Microbial ecology approach for evaluating the effects of contaminants on soil and water ecosystems

Traditional parameters used for the Environmental Risk Assessment (ERA) of environmental contaminants are principally chemiodynamic and physico-chemical properties. Furthermore ecotoxicological effects on organisms in water and soil are assessed with standard acute and chronic ecotoxicologic tests on freshwater, marine and soil organisms. Microbial communities are valuable indicators of the occurrence of disturbances due to exogenous physico-chemical stressors. The assessment of variations in microbial community structure is of basic importance in order to evaluate the impact of an environmental stressor. Complex microbial communities may serve as ideal and ecologically relevant toxicity indicators. A number of microbiologically driven processes has been proposed to evaluate the effects of xenobiotics on ecosystems. Proteins, genes, metabolites, or lipids that, when expressed, present a pattern of molecular change in an organism in response to a specific environmental stressor, can be defined as environmental biomarkers. The number of techniques to study microbial communities has increased exponentially over the last 20 years and the advent of culture-independent methods, such as molecular biological techniques, has changed the view of microbial diversity. Among these techniques epifluorescence microscopy ones, such as direct count of bacterial abundance (DAPI count), vitality (Live/Dead cell viability assay), and Fluorescence In Situ Hybridization (FISH) have been showing effective tools for studying specific microbial populations in soil and water ecosystems. We show how the applications of these techniques to contaminated soil and water ecosystems allow to highlight the presence of particular bacterial groups involved in chemical degradation.