Core-satellite populations and seasonality of water meter biofilms in a metropolitan drinking water distribution system

Handwashing basins and healthcare associated infections: Bacterial diversity in biofilms on faucets and drains

BACKGROUND

Increasingly, hospital handwashing basins have been identified as a source of healthcare-associated infections. Biofilms formed on the faucet and drains of handbasins can potentially harbour pathogenic microbes and promote the dissemination of antimicrobial resistance. However, little is known about the diversity of these biofilm communities and the routes of contamination.

AIM

The aim of this paper was to use 16S rRNA gene amplicon sequencing to investigate the diversity of prokaryote communities present in faucet and drain biofilm samples taken from hospital and residential handbasins.

FINDINGS

The biofilm prokaryotes communities were diverse, with high abundances of potentially corrosive, biofilm forming and pathogenic genera, including those that are not typically waterborne. The β-diversity showed statistically significant differences in the variation of bacterial communities on the basis on building type (hospital vs residential p = 0.0415). However, there was no statistically significant clustering based on sampling site (faucet vs drain p = 0.46). When examining the β-diversity between individual factors, there was a significant difference between drain biofilms of different buildings (hospital drain vs residential drain p = 0.0338).

CONCLUSION

This study demonstrated that biofilms from hospital and residential handbasins contain complex and diverse microbial communities that differ significantly by building type. It also showed biofilms formed on the faucet and drain of a hospital's handbasins were not significantly different. Future research is needed to understand the potential mechanisms of transfer between drains and faucets of hospital handbasins. This information will inform improved infection control guidelines to control this underrecognized source of infections.

What is the Difference between Conventional Drinking Water, Potable Reuse Water, and Nonpotable Reuse Water? A Microbiome Perspective

As water reuse applications expand, there is a need for more comprehensive means to assess water quality. Microbiome analysis could provide the ability to supplement fecal indicators and pathogen profiling toward defining a "healthy" drinking water microbiota while also providing insight into the impact of treatment and distribution. Here, we utilized 16S rRNA gene amplicon sequencing to identify signature features in the composition of microbiota across a wide spectrum of water types (potable conventional, potable reuse, and nonpotable reuse). A clear distinction was found in the composition of microbiota as a function of intended water use (e.g., potable vs nonpotable) across a very broad range of U.S. water systems at both the point of compliance (Betadisper p > 0.01; ANOSIM p < 0.01, r-stat = 0.71) and point of use (Betadisper p > 0.01; ANOSIM p < 0.01, r-stat = 0.41). Core and discriminatory analysis further served in identifying distinct differences between potable and nonpotable water microbiomes. Taxa were identified at both the phylum (Desulfobacterota, Patescibacteria, and Myxococcota) and genus (Aeromonas and NS11.12_marine_group) levels that effectively discriminated between potable and nonpotable waters, with the most discriminatory taxa being core/abundant in nonpotable waters (with few exceptions, such as Ralstonia being abundant in potable conventional waters). The approach and findings open the door to the possibility of microbial community signature profiling as a water quality monitoring approach for assessing efficacy of treatments and suitability of water for intended use/reuse application.

Bacterial assembly and succession patterns in conventional and advanced drinking water systems: From source to tap

Bacteria are pivotal to drinking water treatment and public health. However, the mechanisms of bacterial assembly and their impact on species coexistence remain largely unexplored. This study explored the assembly and succession of bacterial communities in two full-scale drinking water systems over one year. We observed a decline in bacterial biomass, diversity, and co-occurrence network complexity along the treatment processes, except for the biological activated carbon filtration stage. The conventional plant showed higher bacterial diversity than the advanced plant, despite similar bacterial concentrations and better removal efficiency. The biological activated carbon filter exhibited high phylogenetic diversity, indicating enhanced bacterial metabolic functionality for organic matter removal. Chlorination inactivated most bacteria but favored some chlorination-resistant and potentially pathogenic species, such as Burkholderia, Bosea, Brevundimonas, and Acinetobacter. Moreover, the spatiotemporal dynamics of the bacterial continuum were primarily driven by stochastic processes, explaining more than 78% of the relative importance. The advanced plant's bacterial community was less influenced by dispersal limitation and more by homogeneous selection. The stochastic process regulated bacterial diversity and influenced the complexity of the species co-occurrence network. These findings deepen our understanding of microbial ecological mechanisms and species interactions, offering insights for enhancing hygienic safety in drinking water systems.

Drinking Water Microbiota, Entero-Mammary Pathways, and Breast Cancer: Focus on Nontuberculous Mycobacteria

The prospect of drinking water serving as a conduit for gut bacteria, artificially selected by disinfection strategies and a lack of monitoring at the point of use, is concerning. Certain opportunistic pathogens, notably some nontuberculous mycobacteria (NTM), often exceed coliform bacteria levels in drinking water, posing safety risks. NTM and other microbiota resist chlorination and thrive in plumbing systems. When inhaled, opportunistic NTM can infect the lungs of immunocompromised or chronically ill patients and the elderly, primarily postmenopausal women. When ingested with drinking water, NTM often survive stomach acidity, reach the intestines, and migrate to other organs using immune cells as vehicles, potentially colonizing tumor tissue, including in breast cancer. The link between the microbiome and cancer is not new, yet the recognition of intratumoral microbiomes is a recent development. Breast cancer risk rises with age, and NTM infections have emerged as a concern among breast cancer patients. In addition to studies hinting at a potential association between chronic NTM infections and lung cancer, NTM have also been detected in breast tumors at levels higher than normal adjacent tissue. Evaluating the risks of continued ingestion of contaminated drinking water is paramount, especially given the ability of various bacteria to migrate from the gut to breast tissue via entero-mammary pathways. This underscores a pressing need to revise water safety monitoring guidelines and delve into hormonal factors, including addressing the disproportionate impact of NTM infections and breast cancer on women and examining the potential health risks posed by the cryptic and unchecked microbiota from drinking water.

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

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

A review of research advances on disinfection strategies for biofilm control in drinking water distribution systems

The presence of biofilms in drinking water distribution systems (DWDS) is responsible for water quality deterioration and a possible source of public health risks. Different factors impact the biological stability of drinking water (DW) in the distribution networks, such as the presence and concentration of nutrients, water temperature, pipe material composition, hydrodynamic conditions, and levels of disinfectant residual. This review aimed to evaluate the current state of knowledge on strategies for DW biofilm disinfection through a qualitative and quantitative analysis of the literature published over the last decade. A systematic review method was performed on the 562 journal articles identified through database searching on Web of Science and Scopus, with 85 studies selected for detailed analysis. A variety of disinfectants were identified for DW biofilm control such as chlorine, chloramine, UV irradiation, hydrogen peroxide, chlorine dioxide, ozone, and others at a lower frequency, namely, electrolyzed water, bacteriophages, silver ions, and nanoparticles. The disinfectants can impact the microbial communities within biofilms, reduce the number of culturable cells and biofilm biomass, as well as interfere with the biofilm matrix components. The maintenance of an effective residual concentration in the water guarantees long-term prevention of biofilm formation and improves the inactivation of detached biofilm-associated opportunistic pathogens. Additionally, strategies based on multi-barrier processes by optimization of primary and secondary disinfection combined with other water treatment methods improve the control of opportunistic pathogens, reduce the chlorine-tolerance of biofilm-embedded cells, as well as decrease the corrosion rate in metal-based pipelines. Most of the studies used benchtop laboratory devices for biofilm research. Even though these devices mimic the conditions found in real DWDS, future investigations on strategies for DW biofilm control should include the validity of the promising strategies against biofilms formed in real DW networks.

