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

Stress response and tolerance mechanisms of spirobudiclofen exposure based on multiomics in Panonychus citri (Acari: Tetranychidae)

The toxicity of insecticides used in the field decreases gradually to sublethal concentrations over time. Therefore, it is necessary to study sublethal effects of pesticides for controlling population explosion. Panonychus citri is a global pest which control is based on insecticides. This study explores the stress responses of spirobudiclofen on the P. citri. Spirobudiclofen significantly inhibited survival and reproduction of P. citri, and the effects aggravated as concentration increased. The transcriptomes and metabolomes of spirobudiclofen-treated and control were compared to characterize spirobudiclofen molecular mechanism. Transcriptomics indicated stress induced by spirobudiclofen stimulated immune defense, antioxidative system, cuticle formation, and lipid metabolism, as deduced from RNA-seq analysis. Meanwhile, our study found that tolerance metabolism in P. citri was regulated by promoting the metabolism of glycerophospholipids, glycine, serine, and threonine. The results of this study can provide a basis for exploring the adaptation strategies of P. citri to spirobudiclofen stress.

Molecular mechanisms of zinc toxicity in the potworm Enchytraeus crypticus, analysed by high-throughput gene expression profiling

Zinc (Zn) is known to be relatively toxic to some soil-living invertebrates including the ecologically important enchytraeid worms. To reveal the molecular mechanisms of zinc toxicity we assessed the gene expression profile of Enchytraeus crypticus (Enchytraeidae), exposed to the reproduction effect concentrations EC₁₀ and EC₅₀, over 4 consecutive days, using a high-throughput microarray (species customized). Three main mechanisms of toxicity to Zn were observed: 1) Zn trafficking (upregulation of zinc transporters, a defence response to regulate the cellular zinc level), 2) oxidative stress (variety of defence mechanisms, triggered by Reactive Oxygen Species (ROS)), and 3) effects on the nervous system (possibly the primary lesion explaining the avoidance behaviour and also why enchytraeids are relatively susceptible to Zn). The adverse outcome at the organism level (reproduction EC₅₀) could be predicted based on gene expression (male gonad development, oocyte maturation), with Zn at the EC₅₀ affecting processes related to higher stress levels. The gene expression response was time-dependent and reflected the cascade of events taking place over-time. The 1 to 4 days of exposure design was a good strategy as it captured the time for sequence of events towards zinc adverse outcomes in E. crypticus.

Comparative transcriptome analysis of the gills and hepatopancreas from Macrobrachium rosenbergii exposed to the heavy metal Cadmium (Cd2+)

Heavy metal Cadmium (Cd²⁺) pollution has become a severe environmental problem for aquatic organisms. In crustaceans, gills (Gi) and hepatopancreas (Hp) play a vital role in the toxicology. However, in Macrobrachium rosenbergill, there are few researches about gill and hepatopancreases responding to Cd²⁺ stress at a molecular level. In this study, transcriptomic analysis was applied to characterize gene expression profiles of gills and hepatopancreas of M. rosenbergill after Cd²⁺ exposure for 0 h, 3 h and 3 d. Six cDNA libraries (Gi 0 h, Gi 3 h, Gi 3 d, Hp 0 h, Hp 3 h, and Hp 3 d) were constructed and a total of 66,676 transcripts and 48,991 unigenes were annotated. Furthermore, differentially expressed genes (DEGs) were isolated by comparing the Cd²⁺ treated time-point libraries (3 h and 3 d group) with the control library (0 h group). The results showed that most of the DEGs were down-regulated after Cd²⁺ exposure and the number of DEGs among gill groups were significantly higher than those among hepatopancreas groups. GO functional and KEGG pathway analysis suggested many key DEGs in response to the Cd²⁺ stress, such as metallothionein and Hemocyanin. Additionally, a total of six DEGs were randomly selected to further identify their expressional profile by qPCR. The results indicated that these DEGs were involved in the response to Cd²⁺. This comparative transcriptome provides valuable molecular information on the mechanisms of responding to Cd²⁺ stress in M. rosenbergii, which lays the foundation for further understanding of heavy metal stress.

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.

