Effects of soil properties and time of exposure on gene expression of Enchytraeus albidus (Oligochaeta).
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ABSTRACT:
ORGANISM(S): Enchytraeus albidus
PROVIDER: GSE27700 | GEO | 2011/09/07
SECONDARY ACCESSION(S): PRJNA138143
REPOSITORIES: GEO
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Project description:Changes in soil properties (e.g. pH, organic matter content, granulometry) can influence chemical toxicity to organisms and act alone as stressors. Previous studies on Enchytraeus albidus showed that changes in soil properties caused effects on reproduction and avoidance behavior and also oxidative stress. In addition, results at the transcritptomic level indicated changes in gene expression profile due to soil properties changes. In this study, E. albidus was exposed to modified versions of the artificial standard OECD soil (different pH, OM and clay content) in different exposure times (2, 4 and 8 days). The gene expression profile was characterized using a class comparison statistical analysis. Results indicated that the transcriptional response was time dependent, with different genes being affected at different time points. Results also showed some genes (and biological functions) being affected in a soil specific way. Fluorescently labelled cDNA, from enchytraeids exposed during 2, 4 and 8 days OECD standard soil (Cy3) and to the different exposure conditions (modified OECD soil) (Cy5), was synthesized for microarray analysis and hybridizations were performed. After scanning (Agilent Microarray Scanner from Agilent Technologies), spots were identified and ratios quantified using Quantarray (Packard Biochip Technologies). Statistical analysis of the microarrays was performed using BRB Array Tools version 3.8.1 Stable Release (http://linus.nci.nih.gov/BRB-ArrayTools.html). After background subtraction, the replicated spots within each array were averaged, and microarrays were normalized using loess method (Smith and Speed, 2003). Statistical class comparison between groups of arrays was performed between each exposure condition and the respective “control” (exposure in OECD standard soil, for each time of exposure) using two-sample T-test and 95% of confidence level for the assessment of differentially expressed genes.
2011-09-06 | E-GEOD-27700 | biostudies-arrayexpress
Project description: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 gene expression in E. albidus during exposure periods of 2 days, 4 days and 3 weeks, 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 a clear influence of exposure time in 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 at energy metabolism and cell growth level.
2011-09-01 | GSE26896 | GEO
Project description:Due to its antimicrobial activity, silver nanoparticles (Ag-NPs) are among the most used NPs worldwide, yet little information is available regarding their effects, particularly in soil dwelling organisms. Enchytraeids (Oligochaeta) are important members of the soil fauna which actively contribute to the acceleration of organic matter decomposition and nutrient recycling processes. Hence, for hazard and risk assessment it is important to provide toxicity data for these organisms and to understand more in regard to the mode of action of Ag-NPs within organism. To study this we conducted toxicity experiments using the OECD standard guideline, testing Ag-NPs and AgNO3, having assessed survival, reproduction and differential gene expression. Population toxicity responses were assessed showing higher toxicity for the AgNO3. In an attempt to understand the mode of action we performed transcription profiling using the microarray. Gene expression profile of Enchytraeus albidus was analysed after 2 days of exposure to 100 and 200 mg/kg of two silver forms (nanoparticles and salt_silver nitrate) in OECD soil. Three biological replicates per test treatment and control (clean OECD soil) were used.
2013-05-22 | E-GEOD-42431 | biostudies-arrayexpress
Project description: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 gene expression in E. albidus during exposure periods of 2 days, 4 days and 3 weeks, 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 a clear influence of exposure time in 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 at energy metabolism and cell growth level. Fluorescently labelled cDNA, from enchytraeids exposed during 4 days and 3 weeks to control soil (LUFA 2.2) and to the different exposure conditions was synthesized for microarray analysis and hybridizations were performed. After scanning, spots were identified and ratios quantified using the QuantArray (Packard Biochip Technologies). Statistical analysis of the microarrays was performed using limmaGUI package (1.18.0) (Smyth, 2005) in the R (2.8.0) software environment (http://www.R-project.org/). After being submitted to local background subtraction, microarrays were normalized using global loess method. To statistically evaluate the differential gene expression between the different conditions, a gene-per-gene linear model (limma – linear model for microarray analysis) and empirical Bayes methods were applied. The results were then corrected for multiple testing using the Benjamini-Hochberg’s method (adjusted p<0.05 was considered significant) (Benjamini and Hochberg, 1995).
