Gene expression analysis of collembola in cadmium containing soil

A Dirt(y) World in a Changing Climate: Importance of Heat Stress in the Risk Assessment of Pesticides for Soil Arthropods

The rise in global temperatures and increasing severity of heat waves pose significant threats to soil organisms, disrupting ecological balances in soil communities. Additionally, the implications of environmental pollution are exacerbated in a warmer world, as changes in temperature affect the uptake, transformation and elimination of toxicants, thereby increasing the vulnerability of organisms. Nevertheless, our understanding of such processes remains largely unexplored. The present study examines the impact of high temperatures on the uptake and effects of the fungicide fluazinam on the springtail Folsomia candida (Collembola, Isotomidae). Conducted under non-optimum but realistic high temperatures, the experiments revealed that increased temperature hampered detoxification processes in F. candida, enhancing the toxic effects of fluazinam. High temperatures and the fungicide exerted synergistic interactions, reducing F. candida's reproduction and increasing adult mortality beyond what would be predicted by simple addition of the heat and chemical effects. These findings highlight the need to reevaluate the current ecological risk assessment and the regulatory framework in response to climate changes. This research enhances our understanding of how global warming affects the toxicokinetics and toxicodynamics (TK-TD) of chemicals in terrestrial invertebrates. In conclusion, our results suggest that adjustments to regulatory threshold values are necessary to address the impact of a changing climate.

Exploring ecological effects of arsenic and cadmium combined exposure on cropland soil: from multilevel organisms to soil functioning by multi-omics coupled with high-throughput quantitative PCR

Arsenic (As) and cadmium (Cd) pose potential ecological threats to cropland soils; however, few studies have investigated their combined effects on multilevel organisms and soil functioning. Here, we used collembolans and soil microbiota as test organisms to examine their responses to soil As and Cd co-contamination at the gene, individual, and community levels, respectively, and further uncovered ecological relationships between pollutants, multilevel organisms, and soil functioning. At the gene level, collembolan transcriptome revealed that elevated As concentrations stimulated As-detoxifying genes AS3MT and GST, whereas the concurrent Cd restrained GST gene expression. At the individual level, collembolan reproduction was sensitive to pollutants while collembolan survival wasn't. At the community level, significant but inconsistent correlations were observed between the biodiversity of different soil keystone microbial clusters and soil As levels. Moreover, soil functioning related to nutrient (e.g., carbon, nitrogen, phosphorus, and sulfur) cycles was inhibited under As and Cd co-exposure only through the mediation of plant pathogens. Overall, these findings suggested multilevel bioindicators (i.e., AS3MT gene expression in collembolans, collembolan reproduction, and biodiversity of soil keystone microbial clusters) in cropland soils co-contaminated with As and Cd, thus improving the understanding of the ecotoxicological impact of heavy metal co-contamination on soil ecosystems.

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.

Heat stress delays detoxification of phenanthrene in the springtail Folsomia candida

Climate change has intensified the occurrence of heat waves, resulting in organisms being exposed to thermal and chemical stress at the same time. The effects of mild heat shock combined with sublethal concentrations of phenanthrene (PHE) on defense mechanisms in springtails Folsomia candida were investigated. The transcription of Heat Shock Protein 70 (HSP70) was significantly upregulated by heat shock but tended to reach the control levels after 42 h of recovery. The transcription of cytochrome P450 3A13 (CYP3A13) was upregulated 3-13 fold by PHE but suppressed by heat shock. The suppression by heat shock might contribute to the reduced detoxification of PHE during high-temperature exposure. In line with this, we found that the internal PHE concentration was approximately 70% higher in heat-shocked springtails than in animals kept at control temperature. In general, the transcription of genes encoding enzymes of detoxification phase Ⅱ (glutathione S-transferase 3) and phase Ⅲ (ABC transporter 1) and the activity of antioxidant defense enzymes (superoxide dismutase and catalase) were less influenced than genes encoding phase I detoxification mechanisms (CYP3A13). These results indicate that heat shock delays the detoxification of PHE in springtails.

Species-specific environmental DNA analysis of the index species in soil ecosystem, Allonychiurus kimi (Collembola: Onychiuridae)

Collembola are abundant and have significant roles in the soil ecosystem. Therefore, the phenotypic endpoints of Collembola population or community have been used as an effective bioindicator for assessing soil quality. Since the identification and counting the collembolans in the soil is a laborious and costly procedure, environmental DNA (eDNA)-based biomonitoring was proposed as an analysis tool of collembolan species found in the soil. In this study, standard primer sets for the species-specific eDNA analysis using Allonychiurus kimi, a soil bioindicator species was selected. Then, the primers were tested for specificity and sensitivity from the soil samples. Two different eDNA samples were tested: (1) eDNA samples were extracted from the soil with A. kimi individuals (intra-organismal eDNA). (2) The samples from the soil without A. kimi individuals (extra-organismal eDNA). The two primers were confirmed in their sensitivity and specificity to the two types of eDNA samples selected. C t-values from both intra- and extra-organismal eDNA showed the significant correlations to the number of inoculated A. kimi (adj. R 2 = 0.7453-0.9489). These results suggest that in excretion, egg, and other exuviae had a significant effect on eDNA analysis from soil samples taken. Furthermore, our results suggest that environmental factors should be considered when analyzing eDNA collected from soil.

