Impact of Water Chemistry, Pipe Material and Stagnation on the Building Plumbing Microbiome

Persistence of viable but nonculturable Legionella pneumophila state in hospital water systems: A hidden enemy?

There is little evidence of the long-term consequences of maintaining sanitary hot water at high temperatures on the persistence of Legionella in the plumbing system. The aims of this study were to describe the persistence and genotypic variability of L. pneumophila in a hospital building with two entirely independent hot water distribution systems, and to estimate the thermotolerance of the genotypic variants by studying the quantity of VBNC L. pneumophila. Eighty isolates from 55 water samples obtained between the years 2012-2017 were analyzed. All isolates correspond to L. pneumophila serogroup 6. The isolates were discriminated in four restriction patterns by pulsed-field gel electrophoresis. In one installation, pattern A + Aa predominated, accounting for 75.8 % of samples, while the other installation exhibited pattern B as the most frequent (81.8 % of samples; p < 0.001). The mean temperature of the isolates was: 52.6 °C (pattern A + Aa) and 55.0 °C (pattern B), being significantly different. Nine strains were selected as representative among patterns to study their thermotolerance by flow-cytometry after 24 h of thermic treatment. VBNC bacteria were detected in all samples. After thermic treatment at 50 °C, 52.0 % of bacteria had an intact membrane, and after 55 °C this percentage decreased to 23.1 %. Each pattern exhibited varying levels of thermotolerance. These findings indicate that the same hospital building can be colonized with different predominant types of Legionella if it has independent hot water installations. Maintaining a minimum temperature of 50 °C at distal points of the system would allow the survival of replicative L. pneumophila. However, the presence of Legionella in hospital water networks is underestimated if culture is considered as the standard method for Legionella detection, because VBNC do not grow on culture plates. This phenomenon can carry implications for the Legionella risk management plans in hospitals that adjust their control measures based on the microbiological surveillance of water.

Domestic hot-water boilers harbour active thermophilic bacterial communities distinctly different from those in the cold-water supply

Running cold and hot water in buildings is a widely established commodity. However, interests regarding hygiene and microbiological aspects had so far been focussed on cold water. Little attention has been given to the microbiology of domestic hot-water installations (DHWIs), except for aspects of pathogenic Legionella. World-wide, regulations consider hot (or warm) water as 'heated drinking water' that must comply (cold) drinking water (DW) standards. However, the few reports that exist indicate presence and growth of microbial flora in DHWIs, even when supplied with water with disinfectant residual. Using flow cytometric (FCM) total cell counting (TCC), FCM-fingerprinting, and 16S rRNA-gene-based metagenomic analysis, the characteristics and composition of bacterial communities in cold drinking water (DW) and hot water from associated boilers (operating at 50 - 60 °C) was studied in 14 selected inhouse DW installations located in Switzerland and Austria. A sampling strategy was applied that ensured access to the bulk water phase of both, supplied cold DW and produced hot boiler water. Generally, 1.3- to 8-fold enhanced TCCs were recorded in hot water compared to those in the supplied cold DW. FCM-fingerprints of cold and corresponding hot water from individual buildings indicated different composition of cold- and hot-water microbial floras. Also, hot waters from each of the boilers sampled had its own individual FCM-fingerprint. 16S rRNA-gene-based metagenomic analysis confirmed the marked differences in composition of microbiomes. E.g., in three neighbouring houses supplied from the same public network pipe each hot-water boiler contained its own thermophilic bacterial flora. Generally, bacterial diversity in cold DW was broad, that in hot water was restricted, with mostly thermophilic strains from the families Hydrogenophilaceae, Nitrosomonadaceae and Thermaceae dominating. Batch growth assays, consisting of cold DW heated up to 50 - 60 °C and inoculated with hot water, resulted in immediate cell growth with doubling times between 5 and 10 h. When cold DW was used as an inoculum no significant growth was observed. Even boilers supplied with UVC-treated cold DW contained an actively growing microbial flora, suggesting such hot-water systems as autonomously operating, thermophilic bioreactors. The generation of assimilable organic carbon from dissolved organic carbon due to heating appears to be the driver for growth of thermophilic microbial communities. Our report suggests that a man-made microbial ecosystem, very close to us all and of potential hygienic importance, may have been overlooked so far. Despite consumers having been exposed to microbial hot-water flora for a long time, with no major pathogens so far been associated specifically with hot-water usage (except for Legionella), the role of harmless thermophiles and their interaction with potential human pathogens able to grow at elevated temperatures in DHWIs remains to be investigated.

Four buildings and a flush: Lessons from degraded water quality and recommendations on building water management

A reduction in building occupancy can lead to stagnant water in plumbing, and the potential consequences for water quality have gained increasing attention. To investigate this, a study was conducted during the COVID-19 pandemic, focusing on water quality in four institutional buildings. Two of these buildings were old (>58 years) and large (>19,000 m2), while the other two were new (>13 years) and small (<11,000 m2). The study revealed significant decreases in water usage in the small buildings, whereas usage remained unchanged in the large buildings. Initial analysis found that residual chlorine was rarely detectable in cold/drinking water samples. Furthermore, the pH, dissolved oxygen, total organic carbon, and total cell count levels in the first draw of cold water samples were similar across all buildings. However, the ranges of heavy metal concentrations in large buildings were greater than observed in small buildings. Copper (Cu), lead (Pb), and manganese (Mn) sporadically exceeded drinking water limits at cold water fixtures, with maximum concentrations of 2.7 mg Cu L-1, 45.4 μg Pb L-1, 1.9 mg Mn L-1. Flushing the plumbing for 5 min resulted in detectable residual at fixtures in three buildings, but even after 125 min of flushing in largest and oldest building, no residual chlorine was detected at the fixture closest to the building's point of entry. During the pandemic, the building owner conducted fixture flushing, where one to a few fixtures were operated per visit in buildings with hundreds of fixtures and multiple floors. However, further research is needed to understand the fundamental processes that control faucet water quality from the service line to the faucet. In the absence of this knowledge, building owners should create and use as-built drawings to develop flushing plans and conduct periodic water testing.

Responses of drinking water bulk and biofilm microbiota to elevated water age in bench-scale simulated distribution systems

Reductions in nonresidential water demand during the COVID-19 pandemic highlighted the importance of understanding how water age impacts drinking water quality and microbiota in piped distribution systems. Using benchtop model distribution systems, we aimed to characterize the impacts of elevated water age on microbiota in bulk water and pipe wall biofilms. Five replicate constant-flow reactors were fed with municipal chloraminated tap water for 6 months prior to building closures and 7 months after. After building closures, chloramine levels entering the reactors dropped; in the reactor bulk water and biofilms the mean cell counts and ATP concentrations increased over an order of magnitude while the detection of opportunistic pathogens remained low. Water age, and the corresponding physicochemical changes, strongly influenced microbial abundance and community composition. Differential initial microbial colonization also had a lasting influence on microbial communities in each reactor (i.e., historical contingency).

Microbial ecology of drinking water from source to tap

As drinking water travels from its source, through various treatment processes, hundreds to thousands of kilometres of distribution network pipes, to the taps in private homes and public buildings, it is exposed to numerous environmental changes, as well as other microbes living in both water and on surfaces. This review aims to identify the key locations and factors that are associated with changes in the drinking water microbiome throughout conventional urban drinking water systems from the source to the tap water. Over the past 15 years, improvements in cultivation-independent methods have enabled studies that allow us to answer such questions. As a result, we are beginning to move towards predicting the impacts of disturbances and interventions resulting ultimately in management of drinking water systems and microbial communities rather than mere observation. Many challenges still exist to achieve effective management, particularly within the premise plumbing environment, which exhibits diverse and inconsistent conditions that may lead to alterations in the microbiota, potentially presenting public health risks. Finally, we recommend the establishment of global collaborative projects on the drinking water microbiome that will enhance our current knowledge and lead to tools for operators and researchers alike to improve global access to high-quality drinking water.

Assessing Freshwater Microbiomes from Different Storage Sources in the Caribbean Using DNA Metabarcoding

Next-generation sequencing (NGS) and the technique of DNA metabarcoding have provided more efficient and comprehensive options for testing water quality compared to traditional methods. Recent studies have shown the efficacy of DNA metabarcoding in characterizing the bacterial microbiomes of varied sources of drinking water, including rivers, reservoirs, wells, tanks, and lakes. We asked whether DNA metabarcoding could be used to characterize the microbiome of different private sources of stored freshwater on the Caribbean Island nation of Antigua and Barbuda. Two replicate water samples were obtained from three different private residential sources in Antigua: a well, an above-ground tank, and a cistern. The bacterial microbiomes of different freshwater sources were assessed using 16S rRNA metabarcoding. We measured both alpha diversity (species diversity within a sample) and beta diversity (species diversity across samples) and conducted a taxonomic analysis. We also looked for the presence of potentially pathogenic species. Major differences were found in the microbiome composition and relative abundances depending on the water source. A lower alpha diversity was observed in the cistern sample compared to the others, and distinct differences in the microbiome composition and relative abundance were noted between the samples. Notably, pathogenic species, or genera known to harbor such species, were detected in all the samples. We conclude that DNA metabarcoding can provide an effective and comprehensive assessment of drinking water quality and has the potential to identify pathogenic species overlooked using traditional methods. This method also shows promise for tracing the source of disease outbreaks due to waterborne microorganisms. This is the first study from small island countries in the Caribbean where metabarcoding has been applied for assessing freshwater water quality.

