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ABSTRACT: Copper contaminated soil aggregate samples

PROVIDER: PRJNA902313 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22358900_1.fastq.gz	Fastqsanger.gz
	SRR22358900_2.fastq.gz	Fastqsanger.gz
	SRR22358901_1.fastq.gz	Fastqsanger.gz
	SRR22358901_2.fastq.gz	Fastqsanger.gz
	SRR22358902_1.fastq.gz	Fastqsanger.gz

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Project description:Copper contaminated soil samples

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

Project description:Copper has long been applied for agricultural practices. 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 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 explained the history of copper contamination, while gene expression analysis of F. candida is associated with the current level of bioavailable copper. Combined analysis at various trophic levels is highly relevant in the context of assessing long-term soil pollution. A single channel, interwoven loop design was used to test animals exposed to the copper-spiked field soil samples. The field soil was spiked with 4 copper and 4 pH treatments yielding 16 combinations. Combinations are displayed in the Sample descriptions, with 1 M-bM-^@M-^S 4 representing the copper concentrations from low to high, and A-D representing the soil pH from low to high. 4 biological replicates per copper/pH combination were used. Each replicate contained 25 grams of soil and thirty 23-day-old animals.

2012-04-03 | E-GEOD-29644 | biostudies-arrayexpress

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

2012-04-04 | GSE29644 | GEO

Plasmid metagenomes from copper sulfate contaminated soil samples and corresponding control samples from Hygum,DENMARK

Project description:Plasmid metagenomes from copper sulfate contaminated soil samples and corresponding control samples from Hygum, DENMARK

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Project description:Biological community diversity in copper-contaminated soil

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Project description:The bacterial communities in copper contaminated soil

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Role of Mac1 in gene regulation under copper limiting conditions in Fusarium oxysporum [ChIP-seq]

Project description:The transcription factor Mac1 is a key regulator of copper homeostasis and controls the transcriptional response to copper-limiting conditions in fungi. Expression analyses performed in the soil-borne plant pathogen Fusarium oxysporum revealed that almost all copper starvation-induced genes are downregulated in the absence of the regulator Mac1. The aim of this ChIP-seq analysis is to elucidate which of these genes are direct targets of Mac1.

2024-11-07 | GSE244102 | GEO

Project description:Metagenomic-135 soil aggregate samples

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Project description:135 soil aggregate metagenomic samples

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Classifier analysis of gene expression profiles reveals a discriminatory gene set for soil containing different metals

Project description: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 (USC) 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.

2010-02-05 | GSE19353 | GEO

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