Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA241255 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1206522.fastq.gz | Fastqsanger.gz | |||
| SRR1206652.fastq.gz | Fastqsanger.gz | |||
| SRR1206633.fastq.gz | Fastqsanger.gz | |||
| SRR1206495.fastq.gz | Fastqsanger.gz | |||
| SRR1206525.fastq.gz | Fastqsanger.gz |
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Project description:We investigated the toxicity of soil samples derived from a former municipal landfill site in the South of the Netherlands, where a bioremediation project is running aiming at reusing the site for recreation. Both an organic soil extract and the original soil sample was investigated using the ISO standardised Folsomia soil ecotoxicological testing and gene expression analysis. The 28 day survival/reproduction test revealed that the ecologically more relevant original soil sample was more toxic than the organic soil extract. Microarray analysis showed that the more toxic soil samples induced gene regulatory changes in twice as less genes compared to the soil extract. Consequently gene regulatory changes were highly dependent on sample type, and were to a lesser extent caused by exposure level. An important biological process shared among the two sample types was the detoxification pathway for xenobiotics (biotransformation I, II and III) suggesting a link between compound type and observed adverse effects. Finally, we were able to retrieve a selected group of genes that show highly significant dose-dependent gene expression and thus were tightly linked with adverse effects on reproduction. Expression of four cytochrome P450 genes showed highest correlation values with reproduction, and maybe promising genetic markers for soil quality. However, a more elaborate set of environmental soil samples is needed to validate the correlation between gene expression induction and adverse phenotypic effects.
2012-04-16 | GSE37154 | GEO
Project description:MIMS Environmental/Metagenome sample from soil metagenome
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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:We investigated the toxicity of soil samples derived from a former municipal landfill site in the South of the Netherlands, where a bioremediation project is running aiming at reusing the site for recreation. Both an organic soil extract and the original soil sample was investigated using the ISO standardised Folsomia soil ecotoxicological testing and gene expression analysis. The 28 day survival/reproduction test revealed that the ecologically more relevant original soil sample was more toxic than the organic soil extract. Microarray analysis showed that the more toxic soil samples induced gene regulatory changes in twice as less genes compared to the soil extract. Consequently gene regulatory changes were highly dependent on sample type, and were to a lesser extent caused by exposure level. An important biological process shared among the two sample types was the detoxification pathway for xenobiotics (biotransformation I, II and III) suggesting a link between compound type and observed adverse effects. Finally, we were able to retrieve a selected group of genes that show highly significant dose-dependent gene expression and thus were tightly linked with adverse effects on reproduction. Expression of four cytochrome P450 genes showed highest correlation values with reproduction, and maybe promising genetic markers for soil quality. However, a more elaborate set of environmental soil samples is needed to validate the correlation between gene expression induction and adverse phenotypic effects. paired reference design was used testing animals exposed to two concentrations of an environemntal soil sample and two concentrations of the subsequent soil extract. 4 biological replicates per condition containing 25 grams of soil and 10 23day-old animals per replicate.
2012-04-15 | E-GEOD-37154 | biostudies-arrayexpress
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
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Project description:Metaproteome analysis of a forest soil and a potting soil. Different protein extraction methods were compared to investigate protein extraction efficiency and compatibility with sample downstream processing.
2015-03-26 | PRD000542 | Pride
Project description:Metagenome or environmental sample Metagenome
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