Functional traits and health implications of the global household drinking-water microbiome retrieved using an integrative genome-centric approach

The biological safety of drinking water plays a crucial role in public health protection. However, research on the drinking water microbiome remains in its infancy, especially little is known about the potentially pathogenic bacteria in and functional characteristics of the microbiome in household tap water that people are directly exposed to. In this study, we used a genomic-centric approach to construct a genetic catalogue of the drinking water microbiome by analysing 116 metagenomic datasets of household tap water worldwide, spanning nine countries/regions on five continents. We reconstructed 859 high-quality metagenome-assembled genomes (MAGs) spanning 27 bacterial and 2 archaeal phyla, and found that the core MAGs belonging to the phylum Proteobacteria encoded the highest metabolic functional diversity of the 33 key complete metabolic modules. In particular, we found that two core MAGs of Brevibacillus and Methylomona encoded genes for methane metabolism, which may support the growth of heterotrophic organisms observed in the oligotrophic ecosystem. Four MAGs of complete ammonia oxidation (comammox) Nitrospira were identified and functional metabolic analysis suggested these may enable mixotrophic growth and encode genes for reactive oxygen stress defence and arsenite reduction that could aid survival in the environment of oligotrophic drinking water systems. Four MAGs were annotated as potentially pathogenic bacteria (PPB) and thus represented a possible public health concern. They belonged to the genera Acinetobacter (n = 3) and Mycobacterium (n = 1), with a total relative abundance of 1.06 % in all samples. The genomes of PPB A. junii and A. ursingii were discovered to contain antibiotic resistance genes and mobile genetic elements that could contribute to antimicrobial dissemination in drinking water. Further network analysis suggested that symbiotic microbes which support the growth of pathogenic bacteria can be targets for future surveillance and removal.

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.

Shedding light on the total and active core microbiomes in slow sand filters for drinking water production

Slow sand filters (SSF) are widely used in the production of drinking water as a last barrier in the removal of pathogens. This removal mainly depends on the 'Schmutzdecke', a biofilm-like layer on the surface of the sand bed. Most previous studies focused on the total community as revealed by DNA analysis rather than on the active community, which may lead to an incorrect understanding of the SSF ecology. In the current study, we determined and compared the DNA- (total) and RNA-displayed (active) communities in the Schmutzdecke layer from 10 full-scale slow sand filters and further explored the SSF core microbiome in terms of both presence (DNA) and activity (RNA). Discrepancies were observed between the total and the active community, although there was a consistent grouping in the PCoA analysis. The DNA-displayed community may be somewhat inflated, while the RNA-displayed community could reveal low abundance (or rare) but active community members. The overall results imply that both DNA (presence) and RNA (activity) data should be considered to prevent the underestimation of organisms of functional importance but lower abundance. Microbial communities of studied mature Schmutzdecke were shaped by the influent water. Nevertheless, a core microbiome was shared by the mature Schmutzdeckes from independent filters, representing the dominant and consistent microbial community composition in slow sand filters. In the DNA samples, a total of 33 VSC families ('very strict core', with a relative abundance >0.1% and 100% prevalence) were observed across all filters. Among the RNA samples, there were 18 VSC families, including 16 families that overlapped with the DNA VSC families and 2 unique RNA VSC families. The core microbial community structure was influenced by the operational parameters, including the Schmutzdecke age and the sand size, and was less influenced by water flow. In addition, indicator organisms ('biomarkers') for the Schmutzdecke age, which show the longest duration that SSF can maintain a good operation, were observed in our study. The abundant presence of bacteria belonging to bacteriap25 and Caldilineaceae was associated with older Schmutzdeckes, revealing longer periods of stable operation performance of the filter, while the high abundance of bacteria belonging to Bdellovibrionaceae and Bryobacteraceae related to short periods of stable operation performance.

Validation of 16S rRNA gene sequencing and metagenomics for evaluating microbial immigration in a methanogenic bioreactor

To quantitatively evaluate the impact of microbial immigration from an upstream community on the microbial assembly of a downstream community, an ecological genomics (ecogenomics)-based mass balance (EGMB) model coupled with 16S rRNA gene sequencing was previously developed. In this study, a mock community was used to further validate the EGMB models and demonstrate the feasibility of using metagenome-based EGMB model to reveal both microbial activity and function. The mock community consisting of Aeromonas, Escherichia, and Pseudomonas was fed into a lab-scale methanogenic bioreactor together with dissolved organic substrate. Using qPCR, 16S rRNA gene, 16S rRNA gene copy number normalization (GCN), and metagenome, results showed highly comparable community profiles in the feed. In the bioreactor, Aeromonas and Pseudomonas exhibited negative growth rates throughout the experiment by all approaches. Escherichia's growth rate was negative by most biomarkers but was slightly positive by 16S rRNA gene. Still, all approaches showed a decreasing trend toward negative in the growth rate of Escherichia as reactor operation time increased. Uncultivated populations of phyla Desulfobacterota, Chloroflexi, Actinobacteriota, and Spirochaetota were observed to increase in abundance, suggesting their contribution in degrading the feed biomass. Based on metabolic reconstruction of metagenomes, these populations possessed functions of hydrolysis, fermentation, fatty acid degradation, or acetate oxidation. Overall results supported the application of both 16S rRNA gene- and metagenome-based EGMB models to measure the growth rate of microbes in the bioreactor, and the latter had advantage in providing insights into the microbial functions of uncultivated populations.

Seasonality Determines the Variations of Biofilm Microbiome and Antibiotic Resistome in a Pilot-Scale Chlorinated Drinking Water Distribution System Deciphered by Metagenome Assembly

Understanding the biofilm microbiome and antibiotic resistome evolution in drinking water distribution systems (DWDSs) is crucial to ensure the safety of drinking water. We explored the 10 month evolution of the microbial community, antibiotic resistance genes (ARGs), mobile gene elements (MGEs) co-existing with ARGs and pathogenic ARG hosts, and the ARG driving factors in DWDS biofilms using metagenomics assembly. Sampling season was critical in determining the microbial community and antibiotic resistome shift. Pseudomonas was the primary biofilm colonizer, and biofilms diversified more as the formation time increased. Most genera tended to cooperate to adapt to an oligotrophic environment with disinfectant stress. Biofilm microbial community and antibiotic resistome assembly were mainly determined by stochastic processes and changed with season. Metagenome assembly provided the occurrence and fates of MGEs co-existing with ARGs and ARG hosts in DWDS biofilms. The abundance of ARG- and MGE-carrying pathogen Stenotrophomonas maltophilia was high in summer. It primarily harbored the aph(3)-IIb, multidrug transporter, smeD, and metallo-beta-lactamase ARGs, which were transferred via recombination. The microbial community was the most crucial factor driving the antibiotic resistance shift. We provide novel insights about the evolution of pathogens and ARGs and their correlations in DWDS biofilms to ensure the safety of drinking water.

Biogas Residues Improved Microbial Diversity and Disease Suppression Function under Extent Indigenous Soil Microbial Biomass

Indigenous soil microbial biomass (ISMB) plays a key role in maintaining essential functions and biodiversity of soil health. One of the critical unknowns is how the indigenous microorganisms respond to different fertilizers which is directly related to agricultural production. Therefore, we used Mi-Seq sequencing and network analyses to compare the response of ISMB to biogas residue and chemical fertilizers. The results showed that crop production was profoundly influenced by levels of ISMB present and is further dependent on the strategy of fertilizer application. Higher ISMB primarily manifests through retention of richer microbial abundance, a balanced community structure, and tightened co-occurrence within a certain proportion of Nitrospirae, Rhizophlyctidaceae, and Gemmatimonadetes. Compared to chemical fertilizer, biogas residue resulted in higher production with more strongly linked nodes such as Actinobacteria, Chloroflexi and Gemmatimonadetes. Under the same level of ISMB, the microbial diversity was richer and co-occurrence was tighter when biogas residues were applied compared with chemical fertilizer. In addition, the higher level of ISMB with biogas residue applied had a lower abundance of potential fungal pathogens in both bulk and rhizosphere soil compared with chemical fertilizer. This study provides critical data to understand the influence of ISMB and biogas residue on soil ecological system.

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.