Effects of single and combined exposure to nano and bulk zinc-oxide and propiconazole on Enchytraeus albidus

Organisms in soil are often exposed to different mixtures of contaminants. These contaminants may interact with each other and, consequently, may have a different effect on organisms than each of them alone. We wanted to investigate possible effects of ZnO mixtures in bulk and nano form and fungicide propiconazole (PCZ) on biochemical parameters and reproduction in Enchytreus albidus. These compounds were applied separately and in binary mixture. In the single exposure experiment the EC₅₀ values for the number of juveniles were calculated: nano ZnO (641.21 ± 88.82 mg kg^-1), bulk ZnO (445.78 ± 148.4 mg kg^-1) and PCZ (3.63 ± 1.68 mg kg-1), respectively. These concentrations were subsequently used in the binary exposure experiment. Calculated combination indices (CI), that allow quantitative determination of chemical interactions at different concentration and effect level, indicated additive or antagonistic interactions (CI ≥ 1) of applied mixture ratios. The only ratio that showed synergistic interaction (CI < 1) was 75% EC₅₀ nZnO/25% EC₅₀ PCZ. Both ZnO forms caused acetylcholinesterase (AChE) activity increase of up to 40% of control level, as well as increased catalase (CAT) and glutathione S-transferase (GST) activities and malondialdehyde (MDA) level. PCZ did not affect AChE and CAT activities, yet it increased GST activity and MDA level. Induced levels of measured biomarkers indicate an oxidative stress after binary exposure, as well. These effects were not enhanced after binary exposure but reflected the effects on biomarkers that corresponding concentrations of these compounds generated in a single exposure experiment.

High-throughput gene expression in soil invertebrate embryos - Mechanisms of Cd toxicity in Enchytraeus crypticus

Gene expression can vary with the organisms' life stage. It is known that embryos can be more sensitive to toxicant exposure, as previously demonstrated for Enchytraeus crypticus (Oligochaeta) exposed to cadmium (Cd), known to cause embryotoxicity and hatching delay. It was shown that Ca enters embryos via the L-type Ca channels in the cocoon membrane, this being affected in Cd exposed embryos (Cd-Ca competition is well-known). In the present study, the embryotoxic mechanisms of Cd were studied via high-throughput gene expression for E. crypticus. Cocoons (1-2 days old), instead of the adult organism, were exposed in Cd spiked LUFA 2.2 soil during 1 day. Results showed that Cd affected Ca homeostasis which is implicated in several other molecular processes. Several of the major modulators of Cd toxicity (e.g., impaired gene expression, cell cycle arrest, DNA and mitochondrial damage) were identified in the embryos showing its relevancy as a model in ecotoxicogenomics. The draft Adverse Outcome Pathway was improved. Previously was hypothesized that gene regulation mechanisms were activated to synthesize more Ca channel proteins - this was confirmed here. Further, novel evidences were that, besides the extracellular competition, Cd competes intracellularly which causes a reduction in Ca efflux, and potentiates Cd embryotoxicity.

Mechanisms of (photo)toxicity of TiO2 nanomaterials (NM103, NM104, NM105): using high-throughput gene expression in Enchytraeus crypticus

Titanium dioxide (TiO2) based nanomaterials (NMs) are among the most produced NMs worldwide. When irradiated with light, particularly UV, TiO2 is photoactive, a property that is explored for several purposes. There are an increasing number of reports on the negative effects of photoactivated TiO2 on non-target organisms. We have here studied the effect of a suite of reference type TiO2 NMs (i.e. NM103, NM104, and NM105 and compared these to the bulk) with and without UV radiation to the oligochaete Enchytraeus crypticus. High-throughput gene expression was used to assess the molecular mechanisms, while also anchoring it to the known effects at the organism level (i.e., reproduction). Results showed that the photoactivity of TiO2 (UV exposed) played a major role in enhancing TiO2 toxicity, activating the transcription of oxidative stress, lysosome damage and apoptosis mechanisms. For non-UV activated TiO2, where toxicity at the organism level (reproduction) was lower, results showed potential for long-term effects (i.e., mutagenic and epigenetic). NM specific mechanisms were identified: NM103 affected transcription and translation, NM104_UV negatively affected the reproductive system/organs, and NM105_UV activated superoxide anion response. Results provided mechanistic information on UV-related phototoxicity of TiO2 materials and evidence for the potential long-term effects.

