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| 2. |
- Breznau, Nate, et al.
(författare)
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Observing many researchers using the same data and hypothesis reveals a hidden universe of uncertainty
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 119:44
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Tidskriftsartikel (refereegranskat)abstract
- This study explores how researchers analytical choices affect the reliability of scientific findings. Most discussions of reliability problems in science focus on systematic biases. We broaden the lens to emphasize the idiosyncrasy of conscious and unconscious decisions that researchers make during data analysis. We coordinated 161 researchers in 73 research teams and observed their research decisions as they used the same data to independently test the same prominent social science hypothesis: that greater immigration reduces support for social policies among the public. In this typical case of social science research, research teams reported both widely diverging numerical findings and substantive conclusions despite identical start conditions. Researchers expertise, prior beliefs, and expectations barely predict the wide variation in research outcomes. More than 95% of the total variance in numerical results remains unexplained even after qualitative coding of all identifiable decisions in each teams workflow. This reveals a universe of uncertainty that remains hidden when considering a single study in isolation. The idiosyncratic nature of how researchers results and conclusions varied is a previously underappreciated explanation for why many scientific hypotheses remain contested. These results call for greater epistemic humility and clarity in reporting scientific findings.
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| 3. |
- Chan, Sandy, et al.
(författare)
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Bacterial release from pipe biofilm in a full-scale drinking water distribution system
- 2019
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Ingår i: npj Biofilms and Microbiomes. - : Springer Science and Business Media LLC. - 2055-5008. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- Safe drinking water is delivered to the consumer through kilometres of pipes. These pipes are lined with biofilm, which is thought to affect water quality by releasing bacteria into the drinking water. This study describes the number of cells released from this biofilm, their cellular characteristics, and their identity as they shaped a drinking water microbiome. Installation of ultrafiltration (UF) at full scale in Varberg, Sweden reduced the total cell count to 1.5 × 10 3 ± 0.5 × 10 3 cells mL −1 in water leaving the treatment plant. This removed a limitation of both flow cytometry and 16S rRNA amplicon sequencing, which have difficulties in resolving small changes against a high background cell count. Following installation, 58% of the bacteria in the distributed water originated from the pipe biofilm, in contrast to before, when 99.5% of the cells originated from the treatment plant, showing that UF shifts the origin of the drinking water microbiome. The number of bacteria released from the biofilm into the distributed water was 2.1 × 10 3 ± 1.3 × 10 3 cells mL −1 and the percentage of HNA (high nucleic acid) content bacteria and intact cells increased as it moved through the distribution system. DESeq2 analysis of 16S rRNA amplicon reads showed increases in 29 operational taxonomic units (OTUs), including genera identified as Sphingomonas, Nitrospira, Mycobacterium, and Hyphomicrobium. This study demonstrated that, due to the installation of UF, the bacteria entering a drinking water microbiome from a pipe biofilm could be both quantitated and described.
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| 4. |
- Chan, Sandy, et al.
(författare)
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Monitoring biofilm function in new and matured full-scale slow sand filters using flow cytometric histogram image comparison (CHIC)
- 2018
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Ingår i: Water Research. - : Elsevier BV. - 0043-1354. ; 138, s. 27-36
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Tidskriftsartikel (refereegranskat)abstract
- While slow sand filters (SSFs) have produced drinking water for more than a hundred years, understanding of their associated microbial communities is limited. In this study, bacteria in influent and effluent water from full-scale SSFs were explored using flow cytometry (FCM) with cytometric histogram image comparison (CHIC) analysis; and routine microbial counts for heterotrophs, total coliforms and Escherichia coli. To assess if FCM can monitor biofilm function, SSFs differing in age and sand composition were compared. FCM profiles from two established filters were indistinguishable. To examine biofilm in the deep sand bed, SSFs were monitored during a scraping event, when the top layer of sand and the schmutzdecke are removed to restore flow through the filter. The performance of an established SSF was stable: total organic carbon (TOC), pH, numbers of heterotrophs, coliforms, E. coli, and FCM bacterial profile were unaffected by scraping. However, the performance of two newly-built SSFs containing new and mixed sand was compromised: breakthrough of both microbial indicators and TOC occurred following scraping. The compromised performance of the new SSFs was reflected in distinct effluent bacterial communities; and, the presence of microbial indicators correlated to influent bacterial communities. This demonstrated that FCM can monitor SSF performance. Removal of the top layer of sand did not alter the effluent water from the established SSF, but did affect that of the SSFs containing new sand. This suggests that the impact of the surface biofilm on effluent water is greater when the deep sand bed biofilm is not established.
