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Pluym T, Waegenaar F, De Gusseme B, Boon N. Microbial drinking water monitoring now and in the future. Microb Biotechnol 2024; 17:e14532. [PMID: 39051617 PMCID: PMC11270321 DOI: 10.1111/1751-7915.14532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024] Open
Abstract
Over time, humanity has addressed microbial water contamination in various ways. Historically, individuals resorted to producing beer to combat the issue. Fast forward to the 19th century, and we witnessed a scientific approach by Robert Koch. His groundbreaking gelatine plating method aimed to identify and quantify bacteria, with a proposed limit of 100 colony-forming units per millilitre (CFU/mL) to avoid Cholera outbreaks. Despite considerable advancements in plating techniques through experimentation with media compositions and growth temperatures, the reliance on a century-old method for water safety remains the state-of-the-art. Even though most countries succeed in producing qualitative water at the end of the production centres, it is difficult to control, and guarantee, the same quality during distribution. Rather than focusing solely on specific sampling points, we propose a holistic examination of the entire water network to ensure comprehensive safety. Current practices leave room for uncertainties, especially given the low concentrations of pathogens. Innovative methods like flow cytometry and flow cytometric fingerprinting offer the ability to detect changes in the microbiome of drinking water. Additionally, molecular techniques and emerging sequencing technologies, such as third-generation sequencing (MinION), mark a significant leap forward, enhancing detection limits and emphasizing the identification of unwanted genes rather than the unwanted bacteria/microorganisms itself. Over the last decades, there has been the realization that the drinking water distribution networks are complex ecosystems that, beside bacteria, comprise of viruses, protozoans and even isopods. Sequencing techniques to find eukaryotic DNA are necessary to monitor the entire microbiome of the drinking water distribution network. Or will artificial intelligence, big data and machine learning prove to be the way to go for (microbial) drinking water monitoring? In essence, it is time to transcend century-old practices and embrace modern technologies to ensure the safety of our drinking water from production to consumption.
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Affiliation(s)
- Thomas Pluym
- Center for Microbial Ecology and Technology (CMET), Department of BiotechnologyGhent UniversityGhentBelgium
- Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE)GhentBelgium
| | - Fien Waegenaar
- Center for Microbial Ecology and Technology (CMET), Department of BiotechnologyGhent UniversityGhentBelgium
- Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE)GhentBelgium
| | - Bart De Gusseme
- Center for Microbial Ecology and Technology (CMET), Department of BiotechnologyGhent UniversityGhentBelgium
- Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE)GhentBelgium
- Farys, Department R&D – Innovation WaterGhentBelgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Department of BiotechnologyGhent UniversityGhentBelgium
- Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE)GhentBelgium
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Hong JK, Kim SB, Wee GN, Kang BR, No JH, Nishu SD, Park J, Lee TK. Assessing long-term ecological impacts of PCE contamination in groundwater using a flow cytometric fingerprint approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172698. [PMID: 38688365 DOI: 10.1016/j.scitotenv.2024.172698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/09/2024] [Accepted: 04/21/2024] [Indexed: 05/02/2024]
Abstract
This study aims to develop and validate a comprehensive method for assessing ecological disturbances in groundwater ecosystems caused by tetrachloroethylene (PCE) contamination, utilizing flow cytometry (FCM) fingerprint approach. We hypothesized that the ecological disturbance resulting from PCE contamination would exhibit 'press disturbance', persisting over extended periods, and inducing notable phenotypic differences in the microbial community compared to undisturbed groundwater. We collected 40 groundwater samples from industrial district with a history of over twenty years of PCE contamination, along with 56 control groundwater from the national surveillance groundwater system. FCM revealed significant alterations in the phenotypic diversity of microbial communities in PCE-contaminated groundwater, particularly during the dry season. The presence of specific dechlorinating bacteria (Dehalococcoides, Dehalogenimonas, and Geobacter) and their syntrophic partners was identified as an indicator of contamination. Phenotypic diversity measures provided clearer and more direct reflections of contamination impact compared to taxonomic diversity measures. This study establishes FCM fingerprinting as a simple, robust, and accurate method for evaluating ecological disturbances, with potential applications in early warning systems and continuous monitoring of groundwater contamination. The findings not only underscore the sensitivity of FCM in detecting phenotypic variations induced by environmental stressors but also highlight its utility in understanding the complex dynamics of microbial communities in contaminated groundwater ecosystems.
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Affiliation(s)
- Jin-Kyung Hong
- Department of Environmental and Energy Engineering, Yonsei University, Wonju 26493, Republic of Korea
| | - Soo Bin Kim
- Department of Environmental and Energy Engineering, Yonsei University, Wonju 26493, Republic of Korea
| | - Gui Nam Wee
- Department of Environmental and Energy Engineering, Yonsei University, Wonju 26493, Republic of Korea
| | - Bo Ram Kang
- Department of Environmental and Energy Engineering, Yonsei University, Wonju 26493, Republic of Korea
| | - Jee Hyun No
- Department of Environmental and Energy Engineering, Yonsei University, Wonju 26493, Republic of Korea
| | - Susmita Das Nishu
- Department of Environmental and Energy Engineering, Yonsei University, Wonju 26493, Republic of Korea
| | - Joonhong Park
- Department of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Tae Kwon Lee
- Department of Environmental and Energy Engineering, Yonsei University, Wonju 26493, Republic of Korea.
