Biofilm community dynamics in bench-scale annular reactors simulating arrestment of chloraminated drinking water nitrification

Seasonal variations of biofilm C, N and S cycling genes in a pilot-scale chlorinated drinking water distribution system

Biofilms in drinking water distribution systems (DWDS) host diverse microorganisms. However, the functional attributes of DWDS biofilms and their associations with seasonality remain unclear. This study aims to characterize variations in the microbial metabolic traits of DWDS biofilms collected during different seasons, using a pilot-scale DWDS in dark under plug-flow conditions during one-year operation period. Network analysis was used to predict the functional gene hosts. The overall functional attributes determined by shotgun metagenomics exhibited significant differences among seasons. Genes associated with aromatic metabolism, fatty acid biosynthesis and degradation, and capsular extracellular polymeric substance (EPS) were significantly upregulated in summer owing to the higher temperatures and chlorine in the influent of the DWDS. Moreover, the pathways associated with nitrogen, sulfur, glycolysis, and tricarboxylic acid (TCA) cycling, as well as carbon fixation were reconstructed and displayed according to the sampling season. Nitrogen reduction pathways [dissimilatory nitrate reduction to ammonium (DNRA) 73 %, assimilatory nitrate reduction to ammonium (ANRA) 21 %] were identified in DWDS biofilms, but nitrogen oxidation pathways were not. Sulfur cycling were involved in diverse pathways and genes. Glycolysis and TCA cycling offered electron donors and energy sources for nitrogen and sulfur reduction in biofilms. Carbon fixation was observed in DWDS biofilms, with the predominant pathway for fixing carbon dioxide being the reductive citrate cycle (38 %). Constructed functional gene networks composed of carbon, nitrogen, and sulfur cycling-related genes demonstrated synergistic effects (Positive proportion: 63.52-71.09 %). In addition, from spring to autumn, the network complexity decreased and network modularity increased. The assembly mechanism of carbon, nitrogen and sulfur cycling-related genes was driven by stochastic processes for all samples. These results highlight the diverse functional genes in DWDS biofilms, their synergetic interrelationships, and the seasonality effect on functional attributes.

Evaluating the rhizospheric and endophytic bacterial microbiome of pioneering pines in an aggregate mining ecosystem post-disturbance

AIMS

Despite little soil development and organic matter accumulation, lodgepole pine (Pinus contorta var. latifolia) consistently shows vigorous growth on bare gravel substrate of aggregate mining pits in parts of Canadian sub-boreal forests. This study aimed to investigate the bacterial microbiome of lodgepole pine trees growing at an unreclaimed gravel pit in central British Columbia and suggest their potential role in tree growth and survival following mining activity.

METHODS

We characterized the diversity, taxonomic composition, and relative abundance of bacterial communities in rhizosphere and endosphere niches of pine trees regenerating at the gravel pit along with comparing them with a nearby undisturbed forested site using 16S rRNA high-throughput sequencing. Additionally, the soil and plant nutrient contents at both sites were also analyzed.

RESULTS

Although soil N-content at the gravel pit was drastically lower than the forest site, pine tissue N-levels at both sites were identical. Beta-diversity was affected by site and niche-type, signifying that the diversity of bacterial communities harboured by pine trees was different between both sites and among various plant-niches. Bacterial alpha-diversity was comparable at both sites but differed significantly between belowground and aboveground plant-niches. In terms of composition, pine trees predominantly associated with taxa that appear plant-beneficial including phylotypes of Rhizobiaceae, Acetobacteraceae, and Beijerinckiaceae at the gravel pit and Xanthobacteraceae, Acetobacteraceae, Beijerinckiaceae and Acidobacteriaceae at the forest site.

CONCLUSIONS

Our results suggest that, following mining activity, regenerating pine trees recruit bacterial communities that could be plant-beneficial and support pine growth in an otherwise severely N-limited disturbed environment.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11104-022-05327-2.