Lead (Pb) deposition onto new and biofilm-laden potable water pipes

Heavy metals' interactions with plumbing materials are complicated due to the differential formation of biofilms within pipes that can modulate, transform, and/or sequester heavy metals. This research aims to elucidate the mechanistic role of biofilm presence on Lead (Pb) accumulation onto crosslinked polyethylene (PEX-A), high-density polyethylene (HDPE), and copper potable water pipes. For this purpose, biofilms were grown on new pipes for three months. Five-day Pb exposure experiments were conducted to examine the kinetics of Pb accumulation onto the new and biofilm-laden pipes. Additionally, the influence of Pb initial concentration on the rate of its accumulation onto the pipes was examined. The results revealed greater biofilm biomass on the PEX-A pipes compared to the copper and HDPE pipes. More negative zeta potential was found for the biofilm-laden plastic pipes compared to the new plastic pipes. After five days of Pb exposure under stagnant conditions, the biofilm-laden PEX-A (980 μg m-2) and HDPE (1170 μg m-2) pipes accumulated more than three times the Pb surface loading compared to the new PEX-A (265 μg m-2) and HDPE pipes (329 μg m-2), respectively. However, under flow conditions, Pb accumulation on biofilm-laden plastic pipes was lower than on the new pipes. Moreover, with increasing the initial Pb concentration, greater rates of Pb surface accumulation were found for the biofilm-laden pipes compared to the new pipes under stagnant conditions. First-order kinetics model best described the Pb accumulation onto both new and biofilm-laden water pipes under both stagnant and flow conditions.

Assessing residential activity in a home plumbing system simulator: monitoring the occurrence and relationship of major opportunistic pathogens and phagocytic amoebas

Opportunistic premise plumbing pathogens (OPPPs) have been detected in buildings' plumbing systems causing waterborne disease outbreaks in the United States. In this study, we monitored the occurrence of OPPPs along with free-living amoeba (FLA) and investigated the effects of residential activities in a simulated home plumbing system (HPS). Water samples were collected from various locations in the HPS and analyzed for three major OPPPs: Legionella pneumophila, nontuberculous mycobacterial species (e.g., Mycobacterium avium, M. intracellulare, and M. abscessus), and Pseudomonas aeruginosa along with two groups of amoebas (Acanthamoeba and Vermamoeba vermiformis). A metagenomic approach was also used to further characterize the microbial communities. Results show that the microbial community is highly diverse with evidence of spatial and temporal structuring influenced by environmental conditions. L. pneumophila was the most prevalent pathogen (86% of samples), followed by M. intracellulare (66%) and P. aeruginosa (21%). Interestingly, M. avium and M. abscessus were not detected in any samples. The data revealed a relatively low prevalence of Acanthamoeba spp. (4%), while V. vermiformis was widely detected (81%) across all the sampling locations within the HPS. Locations with a high concentration of L. pneumophila and M. intracellulare coincided with the highest detection of V. vermiformis, suggesting the potential growth of both populations within FLA and additional protection in drinking water. After a period of stagnation lasting at least 2-weeks, the concentrations of OPPPs and amoeba immediately increased and then decreased gradually back to the baseline. Furthermore, monitoring the microbial population after drainage of the hot water tank and partial drainage of the entire HPS demonstrated no significant mitigation of the selected OPPPs. This study demonstrates that these organisms can adjust to their environment during such events and may survive in biofilms and/or grow within FLA, protecting them from stressors in the supplied water.

The composition of planktonic prokaryotic communities in a hospital building water system depends on both incoming water and flow dynamics

In recent years, the frequency of nosocomial infections has increased. Hospital water systems support the growth of microbes, especially opportunistic premise plumbing pathogens. In this study, planktonic prokaryotic communities present in water samples taken from hospital showers and hand basins, collected over three different sampling phases, were characterized by 16S rRNA gene amplicon sequencing. Significant differences in the abundance of various prokaryotic taxa were found through univariate and multivariate analysis. Overall, the prokaryotic communities of hospital water were taxonomically diverse and dominated by biofilm forming, corrosion causing, and potentially pathogenic bacteria. The phyla Proteobacteria, Actinobacteriota, Bacteroidota, Planctomycetota, Firmicutes, and Cyanobacteria made up 96% of the relative abundance. The α-diversity measurements of prokaryotic communities showed no difference in taxa evenness and richness based on sampling sites (shower or hand basins), sampling phases (months), and presence or absence of Vermamoeba vermiformis. However, β-diversity measurements showed significant clustering of prokaryotic communities based on sampling phases, with the greatest difference observed between the samples collected in phase 1 vs phase 2/3. Importantly, significant difference was observed in prokaryotic communities based on flow dynamics of the incoming water. The Pielou's evenness diversity index revealed a significant difference (Kruskal Wallis, p < 0.05) and showed higher species richness in low flow regime (< 13 minutes water flushing per week and ≤ 765 flushing events per six months). Similarly, Bray-Curtis dissimilarity index found significant differences (PERMANOVA, p < 0.05) in the prokaryotic communities of low vs medium/high flow regimes. Furthermore, linear discriminant analysis effect size showed that several biofilm forming (e.g., Pseudomonadales), corrosion causing (e.g., Desulfobacterales), extremely environmental stress resistant (e.g., Deinococcales), and potentially pathogenic (e.g., Pseudomonas) bacterial taxa were in higher amounts under low flow regime conditions. This study demonstrated that a hospital building water system consists of a complex microbiome that is shaped by incoming water quality and the building flow dynamics arising through usage.

Building water quality deterioration during water supply restoration after interruption: Influences of premise plumbing configuration

Premise plumbing plays an essential role in determining the final quality of drinking water consumed by customers. However, little is known about the influences of plumbing configuration on water quality changes. This study selected parallel premise plumbing in the same building with different configurations, i.e., laboratory and toilet plumbing. Water quality deteriorations induced by premise plumbing under regular and interrupted water supply were investigated. The results showed that most of the water quality parameters did not vary under regular supply, except Zn, which was significantly increased by laboratory plumbing (78.2 to 260.7 µg/l). For the bacterial community, the Chao1 index was significantly increased by both plumbing types to a similar level (52 to 104). Laboratory plumbing significantly changed the bacterial community, but toilet plumbing did not. Remarkably, water supply interruption/restoration led to serious water quality deterioration in both plumbing types but resulted in different changes. Physiochemically, discoloration was observed only in laboratory plumbing, along with sharp increases in Mn and Zn. Microbiologically, the increase in ATP was sharper in toilet plumbing than in laboratory plumbing. Some opportunistic pathogen-containing genera, e.g., Legionella spp. and Pseudomonas spp., were present in both plumbing types but only in disturbed samples. This study highlighted the esthetic, chemical, and microbiological risks associated with premise plumbing, for which system configuration plays an important role. Attention should be given to optimizing premise plumbing design for managing building water quality.

Controlling Legionella pneumophila in Showerheads: Combination of Remedial Intervention and Preventative Flushing

Shock chlorination and remedial flushing are suggested to address Legionella pneumophila (Lp) contamination in buildings or during their (re)commissioning. However, data on general microbial measurements (adenosine tri-phosphate [ATP], total cell counts [TCC]), and the abundance of Lp are lacking to support their temporary implementation with variable water demands. In this study, the weekly short-term (3-week) impact of shock chlorination (20-25 mg/L free chlorine, 16 h) or remedial flushing (5-min flush) combined with distinct flushing regimes (daily, weekly, stagnant) was investigated in duplicates of showerheads in two shower systems. Results showed that the combination of stagnation and shock chlorination prompted biomass regrowth, with ATP and TCC in the first draws reaching large regrowth factors of 4.31-7.07-fold and 3.51-5.68-fold, respectively, from baseline values. Contrastingly, remedial flushing followed by stagnation generally resulted in complete or larger regrowth in Lp culturability and gene copies (gc). Irrespective of the intervention, daily flushed showerheads resulted in significantly (p < 0.05) lower ATP and TCC, as well as lower Lp concentrations than weekly flushes, in general. Nonetheless, Lp persisted at concentrations ranging from 11 to 223 as the most probable number per liter (MPN/L) and in the same order of magnitude (10³-10⁴ gc/L) than baseline values after remedial flushing, despite daily/weekly flushing, unlike shock chlorination which suppressed Lp culturability (down 3-log) for two weeks and gene copies by 1-log. This study provides insights on the most optimal short-term combination of remedial and preventative strategies that can be considered pending the implementation of suitable engineering controls or building-wide treatment.

