Soil microbes play major agricultural functions such as the transformation of soil organic matter into plant fertilizers. The effects of agricultural practices on soil microbes at the scale of plots, from meters to hectare, are well documented. However, the impact at soil microscale, from micrometers to millimeters, is much less known. Therefore, we studied bacterial community density and diversity at microscale in crop soil under grassland, tillage, and no tillage. We fractionated macroaggregates, from 2,000 to 250 mu m and from 250 to 63 mu m; microaggregates, from 63-20 mu m and 20-2 mu m; and clay particles, lower than 2 mu m. We measured the bacterial density and diversity by real-time PCR and 454-pyrosequencing of 16S rRNA genes of soil DNA, respectively. Results show that bacterial density and diversity were heterogeneous among size aggregates. Tillage decreased bacterial density from 22 to 74 %, and diversity from 4 to 11 %, and changed taxonomic groups in micro- and macroaggregates. This change led to the homogenization of bacterial communities and is explained by a higher protection of microaggregates. As a consequence, microaggregates contained similar bacterial communities whatever the land management is, whereas strong differences were observed between communities inhabiting macroaggregates. These findings demonstrate that bacterial diversity in microaggregates was mainly controlled by historical contingency, whereas bacterial communities in macroaggregates are shaped by contemporary perturbations. Our findings thus revealed unprecedented insights of the effect of agriculture on soil microbes. Potential applications include using crop management options that preserve macroaggregate structure to promote soil heterogeneity and therefore microbial diversity.