Microbial Nitrogen Metabolism in Chloraminated Drinking Water Reservoirs

Analysis of gill and skin microbiota in Larimichthys crocea reveals bacteria associated with cryptocaryoniasis resistance potential

Cryptocaryoniasis, caused by the ciliate parasite Cryptocaryon irritans, poses a significant threat to the large yellow croaker (Larimichthys crocea) in intensive marine aquaculture. This study explores the interaction between skin and gill microbiota and C. irritans infection, focusing on the role of commensal microbes in disease resistance. Fish were challenged with 100 theronts per gram of body weight, leading to substantial microbial dysbiosis, characterized by decreased alpha diversity and disrupted co-occurrence networks, particularly on the skin. Post-infection, Vibrio abundance significantly increased in both gills and skin, suggesting potential for secondary infections. Conversely, lower Vibrio levels correlated with higher populations of Bdellovibrio-like organisms (BALOs), which may play a beneficial role in microbial balance. Fish showed varying susceptibility, with mildly infected individuals exhibiting less histopathological damage and a stronger immune response, indicated by elevated interleukin-1β (IL-1β) and interleukin-8 (IL-8) levels. Correlation analyses revealed significant relationships between relative infection intensity (RII) and microbial composition, with certain bacteria known for anti-eukaryotic microbial properties showing negative correlations with RII. Additionally, the abundance of nitrogen-metabolizing bacteria also correlated negatively with RII. Functional predictions indicated increased bacterial genes related to denitrification and vitamin biosynthesis post-infection. Notably, Candidatus Midichloria was identified as a potential biomarker for C. irritans infection and is thought to be an endosymbiont of C. irritans, with its presence validated through PCR analysis. These findings illuminate microbial dynamics during C. irritans infection and suggest probiotic candidates for managing cryptocaryoniasis.

Denitrification dominates nitrate attenuation and nitrous oxide effluxes under water table fluctuations

Agricultural soils in riparian zones near rivers often experience frequent water table fluctuations, which can lead to increased nitrogen losses and greenhouse gas emissions via the nitrogen biogeochemical processes. However, the influence of water table fluctuations on the multiple nitrogen transformation processes that dominate nitrate attenuation and nitrous oxide (N2O) effluxes remains poorly understood. In this study, the dynamic changes in depth-dependent nitrate attenuation and soil N2O effluxes, and the responses of microbial communities influenced by water table fluctuations were studied using a series of large column experiments. Our results revealed that dissolved oxygen (DO) concentrations at a depth of -10 cm in sand columns with three different grain sizes (fine→medium→coarse) oscillated, producing oxidizing conditions during drainage and reducing conditions during imbibition periods. DO micro-sensors installed in a layered (sand and sandy loam) column as well as in two sandy loam columns with different regimes in induced water table changes all revealed steady hypoxic conditions. The diversity of the microbial community was significantly correlated with total nitrogen, total organic carbon, and nitrate concentrations, as well as potential denitrification rates. The dominant microbial populations related to the nrfA gene were Methanothrix and Sedimentibacte, whereas those related to denitrification (nirK, nirS, and nosZ) were Pseudomonas and Sulfuricaulis. These findings improve our understanding of the effects of water table fluctuations on groundwater nitrate loss in riparian corridors.

Long-term impacts of free chlorine and monochloramine on the development of drinking water biofilm

Biofilm formation in drinking water distribution systems is primarily managed by disinfectants such as free chlorine (FC) and monochloramine (MC). However, there is limited understanding of their long-term and dynamic effects on biofilm development. To address this, a 56-week study was conducted to comprehensively assess biofilm development in terms of microbial quantity and community under different disinfection regimes: no chlorine (NC), FC (0.1 mg/L), and MC (0.4 mg/L). The results showed that both FC and MC significantly inhibited biofilm growth compared to the NC condition while shaping distinct biofilm communities. Notably, FC drastically reduced biofilm biomass and community diversity, resulting in a more uniform biofilm community predominantly composed of Proteobacteria (e.g., Rhizobacter spp., Pseudomonas spp., and Hyphomicrobium spp.), indicating stronger selection pressures on the microbial population. In contrast, though MC effectively reduced the biofilm biomass to a level comparable to that of FC, it maintained a high diversity comparable to that of NC (dominated by Sphingobium spp. and Nocardioides spp.), reflecting weaker selection pressure on bacterial community. Temporally, biofilm communities under all conditions started from nearly identical states. From week-19 and week-36 onwards, deterministic processes predominantly governed biofilm formation under FC and NC conditions, signifying that these biofilms reached a stable state. Differently, under MC condition, the community assembly was continually influenced by stochastic processes, with the biofilm not achieving stability until week-56. Overall, this study provides valuable insights into the long-term dynamics of biofilm development and evidenced that FC is better than MC in controlling biofilm formation, particularly from the community diversity perspective. This challenges classical views that MC is more effective than FC in penetrating and controlling biofilm, which may change the popularity of MC as a disinfectant in water utilities.