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| 5. |
- Chan, Sandy
(författare)
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Processes governing the drinking water microbiome
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- AbstractSafe drinking water is far from sterile and can contain 10^3-10^5 bacteria/mL. This water microbiome can be altered through various treatment processes in the drinking water treatment plant (DWTP), particularity when it comes in contact with biofilms. Biofilms cover surfaces in the drinking water systems and contain diverse bacterial communities that interact with the water. In this thesis, the bacterial communities in biofilms living on surfaces in a full-scale drinking water distribution system (DWDS), and within different slow sand filters (SSFs), were investigated to understand how they shape and interact with the water microbiome. The installation of ultrafiltration (UF) in a DWTP resulted in extensive removal of bacteria from the distributed water. This permitted the addition of bacteria to the water from the DWDS biofilm to be quantitated in a full-scale system, and was estimated using flow cytometry to account for 58 % of the total bacterial content in the water. Using this estimate and bacterial counts from before UF was installed, when many more bacteria originated from the DWTP, the biofilm then contributed only 0.5 % of bacteria to the water microbiome. DESeq2 analysis of 16S rRNA gene sequences identified specific bacterial taxa released from the biofilm including genera Nitrospira, Sphingomonas and Hyphomicrobium. This study showed that the origin of the water microbiome is complex as it can include dynamic contributions from both the DWTP and the DWDS biofilm.In a DWTP, biofilters alter the water microbiome in ways that can persist throughout the DWDS. To identify factors in these filters that govern this transformation of the water microbiome, different SSFs were compared using flow cytometry with cytometric histogram image comparison (CHIC), and 16S rRNA gene sequencing. In contrast to that seen for new SSFs, removal of the top layer of sand, including the Schmutzdecke, did not affect the removal of E. coli and coliforms, or the transformation of the water microbiome by an established SSF. Using washed sand as an inoculum for new SSF gave a more rapid development of the surface sand community towards that was observed in the established filter. A specific transformation of the water microbiome, including an increase in intact bacteria, and bacteria with low nucleic acid (LNA) content, higher community evenness, and higher abundance of certain bacterial taxa, including Planctomycetes and Pseudomonas, are proposed as a microbial signature for desirable SSF function. This thesis has demonstrated how several technological alterations in DWTPs altered the water microbiome, and contributed to the understanding of how processes can govern the microbiome of drinking water, which is essential for control and management of this important resource.
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| 6. |
- Högmander, Milla, et al.
