Investigation of Archaeal and Bacterial community structure of five different small drinking water networks with special regard to the nitrifying microorganisms

Niche Differentiation of Biofilm Microorganisms in a Full-scale Municipal Drinking Water Distribution System in China and Their Implication for Biofilm Control

Biofilms on the inner surface of a drinking water distribution system (DWDS) affect water quality and stability. Understanding the niche differentiation of biofilm microbial communities is necessary for the efficient control of DWDS biofilms. However, biofilm studies are difficult to conduct in the actual DWDS because of inaccessibility to the pipes buried underground. Taking the opportunity of infrastructure construction and relevant pipeline replacement in China, biofilms in a DWDS (a water main and its branch pipes) were collected in situ, followed by analysis on the abundances and community structures of bacterial and archaeal using quantitative PCR and high-throughput sequencing, respectively. Results showed that archaea were detected only in the biofilms of the water main, with a range of 9.4×103~1.1×105 copies/cm2. By contrast, bacteria were detected in the biofilms of branch pipes and the distal part of the water main, with a range of 8.8×103~9.6×106 copies/cm2. Among the biofilm samples, the archaeal community in the central part of the water main showed the highest richness and diversity. Nitrosopumilus was found to be predominant (86.22%) in the biofilms of the proximal part of the water main. However, Methanobrevibacter (87.15%) predominated in the distal part of the water main. The bacterial community of the water main and branch pipes was primarily composed of Firmicutes and Proteobacteria at the phylum level, respectively. Regardless of archaea or bacteria, only few operational taxonomic units (OTUs) (<0.5% of total OTUs) were shared by all the biofilms, indicating the niche differentiation of biofilm microorganisms. Moreover, the high Mn content in the biofilms of the distal sampling location (D3) in the water main was linked to the predominance of Bacillus. Functional gene prediction revealed that the proportion of infectious disease-related genes was 0.44-0.67% in the tested biofilms. Furthermore, functional genes related to the resistance of the bacterial community to disinfections and antibiotics were detected in all the samples, that is, glutathione metabolism-relating genes (0.14-0.65%) and beta-lactam resistance gene (0.01-0.05%). The results of this study indicate the ubiquity of archaea and bacteria in the biofilms of water main and branch pipes, respectively, and pipe diameters could be a major influencing factor on bacterial community structure. In the water main, the key finding was the predominant existence of archaea, particularly Nitrosopumilus and methanogen. Hence, their routine monitoring and probable influences on water quality in pipelines with large diameter should be given more attention. Besides, since Mn-related Bacillus and suspected pathogenic Enterococcus were detected in the biofilm, supplementation of disinfectant may be a feasible strategy for inhibiting their growth and ensuring water quality. In addition, the monitoring on their abundance variation could help to determine the frequency and methods of pipeline maintenance.

Seasonal variations of microbial community and antibiotic resistome in a suburb drinking water distribution system in a northern Chinese city

Antibiotic resistance genes (ARGs) are an emerging issue for drinking water safety. However, the seasonal variation of ARGs in drinking water distribution systems (DWDS) is still unclear. This work revealed the tempo-spatial changes of microbial community, ARGs, mobile genetic elements (MGEs) co-occurring with ARGs, ARG hosts in DWDS bulk water by means of metagenome assembly. The microbial community and antibiotic resistome varied with sampling season and site. Temperature, ammonia, chlorite and total plate count (TPC) drove the variations of microbial community structure. Moreover, environmental parameters (total organic carbon (TOC), chlorite, TPC and hardness) shifted antibiotic resistome. ARGs and MGEs co-occurring with ARGs showed higher relative abundance in summer and autumn, which might be attributed to detached pipe biofilm. In particular, ARG-bacitracin and plasmid were the predominant ARG and MGE, respectively. ARG hosts changed with season and site and were more diverse in summer and autumn. In winter and spring, Limnohabitans and Mycobacterium were the major ARG hosts as well as the dominant genera in microbial community. In addition, in summer and autumn, high relative abundance of Achromobacter and Stenotrophomonas were the hosts harboring many kinds of ARGs and MGEs at site in a residential zone (0.4 km from the water treatment plant). Compared with MGEs, microbial community had a greater contribution to the variation of antibiotic resistome. This work gives new insights into the dynamics of ARGs in full-scale DWDS and the underlying factors.