Ammonia nitrogen affects bacterial virulence and conditional pathogenic bacterial growth by regulating biofilm microbial metabolism and EPS secretion in laboratory scale distribution systems

The control of conditional pathogenic bacteria and inhibition of their virulence factors (VFs) in drinking water distribution systems (DWDSs) is vital for drinking water safety. This study adopted two groups of DWDSs to investigate how ammonia nitrogen affects bacterial VFs and conditional pathogenic bacterial growth in biofilms. Our results indicated that Acidimicrobium (95,916.62 ± 119.24 TPM), Limnohabitans (30,338.81 ± 139.14 TPM), and Sediminibacterium (10,658.01 ± 48.94 TPM) were predominant in the biofilm bacterial community of DWDSs with NH3-N addition. Under these conditions, the abundances of various bacterial metabolites, such as L-glutamate (1.45-fold), 2-oxoglutarate (1.24-fold), pyruvate (2.10-fold), and adenosine monophosphate (AMP, 5.29-fold), were significantly upregulated, which suggested the upregulation of amino acid, carbohydrate, nucleotide, lipid, pyrimidine and purine metabolism. These metabolic pathways accelerated extracellular polymeric substance (EPS) secretion. The protein concentration in EPS also increased to 187.59 ± 0.58 μg/cm2. The increased EPS secretion promoted the amide I CO group of the EPS protein to interact with the surface of the DWDSs, thus enhancing the ability of bacteria (especially conditional pathogenic bacteria) to adhere to the pipe surface to form biofilms. Due to EPS protection, the abundance of the adherence subtype of VFs and the plate counts of Pseudomonas aeruginosa increased to 5912.8 ± 21.89 TPM and 655.78 ± 27.10 CFU/cm2, respectively. Therefore, NH3-N in DWDSs increased bacterial VFs levels and promoted the growth of some conditional pathogenic bacteria by regulating biofilm microbial metabolic pathways and EPS secretion, ultimately impacting the interaction between EPS and the pipe surface.

Comparative analyses on nitrogen removal microbes and functional genes within anaerobic-anoxic-oxic and deoxidation ditch sewage-treating processes in Wuhan and Xi'an cities, China

Introduction

Anaerobic-anoxic-oxic (A2/O) and deoxidation ditch (DOD) processes are being increasingly preferred owing to their effectiveness in treating various wastes in wastewater treatment plants (WWTPs). Considering seasonal variations is crucial in optimizing treatment processes, ensuring compliance with regulations, and maintaining the overall efficiency and effectiveness of WWTPs. This study aimed to determine the influence of seasonality on nitrogen removing microbes and functional genes within A2/O and DOD processes in the humid Wuhan and semi-arid Xi'an cities, China.

Methods

The physicochemical parameters of water quality were determined, and molecular and bioinformatic analyses of the bacterial community and nitrogen metabolism functional genes in the two different treatment processes of two WWTPs were performed over four seasons.

Results and discussion

Our analyses revealed a significant difference in all physicochemical parameters across all experimental groups (p < 0.05). At the genus level, the abundance of Dokdonella, one unidentified genus of Nitrospiraceae, Terrimonas, and one unidentified genus of Chloroflexi was the highest in all groups. Generally, warmer seasons exhibited higher biodiversity indices. The A2/O system exhibited higher values in terms of most nitrogen metabolism functional genes than those of the DOD sewage treatment system. In both WWTPs, the abundance of most genes in spring and summer were higher than that of autumn and winter seasons. Taken together, changes in temperature, caused by seasonal changes, may contribute to changes in abundance of nitrogen metabolic functional genes.

New Drinking Water Genome Catalog Identifies a Globally Distributed Bacterial Genus Adapted to Disinfected Drinking Water Systems

Genome-resolved insights into the structure and function of the drinking water microbiome can advance the effective management of drinking water quality. To enable this, we constructed and curated thousands of metagenome-assembled and isolate genomes from drinking water distribution systems globally to develop a Drinking Water Genome Catalog (DWGC). The current DWGC disproportionately represents disinfected drinking water systems due to a paucity of metagenomes from nondisinfected systems. Using the DWGC, we identify core genera of the drinking water microbiome including a genus (UBA4765) within the order Rhizobiales that is frequently detected and highly abundant in disinfected drinking water systems. We demonstrate that this genus has been widely detected but incorrectly classified in previous amplicon sequencing-based investigations of the drinking water microbiome. Further, we show that a single genome variant (genomovar) within this genus is detected in 75% of drinking water systems included in this study. We propose a name for this uncultured bacterium as "Raskinella chloraquaticus" and describe the genus as "Raskinella" (endorsed by SeqCode). Metabolic annotation and modeling-based predictions indicate that this bacterium is capable of necrotrophic growth, is able to metabolize halogenated compounds, proliferates in a biofilm-based environment, and shows clear indications of disinfection-mediated selection.