Soil Ecotoxicology Needs Robust Biomarkers: A Meta-Analysis Approach to Test the Robustness of Gene Expression-Based Biomarkers for Measuring Chemical Exposure Effects in Soil Invertebrates

Gene expression-based biomarkers are regularly proposed as rapid, sensitive, and mechanistically informative tools to identify whether soil invertebrates experience adverse effects due to chemical exposure. However, before biomarkers could be deployed within diagnostic studies, systematic evidence of the robustness of such biomarkers to detect effects is needed. In our study, we present an approach for conducting a meta-analysis of the robustness of gene expression-based biomarkers in soil invertebrates. The approach was developed and trialed for two measurements of gene expression commonly proposed as biomarkers in soil ecotoxicology: earthworm metallothionein (MT) gene expression for metals and earthworm heat shock protein 70 (HSP70) gene expression for organic chemicals. We collected 294 unique gene expression data points from the literature and used linear mixed-effect models to assess concentration, exposure duration, and species effects on the quantified response. The meta-analysis showed that the expression of earthworm MT was strongly metal concentration dependent, stable over time and species independent. The metal concentration-dependent response was strongest for cadmium, indicating that this gene is a suitable biomarker for this metal. For copper, no clear concentration-dependent response of MT gene expression in earthworms was found, indicating MT is not a reliable biomarker for this metal. For HSP70, overall marginal up-regulation and lack of a concentration-dependent response indicated that this gene is not suitable as a biomarker for organic pollutant effects in earthworms. The present study demonstrates how meta-analysis can be used to assess the status of biomarkers. We encourage colleagues to apply this open-access approach to other biomarkers, as such quantitative assessment is a prerequisite to ensuring that the suitability and limitations of proposed biomarkers are known and stated. Environ Toxicol Chem 2022;41:2124-2138. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Employing gene chip technology for monitoring and assessing soil heavy metal pollution

Soil heavy metals pollution can cause many serious environment problems because of involving a very complex pollution process for soil health. Therefore, it is very important to explore methods that can effectively evaluate heavy metal pollution. Researchers were actively looking for new ideas and new methods for evaluating and predicting levels of soil heavy metal pollution. The study on microbial communities is one of the effective methods using gene chip technology. Gene chip technology, as a high-throughput metagenomics analysis technique, has been widely used for studying the structure and function of complex microbial communities in different polluted environments from different pollutants, including the soil polluted by heavy metals. However, there is still a lack of a systematic summarization for the polluted soil by heavy metals. This paper systematically analyzed soil heavy metals pollution via reviewing previous studies on applying gene chip technology, including single species, tolerance mechanisms, enrichment mechanisms, anticipation and evaluation of soil remediation, and multi-directional analysis. The latest gene chip technologies and corresponding application cases for discovering critical species and functional genes via analyzing microbial communities and evaluating heavy metal pollution of soil were also introduced in this paper. This article can provide scientific guidance for researchers actively investigating the soil polluted by heavy metals.

First characterization of multixenobiotic activity in Collembola: An approach on cadmium-induced response

ATP-binding cassette (ABC) efflux pumps mediate the activity of the Multixenobiotic Resistance (MXR) mechanism and have been proposed as a biomarker of environmental pollution mainly in aquatic invertebrates. MXR activity was never investigated in Collembola and represents a potential tool for soil biomonitoring. This study aimed to characterize for the first time the activity of ABC efflux pumps in the gut of collembolan species, and investigate its responsiveness to cadmium (Cd), a common stressor found in polluted soils. We performed in vitro rhodamine-B accumulation assays in the presence of model inhibitors of ABC efflux pumps: verapamil hydrochloride as P-gp (P-glycoprotein) inhibitor, and MK571, as MRPs (multidrug resistance-related proteins) inhibitor. We also performed rhodamine-B accumulation assays under Cd-exposure (209 μg/L;1 μM). Our results showed that all species presented basal (noninduced) level of MXR activity in their gut. Efflux pumps P-gp and/or MRPs activity were confirmed in Cyphoderus innominatus, Cyphoderus similis, and Folsomia candida, the standard species. The rhodamine-B accumulation assays performed with Cd, applied as soil pollutant, showed that the gut of non-standard species C. similis and Trogolaphysa sp. presented an increase of MXR activity for both P-gp and MRP transporters, indicating the potential of these species as test organisms for soil ecotoxicology studies in Neotropical region. Our findings suggest a functional role of ABC transporters in the collembolan gut and their cellular involvement in Cd defense response, corroborating that MXR phenotype in Collembola can be a promising tool for bioindication of soil contamination.

Species-specific effects of arsenic on the soil collembolan gut microbiota

It is well established that arsenic (As) pollution has a severe threat to food security and soil non-target organisms, however, its influences on soil fauna gut microbiota are poorly understood. The gut microbiota of soil fauna play an important role in host health and nutrient cycling. Here, we used dietary exposure to investigate the effects of As on the mortality and gut microbiota of two model soil collembolans (Folsomia candida and Onychiurus yodai) and determine the accumulation of As in collembolan body tissues. The results showed that, although As exposure did not induce the mortality of the two species, dose dependence of As accumulation was indeed detected in their body tissues. Oral As exposure (500 μg g^-1 yeast) significantly altered the community structure (P < 0.05) of F. candida gut microbiota and reduced its diversity (by more than 20%; P < 0.05) compared to the control; however, no significant effects were observed in O. yodai gut microbiota. The two collembolan species possess significantly different gut microbiota (P < 0.05), which may partly explain the differences of the two collembolan gut microbiota response to As exposure. We further found that the genera Ochrobactrum, Geobacter and Staphylococcus were sensitive to As exposure in F. candida (P < 0.05), but these bacteria were low abundance and not altered in O. yodai. Moreover, the relative abundance of these bacteria was significantly correlated with As bioaccumulation in F. candida body tissues (P < 0.05, R² > 0.6). Higher As bioaccumulation factor was also found in O. yodai body tissues compared to the F. candida. These results indicate that collembolan gut microbiota present a species-specific response to As and may be a more sensitive indicator than the mortality of collembolan.

