While microbes can interact with each other in numerous ways, little is known about the contribution of these interactions to microbial community assembly. Here, we manipulated soil microbial communities to assess the importance of interactions between microorganisms. For this purpose, we first subjected a soil microbial community to 18 different removal treatments before reinoculation in its native, but sterilized, soil. Shifts in microbial communities were assessed by 16S rRNA MiSeq sequencing and soil functions were investigated using proxies for C and N cycling. We found that 47% of the dominant OTUs across removal treatments exhibited increased relative fitness after 45 days of incubation. To test the hypothesis that depletion of competitors by the removal treatments was behind the increased relative fitness, we then used a coalescence approach by mixing the depleted and control communities and postulated that it would re-establish the initial interactions. The coalescence approach not only revealed the importance of density-dependent interactions in microbial community assembly but also allowed to restore partly or fully community diversity and soil functions. We found that shifts in both inorganic nitrogen pools and soil pH after microbial community manipulation were related to the proportion of ammonia-oxidizing bacteria. Our work provides new insights into the understanding of the importance of microbial interactions in soil. Our top-down approach combining removal and coalescence manipulation also allowed linking community structure and ecosystem functions. Furthermore, these results highlight the potential of manipulating microbial communities for restoration of soil ecosystems