Interaction between Microbes and Host in Sow Vaginas in Early Pregnancy

Extensive research has explored the causes of embryo losses during early pregnancy by analyzing interaction mechanisms in sows' uterus, ignoring the importance of the lower reproductive tract in pregnancy development regulation. Despite recent progress in understanding the diversity of vaginal microbes under different physiological states, the dynamic of sows' vaginal microbiotas during pregnancy and the interaction between vaginal microbes and the host are poorly understood. Here, we performed a comprehensive analysis of sows' vaginal microbial communities in early pregnancy coupled with overall patterns of vaginal mucosal epithelium gene expression. The vaginal microbiota was analyzed by 16s rRNA or metagenome sequencing, and the vaginal mucosal epithelium transcriptome was analyzed by RNA sequencing, followed by integration of the data layers. We found that the sows' vaginal microbiotas in early pregnancy develop dynamically, and there is a homeostasis balance of Firmicutes and Proteobacteria. Subsequently, we identified two pregnancy-specific communities, which play diverse roles. The microbes in the vagina stimulate the epithelial cells, while vaginal epithelium changes its structure and functions in response to stimulation. These changes produce specific inflammation responses to promote pregnancy development. Our findings demonstrate the interaction between microbes and host in the sow vagina in early pregnancy to promote pregnancy development, meanwhile providing a reference data set for the study of targeted therapies of microbial homeostasis dysregulation in the female reproductive tract. IMPORTANCE This work sheds light on the dynamics of the sow vaginal microbiotas in early pregnancy and its roles in pregnancy development. Furthermore, this study provides insight into the functional mechanisms of reproductive tract microbes by outlining vaginal microbe-host interactions, which might identify new research and intervention targets for improving pregnancy development by modulating lower reproductive tract microbiota.

Spatiotemporal distribution of opportunistic pathogens and microbial community in centralized rural drinking water: One year survey in China

Centralized water supply in rural areas, supported by small waterworks (small-central mode) and by municipal water treatment plants (urban-extension mode), is an important guarantee to implement the Rural Revitalization Strategy Plan (2018-2022) in China. Opportunistic pathogens (OPs) could not be evaluated by the national drinking water sanitation standards in China (GB 5749-2022), posing potential microbial risks in rural drinking water. In this study, the spatiotemporal distribution of OPs, microbial community and the associated functional composition under two central water supply modes were investigated by molecular approaches. The results indicated that OPs were widely presented in the rural drinking water regardless of water supply modes, and were more abundant than those in the urban tap water. The insufficient residual chlorine and higher turbidity triggered more microbial proliferation, posing a seasonal variation of OPs gene copy numbers and bacterial community compositions. In warm seasons of summer and autumn, the gene copies of E. coli, M. avium, Pseudomonas spp. and the amoeba host Acanthamoeba spp. achieved up to 4.92, 3.94, 6.75 and 3.74 log₁₀ (gene copies/mL), respectively. Potential functional prediction indicated higher relative abundance of pathogenic genes and infectious risks associated with the rural drinking water under small-central water supply mode. This one-year survey of the spatiotemporal distribution of OPs and microbial community provided scientific insights into microbial safety of rural drinking water, prompting attention on small-central water supply mode against OPs risks.

Dynamics of the Microbial Community and Opportunistic Pathogens after Water Stagnation in the Premise Plumbing of a Building

In premise plumbing, microbial water quality may deteriorate under certain conditions, such as stagnation. Stagnation results in a loss of disinfectant residual, which may lead to the regrowth of microorganisms, including opportunistic pathogens. In the present study, microbial regrowth was investigated at eight faucets in a building over four seasons in one year. Water samples were obtained before and after 24 h of stagnation. In the first 100‍ ‍mL after stagnation, total cell counts measured by flow cytometry increased 14- to 220-fold with a simultaneous decrease in free chlorine from 0.17–0.36‍ ‍mg L^–1 to <0.02‍ ‍mg L^–1. After stagnation, total cell counts were not significantly different among seasons; however, the composition of the microbial community varied seasonally. The relative abundance of Pseudomonas spp. was dominant in winter, whereas Sphingomonas spp. were dominant in most faucets after stagnation in other seasons. Opportunistic pathogens, such as Legionella pneumophila, Mycobacterium avium, Pseudomonas aeruginosa, and Acanthamoeba spp., were below the quantification limit for real-time quantitative PCR in all samples. However, sequences related to other opportunistic pathogens, including L. feeleii, L. maceachernii, L. micdadei, M. paragordonae, M. gordonae, and M. haemophilum, were detected. These results indicate that health risks may increase after stagnation due to the regrowth of opportunistic pathogens.

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.

Effect of disinfectant exposure and starvation treatment on the detachment of simulated drinking water biofilms

Biofilms were one of the main habitats of microbes in the drinking water distribution system. The variation of environmental conditions can lead to the detachment of biofilms and the deterioration of water quality. In this study, the effects of disinfectant exposure and starvation treatment on the detachment of biofilms were investigated. The results showed that detaching rate increased with the concentration of chloramine in the inlet water and 1.0 mg/L of chloramine led to the largest detached biomass. The starvation treatment resulted in less biofilm biomass but the detaching rates of treated biofilms were higher than those without starvation. The 16S rRNA sequencing results showed that detached and stubborn biofilms had a significant difference in microbial diversity and richness. The microbial community composition of the two types of biofilm showed the difference in the abundance of Nitrospira, Bryobacter, Hyphomicrobium, and Pedomicrobium. Chloramine exposure did not have a significant impact on the microbial community while the starvation treatment led to a higher abundance of chemolithotrophs bacteria. Metagenomic results indicated that detached biofilms had higher abundances of ARGs and starvation treatment could enrich the ARGs. The results of this research could provide the knowledge of biofilm sloughing and help understand the health risk of antibiotic resistance in drinking water.

Characterizing the premise plumbing microbiome in both water and biofilms of a 50-year-old building

The premise plumbing portion of drinking water distribution systems (DWDS) has several characteristics that may favor microbial growth in the form of biofilms. These microbial communities are implicated as infectious sources for the spread of opportunistic waterborne pathogens by supporting their complex ecology and transmission through DWDS outlets to susceptible individuals. However, there is limited understanding of the drinking water biofilms in real premise plumbing networks due to challenges with accessibility. Using a combination of culture-dependent and culture-independent approaches, this study comprehensively characterized the premise plumbing microbiome of a 50-year-old university building, inclusive of water and biofilm samples. Microbial diversity in the water samples were more taxonomically diverse in comparison to the mature drinking water biofilms, which were dominated with biofilm-formers and opportunistic pathogens, such as Mycobacterium spp. A model opportunistic pathogen, Legionella spp., was only detectable in water samples using quantitative PCR but could not be detected in any of the drinking water biofilms using either qPCR or culture-dependent approaches, highlighting the limitations of detection methods in these environments. This study presents preliminary findings on the microbial dynamics and complexity in premise plumbing networks, which may support public health management and the development of strategies to eliminate microbial risks to human health.

