Using time-lapse omics correlations to integrate toxicological pathways of a formulated fungicide in a soil invertebrate

Integrated analysis of transcriptome and metabolome reveals chronic low salinity stress responses in the muscle of Exopalaemon carinicauda

Low salinity environment is one of the key factors threatening the survival of aquatic organisms. Due to the strong adaptability of low salinity, Exopalaemon carinicauda is an ideal model to study the low salinity adaptation mechanism of crustaceans. In this study, E. carinicauda from the same family were divided into two groups, which were reared at salinity of 4 ‰ and 30 ‰, respectively. Integrated analysis of transcriptome and metabolome was used to uncover the mechanisms of E. carinicauda adaptation to chronic low salinity environment. Under the chronic low salinity stress, a total of 651 differentially expressed genes (DEGs) and 386 differential metabolites (DMs) were obtained, with the majority showing downregulation. These DEGs mainly involved MAPK signal transduction pathway and structural constituent of cuticle. Besides, chitin binding and chitin metabolism process were inhibited significantly. Among the DMs, lipids and lipid-like molecules, flavor amino acids and nucleotides were detected, which may be related to the adjustment of energy metabolism and flavor of muscle. In addition, ubiquinone and other terpenoid-quinone biosynthesis pathway and alanine, aspartate, and glutamate metabolic pathway were induced. These results will enrich our understanding of the molecular mechanism underlying the chronic low salinity tolerance in E. carinicauda, providing an important theoretical basis and practical guidance for the research and breeding, thereby promoting the sustainable development of aquaculture.

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

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

Combining time-resolved transcriptomics and proteomics data for Adverse Outcome Pathway refinement in ecotoxicology

Conventional Environmental Risk Assessment (ERA) of pesticide pollution is based on soil concentrations and apical endpoints, such as the reproduction of test organisms, but has traditionally disregarded information along the organismal response cascade leading to an adverse outcome. The Adverse Outcome Pathway (AOP) framework includes response information at any level of biological organization, providing opportunities to use intermediate responses as a predictive read-out for adverse outcomes instead. Transcriptomic and proteomic data can provide thousands of data points on the response to toxic exposure. Combining multiple omics data types is necessary for a comprehensive overview of the response cascade and, therefore, AOP development. However, it is unclear if transcript and protein responses are synchronized in time or time lagged. To understand if analysis of multi-omics data obtained at the same timepoint reveal one synchronized response cascade, we studied time-resolved shifts in gene transcript and protein abundance in the springtail Folsomia candida, a soil ecotoxicological model, after exposure to the neonicotinoid insecticide imidacloprid. We analyzed transcriptome and proteome data every 12 h up to 72 h after onset of exposure. The most pronounced shift in both transcript and protein abundances was observed after 48 h exposure. Moreover, cross-correlation analyses indicate that most genes displayed the highest correlation between transcript and protein abundances without a time-lag. This demonstrates that a combined analysis of transcriptomic and proteomic data from the same time-point can be used for AOP improvement. This data will promote the development of biomarkers for the presence of neonicotinoid insecticides or chemicals with a similar mechanism of action in soils.

Insights into the molecular mechanisms of pesticide tolerance in the Aporrectodea caliginosa earthworm

Diffuse pollution of the environment by pesticides has become a major soil threat to non-target organisms, such as earthworms for which declines have been reported. However some endogeic species are still abundant and persist in intensively cultivated fields, suggesting they become tolerant to long-term anthropogenic pressure. We thus considered the working hypothesis that populations of Aporrectodea caliginosa earthworms from conventionally managed fields developed a tolerance to pesticides compared with those from organically managed fields. To investigate this hypothesis, we studied earthworm populations of the same genetic lineage from soils that were either lowly or highly contaminated by pesticides to detect any constitutive expression of differentially expressed molecular pathways between these populations. Earthworm populations were then experimentally exposed to a fungicide-epoxiconazole-in the laboratory to identify different molecular responses when newly exposed to a pesticide. State-of-the-art omics technology (RNA sequencing) and bioinformatics were used to characterize molecular mechanisms of tolerance in a non-targeted way. Additional physiological traits (respirometry, growth, bioaccumulation) were monitored to assess tolerance at higher levels of biological organization. In the present study, we generated the de novo assembly transcriptome of A. caliginosa consisting of 64,556 contigs with N50 = 2862 pb. In total, 43,569 Gene Ontology terms were identified for 21,593 annotated sequences under the three main ontologies (biological processes, cellular components and molecular functions). Overall, we revealed that two same lineage populations of A. caliginosa earthworms, inhabiting similar pedo-climatic environment, have distinct gene expression pathways after they long-lived in differently managed agricultural soils with a contrasted pesticide exposure history for more than 22 years. The main difference was observed regarding metabolism, with upregulated pathways linked to proteolytic activities and the mitochondrial respiratory chain in the highly exposed population. This study improves our understanding of the long-term impact of chronic exposure of soil engineers to pesticide residues.

