PCA) further correlated these responses with specific health condition categories, strongly differentiating good, poor, and bad condition ranks. We conclude that molecular profiling is an informative and useful tool that could be applied to indicate and monitor numerous population-level parameters of management interest.

Functional environmental genomics of a municipal landfill soil

We investigated the toxicity of soil samples derived from a former municipal landfill site in the South of the Netherlands, where a bioremediation project is running aiming at reusing the site for recreation. Both an organic soil extract and the original soil sample was investigated using the ISO standardized Folsomia soil ecotoxicological testing and gene expression analysis. The 28 day survival/reproduction test revealed that the ecologically more relevant original soil sample was more toxic than the organic soil extract. Microarray analysis showed that the more toxic soil samples induced gene regulatory changes in twice as less genes compared to the soil extract. Consequently gene regulatory changes were highly dependent on sample type, and were to a lesser extent caused by exposure level. An important biological process shared among the two sample types was the detoxification pathway for xenobiotics (biotransformation I, II, and III) suggesting a link between compound type and observed adverse effects. Finally, we were able to retrieve a selected group of genes that show highly significant dose-dependent gene expression and thus were tightly linked with adverse effects on reproduction. Expression of four cytochrome P450 genes showed highest correlation values with reproduction, and maybe promising genetic markers for soil quality. However, a more elaborate set of environmental soil samples is needed to validate the correlation between gene expression induction and adverse phenotypic effects.

Organic carbon source in formulated sediments influences life traits and gene expression of Caenorhabditis elegans

River water quality is strongly influenced by their sediments and their associated pollutants. To assess the toxic potential of sediments, sediment toxicity tests require reliable control sediments, potentially including formulated control sediments as one major option. Although some standardization has been carried out, one critical issue still remains the quality of sediment organic matter (SOM). Organic carbon not only binds hydrophobic contaminants, but may be a source of mild toxicity, even if the SOM is essentially uncontaminated. We tested two different sources of organic carbon and the mixture of both (Sphagnum peat (P) and one commercial humic substances preparation-HuminFeed(®), HF) in terms of life trait variables and expression profiles of selected life performance and stress genes of the nematode Caenorhabditis elegans. In synchronous cultures, gene expression profiling was done after 6 and 48 h, respectively. The uncontaminated Sphagnum P reduced growth, but increased numbers of offspring, whereas HF did not significantly alter life trait variables. The 6 h expression profile showed most of the studied stress genes repressed, except for slight to strong induction in cyp-35B1 (all exposures), gst-38 (only mixture), and small hsp-16 genes (all exposures). After 48 h, the expression of almost all studied genes increased, particularly genes coding for antioxidative defense, multiple xenobiotic resistance, vitellogenin-like proteins, and genes regulating lifespan. Overall, even essentially uncontaminated SOM may induce several modes of action on the molecular level in C. elegans which may lead to false results if testing synthetic xenobiotics. This contribution is a plea for a strict standardization of the SOM quality in formulated sediments and to check for corresponding effects in other model sediment organisms, especially if using molecular toxicity endpoints.

Toxicogenomic investigation of Tetrahymena thermophila exposed to dichlorodiphenyltrichloroethane (DDT), tributyltin (TBT), and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)

Dichlorodiphenyltrichloroethane (DDT), tributyltin (TBT), and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) are persistent in the environment and cause continuous toxic effects in humans and aquatic life. Tetrahymena thermophila has the potential for use as a model for research regarding toxicants. In this study, this organism was used to analyze a genome-wide microarray generated from cells exposed to DDT, TBT and TCDD. To accomplish this, genes differentially expressed when treated with each toxicant were identified, after which their functions were categorized using GO enrichment analysis. The results suggested that the responses of T. thermophila were similar to those of multicellular organisms. Additionally, the context likelihood of relatedness method (CLR) was applied to construct a TCDD-relevant network. The T-shaped network obtained could be functionally divided into two subnetworks. The general functions of both subnetworks were related to the epigenetic mechanism of TCDD. Based on analysis of the networks, a model of the TCDD effect on T. thermophila was inferred. Thus, Tetrahymena has the potential to be a good unicellular eukaryotic model for toxic mechanism research at the genome level.

