In a food web, nutrients flow via trophic links. For this reason, trophic interactions have a fundamental character due to the principle of mass conservation. To further comply with this principle, we consider a food web model that includes nutrient cycling. Non-trophic effects amongst species of the food web are modelled as interaction modifications, i.e., a functional change in the trophic interaction between two species caused by a third species (a three-party interaction that we call ‘‘rheagogy’’).We also consider that the ecological communities modelled by the food webs result from an assembly process that involves colonisations and extinctions. We find that two distinct classes of ecological communities must be distinguished: (a) ‘‘superefficient’’ communities, in which almost all available nutrients are incorporated into the biomass and (b) ‘‘sub-efficient’’ ones, in which a large proportion of nutrients is not fixed by living organisms. We show that rheagogies (that model non-trophic interactions) are crucial: the larger the effects of rheagogies, the easier the construction of super-efficient communities. These communities are characterized by positive rheagogies, meaning that a certain proportion of mutualistic interactions is necessary. Systems with few or weak rheagogies are less likely to use available abiotic resources efficiently. Although richness (i.e., number of species) is also positively related to efficient nutrient use, its importance is much smaller than that of rheagogies.