2011-08-31 | E-GEOD-26896 | biostudies-arrayexpress
Project description: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.
2011-03-30 | GSE18569 | GEO
Project description:Despite the increased utilization of nanoparticles, the behavior and effect in the environment is largely unknown and few resources are available for health and environmental effect studies. Enchytraeids are extensively used in studies of soil ecotoxicology and recently, a cDNA microarray for Enchytraeus albidus was developed, allowing also toxicogenomic studies in this species. These organisms are ecologically relevant small worms that indirectly contribute to the regulation and degradation of organic matter. In this study we compared the gene expression profiles of E. albidus when exposed to copper-salt (CuCl2) and copper nanoparticles (Cu-NP) spiked soil. The worms were exposed for 48 hours in soil to a range of concentrations. Microarray hybridizations revealed different response patterns between copper-salt and copper nanoparticles exposed organisms, these differences are mainly related with transcripts involved in the energy metabolism of the organisms. Despite unknown gene function in the data-set there are indications that Cu-salt and Cu-NP exposure induced specific gene level responses.
2011-09-08 | GSE26331 | GEO
Project description:It has long been recognized that species occupy a specific ecological niche within their ecosystem. The ecological niche is defined as the number of conditions and resources that limit species distribution. Within their ecological niche, species do not exist in a single physiological state but in a number of states we call the Natural Operating Range. In this paper we link ecological niche theory to physiological ecology by measuring gene expression levels of collembolans exposed to various natural conditions. The soil-dwelling collembolan Folsomia candida was exposed to 26 natural soils with different soil characteristics (soil type, land use, practice, etc). The animals were exposed for two days and gene expression levels were measured. The main factor found to regulate gene expression was the soil type (sand or clay), in which 18.5% of the measured genes were differentially expressed. Gene Ontology analysis showed animals exposed to sandy soils experience general stress, affecting cell homeostasis and replication. Multivariate analysis linking soil chemical data to gene expression data revealed that soil fertility influences gene expression. Land-use and practice had less influence on gene expression; only forest soils showed a different expression pattern. A variation in gene expression variation analysis showed overall low variance in gene expression. The large difference in response to soil type was caused by the soil physicochemical properties where F. candida experiences clay soils and sandy soils as very different from each other. This collembolan prefers fertile soils with high organic matter content, as soil fertility was found to correlate with gene expression and animals exposed to sandy soils (which, in general, have lower organic matter content) experience more general stress. Finally, we conclude that there is no such thing as a fixed physiological state for animals in their ecological niche and the boundary between the ecological niche and a stressed state depends on the genes/pathways investigated.
2011-02-15 | GSE21213 | GEO
Project description: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 stressM-bM-^@M-^Sinduced 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. Fluorescently labelled cDNA, from enchytraeids exposed during 2 days to control LUFA 2.2 (Cy3) soil and to the different exposure conditions (Cy5), was synthesized for microarray analysis and hybridizations were performed. After scanning, spots were identified and ratios quantified using the Genepix software 5.0 (Axon Instruments). Statistical analysis of the microarrays was performed using limmaGUI package (1.18.0) (Smyth, 2005) in the R (2.8.0) software environment (http://www.R-project.org/). After being submitted to local background subtraction, microarrays were normalized using global loess method. To statistically evaluate the differential gene expression between the different conditions, a gene-per-gene linear model (limma M-bM-^@M-^S linear model for microarray analysis) and empirical Bayes methods were applied. The results were then corrected for multiple testing using the Benjamini-HochbergM-bM-^@M-^Ys method (adjusted p<0.05 was considered significant) (Benjamini and Hochberg, 1995).
