The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms

Diverse metabolism drives comammox in continental-scale agricultural streams: Important ammonia oxidation but low N2O production

Agriculture receives approximately 25 % of the annual global nitrogen input, 37 % of which subsequently runs off into adjacent low-order streams and surface water, where it may contribute to high nitrification and nitrous oxide (N2O). However, the mechanisms of nitrification and the pathways controlling N2O production in agricultural streams remain unknown. Here, we report that the third microbial ammonia oxidation process, complete ammonia oxidation (comammox), is widespread and contributes to important ammonia oxidation with low ammonia-N2O conversion in both basin- and continental-scale agricultural streams. The contribution of comammox to ammonia oxidation (21.5 ± 2.3 %) was between that of bacterial (68.6 ± 2.7 %) and archaeal (9.9 ± 1.8 %) ammonia oxidation. Interestingly, N2O production by comammox (18.5 ± 2.1 %) was higher than archaeal (10.5 ± 1.9 %) but significantly lower than bacterial (70.2 ± 2.6 %) ammonia oxidation. The first metagenome-assembled genome (MAG) of comammox bacteria from agricultural streams further revealed their potential extensive diverse and specific metabolism. Their wide habitats might be attributed to the diverse metabolism, i.e. harboring the functional gene of nitrate reduction to ammonia, while the lower N2O would be attributed to their lacking biological function to produce N2O. Our results highlight the importance of widespread comammox in agricultural streams, both for the fate of ammonia fertilizer and for climate change. However, it has not yet been routinely included in Earth system models and IPCC global assessments. Synopsis Widespread but overlooked comammox contributes to important ammonia oxidation but low N2O production, which were proved by the first comammox MAG found in agricultural streams.

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.

Biological Oxygen-dosed Activated Carbon (BODAC) filters - A bioprocess for ultrapure water production removing organics, nutrients and micropollutants

Biological oxygen-dosed activated carbon (BODAC) filters in an Ultrapure water plant were demonstrated to have the potential to further treat secondary wastewater treatment effluent. The BODAC filters were operated for 11 years without carbon regeneration or replacement, while still functioning as pre-treatment step to reverse osmosis (RO) membranes by actively removing organic micropollutants (OMPs) and foulants. In this study, the removal of nutrients and 13 OMPs from secondary wastewater treatment effluent was investigated for 2 years and simultaneously, the granules' characterization and microbial community analysis were conducted to gain insights behind the stable long-term operation of the BODAC filters. The results showed that the BODAC granules' surface area was reduced by ∼70 % of what is in virgin carbon granules and covered by biofilm and inorganic depositions. The BODAC filters reduced the concentration of soluble organics, mainly proteins, performed as an effective nitrification system, and almost completely removed manganese. During the 2 years of observation, the filters consistently removed some OMPs such as hydrochlorothiazide, metoprolol, sotalol, and trimethoprim by at least 70 %. Finally, through microbial community analysis, we found that nitrifying and manganese-oxidizing bacteria were detected in high relative abundance on BODAC granules, supporting BODAC performance in removing OMPs and manganese as well as converting nitrogenous species in the water.

Multi-scale Investigation of Ammonia-Oxidizing Microorganisms in Biofilters Used for Drinking Water Treatment

Ammonia-oxidizing microorganisms (AOMs) include ammonia-oxidizing bacteria (AOB), archaea (AOA), and Nitrospira spp. sublineage II capable of complete ammonia oxidation (comammox). These organisms can affect water quality not only by oxidizing ammonia to nitrite (or nitrate) but also by cometabolically degrading trace organic contaminants. In this study, the abundance and composition of AOM communities were investigated in full-scale biofilters at 14 facilities across North America and in pilot-scale biofilters operated for 18 months at a full-scale water treatment plant. In general, the relative abundance of AOM in most full-scale biofilters and in the pilot-scale biofilters was as follows: AOB > comammox Nitrospira > AOA. The abundance of AOB in the pilot-scale biofilters increased with increasing influent ammonia concentration and decreasing temperature, whereas AOA and comammox Nitrospira exhibited no correlations with these parameters. The biofilters affected AOM abundance in the water passing through the filters via collecting and shedding but exhibited a minor influence on the composition of AOB and Nitrospira sublineage II communities in the filtrate. Overall, this study highlights the relative importance of AOB and comammox Nitrospira compared to AOA in biofilters and the influence of filter influent water quality on AOM in biofilters and their release into the filtrate.