(författare)
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Luminometric Label Array for Counting and Differentiation of Bacteria
- 2017
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Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 89:5, s. 3208-3216
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Tidskriftsartikel (refereegranskat)abstract
- Methods for simple and fast detection and differentiation of bacterial species are required, for instance, in medicine, water quality monitoring, and the food industry. Here, we have developed a novel label array method for the counting and differentiation of bacterial species. This method is based on the nonspecific interactions of multiple unstable lanthanide chelates and selected chemicals within the sample leading to a luminescence signal profile that is unique to the bacterial species. It is simple, cost-effective, and/or user-friendly compared to many existing methods, such as plate counts on selective media, automatic (hemocytometer-based) cell counters, flow cytometry, and polymerase chain reaction (PCR)-based methods for identification. The performance of the method was demonstrated with nine single strains of bacteria in pure culture. The limit of detection for counting was below 1000 bacteria per mL, with an average coefficient of variation of 10% achieved with the developed label array. A predictive model was trained with the measured luminescence signals and its ability to differentiate all tested bacterial species from each other, including members of the same genus Bacillus licheniformis and Bacillus subtilis, was confirmed via leave-one-out cross-validation. The suitability of the method for analysis of mixtures of bacterial species was shown with ternary mixtures of Bacillus licheniformis, Escherichia coli JM109, and Lactobacillus reuteri ATCC PTA 4659. The potential future application of the method could be monitoring for contamination in pure cultures; analysis of mixed bacterial cultures, where examining one species in the presence of another could inform industrial microbial processes; and the analysis of bacterial biofilms, where nonspecific methods based on physical and chemical characteristics are required instead of methods specific to individual bacterial species.
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| 7. |
- Paul, Catherine J., et al.
(författare)
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Assessment of the mobile biofilm microbiome in distributed drinking water following installation of hybrid ultrafiltration process, in Varberg, Sweden.
- 2018
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Konferensbidrag (refereegranskat)abstract
- Drinking water is delivered from the treatment plant to the consumer through kilometres of pipes. Lining these pipes are communities of bacteria living as biofilms. Little is known about the microbial ecology of these biofilms, as access to drinking water pipes for sampling is often limited to pipes sporadically removed for repair or replacement. Bacteria are constantly exchanged between the biofilm and flowing water, however with bacteria in the water leaving the treatment plant reaching numbers as high as 700 000 cells per millilitre, identifying those cells originating from the biofilm is difficult.Membrane hybrid processes—coagulation coupled with ultrafiltration (UF)—have become a common method to comply with the legal, chemical, and microbiological requirements for drinking water. The main advantages of integrating coagulation with membrane filtration are the enhanced removal of natural organic matter (NOM) and reduced membrane fouling. Therefore, in November 2016, the Kvarnagården WTP in Varberg, Sweden was upgraded with a UF facility (capacity of 1080 m3 h−1 net permeate flow rate). The commissioning of the UF treatment process at Kvarnagården WTP, provided the opportunity to observe the microbial consequences of exposing a distribution system previously exposed to high cellular counts, to a virtually cell-free water phase. By observing which bacteria entered this new water phase, particularly those appearing after an extended time within the distribution system, a snapshot would be obtained of which bacteria can enter the water phase from the pipe biofilm.Water samples were taken before, three days after, and for one month after, installation of UF for flow cytometry (FCM) and Illumina 16S rRNA gene sequencing. FCM gives total cell counts and some additional parameters (%intact cells, %HNA) to describe the bacterial community, while DNA sequencing provides detailed genetic descriptions. Samples from the UF feed showed an average of 8 x105 cells/mL while filtered water contained 2.4 x 104 cells/mL. FCM also showed that UF removed intact cells, but that filtration by this method did not show a preference for either high (HNA) or low (LNA) nucleic acid-containing bacteria. Water samples from three locations at increasing distance from the treatment plant were taken within the distribution system. These samples showed an increase in total cells, with, on average, an addition of 0.6 x 104 cells/ mL, contributed from bacteria leaving the biofilm. These bacteria from the biofilm were further characterized by FCM as intact cells containing an increased percentage of HNA cells, relative to the water leaving the treatment plant. DNA sequencing of all samples, followed by the bioinformatics pipeline QIIME, further revealed the community present in the filtered water originating from the biofilm. Community content in the distributed water was distinct from the finished water, and also differed with respect to location within the distribution system. Both species richness and diversity in the distributed water decreased following installation of UF, as measured by Chao´s richness and Shannon diversity index. Differential analysis of the sequencing reads counts by DESeq2 were used to detect statistical significant operational taxonomic units (OTUs) that have changed over the travel across the pipes. Several groups of bacteria were identified associated with filtered water that had, and had not been, in contact with biofilm. These included Hyphomicrobium, Pedomicrobium, Nitrospira, Sphingomonas, Mycobacterium and Rhodobacter as well as several unidentified genera. This suggests that these are the most mobile members of the pipe biofilms in this distribution system. How the mobility of these groups change over seasons or how the overall microbiome of both the biofilm and the water phase in this distribution system will adapt to the filtered water over a longer time period will provide additional information about how pipe biofilms respond to large changes in the microbiology of distributed water.