Antimicrobial activity and carbohydrate metabolism in the bacterial metagenome of the soil-living invertebrate Folsomia candida

The microbiome associated with an animal's gut and other organs is considered an integral part of its ecological functions and adaptive capacity. To better understand how microbial communities influence activities and capacities of the host, we need more information on the functions that are encoded in a microbiome. Until now, the information about soil invertebrate microbiomes is mostly based on taxonomic characterization, achieved through culturing and amplicon sequencing. Using shotgun sequencing and various bioinformatics approaches we explored functions in the bacterial metagenome associated with the soil invertebrate Folsomia candida, an established model organism in soil ecology with a fully sequenced, high-quality genome assembly. Our metagenome analysis revealed a remarkable diversity of genes associated with antimicrobial activity and carbohydrate metabolism. The microbiome also contains several homologs to F. candida genes that were previously identified as candidates for horizontal gene transfer (HGT). We suggest that the carbohydrate- and antimicrobial-related functions encoded by Folsomia's metagenome play a role in the digestion of recalcitrant soil-born polysaccharides and the defense against pathogens, thereby significantly contributing to the adaptation of these animals to life in the soil. Furthermore, the transfer of genes from the microbiome may constitute an important source of new functions for the springtail.

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.

The comet assay in Folsomia candida: A suitable approach to assess genotoxicity in collembolans

The present study shows the comet assay technique being successfully applied for the first time to one of the most widely used soil organisms in standardized ecotoxicological tests, Folsomia candida, providing a step forward in assessing the genotoxicity induced by xenobiotics. Because collembolans have a high content of chitin, a new methodology was developed in which the heads of the collembolans were separated from the rest of the body, allowing the hemolymph to leak out. This procedure allows the cells to be released, and after lysis the genetic material is available for the comet assay. Among other key procedures, the use of 30 organisms (20- to 22-d-old adults) per replicate and the correct amount of cells with genetic material (translated as 10 μL of suspension) applied on the agarose gel were determinants for the success of the results obtained. The methodology was validated by exposing F. candida to a representative metallic element (cadmium) and a representative of organophosphates, the insecticide dimethoate, for a shorter time period of 10 d, compared with the 28 d for the International Organization for Standardization 11267 method. Within this method, the relatively low percentage of DNA damage (30%) observed in controls and the significant increase in terms of percentage of DNA damage for almost all the concentrations of dimethoate and Cd (reaching 52% and 56% of damage in the highest concentrations, respectively) confirmed the genotoxic effect of both compounds and validated this technique. The comet assay proved to be a sensitive technique to detect DNA strand breaks in collembolans' cells. Environ Toxicol Chem 2017;36:2514-2520. © 2017 SETAC.

Draft Genome Sequence of Bacillus toyonensis VU-DES13, Isolated from Folsomia candida (Collembola: Entomobryidae)

We present here the draft genome of Bacillus toyonensis VU-DES13, which was isolated from the midgut of the soil-living springtail Folsomia candida. Previous research revealed the presence of gene clusters for the biosynthesis of various secondary metabolites, including β-lactam antibiotics, in the host's genome. The genome data are discussed in the light of the antimicrobial properties against fungi and oomycetes and a high level of β-lactam resistance of the isolate.

Bioavailability and Toxicity of Copper, Manganese, and Nickel in Paronychiurus kimi (Collembola), and Biomarker Discovery for Their Exposure

Bioavailability and toxicity of Cu, Mn, and Ni in Paronychiurus kimi were investigated after 28 days of exposure to OECD artificial soil spiked with these metals. Uptake and effect of Cu, Mn, and Ni on the reproduction of P. kimi were related to different metal fractions (water-soluble, 0.01 M CaCl₂-extractable or porewater metal concentrations). Cu and Mn concentrations in P. kimi increased with increasing Cu and Mn concentrations in the soil, while Ni contents in P. kimi reached a plateau at a concentration higher than 200 mg/kg in soil. Both uptake and juvenile production related well to different metal fractions, suggesting that these metal fractions are suitable for assessing bioavailability and toxicity of metals in P. kimi. When toxicity for reproduction was compared, as reflected by EC₅₀ values, the order of metal toxicity varied depending upon how exposure concentration was expressed. Moreover, the results of proteomic analysis showed that several proteins involved in the immune system, neuronal outgrowth, and metal ion binding were up-regulated in P. kimi following short-term (7 days) exposure to sublethal level (corresponding to 50% of the EC₅₀) of Cu, Mn, or Ni, respectively. This suggests that the ecotoxicoproteomic approach seems to be a promising tool for early exposure warnings below which significant adverse effects are unlikely to occur. This study demonstrated that a combination of chemical and biological measures can provide information about metal bioavailability and toxicity to which P. kimi has been exposed.

Does long term low impact stress cause population extinction?

This study assessed and monitored 40 consecutive reproduction tests - multigenerational (MG) - of continuous exposure to Cd (at 2 reproduction Effect Concentrations (EC): EC10 and EC50) using the standard soil invertebrate Folsomia candida, in total 3.5 years of data were collected. Endpoints included survival, reproduction, size and metallothionein (MTc) gene expression. Further, to investigate adaptation to the toxicant, additional standard toxicity experiments were performed with the MG organisms of F₆, F₁₀, F₂₆, F₃₄ and F₄₀ generations of exposure. Exposure to Cd EC10 caused population extinction after one year, whereas populations survived exposure to Cd EC50. Cd induced the up-regulation of the MTc gene, this being higher for the higher Cd concentration, which may have promoted the increased tolerance at the EC50. Moreover, EC10 induced a shift towards organisms of smaller size (positive skew), whereas EC50 induced a shift towards larger size (negative skew). Size distribution shifts could be an effect predictor. Sensitivity increased up to F₁₀, but this was reverted to values similar to F₀ in the next generations. The maximum Cd tolerance limits of F. candida increased for Cd EC50 MG. The consequences for risk assessment are discussed.

