The effects of disturbance and management and ecosystem type on 16S rRNA libraries were studied in tilled and no-tillage cropland and land with 30 y. regrowth (New Forest, NF), and 65 y. regrowth (Old Forest, OF) forested sites at Horseshoe Bend in the southern Piedmont of Georgia (USA), and compared with those of forested lands in the Southern Appalachians of western North Carolina (Coweeta LTER site). Alpha-proteobacteria and Actinobacteria were the most abundant groups within the clones. The observed bacterial species richness varied between 50 and 70 across all sites, and the Chao1 estimator varied between 90 and 450. The agricultural libraries were very different from the OF library. The new forest plot represented a transitional phase in the soil regimes and properties. Even after > 30 y., the effects of agriculture on NF bacterial communities were still discernible. The OF library was more similar to two sites of lower-elevation forest occurring on similar soil types (Ultisols) 160 km. distant from HSB than to communities only 150 m. apart in the tilled plots. We infer that system-level differences (soils and vegetation) have a greater influence on microbial communities than site differences.