Biofilm-Forming Capacity of Escherichia coli Isolated from Cattle and Beef Packing Plants: Relation to Virulence Attributes, Stage of Processing, Antimicrobial Interventions, and Heat Tolerance

Despite the importance of biofilm formation in the contamination of meat by pathogenic Escherichia coli at slaughter plants, drivers for biofilm remain unclear. To identify selection pressures for biofilm, we evaluated 745 isolates from cattle and 700 generic E. coli isolates from two beef slaughter plants for motility, the expression of curli and cellulose, and biofilm-forming potential. Cattle isolates were also screened for serogroup, stx₁, stx₂, eae, and rpoS. Generic E. coli isolates were compared by source (hide of carcass, hide-off carcass, and processing equipment) before and after the implementation of antimicrobial hurdles. The proportion of E. coli isolates capable of forming biofilms was lowest (7.1%; P < 0.05) for cattle isolates and highest (87.3%; P < 0.05) from equipment. Only one enterohemorrhagic E. coli (EHEC) isolate was an extremely strong biofilm former, in contrast to 73.4% of E. coli isolates from equipment. Isolates from equipment after sanitation had a greater biofilm-forming capacity (P < 0.001) than those before sanitation. Most cattle isolates were motile and expressed curli, although these traits along with the expression of cellulose and the detection of rpoS were not necessary for biofilm formation. In contrast, isolates capable of forming biofilms on equipment were almost exclusively motile and able to express curli. The results of the present study indicate that cattle rarely carry EHEC capable of making strong biofilms in slaughter plants. However, if biofilm-forming EHEC contaminates equipment, current sanitation procedures may not eliminate the most robust biofilm-forming strains. Accordingly, new and effective antibiofilm hurdles for meat-processing equipment are required to reduce future instances of foodborne disease. IMPORTANCE As the majority of enterohemorrhagic E. coli (EHEC) isolates are not capable of forming biofilms, sources were undetermined for biofilm-forming EHEC isolated from "high-event periods" in beef slaughter plants. This study demonstrated that sanitation procedures used on beef-processing equipment may inadvertently lead to the survival of robust biofilm-forming strains of E. coli. Cattle only rarely carry EHEC capable of forming strong biofilms (1/745 isolates evaluated), but isolates with greater biofilm-forming capacity were more likely (P < 0.001) to survive equipment sanitation. In contrast, chilling carcasses for 3 days at 0°C reduced (P < 0.05) the proportion of biofilm-forming E. coli. Consequently, an additional antibiofilm hurdle for meat-processing equipment, perhaps involving cold exposure, is necessary to further reduce the risk of foodborne disease.

Linking population dynamics to microbial kinetics for hybrid modeling of bioelectrochemical systems

Mechanistic and data-driven models have been developed to provide predictive insights into the design and optimization of engineered bioprocesses. These two modeling strategies can be combined to form hybrid models to address the issues of parameter identifiability and prediction interpretability. Herein, we developed a novel and robust hybrid modeling strategy by incorporating microbial population dynamics into model construction. The hybrid model was constructed using bioelectrochemical systems (BES) as a platform system. We collected 77 samples from 13 publications, in which the BES were operated under diverse conditions, and performed holistic processing of the 16S rRNA amplicon sequencing data. Community analysis revealed core populations composed of putative electroactive taxa Geobacter, Desulfovibrio, Pseudomonas, and Acinetobacter. Primary Bayesian networks were trained with the core populations and environmental parameters, and directed Bayesian networks were trained by defining the operating parameters to improve the prediction interpretability. Both networks were validated with Bray-Curtis similarly, relative root-mean-square error (RMSE), and a null model. A hybrid model was developed by first building a three-population mechanistic component and subsequently feeding the estimated microbial kinetic parameters into network training. The hybrid model generated a simulated community that shared a Bray-Curtis similarity of 72% with the actual microbial community at the genus level and an average relative RMSE of 7% for individual taxa. When examined with additional samples that were not included in network training, the hybrid model achieved accurate prediction of current production with a relative error-based RMSE of 0.8 and outperformed the data-driven models. The genomics-enabled hybrid modeling strategy represents a significant step toward robust simulation of a variety of engineered bioprocesses.

Density-dependent microbial calcium carbonate precipitation by drinking water bacteria via amino acid metabolism and biosorption

Drinking water plumbing systems appear to be a unique environment for microorganisms as they contain few nutrients but a high mineral concentration. Interactions between mineral content and bacteria, such as microbial calcium carbonate precipitation (MCP) however, has not yet attracted too much attention in drinking water sector. This study aims to carefully examine MCP behavior of two drinking water bacteria species, which may potentially link scaling and biofouling processes in drinking water distribution systems. Evidence from cell density evolution, chemical parameters, and microscopy suggest that drinking water isolates can mediate CaCO₃ precipitation through previously overlooked MCP mechanisms like ammonification or biosorption. The results also illustrate the active control of bacteria on the MCP process, as the calcium starts to concentrate onto cell surfaces only after reaching a certain cell density, even though the cell surfaces are shown to be the ideal location for the CaCO₃ nucleation.

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.

Microbial composition and diversity of drinking water: A full scale spatial-temporal investigation of a city in northern China

The microbiological water quality of drinking water distribution systems (DWDSs) is of primary importance for public health. The detachment of biofilm attached on the pipe wall attribution to water source switch and the occurrence of potentially pathogenic chlorine-resistant bacteria (CRB) under chlorine disinfection get lots of attention. Studies examining microbial communities after the water source switch, particularly in low-salinity water, have been scant. The UV‑chlorine combined disinfection applied in one of the investigated drinking water plants provided insight into the control of CRBs. We applied high-throughput sequencing of the 16S rRNA gene to characterize the bacterial communities of the DWDS in northern China over 1 year. A network comprising four different DWDSs was sampled at 48 sites every season (temperate continental monsoon climate), and the impact of key spatial-temporal and physicochemical parameters was investigated. Overall, the entire bacterial community was not significantly different among the four DWDSs (spatial parameter) but varied with seasons (temporal parameter). The switch in water sources might increase the relative abundance of potentially opportunistic pathogens in DWDSs. UV‑chlorine combined disinfection can decrease community diversity and is likely to control the growth of potential opportunistic pathogens in DWDSs.

Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir

BACKGROUND

Freshwater salinization may result in significant changes of microbial community composition and diversity, with implications for ecosystem processes and function. Earlier research has revealed the importance of large shifts in salinity on microbial physiology and ecology, whereas studies on the effects of smaller or narrower shifts in salinity on the microeukaryotic community in inland waters are scarce. Our aim was to unveil community assembly mechanisms and the stability of microeukaryotic plankton networks at low shifts in salinity.

RESULTS

Here, we analyzed a high-resolution time series of plankton data from an urban reservoir in subtropical China over 13 consecutive months following one periodic salinity change ranging from 0 to 6.1‰. We found that (1) salinity increase altered the community composition and led to a significant decrease of plankton diversity, (2) salinity change influenced microeukaryotic plankton community assembly primarily by regulating the deterministic-stochastic balance, with deterministic processes becoming more important with increased salinity, and (3) core plankton subnetwork robustness was higher at low-salinity levels, while the satellite subnetworks had greater robustness at the medium-/high-salinity levels. Our results suggest that the influence of salinity, rather than successional time, is an important driving force for shaping microeukaryotic plankton community dynamics.

CONCLUSIONS

Our findings demonstrate that at low salinities, even small increases in salinity are sufficient to exert a selective pressure to reduce the microeukaryotic plankton diversity and alter community assembly mechanism and network stability. Our results provide new insights into plankton ecology of inland urban waters and the impacts of salinity change in the assembly of microbiotas and network architecture. Video abstract.

The Bacterial Community Diversity of Bathroom Hot Tap Water Was Significantly Lower Than That of Cold Tap and Shower Water

Microbial drinking water quality in premise plumbing systems (PPSs) strongly affects public health. Bacterial community structure is the essential aspect of microbial water quality. Studies have elucidated the microbial community structure in cold tap water, while the microbial community structures in hot tap and shower water are poorly understood. We sampled cold tap, hot tap, and shower water from a simulated PPS monthly for 16 consecutive months and assessed the bacterial community structures in those samples via high-throughput sequencing of bacterial 16S rRNA genes. The total relative abundance of the top five most abundant phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes) was greater than 90% among the 24 identified phyla. The most abundant families were Burkholderiaceae, Sphingomonadaceae, unclassified Alphaproteobacteria, unclassified Corynebacteriales, and Mycobacteriaceae. A multiple linear regression suggests that the bacterial community diversity increased with water temperature and the age of the simulated PPS, decreased with total chlorine residual concentration, and had a limited seasonal variation. The bacterial community in hot tap water had significantly lower Shannon and Inverse Simpson diversity indices (p < 0.05) and thus a much lower diversity than those in cold tap and shower water. The paradoxical results (i.e., diversity increased with water temperature, but hot tap water bacterial community was less diverse) were presumably because (1) other environmental factors made hot tap water bacterial community less diverse, (2) the diversity of bacterial communities in all types of water samples increased with water temperature, and (3) the first draw samples of hot tap water could have a comparable or even lower temperature than shower water samples and the second draw samples of cold tap water. In both a three-dimensional Non-metric multidimensional scaling ordination plot and a phylogenetic dendrogram, the samples of cold tap and shower water cluster and are separate from hot tap water samples (p < 0.05). In summary, the bacterial community in hot tap water in the simulated PPS had a distinct structure from and a much lower diversity than those in cold tap and shower water.