Selective Enrichment of Nitrososphaera viennensis-Like Ammonia-Oxidizing Archaea over Ammonia-Oxidizing Bacteria from Drinking Water Biofilms

Ammonia-oxidizing archaea (AOA) can oxidize ammonia to nitrite for energy gain. They have been detected in chloraminated drinking water distribution systems (DWDS) along with the more common ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). To date, no members of the AOA have been isolated or enriched from drinking water environments. To begin the investigation of the role of AOA in chloraminated DWDS, we developed a selective approach using biofilm samples from a full-scale operational network as inoculum. A Nitrososphaera viennensis-like AOA taxon was enriched from a mixed community that also included Nitrosomonas-like AOB while gradually scaling up the culture volume. Dimethylthiourea (DMTU) and pyruvate at 100 μM were added to promote the growth of AOA while inhibiting AOB. This resulted in the eventual washout of AOB, while NOB were absent after 2 or 3 rounds of amendment with 24 μM sodium azide. The relative abundance of AOA in the enrichment increased from 0.2% to 39.5% after adding DMTU and pyruvate, and further to 51.6% after filtration through a 0.45-μm pore size membrane, within a period of approximately 6 months. IMPORTANCE Chloramination has been known to increase the risk of nitrification episodes in DWDS due to the presence of ammonia-oxidizing microorganisms. Among them, AOB are more frequently detected than AOA. All publicly available cultures of AOA have been isolated from soil, marine or surface water environments, meaning they are allochthonous to DWDS. Hence, monochloramine exposure studies involving these strains may not accurately reflect their role in DWDS. The described method allows for the rapid enrichment of autochthonous AOA from drinking water nitrifying communities. The high relative abundance of AOA in the resulting enrichment culture reduces any confounding effects of co-existing heterotrophic bacteria when investigating the response of AOA to varied levels of monochloramine in drinking water.

Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems

Nitrification, the oxidation of ammonia to nitrate via nitrite, is important for many engineered water treatment systems. The sequential steps of this respiratory process are carried out by distinct microbial guilds, including ammonia-oxidizing bacteria (AOB) and archaea (AOA), nitrite-oxidizing bacteria (NOB), and newly discovered members of the genus Nitrospira that conduct complete ammonia oxidation (comammox). Even though all of these nitrifiers have been identified within water treatment systems, their relative contributions to nitrogen cycling are poorly understood. Although AOA contribute to nitrification in many wastewater treatment plants, they are generally outnumbered by AOB. In contrast, AOA and comammox Nitrospira typically dominate relatively low ammonia environments such as drinking water treatment, tertiary wastewater treatment systems, and aquaculture/aquarium filtration. Studies that focus on the abundance of ammonia oxidizers may misconstrue the actual role that distinct nitrifying guilds play in a system. Understanding which ammonia oxidizers are active is useful for further optimization of engineered systems that rely on nitrifiers for ammonia removal. This review highlights known distributions of AOA and comammox Nitrospira in engineered water treatment systems and suggests future research directions that will help assess their contributions to nitrification and identify factors that influence their distributions and activity.

Variation of carbonaceous disinfectants by-products precursors and their correlation with molecular characteristics of dissolved organic matter and microbial communities in a raw water distribution system

The raw water distribution systems (RWDSs) play key roles in urban water supply systems. The changes of disinfection byproducts (DBPs) precursors of trihalomethanes (THMs), haloacetic acids (HAAs) and halogenated acetaldehydes (HALs) in the RWDS in Taihu Basin were investigated by formation potentials. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) method and 454-pyrosequencing were employed to study the variation of molecular characteristics of low molecular weight-dissolved organic matter (LMW-DOM) and microbial communities of pipeline biofilms respectively, which played crucial roles in the variation of DBPs precursors. The results showed that both DBPs precursors and the molecular characteristics of LMW-DOM in the RWDS had changed. Moreover, the LMW-DOM could be an indicator due to the good positive correlation with precursors of HAAs and HALs. Specifically, the LMW-DOM showed continuous accumulation in the RWDS. The LMW-DOM tended to possess higher m/z and more CH₂ or long alkyl chains while pre-chlorination controlled this trend. The LMW-DOM in the pre-chlorinated pipe section also possessed higher saturation. Additionally, lignins served as an important part of DBPs precursors and dominated the LMW-DOM. The microbial diversity decreased in the RWDS, and the abundance and diversity of the microbial community in the pre-chlorinated section were significantly lower than those in the no-chlorinated section. Finally, most DBPs precursors had positive correlation with dominant phylum and genus in RWDS. This study reveals variation of DBPs precursors, LMW-DOM and microbial pipeline biofilms as well, and provide important data for further research on raw water safety and stability in RWDSs.

