In this study, we used genome-resolved metagenomics and gene-centric approaches to analyze microbial communities in a Dutch DWTP, with a special focus on ammonia and methane-oxidizing microorganisms.
Elevated concentrations of ammonium and methane in groundwater can cause severe problems during drinking water production. To avoid their accumulation, raw water in the Netherlands, and many other countries, is purified by sand filtration. These drinking water filtration systems select for microbial communities that mediate the biodegradation of organic and inorganic compounds. In this study, the active layers and wall biofilms were sampled at different locations along the filtration units of the drinking water treatment plant (DWTP) Breehei, the Netherlands, over three years. We used high-throughput sequencing in combination with differential coverage and sequence composition-based binning to recover 56 near-complete metagenome-assembled genomes (MAGs) with an estimated completion of =70% and with =10% redundancy. These MAGs were used to characterize the microbial communities involved in ammonia and methane conversion. The methanotrophic microbial communities colonizing the wall biofilm (WB) and the granular material of the primary rapid sand filter (P-RSF) were dominated by members of the Methylococcaceae and Methylophilaceae. The abundance of these bacteria drastically decreased in the secondary rapid sand filter (S-RSF) samples. In all samples, complete ammonia-oxidizing (comammox) Nitrospira were the most abundant nitrifying guild. Clade A comammox Nitrospira dominated the P-RSF, while clade B was most abundant in WB and S-RSF, where ammonia concentrations were much lower. In conclusion, the knowledge obtained in this study will help to advance our understanding of the role of microorganisms in the removal of carbon and nitrogen compounds during drinking water production. We furthermore found that drinking water treatment plants represent valuable model systems to study microbial community function and interaction.