Microbial abundance and community composition in biofilms on in-pipe sensors in a drinking water distribution system

Collecting biofilm samples from drinking water distribution systems (DWDSs) is challenging due to limited access to the pipes during regular operations. We report here the analysis of microbial communities in biofilm and water samples collected from sensors installed in a DWDS where monochloramine is used as a residual disinfectant. A total of 52 biofilm samples and 14 bulk water samples were collected from 17 pipe sections representing different water ages. Prokaryotic genome copies (bacterial and archaeal 16S rRNA genes, Mycobacterium spp., ammonia-oxidizing bacteria (AOB), and cyanobacteria) were quantified with droplet digital PCR, which revealed the abundance of these genes in both biofilm and water samples. Prokaryotic 16S rRNA gene sequencing analysis was carried out for a subset of the samples (12 samples from four sites). Mycobacterium and AOB species were dominant in the DWDS sections with low water age and sufficient residual monochloramine, whereas Nitrospira species (nitrite-oxidizing bacteria) dominated in the sections with higher water age and depleted monochloramine level, suggesting the occurrence of nitrification in the studied DWDS. The present study provides novel information on the abundance and identity of prokaryotes in biofilms and water in a full-scale operational DWDS.

Occurrence and quantification of culturable and viable but non-culturable (VBNC) pathogens in biofilm on different pipes from a metropolitan drinking water distribution system

Waterborne pathogens have been found in biofilms grown in drinking water distribution system (DWDS). However, there is a lack of quantitative study on the culturability of pathogens in biofilms from metropolitan DWDS. In this study, we quantified culturable and viable but non-culturable (VBNC) Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa and Vibrio cholerae in biofilms collected from five kinds of pipes (galvanized steel pipe, steel pipe, stainless steel clad pipe, ductile cast iron pipe and polyethylene pipe) and associated drinking water at an actual chlorinated DWDS in use from China. The results of these comprehensive analyses revealed that pipe material is a significant factor influencing the culturability of pathogen and microbial communities. Network analysis of the culturable pathogens and 16S rRNA gene inferred potential interactions between microbiome and culturability of pathogens. Although the water quality met the Chinese national standard of drinking water, however, VBNC pathogens were detected in both biofilms and water from the DWDS. This investigation suggests that stainless steel clad pipe (SSCP) was a better choice for pathogen control compared with other metal pipes. To our knowledge, this is the first study on culturable and VBNC pathogens in biofilms of different pipe materials in metropolitan DWDS.

Changes in biofilm composition and microbial water quality in drinking water distribution systems by temperature increase induced through thermal energy recovery

Drinking water distribution systems (DWDSs) have been thoroughly studied, but the concept of thermal energy recovery from DWDSs is very new and has been conceptualized in the past few years. Cold recovery results in a temperature increase of the drinking water. Its effects on drinking water quality and biofilm development are unclear. Hence, we studied both bulk water and biofilm phases for 232 days in two parallel pilot scale distribution systems with two temperature settings after cold recovery, 25 °C and 30 °C, and compared these with a reference pilot system without cold recovery. In all three pilot distributions systems (DSs) our results showed an initial increase in biomass (ATP) in the biofilm phase, along with occurrence of primary colonizers (Betaproteobacteriales) and subsequently a decrease in biomass and an increasing relative abundance of other microbial groups (amoeba resisting groups; Xanthobacteraceae, Legionellales), including those responsible for EPS formation in biofilms (Sphingomonadaceae). The timeline for biofilm microbial development was different for the three pilot DSs: the higher the temperature, the faster the development took place. With respect to the water phase within the three pilot DSs, major microbial contributions came from the feed water (17-100%) and unkown sources (2-80%). Random contributions of biofilm (0-70%) were seen between day 7-77. During this time period six-fold higher ATP concentration (7-11 ng/l) and two-fold higher numbers of high nucleic acid cells (5.20-5.80 × 10⁴ cells/ml) were also observed in the effluent water from all three pilot DSs, compared to the feed water. At the end of the experimental period the microbial composition of effluent water from three pilot DSs revealed no differences, except the presence of a biofilm related microbial group (Sphingomonadaceae), within all three DSs compared to the feed water. In the biofilm phase higher temperatures initiated the growth of primary colonizing bacteria but this did not lead to differences in microbial diversity and composition at the end of the experimental period. Hence, we propose that the microbiological water quality of DWDSs with cold recovery should be monitored more frequently during the first 2-3 months of operation.

Epilithic biofilm as a reservoir for functional virulence factors in wastewater-dominant rivers after WWTP upgrade

Virulence factors (VFs) confer upon pathogens the ability to cause various types of damage or diseases. Wastewater treatment plants (WWTPs) are important point sources for the emission of pathogens and VFs into receiving rivers. Conventional WWTP upgrades are often implemented to improve the water quality of receiving ecosystems. However, knowledge on the pathogens, VFs, and health risks to receiving aquatic ecosystems after upgrade remains limited. In this study, we investigated detailed pathogenic information, including taxa, pathogenicity, and health risk, in two wastewater-dominant rivers after WWTP upgrade. Using 16S rRNA gene sequencing, we screened 14 potential pathogens in water and epilithic biofilm samples, though they were significantly more enriched in the biofilms. Combining 16S rRNA and metagenomic sequencing data, we identified Pseudomonas and Aeromonas as the dominant pathogenic taxa carrying functional VFs (e.g., mobility and offensive) in the epilithic biofilm. Moreover, strong pathogen-specific VF-host co-occurrence events were observed in the epilithic biofilm samples, indicating the importance of biofilms as reservoirs and vehicles for VFs. Further, we demonstrated that mobility VF is crucial for biofilm formation and pathogens in biofilm carrying offensive VF may be highly invasive. Quantification and health risk assessment suggested that the skin contact risk of P. aeruginosa carrying VFs was higher than the acceptable probability of 10^-4 in both water and epilithic biofilm samples, which may threaten ecological and human health.

Combined effects of seasonality and stagnation on tap water quality: Changes in chemical parameters, metabolic activity and co-existence in bacterial community

In drinking water distribution pipeline systems, the tap water quality is regulated by several biotic and abiotic factors, which can threaten the health of consumers. Stagnation is inevitable in the water distribution pipeline however, the combined effects of seasonal changes and stagnation on tap water quality are not well understood. Here, we investigated the seasonal variations in the chemical and biological quality of water after overnight stagnation for a period of one year. The results showed that the tap water quality deteriorated after overnight stagnation, with up to a 2.7-fold increase in the total iron concentrations. The total bacterial cell concentrations increased by 59-231% after overnight stagnation. The total cell and cell-bound adenosine triphosphate (ATP) of the stagnant water samples peaked in summer. In addition, Biolog analysis showed that the metabolic activities of microbes were higher in spring. The bacterial community based on Illumina Miseq DNA sequence analysis found that Proteobacteria dominated the drinking water bacterial community. The bacterial community structure varied significantly among different seasons, where the diversity and richness of the community were much higher in spring. Structural equation modeling (SEM) was constructed to determine the correlations between bacterial metabolic functions and the community structure. The redundancy analysis (RDA) indicated that the residual chlorine played a critical role in the construction of the bacterial community. Altogether, the overall findings from the present work provide novel insights into how the quality of tap water quality impacted by the seasonal changes and overnight stagnation.