Bacterial Genes Encoding Resistance Against Antibiotics and Metals in Well-Maintained Drinking Water Distribution Systems in Finland

Information on the co-occurrence of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) among bacterial communities in drinking water distribution systems (DWDSs) is scarce. This study characterized ARGs and MRGs in five well-maintained DWDSs in Finland. The studied DWDSs had different raw water sources and treatment methods. Two of the waterworks employed artificially recharged groundwater (ARGW) and used no disinfection in the treatment process. The other three waterworks (two surface and one groundwater source) used UV light and chlorine during the treatment process. Ten bulk water samples (two from each DWDS) were collected, and environmental DNA was extracted and then sequenced using the Illumina HiSeq platform for high-throughput shotgun metagenome sequencing. A total of 430 ARGs were characterized among all samples with the highest diversity of ARGs identified from samples collected from non-disinfected DWDSs. Furthermore, non-disinfected DWDSs contained the highest diversity of bacterial communities. However, samples from DWDSs using disinfectants contained over double the ratio of ARG reads to 16S rRNA gene reads and most of the MRG (namely mercury and arsenic resistance genes). The total reads and types of ARGs conferring genes associated with antibiotic groups namely multidrug resistance, and bacitracin, beta-lactam, and aminoglycoside and mercury resistance genes increased in waterworks treating surface water with disinfection. The findings of this study contribute toward a comprehensive understanding of ARGs and MRGs in DWDSs. The occurrence of bacteria carrying antibiotic or metal resistance genes in drinking water causes direct exposure to people, and thus, more systematic investigation is needed to decipher the potential effect of these resistomes on human health.

Combined impact of TiO2 nanoparticles and antibiotics on the activity and bacterial community of partial nitrification system

The effects of TiO2 nanoparticles (nano-TiO2) together with antibiotics leaking into wastewater treatment plants (WWTPs), especially the partial nitrification (PN) process remain unclear. To evaluate the combined impact and mechanisms of nano-TiO2 and antibiotics on PN systems, batch experiments were carried out with six bench-scale sequencing batch reactors. Nano-TiO2 at a low level had minimal effects on the PN system. In combination with tetracycline and erythromycin, the acute impact of antibiotics was enhanced. Both steps of nitrification were retarded due to the decrease of bacterial activity and abundance, while nitrite-oxidizing bacteria were more sensitive to the inhibition than ammonia-oxidizing bacteria. Proteobacteria at the phylum level and Nitrosospira at the genus level remained predominant under single and combined impacts. The flow cytometry analysis showed that nano-TiO2 enhanced the toxicity of antibiotics through increasing cell permeability. Our results can help clarify the risks of nano-TiO2 combined with antibiotics to PN systems and explaining the behavior of nanoparticles in WWTPs.

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.

An assessment of the persistence of putative pathogenic bacteria in chloraminated water distribution systems

This study investigated how a chloramine loss and nitrifying conditions influenced putative pathogenic bacterial diversity in bulk water and biofilm of a laboratory- and a full-scale chloraminated water distribution systems. Fifty-four reference databases containing full-length 16S rRNA gene sequences obtained from the National Centre for Biotechnology Information database were prepared to represent fifty-four pathogenic bacterial species listed in the World Health Organisation and Australian Drinking Water Quality Guidelines. When 16S rRNA gene sequences of all samples were screened against the fifty-four reference pathogenic databases, a total of thirty-one putative pathogenic bacteria were detected in both laboratory- and full-scale systems where total chlorine residuals ranged between 0.03 - 2.2 mg/L. Pathogenic bacterial species Mycolicibacterium fortuitum and Pseudomonas aeruginosa were noted in all laboratory (i.e. in bulk water and biofilm) and in bulk water of full-scale samples and Mycolicibacterium fortuitum dominated when chloramine residuals were high. Other different pathogenic bacterial species were observed dominant with decaying chloramine residuals. This study for the first time reports the diverse abundance of putative pathogenic bacteria resilient towards chloramine and highlights that metagenomics surveillance of drinking water can serve as a rapid assessment and an early warning of outbreaks of a large number of putative pathogenic bacteria.

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.