Downflow sponge biofilm reactors for polluted raw water treatment: Performance optimisation, kinetics, and microbial community

Water outages caused by elevated ammonium (NH4+-N) levels are a prevalent problem faced by conventional raw water treatment plants in developing countries. A treatment solution requires a short hydraulic retention time (HRT) to overcome nitrification rate limitation in oligotrophic conditions. In this study, the performance of polluted raw water treatment using a green downflow sponge biofilm (DSB) technology was evaluated. We operated two DSB reactors, DSB-1 and DSB-2 under different NH4+-N concentration ranges (DSB-1: 3.2-5.0 mg L-1; DSB-2: 1.7-2.6 mg L-1) over 360 days and monitored their performance under short HRT (60 min, 30 min, 20 min, and 15 min). The experimental results revealed vertical segregation of organic removal in the upper reactor depths and nitrification in the lower depths. Under the shortest HRT of 15 min, both DSB reactors achieved stable NH4+-N and chemical oxygen demand removal (≥95%) and produced minimal effluent nitrite (NO2--N). DSB system could facilitate complete NH4+-N oxidation to nitrate (NO3--N) without external aeration energy requirement. The 16S rRNA sequencing data revealed that nitrifying bacteria Nitrosomonas and Nitrospira in the reactor were stratified. Putative comammox bacteria with high ammonia affinity was successfully enriched in DSB-2 operating at a lower NH4+-N loading rate, which is advantageous in oligotrophic treatment. This study suggests that a high hydraulic rate DSB system with efficient ammonia removal could incorporate ammonia treatment capability into polluted raw water treatment process and ensure safe water supply in many developing countries.

Comparative analysis of chlorine-resistant bacteria after chlorination and chloramination in drinking water treatment plants

Chlorine-resistant bacteria (CRB) in drinking water treatment plants (DWTPs) jeopardize water quality and pose a potential risk to human health. However, the specific response of CRB to chlorination and chloramination remains uncharacterized. Therefore, we analyzed 16 S rRNA sequencing data from water samples before and after chlorination and chloramination taken between January and December 2020. Proteobacteria and Firmicutes dominated all finished water samples. After chloramination, Acinetobacter, Pseudomonas, Methylobacterium, Ralstonia, and Sphingomonas were the dominant CRB, whereas Ralstonia, Bacillus, Acinetobacter, Pseudomonas, and Enterococcus were prevalent after chlorination. Over 75% of the CRB e.g. Acinetobacter, Pseudomonas, Bacillus, and Enterococcus were shared between the chlorination and chloramination, involving potentially pathogens, such as Acinetobacter baumannii and Pseudomonas aeruginosa. Notably, certain genera such as Faecalibacterium, Geobacter, and Megasphaera were enriched as strong CRB after chloramination, whereas Vogesella, Flavobacterium, Thalassolituus, Pseudoalteromonas, and others were enriched after chlorination according to LEfSe analysis. The shared CRB correlated with temperature, pH, and turbidity, displaying a seasonal pattern with varying sensitivity to chlorination and chloramination in cold and warm seasons. These findings enhance our knowledge of the drinking water microbiome and microbial health risks, thus enabling better infectious disease control through enhanced disinfection strategies in DWTPs.

Biofilm formation and antioxidation were responsible for the increased resistance of N. eutropha to chloramination for drinking water treatment

Chloramination is an effective strategy for eliminating pathogens from drinking water and repressing their regrowth in water distribution systems. However, the inevitable release of NH4+ potentially promotes nitrification and associated ammonia-oxidizing bacteria (AOB) contamination. In this study, AOB (Nitrosomona eutropha) were isolated from environmental water and treated with two disinfection stages (chloramine disinfection and chloramine residues) to investigate the occurrence mechanisms of AOB in chloramination. The results showed that N. eutropha had considerable resistance to monochloramine compared to Escherichia coli, whose inactivation rate constant was 19.4-fold lower. The higher resistance was attributed to high levels of extracellular polymer substances (EPS) in AOB, which contribute to AOB surviving disinfection and entering the distribution system. In AOB response to the chloramine residues stage, the respiratory activity of N. eutropha remained at a high level after three days of continuous exposure to high chloramine residue concentrations (0.5-1.5 mg/L). Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) suggested that the mechanism of N. eutropha tolerance involved a significantly high expression of the intracellular oxidative stress-regulating (sodB, txrA) and protein-related (NE1545, NE1546) genes. Additionally, this process enhanced EPS secretion and promoted biofilm formation. Adhesion predictions based on the XDLVO theory corroborated the trend of biofilm formation. Overall, the naturally higher resistance contributed to the survival of AOB in primary disinfection; the enhanced antioxidant response of surviving N. eutropha accompanied by biofilm formation was responsible for their increased resistance to the residual chloramines.