Novel computational identification of highly selective biomarkers of pollutant exposure

The use of in vivo biosensors to acquire environmental pollution data is an emerging and promising paradigm. One major challenge is the identification of highly specific biomarkers that selectively report exposure to a target pollutant, while remaining quiescent under a diverse set of other, often unknown, environmental conditions. This study hypothesized that a microarray data mining approach can identify highly specific biomarkers, and, that the robustness property can generalize to unforeseen environmental conditions. Starting with Arabidopsis thaliana microarray data measuring responses to a variety of treatments, the study used the top scoring pair (TSP) algorithm to identify mRNA transcripts that respond uniquely to phenanthrene, a model polycyclic aromatic hydrocarbon. Subsequent in silico analysis with a larger set of microarray data indicated that the biomarkers remained robust under new conditions. Finally, in vivo experiments were performed with unforeseen conditions that mimic phenanthrene stress, and the biomarkers were assayed using qRT-PCR. In these experiments, the biomarkers always responded positively to phenanthrene, and never responded to the unforeseen conditions, thereby supporting the hypotheses. This data mining approach requires only microarray or next-generation RNA-seq data, and, in principle, can be applied to arbitrary biomonitoring organisms and chemical exposures.

Omic approaches in environmental issues

Biomonitoring requires the application of batteries of different biomarkers, as environmental contaminants induce multiple responses in organisms that are not necessarily correlated. Omic technologies were proposed as an alternative to conventional biomarkers since these techniques quantitatively monitor many biological molecules in a high-throughput manner and thus provide a general appraisal of biological responses altered by exposure to contaminants. As the studies using omic technologies increase, it is becoming clear that any single omic approach may not be sufficient to characterize the complexity of ecosystems. This work aims to provide a preliminary working scheme for the use of combined transcriptomic and proteomic methodologies in environmental biomonitoring. There are difficulties in working with nonmodel organisms as bioindicators when combining several omic approaches. As a whole, our results with heterologous microarrays in M. spretus and suppressive subtractive hybridization (SSH) in P. clarkii indicated that animals sustaining a heavy pollution burden exhibited an enhanced immune response and/or cell apoptosis. The proteomic studies, although preliminary, provide a holistic insight regarding the manner by which pollution shifts protein intensity in two-dimensional gel electrophoresis (2-DE), completing the transcriptomic approach. In our study, the sediment element concentration was in agreement with the intensity of protein expression changes in C. maenas crabs. In conclusion, omics are useful technologies in addressing environmental issues and the determination of contamination threats.

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

Diverse anthropogenic activities often lead to the accumulation of inorganic and organic residues in topsoils. Biota living in close contact with contaminated soils may experience stress at different levels of biological organisation throughout the continuum from the molecular-genetic to ecological and community levels. To date, the relationship between changes at the molecular (mRNA expression) and biochemical/physiological levels evoked by exposures to chemical compounds has been partially established in a limited number of terrestrial invertebrate species. Recently, the advent of a family of transcriptomic tools (e.g. Real-time PCR, Subtractive Suppressive Hybridization, Expressed Sequence Tag sequencing, pyro-sequencing technologies, Microarray chips), together with supporting informatic and statistical procedures, have permitted the robust analyses of global gene expression changes within an ecotoxicological context. This review focuses on how transcriptomics is enlightening our understanding of the molecular-genetic responses of three contrasting terrestrial macroinvertebrate taxa (nematodes, earthworms, and springtails) to inorganics, organics, and agrochemicals.

Systems toxicology approaches for understanding the joint effects of environmental chemical mixtures

Environmental mixtures of chemicals constitute a prevalent issue in ecotoxicology and the development of new methods to reduce the uncertainties associated with their ecological risk assessment is a critical research need. Historically, a number of models have been explored to predict the potential combined effects of chemicals on species. These models, especially concentration addition and the independent action, have been applied to a number of mixtures. While often providing a good prediction of joint effect, there are cases where these models can have limitations: notably in cases where there are interactions for which they fail to adequately predict joint effects. To support the better mechanistic understanding of interactions in mixture toxicology a framework to support experimental studies to investigate the basis of observed interactions is proposed. The conceptual framework is derived from the extension of a three stage scheme which has previously been applied to understand chemical bioavailability. The framework considers that interactions in mixtures result from processes related to 1) the speciation, binding and transport of chemicals in the exposure medium (external exposure); 2) the adsorption, distribution, metabolism and excretion of chemicals within the organisms (toxicokinetics); 3) associations governing the binding and toxicity of the chemical(s) at the target site (toxicodynamics). The current state of the art in (eco)toxicology in relation to investigation of the mechanisms of interactions between chemicals is discussed with particular emphasis towards the multi-disciplinary tools and techniques within environmental chemistry; toxicology; biochemistry and systems biology that can be used to address such effects.