Biochemical pathways supporting beta-lactam biosynthesis in the springtail Folsomia candida

Recently, an active set of beta-lactam biosynthesis genes was reported in the genome of the arthropod springtail Folsomia candida (Collembola). Evidence was provided that these genes were acquired through horizontal gene transfer. However, successful integration of fungal- or bacterial-derived beta-lactam biosynthesis into the metabolism of an animal requires the beta-lactam precursor L-α-aminoadipic acid and a phosphopantetheinyl transferase for activation of the first enzyme of the pathway, δ-(L-α-aminoadipoyl)-L-cysteinyl-D-valine synthetase (ACVS). In this study, we characterized these supporting pathways and their transcriptional regulation in F. candida. We identified one phosphopantetheinyl transferase and three pathways for L-α-aminoadipic acid production, distinct from the pathways utilized by microorganisms. We found that after heat shock, the phosphopantetheinyl transferase was co-regulated with ACVS, confirming its role in activating ACVS. Two of the three L-α-aminoadipic acid production pathways were downregulated, while PIPOX, an enzyme participating in the pipecolate pathway, was slightly co-regulated with ACVS. This indicates that L-α-aminoadipic acid may not be a limiting factor in beta-lactam biosynthesis in F. candida, in contrast to microorganisms. In conclusion, we show that all components for L-α-aminoadipic acid synthesis are present and transcriptionally active in F. candida. This demonstrates how springtails could have recruited native enzymes to integrate a beta-lactam biosynthesis pathway into their metabolism after horizontal gene transfer.

Summary: Analysis of phosphopantetheinyl transferases and metabolic pathways for L-α-aminoadipic acid that are required for beta-lactam biosynthesis in the arthropod Folsomia candida.

Effect of silver nanoparticles on the standard soil arthropod Folsomia candida (Collembola) and the eukaryote model organism Saccharomyces cerevisiae

BACKGROUND

Because of their antimicrobial properties, silver nanoparticles (AgNPs) have been widely used and have come into contact with the environment. In the present work, an effect of AgNPs on a standard soil organism, Folsomia candida, was studied (in comparison to silver nitrate) focusing on molecular and cellular alterations as ecotoxicological endpoints.

RESULTS

At the molecular level, an up-regulation of metallothionein-containing protein (MTC) mRNA in AgNP-treated groups indicated toxic heavy metal stress effects caused by the release of silver ions from AgNPs, which is similar to animal groups treated with silver nitrate. Alteration of the steady-state level of glutathione S-transferase (GST) mRNA was detected in animal treated with AgNPs and AgNO₃. At the cellular level, the relation between GST activity and the size of the glutathione (GSH) was examined. Change of GST activity from different animal groups was not significant, whereas the GSH pool (reduced and oxidized forms) decreased with increasing concentration of AgNPs. In order to obtain direct evidence whether AgNPs cause oxidative stress, treated animals were incubated with the non-fluorescent probe, 2',7'-dichlorodihydrofluorescein diacetate (DCFH-DA). A fluorescence signal was observed in both AgNPs- and AgNO₃-treated groups pointing to the production of reactive species (RS). Since RS formation in F.candida is difficult to quantify, yeast strain BY4742 (wild-type) and mutants lacking of oxidative stress-related protective enzymes were exploited as a further eukaryote model organism. AgNPs and AgNO₃ were found to also affect growth of yeast and induced oxidative stress.

CONCLUSIONS

An effect of AgNPs on Collembola and yeast strains is similar to the one from AgNO₃. However, AgNPs is less toxic due to the slow release of silver ions. In summary, the toxic effect of AgNPs on F. candida is caused by the combination of the release of silver ions from AgNPs and the formation of reactive species.

Combined Transcriptomics Analysis for Classification of Adverse Effects As a Potential End Point in Effect Based Screening

Environmental risk assessment relies on the use of bioassays to assess the environmental impact of chemicals. Gene expression is gaining acceptance as a valuable mechanistic end point in bioassays and effect-based screening. Data analysis and its results, however, are complex and often not directly applicable in risk assessment. Classifier analysis is a promising method to turn complex gene expression analysis results into answers suitable for risk assessment. We have assembled a large gene expression data set assembled from multiple studies and experiments in the springtail Folsomia candida, with the aim of selecting a set of genes that can be trained to classify general toxic stress. By performing differential expression analysis prior to classifier training, we were able to select a set of 135 genes which was enriched in stress related processes. Classifier models from this set were used to classify two test sets comprised of chemical spiked, polluted, and clean soils and compared to another, more traditional classifier feature selection. The gene set presented here outperformed the more traditionally selected gene set. This gene set has the potential to be used as a biomarker to test for adverse effects caused by chemicals in springtails to provide end points in environmental risk assessment.

Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life

Background

Collembola (springtails) represent a soil-living lineage of hexapods in between insects and crustaceans. Consequently, their genomes may hold key information on the early processes leading to evolution of Hexapoda from a crustacean ancestor.

Method

We assembled and annotated transcriptomes of the Collembola Folsomia candida and Orchesella cincta, and performed comparative analysis with protein-coding gene sequences of three crustaceans and three insects to identify adaptive signatures associated with the evolution of hexapods within the pancrustacean clade.

Results

Assembly of the springtail transcriptomes resulted in 37,730 transcripts with predicted open reading frames for F. candida and 32,154 for O. cincta, of which 34.2% were functionally annotated for F. candida and 38.4% for O. cincta. Subsequently, we predicted orthologous clusters among eight species and applied the branch-site test to detect episodic positive selection in the Hexapoda and Collembola lineages. A subset of 250 genes showed significant positive selection along the Hexapoda branch and 57 in the Collembola lineage. Gene Ontology categories enriched in these genes include metabolism, stress response (i.e. DNA repair, immune response), ion transport, ATP metabolism, regulation and development-related processes (i.e. eye development, neurological development).

Conclusions

We suggest that the identified gene families represent processes that have played a key role in the divergence of hexapods within the pancrustacean clade that eventually evolved into the most species-rich group of all animals, the hexapods. Furthermore, some adaptive signatures in collembolans may provide valuable clues to understand evolution of hexapods on land.