The microbial ecology of a Mediterranean chlorinated drinking water distribution systems in the city of Valencia (Spain)

Drinking water distribution systems host extensive microbiomes with diverse biofilm communities regardless of treatment, disinfection, or operational practices. In Mediterranean countries higher temperatures can accelerate reactions and microbial growth that may increase aesthetic water quality issues, particularly where material deposits can develop as a result of net zero flows within looped urban networks. This study investigated the use of flow and turbidity monitoring to hydraulically manage mobilisation of pipe wall biofilms and associated material from the Mediterranean city of Valencia (Spain). Pipe sections of different properties were subjected to controlled incremental flushing with monitoring and sample collection for physico-chemical and DNA analysis with Illumina sequencing of bacterial and fungal communities. A core microbial community was detected throughout the network with microorganisms like Pseudomonas, Aspergillus or Alternaria increasing during flushing, indicating greater abundance in underlying and more consolidated material layers. Bacterial and fungal communities were found to be highly correlated, with bacteria more diverse and dynamic during flushing whilst fungi were more dominant and less variable between sampling sites. Results highlight that water quality management can be achieved through hydraulic strategies yet understanding community dynamics, including the fungal component, will be key to maintaining safe and ultimately beneficial microbiomes in drinking water distribution systems.

Exploring the Bacterial Communities of the Kaiafas Thermal Spring Anigrides Nymphes in Greece Prior to Rehabilitation Actions

Anigrides Nymphes of Lake Kaiafas is a thermal spring that is well known for its therapeutical properties, as the hot water (32-34 °C) is rich in sulfur compounds and minerals. Nowadays, efforts are made from the Hellenic Republic to modernize the existing facilities and infrastructure networks of the area. To study the complex ecosystem of the thermal spring, we collected water from four sampling points (Lake, and Caves 1, 2, and 3). Filtration method was used for microbial enumeration. In parallel, total bacterial DNA was extracted and subjected to next-generation sequencing (NGS). A total of 166 different bacterial families were detected. Differences in families, genera, and species abundances were detected between the different sampling points. Specifically, Comamonadaceae was the most common family detected in Lake and Cave 3. Similarly, in Caves 1 and 2, Rhodobacteraceae was detected at a higher percentage compared to the rest of the families. Moreover, the detection of sequences assigned to waterborne or opportunistic pathogens, i.e., Enterobacteriaceae, Legionellaceae, Coxiellaceae, and Clostridiaceae, as well as Enterococcus and Vibrio, is of great importance. Although the presence of pathogens was not examined by quantitative PCR, the detection of their sequences strengthens the need of the planned rehabilitation actions of this natural environment in order to allow human swimming.

Metagenomic and network analyses decipher profiles and co-occurrence patterns of antibiotic resistome and bacterial taxa in the reclaimed wastewater distribution system

Metagenomic and network analyses were applied to decipher the profiles and co-occurrence of resistome and microbial taxa in the reclaimed wastewater distribution system, including reclaimed wastewater and two types of biofilms, i.e., surface layer biofilms and inner layer biofilms. The effects of chlorination, UV irradiation and no disinfection treatment on ARG relative abundance and composition were systemically investigated. The reclaimed wastewater possesses more diverse and abundant ARGs than biofilms and total ARG relative abundance followed the order of reclaimed wastewater samples > surface layer biofilms > inner layer biofilms. Multidrug, bacitracin, sulfonamide, aminoglycoside, beta-lactam, and macrolide-lincosamide-streptogramin resistance genes were the six most dominant ARG types and their sum accounted for 90.1 %-96.0 % of the total ARG relative abundance in different samples. Beta-lactam resistance gene was the discriminative ARG type for reclaimed wastewater. Bacitracin resistance gene and bacA were the discriminative ARG type and subtype for biofilms. Chlorination significantly reduced ARG relative abundance in the reclaimed wastewater. Nevertheless, it could not reduce ARG relative abundance in biofilms. Regarding to the total ARG profiles, there were no obvious increasing or decreasing trends over time during one year period. Co-occurrence results revealed twenty-six genera were deduced as the potential hosts of twenty-two ARG subtypes.

Metagenomics for taxonomy profiling: tools and approaches

The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about specific genes, microbial communities and its metabolic pathways. More specific drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this 'targeted based metagenomics' approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.

Prevalence of antibiotic resistance genes in drinking water and biofilms: The correlation with the microbial community and opportunistic pathogens

The emergence of antibiotic resistance genes (ARGs) and opportunistic pathogens (OPs) in drinking water system posed potential risks to human health. However, the occurrence of ARGs and OPs in drinking water biofilms is still at its infancy. In this study, we investigated the occurrence of ARGs and OPs in both water and biofilm samples from a drinking water system, and the correlation between ARGs and microbial communities was analyzed. The quantitative PCR results showed that the drinking water treatment process effectively decreased the absolute abundances of ARGs. However, the relative concentration of ARGs did not show a significant difference between raw water and treated water samples. Compared with bulk water and tap water samples, biofilms had higher relative abundances of ARGs. 16 S Illumina Miseq sequencing results showed that microbial communities of biofilms were distinguished with water samples. Meanwhile, qPCR results of OPs also showed that biofilms had higher relative abundances of OPs compared with water samples. Furthermore, the Spearman correlation analysis indicated that Dechloromonas, Desulfovibrio, Methylobacterium and Propionivibrio correlated well with the relative abundance of ARGs. The absolute concentrations of OPs and ARGs also showed a significant correlation. Results of this study suggest that biofilms could serve as the reservoirs for the spread of ARGs and the interaction between biofilms and bulk water requires further research.

Influence of phosphate dosing on biofilms development on lead in chlorinated drinking water bioreactors

Phosphate dosing is used by water utilities to prevent plumbosolvency in water supply networks. However, there is a lack of knowledge regarding biofilm formation on lead and plastic materials when phosphate concentrations are modified in drinking water systems. In this study, biofilms were grown over lead coupons and PVC tubes in bioreactors supplied with local drinking water treated to provide different phosphate doses (below 1, 1 and 2 mg/L) over a period of 28 days. A range of commercial iron pellets (GEH104 and WARP) were tested aiming to maintain phosphate levels below the average 1 mg/L found in drinking water. Changes in biofilm community structure in response to three different phosphate treatments were characterised by Illumina sequencing of the 16S rRNA gene for bacteria and the ITS2 gene for fungi. Scanning electron microscopy was used to visualise physical differences in biofilm development in two types of materials, lead and PVC. The experimental results from the kinetics of phosphate absorption showed that the GEH104 pellets were the best option to, in the long term, reduce phosphate levels while preventing undesirable turbidity increases in drinking water. Phosphate-enrichment promoted a reduction of bacterial diversity but increased that of fungi in biofilms. Overall, higher phosphate levels selected for microorganisms with enhanced capabilities related to phosphorus metabolism and heavy metal resistance. This research brings new insights regarding the influence of different phosphate concentrations on mixed-species biofilms formation and drinking water quality, which are relevant to inform best management practices in drinking water treatment.

Microbiome of Drinking Water Biofilters is Influenced by Environmental Factors and Engineering Decisions but has Little Influence on the Microbiome of the Filtrate

Bacterial communities in biofilters can improve drinking water quality through the biodegradation of dissolved contaminants but also pose potential risks by harboring and shedding microbes into the drinking water distribution system. In this study, pilot-scale granular activated carbon (GAC)-sand and anthracite-sand pilot-scale biofilters were investigated to determine the effects of filter design and operation on the microbiome of the filter media and its relationship to the microbiome in the filter effluent water. Bacterial abundance in the biofilters was relatively stable over time. Bacterial community composition exhibited spatial variation (i.e., with bed depth) and temporal variation linked to water quality changes. Bacterial community composition was significantly affected by the media type (GAC vs anthracite) and backwashing strategy (chloraminated water vs nonchloraminated water). The biofilters reduced bacterial abundance in the water (∼70%) but had only a minor effect on the bacterial community composition in the filtrate. Overall, our results suggest that the bacterial communities growing on biofilters affect filtered water quality primarily through the biotransformation of pollutants and nutrients rather than by altering the microbial community composition of the water as it passes through the filter.

