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

   https://doi.org/10.1128/Spectrum.01434-21  

   Vosloo, Solize; Huo, Linxuan; Anderson, Christopher L.; Dai, Zihan; Sevillano, Maria; Pinto, Ameet (December 2021, Microbiology Spectrum)

   Gralnick, Jeffrey A. (Ed.)

   ABSTRACT 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. 

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2. Microbial Nitrogen Metabolism in Chloraminated Drinking Water Reservoirs

   https://doi.org/10.1128/mSphere.00274-20  

   Potgieter, Sarah C.; Dai, Zihan; Venter, Stephanus N.; Sigudu, Makhosazana; Pinto, Ameet J.; McMahon, Katherine (April 2020, mSphere)

   ABSTRACT Ammonia availability due to chloramination can promote the growth of nitrifying organisms, which can deplete chloramine residuals and result in operational problems for drinking water utilities. In this study, we used a metagenomic approach to determine the identity and functional potential of microorganisms involved in nitrogen biotransformation within chloraminated drinking water reservoirs. Spatial changes in the nitrogen species included an increase in nitrate concentrations accompanied by a decrease in ammonium concentrations with increasing distance from the site of chloramination. This nitrifying activity was likely driven by canonical ammonia-oxidizing bacteria (i.e., Nitrosomonas ) and nitrite-oxidizing bacteria (i.e., Nitrospira ) as well as by complete-ammonia-oxidizing (i.e., comammox) Nitrospira -like bacteria. Functional annotation was used to evaluate genes associated with nitrogen metabolism, and the community gene catalogue contained mostly genes involved in nitrification, nitrate and nitrite reduction, and nitric oxide reduction. Furthermore, we assembled 47 high-quality metagenome-assembled genomes (MAGs) representing a highly diverse assemblage of bacteria. Of these, five MAGs showed high coverage across all samples, which included two Nitrosomonas, Nitrospira, Sphingomonas , and Rhizobiales -like MAGs. Systematic genome-level analyses of these MAGs in relation to nitrogen metabolism suggest that under ammonia-limited conditions, nitrate may be also reduced back to ammonia for assimilation. Alternatively, nitrate may be reduced to nitric oxide and may potentially play a role in regulating biofilm formation. Overall, this study provides insight into the microbial communities and their nitrogen metabolism and, together with the water chemistry data, improves our understanding of nitrogen biotransformation in chloraminated drinking water distribution systems. IMPORTANCE Chloramines are often used as a secondary disinfectant when free chlorine residuals are difficult to maintain. However, chloramination is often associated with the undesirable effect of nitrification, which results in operational problems for many drinking water utilities. The introduction of ammonia during chloramination provides a potential source of nitrogen either through the addition of excess ammonia or through chloramine decay. This promotes the growth of nitrifying microorganisms and provides a nitrogen source (i.e., nitrate) for the growth for other organisms. While the roles of canonical ammonia-oxidizing and nitrite-oxidizing bacteria in chloraminated drinking water systems have been extensively investigated, those studies have largely adopted a targeted gene-centered approach. Further, little is known about the potential long-term cooccurrence of complete-ammonia-oxidizing (i.e., comammox) bacteria and the potential metabolic synergies of nitrifying organisms with their heterotrophic counterparts that are capable of denitrification and nitrogen assimilation. This study leveraged data obtained for genome-resolved metagenomics over a time series to show that while nitrifying bacteria are dominant and likely to play a major role in nitrification, their cooccurrence with heterotrophic organisms suggests that nitric oxide production and nitrate reduction to ammonia may also occur in chloraminated drinking water systems. 

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3. Case report: contamination of a drinking water distribution system by Exophiala-dominated biofilm in the Midwestern United States

   https://doi.org/10.2166/wh.2025.173  

   King, Jon C; Lancaster, Emma; Myers, Alicia; Lee, Jiyoung; Dannemiller, Karen C (February 2025, Journal of Water and Health)

   Fungal contamination of drinking water distribution systems can impact water quality with implications for public health. We document an instance of Exophiala spp. biofilm contamination of customer taps in the Midwest United States following consumer complaints. Three samples of black biofilm were collected from customer taps in Ohio and then processed using next-generation DNA sequencing of the bacterial 16S and fungal ITS regions. Two samples with successful ITS sequencing were dominated by Exophiala spp., putatively identified as E. cancerae and E. lecanii-corni. Dominant bacterial phyla in samples included Proteobacteria, Bacteroidetes, Actinobacteria, and Acidobacteria. Bacterial composition varied substantially at the family and genus levels, and potentially pathogenic bacteria (i.e., Acinetobacter spp., Legionella spp., Mycobacterium spp., and Pseudomonas spp.) were detected. The potential for fungal contamination of drinking water distribution systems should be evaluated when biofilms are observed. 

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4. The Municipal Drinking Water Database

   https://doi.org/10.1371/journal.pwat.0000081  

   Hughes, Sara; Kirchhoff, Christine J.; Conedera, Katelynn; Friedman, Mirit (April 2023, PLOS Water)

   Herrera, Manuel (Ed.)

   Drinking water services in the U.S. are critical for public health and economic development but face technical, political, and administrative challenges. Understanding the root cause of these challenges and how to overcome them is hindered by the lack of integrative, comprehensive data about drinking water systems and the communities they serve. The Municipal Drinking Water Database (MDWD) combines financial, institutional, demographic, and environmental conditions of U.S. municipalities and their community water systems (CWS). Municipally owned and operated CWS are ubiquitous and play a critical role in ensuring safe, affordable drinking water services for most Americans; they also offer important opportunities for understanding municipal government behavior and decision making. The MDWD is publicly available and will enable researchers and practitioners interested in viewing or tracking drinking water spending, the financial condition of municipal governments, or myriad demographic, political, institutional, and physical characteristics of municipal drinking water systems to access the data quickly and easily. This paper describes the database and its creation, details examples of how the data can be used and discusses illustrative analyses of trends and insights that can be gleaned from the database. Building and sharing more integrated datasets provides new opportunities for asking novel questions about the drivers and consequences of local decision making about drinking water. 

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5. Disparities in drinking water quality: evidence from California

   https://doi.org/10.2166/wp.2023.068  

   Acquah, Sarah; Allaire, Maura (February 2023, Water Policy)

   Abstract Reducing disparities in drinking water quality is a state-level priority in California, yet targeting communities for assistance is hindered by the lack of empirical evidence regarding populations disproportionately affected. The study addresses this gap by analyzing drinking water quality violations and identifying the types of communities disproportionately burdened by water contaminants. Using a sample of 1,710 Community Water Systems (CWSs) and probit regression models, we analyzed the likelihood of violation as a function of low-income, minority groups, and vulnerable populations. Results indicate that environmental justice concerns are prevalent. Low-income communities and minority groups (Hispanics and non-Whites) face greater likelihood of water quality violations. Low-income communities are 1.77% more likely to have any health-related violations. Severely disadvantaged communities face greater likelihood (3.44%) of water quality violations. Tribal water systems are 2% more likely to violate the Total Coliform Rule. Children aged five and under are 3% more likely to be exposed to health-based water quality violations. Failure to address prior violations leads to greater likelihood (38.94%) of future violations, while large utility systems and purchased water sources have the propensity to reduce violations. Overall, these findings can guide policy decisions to prioritize assistance to communities disproportionately impacted by poor water quality. 

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