We present research aimed at determining the role of soil structure in the organization of microbial communities in soil. We have focused on the microbial communities involved in functional roles within the nitrogen cycle, particularly nitrogen fixation. We have studied how different aggregate structures of varying size and stability provide different environments for these communities. Initially, we compared the nitrogen-fixing communities between aggregate structures obtained from soils from arctic, temperate and tropical environments. We also compared the communities involved in nitrogen fixation, nitrate reduction and ammonia oxidation from adjacent agricultural plots under different tillage regimes. We continued to monitor the community composition of nitrogen fixers at the aggregate scale through the following year and season after a tillage disturbance. We further narrowed down our scale by comparing the total diversity and functional diversity of an individual microaggregate and compared it with others. We then looked that the effect of disturbance at larger time scales in forest soil plots of old and secondary forest growth over one hundred years after recovery. We have determined that very different functional community structure can be found across all aggregate fractions in soils from all over the world, as well as from adjacent plots. Tillage has a major effect on the community composition of communities involved in the nitrogen cycle evidenced at all aggregate scales. This disturbance also affects the overall activity of nitrogen fixers measured in soil. However, the community recovers a year after the tillage disturbance, both in terms of community composition and activity of nitrogen fixers. Individual microaggregates are different from each other in terms of overall community structure, but the functional community composition seems to be homogeneous and representative of the composition observed in a pooled microaggregate fraction. Prolonged agricultural activities significantly altered the communities obtained from secondary growth forests when compared to adjacent old forest soils. Different aggregate structures provide environments for very different microbial communities involved in the nitrogen cycle. However, even the most stable of these structures is affected by tillage at the level of community composition and activity. This work describes not only the extent of this community and niche disturbance and their ability to recover, but also the extent of functional diversity at the micro-scale of the most complex of natural environments.