Rapid initiation of a single-stage partial nitritation-anammox process treating low-strength ammonia wastewater: Novel insights into biofilm development on porous polyurethane hydrogel carrier

Media-supported biofilm is a powerful strategy for growth and enrichment of slow-growing microorganisms. In this study, a single-stage nitritation-anammox process treating low-strength wastewater was successfully started to investigate the biofilm development on porous polyurethane hydrogel carrier. Suspended biomass migration into the carrier and being entrapment by its internal interconnected micropores dominated the fast initial colonization stage. Both surface-attached growth and embedded growth of microbes occurred during the following accumulation stage. Fluorescence in situ hybridization analysis of mature biofilm indicated that ammonium-oxidizing bacteria located at the outer layers featured a surface-attached growth, while anammox microcolonies housed in the inner layers proliferated as an embedded-like growth. In this way, the growth rate of anammox bacteria (predominated by Candidatus Kuenenia) could be 0.079 d^-1. The anammox potential of the biofilm reactor reached 1.65 ± 0.3 kg/m³/d within two months. This study provides novel insights into nitritation-anammox biofilm formation on the porous polyurethane hydrogel carrier.

Enhanced bacterial inactivation by activated carbon modified with nano-sized silver oxides: Performance and mechanism

In this study, nano-sized silver oxides were loaded on activated carbon (nAg2O/AC) through a facile impregnation-calcination method for enhanced bacterial inactivation from drinking water, in which Escherichia coli (E. coli) was used as target bacteria. XRD and SEM characterization confirmed that nano-sized Ag2O particles (50-200 nm) were successfully prepared and uniformly distributed on the surfaces and pores of AC. Due to the structural reducing groups of AC, surface-bound Ag(I) was partially converted to Ag in the nAg2O matrix and the resulted Ag could sterilize E. coli directly. More importantly, surface-bound Ag could catalyze O2 and H2O to generate reactive oxygen species (ROS) for oxidation sterilization, thus significantly enhanced the inactivation efficiency from 0.8 log10 CFU/mL (nAg2O control) and 0.2 log10 CFU/mL (AC control) to 6.0 log10 CFU/mL in the nAg2O/AC system. The inactivation process was highly pH-dependent, and neutral pH was favorable for sterilization. A sterilization efficiency of 5.2 log10 CFU/mL could still be achieved after 5 running cycles, indicating stable sterilization performance of nAg2O/AC. In addition, the nAg2O/AC also exhibited excellent renewability since a sterilization efficiency of 5.8 log10 CFU/mL was obtained after nAg2O being stripped and reloaded on the AC. These results demonstrated that nAg2O-modified AC is an efficient material for sterilization in water treatment.

Contaminants of Emerging Concern in the Lower Volta River, Ghana, West Africa: The Agriculture, Aquaculture, and Urban Development Nexus

Contaminants of emerging concern (CECs) are ubiquitous in aquatic environments across all continents and are relatively well known in the developed world. However, few studies have investigated their presence and biological effects in low- and middle-income countries. We provide a survey of CEC presence in the Volta River, Ghana, and examine the microbial consequences of anthropogenic activities along this economically and ecologically important African river. Water and sediment samples were taken by boat or from shore at 14 sites spanning 118 km of river course from the Volta estuary to the Akosombo dam. Sample extracts were prepared for targeted analysis of antimicrobial CECs, N,N-diethyl-meta-toluamide, and per- and polyfluoroalkyl substances (PFAS; water only). Concurrent samples were extracted to characterize the microbial community and antibiotic-resistant genes (ARGs). Antibiotics and PFAS (PFAS, 2-20 ng/L) were found in all water samples; however, their concentrations were usually in the low nanograms per liter range and lower than reported for other African, European, and North American studies. N,N-Diethyl-meta-toluamide was present in all samples. The number of different genes detected (between one and 10) and total ARG concentrations varied in both water (9.1 × 10^-6 to 8.2 × 10^-3 ) and sediment (2.2 × 10^-4 to 5.3 × 10^-2 ), with increases in gene variety at sites linked to urban development, sand mining, agriculture, and shellfish processing. Total ARG concentration spikes in sediment samples were associated with agriculture. No correlations between water quality parameters, CEC presence, and/or ARGs were noted. The presence of CECs in the lower Volta River highlights their global reach. The overall low concentrations of CECs detected is encouraging and, coupled with mitigation measures, can stymie future CEC pollution in the Volta River. Environ Toxicol Chem 2022;41:369-381. © 2021 SETAC.

