Folsomia candida
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA255666 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Increasing concern about pollution of our environment calls for advanced and rapid methods to estimate ecological toxicity. The use of gene expression microarrays in environmental studies can potentially meet this challenge. We present a novel method to examine soil toxicity. We exposed the collembolan Folsomia candida to soil containing an ecologically relevant cadmium concentration, and found a cumulative total of 1586 differentially expressed transcripts across three exposure durations, including transcripts involved in stress response, detoxification, and hypoxia. Additional enrichment analysis of gene ontology (GO) terms revealed that antibiotic biosynthesis is important at all time points examined. Interestingly, genes involved in the "penicillin and cephalosporin biosynthesis pathway" have never been identified in animals before, but are expressed in F. candida’s tissue. The synthesis of antibiotics can possibly be a response to increased cadmium-induced susceptibility to invading pathogens, which might be caused by repression of genes involved in the immune-system (C-type lectins and Toll receptor). This study presents a first global view on the environmental stress response of an arthropod species exposed to contaminated soil,and provides a mechanistic basis for the development of a gene expression soil quality test. Keywords: cadmium, soil, Collembola, environmental genomics
2008-08-08 | GSE11122 | GEO
Project description:Polycyclic aromatic hydrocarbons are common pollutants in soil, have negative effects on soil ecosystems, and are potentially carcinogenic. The Springtail (Collembola) Folsomia candida is often used as an indicator species for soil toxicity. Here we report a toxicogenomic study that translates the ecological effects of the polycyclic aromatic hydrocarbon phenanthrene in soil to the early transcriptomic responses in Folsomia candida. Microarrays were used to examine two different exposure concentrations of phenanthrene, namely the EC10 (24.95 mg kg-1 soil) and EC50 (45.80 mg kg-1 soil) on reproduction of this springtail, which evoked 405 and 251 differentially expressed transcripts, respectively. Fifty transcripts were differential in response to either concentration. Many transcripts encoding xenobiotic detoxification and biotransformation enzymes (phases I, II, and III) were upregulated in response to either concentration. Furthermore, indications of general and oxidative stress were found in response to phenanthrene. Chitin metabolism appeared to be disrupted particularly at the low concentration, and protein translation appeared suppressed at the high concentration of phenanthrene; most likely in order to reallocate energy budgets for the detoxification process. Finally, an immune response was evoked especially in response to the high effect concentration, which was also described in a previous transcriptomic study using the same effect concentration (EC50) of cadmium. Our study provides new insights in the molecular mode of action of the important polluting class of polycyclic aromatic hydrocarbons in soil animals. Furthermore, we present a fast, sensitive, and specific soil toxicity test which enhances traditional tests and may help to improve current environmental risk assessments and monitoring of potentially polluted sites.
2009-05-21 | GSE14207 | GEO
Project description:Ecogenomic assessment of soil toxicity associated with the production chain of 2,5-furandicarboxylic acid (FDCA), a candidate bio-based green chemical building block
| PRJNA301049 | ENA
Project description:INTEGRATING TRANSCRIPTOMICS INTO TRIAD-BASED SOIL QUALITY ASSESSMENT
| PRJNA227772 | ENA
Project description:The present invention relates to methods for determining soil quality, and especially soil pollution, using the invertebrate soil organism Folsomia candida also designated as springtail. Specifically, the present invention relates to a method for determining soil quality comprising: contacting Folsomia Candida with a soil sample to be analysed during a time period of 1 to 5 days; isolating said soil contacted Folsomia Candida; extracting RNA from said isolated soil contacted Folsomia Candida; determing a gene expression profile based on said extracted RNA using microarray technology; comparing said gene expression profile with a reference gene expression profile; and determing soil quality based expression level differences between said gene expression profile and said control expression profile.
