DNA microarrays detect effects of soil contamination on Arabidopsis thaliana gene expression

Soil contamination, such as heavy metals and benzene compounds, is a widespread problem on military installations. It is important to be able to determine the effects of soil contamination before any adverse effects appear in organisms in surrounding areas. We examined gene expression in Arabidopsis thaliana grown in soil from three sites at the Radford Army Ammunition Plant in Radford, Virginia, USA, using DNA microarrays. We analyzed soil, germination, and growth rate to compare with the microarray data. Soil contamination affected both external phenotype and gene expression. Plants grown in soil with high levels of contaminants were chloritic and were smaller than control plants grown in potting soil. Plants grown in soil with the highest copper concentration had the lowest growth rates and had genes up-regulated across several functional groups. Plants grown in soils with elevated lead had many genes down-regulated that were related to photosystem II, metabolism, cellular transport, and protein synthesis. Genes consistently up-regulated across most microarrays were genes related to photosystem I, genes related to water deprivation and oxidative stress response, heat shock proteins, and toxin catabolism genes such as glutathiones. DNA microarrays, in concert with a model genetic organism such as A. thaliana, were an effective assessment tool to determine the presence of toxic substances in soil at a site used for the production of military explosives.