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3
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Dowdell KS, Olsen K, Martinez Paz EF, Sun A, Keown J, Lahr R, Steglitz B, Busch A, LiPuma JJ, Olson T, Raskin L. Investigating the suitability of online flow cytometry for monitoring full-scale drinking water ozone system disinfection effectiveness. WATER RESEARCH 2024; 257:121702. [PMID: 38749337 DOI: 10.1016/j.watres.2024.121702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/02/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024]
Abstract
While online monitoring of physicochemical parameters has widely been incorporated into drinking water treatment systems, online microbial monitoring has lagged behind, resulting in the use of surrogate parameters (disinfectant residual, applied dose, concentration × time, CT) to assess disinfection system performance. Online flow cytometry (online FCM) allows for automated quantification of total and intact microbial cells. This study sought to investigate the feasibility of online FCM for full-scale drinking water ozone disinfection system performance monitoring. A water treatment plant with high lime solids turbidity in the ozone contactor influent was selected to evaluate the online FCM in challenging conditions. Total and intact cell counts were monitored for 40 days and compared to surrogate parameters (ozone residual, ozone dose, and CT) and grab sample assay results for cellular adenosine triphosphate (cATP), heterotrophic plate counts (HPC), impedance flow cytometry, and 16S rRNA gene sequencing. Online FCM provided insight into the dynamics of the full-scale ozone system, including offering early warning of increased contactor effluent cell concentrations, which was not observed using surrogate measures. Positive correlations were observed between online FCM intact cell counts and cATP levels (Kendall's tau=0.40), HPC (Kendall's tau=0.20), and impedance flow cytometry results (Kendall's tau=0.30). Though a strong correlation between log intact cell removal and CT was not observed, 16S rRNA gene sequencing results showed that passage through the ozone contactor significantly changed the microbial community (p < 0.05). Potential causes of the low overall cell inactivation in the contactor and the significant changes in the microbial community after ozonation include regrowth in the later chambers of the contactor and varied ozone resistance of drinking water microorganisms. This study demonstrates the suitability of direct, online microbial analysis for monitoring full-scale disinfection systems.
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Affiliation(s)
- Katherine S Dowdell
- Department of Civil and Environmental Engineering, University of Michigan, 1353 Beal Ave., Ann Arbor, MI 48109, USA
| | - Kirk Olsen
- Department of Civil and Environmental Engineering, University of Michigan, 1353 Beal Ave., Ann Arbor, MI 48109, USA
| | - Ernesto F Martinez Paz
- Department of Civil and Environmental Engineering, University of Michigan, 1353 Beal Ave., Ann Arbor, MI 48109, USA
| | - Aini Sun
- Department of Civil and Environmental Engineering, University of Michigan, 1353 Beal Ave., Ann Arbor, MI 48109, USA
| | - Jeff Keown
- Ann Arbor Water Treatment Plant, City of Ann Arbor, 919 Sunset Rd., Ann Arbor, MI 48103, USA
| | - Rebecca Lahr
- Ann Arbor Water Treatment Plant, City of Ann Arbor, 919 Sunset Rd., Ann Arbor, MI 48103, USA
| | - Brian Steglitz
- Ann Arbor Water Treatment Plant, City of Ann Arbor, 919 Sunset Rd., Ann Arbor, MI 48103, USA
| | - Andrea Busch
- Great Lakes Water Authority, 9300W. Jefferson Ave, Detroit, MI 48209, USA
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, 8323 MSRB III, SPC5646, 1150W. Med Cntr Dr., Ann Arbor, MI 48109, USA
| | - Terese Olson
- Department of Civil and Environmental Engineering, University of Michigan, 1353 Beal Ave., Ann Arbor, MI 48109, USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, University of Michigan, 1353 Beal Ave., Ann Arbor, MI 48109, USA.
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Waegenaar F, García-Timermans C, Van Landuyt J, De Gusseme B, Boon N. Impact of operational conditions on drinking water biofilm dynamics and coliform invasion potential. Appl Environ Microbiol 2024; 90:e0004224. [PMID: 38647288 PMCID: PMC11107155 DOI: 10.1128/aem.00042-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/27/2024] [Indexed: 04/25/2024] Open
Abstract
Biofilms within drinking water distribution systems serve as a habitat for drinking water microorganisms. However, biofilms can negatively impact drinking water quality by causing water discoloration and deterioration and can be a reservoir for unwanted microorganisms. In this study, we investigated whether indicator organisms for drinking water quality, such as coliforms, can settle in mature drinking water biofilms. Therefore, a biofilm monitor consisting of glass rings was used to grow and sample drinking water biofilms. Two mature drinking water biofilms were characterized by flow cytometry, ATP measurements, confocal laser scanning microscopy, and 16S rRNA sequencing. Biofilms developed under treated chlorinated surface water supply exhibited lower cell densities in comparison with biofilms resulting from treated groundwater. Overall, the phenotypic as well as the genotypic characteristics were significantly different between both biofilms. In addition, the response of the biofilm microbiome and possible biofilm detachment after minor water quality changes were investigated. Limited changes in pH and free chlorine addition, to simulate operational changes that are relevant for practice, were evaluated. It was shown that both biofilms remained resilient. Finally, mature biofilms were prone to invasion of the coliform, Serratia fonticola. After spiking low concentrations (i.e., ±100 cells/100 mL) of the coliform to the corresponding bulk water samples, the coliforms were able to attach and get established within the mature biofilms. These outcomes emphasize the need for continued research on biofilm detachment and its implications for water contamination in distribution networks. IMPORTANCE The revelation that even low concentrations of coliforms can infiltrate into mature drinking water biofilms highlights a potential public health concern. Nowadays, the measurement of coliform bacteria is used as an indicator for fecal contamination and to control the effectiveness of disinfection processes and the cleanliness and integrity of distribution systems. In Flanders (Belgium), 533 out of 18,840 measurements exceeded the established norm for the coliform indicator parameter in 2021; however, the source of microbial contamination is mostly unknown. Here, we showed that mature biofilms, are susceptible to invasion of Serratia fonticola. These findings emphasize the importance of understanding and managing biofilms in drinking water distribution systems, not only for their potential to influence water quality, but also for their role in harboring and potentially disseminating pathogens. Further research into biofilm detachment, long-term responses to operational changes, and pathogen persistence within biofilms is crucial to inform strategies for safeguarding drinking water quality.
