Microbial Community of Municipal Drinking Water in Hangzhou Using Metagenomic Sequencing

While traditional culture-dependent methods effectively detect certain microorganisms, the comprehensive composition of the municipal drinking water (DW) microbiome, including bacteria, archaeal, and viruses, remains unknown. Metagenomic sequencing has opened the door to accurately determine and analyze the entire microbial community of DW, providing a comprehensive understanding of DW’s species diversity, especially in the context of public health concerns during the COVID-19 era. In this study, we found that most of the culturable bacteria and some fecal indicator bacteria, such as Escherichia coli and Pseudomonas aeruginosa, were not detected using culture-dependent methods in all samples. However, metagenomic analysis showed that the predominant bacterial species in the DW samples belonged to the Proteobacteria and Planctomycetes phyla. Notably, the Methylobacterium genus was the most abundant in all water samples, followed by Sphingomonas, Gemmata, and Azospirilum. While low levels of virulence-associated factors, such as the Esx-5 type VII secretion system (T7SS) and DevR/S, were detected, only the erythromycin resistance gene erm(X), an rRNA methyltransferase, was identified at low abundance in one sample. Hosts corresponding to virulence and resistance genes were identified in some samples, including Mycobacterium spp.. Archaeal DNA (Euryarchaeot, Crenarchaeota) was detected in trace amounts in some DW samples. Viruses like rotavirus, coxsackievirus, human enterovirus, and SARS-CoV-2, were all negative in all DW using colloidal gold and real-time reverse transcription polymerase chain reaction (RT-PCR) methods. However, DNA encoding a new order of reverse-transcribing viruses (ortervirales) and herpesvirales were detected in some DW samples. The metabolism pathways of the entire microbial community involve cell-cell communication and the secretion of signals, contributing to cooperation between different microbial populations in the water. This study gained insight into the microbial community and metabolism process of DW in Hangzhou, China, utilizing both culture-dependent methods and metagenomic sequencing combined with bioinformatics tools during the COVID-19 pandemic era.