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.

Response of high-, mid- and low-abundant taxa and potential pathogens to eight disinfection methods and their interactions in domestic hot water system

Eight disinfection methods were applied to control biofilm contamination in domestic hot water system. The inactivation efficiency, responses of high- (≥1%), mid- (0.1% ~ 1%) and low-abundant taxa (≤0.1%) to disinfection, and interactions within and across three sub-communities were investigated. Ultraviolet was the most effective disinfection method for total bacteria and Escherichia coli, and chlorine dioxide had the highest inactivation efficiency on heterotrophic bacteria, while silver ions exhibited poor performance on all of them. At the phylum level, the responses of microorganisms to eight disinfection methods were different, but Proteobacteria and Firmicutes dominated in most samples. Eight disinfection methods had a greater impact on the proportion of high- and mid-abundant taxa than that of low-abundant taxa, and led to dissimilar transformations of genera among high-, mid- and low-abundant taxa in each sample. High-, mid- and low-abundant taxa of different samples showed similar structures and were roughly clustered into three Groups. Moreover, high-abundant taxa had more complex internal interactions than mid- and low-abundant taxa, and mainly presented co-occurrence patterns. The associations between high- and low-abundant taxa were close, and some low-abundant genera were identified as hub bacteria, such as Paracoccus, Thioalkalispira and Flavitalea. Furthermore, a total of 23 potential pathogens were detected in this study, and they mainly showed positive interactions, with Mycobacteria and Streptococcus as keystone genera. These results highlight the dissimilar responses of high-, mid- and low-abundant taxa to disinfection, and the critical role of some low-abundant genera in the microbial network, as well as the co-occurrence patterns among potential pathogens.

Decreased natural organic matter in water distribution decreases nitrite formation in non-disinfected conditions, via enhanced nitrite oxidation

Nitrite in drinking water is a potentially harmful substance for humans, and controlling nitrite formation in drinking water distribution systems (DWDSs) is highly important. The effect of natural organic matter (NOM) on the formation of nitrite in simulated distribution systems was studied. The objective was to inspect how a reduced NOM concentration affected nitrite development via nitrification, separated from the effects of disinfection. We observed that nitrite formation was noticeably sensitive to the changes in the NOM concentrations. Nitrite declined with reduced NOM (TOC 1.0 mg L^-1) but increased with the normal NOM concentration of tap water (TOC 1.6 mg L^-1). Ammonium oxidation was not altered by the reduced NOM, however, nitrite oxidation was enhanced significantly according to the pseudo-first order reaction rate model interpretation. The enhanced nitrite oxidation was observed with both ammonium and nitrite as the initial nitrogen source. The theoretical maximum nitrite concentrations were higher with the normal concentration of NOM than with reduced NOM. The results suggest that the role of nitrite oxidation may be quite important in nitrite formation in DWDSs and worth further studies. As a practical result, our study supported enhanced NOM removal in non-disinfected DWDSs.

