Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.
E-GEOD-52393 - INTEGRATING TRANSCRIPTOMICS INTO TRIAD-BASED SOIL QUALITY ASSESSMENT
Released on 1 February 2014, last updated on 3 June 2014
This study examined how transcriptomics tools can be included in a Triad-based soil quality assessment to assess the toxicity of soils from river banks polluted by metals. To that end we measured chemical soil properties and used the standardized ISO guideline for ecotoxicological tests and a newly developed microarray for gene expression in the indicator soil arthropod, Folsomia candida. Microarray analysis revealed that the oxidative stress response pathway was significantly affected in all soils except one. The data indicate that changes in cell redox homeostasis are a significant signature of metal stress. Finally, 32 genes showed significant dose-dependent expression with metal concentrations. They are promising genetic markers providing an early indication of the need for higher tier testing in soil quality. One of the least polluted soils showed toxicity in the bioassay that could be removed by sterilization. The gene expression profile for this soil did not show a metal-related signature, confirming that another factor than metals (most likely of biological origin) caused the toxicity. This study demonstrates the feasibility and advantages of integrating transcriptomics into Triad-based soil quality assessment. Combining molecular and organismal life-history trait’s stress responses helps identifying causes of adverse effect in bioassays. Further validation is needed for verifying the set of genes with dose-dependent expression patterns linked with toxic stress. We used a one-color microarray design where each sample was hybridized to a single array
transcription profiling by array
Tjalf de Boer <TE.de.Boer@vu.nl>, Cornelis A van Gestel, Dick Roelofs, Guangquan Chen, Marlea Wagelmans, Nico M van Straalen, Tjalf E de Boer