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.

黑暗发酵的研究强调了生物反应器的工程学观点，忽视了其与过程生态动力学的整合。微生物相互作用驱动的生态动力学影响生物反应器的性能，对于理解黑暗发酵的机理基础至关重要。我们提出了一个由“描述”，“关联”和“建模”组成的分析框架”阶段或查询级别，以阐明与生物反应器相关的微生物联盟中潜在的生态相互作用。每个阶段都会深入了解生物反应器中微生物行为的机理。我们提供一个研究案例，以说明框架的每个步骤，它们的局限性和机会。我们表明整合代谢数据和微生物多样性的分析框架使人们深入了解了黑​​暗发酵生物反应器性能的生态过程，并可以通过知情的假设指导未来的研究。