Drinking water microbiota: from the source to the tap

Drinking water quality is a public health concern worldwide. Growing evidences depict drinking water as a complex matrix, in which a wide diversity of microorganisms interacts in a dynamic network. Dealing with environmental samples, the “great plate count anomaly” must be taken into account: only a minimal portion of bacteria can grow on cultured media. Molecular techniques can give a deeper knowledge, going beyond the limit of culture-dependent methods, even if the living/death distinction is a traditional limitation. We collected water samples during an extended monitoring campaign of drinking water treatment plants (DWTPs) located in Milan (Italy). We analysed the microbial community at different steps of the potabilization processes, from the source to the tap: i) raw water from the groundwater, ii) after the passage across granular activated carbon filters and iii) after chlorination. We first evaluated and standardized a new pipeline for microorganisms concentration, environmental DNA extraction and amplification, suitable for molecular analysis and optimized for High-Throughput DNA Sequencing (HTS) approaches. Since molecular techniques are unable to differentiate between viable and nonviable microorganisms, live/dead ratio of microorganisms for each sampling point was estimated using fluorescent staining coupled with microscopy visualization. From our observations chlorination does not exert a full-scale effect. We further analysed the presence and the relative abundance of microorganisms across the DWTP through Real Time PCR. The occurrence of antibiotic resistance genes (ARGs) was detected across the entire DWTP, highlighting the presence of native resistance genes in groundwater and their permanence after potabilization processes. The presence of ARGs in water is becoming an issue of great interest as the mobile resistome (i. e. the collection of all the resistance genes of an ecosystem) can easily spread among species. Recent studies revealed that drinking water treatment process can affect the microbiota structure. Our results agree with these findings: carbon filters play a key role in shaping the bacterial community. Likely filters harbour a microbial community that seeds and shapes water microbiota downstream, even after chlorination. These evidences can help to unravel the dynamics underlying water microbiota changes. We reported for the first time the presence of the so-called nanobacteria in the entire DWTP, even after chlorination. Nanobacteria showed a differential distribution across the DWTP, emphasising the role of carbon filters in shaping the nano-microbial community downstream. Our main result is that DWTP is not an inert system, but an ecosystem: complex biological processes take place between the source and the tap. A better knowledge of these networks is crucial to improve the management of drinking water facilities.