Nitrifying niche differentiation in biofilms from full-scale chloraminated drinking water distribution system

Tropical conditions favour the auto-decomposition of monochloramine (MCA) leading to disinfectant decay and free ammonia in drinking water distribution systems (DWDS); thus, they promote the growth of nitrifiers and the development of biofilms on the inner-pipe surface. Biofilms can adversely impact the provision of safe and biologically stable water. Moreover, there is a general lack of understanding of the role of microbial communities in DWDS in regions with warm temperatures and no distinct seasons. Here, we report a survey on biofilms from full-scale monochloraminated DWDS in a highly urbanised metropolis using next generation sequencing tools. The monitoring campaign consisted of sampling biofilms and bulk waters from 21 in-service pipes. We characterized the microbial community with emphasis on nitrifying bacteria and archaea using 16S rRNA gene amplicon sequencing and potential nitrification activity. Samples grouped into two clusters, characterized by their low (Cluster LD) and high (Cluster HD) α-diversity. Both clusters harbour microorganisms related to nitrification: i) Nitrosomonas (24.9-68.8%), an ammonia oxidising bacterium (AOB) that dominated Cluster LD, and ii) a co-aggregation of genus Nitrospira (9.8-32.5%), a nitrite oxidising bacterium (NOB), and Thaumarchaeota (1.4-10.9%), chemolithotrophic ammonia oxidising (AOA) archaea that were among the most abundant OTUs in Cluster HD. Activity tests performed with fresh biofilm samples confirmed that these two clusters represent distinctive biofilm niches performing different stages of the nitrification process. Cluster LD correlated with a high concentration of MCA, which caused dysbiosis and resulted in high unevenness of the cluster. In cluster HD, with more biomass, chemical reactions involving nitrite increased the MCA demand, releasing ammonia and allowing more nitrifiers to grow, like AOA and NOB. From this study, we conclude that an MCA residual gradient along the DWDS drives and shapes the microbial community assembly and should be considered when designing effective disinfection strategies.

Nitrite accumulation stability evaluation for low-strength ammonium wastewater by adsorption and biological desorption of zeolite under different operational temperature

How to achieve stable nitrite accumulation was still a huge challenge for low-carbon and energy-saving biological nitrogen removal of low-strength ammonium wastewater. This study proposed a new way to solve this problem with zeolite biological fixed bed (ZBFB) by cycle operation of adsorption and biological desorption. In order to evaluate nitritation performance of this reactor, the influence of operational temperature on nitrite accumulation stability was investigated by 126 cycles operation in four parallel ZBFB reactors for low-strength ammonium wastewater (50 mg/L NH₄⁺-N). It was found that higher operational temperature (i.e., 36.0 °C), rather than other temperature (i.e., 27.0 °C, 30.0 °C, 33.0 °C), could maintain stable nitrite accumulation with nitrite production rate of 0.312 kg NO₂^--N·m^-3 zeolite·day^-1 and nitrite accumulation ratio higher than 95.0% after biological desorption. High-throughput sequencing analysis results showed that bacterial structure significantly changed in ZBFB under different operational temperature, and obvious enrichment of genus Nitrosomonas (AOB) and gradually enhanced free ammonia (FA) inhibition on genus Nitrospira and Nitrobacter (NOB) were found by elevation of operational temperature, leading to different nitrite accumulation performance in ZBFB reactors. The mechanism for stable nitrite accumulation performance by ZBFB might be attributed to overwhelming growth rate of AOB than NOB, faster ammonium desorption and enhanced FA inhibition on NOB under operational temperature (i.e., 36.0 °C). All in all, keeping high temperature for biological desorption step should be extremely crucial for stable nitrite accumulation by ZBFB, which could facilitate further low-carbon and energy-saving biological nitrogen removal for low-strength ammonium wastewater treatment.

Effects of geographic location and water quality on bacterial communities in full-scale biofilters across North America

Spatial patterns of bacterial community composition often follow a distance-decay relationship in which community dissimilarity increases with geographic distance. Such a relationship has been commonly observed in natural environments, but less so in engineered environments. In this study, bacterial abundance and community composition in filter media samples (n = 57) from full-scale rapid biofilters at 14 water treatment facilities across North America were determined using quantitative polymerase chain reaction and Illumina HiSeq high-throughput sequencing targeting the 16S rRNA gene, respectively. Bacteria were abundant on the filter media (108.8±0.3 to 1010.7±0.2 16S rRNA gene copies/cm3 bed volume) and the bacterial communities were highly diverse (Shannon index: 5.3 ± 0.1 to 8.4 ± 0.0). Significant inter-filter variations in bacterial community composition were observed, with weighted UniFrac dissimilarity values following a weak but highly significant distance-decay relationship (z = 0.0057 ± 0.0006; P = 1.8 × 10-22). Approximately 50% of the variance in bacterial community composition was explained by the water quality parameters measured at the time of media sample collection (i.e. pH, temperature and dissolved organic carbon concentration). Overall, this study suggested that the microbiomes of biofilters are primarily shaped by geographic location and local water quality conditions but the influence of these factors on the microbiomes is tempered by filter design and operating conditions.

Assessing the transition effects in a drinking water distribution system caused by changing supply water quality: an indirect approach by characterizing suspended solids

Worldwide, it is common that the drinking water distribution systems (DWDSs) may be subjected to changes of supply water quality due to the needs of upgrading the treatment processes or switching the source water. However, the potential impacts of quality changed supply water on the stabilized ecological niches within DWDSs and the associated water quality deterioration risks were poorly documented. In the present study, such transition effects caused by changing the supply water quality that resulted from destabilization of biofilm and loose deposits in DWDS were investigated by analyzing the physiochemical and microbiological characteristics of suspended particles before (T₀), during (T_3-weeks) and after upgrading the treatments (T_6-months) in an unchlorinated DWDS in the Netherlands. Our results demonstrated that after 6 months' time the upgraded treatments significantly improved the water quality. Remarkably, water quality deterioration was observed at the initial stage when the quality-improved treated water distributed into the network at T_3-weeks, observed as a spike of total suspended solids (TSS, 50-260%), active biomass (ATP, 95-230%) and inorganic elements (e.g. Mn, 130-250%). Furthermore, pyrosequencing results revealed sharp differences in microbial community composition and structure for the bacteria associated with suspended particles between T₀ and T_3-weeks, which re-stabilized after 6 months at T_6-months. The successful capture of transition effects was especially confirmed by the domination of Nitrospira spp. and Polaromonas spp. in the distribution system at T_3-weeks, which were detected at rather low relative abundance at treatment plant. Though the transitional effects were captured, this study shows that the introduction of softening and additional filtration did not have an effect on the water quality for the consumer which improved considerably after 6-months' period. The methodology of monitoring suspended particles with MuPFiSs and additional analysis is capable of detecting transitional effects by monitoring the dynamics of suspended particles and its physiochemical and microbiological composition.

Bringing Community Ecology to Bear on the Issue of Antimicrobial Resistance

Antimicrobial resistance (AMR) is a global concern, pertaining not only to human health but also to the health of industry and the environment. AMR research has traditionally focused on genetic exchange mechanisms and abiotic environmental constraints, leaving important aspects of microbial ecology unresolved. The genetic and ecological aspects of AMR, however, not only contribute separately to the problem but also are interrelated. For example, mutualistic associations among microbes such as biofilms can both serve as a barrier to antibiotic penetration and a breeding ground for horizontal exchange of antimicrobial resistance genes (ARGs). In this review, we elucidate how species interactions promote and impede the establishment, maintenance, and spread of ARGs and indicate how management initiatives might benefit from leveraging the principles and tools of community ecology to better understand and manipulate the processes underlying AMR.