Multi-Omics Methods Applied to Flower Development

Developmental processes in multicellular organisms depend on the proficiency of cells to orchestrate different gene expression programs. Over the past years, several studies of reproductive organ development have considered genomic analyses of transcription factors and global gene expression changes, modeling complex gene regulatory networks. Nevertheless, the dynamic view of developmental processes requires, as well, the study of the proteome in its expression, complexity, and relationship with the transcriptome. In this chapter, we describe a dual extraction method-for protein and RNA-for the characterization of genome expression at proteome level and its correlation to transcript expression data. We also present a shotgun proteomic procedure (LC-MS/MS) followed by a pipeline for the imputation of missing values in mass spectrometry results.

Stress response markers in the blood of São Tomé green sea turtles (Chelonia mydas) and their relation with accumulated metal levels

Metals are persistent worldwide being harmful for diverse organisms and having complex and combined effects with other contaminants in the environment. Sea turtles accumulate these contaminants being considered good bioindicator species for marine pollution. However, very little is known on how this is affecting these charismatic animals. São Tomé and Príncipe archipelago harbours important green sea turtle (Chelonia mydas) nesting and feeding grounds. The main goal of this study was to determine metal and metalloid accumulation in the blood of females C. mydas nesting in São Tomé Island, and evaluate the possible impacts of this contamination by addressing molecular stress responses. Gene expression analysis was performed in blood targeting genes involved in detoxification/sequestration and metal transport (mt, mtf and fer), and in antioxidant and oxidative stress responses (cat, sod, gr, tdx, txrd, selp and gclc). Micronuclei analysis in blood was also addressed as a biomarker of genotoxicity. Present results showed significant correlations between different gene expressions with the metals evaluated. The best GLM models and significant relationships were found for mt expression, for which 78% of the variability was attributed to metal levels (Al, Cu, Fe, Hg, Pb and Zn), followed by micronuclei count (65% - Cr, Cu, Fe, Hg, Mn and Zn), tdx expression (52% - Cd, Fe, Mn, Pb and Se), and cat expression (52% - As, Fe, Se and Cd x Hg). Overall, this study demonstrates that these green sea turtles are trying to adapt to the oxidative stress and damage produced by metals through the increased expression of antioxidants and other protectors, which raises concerns about the impacts on these endangered organisms' fitness. Furthermore, promising biomarker candidates associated to metal stress were identified in this species that may be used in future biomonitoring studies using C. mydas' blood, allowing for a temporal follow-up of the organisms.

Multigenerational exposure of the collembolan Folsomia candida to soil metals: Adaption to metal stress in soils polluted over the long term

Multigenerational tests provide a comprehensive assessment of the long-term toxicity of pollutants. Here, the multigenerational effects of soil metal contamination on Folsomia candida were investigated over five generations (generations 1-5: F1-F5). Nine soils with varying physicochemical properties and degrees of metal pollution were studied. The selected endpoints were survival, reproduction, body size and body metal concentrations. F. candida was cultured only up to the fifth generation with high reproduction in contaminated acid soils where reproduction was at least 5 times that in neutral soils and 20 times that in calcareous soils. Correlation analysis indicated that soil pH (68.9% contribution) and cation exchange capacity (CEC, 15.4% contribution) were more important factors than pollution level affecting the reproduction of F. candida. No significant difference was observed in adult survival or adult length over five generations. The highest collembolan body Cd concentrations in soils A1-A3 were 3.15, 2.93 and 3.23 times those in F1, with similar results for body Pb. A similar trend in reproduction and juvenile length was observed with an initial decrease (p < 0.05) and then an increase (p < 0.05) over the generations in each acid soil; the opposite trend occurred in the changes in body cadmium (Cd) and lead (Pb) concentrations which increased initially (p < 0.05) and then decreased (p < 0.05) compared to the original concentrations of the first generation. The results indicate that F. candida can adapt to soil metal stress during multigenerational exposure and the adaption energy may be related to a tradeoff between reproduction or growth of juveniles and the detoxification of metals accumulated in the body. Soil properties, especially pH and CEC, had a substantial influence on the long-term survival of the collembolan in the metal-polluted soils.