A Critical Review on the Factors that Influence Opportunistic Premise Plumbing Pathogens: From Building Entry to Fixtures in Residences

Residential buildings provide unique conditions for opportunistic premise plumbing pathogen (OPPP) exposure via aerosolized water droplets produced by showerheads, faucets, and tubs. The objective of this review was to critically evaluate the existing literature that assessed the impact of potentially enhancing conditions to OPPP occurrence associated with residential plumbing and to point out knowledge gaps. Comprehensive studies on the topic were found to be lacking. Major knowledge gaps identified include the assessment of OPPP growth in the residential plumbing, from building entry to fixtures, and evaluation of the extent of the impact of typical residential plumbing design (e.g., trunk and branch and manifold), components (e.g., valves and fixtures), water heater types and temperature setting of operation, and common pipe materials (copper, PEX, and PVC/CPVC). In addition, impacts of the current plumbing code requirements on OPPP responses have not been assessed by any study and a lack of guidelines for OPPP risk management in residences was identified. Finally, the research required to expand knowledge on OPPP amplification in residences was discussed.

Flushing Temporarily Improves Microbiological Water Quality for Buildings Supplied with Chloraminated Surface Water but Has Little Effect for Groundwater Supplies

Microbial communities in premise plumbing systems were investigated after more than 2 months of long-term stagnation, during a subsequent flushing event, and during post-flush stagnation. Water samples were collected from showers in buildings supplied with chlorinated groundwater, untreated groundwater, and chloraminated surface water. The building supplied with chlorinated groundwater generally had the lowest bacterial concentrations across all sites (ranging from below quantification limit to 5.2 log copies/L). For buildings supplied with untreated groundwater, bacterial concentrations (5.0 to 7.6 log copies/L) and microbial community diversity index (ACE) values were consistent throughout sampling. Nontuberculous mycobacteria (NTM) and Legionella pneumophila were not detected in any groundwater-supplied buildings. Total bacteria, Legionella spp., and NTM were abundant in the surface water-supplied buildings following long-term stagnation (up to 7.6, 6.2, and 7.6 log copies/L, respectively). Flushing decreased these concentrations by ∼1 to >4 log units and reduced microbial community diversity, but the communities largely recovered within a week of post-flush stagnation. The results suggest that buildings supplied with disinfected surface water are more likely than buildings supplied with treated or untreated groundwater to experience deleterious changes in microbiological water quality during stagnation and that the water quality improvements from flushing with chloraminated water, while substantial, are short-lived.

Legionella pneumophila Risk from Air–Water Cooling Units Regarding Pipe Material and Type of Water

Legionellosis is a respiratory disease related to environmental health. There have been manifold studies of pipe materials, risk installations and legionellosis without considering the type of transferred water. The objective of this study was to determine the potential development of the causative agent Legionella pneumophila regarding air–water cooling units, legislative compliance, pipe material and type of water. Forty-four hotel units in Andalusia (Spain) were analysed with respect to compliance with Spanish health legislation for the prevention of legionellosis. The chi-square test was used to explain the relationship between material–water and legislative compliance, and a biplot of the first two factors was generated. Multiple correspondence analysis (MCA) was performed on the type of equipment, legislative compliance, pipe material and type of water, and graphs of cases were constructed by adding confidence ellipses by categories of the variables. Pipe material–type of water (p value = 0.29; p < 0.05) and legislative compliance were not associated (p value = 0.15; p < 0.05). Iron, stainless steel, and recycled and well water contributed the most to the biplot. MCA showed a global pattern in which lead, iron and polyethylene were well represented. Confidence ellipses around categories indicated significant differences among categories. Compliance with Spanish health legislation regarding the prevention and control of legionellosis linked to pipe material and type of water was not observed.

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.

Impact of Pipe Material and Temperature on Drinking Water Microbiome and Prevalence of Legionella, Mycobacterium, and Pseudomonas Species

In drinking water distribution systems (DWDSs), pipe material and water temperature are some of the critical factors affecting the microbial flora of water. Six model DWDSs consisting of three pipe materials (galvanized steel, copper, and PEX) were constructed. The temperature in three systems was maintained at 22 °C and the other 3 at 32 °C to study microbial and elemental contaminants in a 6-week survey using 16S rRNA next-generation sequencing (NGS) and inductively coupled plasma-optical emission spectrometry (ICP-OES). Pipe material and temperature were preferentially linked with the composition of trace elements and the microbiome of the DWDSs, respectively. Proteobacteria was the most dominant phylum across all water samples ranging from 60.9% to 91.1%. Species richness (alpha diversity) ranking was PEX < steel ≤ copper system and elevated temperature resulted in decreased alpha diversity. Legionellaceae were omni-prevalent, while Mycobacteriaceae were more prevalent at 32 °C (100% vs. 58.6%) and Pseudomonadaceae at 22 °C (53.3% vs. 62.9%). Heterogeneity between communities was disproportionately driven by the pipe material and water temperature. The elevated temperature resulted in well-defined microbial clusters (high pseudo-F index) in all systems, with the highest impact in PEX (10.928) followed by copper (9.696) and steel (5.448). Legionellaceae and Mycobacteriaceae are preferentially prevalent in warmer waters. The results suggest that the water temperature has a higher magnitude of impact on the microbiome than the pipe material.

Microplastics in urban waters and its effects on microbial communities: a critical review

Microplastic (MP) pollution is one of the emerging threats to the water and terrestrial environment, forcing a new environmental challenge due to the growing trend of plastic released into the environment. Synthetic and non-synthetic plastic components can be found in rivers, lakes/reservoirs, oceans, mountains, and even remote areas, such as the Arctic and Antarctic ice sheets. MPs' main challenge is identifying, measuring, and evaluating their impacts on environmental behaviors, such as carbon and nutrient cycles, water and wastewater microbiome, and the associated side effects. However, until now, no standardized methodical protocols have been proposed for comparing the results of studies in different environments, especially in urban water and wastewater. This review briefly discusses MPs' sources, fate, and transport in urban waters and explains methodological uncertainty. The effects of MPs on urban water microbiomes, including urban runoff, sewage wastewater, stagnant water in plumbing networks, etc., are also examined in depth. Furthermore, this study highlights the pathway of MPs and their transport vectors to different parts of ecosystems and human life, particularly through mediating microbial communities, antibiotic-resistant genes, and biogeochemical cycles. Overall, we have briefly highlighted the present research gaps, the lack of appropriate policy for evaluating microplastics and their interactions with urban water microbiomes, and possible future initiatives.

Stagnation trigger changes to tap water quality in winter season: Novel insights into bacterial community activity and composition

The drinking water distribution system is important for water supply and it affects the quality of the drinking water. Indoor pipeline water quality is regulated by physical, hydraulic and biological elements, such as indoor temperature and stagnation. In this work, the effects of indoor heating and overnight stagnation on the variation in bacterial community structure and the total cell count were assessed by full-length 16S rRNA gene sequencing and flow cytometry, respectively. The results exhibited that the average intact cell count was 6.99 × 10⁴ cells/mL and the low nucleic acid (LNA) bacteria was 4.48 × 10⁴ cells/mL after stagnation. The average concentration of total and intracellular adenosine triphosphate (ATP) was 3.64 × 10^-12 gATP/mL and 3.13 × 10^-17 gATP/cell in stagnant water, respectively. The growth of LNA cells played a crucial role in increasing ATP. The dominant phylum observed was Proteobacteria (87.21 %), followed by Actinobacteria (8.25 %). Opportunistic pathogens increased the risk of disease in stagnant water (up to 1.2-fold for Pseudomonas sp. and 5.8-fold for Mycobacterium sp.). Meanwhile, structural equation model (SEM) and redundancy analysis (RDA) also illustrated that water temperature, residual chlorine and Fe significantly affected the abundance and composition of bacterial community. Taking together, these results show response of tap water quality to overnight stagnation and indoor heating, and provide scientific basis for drinking water security management in winter season.

Keystone Taxa and Predictive Functional Analysis of Sphagnum palustre Tank Microbiomes in Erxianyan Peatland, Central China

Sphagnum is a fundamental ecosystem of engineers, including more than 300 species around the world. These species host diverse microbes, either endosymbiotic or ectosymbiotic, and are key to carbon sequestration in peatland ecosystems. However, the linkages between different types of Sphagnum and the diversity and ecological functions of Sphagnum-associated microbiomes are poorly known, and so are their joint responses to ecological functions. Here, we systematically investigated endophytes in Sphagnum palustre via next-generation sequencing (NGS) techniques in the Erxianyan peatland, central China. The total bacterial microbiome was classified into 38 phyla and 55 classes, 122 orders and 490 genera. The top 8 phyla of Proteobacteria (33.69%), Firmicutes (11.94%), Bacteroidetes (9.42%), Actinobacteria (6.53%), Planctomycetes (6.37%), Gemmatimonadetes (3.05%), Acidobacteria (5.59%) and Cyanobacteria (1.71%) occupied 78.31% of total OTUs. The core microbiome of S. palustre was mainly distributed mainly in 7 phyla, 9 classes, 15 orders, 22 families and 43 known genera. There were many differences in core microbiomes compared to those in the common higher plants. We further demonstrate that the abundant functional groups have a substantial potential for nitrogen fixation, carbon cycle, nitrate metabolism, sulfate respiration and chitinolysis. These results indicate that potential ecological function of Sphagnum palustre in peatlands is partially rooted in its microbiomes, and that incorporating into functional groups of Sphagnum-associated microbiomes can promote mechanistic understanding of Sphagnum ecology in subalpine peatlands.