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Affiliation(s)
- Fien Waegenaar
- Department of Biotechnology, Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
- Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Ghent, Belgium
| | - Cristina García-Timermans
- Department of Biotechnology, Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
- Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Ghent, Belgium
| | - Josefien Van Landuyt
- Department of Biotechnology, Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
- Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Ghent, Belgium
| | - Bart De Gusseme
- Department of Biotechnology, Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
- Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Ghent, Belgium
- Farys, Department R&D – Innovation Water, Ghent, Belgium
| | - Nico Boon
- Department of Biotechnology, Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
- Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Ghent, Belgium
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Egli T, Campostrini L, Leifels M, Füchslin HP, Kolm C, Dan C, Zimmermann S, Hauss V, Guiller A, Grasso L, Shajkofci A, Farnleitner AH, Kirschner AKT. Domestic hot-water boilers harbour active thermophilic bacterial communities distinctly different from those in the cold-water supply. WATER RESEARCH 2024; 253:121109. [PMID: 38377920 DOI: 10.1016/j.watres.2024.121109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 02/22/2024]
Abstract
Running cold and hot water in buildings is a widely established commodity. However, interests regarding hygiene and microbiological aspects had so far been focussed on cold water. Little attention has been given to the microbiology of domestic hot-water installations (DHWIs), except for aspects of pathogenic Legionella. World-wide, regulations consider hot (or warm) water as 'heated drinking water' that must comply (cold) drinking water (DW) standards. However, the few reports that exist indicate presence and growth of microbial flora in DHWIs, even when supplied with water with disinfectant residual. Using flow cytometric (FCM) total cell counting (TCC), FCM-fingerprinting, and 16S rRNA-gene-based metagenomic analysis, the characteristics and composition of bacterial communities in cold drinking water (DW) and hot water from associated boilers (operating at 50 - 60 °C) was studied in 14 selected inhouse DW installations located in Switzerland and Austria. A sampling strategy was applied that ensured access to the bulk water phase of both, supplied cold DW and produced hot boiler water. Generally, 1.3- to 8-fold enhanced TCCs were recorded in hot water compared to those in the supplied cold DW. FCM-fingerprints of cold and corresponding hot water from individual buildings indicated different composition of cold- and hot-water microbial floras. Also, hot waters from each of the boilers sampled had its own individual FCM-fingerprint. 16S rRNA-gene-based metagenomic analysis confirmed the marked differences in composition of microbiomes. E.g., in three neighbouring houses supplied from the same public network pipe each hot-water boiler contained its own thermophilic bacterial flora. Generally, bacterial diversity in cold DW was broad, that in hot water was restricted, with mostly thermophilic strains from the families Hydrogenophilaceae, Nitrosomonadaceae and Thermaceae dominating. Batch growth assays, consisting of cold DW heated up to 50 - 60 °C and inoculated with hot water, resulted in immediate cell growth with doubling times between 5 and 10 h. When cold DW was used as an inoculum no significant growth was observed. Even boilers supplied with UVC-treated cold DW contained an actively growing microbial flora, suggesting such hot-water systems as autonomously operating, thermophilic bioreactors. The generation of assimilable organic carbon from dissolved organic carbon due to heating appears to be the driver for growth of thermophilic microbial communities. Our report suggests that a man-made microbial ecosystem, very close to us all and of potential hygienic importance, may have been overlooked so far. Despite consumers having been exposed to microbial hot-water flora for a long time, with no major pathogens so far been associated specifically with hot-water usage (except for Legionella), the role of harmless thermophiles and their interaction with potential human pathogens able to grow at elevated temperatures in DHWIs remains to be investigated.
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Affiliation(s)
- Thomas Egli
- Microbes-in-Water GmbH, Feldmeilen CH-8706, Switzerland.
| | - Lena Campostrini
- Institute for Hygiene and Applied Immunology, Water Microbiology, Medical University of Vienna, Vienna A-1090, Austria; Interuniversity Cooperation Centre Water & Health, Austria
| | - Mats Leifels
- Division of Water Quality and Health, Dept. Pharmacology, Physiology and Microbiology, Karl Landsteiner University, Krems A-3500, Austria; Interuniversity Cooperation Centre Water & Health, Austria
| | | | - Claudia Kolm
- Division of Water Quality and Health, Dept. Pharmacology, Physiology and Microbiology, Karl Landsteiner University, Krems A-3500, Austria; Centre for Water Resource Systems, Vienna University of Technology, Vienna A-1040, Austria; Interuniversity Cooperation Centre Water & Health, Austria
| | - Cheng Dan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | | | - Vivian Hauss
- bNovate Technologies SA, Zurich CH-8045, Switzerland
| | | | | | | | - Andreas H Farnleitner
- Division of Water Quality and Health, Dept. Pharmacology, Physiology and Microbiology, Karl Landsteiner University, Krems A-3500, Austria; Centre for Water Resource Systems, Vienna University of Technology, Vienna A-1040, Austria; Interuniversity Cooperation Centre Water & Health, Austria
| | - Alexander K T Kirschner
- Institute for Hygiene and Applied Immunology, Water Microbiology, Medical University of Vienna, Vienna A-1090, Austria; Division of Water Quality and Health, Dept. Pharmacology, Physiology and Microbiology, Karl Landsteiner University, Krems A-3500, Austria; Interuniversity Cooperation Centre Water & Health, Austria.