Instructive analysis of engineered carbon materials for potential application in water and wastewater treatment

Water remediation is an essential component for sustainable development. Increasing population and rapid industrialization have contributed to the deterioration of water resources. In particular, effluents from chemical, pharmaceutical, petroleum industries, and anthropogenic activities have led to severe ecological degradation. Many of these detrimental pollutants are highly toxic even at low concentrations, acting as carcinogens and inflicting severe long-lasting effects on human health. This review underscores the potential applications of engineered carbon-based materials for effective wastewater treatment. It focuses on the performance as well as efficiency of activated carbon, graphene nanomaterial, and carbon nanotubes, both with and without chemical functionalization. Plausible mechanisms of action between the chemically functionalized adsorbent and pollutants are also discussed. Based on the keywords from the literature published in the recent five years, a statistical practicality-vs-applicability analysis of these three materials is also provided. The review will provide a deep understanding of the physical or chemical interactions of the wastewater pollutants with carbon materials.

Machine learning in natural and engineered water systems

Water resources of desired quality and quantity are the foundation for human survival and sustainable development. To better protect the water environment and conserve water resources, efficient water management, purification, and transportation are of critical importance. In recent years, machine learning (ML) has exhibited its practicability, reliability, and high efficiency in numerous applications; furthermore, it has solved conventional and emerging problems in both natural and engineered water systems. For example, ML can predict various water quality indicators in situ and real-time by considering the complex interactions among water-related variables. ML approaches can also solve emerging pollution problems with proven rules or universal mechanisms summarized from the related research. Moreover, by applying image recognition technology to analyze the relationships between image information and physicochemical properties of the research object, ML can effectively identify and characterize specific contaminants. In view of the bright prospects of ML, this review comprehensively summarizes the development of ML applications in natural and engineered water systems. First, the concept and modeling steps of ML are briefly introduced, including data preparation, algorithm selection and model evaluation. In addition, comprehensive applications of ML in recent studies, including predicting water quality, mapping groundwater contaminants, classifying water resources, tracing contaminant sources, and evaluating pollutant toxicity in natural water systems, as well as modeling treatment techniques, assisting characterization analysis, purifying and distributing drinking water, and collecting and treating sewage water in engineered water systems, are summarized. Finally, the advantages and disadvantages of commonly used algorithms are analyzed according to their structures and mechanisms, and recommendations on the selection of ML algorithms for different studies, as well as prospects on the application and development of ML in water science are proposed. This review provides references for solving a wider range of water-related problems and brings further insights into the intelligent development of water science.

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.

Understanding structure/function relationships in nitrifying microbial communities after cross-transfer between freshwater and seawater

In this study, nitrification before and after abrupt cross-transfer in salinity was investigated in two moving bed biofilm reactors inoculated with nitrifying cultures that had adaptation to freshwater (FR) and seawater salinities (SR). FR and SR MBRRs were exposed to short and long term cross-transfer in salinity, and the functional capacity of nitrifying microbial communities was quantified by the estimation of ammonia and nitrite oxidation rates. Salinity induced successions were evaluated before and after salinity change by deep sequencing of 16S rRNA gene amplicons and statistical analysis. The bacterial community structure was characterized and Venn diagrams were included. The results indicated that after salinity cross-transfer, the FR was not significantly recovered at seawater salinity whereas SR showed high resistance to stress caused by low-salt. Succession and physiological plasticity were the main mechanisms of the long-term adaption of the nitrifying communities exposed to abrupt salinity changes. Independently of salinity, some nitrifiers presented high physiological plasticity towards salinity and were very successful at both zero and full seawater salinity. SR culture is robust and suitable inoculum for ammonium removal from recirculating aquaculture systems and industrial wastewaters with variable and fast salinity changes. Our findings contradict the current perspective of the significance of salinity on the structure of nitrifying communities.