Transcriptional profiling of the soil invertebrate Folsomia candida in pentachlorophenol-contaminated soil

Pentachlorophenol (PCP), a widely used pesticide, is considered to be an endocrine disruptor. The molecular effects of chemicals with endocrine-disrupting potential on soil invertebrates are largely unknown. In the present study, the authors explored the transcriptional expression changes of collembola (Folsomia candida) in response to PCP contamination. A total of 92 genes were significantly differentially expressed at all exposure times, and the majority of them were found to be downregulated. In addition to the transcripts encoding cytochrome P450s and transferase enzymes, chitin-binding protein was also identified in the list of common differentially expressed genes. Analyses of gene ontology annotation and enrichment revealed that cell cycle-related transcripts were significantly induced by PCP, indicating that PCP can stimulate cell proliferation in springtail, as has been reported in human breast cancer cells. Enrichment of functional terms related to steroid receptors was observed, particularly in 20 significant differentially expressed genes involved in chitin metabolism in response to PCP exposure. Combined with confirmation by quantitative polymerase chain reaction, the results indicate that the adverse effects on reproduction of springtails after exposure to PCP can be attributed to a chemical-induced delay in the molting cycle and that molting-associated genes may serve as possible biomarkers for assessing toxicological effects.

Ecotoxicogenomic assessment of diclofenac toxicity in soil

Diclofenac is widely used as nonsteroidal anti-inflammatory drug leaving residues in the environment. To investigate effects on terrestrial ecosystems, we measured dissipation rate in soil and investigated ecotoxicological and transcriptome-wide responses in Folsomia candida. Exposure for 4 weeks to diclofenac reduced both survival and reproduction of F. candida in a dose-dependent manner. At concentrations ≥ 200 mg/kg soil diclofenac remained stable in the soil during a 21-day incubation period. Microarrays examined transcriptional changes at low and high diclofenac exposure concentrations. The results indicated that development and growth were severely hampered and immunity-related genes, mainly directed against bacteria and fungi, were significantly up-regulated. Furthermore, neural metabolic processes were significantly affected only at the high concentration. We conclude that diclofenac is toxic to non-target soil invertebrates, although its mode of action is different from the mammalian toxicity. The genetic markers proposed in this study may be promising early markers for diclofenac ecotoxicity.

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.

Biomass estimation of the terrestrial ecotoxicological species Folsomia candida (Collembola) using a real-time polymerase chain reaction

The abundance and growth of the Folsomia candida soil arthropod have been widely used to assess the environmental impact of a range of soil pollutants, and increasing concerns about environmental pollution require advanced and rapid methods to estimate ecological toxicity. Here, we developed a quantitative polymerase chain reaction (qPCR)-based assay for determining the biomass of F. candida. Prior to DNA extraction, an appropriate amount of an artificial sequence was spiked into the test samples, allowing us to assess the extraction efficiency used for normalisation. We designed primers based on the sequencing information of the nuclear RNA polymerase II (Pol II) and mitochondrial cytochrome c oxidase subunit I (mtCOI) genes of F. candida. Assays were performed on samples containing a different number of individuals at the same body length (individually same biomass; same age) and samples containing the same number of individuals at a different body length (individually different biomass; different age). Biomass was estimated from the body lengths of collembolan samples. For both genes, DNA quantity showed a significant linear relationship between increased collembolan numbers and the estimated biomass; DNA quantity in different ages of collembolans showed a significant correlation with body length and a linear relationship with the estimated biomass. We believe that this rapid and accurate technique could be used to detect and quantify soil animals and thus would improve ecotoxicological testing.

Integrated transcriptomic and proteomic analysis of the global response of Wolbachia to doxycycline-induced stress

The bacterium Wolbachia (order Rickettsiales), representing perhaps the most abundant vertically transmitted microbe worldwide, infects arthropods and filarial nematodes. In arthropods, Wolbachia can induce reproductive alterations and interfere with the transmission of several arthropod-borne pathogens. In addition, Wolbachia is an obligate mutualist of the filarial parasites that cause lymphatic filariasis and onchocerciasis in the tropics. Targeting Wolbachia with tetracycline antibiotics leads to sterilisation and ultimately death of adult filariae. However, several weeks of treatment are required, restricting the implementation of this control strategy. To date, the response of Wolbachia to stress has not been investigated, and almost nothing is known about global regulation of gene expression in this organism. We exposed an arthropod Wolbachia strain to doxycycline in vitro, and analysed differential expression by directional RNA-seq and label-free, quantitative proteomics. We found that Wolbachia responded not only by modulating expression of the translation machinery, but also by upregulating nucleotide synthesis and energy metabolism, while downregulating outer membrane proteins. Moreover, Wolbachia increased the expression of a key component of the twin-arginine translocase (tatA) and a phosphate ABC transporter ATPase (PstB); the latter is associated with decreased susceptibility to antimicrobials in free-living bacteria. Finally, the downregulation of 6S RNA during translational inhibition suggests that this small RNA is involved in growth rate control. Despite its highly reduced genome, Wolbachia shows a surprising ability to regulate gene expression during exposure to a potent stressor. Our findings have general relevance for the chemotherapy of obligate intracellular bacteria and the mechanistic basis of persistence in the Rickettsiales.

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

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

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

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

Toxicity of profenofos to the springtail, Folsomia candida, and ammonia-oxidizers in two agricultural soils

Extensive use of organophosphorus insecticide profenofos (PFF) for agricultural and house-hold purposes has led to serious environmental pollution, with potential risk to organisms in the ecosystem. This study examined the toxicity of PFF to the soil springtail Folsomia candida and ammonia-oxidizers through a series of toxicity tests conducted on two agricultural soils. It was found that the survival, reproduction, hsp70 gene expression of F. candida and the soil potential nitrification rate (PNR) were sensitive to the PFF, whereas no apparent change was observed in the abundance of ammonia-oxidizers. The reproduction of F. candida was the most sensitive endpoint (mean 0.10 mg/kg of EC(50) value) for PFF, although the test was more time-consuming. The results of the acute toxicity tests suggested that the survival of F. candida could be considered as the most suitable bioindicator for fast screening of PFF toxicity because of its fast and easy test procedure. In addition, the hsp70 gene expression in F. candida and the PNR could be used as important parameters for assessment of PFF toxicity. The threshold concentration based on the obtained endpoints differed in the two soils, and consequently the soil property should be considered in toxicity assessments of contaminated soils.

