Revisiting the linkage between engineered ecosystem function and the microbial community: A review from ecological perspectives

Biological waste treatment technology is currently the world's largest application process, and its functional achievement mainly relies on complex microbial communities. However, the microbial system in such engineered ecosystems has been considered a "black box." Over the past decade, with the development of molecular biotechnology and next-generation sequencing technologies, the exploration of such "black boxes" has gradually deepened. In particular, the role of ecological forces in uncovering and regulating microbial communities has been largely recognized and has provided novel insights into the link between microbial communities and engineering objectives. However, the study of community ecology in engineered ecosystems is still in its early infancy and faces grand challenges in bridging engineering principles with microbial ecology theory. In this review, we discuss recent advances in the understanding of microbial community behavior in biological waste treatment systems, including biodiversity and its influencing factors, the role of neglected rare species, microbial interactions, and community assembly mechanisms. We emphasize the importance of these ecological perspectives in revealing and regulating microbial communities and functions, such as the enhancement of contaminant removal and operational stability in engineered ecosystems. In particular, cross-validation of the microbial community analysis results is necessary to yield valid real information to guide the improvement and stability of engineering ecosystem performance. Multi-omics approaches and synthetic community biology are preferred ways to link ecological theory and engineering objectives.