Metagenomic profiling of ammonia- and methane-oxidizing microorganisms in a Dutch drinking water treatment plant

Abstract

Highlights 10• Microbial distribution was mainly influenced by sampling location within the DWTP.• Clade A comammox Nitrospira were the most abundant nitrifying guild in samples from the primary sand filter, while clade B dominated in samples from wall biofilm and the secondary filter.• A novel methanotrophic bacterium affiliated with the Methylophilaceae family comprised 15 the largest bacterial fraction in the primary sand filter. AbstractElevated 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 20 for microbial communities that mediate the biodegradation of organic and inorganic compounds.In this study, the active layers and wall biofilm of a Dutch drinking water treatment plant (DWTP) were sampled at different locations along the filtration units of the plant over three years. We used high-throughput sequencing in combination with differential coverage and sequence compositionbased binning to recover 56 near-complete metagenome-assembled genomes (MAGs) with an 25 estimated completion of ≥70% and with ≤10% redundancy. These MAGs were used to characterize the microbial communities involved in the conversion of ammonia and methane. 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 30 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 ammonium concentrations were much lower. In conclusion, the knowledge obtained in this study contributes to understanding the role of microorganisms in the removal of carbon and nitrogen compounds during drinking 35 water production. We furthermore found that drinking water treatment plants represent valuable model systems to study microbial community function and interaction. Methane uptakeMethane-oxidizing capacity was determined for the P-RSF and WB samples collected in 2016. 115For the P-RSF, 2.5, 5, 10, and 20 g of sand material were mixed with 20 ml top water. After settling of the sand, overlaying water samples (20 ml) were transferred into 120 ml serum bottles with Deep aquifer Clay Shallow aquifer Sand and gravel NH 4 + CH 4 Fe H 2 S Mn Groundwater Air supply Air supply WB P-RSF S-RSF Storage and distribution Wall

Microbial ecology of biofiltration used for producing safe drinking water

“…Tatari et al (2017) reported a high abundance of Nitrospira (5−10% of the total community) consistently in RSF filters and up to 2 to 4 orders of magnitude more abundant than Nitrobacter and canonical AOBs, respectively. The high abundance of Nitrospira in nitrifying guilds is also reported by other studies (Poghosyan et al 2020).…”

“…It was shown that the biological nitrification process is responsible for the reduction of the ammonia concentration in water in RSF filters (Oh et al 2018;Poghosyan et al 2020). The consistency of spatial dissimilarity of the ammonium removal capacity with the spatial heterogeneity of nitrifying guilds in RSF filters further supports the above hypothesis (Lee et al 2014).…”

“…Although bacteria are overall predominantly present in RSF, GACF, and SSF, biofilter community dissimilarity is still found between and within DWTPs (Lautenschlager et al 2014;Gülay et al 2016;Palomo et al 2016;Oh et al 2018;Poghosyan et al 2020). In general, differences in community composition amongst DWTPs are greater than within DWTPs.…”

“…Besides, RSF has a proven effect on removing iron (28.6-97%) and manganese (50-97%) and to a less extent on removing unpleasant odour and taste, bacteria (0.3-3 log 10 ), and organic matters (e.g. 99% methane) (Bishaw and Kebede 1999;Lee et al 2014;Asami et al 2016;Poghosyan et al 2020) (Table S1).…”

“…Within the microbial communities in RSF filters, the nitrifying guilds including ammonia-oxidising bacteria (AOB) (Nitrosomonas and Nitrosospira), ammonia-oxidising archaea (AOA) (Nitrosopumilus), and nitrite-oxidising bacteria (NOB) Nitrobacter and Nitrospira have been frequently observed and studied (Lautenschlager et al 2014;Gülay et al 2016;Palomo et al 2016;Oh et al 2018;Poghosyan et al 2020). Tatari et al (2017) reported a high abundance of Nitrospira (5−10% of the total community) consistently in RSF filters and up to 2 to 4 orders of magnitude more abundant than Nitrobacter and canonical AOBs, respectively.…”