Effective chloramine management without "burn" in biofilm affected nitrifying tanks using a low dose of copper

This paper highlights the potential to effectively inhibit nitrification and restore chloramine levels using a low copper concentration in a biofilm-affected (surface-to-volume ratio 16 m-1) continuous-flow laboratory-scale chloraminated system. High nitrite and low chloramine containing tanks are always recovered with chlorine "burn" by water utilities. The "burn" is not only costly and operationally complex, but also compromises the water quality, public health, and customer relations. A laboratory system comprising five reactors connected in series was operated. Each reactor simulated conditions typically encountered in full-scale systems. Low amount of copper (0.1-0.2 mg-Cu L-1) was dosed once per day into nitrified reactors. At any given time, only one reactor was dosed with copper. Not only inhibition of nitrification, chloramine decay associated with bulk water, biofilm and sediments also improved. However, the improvement was quicker and more significant when the influent to the reactor contained a high chloramine and a low nitrite concentration. Ammonia oxidising microbes exhibited resilience when exposed to low copper and chloramine concentrations for an extended period. Chloramine decay due to planktonic microbes and chemical reactions in bulk water decreased more rapidly than decay attributed to biofilm and sediments. The concept "biostable residual chlorine" explained how copper and chloramine can inhibit nitrification. Once nitrification was inhibited, the chloramine supplied from upstream effectively continued to suppress downstream nitrification, and this effect lasted more than 50 days even at 22 °C. The findings could be used to develop short-term copper dosing strategies and prevent negative impacts of nitrification and breakpoint chlorination.

Involvement of functional metabolism promotes the enrichment of antibiotic resistome in drinking water: Based on the PICRUSt2 functional prediction

Biofilters are the important source and sink of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARB) in the drinking water. Current studies generally ascribed the prevalence of BAR in biofilter from the perspective of gene behavior, i.e. horizontal gene transfer (HGT), little attentions have been paid on the ARGs carrier- ARB. In this study, we proposed the hypothesis that ARB participating in pollutant metabolism processes and becoming dominant is an important way for the enrichment of ARGs. To verify this, the antibiotic resistome and bacterial functional metabolic pathways of a sand filter was profiled using heterotrophic bacterial plate counting method (HPC), high-throughput qPCR, Illumina Hiseq sequencing and PICRUSt2 functional prediction. The results illustrated a significant leakage of ARB in the effluent of the sand filter with an average absolute abundance of approximately 102-103 CFU/mL. Further contribution analysis revealed that the dominant genera, such as Acinetobacter spp., Aeromonas spp., Elizabethkingia spp., and Bacillus spp., were primary ARGs hosts, conferring resistance to multiple antibiotics including sulfamethoxazole, tetracycline and β-lactams. Notably, these ARGs hosts were involved in nitrogen metabolism, including extracellular nitrate/nitrite transport and nitrite reduction, which are crucial in nitrification and denitrification in biofilters. For example, Acinetobacter spp., the dominant bacteria in the filter (relative abundance 69.97 %), contributed the majority of ARGs and 53.79 % of nitrite reduction function. That is, ARB can predominate by participating in the nitrogen metabolism pathways, facilitating the enrichment of ARGs. These findings provide insights into the stable presence of ARGs in biofilters from a functional metabolism perspective, offering a significant supplementary to the mechanisms of the emergence, maintenance, and transmission of BARin drinking water.

Extended chloramination significantly enriched intracellular antibiotic resistance genes in drinking water treatment plants

Chloramination and chlorination are both strong barriers that prevent the transmission of potential pathogens to humans through drinking water. However, the comparative effects of chloramination and chlorination on the occurrence of antibiotic resistance genes (ARGs) in drinking water treatment plants (DWTPs) remain unknown. Herein, the antibiotic resistome in water before and after chloramination or chlorination was analyzed through metagenomic sequencing and then verified through quantitative real-time polymerase chain reaction (qPCR). After the treatment of 90 min, chloramination led to higher enrichment of the total relative abundance of intracellular ARGs (iARGs) in water than chlorination, whereas chlorination facilitated the release of more extracellular ARGs (eARGs) than chloramination. According to redundancy and Pearson's analyses, the total concentration of the observed iARGs in the finished water exhibited a strong positive correlation with ammonium nitrogen (NH₄⁺-N) concentration, presenting a linear upward trend with an increase in the NH₄⁺-N concentration. This indicated that NH₄⁺-N is a crucial driving factor for iARG accumulation during chloramination. iARG enrichment ceases if the duration of chloramination is shortened to 40 min, suggesting that shortening the duration would be a better strategy for controlling iARG enrichment in drinking water. These findings emphasized the potential risk of antibiotic resistance after extended chloramination, shedding light on the control of transmission of antibiotic-resistant bacteria through water by optimizing disinfection procedures in DWTPs.

