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Title: The influence of long-term copper contaminated agricultural soil at different pH levels on microbial communities and springtail transcriptional regulation      
dateReleased:
04-03-2012
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 – 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.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-29644
refinement:
raw
alternateIdentifiers:
29644
keywords:
functional genomics
dateModified:
04-11-2012
availability:
available
types:
gene expression
name:
Folsomia candida
ID:
A-GEOD-7150
name:
ISQ Chip Folsomia candida Collembola VU 15.7K version 2.0
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-29644/E-GEOD-29644.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-29644/E-GEOD-29644.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29644
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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