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6
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Claveau L, Hudson N, Jeffrey P, Hassard F. To gate or not to gate: Revisiting drinking water microbial assessment through flow cytometry fingerprinting. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169138. [PMID: 38070556 DOI: 10.1016/j.scitotenv.2023.169138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/20/2023] [Accepted: 12/04/2023] [Indexed: 01/18/2024]
Abstract
Flow cytometry has been utilized for over a decade as a rapid and reproducible approach to assessing microbial quality of drinking water. However, the need for specialized expertise in gating-a fundamental strategy for distinguishing cell populations-introduces the potential for human error and obstructs the standardization of methods. This work conducts a comprehensive analysis of various gating approaches applied to flow cytometric scatter plots, using a dataset spanning a year. A sensitivity analysis is carried out to examine the impact of different gating strategies on final cell count results. The findings show that dynamic gating, which requires user intervention, is essential for the analysis of highly variable raw waters and distributed water. In contrast, static gating proved suitable for more stable water sources, interstage sample locations, and water presenting a particularly low cell count. Our conclusions suggest that cell count analysis should be supplemented with fluorescence fingerprinting to gain a more complete understanding of the variability in microbial populations within drinking water supplies. Establishing dynamic baselines for each water type in FCM monitoring studies is essential for choosing the correct gating strategy. FCM fingerprinting offers a dynamic approach to quantify treatment processes, enabling options for much better monitoring and control. This study offers new insights into the vagaries of various flow cytometry gating strategies, thereby substantially contributing to best practices in the water industry. The findings foster more efficient and reliable water analysis, improving of standardizing methods in microbial water quality assessment using FCM.
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Affiliation(s)
- L Claveau
- Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK
| | - N Hudson
- South East Water, Rocfort Road, Snodland, Kent ME6 5AH, UK
| | - P Jeffrey
- Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK
| | - F Hassard
- Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK.
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7
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Sabbe K, D'Haen L, Boon N, Ganigué R. Predicting the performance of chain elongating microbiomes through flow cytometric fingerprinting. WATER RESEARCH 2023; 243:120323. [PMID: 37459796 DOI: 10.1016/j.watres.2023.120323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 09/07/2023]
Abstract
As part of the circular bio-economy paradigm shift, waste management and valorisation practices have moved away from sanitation and towards the production of added-value compounds. Recently, the development of mixed culture bioprocess for the conversion of waste(water) to platform chemicals, such as medium chain carboxylic acids, has attracted significant interest. Often, the microbiology of these novel bioprocesses is less diverse and more prone to disturbances, which can lead to process failure. This issue can be tackled by implementing an advanced monitoring strategy based on the microbiology of the process. In this study, flow cytometry was used to monitor the microbiology of lactic acid chain elongation for the production of caproic acid, and assess its performance both qualitatively and quantitatively. Two continuous stirred tank reactors for chain elongation were monitored flow cytometrically for over 336 days. Through community typing, four specific community types could be identified and correlated to both a specific functionality and genotypic diversity. Additionally, the machine-learning algorithms trained in this study demonstrated the ability to predict production rates of, amongst others, caproic acid with high accuracy in the present (R² > 0.87) and intermediate accuracy in the near future (R² > 0.63). The identification of specific community types and the development of predictive algorithms form the basis of advanced bioprocess monitoring based on flow cytometry, and have the potential to improve bioprocess control and optimization, leading to better product quality and yields.
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Affiliation(s)
- Kevin Sabbe
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052 Ghent, Belgium
| | - Liese D'Haen
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052 Ghent, Belgium
| | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052 Ghent, Belgium.
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Mermans F, Mattelin V, Van den Eeckhoudt R, García-Timermans C, Van Landuyt J, Guo Y, Taurino I, Tavernier F, Kraft M, Khan H, Boon N. Opportunities in optical and electrical single-cell technologies to study microbial ecosystems. Front Microbiol 2023; 14:1233705. [PMID: 37692384 PMCID: PMC10486927 DOI: 10.3389/fmicb.2023.1233705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/03/2023] [Indexed: 09/12/2023] Open
Abstract
New techniques are revolutionizing single-cell research, allowing us to study microbes at unprecedented scales and in unparalleled depth. This review highlights the state-of-the-art technologies in single-cell analysis in microbial ecology applications, with particular attention to both optical tools, i.e., specialized use of flow cytometry and Raman spectroscopy and emerging electrical techniques. The objectives of this review include showcasing the diversity of single-cell optical approaches for studying microbiological phenomena, highlighting successful applications in understanding microbial systems, discussing emerging techniques, and encouraging the combination of established and novel approaches to address research questions. The review aims to answer key questions such as how single-cell approaches have advanced our understanding of individual and interacting cells, how they have been used to study uncultured microbes, which new analysis tools will become widespread, and how they contribute to our knowledge of ecological interactions.