Identifying Eukaryotes and Factors Influencing Their Biogeography in Drinking Water Metagenomes

The biogeography of eukaryotes in drinking water systems is poorly understood relative to that of prokaryotes or viruses, limiting the understanding of their role and management. A challenge with studying complex eukaryotic communities is that metagenomic analysis workflows are currently not as mature as those that focus on prokaryotes or viruses. In this study, we benchmarked different strategies to recover eukaryotic sequences and genomes from metagenomic data and applied the best-performing workflow to explore the factors affecting the relative abundance and diversity of eukaryotic communities in drinking water distribution systems (DWDSs). We developed an ensemble approach exploiting k-mer- and reference-based strategies to improve eukaryotic sequence identification and identified MetaBAT2 as the best-performing binning approach for their clustering. Applying this workflow to the DWDS metagenomes showed that eukaryotic sequences typically constituted small proportions (i.e., <1%) of the overall metagenomic data with higher relative abundances in surface water-fed or chlorinated systems with high residuals. The α and β diversities of eukaryotes were correlated with those of prokaryotic and viral communities, highlighting the common role of environmental/management factors. Finally, a co-occurrence analysis highlighted clusters of eukaryotes whose members' presence and abundance in DWDSs were affected by disinfection strategies, climate conditions, and source water types.

Nitrogen-metabolising microorganism analysis in rapid sand filters from drinking water treatment plant

Sand filters (SFs) are common treatment processes for nitrogen pollutant removal in drinking water treatment plants (DWTPs). However, the mechanisms on the nitrogen-cycling role of SFs are still unclear. In this study, 16S rRNA gene amplicon sequencing was used to characterise the diversity and composition of the bacterial community in SFs from DWTPs. Additionally, metagenomics approach was used to determine the functional microorganisms involved in nitrogen cycle in SFs. Our results showed that Pseudomonadota, Acidobacteria, Nitrospirae and Chloroflexi dominated in SFs. Subsequently, 85 high-quality metagenome-assembled genomes (MAGs) were retrieved from metagenome datasets of selected SFs involving nitrification, assimilatory nitrogen reduction, denitrification and anaerobic ammonia oxidation (anammox) processes. Read mapping to reference genomes of Nitrospira and the phylogenetic tree of the ammonia monooxygenase subunit A gene, amoA, suggested that Nitrospira is abundantly found in SFs. Furthermore, according to their genetic content, a nitrogen metabolic model in SFs was proposed using representative MAGs and pure culture isolate. Quantitative real-time polymerase chain reaction (qPCR) showed that ammonia-oxidising bacteria (AOB) and archaea (AOA), and complete ammonia oxidisers (comammox) were ubiquitous in the SFs, with the abundance of comammox being higher than that of AOA and AOB. Moreover, we identified a bacterial strain with a high NO₃-N removal rate as Pseudomonas sp. DW-5, which could be applied in the bioremediation of micro-polluted drinking water sources. Our study provides insights into functional nitrogen-metabolising microbes in SFs of DWTPs.

Gradual Recovery of Building Plumbing-Associated Microbial Communities after Extended Periods of Altered Water Demand during the COVID-19 Pandemic

COVID-19 pandemic-related building restrictions heightened drinking water microbiological safety concerns post-reopening due to the unprecedented nature of commercial building closures. Starting with phased reopening (i.e., June 2020), we sampled drinking water for 6 months from three commercial buildings with reduced water usage and four occupied residential households. Samples were analyzed using flow cytometry and full-length 16S rRNA gene sequencing along with comprehensive water chemistry characterization. Prolonged building closures resulted in 10-fold higher microbial cell counts in the commercial buildings [(2.95 ± 3.67) × 105 cells mL-1] than in residential households [(1.11 ± 0.58) × 104 cells mL-1] with majority intact cells. While flushing reduced cell counts and increased disinfection residuals, microbial communities in commercial buildings remained distinct from those in residential households on the basis of flow cytometric fingerprinting [Bray-Curtis dissimilarity (dBC) = 0.33 ± 0.07] and 16S rRNA gene sequencing (dBC = 0.72 ± 0.20). An increase in water demand post-reopening resulted in gradual convergence in microbial communities in water samples collected from commercial buildings and residential households. Overall, we find that the gradual recovery of water demand played a key role in the recovery of building plumbing-associated microbial communities as compared to short-term flushing after extended periods of reduced water demand.

