We developed the concept of Aggregatomics to study soil aggregates as functional biological entities. These entities, which are dynamic in space and time, control the flow of energy and substrates in soils. Soil aggregates are associations of viable microorganisms, organic material at different stages of decay, and mineral particles. The specific living-conditions inside and on the surface of aggregates strongly determine how soils function and the services they provide for the ecosystem and on a global scale. The biological activities of aggregates not only depend on their associated organisms but are also strongly affected by physicochemical interactions with the abiotic environment. Aggregatomics aims at capturing the total diversity and quantity of biomolecules independent of the individual organisms. This includes information carrying macromolecules, i.e. nucleic acids (DNA, RNA) and proteins, as well as microbial metabolites. In our current work, we analyze microbial communities of soil aggregates at the DNA-level in order to determine their diversity and characterize their interactions.