An integrative omics approach to unravel toxicity mechanisms of environmental chemicals: effects of a formulated herbicide

The use of integrative molecular approaches can aid in a comprehensive understanding of the effects of toxicants at different levels of biological organization, also supporting risk assessment. The present study aims to unravel the toxicity mechanisms of a widely used herbicide to the arthropod Folsomia candida exposed in a natural soil, by linking effects on reproduction, proteomics and genome-wide gene expression. The EC50 effects on reproduction over 4 weeks was 4.63 mg glyphosate/kg of soil. The formulation included a polyethoxylated tallowamine as an adjuvant, which at 50% effect on reproduction had an estimated concentration of 0.87-1.49 mg/kg of soil. No effects were observed on survival and reproduction when using the isolated active substance, pointing the toxicity of the formulated product to the co-formulant instead of the active ingredient, glyphosate. RNA sequencing and shotgun proteomics were applied to assess differential transcript and protein expressions between exposed and control organisms in time, respectively. Specific functional categories at protein and transcriptome levels were concordant with each other, despite overall limited correlations between datasets. The exposure to this formulation affected normal cellular respiration and lipid metabolism, inducing oxidative stress and leading to impairment in biological life cycle mechanisms such as molting and reproduction.

High-throughput tool to discriminate effects of NMs (Cu-NPs, Cu-nanowires, CuNO3, and Cu salt aged): transcriptomics in Enchytraeus crypticus

The current testing of nanomaterials (NMs) via standard toxicity tests does not cover many of the NMs specificities. One of the recommendations lays on understanding the mechanisms of action, as these can help predicting long-term effects and safe-by-design production. In the present study, we used the high-throughput gene expression tool, developed for Enchytraeus crypticus (4 × 44k Agilent microarray), to study the effects of exposure to several copper (Cu) forms. The Cu treatments included two NMs (spherical and wires) and two copper-salt treatments (CuNO₃ spiked and Cu salt field historical contamination). To relate gene expression with higher effect level, testing was done with reproduction effect concentrations (EC₂₀, EC₅₀), using 3 and 7 days as exposure periods. Results showed that time plays a major role in the transcriptomic response, most of it occurring after 3 days. Analysis of gene expression profiles showed that Cu-salt-aged and Cu-nanowires (Nwires) differed from CuNO₃ and Cu-nanoparticles (NPs). Functional analysis revealed specific mechanisms: Cu-NPs uniquely affected senescence and cuticle pattern formation, which can result from the contact of the NPs with the worms' tegument. Cu-Nwires affected reproduction via male gamete generation and hermaphrodite genitalia development. CuNO₃ affected neurotransmission and locomotory behavior, both of which can be related with avoidance response. Cu salt-aged uniquely affected phagocytosis and reproductive system development (via different mechanisms than Cu-Nwires). For the first time for Cu (nano)materials, the adverse outcome pathways (AOPs) drafted here provide an overview for common and unique effects per material and linkage with apical effects.

Influence of climate change on the multi-generation toxicity to Enchytraeus crypticus of soils polluted by metal/metalloid mining wastes

This study aimed at assessing the effects of increased air temperature and reduced soil moisture content on the multi-generation toxicity of a soil polluted by metal/metalloid mining wastes. Enchytraeus crypticus was exposed to dilution series of the polluted soil in Lufa 2.2 soil under different combinations of air temperature (20 °C and 25 °C) and soil moisture content (50% and 30% of the soil water holding capacity, WHC) over three generations standardized on physiological time. Generation time was shorter with increasing air temperature and/or soil moisture content. Adult survival was only affected at 30% WHC (∼30% reduction at the highest percentages of polluted soil). Reproduction decreased with increasing percentage of polluted soil in a dose-related manner and over generations. Toxicity increased at 30% WHC (>50% reduction in EC₅₀ in F0 and F1 generations) and over generations in the treatments at 20 °C (40-60% reduction in EC₅₀ in F2 generation). At 25 °C, toxicity did not change when combined with 30% WHC and only slightly increased with 50% WHC. So, higher air temperature and/or reduced soil moisture content does affect the toxicity of soils polluted by metal/metalloid mining wastes to E. crypticus and this effect may exacerbate over generations.