Land-Water Transport and Sources of Nitrogen Pollution Affecting the Structure and Function of Riverine Microbial Communities

The characterization of variations in riverine microbiota that stem from contaminant sources and transport modes is important for understanding biogeochemical processes. However, the association between complex anthropogenic nitrogen pollution and bacteria has not been extensively investigated owing to the difficulties faced while determining the distribution of nitrogen contaminants in watersheds. Here, we employed the Soil and Water Assessment Tool alongside microbiological analysis to explore microbial characteristics and their responses to complex nitrogen pollution patterns. Significant variations in microbial communities were observed in sub-basins with distinct land-water pollution transport modes. Point source-dominated areas (PSDAs) exhibited reduced microbial diversity, high number of denitrification groups, and increased nitrogen cycling compared with others. The negative relative deviations (-3.38) between the measured and simulated nitrate concentrations in PSDAs indicated that nitrate removal was more effective in PSDAs. Pollution sources were also closely associated with microbiota. Effluents from concentrated animal feeding operations were the primary factors relating to the microbiota compositions in PSDAs and balanced areas. In nonpoint source-dominated areas, contaminants from septic tanks become the most relevant sources to microbial community structures. Overall, this study expands our knowledge regarding microbial biogeochemistry in catchments and beyond by linking specific nitrogen pollution scenarios to microorganisms.

A comparative analysis employing a gene- and genome-centric metagenomic approach reveals changes in composition, function, and activity in waterworks with different treatment processes and source water in Finland

The emergence and development of next-generation sequencing technologies (NGS) has made the analysis of the water microbiome in drinking water distribution systems (DWDSs) more accessible and opened new perspectives in microbial ecology studies. The current study focused on the characterization of the water microbiome employing a gene- and genome-centric metagenomic approach to five waterworks in Finland with different raw water sources, treatment methods, and disinfectant. The microbial communities exhibit a distribution pattern of a few dominant taxa and a large representation of low-abundance bacterial species. Changes in the community structure may correspond to the presence or absence and type of disinfectant residual which indicates that these conditions exert selective pressure on the microbial community. The Archaea domain represented a small fraction (up to 2.5%) and seemed to be effectively controlled by the disinfection of water. Their role particularly in non-disinfected DWDS may be more important than previously considered. In general, non-disinfected DWDSs harbor higher microbial richness and maintaining disinfectant residual is significantly important for ensuring low microbial numbers and diversity. Metagenomic binning recovered 139 (138 bacterial and 1 archaeal) metagenome-assembled genomes (MAGs) that had a >50% completeness and <10% contamination consisting of 20 class representatives in 12 phyla. The presence and occurrence of nitrite-oxidizing bacteria (NOB)-like microorganisms have significant implications for nitrogen biotransformation in drinking water systems. The metabolic and functional complexity of the microbiome is evident in DWDSs ecosystems. A comparative analysis found a set of differentially abundant taxonomic groups and functional traits in the active community. The broader set of transcribed genes may indicate an active and diverse community regardless of the treatment methods applied to water. The results indicate a highly dynamic and diverse microbial community and confirm that every DWDS is unique, and the community reflects the selection pressures exerted at the community structure, but also at the levels of functional properties and metabolic potential.

Monochloramine Induces Release of DNA and RNA from Bacterial Cells: Quantification, Sequencing Analyses, and Implications

Monochloramine (MCA) is a widely used secondary disinfectant to suppress microbial growth in drinking water distribution systems. In monochloraminated drinking water, a significant amount of extracellular DNA (eDNA) has been reported, which has many implications ranging from obscuring DNA-based drinking water microbiome analyses to posing potential health concerns. To address this, it is imperative for us to know the origin of the eDNA in drinking water. Using Pseudomonas aeruginosa as a model organism, we report for the first time that MCA induces the release of nucleic acids from both biofilms and planktonic cells. Upon exposure to 2 mg/L MCA, massive release of DNA from suspended cells in both MilliQ water and 0.9% NaCl was directly visualized using live cell imaging in a CellASIC ONIX2 microfluidic system. Exposing established biofilms to MCA also resulted in DNA release from the biofilms, which was confirmed by increased detection of eDNA in the effluent. Intriguingly, massive release of RNA was also observed, and the extracellular RNA (eRNA) was also found to persist in water for days. Sequencing analyses of the eDNA revealed that it could be used to assemble the whole genome of the model organism, while in the water, certain fragments of the genome were more persistent than others. RNA sequencing showed that the eRNA contains non-coding RNA and mRNA, implying its role as a possible signaling molecule in environmental systems and a snapshot of the past metabolic state of the bacterial cells.