Metagenomics approach and canonical correspondence analysis of novel nitrifiers and ammonia-oxidizing archaea in full scale anaerobic-anoxic-oxic (A2/O) and oxidation ditch processes

Various microorganisms are involved in nitrogen removal, and their group compositions depend closely on operating parameters. The structures and functions of nitrification microorganisms in full-scale anaerobic-anoxic-oxic (A2/O) and oxidation ditch processes were analyzed using metagenomics and canonical correspondence analysis. The community structure of ammonia-oxidizing archaea in the oxidation ditch was 3.8 (winter) - 6.3 (summer) times higher than in A2/O, and the complete ammonia oxidizer was only found in the oxidation ditch process. The canonical correspondence analysis of various environmental variables showed that Nitrosomonadales, Crenarchaeota, and Nitrospira inopinata correlate highly with nitrification, and Nitrospira was involved in NO₂^--N oxidation rather than Nitrobacter. The longer solid and hydraulic retention times in the oxidation ditch were more effective in achieving a wider range of novel nitrification than A2/O. This result indicates that microbial communities of novel nitrifiers and ammonia-oxidizing archaea improved in the oxidation ditch process, significantly contributing to stable nitrogen removal.

Effect of Flow Configuration on Nitrifiers in Biological Activated Carbon Filters for Potable Water Production

Up-flow biological activated carbon (BAC) filters have been empirically employed in drinking water treatment plants (DWTPs) to address the challenges of its down-flow counterparts (e.g., high head loss and insufficient use of BAC beds), yet their performances and mechanisms toward ammonia removal are not fully evaluated. This study characterized the occurrence, distribution, and diversities of nitrifiers in up-flow and down-flow BAC filters by investigating 18 full-scale drinking water treatment trains in different geographic locations. Quantitative polymerase chain reaction analysis of gene markers of target microorganisms demonstrated higher numbers of total bacteria, ammonia-oxidizing bacteria (AOB), and Nitrospira in the up-flow filters relative to the down-flow filters (P < 0.05), implying enhanced biological activities and nitrification potential within up-flow filters. The dominance of ammonia-oxidizing archaea (AOA) over AOB (i.e., 1.3-4.0 log₁₀ gene copies higher) in 17 BAC filters illustrated the critical role of AOA in drinking water nitrification. Stratification of biomass was mainly found in the down-flow filters rather than the up-flow filters, suggesting better mixing of filter media across up-flow filter beds. Analysis of similarity results revealed that the AOA and Nitrospira community compositions were mainly affected by water sources and locations (P < 0.05) but not flow configurations. These results provide insight into nitrification mechanisms in BAC filters with different flow configurations in real-world DWTPs.

Efficient removal of 17α-ethinylestradiol from secondary wastewater treatment effluent by a biofilm process incorporating biogenic manganese oxide and Pseudomonas putida strain MnB1

This study proposes a biofilm process to immobilize biogenic manganese oxide (BMO) and Pseudomonas putida MnB1 (BMO-MnB1), which shows excellent synergistic effects for 17α-ethinylestradiol (EE2) from secondary wastewater treatment effluent (WWTE). Modified granular activated carbon (M-GAC) was used as the packing carrier, inoculated with Pseudomonas putida MnB1 and Mn(II) to form the BMO-MnB1 biofilm. Feasibility tests were performed to compare the EE2 removal efficiency with that of the conventional biofilm process (BAC) for heterogeneous microbial communities. Results show that in the BAC, EE2 was removed mainly by adsorption, with biodegradation contributing only slightly to the overall performance. In contrast, the BMO-MnB1 biofilter outperformed the BAC. Furthermore, less than 4% of the total EE2 removed was extracted from the biofilter medium over 150 days of operation, confirming that EE2 was biodegraded by P. putida MnB1 or chemically oxidized by BMO. Our results suggest that BMO-MnB1 biofilm processes have high potential for practical applications in removal of endocrine disrupting compounds from wastewater effluent.

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.

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.

