Determining the structure of bacterial communities and their response to stimuli is key to understanding community function and the interactions that occur between micro-organisms and the environment. However, bacterial communities often comprise complex assemblages of large numbers of different bacterial populations. An approach is presented which allows bacterial community structure to be determined by fractionation of the complex mixture of total bacterial community DNA using the DNA-binding dye bisbenzimidazole which imposes G+C-dependent changes in the buoyant density of DNA. Bacterial community structure presented as percentage of total DNA vs. percentage G+C content of DNA is an indication of the relative abundance of phylogenetic groups of bacteria. Changes in the composition of a soil bacterial community in response to perturbations in the form of carbon amendment and altered water status were monitored.