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Affiliation(s)
- Fabian Mermans
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
- Department of Oral Health Sciences, KU Leuven, Leuven, Belgium
| | - Valérie Mattelin
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Ruben Van den Eeckhoudt
- Micro- and Nanosystems (MNS), Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
| | - Cristina García-Timermans
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Josefien Van Landuyt
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Yuting Guo
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Irene Taurino
- Micro- and Nanosystems (MNS), Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
- Semiconductor Physics, Department of Physics and Astronomy, KU Leuven, Leuven, Belgium
| | - Filip Tavernier
- MICAS, Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
| | - Michael Kraft
- Micro- and Nanosystems (MNS), Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
- Leuven Institute of Micro- and Nanoscale Integration (LIMNI), KU Leuven, Leuven, Belgium
| | - Hira Khan
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
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9
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Park JW, Boxall J, Maeng SK. Predicting heterotrophic plate count exceedance in tap water: A binary classification model supervised by culture-independent data. WATER RESEARCH 2023; 242:120172. [PMID: 37307683 DOI: 10.1016/j.watres.2023.120172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/14/2023]
Abstract
Culture-independent data can be utilized to identify heterotrophic plate count (HPC) exceedances in drinking water. Although HPC represents less than 1% of the bacterial community and exhibits time lags of several days, HPC data are widely used to assess the microbiological quality of drinking water and are incorporated into drinking water standards. The present study confirmed the nonlinear relationships between HPC, intact cell count (ICC), and adenosine triphosphate (ATP) in tap water samples (stagnant and flushed). By using a combination of ICC, ATP, and free chlorine data as inputs, we show that HPC exceedance can be classified using a 2-layer feed-forward artificial neural network (ANN). Despite the nonlinearity of HPC, the best binary classification model showed accuracies of 95%, sensitivity of 91%, and specificity of 96%. ICC and chlorine concentrations were the most important features for classifiers. The main limitations, such as sample size and class imbalance, were also discussed. The present model provides the ability to convert data from emerging measurement techniques into established and well-understood measures, overcoming culture dependence and offering near real-time data to help ensure the biostability and safety of drinking water.
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Affiliation(s)
- Ji Won Park
- Department of Civil and Environmental Engineering, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul 05006, Republic of Korea
| | - Joby Boxall
- Department of Civil and Structural Engineering, University of Sheffield, S13JD, United Kingdom
| | - Sung Kyu Maeng
- Department of Civil and Environmental Engineering, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul 05006, Republic of Korea.
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10
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López-Gálvez J, Schiessl K, Besmer MD, Bruckmann C, Harms H, Müller S. Development of an Automated Online Flow Cytometry Method to Quantify Cell Density and Fingerprint Bacterial Communities. Cells 2023; 12:1559. [PMID: 37371029 DOI: 10.3390/cells12121559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/09/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Cell density is an important factor in all microbiome research, where interactions are of interest. It is also the most important parameter for the operation and control of most biotechnological processes. In the past, cell density determination was often performed offline and manually, resulting in a delay between sampling and immediate data processing, preventing quick action. While there are now some online methods for rapid and automated cell density determination, they are unable to distinguish between the different cell types in bacterial communities. To address this gap, an online automated flow cytometry procedure is proposed for real-time high-resolution analysis of bacterial communities. On the one hand, it allows for the online automated calculation of cell concentrations and, on the other, for the differentiation between different cell subsets of a bacterial community. To achieve this, the OC-300 automation device (onCyt Microbiology, Zürich, Switzerland) was coupled with the flow cytometer CytoFLEX (Beckman Coulter, Brea, USA). The OC-300 performs the automatic sampling, dilution, fixation and 4',6-diamidino-2-phenylindole (DAPI) staining of a bacterial sample before sending it to the CytoFLEX for measurement. It is demonstrated that this method can reproducibly measure both cell density and fingerprint-like patterns of bacterial communities, generating suitable data for powerful automated data analysis and interpretation pipelines. In particular, the automated, high-resolution partitioning of clustered data into cell subsets opens up the possibility of correlation analysis to identify the operational or abiotic/biotic causes of community disturbances or state changes, which can influence the interaction potential of organisms in microbiomes or even affect the performance of individual organisms.
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Affiliation(s)
- Juan López-Gálvez
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany
| | | | - Michael D Besmer
- onCyt Microbiology AG, Marchwartstrasse 61, 8038 Zürich, Switzerland
| | - Carmen Bruckmann
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Susann Müller
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany
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11
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Koppanen M, Kesti T, Rintala J, Palmroth M. Can online particle counters and electrochemical sensors distinguish normal periodic and aperiodic drinking water quality fluctuations from contamination? THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162078. [PMID: 36764531 DOI: 10.1016/j.scitotenv.2023.162078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Early warning systems monitoring the quality of drinking water need to distinguish between normal quality fluctuations and those caused by contaminants. Thus, to decrease the number of false positive events, normal water quality fluctuations, whether periodic or aperiodic, need to be characterized. For this, we used a novel flow-imaging particle counter, a light-scattering particle counter, and electrochemical sensors to monitor the drinking water quality of a pressure zone in a building complex for 109 days. Data were analyzed to determine the feasibility of the sensors and particle counters to distinguish periodic and aperiodic fluctuations from real-life contaminants. The concentrations of particles smaller than 10 μm and N, Small, Large, and B particles showed sudden changes recurring daily, likely due to the flow rate changes in the building complex. Conversely, the concentrations of larger than 10 μm particles and C particles, in addition to the responses of electrochemical sensors, remained in their low typical values despite flow rate changes. The aperiodic events, likely resulting from an abnormally high flow rate in the water mains due to maintenance, were detected using particle counters and electrochemical sensors. This study provides insights into choosing water quality sensors by showing that machine learning-based particle classes, such as B, C, F, and particles larger than 10 μm are promising in distinguishing contamination from aperiodic and periodic fluctuations while the use of other particle classes and electrochemical sensors may require dynamic baseline to decrease false positive events in an early warning system.