2011-03-30 | E-GEOD-18569 | biostudies-arrayexpress
Project description:Despite the increased utilization of nanoparticles, the behavior and effect in the environment is largely unknown and few resources are available for health and environmental effect studies. Enchytraeids are extensively used in studies of soil ecotoxicology and recently, a cDNA microarray for Enchytraeus albidus was developed, allowing also toxicogenomic studies in this species. These organisms are ecologically relevant small worms that indirectly contribute to the regulation and degradation of organic matter. In this study we compared the gene expression profiles of E. albidus when exposed to copper-salt (CuCl2) and copper nanoparticles (Cu-NP) spiked soil. The worms were exposed for 48 hours in soil to a range of concentrations. Microarray hybridizations revealed different response patterns between copper-salt and copper nanoparticles exposed organisms, these differences are mainly related with transcripts involved in the energy metabolism of the organisms. Despite unknown gene function in the data-set there are indications that Cu-salt and Cu-NP exposure induced specific gene level responses. Fluorescently labelled cDNA, from enchytraeids exposed during 2 days to control soil (from Hygum site in Denmark) and to the different exposure conditions (Cy5), was synthesized for microarray analysis and hybridizations were performed. After scanning, spots were identified and ratios quantified using the QuantArray (Packard Biochip Technologies). Statistical analysis of the microarrays was performed using limmaGUI package (1.18.0) (Smyth, 2005) in the R (2.8.0) software environment (http://www.R-project.org/). After being submitted to local background subtraction, microarrays were normalized using global loess method. To statistically evaluate the differential gene expression between the different conditions, a gene-per-gene linear model (limma – linear model for microarray analysis) and empirical Bayes methods were applied. The results were then corrected for multiple testing using the Benjamini-Hochberg’s method (adjusted p<0.05 was considered significant) (Benjamini and Hochberg, 1995).
2011-09-07 | E-GEOD-26331 | biostudies-arrayexpress
Project description:It has long been recognized that species occupy a specific ecological niche within their ecosystem. The ecological niche is defined as the number of conditions and resources that limit species distribution. Within their ecological niche, species do not exist in a single physiological state but in a number of states we call the Natural Operating Range. In this paper we link ecological niche theory to physiological ecology by measuring gene expression levels of collembolans exposed to various natural conditions. The soil-dwelling collembolan Folsomia candida was exposed to 26 natural soils with different soil characteristics (soil type, land use, practice, etc). The animals were exposed for two days and gene expression levels were measured. The main factor found to regulate gene expression was the soil type (sand or clay), in which 18.5% of the measured genes were differentially expressed. Gene Ontology analysis showed animals exposed to sandy soils experience general stress, affecting cell homeostasis and replication. Multivariate analysis linking soil chemical data to gene expression data revealed that soil fertility influences gene expression. Land-use and practice had less influence on gene expression; only forest soils showed a different expression pattern. A variation in gene expression variation analysis showed overall low variance in gene expression. The large difference in response to soil type was caused by the soil physicochemical properties where F. candida experiences clay soils and sandy soils as very different from each other. This collembolan prefers fertile soils with high organic matter content, as soil fertility was found to correlate with gene expression and animals exposed to sandy soils (which, in general, have lower organic matter content) experience more general stress. Finally, we conclude that there is no such thing as a fixed physiological state for animals in their ecological niche and the boundary between the ecological niche and a stressed state depends on the genes/pathways investigated. Test animals were exposed to 26 natural soils + 2 control soils. 4 biological replicates per soil containing 25 grams of soil and 30 23-day-old animals per replicate, RNA was isolated after two days of exposure. for the micro-array hybridization design we made use of an interwoven loop design. from the four replicates per soil two were labeled with Cy3 and 2 with Cy5. It was made sure that now two replicates of the same soil were ever hybridized against the same soil.
2011-02-15 | E-GEOD-21213 | biostudies-arrayexpress