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Humans are visiting Antarctica in increasing numbers, and the ecological effect of rapid soil habitat alteration due to human-induced physical disturbance is not well understood. An experimental soil disturbance trial was set up near Scott Base on Ross Island, to investigate the immediate and short-term changes to bacterial community structure, following surface soil disturbance. Three blocks, each comprising an undisturbed control, and an area disturbed by removing the top 2 cm of soil, were sampled over a time series (0, 7, 14, 21, and 35 days), to investigate changes to bacterial community structure using DNA profiling by terminal restriction fragment length polymorphism. The simulated disturbance did not cause any major shifts in the structure of the bacterial communities over the 35-day sampling period. Ordination showed that the bacterial community composition correlated strongly with soil EC (R-2 = 0.55) and soil pH (R-2 = 0.67), rather than the removal of the top 2 cm of surface material. Although the replicate blocks were visually indistinguishable from one another, high local spatial variability of soil chemical properties was found at the study site and different populations of bacterial communities occurred within 2 m of one another, within the same landscape unit. Given the current knowledge of the drivers of bacterial community structure, that is, soil EC, soil pH, and soil moisture content, a follow-up investigation incorporating DNA and RNA-based analyses over a time frame of 2-3 years would lead to a greater understanding of the effects of soil disturbance on bacterial communities.