Biofouling of Polyamide Membranes: Fouling Mechanisms, Current Mitigation and Cleaning Strategies, and Future Prospects

Reverse osmosis and nanofiltration systems are continuously challenged with biofouling of polyamide membranes that are used almost exclusively for these desalination techniques. Traditionally, pretreatment and reactive membrane cleanings are employed as biofouling control methods. This in-depth review paper discusses the mechanisms of membrane biofouling and effects on performance. Current industrial disinfection techniques are reviewed, including chlorine and other chemical and non-chemical alternatives to chlorine. Operational techniques such as reactive membrane cleaning are also covered. Based on this review, there are three suggested areas of additional research offering promising, polyamide membrane-targeted biofouling minimization that are discussed. One area is membrane modification. Modification using surface coatings with inclusion of various nanoparticles, and graphene oxide within the polymer or membrane matrix, are covered. This work is in the infancy stage and shows promise for minimizing the contributions of current membranes themselves in promoting biofouling, as well as creating oxidant-resistant membranes. Another area of suggested research is chemical disinfectants for possible application directly on the membrane. Likely disinfectants discussed herein include nitric oxide donor compounds, dichloroisocyanurate, and chlorine dioxide. Finally, proactive cleaning, which aims to control the extent of biofouling by cleaning before it negatively affects membrane performance, shows potential for low- to middle-risk systems.

Transcriptional activity and diversity of comammox bacteria as a previously overlooked ammonia oxidizing prokaryote in full-scale wastewater treatment plants

The discovery of complete ammonia oxidizing bacteria (CAOB) has fundamentally overturned the traditional recognition of nitrification. However, little was known about the transcriptional activity and diversity of the newly recognized ammonia oxidizing prokaryote in engineered ecosystems. To fill this gap, transcriptional investigations of CAOB amoA genes were carried out comparatively with the canonical ammonia oxidizing bacteria (AOB) and archaea (AOA) in eight full-scale wastewater treatment plants (WWTPs). Remarkably, qPCR results revealed the transcriptional levels of CAOB amoA gene were unexpectedly high in most of samples with the highest 24-fold that of AOB amoA, suggesting CAOB were actively participating in ammonia oxidation while they were previously overlooked. This result also well explained the confusing high abundances of genus Nitrospira which were frequently detected in WWTPs. Furthermore, phylogenetic analysis based on high throughput sequencing indicated the CAOB amoA gene sequences formed three well-supported clusters and Nitrospira nitrosa cluster accounted for 97% of all the retrieved sequences, which was supposed to be the dominant taxon of CAOB in the ammonia-intensive environment due to niche partitioning. This study highlighted the significance of including the newly discovered ammonia oxidizing bacterial member when assessing the nitrification process and ecological function in the future.

Removal Efficacy of Opportunistic Pathogens and Bacterial Community Dynamics in Two Drinking Water Treatment Trains

Drinking water treatment processes (DWTPs) impact pathogen colonization and microbial communities in finished water; however, their efficacies against opportunistic pathogens are not fully understood. In this study, the effects of treatment steps on the removal of Legionella spp., Legionella pneumophila, nontuberculous mycobacteria, Mycobacterium avium, and two amoeba hosts (Vermamoeba vermiformis, Acanthamoeba) are evaluated in two parallel trains of DWTPs equipped with different pretreatment units. Quantitative polymerase chain reaction analysis demonstrates significantly reduced numbers of total bacteria, Legionella, and mycobacteria during ozonation, followed by a rebound in granular activated carbon (GAC) filtration, whereas sand filtration exerts an overarching effect in removing microorganisms in both treatment trains. V. vermiformis is more prevalent in biofilm (34%) than water samples (7.7%), while Acanthamoeba is not found in the two trains of DWTPs. Illumina sequencing of bacterial 16S rRNA genes reveals significant community shifts at different treatment steps, as well as distinct bacterial community structures in water and biofilm samples in parallel units (e.g., ozonation, GAC, sand filtration) between the two trains (analysis of similarities (ANOSIM), p < 0.05), implying the potential influence of different pretreatment steps in shaping the downstream microbiome. Overall, the results provide insights to mitigation of opportunistic pathogens and engineer approaches for managing bacterial communities in DWTPs.