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Affiliation(s)
- Markus Koppanen
- Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, FI-33101, Tampere, Finland.
| | - Tero Kesti
- Uponor Corporation, Kaskimäenkatu 2, FI-33900 Tampere, Finland
| | - Jukka Rintala
- Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, FI-33101, Tampere, Finland
| | - Marja Palmroth
- Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, FI-33101, Tampere, Finland
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12
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Zhang Z, Wei Y, Peng Z, Du P, Du X, Zuo G, Wang C, Li P, Wang J, Wang R. Exploration of microbiome diversity of stacked fermented grains by flow cytometry and cell sorting. Front Microbiol 2023; 14:1160552. [PMID: 37051523 PMCID: PMC10083240 DOI: 10.3389/fmicb.2023.1160552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/06/2023] [Indexed: 03/28/2023] Open
Abstract
Sauce-flavor baijiu is one of the twelve flavor types of Chinese distilled fermented product. Microbial composition plays a key role in the stacked fermentation of Baijiu, which uses grains as raw materials and produces flavor compounds, however, the active microbial community and its relationship remain unclear. Here, we investigated the total and active microbial communities of stacked fermented grains of sauce-flavored Baijiu using flow cytometry and high-throughput sequencing technology, respectively. By using traditional high-throughput sequencing technology, a total of 24 bacterial and 14 fungal genera were identified as the core microbiota, the core bacteria were Lactobacillus (0.08–39.05%), Acetobacter (0.25–81.92%), Weissella (0.03–29.61%), etc. The core fungi were Issatchenkia (23.11–98.21%), Monascus (0.02–26.36%), Pichia (0.33–37.56%), etc. In contrast, using flow cytometry combined with high-throughput sequencing, the active dominant bacterial genera after cell sorting were found to be Herbaspirillum, Chitinophaga, Ralstonia, Phenylobacterium, Mucilaginibacter, and Bradyrhizobium, etc., whereas the active dominant fungal genera detected were Aspergillus, Pichia, Exophiala, Candelabrochaete, Italiomyces, and Papiliotrema, etc. These results indicate that although the abundance of Acetobacter, Monascus, and Issatchenkia was high after stacked fermentation, they may have little biological activity. Flow cytometry and cell sorting techniques have been used in the study of beer and wine, but exploring the microbiome in such a complex environment as Chinese baijiu has not been reported. The results also reveal that flow cytometry and cell sorting are convenient methods for rapidly monitoring complex microbial flora and can assist in exploring complex environmental samples.
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Affiliation(s)
- Ziyang Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
| | - Yanwei Wei
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
| | - Zehao Peng
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
| | - Peng Du
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
| | - Xinyong Du
- Gubeichun Group Co., Ltd., Jinan, Shandong, China
| | - Guoying Zuo
- Gubeichun Group Co., Ltd., Jinan, Shandong, China
| | | | - Piwu Li
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
| | - Junqing Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
- *Correspondence: Junqing Wang,
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
- Ruiming Wang,
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13
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Lyons KJ, Ikonen J, Hokajärvi AM, Räsänen T, Pitkänen T, Kauppinen A, Kujala K, Rossi PM, Miettinen IT. Monitoring groundwater quality with real-time data, stable water isotopes, and microbial community analysis: A comparison with conventional methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:161199. [PMID: 36581300 DOI: 10.1016/j.scitotenv.2022.161199] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Groundwater provides much of the world's potable water. Nevertheless, groundwater quality monitoring programmes often rely on a sporadic, slow, and narrowly focused combination of periodic manual sampling and laboratory analyses, such that some water quality deficiencies go undetected, or are detected too late to prevent adverse consequences. In an effort to address this shortcoming, we conducted enhanced monitoring of untreated groundwater quality over 12 months (February 2019-February 2020) in four shallow wells supplying potable water in Finland. We supplemented periodic manual sampling and laboratory analyses with (i) real-time online monitoring of physicochemical and hydrological parameters, (ii) analysis of stable water isotopes from groundwater and nearby surface waters, and (iii) microbial community analysis of groundwater via amplicon sequencing of the 16S rRNA gene and 16S rRNA. We also developed an early warning system (EWS) for detecting water quality anomalies by automating real-time online monitoring data collection, transfer, and analysis - using electrical conductivity (EC) and turbidity as indirect water quality indicators. Real-time online monitoring measurements were largely in fair agreement with periodic manual measurements, demonstrating their usefulness for monitoring water quality; and the findings of conventional monitoring, stable water isotopes, and microbial community analysis revealed indications of surface water intrusion and faecal contamination at some of the studied sites. With further advances in technology and affordability expected into the future, the supplementary methods used here could be more widely implemented to enhance groundwater quality monitoring - by contributing new insights and/or corroborating the findings of conventional analyses.