Enchytraeus albidus microarray: enrichment, design, annotation and database (EnchyBASE)

Enchytraeus albidus (Oligochaeta) is an ecologically relevant species used as standard test organisms for risk assessment. Effects of stressors in this species are commonly determined at the population level using reproduction and survival as endpoints. The assessment of transcriptomic responses can be very useful e.g. to understand underlying mechanisms of toxicity with gene expression fingerprinting. In the present paper the following is being addressed: 1) development of suppressive subtractive hybridization (SSH) libraries enriched for differentially expressed genes after metal and pesticide exposures; 2) sequencing and characterization of all generated cDNA inserts; 3) development of a publicly available genomic database on E. albidus. A total of 2100 Expressed Sequence Tags (ESTs) were isolated, sequenced and assembled into 1124 clusters (947 singletons and 177 contigs). From these sequences, 41% matched known proteins in GenBank (BLASTX, e-value ≤ 10(-5)) and 37% had at least one Gene Ontology (GO) term assigned. In total, 5.5% of the sequences were assigned to a metabolic pathway, based on KEGG. With this new sequencing information, an Agilent custom oligonucleotide microarray was designed, representing a potential tool for transcriptomic studies. EnchyBASE (http://bioinformatics.ua.pt/enchybase/) was developed as a web freely available database containing genomic information on E. albidus and will be further extended in the near future for other enchytraeid species. The database so far includes all ESTs generated for E. albidus from three cDNA libraries. This information can be downloaded and applied in functional genomics and transcription studies.

Effect of Cu-nanoparticles versus Cu-salt in Enchytraeus albidus (Oligochaeta): differential gene expression through microarray analysis

Despite increased utilization of copper (Cu) nanoparticles, their behaviour and effect in the environment is largely unknown. Enchytraeids are extensively used in studies of soil ecotoxicology. Ecotoxicogenomic tools have shown to be valuable in nanotoxicity interpretation. A cDNA microarray for Enchytraeus albidus has recently been developed, which was used in this study. We compared the gene expression profiles of E. albidus when exposed to Cu-salt (CuCl(2)) and Cu-nanoparticles (Cu-NP) spiked soil. Exposure time was 48 h with a concentration range of 400 to 1000 mg Cu/kg. There were more down-regulated than up-regulated genes. The number of differently expressed genes (DEG) decreased with increasing concentration for CuCl(2) exposure, whereas for Cu-NP, the number did not change. The number of common DEG decreased with increasing concentration. Differences were mainly related to transcripts involved in energy metabolism (e.g. monosaccharide transporting ATPase, NADH dehydrogenase subunit 1, cytochrome c). Overall, our results indicated that Cu-salt and Cu-NP exposure induced different gene responses. Indirect estimates of Cu-NP related ion-release indicated little or no free Cu(2+) activity in soil solutions. Hence, it was concluded that the Cu-NP effects were probably caused by the nanoparticles themselves and not by released ions.

The influence of long-term copper contaminated agricultural soil at different pH levels on microbial communities and springtail transcriptional regulation

Copper has long been applied for agricultural practises. Like other metals, copper is highly persistent in the environment and biologically active long after its use has ceased. Here we present a unique study on the long-term effects (27 years) of copper and pH on soil microbial communities and on the springtail Folsomia candida an important representative of the soil macrofauna, in an experiment with a full factorial, random block design. Bacterial communities were mostly affected by pH. These effects were prominent in Acidobacteria, while Actinobacteria and Gammaroteobacteria communities were affected by original and bioavailable copper. Reproduction and survival of the collembolan F. candida was not affected by the studied copper concentrations. However, the transcriptomic responses to copper reflected a mechanism of copper transport and detoxification, while pH exerted effects on nucleotide and protein metabolism and (acute) inflammatory response. We conclude that microbial community structure reflected the history of copper contamination, while gene expression analysis of F. candida is associated with the current level of bioavailable copper. The study is a first step in the development of a molecular strategy aiming at a more comprehensive assessment of various aspects of soil quality and ecotoxicology.

Differential gene expression analysis in Enchytraeus albidus exposed to natural and chemical stressors at different exposure periods

The soil oligochaete Enchytraeus albidus is a standard test organism used in biological testing for Environmental Risk Assessment (ERA). Although effects are known at acute and chronic level through survival, reproduction and avoidance behaviour endpoints, very little is known at the sub-cellular and molecular levels. In this study, the effects of soil properties (clay, organic matter and pH) and of the chemicals copper and phenmedipham were studied on E. albidus gene expression, during exposure periods of 2, 4 and 21 days, using DNA microarrays based on a normalised cDNA library for this test species (Amorim et al. 2011). The main objectives of this study were: (1) to assess changes in gene expression of E. albidus over time, and (2) to identify molecular markers for natural and chemical exposures. Results showed an influence of exposure time on gene expression. Transcriptional responses to phenmedipham were seen at 2 days while the responses to copper and the different soils were more pronounced at 4 days of exposure. Some genes were differentially expressed in a stress specific manner and, in general, the responses were related with effects in the energy metabolism and cell growth.

Concentrations of selected trace elements in organs and tissues of livestock from a polluted area

The occurrence of cadmium (Cd), nickel (Ni) and lead (Pb) from industrial emissions were determined in the muscle and liver of cattle from agricultural farms near an industrial plant in Eastern Slovakia. In this study cows (n = 25) were slaughtered and the concentrations of Cd, Ni, Pb were analyzed with a the atomic absorption spectrophotometer. Levels reaching the highest permissible hygiene limits for toxic metals Cd, Pb and Ni were determined in 50 samples. The maximum levels of Cd, Pb and Ni were recorded in the liver (0.865; 2.324; 1.140 mg/kg, respectively) and muscle (0.300; 0.854; 0.700 mg/kg, respectively). It was concluded that the exposure to an industrial plant significantly increases the levels of contaminants in the muscle and organs of cattle, as the most susceptible livestock.