Effects of Chloramine and Coupon Material on Biofilm Abundance and Community Composition in Bench-Scale Simulated Water Distribution Systems and Comparison with Full-Scale Water Mains

The vast majority of bacteria in drinking water distribution systems (DWDSs) reside in biofilms on the interior walls of water mains. Little is known about how water quality conditions affect water-main biofilms because of the inherent limitations in experimenting with drinking water supplies and accessing the water mains for sampling. Bench-scale reactors permit experimentation and ease of biofilm sampling, yet questions remain as to how well biofilms in laboratory reactors represent those on water mains. In this study, the effects of DWDS pipe materials and chloramine residual on biofilms were investigated by cultivating biofilms on cement, polyvinyl chloride, and high density polyethylene coupons in CDC reactors for up to 28 months in the presence of chloraminated or dechlorinated tap water. The bench-scale biofilm microbiomes were then compared with the microbiome on a water main from the full-scale system that supplied the water to the reactors. The presence of a chloramine residual (1.74 ± 0.21 mg/L) suppressed biofilm accumulation and selected for Mycobacterium-like and Sphingopyxis-like operational taxonomic units (OTUs) while the destruction of the chloramine residual resulted in a significant increase in biomass quantity and a shift toward a more diverse community dominated by Nitrospira-like OTUs, which, our results suggest, may be complete ammonia oxidizers (comammox). Coupon material, however, had a relatively minor effect on the abundance and community composition of the biofilm bacteria. Although biofilm communities from the chloraminated water reactor and the water mains shared some dominant populations (namely, Mycobacterium- and Nitrosomonas-like OTUs), the communities were significantly different. This manuscript provides novel insights into the effects of dechlorination and pipe material on biofilm community composition. Furthermore, to our knowledge, it is the first study to compare biofilm in a tap water-fed, bench-scale simulated distribution system to biofilm on water mains from the full-scale system supplying the tap water.

Complete ammonia oxidation: an important control on nitrification in engineered ecosystems?

Nitrification has long been considered to be mediated by two distinct microbial guilds, the ammonia-oxidizing bacteria and archaea, and the nitrite-oxidizing bacteria. The process has been widely applied as an environmental biotechnology for ammonium removal during water and wastewater treatment. Recently, bacteria capable of complete nitrification of ammonia to nitrate (a process termed complete ammonia oxidation, or comammox) have been discovered. These novel nitrifiers have been identified in a range of engineered, natural freshwater and terrestrial ecosystems, challenging previously held knowledge on the key microorganisms and biochemical pathways controlling nitrification. This paper discusses the distribution of comammox bacteria with a focus on engineered ecosystems, as well as emerging insights from recent genomic and experimental studies on their ecophysiology.

Density and distribution of nitrifying guilds in rapid sand filters for drinking water production: Dominance of Nitrospira spp

We investigated the density and distribution of total bacteria, canonical Ammonia Oxidizing Bacteria (AOB) (Nitrosomonas plus Nitrosospira), Ammonia Oxidizing Archaea (AOA), as well as Nitrobacter and Nitrospira in rapid sand filters used for groundwater treatment. To investigate the spatial distribution of these guilds, filter material was sampled at four drinking water treatment plants (DWTPs) in parallel filters of the pre- and after-filtration stages at different locations and depths. The target guilds were quantified by qPCR targeting 16S rRNA and amoA genes. Total bacterial densities (ignoring 16S rRNA gene copy number variation) were high and ranged from 10⁹ to 10¹⁰ per gram (10¹⁵ to 10¹⁶ per m³) of filter material. All examined guilds, except AOA, were stratified at only one of the four DWTPs. Densities varied spatially within filter (intra-filter variation) at two of the DWTPs and in parallel filters (inter-filter variation) at one of the DWTPs. Variation analysis revealed random sampling as the most efficient strategy to yield accurate mean density estimates, with collection of at least 7 samples suggested to obtain an acceptable (below half order of magnitude) density precision. Nitrospira was consistently the most dominant guild (5-10% of total community), and was generally up to 4 orders of magnitude more abundant than Nitrobacter and up to 2 orders of magnitude more abundant than canonical AOBs. These results, supplemented with further analysis of the previously reported diversity of Nitrospira in the studied DWTPs based on 16S rRNA and nxrB gene phylogeny (Gülay et al., 2016; Palomo et al., 2016), indicate that the high Nitrospira abundance is due to their comammox (complete ammonia oxidation) physiology. AOA densities were lower than AOB densities, except in the highly stratified filters, where they were of similar abundance. In conclusion, rapid sand filters are microbially dense, with varying degrees of spatial heterogeneity, which requires replicate sampling for a sufficiently precise determination of total microbial community and specific population densities. A consistently high Nitrospira to bacterial and archaeal AOB density ratio suggests that non-canonical pathways for nitrification may dominate the examined RSFs.