The two Caenorhabditis elegans metallothioneins (CeMT-1 and CeMT-2) discriminate between essential zinc and toxic cadmium

The nematode Caenorhabditis elegans expresses two metallothioneins (MTs), CeMT-1 and CeMT-2, that are believed to be key players in the protection against metal toxicity. In this study, both isoforms were expressed in vitro in the presence of either Zn(II) or Cd(II). Metal binding stoichiometries and affinities were determined by ESI-MS and NMR, respectively. Both isoforms had equal zinc binding ability, but differed in their cadmium binding behaviour, with higher affinity found for CeMT-2. In addition, wild-type C. elegans, single MT knockouts and a double MT knockout allele were exposed to zinc (340 microm) or cadmium (25 microm) to investigate effects in vivo. Zinc levels were significantly increased in all knockout strains, but were most pronounced in the CeMT-1 knockout, mtl-1 (tm1770), while cadmium accumulation was highest in the CeMT-2 knockout, mtl-2 (gk125) and the double knockout mtl-1;mtl-2 (zs1). In addition, metal speciation was assessed by X-ray absorption fine-structure spectroscopy. This showed that O-donating, probably phosphate-rich, ligands play a dominant role in maintaining the physiological concentration of zinc, independently of metallothionein status. In contrast, cadmium was shown to coordinate with thiol groups, and the cadmium speciation of the wild-type and the CeMT-2 knockout strain was distinctly different to the CeMT-1 and double knockouts. Taken together, and supported by a simple model calculation, these findings show for the first time that the two MT isoforms have differential affinities towards Cd(II) and Zn(II) at a cellular level, and this is reflected at the protein level. This suggests that the two MT isoforms have distinct in vivo roles.

Ecotoxicogenomics: bridging the gap between genes and populations

Ecotoxicogenomics might help solving open questions that cannot be answered by standard ecotoxicity tests currently used in environmental risk assessment. Changes in gene expression are claimed to serve potentially as early warning indicators for environmental effects and as sensitive and specific ecotoxicological end points. Ecotoxicogenomics focus on the lowest rather than the highest levels of biological organization. Our aim was to explore the links between gene expression responses and population level responses, both mechanistically (conceptual framework) and correlatively (Species Sensitivity Distribution). The effects of cadmium on aquatic species were compared for gene level responses (Lowest Observed Effect Concentrations) and individual level responses (median Lethal Concentrations, LC(50), and No Observed Effect Concentrations, NOEC). Responses in gene expression were on average four times above the NOEC and eleven times below the LC(50) values. Currently, use of gene expression changes as early warning indicators of environmental effects is not underpinned due to a lack of data. To confirm the sensitivity claimed by ecotoxicogenomics more testing at low concentrations is needed. From the conceptual framework, we conclude that for a mechanistic gene population link in risk management, research is required that includes at least one meaningful end point at each level of organization.

Applications of cold temperature stress to age fractionate Caenorhabditis elegans: a simple inexpensive technique

The nematode Caenorhabditis elegans’s (CE) successful use in studies of aging is well documented. Cold temperature stress of mixed populations of CE provides a rapid inexpensive means of obtaining three life stage–specific cohorts. Cohorts are obtained in quantities that allow acquisition of replicate metabolite profiles of changes associated with development, aging, and senescence. The fractionation technique is effective with monoxenic and axenic CE cultures. Cohort Y contains 100% young worms, and Cohort A contains 75% adult worms. Cohort M, prereproductive and reproductive, contains some A and Y due to continuous egg laying and hatch. Principal component analysis of normalized data from metabolite profiles obtained using high-performance liquid chromatography electrochemical analysis clearly separates Cohort Y from Cohort A and monoxenic from axenic cultured worms. Access to replicate quantities of age-defined worms will aid studies of alterations in homeostatic controls associated with aging and senescence.