Integration of transcriptome and proteome reveals molecular mechanisms underlying stress responses of the cutworm, Spodoptera litura, exposed to different levels of lead (Pb)

Heavy metals are major environmental pollutants that affect organisms across different trophic levels. Herbivorous insects play an important role in the bioaccumulation, and eventually, biomagnification of these metals. Although effects of heavy metal stress on insects have been well-studied, the molecular mechanisms underlying their effects remain poorly understood. Here, we used the RNA-Seq profiling and isobaric tags for relative and absolute quantitation (iTRAQ) approaches to unravel these mechanisms in the polyphagous pest Spodoptera litura exposed to lead (Pb) at two different concentrations (12.5 and 100 mg Pb/kg; PbL and PbH, respectively). Altogether, 1392 and 1630 differentially expressed genes (DEGs) and 58, 114 differentially expressed proteins (DEPs) were identified in larvae exposed to PbL and PbH, respectively. After exposed to PbL, the main up-regulated genes clusters and proteins in S. litura larvae were associated with their metabolic processes, including carbohydrate, protein, and lipid metabolism, but the levels of cytochrome P450 associated with the pathway of xenobiotic biodegradation and metabolism were found to be decreased. In contrast, the main up-regulated genes clusters and proteins in larvae exposed to PbH were enriched in the metabolism of xenobiotic by cytochrome P450, drug metabolism-cytochrome P450, and other drug metabolism enzymes, while the down-regulated genes and proteins were found to be closely related to the lipid (lipase) and protein (serine protease, trypsin) metabolism and growth processes (cuticular protein). These findings indicate that S. litura larvae exposed to PbL could enhance food digestion and absorption to prioritize for growth rather than detoxification, whereas S. litura larvae exposed to PbH reduced food digestion and absorption and channelized the limited energy for detoxification rather than growth. These contrasting results explain the dose-dependent effects of heavy metal stress on insect life-history traits, wherein low levels of heavy metal stress induce stimulation, while high levels of heavy metal stress cause inhibition at the transcriptome and proteome levels.

From laboratory to the field: Validating molecular markers of effect in Folsomia candida exposed to a fungicide-based formulation

Under controlled laboratory conditions, toxicity data tend to be less variable than in more realistic in-field studies and responses may thus differ from those in the natural environment, creating uncertainty. The validation of data under environmental conditions is therefore a major asset in environmental risk assessment of chemicals. The present study aimed to validate the mode of action of a commercial fungicide formulation in the soil invertebrate F. candida, under more realistic exposure scenarios (in-field bioassay), by targeting specific molecular biomarkers retrieved from laboratory experiments. Organisms were exposed in soil cores under minimally controlled field conditions for 4 days to a chlorothalonil fungicide dosage causing 75% reduction of reproduction in a previous laboratory experiment (127 mg a.i. kg^-1) and half this concentration (60 mg a.i. kg^-1). After exposure, organisms were retrieved and RNA was extracted from each pool of organisms. According to previous laboratorial omics results with the same formulation, ten genes were selected for gene expression analysis by qRT-PCR, corresponding to key genes of affected biological pathways including glutathione metabolism, oxidation-reduction, body morphogenesis, and reproduction. Six of these genes presented a dose-response trend with higher up- or down-regulation with increasing pesticide concentrations. Highly significant correlations between their expression patterns in laboratory and in-field experiments were observed. This work shows that effects of toxicants can be clearly demonstrated in more realistic conditions using validated biomarkers. Our work outlines a set of genes that can be used to assess the early effects of pesticides in a realistic agricultural scenario.

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

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