Microbial Communities Shaped by Treatment Processes in a Drinking Water Treatment Plant and Their Contribution and Threat to Drinking Water Safety

Bacteria play an important role in water purification in drinking water treatment systems. On one hand, bacteria present in the untreated water may help in its purification through biodegradation of the contaminants. On the other hand, some bacteria may be human pathogens and pose a threat to consumers. The present study investigated bacterial communities using Illumina MiSeq sequencing of 16S rRNA genes and their functions were predicted using PICRUSt in a treatment system, including the biofilms on sand filters and biological activated carbon (BAC) filters, in 4 months. In addition, quantitative analyses of specific bacterial populations were performed by real-time quantitative polymerase chain reaction (qPCR). The bacterial community composition of post-ozonation effluent, BAC effluent and disinfected water varied with sampling time. However, the bacterial community structures at other treatment steps were relatively stable, despite great variations of source water quality, resulting in stable treatment performance. Illumina MiSeq sequencing illustrated that Proteobacteria was dominant bacterial phylum. Chlorine disinfection significantly influenced the microbial community structure, while other treatment processes were synergetic. Bacterial communities in water and biofilms were distinct, and distinctions of bacterial communities also existed between different biofilms. By contrast, the functional composition of biofilms on different filters were similar. Some functional genes related to pollutant degradation were found widely distributed throughout the treatment processes. The distributions of Mycobacterium spp. and Legionella spp. in water and biofilms were revealed by real-time quantitative polymerase chain reaction (qPCR). Most bacteria, including potential pathogens, could be effectively removed by chlorine disinfection. However, some bacteria presented great resistance to chlorine. qPCRs showed that Mycobacterium spp. could not be effectively removed by chlorine. These resistant bacteria and, especially potential pathogens should receive more attention. Redundancy analysis (RDA) showed that turbidity, ammonia nitrogen and total organic carbon (TOC) exerted significant effects on community profiles. Overall, this study provides insight into variations of microbial communities in the treatment processes and aids the optimization of drinking water treatment plant design and operation for public health.

Variation of microbial communities and functional genes during the biofilm formation in raw water distribution systems and associated effects on the transformation of nitrogen pollutants

This study aimed to investigate the variation of microbial communities and functional genes during the biofilm formation in raw water distribution systems without prechlorination and associated effects on the transformation of nitrogen pollutants by using a designed model pipe system. The results showed the transformation of nitrogen pollutants was obvious during the biofilm formation. The richness and diversity of the microbial communities changed significantly. The higher abundance of Nitrospirae in biofilm samples significantly contributed to biological nitrification. In particular, the stable content of Bacteroidetes in the biofilm and soluble microbial products released by the biomass might have enhanced the increase in dissolved organic nitrogen. In addition, the variation tendency of nitrogen functional gene abundances and their strong effects on NH₄⁺-N, NO₂^--N, and NO₃^--N transformation were clearly observed. These findings provide new insights into the evolution of microbial communities and functional genes during the initial operation period of real-world raw water distribution pipes and highlight management and possible safety issues in the subsequent water treatment process.

Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp

Rapid gravity sand filtration is a drinking water production technology widely used around the world. Microbially catalyzed processes dominate the oxidative transformation of ammonia, reduced manganese and iron, methane and hydrogen sulfide, which may all be present at millimolar concentrations when groundwater is the source water. In this study, six metagenomes from various locations within a groundwater-fed rapid sand filter (RSF) were analyzed. The community gene catalog contained most genes of the nitrogen cycle, with particular abundance in genes of the nitrification pathway. Genes involved in different carbon fixation pathways were also abundant, with the reverse tricarboxylic acid cycle pathway most abundant, consistent with an observed Nitrospira dominance. From the metagenomic data set, 14 near-complete genomes were reconstructed and functionally characterized. On the basis of their genetic content, a metabolic and geochemical model was proposed. The organisms represented by draft genomes had the capability to oxidize ammonium, nitrite, hydrogen sulfide, methane, potentially iron and manganese as well as to assimilate organic compounds. A composite Nitrospira genome was recovered, and amo-containing Nitrospira genome contigs were identified. This finding, together with the high Nitrospira abundance, and the abundance of atypical amo and hao genes, suggests the potential for complete ammonium oxidation by Nitrospira, and a major role of Nitrospira in the investigated RSFs and potentially other nitrifying environments.

Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters

Here, we document microbial communities in rapid gravity filtration units, specifically serial rapid sand filters (RSFs), termed prefilters (PFs) and after- filters (AFs), fed with anoxic groundwaters low in organic carbon to prepare potable waters. A comprehensive 16S rRNA-based amplicon sequencing survey revealed a core RSF microbiome comprising few bacterial taxa (29–30 genera) dominated by Nitrospirae, Proteobacteria and Acidobacteria, with a strikingly high abundance (75–87±18%) across five examined waterworks in Denmark. Lineages within the Nitrospira genus consistently comprised the second most and most abundant fraction in PFs (27±23%) and AFs (45.2±23%), respectively, and were far more abundant than typical proteobacterial ammonium-oxidizing bacteria, suggesting a physiology beyond nitrite oxidation for Nitrospira. Within the core taxa, sequences closely related to types with ability to oxidize ammonium, nitrite, iron, manganese and methane as primary growth substrate were identified and dominated in both PFs (73.6±6%) and AFs (61.4±21%), suggesting their functional importance. Surprisingly, operational taxonomic unit richness correlated strongly and positively with sampling location in the drinking water treatment plant (from PFs to AFs), and a weaker negative correlation held for evenness. Significant spatial heterogeneity in microbial community composition was detected in both PFs and AFs, and was higher in the AFs. This is the first comprehensive documentation of microbial community diversity in RSFs treating oligotrophic groundwaters. We have identified patterns of local spatial heterogeneity and dispersal, documented surprising energy–diversity relationships, observed a large and diverse Nitrospira fraction and established a core RSF microbiome.

Metagenomic Evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System

Nitrification plays an important role in regulating the concentrations of inorganic nitrogen species in a range of environments, from drinking water and wastewater treatment plants to the oceans. Until recently, aerobic nitrification was considered to be a two-step process involving ammonia-oxidizing bacteria or archaea and nitrite-oxidizing bacteria. This process requires close cooperation between these two functional guilds for complete conversion of ammonia to nitrate, without the accumulation of nitrite or other intermediates, such as nitrous oxide, a potent greenhouse gas. The discovery of a single organism with the potential to oxidize both ammonia and nitrite adds a new dimension to the current understanding of aerobic nitrification, while presenting opportunities to rethink nitrogen management in engineered systems.

We report metagenomic evidence for the presence of a Nitrospira-like organism with the metabolic potential to perform the complete oxidation of ammonia to nitrate (i.e., it is a complete ammonia oxidizer [comammox]) in a drinking water system. This metagenome bin was discovered through shotgun DNA sequencing of samples from biologically active filters at the drinking water treatment plant in Ann Arbor, MI. Ribosomal proteins, 16S rRNA, and nxrA gene analyses confirmed that this genome is related to Nitrospira-like nitrite-oxidizing bacteria. The presence of the full suite of ammonia oxidation genes, including ammonia monooxygenase and hydroxylamine dehydrogenase, on a single ungapped scaffold within this metagenome bin suggests the presence of recently discovered comammox potential. Evaluations based on coverage and k-mer frequency distribution, use of two different genome-binning approaches, and nucleic acid and protein similarity analyses support the presence of this scaffold within the Nitrospira metagenome bin. The amoA gene found in this metagenome bin is divergent from those of canonical ammonia and methane oxidizers and clusters closely with the unusual amoA gene of comammox Nitrospira. This finding suggests that previously reported imbalances in abundances of nitrite- and ammonia-oxidizing bacteria/archaea may likely be explained by the capacity of Nitrospira-like organisms to completely oxidize ammonia. This finding might have significant implications for our understanding of microbially mediated nitrogen transformations in engineered and natural systems.

IMPORTANCE Nitrification plays an important role in regulating the concentrations of inorganic nitrogen species in a range of environments, from drinking water and wastewater treatment plants to the oceans. Until recently, aerobic nitrification was considered to be a two-step process involving ammonia-oxidizing bacteria or archaea and nitrite-oxidizing bacteria. This process requires close cooperation between these two functional guilds for complete conversion of ammonia to nitrate, without the accumulation of nitrite or other intermediates, such as nitrous oxide, a potent greenhouse gas. The discovery of a single organism with the potential to oxidize both ammonia and nitrite adds a new dimension to the current understanding of aerobic nitrification, while presenting opportunities to rethink nitrogen management in engineered systems.