2014-07-19 | GSE59588 | GEO
Project description:Polycyclic aromatic hydrocarbons are common pollutants in soil, have negative effects on soil ecosystems, and are potentially carcinogenic. The Springtail (Collembola) Folsomia candida is often used as an indicator species for soil toxicity. Here we report a toxicogenomic study that translates the ecological effects of the polycyclic aromatic hydrocarbon phenanthrene in soil to the early transcriptomic responses in Folsomia candida. Microarrays were used to examine two different exposure concentrations of phenanthrene, namely the EC10 (24.95 mg kg-1 soil) and EC50 (45.80 mg kg-1 soil) on reproduction of this springtail, which evoked 405 and 251 differentially expressed transcripts, respectively. Fifty transcripts were differential in response to either concentration. Many transcripts encoding xenobiotic detoxification and biotransformation enzymes (phases I, II, and III) were upregulated in response to either concentration. Furthermore, indications of general and oxidative stress were found in response to phenanthrene. Chitin metabolism appeared to be disrupted particularly at the low concentration, and protein translation appeared suppressed at the high concentration of phenanthrene; most likely in order to reallocate energy budgets for the detoxification process. Finally, an immune response was evoked especially in response to the high effect concentration, which was also described in a previous transcriptomic study using the same effect concentration (EC50) of cadmium. Our study provides new insights in the molecular mode of action of the important polluting class of polycyclic aromatic hydrocarbons in soil animals. Furthermore, we present a fast, sensitive, and specific soil toxicity test which enhances traditional tests and may help to improve current environmental risk assessments and monitoring of potentially polluted sites. Folsomia candida was exposed to phenanthrene spiked soil or untreated (reference/control) soil for 2 days. Two different concentrations of phenanthrene were used, 24.95 and 45.80 mg/kg soil which represent the EC10 and EC50 on reproduction, respectively. For each concentration treatment 4 biological replicates were used, replicate samples consisted of total RNA extracted from ~30 animals exposed in the same jar to either reference or phenanthrene spiked soil. Phenanthrene treated samples were always hybridized to reference samples in an evenly distributed dye-swap manner, which resulted in total in 8 hybridizations of 16 samples.
2010-05-18 | E-GEOD-14207 | biostudies-arrayexpress
Project description:Narcosis or baseline toxicity is the inert toxicity of hydrophobic compounds, supposed to take place at the level of the cellular membranes. Based on the linear relationship between the toxicity (logEC50) and the hydrophobicity (logKow), class I and II narcotizing compounds are recognized, in which the latter group is assumed to exert additional toxic mechanisms by hydrogen bond donor acidity by their polar groups. Chlorinated anilines, which occur often in the environment as degradation products of certain pesticides , are considered to be narcotizing compounds. In this study the transcriptional responses of the soil arthropod Folsomia candida are investigated upon exposure to a series of anilines with increasing chlorination. A discrimination between class1 and class2 narcotizing compound is being made.
2010-02-03 | GSE19929 | GEO
Project description:Narcosis or baseline toxicity is the inert toxicity of hydrophobic compounds, supposed to take place at the level of the cellular membranes. Based on the linear relationship between the toxicity (logEC50) and the hydrophobicity (logKow), class I and II narcotizing compounds are recognized, in which the latter group is assumed to exert additional toxic mechanisms by hydrogen bond donor acidity by their polar groups. Chlorinated anilines, which occur often in the environment as degradation products of certain pesticides , are considered to be narcotizing compounds. In this study the transcriptional responses of the soil arthropod Folsomia candida are investigated upon exposure to a series of anilines with increasing chlorination. A discrimination between class1 and class2 narcotizing compound is being made. Twenty-three day old Folsomia candida were exposed in LUFA 2.2 standard soil for two days to the EC50 concentrations of the following compounds: aniline, 4-chloroaniline, 3.5-dichloroaniline, 2,3,4-trichloroaniline, 2,3,5,6-tetrachloroaniline, pentachloroaniline and 1,2,3,4-tetrachlorobenzene.1,2,3,4-tetrachlrobenzene was included in the experimental design as a posiitive control of a narcotic class 1 compound. Four biological replicates were used for every treatment and a dye swap was used with the Cy3/Cy5 labels. This resulted in 32 samples which were analysed in 16 hybridisations executed in an interwoven loop design. The solvent (for spiking the soil) control was used as the reference treatment in the data analysis.
2010-02-02 | E-GEOD-19929 | biostudies-arrayexpress
Project description: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.
2014-10-01 | GSE59589 | GEO
Project description:The present invention relates to methods for determining soil quality, and especially soil pollution, using the invertebrate soil organism Folsomia candida also designated as springtail. Specifically, the present invention relates to a method for determining soil quality comprising: contacting Folsomia Candida with a soil sample to be analysed during a time period of 1 to 5 days; isolating said soil contacted Folsomia Candida; extracting RNA from said isolated soil contacted Folsomia Candida; determing a gene expression profile based on said extracted RNA using microarray technology; comparing said gene expression profile with a reference gene expression profile; and determing soil quality based expression level differences between said gene expression profile and said control expression profile. A direct design was used where springtails were exposed to 3 field soils (2 polluted and 1 clean) and cadium and microarrays were directly contrased to those from animals exposed to clean LUFA2.2 soil. 4 biological replicates were used with each containing 25 grams of soil and 30 adult, randomly selected, age sychronized springtails
2014-07-19 | E-GEOD-59588 | biostudies-arrayexpress