Investigation of nitrogen pollutants transformation and its pathways along the long-distance prechlorinated raw water distribution system

Understanding the transformation pattern of nitrogen (N) pollutants and its pathways in the prechlorinated raw water distribution system (PRWDS) is vital for controlling the stablitiy and safety of raw water qulity. This study investigated the N transformation, N functional genes and their correlations to find the N transformation pathways along the PRWDS. Results suggested that simultaneous nitrification, anaerobic ammonium oxidation and denitrification (SNAD) contribute to the N transformationin the PRWDS. Along the pipeline, anammox 16S rRNA (9.18 × 10⁷-8.41 × 10⁸ copies/g), limited by prechlorination, was the most abundant N functional genes and anammox process was the main pathway of ammonia nitrogen (NH₄⁺-N). The decreasing NH₄⁺-N was connected with Planctomycetes, Nitrospira and abundance of nxrA attributing to the joint effort of anammox and declined nitrification. The concentration of nitrate (NO₃^--N) increasing at first and then decreasing, was correlated positively with Sphingomonas. because of the declined nitritication and increased denitrification. Besides, the NO₃^--N→NO₂^--N process was considered to be primary NO₃^--N transformation pathways. Increases in the concentration of dissolved organic nitrogen (DON) and nitrite (NO₂^--N) observed in the PRWDS had positive correlation with relative abundance of Pseudomonas. We believe that prechlorination shaped the particular bacterialcharacteristics in biofilms and influenced the N transformation pathways indirectly, resulting in the varying N transformation rules in PRWDSs. Moreover, systematic and extended research is particularly vital for determining the effects of changes in source water quality and environmental conditions on bacterial community structure and N conversion along PRWDSs.

Preparation and characterization of site-specific dechlorinating microbial inocula capable of complete dechlorination enriched in anaerobic microcosms amended with clay mineral

Abstract

Short-chain halogenated aliphatic hydrocarbons (e.g. perchloroethene, trichloroethene) are among the most toxic environmental pollutants. Perchloroethene and trichloroethene can be dechlorinated to non-toxic ethene through reductive dechlorination by Dehalococcoides sp. Bioaugmentation, applying cultures containing organohalide-respiring microorganisms, is a possible technique to remediate sites contaminated with chlorinated ethenes. Application of site specific inocula is an efficient alternative solution. Our aim was to develop site specific dechlorinating microbial inocula by enriching microbial consortia from groundwater contaminated with trichloroethene using microcosm experiments containing clay mineral as solid phase. Our main goal was to develop fast and reliable method to produce large amount (100 L) of bioactive agent with anaerobic fermentation technology. Polyphasic approach has been applied to monitor the effectiveness of dechlorination during the transfer process from bench-scale (500 mL) to industrial-scale (100 L). Gas chromatography measurement and T-RFLP (Terminal Restriction Fragment Length Polymorphism) revealed that the serial subculture of the enrichments shortened the time-course of the complete dechlorination of trichloroethene to ethene and altered the composition of bacterial communities. Complete dechlorination was observed in enrichments with significant abundance of Dehalococcoides sp. cultivated at 8 °C. Consortia incubated in fermenters at 18 °C accelerated the conversion of TCE to ethene by 7–14 days. Members of the enrichments belong to the phyla Bacteroidetes, Chloroflexi, Proteobacteria and Firmicutes. According to the operational taxonomic units, main differences between the composition of the enrichment incubated at 8 °C and 18 °C occurred with relative abundance of acetogenic and fermentative species. In addition to the temperature, the site-specific origin of the microbial communities and the solid phase applied during the fermentation technique contributed to the development of a unique microbial composition.

Graphic abstract

Electronic supplementary material

The online version of this article (10.1007/s11274-020-2806-7) contains supplementary material, which is available to authorized users.

Behavior of Nitrate-Nitrogen and Nitrite-Nitrogen in Drinking Water

Nitrate-nitrogen (NO₃-N) and nitrite-nitrogen (NO₂-N) are constituents of the nitrogen cycle. NO₃-N is toxic to humans, primarily due to its reduction to NO₂-N. In Japan, NO₃-N and NO₂-N levels in tap water must not exceed 10 mg/L and only NO₂-N alone not 0.04 mg/L, respectively. In this study, we verified the effect of microorganisms and ultraviolet (UV) to increase of NO₂-N in water. First, all tested drinking-waters including tap water and commercial mineral water in PET bottles had < 2 mg/L NO₃-N and undetectable levels (< 0.01 mg/L) of NO₂-N. However, we found that NO₂-N was generated in tap water left to stand at room temperature for several days, leading to increases in CF and TC counts and reduction of NO₃-N. We also demonstrated that direct UV and sunlight irradiation of NO₃-N-containing drinking water generated NO₂-N in 1-2 h, with NO₂-N reaching > 0.04 mg/mL by 4-6 h. On the other hand, NO₃-N and NO₂-N were undetectable in commercially purified water.