Characteristics of Antibiotic Resistance Genes and Antibiotic-Resistant Bacteria in Full-Scale Drinking Water Treatment System Using Metagenomics and Culturing

The contamination of antibiotic resistance genes (ARGs) may directly threaten human health. This study used a metagenomic approach to investigate the ARG profile in a drinking water treatment system (DWTS) in south China. In total, 317 ARG subtypes were detected; specifically, genes encoding bacitracin, multidrug, and sulfonamide were widely detected in the DWTS. Putative ARG hosts included Acidovorax (6.0%), Polynucleobacter (4.3%), Pseudomonas (3.4%), Escherichia (1.7%), and Klebsiella (1.5%) as the enriched biomarkers in the DWTS, which mainly carried bacitracin, beta-lactam, and aminoglycoside ARGs. From a further analysis of ARG-carrying contigs (ACCs), Stenotrophomonas maltophilia and Pseudomonas aeruginosa were the most common pathogens among the 49 ACC pathogens in the DWTS. The metagenomic binning results demonstrated that 33 high-quality metagenome-assembled genomes (MAGs) were discovered in the DWTS; particularly, the MAG identified as S. maltophilia-like (bin.195) harbored the greatest number of ARG subtypes (n = 8), namely, multidrug (n = 6; smeD, semE, multidrug_transporter, mexE, semB, and smeC), beta-lactam (n = 1; metallo-beta-lactamase), and aminoglycoside [n = 1; aph(3’)-IIb]. The strong positive correlation between MGEs and ARG subtypes revealed a high ARG dissemination risk in the DWTS. Based on the pure-culture method, 93 isolates that belong to 30 genera were recovered from the DWTS. Specifically, multidrug-resistant pathogens and opportunistic pathogens such as P. aeruginosa, Bacillus cereus, and S. maltophilia were detected in the DWTS. These insights into the DWTS’s antibiotic resistome indicated the need for more comprehensive ARG monitoring and management in the DWTS. Furthermore, more effective disinfection methods need to be developed to remove ARGs in DWTSs, and these findings could assist governing bodies in the surveillance of antibiotic resistance in DWTSs.

Enhanced bio-reductive degradation of fluoroglucocorticoids in the groundwater fluctuation zone by external electron donors: Performance, microbial community, and functional genes

This study evaluated the effectiveness of external electron donors on the bio-reductive degradation enhancement of fluoroglucocorticoids (FGCs) in the groundwater fluctuation zone during the wet season when reverse upward fluctuation of the groundwater table occurs and the dry season after the groundwater table declines. The results showed that the external electron donors, provided by the addition of nano zero-valent iron-modified biochar (nZVI@BC), inhibited the migration and enhanced the reductive defluorination of triamcinolone acetonide (TA), a representative FGC. The accumulation rate constant with temporal fluctuation depth and the attenuation rate constant with vertical fluctuation depth were -2.55 × 10^-3 and 4.20 × 10^-2, respectively, in the groundwater of the natural groundwater fluctuation zone (N-FZ). In contrast, the accumulation and attenuation rate constants were, respectively, 35.6% and 2.64 times higher in the groundwater fluctuation zone amended with nZVI@BC (nZVI@BC-FZ) as compared with those observed in the N-FZ. Furthermore, the decay rate constant of the TA residue in the dry season was 0.843 × 10^-2 μg/d in N-FZ and was 2.19 times higher in nZVI@BC-FZ. This enhancement effect, caused by the addition of external electrons, was positively correlated with the evolution of the microbial community and the expression of functional genes. The microbes evolved into functional genera with reductive dehalogenation (Xylophilus and Hydrogenophaga) and iron-oxidizing (Lysobacter, Pseudoxanthomonas, and Sphingomonas) abilities in the nZVI@BC-FZ system, which increased dehalogenation and iron oxide genes by a 4-5 order of magnitude. The utilization proportion of external electrons for TA metabolism was 50.04%, of which 30.82%, 10.26%, and 8.96% were utilized for defluorination, hydrogenation, and ring-opening, respectively. This study provides an effective method to reduce pollutant diffusion and enhance the bio-reductive degradation caused by groundwater table fluctuation.

