Soil microorganisms form one of the largest biodiversity reservoirs on earth. They also play essential roles in ecosystem functions such as biogeochemical cycling. However, the importance of microbial community diversity and composition for ecosystem functioning is still debated. A sound understanding of the ecological processes governing the assembly of these communities in the environment is also missing. In this talk, I will give examples of how we addressed these knowledge gaps using nitrogen cycling microorganisms as model functional guilds. Nitrogen is the most limiting nutrient for crop production in agriculture. The nitrogen cycle is also one which was pushed by human activities outside critical thresholds representing the safe operating space. I will show that microbial diversity loss can alter nitrogen cycling and discuss studies showing the importance of microbial community composition for emissions and consumption of the greenhouse gas N2O. To explicitly test the role of biotic interactions for microbial community assembly and functioning, we used an alternative top-down approach based on microbial community manipulation by removal of various microbial groups in a native soil community. We found that nearly 50 % of the dominant bacterial taxa were subjected to competitive interactions, underlining the importance of biotic interactions in community assembly. Moreover, evidence for competitive exclusion between members of Bacillales and Proteobacteriales suggested that potential general rules of microbial community assembly can be identified. Finally, I will show that reassembly after removal resulted in greater changes in activities related to N- than to C-cycling. Our approach may represent an alternative avenue to better understand the links between microbial community composition and ecosystem functioning based on the analogy to gene knockout procedures in genomics.