Despite the long history of water research, understanding drinking water microbiome continuum spanning from source water, treatment in the production process, distribution network, and up to the point where water enters a building is rather challenging owing to the complexity in community assembly, water matrices, physical structure, and chemical gradients from source to tap. Previous studies on drinking water microbiomes have primarily investigated “who are there” and “how do they change over time and across space” in selected stages of drinking water systems. However, it is important to ask additional questions that include but are not limited to “what are they doing?”, “why are they there?” and more critically “who is doing what?”, and “what are the interrelationships among them, and between them and their environment?”. To answer these questions, it requires not only the advent of new methods, but also the transformation of drinking water microbiology from a descriptive discipline to a hypothesis-driven science that attempts to elucidate mechanisms with the intention to predict and shape the microbiome continuum.
The studies included in this dissertation resolved the ecological patterns of a groundwater-sourced drinking water microbiome at different scales. At the community level, the treatment process could be viewed as ecological disturbances on the drinking water microbiome continuum over space in the system by combining 16S rRNA gene amplicon sequencing and metagenomics. Abstraction caused a substantial decrease in both the abundance and number of functional genes related to methanogenesis and syntrophs in raw water. The softening process reduced microbial diversity and selected an Exiguobacterium-related population, which was attributed to its ability to use the phosphotransferase system (PTS) as regulatory machinery to control the energy conditions of the cell. After disinfection and entering the distribution system, microbial populations and their functions remained relatively stable. Predation by eukaryotic populations could be another disturbance to the bacterial microbiome, which could further drive the diversification of the bacterial community. At the population level, nine draft genomes of pathogen-related species from the genera Legionella, Mycobacterium, Parachlamydia, and Leptospira were constructed and characterized in relation to their abundance, diversity, potential pathogenicity, genetic exchange, and distribution across the groundwater-sourced drinking water system. The presence/absence of specific virulence machinery could be effectively used to determine the pathogenicity potential of these genomes. Clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins (CRISPR-Cas) genetic signatures were identified as a potential biomarker in the monitoring of Legionella related strains across different drinking water systems. At the multi-species level, methano-/methylo-trophs were investigated, which were overlooked populations dominant and prevalent in drinking water microbiomes of groundwater systems. Using genome-resolved metagenomics, 34 methylotroph-related draft genomes were recovered together with another 133 draft genomes belonging to a variety of taxa. Both Type I and Type II methanotrophs dominated the finished water and distribution system. They mostly possessed methylotrophy pathways involving many enzymes rather than single enzyme systems. Network analysis determined potential species interaction between methanotrophs and a number of non-methanotrophic methylotrophs and other heterotrophs. The latter two groups had the capability to supply essential metabolites to methanotrophs as indicated by metabolic interdependency analysis.
This series of studies established a framework to understand the drinking water microbiome continuum through the inference of evolutionary and ecological processes that shape the microbiome from genomic/metagenomic data. They also offered new perspectives to some questions waiting to be answered by future studies, including “How to define a ‘healthy’ microbiome and microbial indicators?”, “How to effectively monitor opportunistic pathogens in drinking water microbiomes?”, and “Can drinking water microbiomes be predict and intentionally shaped?”