Antioxidant and neurotoxicity markers in the model organism Enchytraeus albidus (Oligochaeta): mechanisms of response to atrazine, dimethoate and carbendazim

The present study aimed to investigate the effects of dimethoate, atrazine and carbendazim on the antioxidant defences and neuronal function of the soil organism Enchytraeus albidus. Effects were studied at concentrations known to affect their reproduction (EC20, EC50 and EC90) and along time (2, 4, 8, 14 and 21 days). In general, responses were more pronounced at periods of exposure longer than 8 days and at the highest concentrations. Multivariate statistics (RDA-PRC) clearly displayed that exposure duration had an effect itself, biomarkers' responses showed interaction for all pesticides and catalase scored consistently high, indicating its relevancy in the group of measured markers. Univariate analysis indicated oxidative stress for all pesticides and atrazine induced oxidative damage in lipids. Atrazine seems to be effectively metabolized by GST of the biotransformation system, as its activity significantly increased after exposure to this pesticide. Dimethoate caused ChE inhibition, indicating an impairment of the neuronal function. Carbendazim impaired the antioxidant system, but no oxidative damage was observed, along with any effects on the ChE activity. The integrated biomarker response analysis was performed but we suggest modifications due to limiting artefacts.

Transcriptome assembly and microarray construction for Enchytraeus crypticus, a model oligochaete to assess stress response mechanisms derived from soil conditions

Background

The soil worm Enchytraeus crypticus (Oligochaeta) is an ecotoxicology model species that, until now, was without genome or transcriptome sequence information. The present research aims at studying the transcriptome of Enchytraeus crypticus, sampled from multiple test conditions, and the construction of a high-density microarray for functional genomic studies.

Results

Over 1.5 million cDNA sequence reads were obtained representing 645 million nucleotides. After assembly, 27,296 contigs and 87,686 singletons were obtained, from which 44% and 25% are annotated as protein-coding genes, respectively, sharing homology with other animal proteomes. Concerning assembly quality, 84% of the contig sequences contain an open reading frame with a start codon while E. crypticus homologs were identified for 92% of the core eukaryotic genes. Moreover, 65% and 77% of the singletons and contigs without known homologs, respectively, were shown to be transcribed in an independent microarray experiment. An Agilent 180 K microarray platform was designed and validated by hybridizing cDNA from 4 day zinc- exposed E. crypticus to the concentration corresponding to 50% reduction in reproduction after three weeks (EC50). Overall, 70% of all probes signaled expression above background levels (mean signal + 1x standard deviation). More specifically, the probes derived from contigs showed a wider range of average intensities when compared to probes derived from singletons. In total, 522 significantly differentially regulated transcripts were identified upon zinc exposure. Several significantly regulated genes exerted predicted functions (e.g. zinc efflux, zinc transport) associated with zinc stress. Unexpectedly, the microarray data suggest that zinc exposure alters retro transposon activity in the E. crypticus genome.

Conclusion

An initial investigation of the E. crypticus transcriptome including an associated microarray platform for future studies proves to be a valuable resource to investigate functional genomics mechanisms of toxicity in soil environments and to annotate a potentially large number of lineage specific genes that are responsive to environmental stress conditions.

Profiling transcriptomic response of Enchytraeus albidus to Cu and Ni: comparison with Cd and Zn

Metals are among the most common contaminants in soils in Europe. Although their effects are relatively well known regarding survival and reproduction to soil invertebrates, their mode of action is poorly understood. Enchytraeus albidus is a model organism in ecotoxicology and with the development of a gene library for this species, transcriptomic studies are now possible. The main aim of this study is to understand the Cu and Ni mechanisms of response in E. albidus, in comparison with Cd and Zn (already studied). E. albidus were exposed to Cu and Ni for 4 days to the reproduction effect concentrations EC50 and EC90. Results indicate that Cu and Ni have similar mechanisms of toxicity. When comparing four elements (hierarchical clustering) it was possible to observe a clear separation of Cd from all other metals. This separation correlates with the available information from other species regarding the toxicokinetics of the tested elements.