Factors That Affect Legionella Positivity in Healthcare Building Water Systems from a Large, National Environmental Surveillance Initiative

Legionella growth in healthcare building water systems can result in legionellosis, making water management programs (WMPs) important for patient safety. However, knowledge is limited on Legionella prevalence in healthcare buildings. A dataset of quarterly water testing in Veterans Health Administration (VHA) healthcare buildings was used to examine national environmental Legionella prevalence from 2015 to 2018. Bayesian hierarchical logistic regression modeling assessed factors influencing Legionella positivity. The master dataset included 201,146 water samples from 814 buildings at 168 VHA campuses. Overall Legionella positivity over the 4 years decreased from 7.2 to 5.1%, with the odds of a Legionella-positive sample being 0.94 (0.90-0.97) times the odds of a positive sample in the previous quarter for the 16 quarters of the 4 year period. Positivity varied considerably more at the medical center campus level compared to regional levels or to the building level where controls are typically applied. We found higher odds of Legionella detection in older buildings (OR 0.92 [0.86-0.98] for each more recent decade of construction), in taller buildings (OR 1.20 [1.13-1.27] for each additional floor), in hot water samples (O.R. 1.21 [1.16-1.27]), and in samples with lower residual biocide concentrations. This comprehensive healthcare building review showed reduced Legionella detection in the VHA healthcare system over time. Insights into factors associated with Legionella positivity provide information for healthcare systems implementing WMPs and for organizations setting standards and regulations.

Water and biofilm in drinking water distribution systems in the Netherlands

To keep the high quality of drinking water in the future for non-chlorinated drinking water systems, knowledge about the variables that most strongly affect this quality is necessary in order to know where to focus on and possibly even change aspects of drinking water production and distribution. Therefore, the aim of this study was to investigate which variables (source of drinking water, growth potential and pipe material type) have the biggest influence on bacterial community composition and biomass concentration of drinking water and biofilm in distribution systems. Ten different distribution systems were sampled for water and biofilm, obtained from four different pipe materials, throughout the Netherlands. The distribution systems are supplied either with drinking water produced from groundwater or surface water, and differ in drinking water quality parameters such as the growth potential. We found a significant relationship for growth potential and ATP concentration in water, but for the ATP in the biofilm none of the parameters showed a significant effect. Furthermore, the source of the drinking water and the pipe material did not significantly affect the ATP concentration in water and biofilm. The bacterial composition of in both water and biofilm was significantly different between distribution systems delivering water with low and high growth potential and between drinking water produced from groundwater or surface water. In contrast, the different pipe materials did not significantly affect composition of biofilm-associated communities. We conclude from these results that the growth potential of the treated water best explains the variation in biomass and bacterial composition in water and biofilm of non-chlorinated drinking water distribution systems followed by the drinking water source, whereas pipe materials seem to be of lesser importance.

Direct evidence of microbiological water quality changes on bacterial quantity and community caused by plumbing system

Drinking water quality deteriorates from treatment plant to customer taps, especially in the plumbing system. There is no direct evidence about what the differences are contributed by plumbing system. This study compared the water quality in the water main and at customer tap by preparing a sampling tap on the water main. The biomass was quantified by adenosine triphosphate (ATP) and the microbial community was profiled by 454 pyrosequencing. The results showed that in distribution pipes, biofilm contributed >94% of the total biomass, while loose deposits showed little contribution (< 2%) because of the low amount of loose deposits. The distribution of biological stable water had minor effects on the microbiocidal water quality regarding both quantity (ATP 1 ng/L vs. 1.7 ng/L) and community of the bacteria. Whereas the plumbing system has significant contribution to the increase of active biomass (1.7 ng/L vs. 2.9 ng/L) and the changes of bacterial community. The relative abundance of Sphingomonas spp. at tap (22%) was higher than that at water main (2%), while the relative abundance of Pseudomonas spp. in tap water (15%) was lower than that in the water from street water main (29%). Though only one location was prepared and studied, the present study showed that the protocol of making sampling tap on water main offered directly evidences about the impacts of plumbing system on tap water quality, which makes it possible to distinguish and study the processes in distribution system and plumbing system separately.

Influence of Metal Concentration and Plumbing Materials on Legionella Contamination

Legionella colonization of water supply pipes is a significant public health problem. The objective of this work was to evaluate Legionella colonization in hotel hot water systems and to investigate the relationship between metal concentrations, piping materials (galvanized iron pipes and plastic pipes), and Legionella proliferation. Concentrations of calcium and magnesium ions and the presence of Legionella pneumophila were determined in a total of 108 water samples from the hot water systems of four hotels in Split-Dalmatia County over a 12-month period, and additional data on piping materials were collected. L. pneumophila was isolated in 23.1% of all samples-in 28.8% (15/52) of water samples from galvanized iron pipes and in 17.8% (10/56) of samples from plastic pipes. L. pneumophila serogroups 2-14 were isolated from all samples. This study found higher prevalence of L. pneumophila at higher concentrations of Ca and Mg ions (except for Mg and plastic pipes). The metal parts of the water supply may be important factors in Legionella contamination due to the possibility of lime scale or roughness of the pipes. Higher Ca and Mg ion concentrations increased the risk of Legionella colonization.

Variation in the Structure and Composition of Bacterial Communities within Drinking Water Fountains in Melbourne, Australia

Modern drinking water distributions systems (DWDSs) have been designed to transport treated or untreated water safely to the consumer. DWDSs are complex environments where microorganisms are able to create their own niches within water, biofilm or sediment. This study was conducted on twelve drinking fountains (of three different types, namely types A, B and C) within the Melbourne (Australia) city area with the aim to (i) characterize the water quality and viable and total counts at each fountain, (ii) compare the differences in the structure and diversity of the bacterial community between bulk water and biofilm and (iii) determine differences between the bacterial communities based on fountain type. Samples of water and biofilm were assessed using both culture-dependent and culture-independent techniques. Heterotrophic plate counts of water samples ranged from 0.5 to 107.5 CFU mL−1, and as expected, total cell counts (cells mL−1) were, on average, 2.9 orders of magnitude higher. Based on the mean relative abundance of operational taxonomic units (OTUs), ANOSIM showed that the structure of the bacterial communities in drinking water and biofilm varied significantly (R = 0.58, p = 0.001). Additionally, ANOSIM showed that across fountain types (in water), the bacterial community was more diverse in fountain type C compared to type A (p < 0.001) and type B (p < 0.001). 16S rRNA next-generation sequencing revealed that the bacterial communities in both water and biofilm were dominated by only seven phyla, with Proteobacteria accounting for 71.3% of reads in water and 68.9% in biofilm. The next most abundant phylum was Actinobacteria (10.4% water; 11.7% biofilm). In water, the genus with the highest overall mean relative abundance was Sphingomonas (24.2%), while Methylobacterium had the highest mean relative abundance in biofilm samples (54.7%). At the level of genus and higher, significant differences in dominance were found across fountain types. In water, Solirubrobacterales (order) were present in type C fountains at a relative abundance of 17%, while the mean relative abundance of Sphingomonas sp. in type C fountains was less than half that in types A (25%) and B (43%). In biofilm, the relative abundance of Sphingomonas sp. was more than double in type A (10%) fountains compared to types B (4%) and C (5%), and Sandarakinorhabdus sp. were high in type A fountains (6%) and low in types B and C (1%). Overall this research showed that there were significant differences in the composition of bacterial communities in water and biofilm from the same site. Furthermore, significant variation exists between microbial communities present in the fountain types, which may be related to age. Long-established environments may lead to a greater chance of certain bacteria gaining abilities such as increased disinfection resistance. Variations between the structure of the bacterial community residing in water and biofilm and differences between fountain types show that it is essential to regularly test samples from individual locations to determine microbial quality.

Microbiome differential abundance methods produce different results across 38 datasets

Identifying differentially abundant microbes is a common goal of microbiome studies. Multiple methods are used interchangeably for this purpose in the literature. Yet, there are few large-scale studies systematically exploring the appropriateness of using these tools interchangeably, and the scale and significance of the differences between them. Here, we compare the performance of 14 differential abundance testing methods on 38 16S rRNA gene datasets with two sample groups. We test for differences in amplicon sequence variants and operational taxonomic units (ASVs) between these groups. Our findings confirm that these tools identified drastically different numbers and sets of significant ASVs, and that results depend on data pre-processing. For many tools the number of features identified correlate with aspects of the data, such as sample size, sequencing depth, and effect size of community differences. ALDEx2 and ANCOM-II produce the most consistent results across studies and agree best with the intersect of results from different approaches. Nevertheless, we recommend that researchers should use a consensus approach based on multiple differential abundance methods to help ensure robust biological interpretations.