Effects of feed water NOM variation on chloramine demand from chloramine-decaying soluble microbial products during rechloramination

Earlier, we reported on soluble microbial products-mediated chloramine decay in nitrifying waters. However, we neither separated the agent(s) nor identified the factors that enhanced the production of chloramine-decaying soluble microbial products (cSMPs). Experiments were conducted by feeding reactor sets (each consisting of five reactors connected in series) with treated water (3-8 mg-DOC.L^-1) obtained from a water treatment plant. The reactors simulated various nitrifying conditions that are experienced in a chloraminated system. In unfiltered samples obtained from nitrified reactors, about 89-93% of the dosed chloramine decayed within 40 h. The cSMP-mediated decay accounted for 21-39% of all chloramine decay in the samples from 0 to 5 mg-C.L^-1 fed reactors and 15% in the samples from 7 to 8 mg-C.L^-1 fed reactors. Microbial processes (mediated by nitrifiers and/or heterotrophs) and biomass-associated microbial products (BMPs) in insoluble form accounted for 13-21% for the reactors fed with 0-5 mg-C.L^-1 and 34% for those fed with 7-8 mg-C.L^-1. The cSMPs were separable with a 30 kDa cut-off membrane but not with 50 or 100 kDa membranes, i.e., they were above 30 kDa but below 50 kDa in size, and were confirmed to be a protein(s). The protein(s) accelerated chloramine decay by accelerating chloramine auto-decomposition and nitrite oxidation. As opposed to the traditional belief, unknown factors accounted for approximately 34-53% in commonly encountered re-chloraminated nitrifying waters (2-5 mg-DOC.L^-1). Understanding the identity and role of these factors - such as cSMPs, BMPs, heterotrophs - will lead to a better control of chloramine.

The Seasonality of Nitrite Concentrations in a Chloraminated Drinking Water Distribution System

We studied the seasonal variation of nitrite exposure in a drinking water distribution system (DWDS) with monochloramine disinfection in the Helsinki Metropolitan Area. In Finland, tap water is the main source of drinking water, and thus the nitrite in tap water increases nitrite exposure. Our data included both the obligatory monitoring and a sampling campaign data from a sampling campaign. Seasonality was evaluated by comparing a nitrite time series to temperature and by calculating the seasonal indices of the nitrite time series. The main drivers of nitrite seasonality were the temperature and the water age. We observed that with low water ages (median: 6.7 h) the highest nitrite exposure occurred during the summer months, and with higher water ages (median: 31 h) during the winter months. With the highest water age (190 h), nitrite concentrations were the lowest. At a low temperature, the high nitrite concentrations in the winter were caused by the decelerated ammonium oxidation. The dominant reaction at low water ages was ammonium oxidation into nitrite and, at high water ages, it was nitrite oxidation into nitrate. These results help to direct monitoring appropriately to gain exact knowledge of nitrite exposure. Also, possible future process changes and additional disinfection measures can be designed appropriately to minimize extra nitrite exposure.

Effect of Metal Ions on the Formation of Trichloronitromethane during Chlorination of Catechol and Nitrite

Catechol, nitrite, and dissolved metals are ubiquitous in source drinking water. Catechol and nitrite have been identified as precursors for halonitromethanes (HNMs), but the effect of metal ions on HNM formation during chlorination remains unclear. The main objective of this study was to investigate the effect of metal ions (Fe, Ti, Al) on the formation of trichloronitromethane (TCNM) (the most representative HNM species in disinfected water) on chlorinating catechol and nitrite. Trichloronitromethane was extracted by methyl tert-butyl ether and detected by gas chromatography. The results show that metal ions promoted the formation of TCNM and that the enhancement efficiency followed the order of Fe > Ti > Al. Trichloronitromethane formation increased greatly within 2 h, and a basic condition (pH 8-9) favored TCNM formation more than acidic or neutral conditions. The conjoint effect of the metal-ion mixtures was shown to be similar to that of the single metal ion having the highest promoting effect on TCNM formation. Our results strongly suggest that metal ions play a significant role in enhancing TCNM formation.