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| 8. |
- Paul, Catherine J., et al.
(författare)
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Disturbance of the bacterial communities in drinking water produced from established and newly-built slow sand filters
- 2016
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Konferensbidrag (refereegranskat)abstract
- IntroductionSlow sand filtration is an established method for drinking water treatment, however, the knowledge about their microbial ecology remains limited. Maintenance of slow sand filters (SSF) includes washing to remove biofilm growth in the sand and restore flow through the filter. Understanding how this impacts produced water is important as the SSF may influence the bacterial flora in the finished drinking water and distribution system biofilms (El-Chakhtoura et al. 2015, Lührig et al. 2016, manuscript in preparation). Routine SSF monitoring after washing includes heterotrophic plate count (HPC) however this only describes a small fraction of the bacteria in the water (Allen, Edberg et al. 2004). Flow cytometry (FC) has been proposed for routine monitoring of bacteria in drinking water. FC counts the cells present in water and generates a fingerprint based on describing differential DNA staining to describe the population of bacteria (Arnoldini et al. 2013). Two full-scale new SSFs were constructed using different types of sand as starting material. Traditional microbial parameters (HPC, coliforms and E. coli) and FC data suggested these SSFs differed from each other and were not performing as well as established SSFs (Chan et al. 2016, manuscript in preparation). This study explored: using FC for routine monitoring of SSFs during washing; and, if the response to washing differed between each of the newly built SSFs when compared to an established SSF. Materials and MethodsInfluent and effluent water were characterized using HPC, the Colilert method (E.coli and coliforms), and FC according to established protocols (Prest et al. 2013). FC data was analyzed with Cytometric Histogram Image Comparison (CHIC) (Koch et al. 2013). Results and ConclusionsTwo new SSFs were built using only new sand (SSF-new), or a mix of new sand with sand previously removed during washing from existing sand filters (SSF-mix). After 6 months, the impact on water quality of disturbance from SSF washing was determined by comparing the bacterial populations of the influent and effluent water from SSF-new, SSF-mix, and an established SSF (SSF-est). No significant log reduction of cells was observed in any effluent water. The fluorescence distribution of effluent differed from that of the influent with each SSF showing a unique fingerprint (Fig 1.1). Figure 1.1 Comparison of fluorescence fingerprints for (left to right) SSF-est, SSF-mix, and SSF-new. Profiles show the combined plot of cell concentration and fluorescence distribution of nucleic acid stained with SYBR Green I in effluent water before wash (blue), and 4 days after washing (red).Fingerprints of effluent water were stable throughout the sampling period for SSF-est, regardless of washing, while for SSF-new and SSF-mix, fingerprints suggested a destabilization of the bacterial population related to washing. This suggested that SSF-new, SSF-mix and SSF-est differed in the population of cells being seeded into their respective effluent waters and this was supported by results from traditional methods and qPCR, showing lowest number of coliforms in the effluent from SSF-est. Analysis by CHIC, showed that the cell populations seeded by SSF-mix were more similar to those from SSF-est, than SSF-new. FC fingerprints from SSF-new were very similar to those of the influent water, suggesting that the biofilm in this SSF had little impact on the water passing through SSF-new. Since SSF-mix included washed sand from established SSFs, this appears to have inoculated the SSF-mix biofilm in a way that was not observed for SSF-new. The fingerprints for SSF-est effluent remained stable, consistent with a biofilm that is resilient to disturbance, and coliform counts demonstrating uninterrupted SSF function. This study thus suggests that washed sand is preferable to new sand for SSF construction and that more than 6 months is required