Many microbiome differential abundance methods are available, but it lacks systematic comparison among them. Here, the authors compare the performance of 14 differential abundance testing methods on 38 16S rRNA gene datasets with two sample groups, and show ALDEx2 and ANCOM-II produce the most consistent results.

The Impact of Pipe Material on the Diversity of Microbial Communities in Drinking Water Distribution Systems

As many cities around the world face the prospect of replacing aging drinking water distribution systems (DWDS), water utilities must make careful decisions on new pipe material (e.g., cement-lined or PVC) for these systems. These decisions are informed by cost, physical integrity, and impact on microbiological and physicochemical water quality. Indeed, pipe material can impact the development of biofilm in DWDS that can harbor pathogens and impact drinking water quality. Annular reactors (ARs) with cast iron and cement coupons fed with chloraminated water from a municipal DWDS were used to investigate the impact of pipe material on biofilm development and composition over 16 months. The ARs were plumbed as closely as possible to the water main in the basement of an academic building to simulate distribution system conditions. Biofilm communities on coupons were characterized using 16S rRNA sequencing. In the cast iron reactors, β-proteobacteria, Actinobacteria, and α-proteobacteria were similarly relatively abundant (24.1, 22.5, and 22.4%, respectively) while in the cement reactors, α-proteobacteria and Actinobacteria were more relatively abundant (36.3 and 35.2%, respectively) compared to β-proteobacteria (12.8%). Mean alpha diversity (estimated with Shannon H and Faith's Phylogenetic Difference indices) was greater in cast iron reactors (Shannon: 5.00 ± 0.41; Faith's PD: 15.40 ± 2.88) than in cement reactors (Shannon: 4.16 ± 0.78; Faith's PD: 13.00 ± 2.01). PCoA of Bray-Curtis dissimilarities indicated that communities in cast iron ARs, cement ARs, bulk distribution system water, and distribution system pipe biofilm were distinct. The mean relative abundance of Mycobacterium spp. was greater in the cement reactors (34.8 ± 18.6%) than in the cast iron reactors (21.7 ± 11.9%). In contrast, the mean relative abundance of Legionella spp. trended higher in biofilm from cast iron reactors (0.5 ± 0.7%) than biofilm in cement reactors (0.01 ± 0.01%). These results suggest that pipe material is associated with differences in the diversity, bacterial composition, and opportunistic pathogen prevalence in biofilm of DWDS.

Human- and infrastructure-associated bacteria in greywater

Greywater, the wastewater from sinks, showers and laundry, is an understudied environment for bacterial communities. Most greywater studies focus on quantifying pathogens, often via proxies used in other wastewater, like faecal indicator bacteria; there is a need to identify more greywater-appropriate surrogates, like Staphylococcus sp. Sequencing-based studies have revealed distinct communities in different types of greywater as well as in different parts of greywater infrastructure, including biofilms on pipes, holding tanks and filtration systems. The use of metagenomic sequencing provides high resolution on both the taxa and genes present, which may be of interest in cases like identifying pathogens and surrogates relevant to different matrices, monitoring antibiotic resistance genes and understanding metabolic processes occurring in the system. Here, we review what is known about bacterial communities in different types of greywater and its infrastructure. We suggest that wider adoption of environmental sequencing in greywater research is important because it can describe the entire bacterial community along with its metabolic capabilities, including pathways for removal of nutrients and organic materials. We briefly describe a metagenomic dataset comparing different types of greywater samples in a college dormitory building to highlight the type of questions these methods can address. Metagenomic sequencing can help further the understanding of greywater treatment for reuse because it allows for identification of new pathogens or genes of concern.

Bacterial Community Analysis and Potential Functions of Core Taxa in Different Parts of the Fungus Cantharellus cibarius

Cantharellus cibarius is a widely distributed, popular, edible fungus with high nutritional and economic value. However, significant challenges persist in the microbial ecology and artificial cultivation of C. cibarius. Based on the 16S rRNA sequencing data, this study analyzed bacterial community structures and diversity of fruit bodies and rhizomorph parts of C. cibarius and mycosphere samples (collected in the Wudang District, Guiyang, Guizhou Province, China). It explored the composition and function of the core bacterial taxa. The analyzed results showed that the rhizomorph bacterial community structure was similar to mycosphere, but differed from the fruit bodies. Members of the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium complex had the highest abundance in the fruit bodies. However, they were either absent or low in abundance in the rhizomorphs and mycosphere. At the same time, members of the Burkholderia-Caballeronia-Paraburkholderia complex were abundant in the fruit bodies and rhizomorphs parts of C. cibarius, as well as mycosphere. Through functional annotation of core bacterial taxa, we found that there was an apparent trend of potential functional differentiation of related bacterial communities in the fruit body and rhizomorph: potential functional groups of core bacterial taxa in the fruit bodies centered on nitrogen fixation, nitrogen metabolism, and degradation of aromatic compounds, while those in rhizomorphs focused on aerobic chemoheterotrophy, chemoheterotrophy, defense against soil pathogens, decomposition of complex organic compounds, and uptake of insoluble inorganic compounds. The analysis of functional groups of bacteria with different structures is of great significance to understand that bacteria promote the growth and development of C. cibarius.

Microbial diversity in full-scale water supply systems through sequencing technology: a review

The prevalence of microorganisms in full-scale water supply systems raises concerns about their pathogenicity and threats to public health. Clean tap water is essential for public health safety. The conditions of the water treatment process from the source water to tap water, including source water quality, water treatment processes, the drinking water distribution system (DWDS), and building water supply systems (BWSSs) in buildings, greatly influence the bacterial community in tap water. Given the importance of drinking water biosafety, the study of microbial diversity from source water to tap water is essential. With the development of molecular biology methods and bioinformatics in recent years, sequencing technology has been applied to study bacterial communities in full-scale water supply systems. In this paper, changes in the bacterial community and the influence of each treatment stage on microbial diversity in full-scale water supply systems are classified and analyzed. Microbial traceability analysis and control are discussed, and suggestions for future drinking water biosafety research and its prospects are proposed.

Evaluation of DNA extraction yield from a chlorinated drinking water distribution system

Desalination technology based on Reverse Osmosis (RO) membrane filtration has been resorted to provide high-quality drinking water. RO produced drinking water is characterized by a low bacterial cell concentration. Monitoring microbial quality and ensuring membrane-treated water safety has taken advantage of the rapid development of DNA-based techniques. However, the DNA extraction process from RO-based drinking water samples needs to be evaluated regarding the biomass amount (filtration volume) and residual disinfectant such as chlorine, as it can affect the DNA yield. We assessed the DNA recovery applied in drinking water microbiome studies as a function of (i) different filtration volumes, (ii) presence and absence of residual chlorine, and (iii) the addition of a known Escherichia coli concentration into the (sterile and non-sterile, chlorinated and dechlorinated) tap water prior filtration, and directly onto the (0.2 μm pore size, 47 mm diameter) mixed ester cellulose membrane filters without and after tap water filtration. Our findings demonstrated that the co-occurrence of residual chlorine and low biomass/cell density water samples (RO-treated water with a total cell concentration ranging between 2.47 × 102-1.5 × 103 cells/mL) failed to provide sufficient DNA quantity (below the threshold concentration required for sequencing-based procedures) irrespective of filtration volumes used (4, 20, 40, 60 L) and even after performing dechlorination. After exposure to tap water containing residual chlorine (0.2 mg/L), we observed a significant reduction of E. coli cell concentration and the degradation of its DNA (DNA yield was below detection limit) at a lower disinfectant level compared to what was previously reported, indicating that free-living bacteria and their DNA present in the drinking water are subject to the same conditions. The membrane spiking experiment confirmed no significant impact from any potential inhibitors (e.g. organic/inorganic components) present in the drinking water matrix on DNA extraction yield. We found that very low DNA content is likely to be the norm in chlorinated drinking water that gives hindsight to its limitation in providing robust results for any downstream molecular analyses for microbiome surveys. We advise that measurement of DNA yield is a necessary first step in chlorinated drinking water distribution systems (DWDSs) before conducting any downstream omics analyses such as amplicon sequencing to avoid inaccurate interpretations of results based on very low DNA content. This study expands a substantial source of bias in using DNA-based methods for low biomass samples typical in chlorinated DWDSs. Suggestions are provided for DNA-based research in drinking water with residual disinfectant.

