Microbial communities are at the heart of all ecosystems and yet, a sound understanding of the ecological processes governing the assembly of these communities in the environment is missing. To address the role of biotic interactions in assembly and functioning of the soil microbiota, we used a top down manipulation approach based on the removal of various populations in a natural microbial community. Suspensions of the soil microbiota were subjected to various biocidal and filtration treatments before being inoculated into the same sterilized soil. We hypothesized that if biotic interactions are an important shaping force of the microbiota assembly, removal of microbial groups should largely affect the fitness of the remaining ones during soil recolonization. We show that nearly half of the dominant bacterial taxa were subjected to competitive interactions, underlining the importance of biotic interactions in the assembly of microbial community in soil. Moreover, evidence for competitive exclusion between members of Bacillales and Proteobacteriales suggests that potential general rules of microbial community assembly can be identified. Our findings also indicate that effects on biotic interactions results in more prominent changes in activities related to N- than to C-cycling. Such removal approach can provide a new avenue to study microbial interactions in complex ecosystems