While traditionally, bacteria have been considered driving much of the Earth’s nitrogen (N) cycle, recent research shows that ecological interactions between meio-, macrofauna and bacteria are important in regulating N cycling in soft sediments. Thus, the INBALANCE Project aims to unveil the quantitative importance of ecological interactions between microorganisms and their benthic invertebrate hosts in regulating N cycling in shallow estuarine sediments. In particular, this project will investigate the identity and activity of bacteria associated with benthic invertebrate hosts, the most abundant functional group of meio- and macrofauna in estuarine systems, across the full range of possible interactions, from strict symbioses to casual associations.