for a resilient SSF biofilm. While total cell numbers did not change significantly across any SSF, SSF-est selectively reduced HPC and coliforms suggesting that this biofilm function is selective compared to newer SSF biofilms. In this study FC was not only useful for monitoring total cell counts to follow changes during SSF washing, but showed a consistent effluent water fingerprint associated with a resilient and functional SSF biofilm. As this was not observed for the newly built SSFs, FC can follow both the character and establishment of SSF biofilms and should be helpful for analyzing the impacts of any potential events on SSF biofilm integrity.ReferencesAllen, M.J., Edberg, S.C. and Reasoner, D.J., (2004). Heterotrophic plate count bacteria—what is their significance in drinking water? International journal of food microbiology, 92(3), pp.265-274.Arnoldini, M., Heck, T., Blanco-Fernández, A. and Hammes, F., (2013). Monitoring of dynamic microbiological processes using real-time flow cytometry. PloS one, 8(11), p.e80117.El-Chakhtoura, J., Prest, E., Saikaly, P., van Loosdrecht, M., Hammes, F. and Vrouwenvelder, H., 2015. Dynamics of bacterial communities before and after distribution in a full-scale drinking water network. Water Research, 74, pp.180-190.Koch, C., Fetzer, I., Harms, H. and Müller, S., (2013). CHIC—an automated approach for the detection of dynamic variations in complex microbial communities. Cytometry Part A, 83(6), pp.561-567.Prest, E.I., Hammes, F., Kötzsch, S., Van Loosdrecht, M.C.M. and Vrouwenvelder, J.S., (2013). Monitoring microbiological changes in drinking water systems using a fast and reproducible flow cytometric method. Water research, 47(19), pp.7131-7142.
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| 9. |
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| 10. |
- Pullerits, Kristjan, et al.
(författare)
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Impact of coagulation–ultrafiltration on long-term pipe biofilm dynamics in a full-scale chloraminated drinking water distribution system
- 2020
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Ingår i: Environmental Science: Water Research & Technology. - 2053-1419. ; 6:11, s. 3044-3056
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Tidskriftsartikel (refereegranskat)abstract
- While pipe biofilms in DWDSs (drinking water distribution systems) are thought to affect the quality of distributed water, studies regarding the microbial processes are impeded by the difficulties in accessing biofilm undisturbed by DWDS maintenance. In this study, pipe sections were removed from a fully operational DWDS for biofilm sampling over two years and three months, and before and after start of ultrafiltration (UF) with coagulation treatment in the drinking water treatment plant (DWTP). Water (n = 31), surface biofilm (obtained by swabbing, n = 34) and deep pipe biofilm (obtained by scraping, n = 34) were analyzed with 16S rRNA gene amplicon sequencing; with flow cytometry, and chemical and natural organic matter (NOM) analysis as additional parameters for water quality. UF with coagulation decreased the total cell concentration in the DWDS bulk water from 6.0 × 105 ± 2.3 × 105 cells per ml to 6.0 × 103 ± 8.3 × 103 cells per ml, including fluctuations due to seasonal change, as well as decreasing most analyzed fractions of NOM. UF treatment of the water revealed that 75% ± 18% of the cells in the water originated from DWDS biofilm, confirmed by SourceTracker analysis, with the rest of the cells likely released from biofilm on DWTP storage tanks. Following UF start, the ASVs (amplicon sequence variants) in the deep pipe biofilm decreased, and Evenness and Shannon diversity indices decreased, reflecting the community's response to the new environment created by the altered water quality. The pipe biofilm community was dominated by ASVs classified as Nitrosomonadaceae, Nitrospira, Hyphomicrobium and Sphingomonas, with relative abundances ranging from 5–78%, and also included ASVs of genus Mycobacterium, genus Legionella and order Legionellales. This community composition, together with the observation that turnover of nitrogen compounds was unchanged by UF start, indicate that nitrification in the DWDS was localized to the pipe biofilm.