Characterisation of Microbial Community Associated with Different Disinfection Treatments in Hospital hot Water Networks

Many disinfection treatments can be adopted for controlling opportunistic pathogens in hospital water networks in order to reduce infection risk for immunocompromised patients. Each method has limits and strengths and it could determine modifications on bacterial community. The aim of our investigation was to study under real-life conditions the microbial community associated with different chemical (monochloramine, hydrogen peroxide, chlorine dioxide) and non-chemical (hyperthermia) treatments, continuously applied since many years in four hot water networks of the same hospital. Municipal cold water, untreated secondary, and treated hot water were analysed for microbiome characterization by 16S amplicon sequencing. Cold waters had a common microbial profile at genera level. The hot water bacterial profiles differed according to treatment. Our results confirm the effectiveness of disinfection strategies in our hospital for controlling potential pathogens such as Legionella, as the investigated genera containing opportunistic pathogens were absent or had relative abundances ≤1%, except for non-tuberculous mycobacteria, Sphingomonas, Ochrobactrum and Brevundimonas. Monitoring the microbial complexity of healthcare water networks through 16S amplicon sequencing is an innovative and effective approach useful for Public Health purpose in order to verify possible modifications of microbiota associated with disinfection treatments.

Nitrification in Premise Plumbing: A Review

Nitrification is a major issue that utilities must address if they utilize chloramines as a secondary disinfectant. Nitrification is the oxidation of free ammonia to nitrite which is then further oxidized to nitrate. Free ammonia is found in drinking water systems as a result of overfeeding at the water treatment plant (WTP) or as a result of the decomposition of monochloramine. Premise plumbing systems (i.e., the plumbing systems within buildings and homes) are characterized by irregular usage patterns, high water age, high temperature, and high surface-to-volume ratios. These characteristics create ideal conditions for increased chloramine decay, bacterial growth, and nitrification. This review discusses factors within premise plumbing that are likely to influence nitrification, and vice versa. Factors influencing, or influenced by, nitrification include the rate at which chloramine residual decays, microbial regrowth, corrosion of pipe materials, and water conservation practices. From a regulatory standpoint, the greatest impact of nitrification within premise plumbing is likely to be a result of increased lead levels during Lead and Copper Rule (LCR) sampling. Other drinking water regulations related to nitrifying parameters are monitored in a manner to reduce premise plumbing impacts. One way to potentially control nitrification in premise plumbing systems is through the development of building management plans.

Performance and diversity responses of nitrifying biofilms developed on varied materials and topographies to stepwise increases of aeration

Nitrifying biofilms were grown on 3D-printed nylon with three different surface characteristics (flat, millimeter-scale indentations, and indentations with activated carbon (AC) coating) and were subjected to sequentially increasing aeration-based shear to determine the interplay between surface, performance, and microbial populations towards improved design of wastewater treatment media. Biofilms were evaluated for nitrification, biomass detachment, and microbial composition based on Illumina 16s rRNA sequencing. Indentations provided greater stability over flat with respect to population diversity after detachment events but did not improve ammonia removal. AC-surface biofilm had significantly higher removal than uncoated surfaces at low aeration (1.0 L/min, fine) and significantly lower at high aeration (5.0 L/min, coarse). Principal component analyses of microbial communities illustrated temporal shifts over two similar cycles of growth and shear-induced biomass loss, demonstrating that biofilms grew similar consortia across all surfaces, but tended to revert to earlier individual compositions after shear events.

Effect of sequential UV/free chlorine disinfection on opportunistic pathogens and microbial community structure in simulated drinking water distribution systems

Drinking water distribution systems (DWDS) may be a "Trojan Horse" for some waterborne diseases caused by opportunistic pathogens (OPs). In this study, two simulated DWDS inoculated with groundwater were treated with chlorine (Cl₂) and ultraviolet/chlorine (UV/Cl₂) respectively to compare their effects on the OPs distributed in four different phases (bulk water, biofilms, corrosion products, and loose deposits) of DWDS. 16S rRNA genes sequencing and qPCR were used to profile microbial community and quantify target genes of OPs, respectively. Results showed that UV/Cl₂ was more effective than single Cl₂ to control the regrowth of OPs in the water with the same residual chlorine concentration. However, the OPs inhabiting the biofilms, corrosion products, and loose deposits seemed to be tolerant to UV/Cl₂ and Cl₂, demonstrating that OPs residing in these phases were resistant to the disinfection processes. Some significant microbial correlations between OPs and Acanthamoeba were found by Spearman correlative analysis (p < 0.05), demonstrating that the ecological interactions may exist in the DWDS. 16S rRNA genes sequencing of water samples revealed a significant different microbial community structure between UV/Cl₂ and Cl₂. This study may give some implications for controlling the OPs in the DWDS disinfected with UV/Cl₂.