Mechanisms of response to silver nanoparticles on Enchytraeus albidus (Oligochaeta): survival, reproduction and gene expression profile

Silver has antimicrobial properties and silver nanoparticles (Ag-NPs) have been some of the most widely used NPs. Information regarding their effects is still insufficient, in particular for soil dwelling organisms. The standard soil Oligochaete Enchytraeus albidus was used to study the effects of Ag in soils, using differential gene expression (microarray) and population (survival, reproduction) response to Ag-NPs (PVP coated) and AgNO₃. Results showed higher toxicity of AgNO₃ (EC₅₀<50 mg/kg) compared to toxicity of Ag-NPs (EC₅₀=225 mg/kg). Based on the biological and material identity, the difference in toxicity between Ag-NPs and AgNO₃ could possibly be explained by a release of Ag(+) ions from the particles or by a slower uptake of Ag-NPs. The indications were that the responses to Ag-NPs reflect an effect of Ag ions and Ag-NPs given the extent of similar/dissimilar genes activated. The particles characterization supports this deduction as there were limited free ions measured in soil extracts, maybe related to little oxidation and/or complexation in the soil matrix. The possibility that gene differences were due to different levels of biological impact (i.e. physiological responses) should not be excluded. Testing of Ag-NPs seem to require longer exposure period to be comparable in terms of effect/risk assessment with other chemicals.

Exposure of Enchytraeus albidus to Cd and Zn - changes in cellular energy allocation (CEA) and linkage to transcriptional, enzymatic and reproductive effects

Cellular energy allocation (CEA) is a measure of the energy status of an organism. The effects of Cd and Zn (reproduction EC(50)s and EC(90)s) on the total energy budget of Enchytraeus albidus (Oligochaeta) were assessed through CEA determination, over periods of time from 0 to 8 d. Results showed reduction on the energy reserves for both metals after 2 d exposure. Lipids were the first reserves to be used and carbohydrates were reduced exclusively after Cd exposure. Electron transport system (ETS) activities were enhanced, suggesting increased metabolism and higher energy requirements for metal detoxification. This was supported by previous results at transcription level, where an up-regulation of genes involved in the mitochondrial oxidative phosphorylation was verified. Additionally, the reduction of CEA may be related with the decrease on the reproductive output. These results showed the relevance of integrating various endpoints, which enabled an overview of various processes and to unravel mechanisms of action of chemicals.

Gene expression responses linked to reproduction effect concentrations (EC 10,20,50,90) of dimethoate, atrazine and carbendazim, in Enchytraeus albidus

Background

Molecular mechanisms of response to pesticides are scarce and information on such responses from soil invertebrates is almost inexistent. Enchytraeus albidus (Oligochaeta) is a standard soil ecotoxicology model species for which effects of many pesticides are known on survival, reproduction and avoidance behaviour. With the recent microarray development additional information can be retrieved on the molecular effects.

Methodology/Principal Findings

Experiments were performed to investigate the transcription responses of E. albidus when exposed to three pesticides – dimethoate (insecticide), atrazine (herbicide) and carbendazim (fungicide) – in a range of concentrations that inhibited reproduction by 10%, 20%, 50% and 90% (EC₁₀, EC₂₀, EC₅₀ and EC₉₀, respectively). The goal of this study was to further identify key biological processes affected by each compound and if dose-related. All three pesticides significantly affected biological processes like translation, regulation of the cell cycle or general response to stress. Intracellular signalling and microtubule-based movement were affected by dimethoate and carbendazim whereas atrazine affected lipid and steroid metabolism (also by dimethoate) or carbohydrate metabolism (also by carbendazim). Response to DNA damage/DNA repair was exclusively affected by carbendazim.

Conclusions

Changes in gene expression were significantly altered after 2 days of exposure in a dose-related manner. The mechanisms of response were comparable with the ones for mammals, suggesting across species conserved modes of action. The present results indicate the potential of using gene expression in risk assessment and the advantage as early markers.