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| 11. |
- Rosenqvist, Tage, et al.
(författare)
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Inoculation with adapted bacterial communities promotes development of full scale slow sand filters for drinking water production
- 2024
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Ingår i: Water Research. - 1879-2448. ; 253
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Tidskriftsartikel (refereegranskat)abstract
- Gravity-driven filtration through slow sand filters (SSFs) is one of the oldest methods for producing drinking water. As water passes through a sand bed, undesired microorganisms and chemicals are removed by interactions with SSF biofilm and its resident microbes. Despite their importance, the processes through which these microbial communities form are largely unknown, as are the factors affecting these processes. In this study, two SSFs constructed using different sand sources were compared to an established filter and observed throughout their maturation process. One SSF was inoculated through addition of sand scraped from established filters, while the other was not inoculated. The operational and developing microbial communities of SSFs, as well as their influents and effluents, were studied by sequencing of 16S ribosomal rRNA genes. A functional microbial community resembling that of the established SSF was achieved in the inoculated SSF, but not in the non-inoculated SSF. Notably, the non-inoculated SSF had significantly (p < 0.01) higher abundances of classes Armatimonadia, Elusimicrobia, Fimbriimonadia, OM190 (phylum Planctomycetota), Parcubacteria, Vampirivibrionia and Verrucomicrobiae. Conversely, it had lower abundances of classes Anaerolineae, Bacilli, bacteriap25 (phylum Myxococcota), Blastocatellia, Entotheonellia, Gemmatimonadetes, lineage 11b (phylum Elusimicrobiota), Nitrospiria, Phycisphaerae, subgroup 22 (phylum Acidobacteriota) and subgroup 11 (phylum Acidobacteriota). Poor performance of neutral models showed that the assembly and dispersal of SSF microbial communities was mainly driven by selection. The temporal turnover of microbial species, as estimated through the scaling exponent of the species-time relationship, was twice as high in the non-inoculated filter (0.946 ± 0.164) compared to the inoculated filter (0.422 ± 0.0431). This study shows that the addition of an inoculum changed the assembly processes within SSFs. Specifically, the rate at which new microorganisms were observed in the biofilm was reduced. The reduced temporal turnover may be driven by inoculating taxa inhibiting growth, potentially via secondary metabolite production. This in turn would allow the inoculation community to persist and contribute to SSF function.
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| 12. |
- Schleich, Caroline, et al.
(författare)
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Mapping Dynamics of Bacterial Communities in a Full-Scale Drinking Water Distribution System Using Flow Cytometry
- 2019
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Ingår i: Water. - : MDPI AG. - 2073-4441. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Microbial monitoring of drinking water is required to guarantee high quality water and to mitigate health hazards. Flow cytometry (FCM) is a fast and robust method that determines bacterial concentrations in liquids. In this study, FCM was applied to monitor the dynamics of the bacterial communities over one year in a full-scale drinking water distribution system (DWDS), following implementation of ultrafiltration (UF) combined with coagulation at the drinking water treatment plant (DWTP). Correlations between the environmental conditions in the DWDS and microbial regrowth were observed, including increases in total cell counts with increasing retention time (correlation coefficient R = 0.89) and increasing water temperature (up to 5.24-fold increase in cell counts during summer). Temporal and spatial biofilm dynamics affecting the water within the DWDS were also observed, such as changes in the percentage of high nucleic acid bacteria with increasing retention time (correlation coefficient R = −0.79). FCM baselines were defined for specific areas in the DWDS to support future management strategies in this DWDS, including a gradual reduction of chloramine.
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