P>1. Positive effects of species diversity on ecosystem functioning have often been demonstrated in 'macrobial' communities. This relation and the responsible mechanisms are far less clear for microbial communities. Most experimental studies on microorganisms have used randomly assembled communities that do not resemble natural communities. It is therefore difficult to predict the consequences of realistic, non-random diversity loss. 2. In this study, we used naturally co-occurring diatom species from intertidal mudflats to assemble communities with realistically decreasing diversity and analysed the effect of non-random species loss on biomass production. 3. Our results demonstrate a highly positive biodiversity effect on production, with mixtures outperforming the most productive component species in more than half of the combinations. These strong positive diversity effects could largely be attributed to positive complementarity effects (including both niche complementarity and facilitation), despite the occurrence of negative selection effects which partly counteracted the positive complementarity effects at higher diversities. 4. Facilitative interactions were, at least in part, responsible for the higher biomass production. For one of the species, Cylindrotheca closterium, we show its ability to significantly increase its biomass production in response to substances leaked into the culture medium by other diatom species. In these conditions, the species drastically reduced its pigment concentration, which is typical for mixotrophic growth. 5. Synthesis. We show that both species richness and identity have strong effects on the biomass production of benthic diatom biofilms and that transgressive overyielding is common in these communities. In addition, we show mechanistic evidence for facilitation which is partly responsible for enhanced production. Understanding the mechanisms by which diversity enhances the performance of ecosystems is crucial for predicting the consequences of species loss for ecosystem functioning.