Bacterial Communities in Concrete Reflect Its Composite Nature and Change with Weathering

Concrete is an extreme but common environment and is home to microbial communities adapted to alkaline, saline, and oligotrophic conditions. Microbes inside the concrete that makes up buildings or roads have received little attention despite their ubiquity and capacity to interact with the concrete. Because concrete is a composite of materials which have their own microbial communities, we hypothesized that the microbial communities of concrete reflect those of the concrete components and that these communities change as the concrete ages. Here, we used a 16S amplicon study to show how microbial communities change over 2 years of outdoor weathering in two sets of concrete cylinders, one prone to the concrete-degrading alkali-silica reaction (ASR) and the other having the risk of the ASR mitigated. After identifying and removing taxa that were likely laboratory or reagent contaminants, we found that precursor materials, particularly the large aggregate (gravel), were the probable source of ∼50 to 60% of the bacteria observed in the first cylinders from each series. Overall, community diversity decreased over 2 years, with temporarily increased diversity in warmer summer months. We found that most of the concrete microbiome was composed of Proteobacteria, Firmicutes, and Actinobacteria, although community composition changed seasonally and over multiyear time scales and was likely influenced by environmental deposition. Although the community composition between the two series was not significantly different overall, several taxa, including Arcobacter, Modestobacter, Salinicoccus, Rheinheimera, Lawsonella, and Bryobacter, appear to be associated with ASR.

IMPORTANCE Concrete is the most-used building material in the world and a biologically extreme environment, with a microbiome composed of bacteria that likely come from concrete precursor materials, aerosols, and environmental deposition. These microbes, though seeded from a variety of materials, are all subject to desiccation, heating, starvation, high salinity, and very high pH. Microbes that survive and even thrive under these conditions can potentially either degrade concrete or contribute to its repair. Thus, understanding which microbes survive in concrete, under what conditions, and for how long has potential implications for biorepair of concrete. Further, methodological pipelines for analyzing concrete microbial communities can be applied to concrete from a variety of structures or with different types of damage to identify bioindicator species that can be used for structural health monitoring and service life prediction.

Next generation sequencing approaches to evaluate water and wastewater quality

The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.

Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health

Aquatic ecosystems are under increasing stress from global anthropogenic and natural changes, including climate change, eutrophication, ocean acidification, and pollution. In this critical review, we synthesize research on the microbiota of aquatic vertebrates and discuss the impact of emerging stressors on aquatic microbial communities using two case studies, that of toxic cyanobacteria and microplastics. Most studies to date are focused on host-associated microbiomes of individual organisms, however, few studies take an integrative approach to examine aquatic vertebrate microbiomes by considering both host-associated and free-living microbiota within an ecosystem. We highlight what is known about microbiota in aquatic ecosystems, with a focus on the interface between water, fish, and marine mammals. Though microbiomes in water vary with geography, temperature, depth, and other factors, core microbial functions such as primary production, nitrogen cycling, and nutrient metabolism are often conserved across aquatic environments. We outline knowledge on the composition and function of tissue-specific microbiomes in fish and marine mammals and discuss the environmental factors influencing their structure. The microbiota of aquatic mammals and fish are highly unique to species and a delicate balance between respiratory, skin, and gastrointestinal microbiota exists within the host. In aquatic vertebrates, water conditions and ecological niche are driving factors behind microbial composition and function. We also generate a comprehensive catalog of marine mammal and fish microbial genera, revealing commonalities in composition and function among aquatic species, and discuss the potential use of microbiomes as indicators of health and ecological status of aquatic ecosystems. We also discuss the importance of a focus on the functional relevance of microbial communities in relation to organism physiology and their ability to overcome stressors related to global change. Understanding the dynamic relationship between aquatic microbiota and the animals they colonize is critical for monitoring water quality and population health.

Indoor heating triggers bacterial ecological links with tap water stagnation during winter: Novel insights into bacterial abundance, community metabolic activity and interactions

The overnight stagnation of tap water in plumbing systems can lead to water quality deterioration. Meanwhile, the indoor heating can improve the indoor temperature in cold areas during winter, which may affect the quality of tap water during stagnation. However, indoor heating drives bacterial ecological links with tap water stagnation during winter are not well understood. The results indicated that the water temperature increased significantly after stagnation during indoor heating periods. Moreover, the average intact cell number and total adenosine triphosphate (ATP) concentration increased 1.53-fold and 1.35-fold after stagnation, respectively (P < 0.01). In addition, the increase in the ATP per cell number indicated that the combined effects of stagnation and indoor heating could enhance the bacterial activity. Biolog data showed that the bacterial community metabolic capacity was significantly higher in stagnant water than that of fresh water. Co-occurrence networks suggested that the bacterial metabolic profile changed after stagnation during the heating periods. DNA analysis indicated that the composition of the bacterial community changed dramatically after stagnation. The abundances of potential pathogens such as Mycobacterium sp. and Pseudomonas sp. also increased after stagnation. These results will give novel insights on comprehensive understanding the combined effects of indoor heating and overnight stagnation on the water bacterial community ecology of plumbing systems, and provide a scientific basis for tap water quality management after overnight stagnation during the indoor heating periods.

Flushing of Stagnant Premise Water Systems after the COVID-19 Shutdown Can Reduce Infection Risk by Legionella and Mycobacterium spp

There is concern about potential exposure to opportunistic pathogens when reopening buildings closed due to the COVID-19 pandemic. In this study, water samples were collected before, during, and after flushing showers in five unoccupied (i.e., for ∼2 months) university buildings with quantification of opportunists via a cultivation-based assay (Legionella pneumophila only) and quantitative PCR. L. pneumophila were not detected by either method; Legionella spp., nontuberculous mycobacteria (NTM), and Mycobacterium avium complex (MAC), however, were widespread. Using quantitative microbial risk assessment (QMRA), the estimated risks of illness from exposure to L. pneumophila and MAC via showering were generally low (i.e., less than a 10^-7 daily risk threshold), with the exception of systemic infection risk from MAC exposure in some buildings. Flushing rapidly restored the total chlorine (as chloramine) residual and decreased bacterial gene targets to building inlet concentrations within 30 min. During the postflush stagnation period, the residual chlorine dissipated within a few days and bacteria rebounded, approaching preflush concentrations after 6-7 days. These results suggest that flushing can quickly improve water quality in unoccupied buildings, but the improvement may only last a few days.

Critical Review: Propensity of Premise Plumbing Pipe Materials to Enhance or Diminish Growth of Legionella and Other Opportunistic Pathogens

Growth of Legionella pneumophila and other opportunistic pathogens (OPs) in drinking water premise plumbing poses an increasing public health concern. Premise plumbing is constructed of a variety of materials, creating complex environments that vary chemically, microbiologically, spatially, and temporally in a manner likely to influence survival and growth of OPs. Here we systematically review the literature to critically examine the varied effects of common metallic (copper, iron) and plastic (PVC, cross-linked polyethylene (PEX)) pipe materials on factors influencing OP growth in drinking water, including nutrient availability, disinfectant levels, and the composition of the broader microbiome. Plastic pipes can leach organic carbon, but demonstrate a lower disinfectant demand and fewer water chemistry interactions. Iron pipes may provide OPs with nutrients directly or indirectly, exhibiting a high disinfectant demand and potential to form scales with high surface areas suitable for biofilm colonization. While copper pipes are known for their antimicrobial properties, evidence of their efficacy for OP control is inconsistent. Under some circumstances, copper's interactions with premise plumbing water chemistry and resident microbes can encourage growth of OPs. Plumbing design, configuration, and operation can be manipulated to control such interactions and health outcomes. Influences of pipe materials on OP physiology should also be considered, including the possibility of influencing virulence and antibiotic resistance. In conclusion, all known pipe materials have a potential to either stimulate or inhibit OP growth, depending on the circumstances. This review delineates some of these circumstances and informs future research and guidance towards effective deployment of pipe materials for control of OPs.

Monitoring of Nitrification in Chloraminated Drinking Water Distribution Systems With Microbiome Bioindicators Using Supervised Machine Learning

Many drinking water utilities in the United States using chloramine as disinfectant treatment in their drinking water distribution systems (DWDS) have experienced nitrification episodes, which detrimentally impact the water quality. Identification of potential predictors of nitrification in DWDS may be used to optimize current nitrification monitoring plans and ultimately helps to safeguard drinking water and public health. In this study, we explored the water microbiome from a chloraminated DWDS simulator operated through successive operational schemes of stable and nitrification events and utilized the 16S rRNA gene dataset to generate high-resolution taxonomic profiles for bioindicator discovery. Analysis of the microbiome revealed both an enrichment and depletion of various bacterial populations associated with nitrification. A supervised machine learning approach (naïve Bayes classifier) trained with bioindicator profiles (membership and structure) were used to classify water samples. Performance of each model was examined using the area under the curve (AUC) from the receiver-operating characteristic (ROC) and precision-recall (PR) curves. The ROC- and PR-AUC gradually increased to 0.778 and 0.775 when genus-level membership (i.e., presence and absence) was used in the model and increased significantly using structure (i.e., distribution) dataset (AUCs = 1.000, p < 0.01). Community structure significantly improved the predictive ability of the model beyond that of membership only regardless of the type of data (sequence- or taxonomy-based model) we used to represent the microbiome. In comparison, an ATP-based model (bulk biomass) generated a lower AUCs of 0.477 and 0.553 (ROC and PR, respectively), which is equivalent to a random classification. A combination of eight bioindicators was able to correctly classify 85% of instances (nitrification or stable events) with an AUC of 0.825 (sensitivity: 0.729, specificity: 0.894) on a full-scale DWDS test set. Abiotic-based model using total Chlorine/NH₂Cl and NH₃ generated AUCs of 0.740 and 0.861 (ROC and PR, respectively), corresponding to a sensitivity of 0.250 and a specificity of 0.957. The AUCs increased to > 0.946 with the addition of NO₂^– concentration, which is indicative of nitrification in the DWDS. This research provides evidence of the feasibility of using bioindicators to predict operational failures in the system (e.g., nitrification).