Narcotic mechanisms of acute toxicity of chlorinated anilines in Folsomia candida (Collembola) revealed by gene expression analysis

In order to clarify the mechanisms of reproductive toxicity in a QSAR approach, the transcriptional signatures upon the 2 day exposure to the 28 days EC₅₀ of a series of increasingly chlorinated aniline compounds and 1,2,3,4-tetrachlorobenzene were measured in Folsomia candida. In general, the transcriptional patterns associated with all compounds revealed toxicity at the cellular membranes and hence components of narcosis type I, but a principal component analysis revealed a deviating response by the pentachloroaniline and 2,3,5,6-tetrachloroaniline exposure. Moreover the expression of a subset of mainly biotransformation related genes showed a significant relationship with the logK(ow,) which stresses the presence of narcosis type I. This was confirmed by GO term enrichment at the level of cellular component. Genes involved in the three phases of xenobiotic biotransformation exhibited strict compound specific transcription patterns, which may reflect biotransformation processes in F. candida. Additional toxic mechanisms were especially observed for the 2,3,5,6-tetrachloroaniline, which possible works as an uncoupler or inhibitor of electron transport systems, which is revealed by the up-regulation of genes that encode different members of the electron transport chain. The aniline and 2,3,4-trichloroaniline exposure caused the induction of genes in the ROS defense system. Additional toxicity mechanisms were less clear, but they include the attack of microbial pathogens for the six other compounds and for 2,3,5,6-tetrachloroaniline an effect on mitochondrial protein folding.

Development of a microarray for Enchytraeus albidus (Oligochaeta): preliminary tool with diverse applications

Standard bioassays allow hazard assessment at the population level, but much remains to be learned about the molecular level response of organisms to stressors. The main aim of this study was the development of a DNA microarray for Enchytraeus albidus, a common soil worm species. Further, this microarray was tested using worms exposed to Cu, phenmedipham, and different soil types. Hybridization onto the developed microarray revealed several genes with homology to known sequences. Genes of interest were confirmed through real-time polymerase chain reaction. It was possible to discriminate between natural and chemical stressors and chemical concentrations. Gene responses were detected under conditions known to have effects in the reproduction of individuals. It was confirmed that the integration of different endpoints improves the assessment process and enhances the understanding of the modes of action of stressors. The chemical stress-induced genes were related to factors such as immune response, stress response, metabolic processes, and/or signal transduction. The present study represents the first step of a gene-level study in the ecologically relevant and standard test species E. albidus. It demonstrates the usefulness of cDNA normalization in the production of cDNA libraries of ecotoxicological standard organisms that are not genome models like E. albidus.

Biomarker discovery and proteomic evaluation of cadmium toxicity on a collembolan species, Paronychiurus kimi (Lee)

The goal of this study was to identify promising new biomarkers of cadmium by identifying differentially expressed proteins in Paronychiurus kimi after exposure to cadmium. Through proteomic analysis of P. kimi using 1-D PAGE and nano-LC-MS/MS, 36 downregulated proteins and 40 upregulated proteins were found. Some of the downregulated and upregulated proteins were verified by LC-MS/MS analysis after 2-D PAGE. Downregulated proteins in response to cadmium exposure were involved in glycolysis and energy metabolism, chaperones, transcription, reproduction, and neuron growth. In contrast, proteins involved in glycolysis and energy production, neurogenesis, defense systems response to bacteria, and protein biosynthesis were upregulated in cadmium-treated collembolans. Cubulin may be a potential biomarker for the detection of cadmium in P. kimi since this biomarker was able to low levels (3.5 mg/kg) of cadmium. The 14-3-3 ζ was also found to be a potential biomarker for the detection of medium levels (14 mg/kg) of cadmium. Collembolans may be an alternative tool to humans because many collembolans proteins show a high homology to human proteins.

Expression of mtc in Folsomia candida indicative of metal pollution in soil

The soil-living springtail Folsomia candida is frequently used in reproduction bioassays to assess soil contamination. Alternatively, the response of genes to contamination is assessed. In this study the expression of F. candida's gene encoding the deduced metallothionein-like motif containing protein (MTC) was assessed, using quantitative PCR, in response to six different metals, each at two concentrations in soil. The expression of mtc was induced after exposure to all metals, except for one chromium concentration. Exposure to soil originating from metal-contaminated field sites also induced mtc, while the expression did not change in response to a polycyclic aromatic hydrocarbon. Since this transcript is induced by most of the tested metals, it may potentially be a good indicator of metal contamination. The presented gene expression assay might become a useful tool to screen potentially polluted sites, in order to identify the ones that need further ecotoxicological investigation.

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

Background

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

Results

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

Conclusions

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

Transcriptional plasticity of a soil arthropod across different ecological conditions

Ecological functional genomics, dealing with the responses of organisms to their natural environment is confronted with a complex pattern of variation and a large number of confounding environmental factors. For gene expression studies to provide meaningful information on conditions deviating from normal, a baseline or normal operating range (NOR) response needs to be established which indicates how an organism's transcriptome reacts to naturally varying ecological factors. Here we determine the transcriptional plasticity of a soil arthropod, Folsomia candida, exposed to various natural environments, as part of a first attempt in establishing such a NOR. Animals were exposed to 26 different field soils after which gene expression levels were measured. The main factor found to regulate gene expression was soil-type (sand or clay). Cell homeostasis and DNA replication were affected in collembolans exposed to sandy soil, indicating general stress. Multivariate analysis identified soil fertility as the main factor influencing gene expression. Regarding land-use, only forest soils showed an expression pattern deviating from the others. No significant effect of land-use, agricultural practice or soil type on fitness was observed, but arsenic concentration was negatively correlated with reproductive output. In conclusion, transcriptional responses remained within a limited range across the different land-uses but were significantly affected by soil-type. This may be caused by the contrasting soil physicochemical properties to which F. candida strongly responds. The broad range of conditions over which this soil-living detritivore is able to survive and reproduce, indicates a strategy of high plasticity, which comes with extensive gene expression regulation.