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Affiliation(s)
- Kevin J Lyons
- Water, Energy and Environmental Engineering Research Unit, University of Oulu, Oulu, Finland.
| | - Jenni Ikonen
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Anna-Maria Hokajärvi
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Teemu Räsänen
- Preventos Informatics Oy, Kuopio, Finland; Department of Environmental Technology, Savonia University of Applied Sciences, Kuopio, Finland
| | - Tarja Pitkänen
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland; Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Ari Kauppinen
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland; Animal Health Diagnostic Unit, Laboratory and Research Division, Finnish Food Authority, Helsinki, Finland
| | - Katharina Kujala
- Water, Energy and Environmental Engineering Research Unit, University of Oulu, Oulu, Finland
| | - Pekka M Rossi
- Water, Energy and Environmental Engineering Research Unit, University of Oulu, Oulu, Finland
| | - Ilkka T Miettinen
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
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14
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Vosloo S, Huo L, Chauhan U, Cotto I, Gincley B, Vilardi KJ, Yoon B, Bian K, Gabrielli M, Pieper KJ, Stubbins A, Pinto AJ. Gradual Recovery of Building Plumbing-Associated Microbial Communities after Extended Periods of Altered Water Demand during the COVID-19 Pandemic. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:3248-3259. [PMID: 36795589 PMCID: PMC9969676 DOI: 10.1021/acs.est.2c07333] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
COVID-19 pandemic-related building restrictions heightened drinking water microbiological safety concerns post-reopening due to the unprecedented nature of commercial building closures. Starting with phased reopening (i.e., June 2020), we sampled drinking water for 6 months from three commercial buildings with reduced water usage and four occupied residential households. Samples were analyzed using flow cytometry and full-length 16S rRNA gene sequencing along with comprehensive water chemistry characterization. Prolonged building closures resulted in 10-fold higher microbial cell counts in the commercial buildings [(2.95 ± 3.67) × 105 cells mL-1] than in residential households [(1.11 ± 0.58) × 104 cells mL-1] with majority intact cells. While flushing reduced cell counts and increased disinfection residuals, microbial communities in commercial buildings remained distinct from those in residential households on the basis of flow cytometric fingerprinting [Bray-Curtis dissimilarity (dBC) = 0.33 ± 0.07] and 16S rRNA gene sequencing (dBC = 0.72 ± 0.20). An increase in water demand post-reopening resulted in gradual convergence in microbial communities in water samples collected from commercial buildings and residential households. Overall, we find that the gradual recovery of water demand played a key role in the recovery of building plumbing-associated microbial communities as compared to short-term flushing after extended periods of reduced water demand.
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Affiliation(s)
- Solize Vosloo
- Department
of Civil and Environmental Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 021115, United States
| | - Linxuan Huo
- School
of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, Georgia 30318, United States
| | - Umang Chauhan
- Department
of Civil and Environmental Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 021115, United States
| | - Irmarie Cotto
- Department
of Civil and Environmental Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 021115, United States
| | - Benjamin Gincley
- School
of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, Georgia 30318, United States
| | - Katherine J. Vilardi
- Department
of Civil and Environmental Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 021115, United States
| | - Bryan Yoon
- Department
of Civil and Environmental Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 021115, United States
| | - Kaiqin Bian
- School
of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, Georgia 30318, United States
| | - Marco Gabrielli
- Dipartimento
di Ingegneria Civile e Ambientale - Sezione Ambientale, Politecnico di Milano, 20133 Milan, Italy
| | - Kelsey J. Pieper
- Department
of Civil and Environmental Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 021115, United States
| | - Aron Stubbins
- Department
of Civil and Environmental Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 021115, United States
| | - Ameet J. Pinto
- School
of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, Georgia 30318, United States
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15
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Lin H, Hu Y. Impact of different source-water switching patterns on the stability of drinking water in an estuarine urban water distribution system. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:49059-49069. [PMID: 35217958 DOI: 10.1007/s11356-022-19117-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Source-water switching can lead to instability in drinking water distribution systems. In estuarine cities using surface water as source water where salt tide occasionally happens, the influence can be particularly complex due to changes of Larson Index (LI). The objective of this study was to investigate the effects of different switching patterns on the stability of water in an estuarine city. Fluctuated LI was found in the current distribution system. LI of the new source water was lower and more stable. Susceptible areas with a high frequency of over standard water quality were identified and pipe scales there were mainly composed of relatively stable iron oxides with dense crystal structures (Fe3O4 and α-FeOOH). Two old pipe sections were used to simulate different switching patterns. The microbial risk did not increase significantly when the original and new water sources were combined in different ratios (2∶8, 5∶5), when multiple water sources were used (3∶3∶4) or when salinity increased. The better water quality, lower LI of the new source water, and stability of the current distribution system together contributed to the biostability. Total iron increased after switching, then declined and stabilized for most switching patterns. Salt tide can lead to sharp iron release. The results provided insightful information for distribution systems that have cast iron pipes and that might encounter source-water switching patterns.