O3-BAC-Cl2: A multi-barrier process controlling the regrowth of opportunistic waterborne pathogens in drinking water distribution systems

Simulated drinking water distribution system (DWDS) treated with O₃-BAC-Cl₂ (ozone-biological activated carbon-chlorine) was constructed to study its effects on the regrowth of five typical opportunistic pathogens (OPs). It was found that O₃-BAC-Cl₂ could significantly reduce the regrowth of target OPs in the effluents of DWDS compared with Cl₂ and O₃-Cl₂ with the same residual chlorine levels. However, the effect of O₃-BAC-Cl₂ on the average numbers of target OPs gene markers in the biofilms of DWDS was not apparent, suggesting that OPs in the biofilms of DWDS were tolerant to the upstream disinfection process. The quantification of target OPs in the BAC-filter column demonstrated that OPs decreased with the increase of depth, which was likely due to the organic nutrient gradient and microbial competition inside the BAC-filter. Increase in the ozone dose could further reduce the OPs at the bottom of the BAC-filter. Spearman correlation analysis demonstrated that some significant correlations existed between target microorganisms, suggesting potential microbial ecological relationships. Overall, our results demonstrated that the BAC-filter may act as a "battlefield" suppressing the OPs through microbial competition. O₃-BAC-Cl₂ could be an effective multi-barrier process to suppress the proliferation of OPs in the bulk water of DWDS. However, OPs protected by the biofilms of DWDS should receive further attention because OPs may be detached and released from the biofilms.

Effects of chlorination/chlorine dioxide disinfection on biofilm bacterial community and corrosion process in a reclaimed water distribution system

In this work, reclaimed water treated with sodium hypochlorite (NaClO) or chlorine dioxide (ClO₂) at 1, 2, and 4 mg/L was operated successively for 30 days respectively, in annular reactors with new cast iron coupons, corresponding to stages I (days 0-30), II (days 31-60), and III (days 61-90). The Illumina HiSeq 2500 sequencing platform was used to analyze the bacterial community composition, scanning electron microscopy and X-ray diffraction analyses were conducted to characterize corrosion scales, and the weight loss method was served to determine the general corrosion rate. Results reveal the precise disinfection effect on biofilm bacteria to be dose dependent and species specific. In stage I, disinfection caused a reduction in the number of operational taxonomic units, but, had little effect on biofilm composition. In stage II, NaClO and ClO₂ induced a reduction of Proteobacteria proportion, but increased the dominance of Firmicutes; the diminished Proteobacteria in NaClO test mainly included Gammaproteobacteria, while, that in ClO₂ test mainly included the Gammaproteobacteria and Betaproteobacteria. In stage III, Firmicutes presented a certain resistance to NaClO and ClO₂ as the accumulation of corrosion scales. Results also indicated that disinfection enhanced the corrosion process, and the promoting effect of ClO₂ was more pronounced than that of NaClO. Moreover, this promoting effect was more obvious in stage I than that in the latter two stages. The strong oxidization effect associated with disinfection in stage I was the dominant factor promoting corrosion, whereas, the bacterial community also played a crucial role in stages II and III.

Effects of graphite nanoparticles on nitrification in an activated sludge system

Graphite nanoparticles (GNPs) might result in unexpected effects during their transportation and transformation in wastewater treatment systems, including strong thermo-catalytic and catalytic effects and microbial cytotoxicity. In particular, the effects of GNPs on the nitrification process in activated sludge systems should be addressed. This study aimed to estimate the influence of GNPs on the nitrification process in a short-term nitrification reactor with exposure to different light sources. The results indicated that GNPs could only improve the efficiency of photothermal transformation slightly in the activated sludge system because of its photothermal effects under the standard illuminant (imitating 1 × sun). However, even with better photothermal effects, the nitrification efficiency still decreased significantly with GNP dosing under the standard illuminant, which might result from stronger cytotoxic effects of GNPs on the nitrifying bacteria. The disappearance of extracellular polymeric substances (EPS) around bacterial cells was observed, and the total quantity of viable bacteria decreased significantly after GNP exposuring. Variation in bacterial groups primarily occurred in nitrifying microbial communities, including Nitrosomonas sp., Nitrosospira sp., Comamonas sp. and Bradyrhizobiace sp. Nitrifiers significantly decreased, while the phyla Gammaproteobacteria, Deinocccus, and Bacteroidetes exhibited greater stability during GNP treatment.