Replicable simulation of distal hot water premise plumbing using convectively-mixed pipe reactors

A lack of replicable test systems that realistically simulate hot water premise plumbing conditions at the laboratory-scale is an obstacle to identifying key factors that support growth of opportunistic pathogens (OPs) and opportunities to stem disease transmission. Here we developed the convectively-mixed pipe reactor (CMPR) as a simple reproducible system, consisting of off-the-shelf plumbing materials, that self-mixes through natural convective currents and enables testing of multiple, replicated, and realistic premise plumbing conditions in parallel. A 10-week validation study was conducted, comparing three pipe materials (PVC, PVC-copper, and PVC-iron; n = 18 each) to stagnant control pipes without convective mixing (n = 3 each). Replicate CMPRs were found to yield consistent water chemistry as a function of pipe material, with differences becoming less discernable by week 9. Temperature, an overarching factor known to control OP growth, was consistently maintained across all 54 CMPRs, with a coefficient of variation <2%. Dissolved oxygen (DO) remained lower in PVC-iron (1.96 ± 0.29 mg/L) than in PVC (5.71 ± 0.22 mg/L) or PVC-copper (5.90 ± 0.38 mg/L) CMPRs as expected due to corrosion. Further, DO in PVC-iron CMPRs was 33% of that observed in corresponding stagnant pipes (6.03 ± 0.33 mg/L), demonstrating the important role of internal convective mixing in stimulating corrosion and microbiological respiration. 16S rRNA gene amplicon sequencing indicated that both bulk water (P_adonis = 0.001, R² = 0.222, P_betadis = 0.785) and biofilm (P_adonis = 0.001, R² = 0.119, P_betadis = 0.827) microbial communities differed between CMPR versus stagnant pipes, consistent with creation of a distinct ecological niche. Overall, CMPRs can provide a more realistic simulation of certain aspects of premise plumbing than reactors commonly applied in prior research, at a fraction of the cost, space, and water demand of large pilot-scale rigs.

Interactive Effects of Copper Pipe, Stagnation, Corrosion Control, and Disinfectant Residual Influenced Reduction of Legionella pneumophila during Simulations of the Flint Water Crisis

Flint, MI experienced two outbreaks of Legionnaires' Disease (LD) during the summers of 2014 and 2015, coinciding with use of Flint River as a drinking water source without corrosion control. Using simulated distribution systems (SDSs) followed by stagnant simulated premise (i.e., building) plumbing reactors (SPPRs) containing cross-linked polyethylene (PEX) or copper pipe, we reproduced trends in water chemistry and Legionella proliferation observed in the field when Flint River versus Detroit water were used before, during, and after the outbreak. Specifically, due to high chlorine demand in the SDSs, SPPRs with treated Flint River water were chlorine deficient and had elevated L. pneumophila numbers in the PEX condition. SPPRs with Detroit water, which had lower chlorine demand and higher residual chlorine, lost all culturable L. pneumophila within two months. L. pneumophila also diminished more rapidly with time in Flint River SPPRs with copper pipe, presumably due to the bacteriostatic properties of elevated copper concentrations caused by lack of corrosion control and stagnation. This study confirms hypothesized mechanisms by which the switch in water chemistry, pipe materials, and different flow patterns in Flint premise plumbing may have contributed to observed LD outbreak patterns.

Microbial contamination in distributed drinking water purifiers induced by water stagnation

Small-scale distributed water purifiers (SSDWPs), providing better quality drinking water, are popularly used both in homes and in the public domain. Non-continuous operation leads to water stagnation and ultimately induces microbial contamination. However, information related to such contamination in these purifiers is reported scarcely. In the present study, an SSDWP, consisting of sand filtration (SF), granular activated carbon (GAC), and ultrafiltration (UF) processes, was established to explore microbial changes induced by water stagnation, based on the aspects of bacterial count, microbial size, microbiome and pathogenic communities. Our results primary showed that: first, compared with drinking water distribution system (DWDS), bacterial counts increased more rapidly in SSDWPs, growing to > 500 cfu/mL after 2.5 h stagnation. The proportion of intact cells also increased with stagnation time. Conversely, microbial size decreased with stagnation time according to changes in forward scatter detected using flow cytometry. Second, microbiome evolution followed the isolated island model, while in stagnated DWDS, microbiome evolved according to the continent island model, and the former had higher abundance of biodiversity. Furthermore, stagnation evidently caused microbiome changes in each unit, and spatial differences contributed to microbiome dissimilarity more significantly than temporal differences. Third, Mycobacterium was the dominant pathogenic genus in the SF and GAC units while Acinetobacter was the most abundant in the UF unit. Pathogenic risks increased with water stagnation time and lower nutrients level contributed to pathogenic community richness. Therefore, terminal disinfection of SSDWPs is strongly advised.

Characterization of the core microbiome in tobacco leaves during aging

Microbiome plays an important role during the tobacco aging process which was an indispensable link in the production and processing of cigarettes. However, the structure and functions of microbiome have not been clarified during the tobacco aging process. In this study, 16S rDNA and ITS amplicon sequencing techniques were used to analyze the core microbiome of 15 tobacco samples from five different aging stages. The whole bacterial microbiome was classified into 29 microbial phyla and 132 orders. Enterobacteriales (63%), Pseudomonadales (16%), Sphingomonadales (8%), Xanthomonadales (4%), Burkholderiales (4%), Rhizobiales (3%), and Bacillales (2%) comprised the core bacterial microbiome. The whole fungal microbiome was classified into five microbial phyla and 52 orders. Incertae_sedis_Eurotiomycetes (27%), Wallemiales (25%), Sporidiobolales (17%), Capnodiales (5%), Eurotiales (2%), an unclassified Ascomycota (12%), and an unidentified Eurotiomycetes (4%) comprised the core fungal microbiome. FAPROTAX function prediction suggested that the core microbiome has a substantial potential for the carbon cycle, nitrate metabolism, aromatic compound degradation, chitinolysis, cellulolysis, and xylanolysis, but simultaneously, the core microbiome is also a source of human pathogens. The dynamics of the bacterial community were primarily determined by the total nitrogen in tobacco leaves during the aging process, while those of the fungal microbiome were primarily determined by total organic carbon. This study indicated that the core microbiome activities may play an important role in regulating the loss of carbon organic compounds and enhancing the secondary metabolites during tobacco leaves aging process.

Presence of Legionella spp. in cooling towers: the role of microbial diversity, Pseudomonas, and continuous chlorine application

Legionnaires' disease (LD) is a severe pneumonia caused by several species of the genus Legionella, most frequently by Legionella pneumophila. Cooling towers are the most common source for large community-associated outbreaks. Colonization, survival, and proliferation of L. pneumophila in cooling towers are necessary for outbreaks to occur. These steps are affected by the chemical and physical parameters of the cooling tower environment. We hypothesize that the bacterial community residing in the cooling tower could also affect the presence of L. pneumophila. A 16S rRNA gene targeted amplicon sequencing approach was used to study the bacterial community of cooling towers and its relationship with the Legionella spp. and L. pneumophila communities. The results indicated that the water source shaped the bacterial community of cooling towers. Several taxa were enriched and positively correlated with Legionella spp. and L. pneumophila. In contrast, Pseudomonas showed a strong negative correlation with Legionella spp. and several other genera. Most importantly, continuous chlorine application reduced microbial diversity and promoted the presence of Pseudomonas creating a non-permissive environment for Legionella spp. This suggests that disinfection strategies as well as the resident microbial population influences the ability of Legionella spp. to colonize cooling towers.

