An integrated analytical approach for assessing the biological status of the soil microbial community

An integrated multicriteria analytical procedure for rapid, cost-effective characterisation of the biological status of soil bacterial community was developped. Commercially-available, light emission-based bioassays were selected for measuring cell density, activity, and diversity. All but Terminal Restriction Fragment Length Polymorphism (T-RFLP) were designed for multiwell-plate formats and high-throughput screening potential. Adenosine Tri Phosphate (ATP) was measured using a bioluminescence assay. Dehydrogenase activity (DHA) was measured on growing cells. Kinetic measurements of the formation of a coloured formazan derivative was used after nutrient broth addition to estimate initial cell concentrations by reference to Escherichia coli added as internal standard. Compared to conventional ATP and DHA determinations in soils, the procedures described here do not require extraction of ATP or formazan derivative from the soil matrix. Metabolic diversity was characterised using the Biolog™ system. T-RFLP was chosen for assessing bacterial community structure. The bioassays were performed on microbial preparations obtained after either direct dilution of soil suspensions or prior density-gradient separation of microbial cells from the soil matrix. Dilution maintains the original structure of native dominant microbial communities. Density-gradient separation of microbial cells is highly selective, drastically modifying metabolic (CLP Profiles) and species (T-RFLP patterns) diversity, as well as activity parameters.

► Soil and cell suspensions differ in terms of metabolic and species diversities.
► Density separation is justified when high purity cell or DNA preparations are required.
► Cultivable microbes are more sensitive indicators than the whole of the soil microflora.
► Combining microbial properties increases the efficiency for assessing ecological impacts.