A framework for integrating functional and microbial data: The case of dark fermentation H2 production

Abstract Research in dark fermentation has emphasized an engineering view of bioreactors overlooking its integration with the ecological dynamics of the process. Ecological dynamics driven by microbial interactions impact bioreactors performance and are critical to understanding the mechanistic bases of dark fermentation. We propose an analytical framework consisting of “description”, “association” and “modeling” phases or inquiry levels to elucidate potential ecological interactions in bioreactor-associated microbial consortia. Each phase deepens into obtaining mechanistic insights of the microbial behavior in bioreactors. We present a study case to illustrate each step of the framework, their limitations and opportunities. We show that analytical frameworks integrating metabolic data and microbial diversity give insights into the ecological processes underlying the performance of dark fermentation bioreactors and can guide future research through informed hypotheses.