Linking Microbial Community Composition in Treated Wastewater with Water Quality in Distribution Systems and Subsequent Health Effects

The increases in per capita water consumption, coupled in part with global climate change have resulted in increased demands on available freshwater resources. Therefore, the availability of safe, pathogen-free drinking water is vital to public health. This need has resulted in global initiatives to develop sustainable urban water infrastructure for the treatment of wastewater for different purposes such as reuse water for irrigation, and advanced waste water purification systems for domestic water supply. In developed countries, most of the water goes through primary, secondary, and tertiary treatments combined with disinfectant, microfiltration (MF), reverse osmosis (RO), etc. to produce potable water. During this process the total bacterial load of the water at different stages of the treatment will decrease significantly from the source water. Microbial diversity and load may decrease by several orders of magnitude after microfiltration and reverse osmosis treatment and falling to almost non-detectable levels in some of the most managed wastewater treatment facilities. However, one thing in common with the different end users is that the water goes through massive distribution systems, and the pipes in the distribution lines may be contaminated with diverse microbes that inhabit these systems. In the main distribution lines, microbes survive within biofilms which may contain opportunistic pathogens. This review highlights the role of microbial community composition in the final effluent treated wastewater, biofilms formation in the distribution systems as the treated water goes through, and the subsequent health effects from potential pathogens associated with poorly treated water. We conclude by pointing out some basic steps that may be taken to reduce the accumulation of biofilms in the water distribution systems.

Composition and Dynamics of Bacterial Communities in a Full-Scale Mineral Water Treatment Plant

The aim of this study was to gain insight into the bacterial composition and dynamics in a mineral water treatment system (MWTS). The bacterial community of a full-scale mineral water treatment plant in the Maofeng Mountain, South China, was studied using high-throughput sequencing combined with cultivation-based techniques in both the dry and wet season. Overall, adenosine tri-phosphate (ATP) concentration (6.47 × 10^-11 – 3.32 × 10^-8 M) and heterotrophic plate counts (HPC) (3 – 1.29 × 10³ CFU/mL) of water samples in the wet season were lower than those (ATP concentration 5.10 × 10^-11 – 6.96 × 10^-8 M, HPC 2 – 1.97 × 10³ CFU/mL) in the dry season throughout the whole MWTS. The microbial activity and biomass of water samples obviously changed along with treatment process. All 300 isolates obtained using cultivation-based techniques were distributed in 5 phyla, 7 classes, and 19 genera. Proteobacteria accounted for 55.7% (167) of the total isolates, among which predominant genus was Pseudomonas (19.3%). Illumina sequencing analysis of 16s rRNA genes revealed 15 bacterial phyla (relative abundance >0.1%) as being identified in all water samples. Among these, Proteobacteria constituted the dominant bacteria microbiota in all water samples. A large shift in the proportion of Bacteroidetes, Actinobacteria, and Firmicutes was obtained during the treatment process, with the proportion of Bacteroidetes, Actinobacteria decreasing sharply, whereas that of Firmicutes increased and predominated in the final water product. The core microbiome, which was still present in whole MWTS comprised several genera including Pseudomonas, Acinetobacter, Clostridium, and Mycobacterium, that contain species that are opportunistic pathogens, suggesting a potential threat for mineral water microbiology safety. This study is the first to investigate the bacterial community of a full-scale mineral water treatment plant in China. The results provided data regarding the bacteria composition and dynamics in an MWTS, which will contribute to the beneficial manipulation of the mineral water microbiome.

Active eukaryotes in drinking water distribution systems of ground and surface waterworks

BACKGROUND

Eukaryotes are ubiquitous in natural environments such as soil and freshwater. Little is known of their presence in drinking water distribution systems (DWDSs) or of the environmental conditions that affect their activity and survival.

METHODS

Eukaryotes were characterized by Illumina high-throughput sequencing targeting 18S rRNA gene (DNA) that estimates the total community and the 18S rRNA gene transcript (RNA) that is more representative of the active part of the community. DWDS cold water (N = 124), hot water (N = 40), and biofilm (N = 16) samples were collected from four cities in Finland. The sampled DWDSs were from two waterworks A-B with non-disinfected, recharged groundwater as source water and from three waterworks utilizing chlorinated water (two DWDSs of surface waterworks C-D and one of ground waterworks E). In each DWDS, samples were collected from three locations during four seasons of 1 year.

RESULTS

A beta-diversity analysis revealed that the main driver shaping the eukaryotic communities was the DWDS (A-E) (R = 0.73, P < 0.001, ANOSIM). The kingdoms Chloroplastida (green plants and algae), Metazoa (animals: rotifers, nematodes), Fungi (e.g., Cryptomycota), Alveolata (ciliates, dinoflagellates), and Stramenopiles (algae Ochrophyta) were well represented and active-judging based on the rRNA gene transcripts-depending on the surrounding conditions. The unchlorinated cold water of systems (A-B) contained a higher estimated total number of taxa (Chao1, average 380-480) than chlorinated cold water in systems C-E (Chao1 ≤ 210). Within each DWDS, unique eukaryotic communities were identified at different locations as was the case also for cold water, hot water, and biofilms. A season did not have a consistent impact on the eukaryotic community among DWDSs.

CONCLUSIONS

This study comprehensively characterized the eukaryotic community members within the DWDS of well-maintained ground and surface waterworks providing good quality water. The study gives an indication that each DWDS houses a unique eukaryotic community, mainly dependent on the raw water source and water treatment processes in place at the corresponding waterworks. In particular, disinfection as well as hot water temperature seemed to represent a strong selection pressure that controlled the number of active eukaryotic species.

Dynamics of the physiochemical and community structures of biofilms under the influence of algal organic matter and humic substances

Increased loading of algal organic matter (AOM) during harmful algal blooms not only burdens water treatment processes but also challenges safe drinking water delivery. While organic constituents promote biofilm growth in drinking water distribution systems (DWDS), the effects of AOM on biofilm formation in DWDS are not well understood. Herein, three parallel biofilm reactors were used to assess and compare how treated AOM- and humic substance (HS)-impacted bulk water, and R2A medium (a control) affect biofilm development for 168 days. The 16S rRNA gene sequencing analysis revealed that the bacterial communities in biofilms were clustered with the organic matter types in bulk water, where Family Comamonadaceae was the most dominant but showed different temporal dynamics depending on the organic matter characteristics in bulk water. Higher diversity was observed in the biofilms grown in AOM-impacted bulk water (BFAOM) than biofilms grown in HS-impacted (BFHS) and R2A-impacted bulk water (BFR2A) as the biofilms matured. In addition, some taxa (e.g., Rhodobacteraceae and Sphingomonadaceae) were enriched in BFAOM compared to BFHS and BFR2A. The biofilm image analysis results indicated that compared to BFHS, BFAOM and BFR2A had relatively thinner and heterogeneous physical structures with lower amounts of cell biomass, extracellular polymeric substances (EPS), and higher EPS protein/polysaccharide ratios. Overall, this study revealed how AOM- and HS-impacted bulk water shape the physiochemical and community structures of biofilms, which can provide insights into assessing biofilm-associated risks and optimizing disinfection practices for biofilm control in DWDS.

mSphere of Influence: Engineering Microbes

Patrick J. McNamara works in the field of environmental engineering. In this mSphere of Influence article, he reflects on how the papers “Bacterial community structure in the drinking water microbiome is governed by filtration processes” (A. J. Pinto, C. Xi, and L.

Patrick J. McNamara works in the field of environmental engineering. In this mSphere of Influence article, he reflects on how the papers “Bacterial community structure in the drinking water microbiome is governed by filtration processes” (A. J. Pinto, C. Xi, and L. Raskin, Environ Sci Technol 46:8851–8859, 2012, https://doi.org/10.1021/es302042t) and “Differential resistance of drinking water bacterial populations to monochloramine disinfection” (T. Chiao, T. M. Clancy, A. Pinto, C. Xi, and L. Raskin, Environ Sci Technol 48:4038–4047, 2014, https://doi.org/10.1021/es4055725) by Lutgarde Raskin and colleagues made an impact on him by providing a foundation for the study of microbial ecology in engineering drinking water treatment plants and drinking water distribution systems.

Understanding the impacts of intermittent supply on the drinking water microbiome

Increasing access to piped water in low-income and middle-income countries combined with the many factors that threaten our drinking water supply infrastructure mean that intermittent water supply (IWS) will remain a common practice around the world. Common features of IWS include water stagnation, pipe drainage, intrusion, backflow, first flush events, and household storage. IWS has been shown to cause degradation as measured by traditional microbial water quality indicators. In this review, we build on new insights into the microbial ecology of continuous water supply systems revealed by sequencing methods to speculate about how intermittent supply conditions may further influence the drinking water microbiome, and identify priorities for future research.

Nontuberculous mycobacteria in drinking water systems - the challenges of characterization and risk mitigation

Nontuberculous mycobacteria (NTM) pulmonary infections are a growing concern worldwide, with a disproportionate incidence in persons with pre-existing health conditions. NTM have frequently been found in municipally-treated drinking water and building plumbing, leading to the hypothesis that an important source of NTM exposure is drinking water. The identification and quantification of NTM in environmental samples are complicated by genetic variability among NTM species, making it challenging to determine if clinically relevant NTM are present. Additionally, their unique cellular features and lifestyles make NTM and their nucleic acids difficult to recover. This review highlights a recent work focused on quantification and characterization of NTM and on understanding the influence of source water, treatment plants, distribution systems, and building plumbing on the abundance of NTM in drinking water.