Ecological forces dictate microbial community assembly processes in bioreactor systems

Microbial communities are increasingly used as biocatalysts in biotechnological processes due to the multifunctional properties of their members. In contrast to genetically defined engineered bacterial strains, which are modified to perform the desired steps of a biochemical transformation as a pure culture, microbial communities distribute the necessary transformation steps among different cell types. The involvement of microbial communities in biotechnological production processes has at least two advantages: One is that engineered organisms often require expensive and specifically refined substrates to produce valuable products. Instead, microbial communities can convert cheap complex materials from agriculture and forestry as well as waste materials, which significantly reduces production costs. Such approaches also lead to reduced use of fossil resources for the production of valuable chemicals and support the shift to a circular economy. Second, the functional capacity in communities is vast, mostly redundant or evolving, and thus offers a huge library of possible metabolic transformation pathways 1, 2. But despite these great benefits, there is a reluctance to use microbial communities more intensively in biotechnology. With the exception of well-known processes such as biogas production, wastewater treatment or the use of microbial communities in the food industry, there are no significant new applications beyond these. In our opinion, the reason for this could be the inability to control complex microbial communities in biotechnological processes. In this statement, we aim to identify the probable causes of process instabilities caused by microbial communities as catalysts and pave the way for solutions to overcome this problem.

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