Evaluating de Novo Assembly and Binning Strategies for Time Series Drinking Water Metagenomes

Reconstructing microbial genomes from metagenomic short-read data can be challenging due to the unknown and uneven complexity of microbial communities. This complexity encompasses highly diverse populations, which often includes strain variants. Reconstructing high-quality genomes is a crucial part of the metagenomic workflow, as subsequent ecological and metabolic inferences depend on their accuracy, quality, and completeness. In contrast to microbial communities in other ecosystems, there has been no systematic assessment of genome-centric metagenomic workflows for drinking water microbiomes. In this study, we assessed the performance of a combination of assembly and binning strategies for time series drinking water metagenomes that were collected over 6 months. The goal of this study was to identify the combination of assembly and binning approaches that result in high-quality and -quantity metagenome-assembled genomes (MAGs), representing most of the sequenced metagenome. Our findings suggest that the metaSPAdes coassembly strategies had the best performance, as they resulted in larger and less fragmented assemblies, with at least 85% of the sequence data mapping to contigs greater than 1 kbp. Furthermore, a combination of metaSPAdes coassembly strategies and MetaBAT2 produced the highest number of medium-quality MAGs while capturing at least 70% of the metagenomes based on read recruitment. Utilizing different assembly/binning approaches also assists in the reconstruction of unique MAGs from closely related species that would have otherwise collapsed into a single MAG using a single workflow. Overall, our study suggests that leveraging multiple binning approaches with different metaSPAdes coassembly strategies may be required to maximize the recovery of good-quality MAGs. IMPORTANCE Drinking water contains phylogenetic diverse groups of bacteria, archaea, and eukarya that affect the esthetic quality of water, water infrastructure, and public health. Taxonomic, metabolic, and ecological inferences of the drinking water microbiome depend on the accuracy, quality, and completeness of genomes that are reconstructed through the application of genome-resolved metagenomics. Using time series metagenomic data, we present reproducible genome-centric metagenomic workflows that result in high-quality and -quantity genomes, which more accurately signifies the sequenced drinking water microbiome. These genome-centric metagenomic workflows will allow for improved taxonomic and functional potential analysis that offers enhanced insights into the stability and dynamics of drinking water microbial communities.

Prospects for multi-omics in the microbial ecology of water engineering

Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions - including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, related developments in both whole community gene expression surveys and metabolite profiling have permitted for direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.

Metagenomic Profile of Microbial Communities in a Drinking Water Storage Tank Sediment after Sequential Exposure to Monochloramine, Free Chlorine, and Monochloramine

Sediment accumulation in drinking water storage facilities may lead to water quality degradation, including biological growth and disinfectant decay. The current research evaluated the microbiome present in a sediment after sequential exposure to monochloramine, free chlorine, and monochloramine. Chemical profiles within the sediment based on microelectrodes showed evidence of nitrification, and monochloramine slowly penetrated the sediment but was not measurable at lower depths. A metagenomic approach was used to characterize the microbial communities and functional potential of top (0-1 cm) and bottom (1-2 cm) layers in sediment cores. Differential abundance analysis revealed both an enrichment and depletion associated with depth of microbial populations. We assembled 30 metagenome-assembled genomes (MAGs) representing bacterial and archaeal microorganisms. Most metabolic functions were represented in both layers, suggesting the capability of the microbiomes to respond to environmental fluctuations. However, niche-specific abundance differences were identified in biotransformation processes (e.g., nitrogen). Metagenome-level analyses indicated that nitrification and denitrification can potentially occur simultaneously in the sediments, but the exact location of their occurrence within the sediment will depend on the localized physicochemical conditions. Even though monochloramine was maintained in the bulk water there was limited penetration into the sediment, and the microbial community remained functionally diverse and active.

Phosphate Dosing in Drinking Water Distribution Systems Promotes Changes in Biofilm Structure and Functional Genetic Diversity

Water utilities treat drinking water by adding phosphate to prevent metal dissolution from water pipe work systems and particularly lead poisoning. Phosphate can be a limiting nutrient for microbial biofilms in DWDS, yet its effects on these microbial consortia are not well understood. This research presents results from phosphate dosing experiments using a real scale chlorinated DWDS, comparing standard phosphate concentrations of United Kingdom drinking water (1 mgP/L) with a double dose (2 mgP/L) commonly used in plumbosolvency treatment. Biofilm development during phosphate treatment experiments was monitored using a holistic approach by combining metagenomics analysis, flow cytometry and SEM characterisation. The increase of phosphate levels in drinking water, reduced biofilm cell numbers and promoted the presence of poorly distributed biofilms on inner pipe surfaces. Metagenomics analysis using genetic markers (16S rRNA and ITS2) showed that phosphate influenced biofilm community structure, particularly fungal composition. Whole metagenome sequencing showed that phosphate enrichment favoured the presence of sequencing reads associated to ATPases, ion transporters and DNA-interacting proteins, whilst reads associated to nitrogen metabolism were predominant in control samples. This research brings new knowledge regarding the influence of phosphate treatment on the composition and structure of biofilms within DWDS, and the implications that this might have for the management of these systems.