During the storage of manure a wide range of microbial processes take place on the inside of the manure. In these processes greenhouse gases are produced such as methane and nitrous oxide. To be able to apply mitigation strategies a good insight in the potential pathways is needed which produce these greenhouse gases. In this research I will study the interaction of nitrification and denitrification pathways responsible for nitrous oxide formation using batch reactors emission experiments. From these results mitigation strategies to reduce nitrous oxide emissions on farms will be proposed and tested in 6 pilot scale storage silo’s.