Effect of temperature and colonization of Legionella pneumophila and Vermamoeba vermiformis on bacterial community composition of copper drinking water biofilms

It is unclear how the water-based pathogen, Legionella pneumophila (Lp), and associated free-living amoeba (FLA) hosts change or are changed by the microbial composition of drinking water (DW) biofilm communities. Thus, this study characterized the bacterial community structure over a 7-month period within mature (> 600-day-old) copper DW biofilms in reactors simulating premise plumbing and assessed the impact of temperature and introduction of Lp and its FLA host, Vermamoeba vermiformis (Vv), co-cultures (LpVv). Sequence and quantitative PCR (qPCR) analyses indicated a correlation between LpVv introduction and increases in Legionella spp. levels at room temperature (RT), while at 37°C, Lp became the dominant Legionella spp. qPCR analysis suggested Vv presence may not be directly associated with Lp biofilm growth at RT and 37°C, but may contribute to or be associated with non-Lp legionellae persistence at RT. Two-way PERMANOVA and PCoA revealed that temperature was a major driver of microbiome diversity. Biofilm community composition also changed over the seven-month period and could be associated with significant shifts in dissolved oxygen, alkalinity and various metals in the influent DW. Hence, temperature, biofilm age, DW quality and transient intrusions/amplification of pathogens and FLA hosts may significantly impact biofilm microbiomes and modulate pathogen levels over extended periods.

Response of Simulated Drinking Water Biofilm Mechanical and Structural Properties to Long-Term Disinfectant Exposure

Mechanical and structural properties of biofilms influence the accumulation and release of pathogens in drinking water distribution systems (DWDS). Thus, understanding how long-term residual disinfectants exposure affects biofilm mechanical and structural properties is a necessary aspect for pathogen risk assessment and control. In this study, elastic modulus and structure of groundwater biofilms was monitored by atomic force microscopy (AFM) and optical coherence tomography (OCT) during three months of exposure to monochloramine or free chlorine. After the first month of disinfectant exposure, the mean stiffness of monochloramine- or free-chlorine-treated biofilms was 4 to 9 times higher than those before treatment. Meanwhile, the biofilm thickness decreased from 120 ± 8 μm to 93 ± 6-107 ± 11 μm. The increased surface stiffness and decreased biofilm thickness within the first month of disinfectant exposure was presumably due to the consumption of biomass. However, by the second to third month during disinfectant exposure, the biofilm mean stiffness showed a 2- to 4-fold decrease, and the biofilm thickness increased to 110 ± 7-129 ± 8 μm, suggesting that the biofilms adapted to disinfectant exposure. After three months of the disinfectant exposure process, the disinfected biofilms showed 2-5 times higher mean stiffness (as determined by AFM) and 6-13-fold higher ratios of protein over polysaccharide, as determined by differential staining and confocal laser scanning microscopy (CLSM), than the nondisinfected groundwater biofilms. However, the disinfected biofilms and nondisinfected biofilms showed statistically similar thicknesses (t test, p > 0.05), suggesting that long-term disinfection may not significantly remove net biomass. This study showed how biofilm mechanical and structural properties vary in response to a complex DWDS environment, which will contribute to further research on the risk assessment and control of biofilm-associated-pathogens in DWDS.

Impact of disinfection on drinking water biofilm bacterial community

Disinfectants are commonly applied to control the growth of microorganisms in drinking water distribution systems. However, the effect of disinfection on drinking water microbial community remains poorly understood. The present study investigated the impacts of different disinfectants (chlorine and chloramine) and dosages on biofilm bacterial community in bench-scale pipe section reactors. Illumina MiSeq sequencing illustrated that disinfection strategy could affect both bacterial diversity and community structure of drinking water biofilm. Proteobacteria tended to predominate in chloraminated drinking water biofilms, while Firmicutes in chlorinated and unchlorinated biofilms. The major proteobacterial groups were influenced by both disinfectant type and dosage. In addition, chloramination had a more profound impact on bacterial community than chlorination.