The relationship with depth of soil microbial communities to several soil characteristics was examined in two 25-cm deep trenches dug in a grass meadow covered with Andropogon gerardii, Plantago lanceolata, Rudbeckia hirta, and other grass species. Most measured soil characteristics tended to decrease in magnitude with distance from the surface to about 10-15 cm, below which the values were approximately constant. pH increased from 0 to 10 cm depth and did not change below that. Change in bacterial abundance with depth was similar to that observed for all soil characteristics except pH. Bacterial and fungal community structures were not highly correlated to one another in either trenches (PB = 0.179 and PD= 0.214). Only bacterial community structure of B trench was significantly correlated with soil characteristics by Mantel test (rM = 0.618, P = 0.010). The lag distance at depth was not significantly associated with either bacterial or fungal community structures at either trench, while soil characteristics were significantly associated.Altogether, surface vegetation (P. lanceolata and R. hirta for B trench, and A. gerardii for D trench) as dominant factor differentiating microbial community structures between trenches with distinctive types of root exudates released from root systems.