Quantifying the contribution of microbial immigration in engineered water systems

Immigration is a process that can influence the assembly of microbial communities in natural and engineered environments. However, it remains challenging to quantitatively evaluate the contribution of this process to the microbial diversity and function in the receiving ecosystems. Currently used methods, i.e., counting shared microbial species, microbial source tracking, and neutral community model, rely on abundance profile to reveal the extent of overlapping between the upstream and downstream communities. Thus, they cannot suggest the quantitative contribution of immigrants to the downstream community function because activities of individual immigrants are not considered after entering the receiving environment. This limitation can be overcome by using an approach that couples a mass balance model with high-throughput DNA sequencing, i.e., ecogenomics-based mass balance. It calculates the net growth rate of individual microbial immigrants and partitions the entire community into active populations that contribute to the community function and inactive ones that carry minimal function. Linking activities of immigrants to their abundance further provides quantification of the contribution from an upstream environment to the downstream community. Considering only active populations can improve the accuracy of identifying key environmental parameters dictating process performance using methods such as machine learning.

Impacts of diel temperature variations on nitrogen removal and metacommunity of anammox biofilm reactors

The influence of diel temperature variations (DTVs) on nitrogen removal and bacterial communities was investigated in two parallel anammox reactors (i.e., control and DTV reactors). The control reactor was operated at a constant temperature of 30 °C, whereas the DTV reactor was operated in a temperature fluctuation mode with a cycle of 12/12 h of high/low temperatures. Nine water temperature variations for the day/night periods were set from 30/30 °C (i.e., Δ0 °C) to 38/22 °C (i.e., Δ16 °C). An increase in DTVs from Δ8 °C (34/26 °C) to Δ16 °C (38/22 °C) caused a significant decline in reactor performance and a shift in bacterial diversity. Compared to the control reactor, for instance, nitrogen removal efficiency decreased (P < 0.05) when temperature fluctuations exceeded Δ8 °C in the DTV reactor with a decreasing ΔNO₃^-/ΔNH₄⁺ ratio (from 0.21 ± 0.15 to 0.16 ± 0.04). The results of 16S rRNA gene sequencing showed that the initial disturbance of temperature variations led to increased levels of bacterial diversity (i.e., alpha diversity) and decreased community levels of anammox consortia whereas they slightly recovered at the end of each DTV phase. Notably, Candidatus Jettenia was more sensitive to strong water temperature fluctuations, with the lower relative abundance at Δ14 °C (17.11 ± 5.01%) and Δ16 °C (17.83 ± 7.22%) than at Δ4 °C (39.82 ± 0.01%). In contrast, Ca. Brocadia and Ca. Kuenenia had higher relative abundance at Δ14 °C (i.e., 0.24 ± 0.07% and 0.09 ± 0.02%, respectively) and Δ16 °C (i.e., 0.28 ± 0.05% and 0.12 ± 0.03%, respectively) compared to that at Δ4 °C (i.e., 0.15 ± 0.04% and 0.04 ± 0.01%, respectively). Nitrifiers (i.e., unidentified_Nitrospiraceae and Nitrosomonas) and denitrifiers (i.e., Denitratisoma) were also capable of tolerating high temperature perturbations. Overall this study furthers our knowledge of responses of the microbial ecology of anammox bacteria to DTVs in anammox processes, which could aid us in optimizing anammox-related wastewater treatment systems and in understanding the nitrogen cycles of natural ecosystems.

Molecular microbial ecology of stable versus failing rice straw anaerobic digesters

Waste rice straw (RS) is generated in massive quantities around the world and is often burned, creating greenhouse gas and air quality problems. Anaerobic digestion (AD) may be a better option for RS management, but RS is presumed to be comparatively refractory under anaerobic conditions without pre-treatment or co-substrates. However, this presumption assumes frequent reactor feeding regimes but less frequent feeding may be better for RS due to slow hydrolysis rates. Here, we assess how feeding frequency (FF) and organic loading rate (OLR) impacts microbial communities and biogas production in RS AD reactors. Using 16S rDNA amplicon sequencing and bioinformatics, microbial communities from five bench-scale bioreactors were characterized. At low OLR (1.0 g VS l-1  day-1 ), infrequently fed units (once every 21 days) had higher specific biogas yields than more frequent feeding (five in 7 days), although microbial community diversities were statistically similar (P > 0.05; ANOVA with Tukey comparison). In contrast, an increase in OLR to 2.0 g VS l-1  day-1 significantly changed Archaeal and fermenting Eubacterial sub-communities and the least frequency fed reactors failed. 'Stable' reactors were dominated by Methanobacterium, Methanosarcina and diverse Bacteroidetes, whereas 'failed' reactors saw shifts towards Clostridia and Christensenellaceae among fermenters and reduced methanogen abundances. Overall, OLR impacted RS AD microbial communities more than FF. However, combining infrequent feeding and lower OLRs may be better for RS AD because of higher specific yields.

Nontuberculous Mycobacteria in Two Drinking Water Distribution Systems and the Role of Residual Disinfection

Nontuberculous mycobacteria (NTM) are frequently found in chloraminated drinking water distribution systems (DWDSs) due to their chloramine tolerance. NTM were investigated in the water-main biofilms and drinking water of a chloraminated DWDS in the United States (initial chloramine residual = 3.8 ± 0.1 mg L^-1) and a DWDS in Norway with minimal residual disinfectant (0.08 ± 0.01 mg L^-1). Total mycobacteria and Mycobacterium avium complex (MAC) were quantified by qPCR targeting, respectively, atpE genes and the internal transcribed spacer region. Mycobacteria concentrations in drinking water did not differ between the two systems (P = 0.09; up to 6 × 10⁴ copies L^-1) but were higher in the biofilms from the chloraminated DWDS (P = 5 × 10^-9; up to 5 × 10⁶ copies cm^-2). MAC were not detected in either system. Sequencing of mycobacterial hsp65 genes indicated that the chloraminated DWDS lacked diversity and consisted almost exclusively of M. gordonae. In contrast, there were various novel mycobacteria in the no-residual DWDS. Finally, Mycobacterium- and Methylobacterium-like 16S rRNA genes were often detected simultaneously, though without correlation as previously observed. We conclude that, though residual chloramine may increase mycobacterial biomass in a DWDS, it may also decrease mycobacterial diversity.

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.

Comparison of the microbiomes of two drinking water distribution systems-with and without residual chloramine disinfection

BACKGROUND

Residual disinfection is often used to suppress biological growth in drinking water distribution systems (DWDSs), but not without undesirable side effects. In this study, water-main biofilms, drinking water, and bacteria under corrosion tubercles were analyzed from a chloraminated DWDS (USA) and a no-residual DWDS (Norway). Using quantitative real-time PCR, we quantified bacterial 16S rRNA genes and ammonia monooxygenase genes (amoA) of Nitrosomonas oligotropha and ammonia-oxidizing archaea-organisms that may contribute to chloramine loss. PCR-amplified 16S rRNA genes were sequenced to assess community taxa and diversity.

RESULTS

The chloraminated DWDS had lower biofilm biomass (P=1×10^-6) but higher N. oligotropha-like amoA genes (P=2×10^-7) than the no-residual DWDS (medians =4.7×10⁴ and 1.1×10³amoA copies cm^-2, chloraminated and no residual, respectively); archaeal amoA genes were only detected in the no-residual DWDS (median =2.8×10⁴ copies cm^-2). Unlike the no-residual DWDS, biofilms in the chloraminated DWDS had lower within-sample diversity than the corresponding drinking water (P<1×10^-4). Chloramine was also associated with biofilms dominated by the genera, Mycobacterium and Nitrosomonas (≤91.7% and ≤39.6% of sequences, respectively). Under-tubercle communities from both systems contained corrosion-associated taxa, especially Desulfovibrio spp. (≤98.4% of sequences).

CONCLUSIONS

Although residual chloramine appeared to decrease biofilm biomass and alpha diversity as intended, it selected for environmental mycobacteria and Nitrosomonas oligotropha-taxa that may pose water quality challenges. Drinking water contained common freshwater plankton and did not resemble corresponding biofilm communities in either DWDS; monitoring of tap water alone may therefore miss significant constituents of the DWDS microbiome. Corrosion-associated Desulfovibrio spp. were observed under tubercles in both systems but were particularly dominant in the chloraminated DWDS, possibly due to the addition of sulfate from the coagulant alum.