POTENTIAL APPLICATION OF A COMMUNITY HYBRIDIZATION TECHNIQUE FOR ASSESSING CHANGES IN THE POPULATION-STRUCTURE OF SOIL MICROBIAL COMMUNITIES

Assessment of changes in the structure of soil microbial communities is hampered by their great complexity and the lack of techniques which are sufficiently global in integrating the plethora of below-ground flora. We have evaluated the application of a DNA hybridization technique which quantifies the extent to which the population structure of microbial communities is similar. DNA is extracted from the communities to be compared and similarity is determined by measuring the relative extent to which DNA from one community cross-hybridizes with that from another. To test the performance of the assay, mixtures of DNA of widely differing complexity (i.e. number of species present) were synthesized using pure cultures of bacteria and fungi, and mixed soil cultures where prokaryotes and eukaryotes were separated using antibiotics. In studies on the effects of hybridization conditions on signal strength, mass of filter-bound target DNA had the greatest effect on the signal to noise ratio (S:N). Observed and theoretical similarity indices based on the mixtures were in broad agreement. However, hybridization signals were strongly decreased by an increase in complexity of the DNA mixture. This resulted in problems with application of the technique to very complex DNA such as was isolated from entire soil communities. However, application to defined, simplified subsets of the soil community, such as the extractable bacterial fraction, was more feasible. The method shows great potential in revealing shifts in soil community structure since it circumvents problems associated with the non-cultivibility of many soil microbes, and provides a holistic measure of the extent to which communities share common microbial species.