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.

Gene expression microarray analysis of heat stress in the soil invertebrate Folsomia candida

Sudden temperature changes in soil can induce stress in soil-dwelling invertebrates. Hyperthermic conditions have an impact on gene expression as one of the first steps. We use a transcriptomics approach using microarrays to identify expression changes in response to heat in the springtail Folsomia candida. An elevation of temperature (Delta 10 degrees C) altered the expression of 142 genes (116 up-, 26 down-regulated). Many up-regulated genes encoded heat shock proteins, enzymes involved in ATP synthesis, oxidative stress responsive enzymes and anion-transporting ATPases. Down-regulated were glycoside hydrolases, involved in catalysis of disaccharides. The small number of altered transcripts suggest a mild response to heat in this soil invertebrate, but further research is needed to confirm this. This study presents candidate genes for future functional studies concerning thermal stress in soil-dwelling invertebrates.

mRNA expression of a cadmium-responsive gene is a sensitive biomarker of cadmium exposure in the soil collembolan Folsomia candida

The gene expression of environmental organisms is useful as a biomarker of environmental pollution. One of its advantages is high sensitivity. We identified the cDNA of a novel cadmium-responsive gene in the soil collembolan Folsomia candida. The deduced protein, designated "metallothionein-like motif containing protein" (MTC), was cysteine-rich and contained a metallothionein-like motif with similarity to metallothionein, but had a much longer sequence than metallothionein and contained repeated sequences of amino acids. Expression of MTC mRNA was sensitively induced by cadmium exposure at 0.3 mg/kg of dry food, a concentration at which toxic effects are not observed, but expression was not affected by gamma-ray exposure (an inducer of oxidative stress). These findings suggest that MTC is involved in cadmium-binding processes rather than in oxidative-stress responses. In conclusion, we suggest that gene expression of MTC may be a candidate biomarker for detecting low levels of cadmium contamination in soil.

The effect of soil pH and temperature on Folsomia candida transcriptional regulation

Differences in abiotic factors like temperature and soil pH can have a significant physiological impact on soil dwelling invertebrates and may confound results in ecotoxicological testing. In this study we exposed Folsomia candida to a range of two abiotic stress treatments (pH and temperature) for 3 days and measured gene expression of a panel of nine stress response genes with real-time Q-PCR. The exposure to different pH values had a minimal effect on the expression of the nine selected genes: only V-ATPase expression was significantly increased due to decreasing pH. ATPase expression was up-regulated, possibly due to increased proton trafficking across the cell membrane, at a lower pH. HSP70 was up-regulated in collembolans exposed to 30 degrees C, and along with HSP40 at 0 degrees C. We speculate that the minor pH effect on gene expression, compared to the temperature treatment, can be explained by the spatial restricted exposure to the external pH in the gut. Our data showed that only 1 or 2 stress response genes were transcriptionally affected by pH and temperature thus exerting minimal effects. The physiological effects of these treatments on F. candida might indicate interesting novel molecular mechanisms.

Effects of mercury on reproduction, avoidance, and heat shock protein gene expression of the soil springtail Folsomia candida

Based on the Cambisols of Beijing (used as agricultural soils), toxicity tests were conducted to investigate the effects of mercury (Hg) on reproduction and avoidance of Folsomia candida (Hexapoda: Collembola), as well as the transcriptional responses of the hsp70 gene, under different Hg concentrations and at different exposure times. Results showed that the hsp70 gene of the springtail was the most sensitive parameter to soil Hg stress, with a half-maximal effective concentration (EC50) of 0.42 mg/kg. The EC50 values based on reproduction and avoidance tests were 9.29 and 3.88 mg/kg, respectively. The expression level of the hsp70 gene was significantly up-regulated when soil Hg concentration was over 0.25 mg/kg (lowest-observed-effect concentration [LOEC]). In addition, responses of this gene expression were strongly induced after 48 h exposure under 1 mg/kg soil Hg, which probably was due to the fast and sensitive response of the gene transcription to Hg stress. Thus, the results suggested that the responses of the hsp70 gene and individual-level effects (reproduction and avoidance) could be integrated to provide helpful information for environmental monitoring and assessment of contaminated soils.

Gene expression analysis reveals a gene set discriminatory to different metals in soil

Environmental pollution is a worldwide problem, and metals are the largest group of contaminants in soil. Microarray toxicogenomic studies with ecologically relevant organisms, such as springtails, supplement traditional ecotoxicological research but are presently rather descriptive. Classifier analysis, a more analytical application of the microarray technique, is able to predict biological classes of unknown samples. We used the uncorrelated shrunken centroid method to classify gene expression profiles of the springtail Folsomia candida exposed to soil spiked with six different metals (barium, cadmium, cobalt, chromium, lead, and zinc). We identified a gene set (classifier) of 188 genes that can discriminate between six different metals present in soil, which allowed us to predict the correct classes for samples of an independent test set with an accuracy of 83% (error rate = 0.17). This study shows further that in order to apply classifier analysis to actual contaminated field soil samples, more insight and information is needed on the transcriptional responses of soil organisms to different soil types (properties) and mixtures of contaminants.

Sugar sweet springtails: on the transcriptional response of Folsomia candida (Collembola) to desiccation stress

Several species of Collembola survive stressful desiccating conditions by absorbing water vapour from the environment. To obtain insight into the transcriptomic responses underlying this 'water vapour absorption' mechanism we subjected Folsomia candida (Collembola) to transcriptome profiling. We show that ecologically relevant desiccation stress leads to strong time-dependent transcriptomic changes. Exposure of F. candida to 98.2% relative humidity over an interval of 174 h resulted in a high number of gene transcripts being differentially expressed (up to 41%; P-value < 0.05). Additional Gene Ontology analyses suggest that carbohydrate transport, sugar catabolism and cuticle maintenance are biological processes involved in combating desiccation. However, many additional pathways seem to be affected; additional experiments are needed to elucidate which responses are primarily linked to desiccation resistance.