The application of molecular tools to study the drinking water microbiome–Current understanding and future needs

Despite the long history of water research, understanding how the drinking water microbiome is shaped at the user end is rather challenging owing to the complexity in community assembly, water matrices, physical structures, and chemical gradients from source to tap. The application of molecular tools that primarily base on the use of rRNA gene sequences has substantially expanded our view of the drinking water microbiome. In this review, we critically evaluate currently available cultivation-independent tools for monitoring the drinking water microbiome and summarize the ecological patterns we have observed so far on the longitudinal and temporal dynamics, geographical distributions, and structural and functional characteristics of the drinking water microbiome (including those in recycled water systems). Studies on four full-scale systems in the United States and Europe further exemplify the application of ecological theory into drinking water microbiome studies. Finally, we discuss how meta-omics are able to provide new perspectives on microbial function and interspecies relationship within the drinking water ecosystem. This review promotes an integral understanding of the drinking water microbiome and the transformation of drinking water microbiology from a descriptive discipline to an ecology-driven science that attempts to elucidate mechanisms for predicting and shaping the microbiome at the user end.