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Affiliation(s)
- Huirong Lin
- Department of Environmental Science and Engineering, College of Chemical Engineering, Huaqiao University, 668 Jimei Road, Xiamen, 361021, Fujian, China.
| | - Yue Hu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
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16
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Cheswick R, Nocker A, Moore G, Jefferson B, Jarvis P. Exploring the use of flow cytometry for understanding the efficacy of disinfection in chlorine contact tanks. WATER RESEARCH 2022; 217:118420. [PMID: 35468557 DOI: 10.1016/j.watres.2022.118420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
A pilot scale chlorine contact tank (CCT) with flexible baffling was installed at an operational water treatment plant (WTP), taking a direct feed from the outlet of the rapid gravity filters (RGF). For the first time, disinfection efficacy was established by direct microbial monitoring in a continuous reactor using flow cytometry (FCM). Disinfection variables of dose, time, and hydraulic efficiency (short circuiting and dispersion) were explored following characterisation of the reactor's residence time distributions (RTD) by tracer testing. FCM enabled distinction to be made between changes in disinfection reactor design where standard culture-based methods could not. The product of chlorine concentration (C) and residence time (t) correlated well with inactivation of microbes, organisms, with the highest cell reductions (N/N0) reaching <0.025 at Ctx¯ of 20 mg.min/L and above. The influence of reactor geometry on disinfection was best shown from the Ct10. This identified that the initial level of microbial inactivation was higher in unbaffled reactors for low Ct10 values, although the highest levels of inactivation of 0.015 could only be achieved in the baffled reactors, because these conditions enabled the highest Ct10 values to be achieved. Increased levels of disinfection were closely associated with increased formation of the trihalomethane disinfection by-products. The results highlight the importance of well-designed and operated CCT. The improved resolution afforded by FCM provides a tool that can dynamically quantify disinfection processes, enabling options for much better process control.
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Affiliation(s)
- Ryan Cheswick
- Cranfield University, Bedford, MK43 0AL, UK; Scottish Water, Castle House, Dunfermline, KY11 8GG, UK
| | | | - Graeme Moore
- Scottish Water, Castle House, Dunfermline, KY11 8GG, UK
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17
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El Mujtar VA, Chirdo F, Lagares A, Wall L, Tittonell P. Soil bacterial biodiversity characterization by flow cytometry: The bottleneck of cell extraction from soil. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Verónica A. El Mujtar
- Agroecology, Environment and Systems Group, Instituto de Investigaciones Forestales y Agropecuarias de Bariloche (IFAB) INTA‐CONICET, San Carlos de Bariloche Río Negro Argentina
| | - Fernando Chirdo
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP)(UNLP‐CONICET), Facultad de Ciencias Exactas Universidad Nacional de La Plata La Plata Argentina
| | - Antonio Lagares
- IBBM—Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas Universidad Nacional de La Plata, CCT‐La Plata CONICET La Plata Argentina
| | - Luis Wall
- Laboratorio de Bioquímica y Microbiología de Suelo, Centro de Bioquímica y Microbiología de Suelos Universidad Nacional de Quilmes Bernal Argentina
| | - Pablo Tittonell
- Agroecology, Environment and Systems Group, Instituto de Investigaciones Forestales y Agropecuarias de Bariloche (IFAB) INTA‐CONICET, San Carlos de Bariloche Río Negro Argentina
- Groningen Institute of Evolutionary Life Sciences Groningen University Groningen The Netherlands
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18
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Thom C, Smith CJ, Moore G, Weir P, Ijaz UZ. Microbiomes in drinking water treatment and distribution: A meta-analysis from source to tap. WATER RESEARCH 2022; 212:118106. [PMID: 35091225 DOI: 10.1016/j.watres.2022.118106] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/12/2022] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
A meta-analysis of existing and available Illumina 16S rRNA datasets from drinking water source, treatment and drinking water distribution systems (DWDS) were collated to compare changes in abundance and diversity throughout. Samples from bulk water and biofilm were used to assess principles governing microbial community assembly and the value of amplicon sequencing to water utilities. Individual phyla relationships were explored to identify competitive or synergistic factors governing DWDS microbiomes. The relative importance of stochasticity in the assembly of the DWDS microbiome was considered to identify the significance of source and treatment in determining communities in DWDS. Treatment of water significantly reduces overall species abundance and richness, with chlorination of water providing the most impact to individual taxa relationships. The assembly of microbial communities in the bulk water of the source, primary treatment process and DWDS is governed by more stochastic processes, as is the DWDS biofilm. DWDS biofilm is significantly different from bulk water in terms of local contribution to beta diversity, type and abundance of taxa present. Water immediately post chlorination has a more deterministic microbial assembly, highlighting the significance of this process in changing the microbiome, although elevated levels of stochasticity in DWDS samples suggest that this may not be the case at customer taps. 16S rRNA sequencing is becoming more routine, and may have several uses for water utilities, including: detection and risk assessment of potential pathogens such as those within the genera of Legionella and Mycobacterium; assessing the risk of nitrification in DWDS; providing improved indicators of process performance and monitoring for significant changes in the microbial community to detect contamination. Combining this with quantitative methods like flow cytometry will allow a greater depth of understanding of the DWDS microbiome.
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Affiliation(s)
- Claire Thom
- Infrastructure and Environment Research Division, James Watt School of Engineering, University of Glasgow, UK; Scottish Water, 6 Castle Drive Dunfermline, KY11 8GG, UK.
| | - Cindy J Smith
- Infrastructure and Environment Research Division, James Watt School of Engineering, University of Glasgow, UK
| | - Graeme Moore
- Scottish Water, 6 Castle Drive Dunfermline, KY11 8GG, UK
| | - Paul Weir
- Scottish Water, 6 Castle Drive Dunfermline, KY11 8GG, UK
| | - Umer Z Ijaz
- Infrastructure and Environment Research Division, James Watt School of Engineering, University of Glasgow, UK
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19
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Zand E, Froehling A, Schoenher C, Zunabovic-Pichler M, Schlueter O, Jaeger H. Potential of Flow Cytometric Approaches for Rapid Microbial Detection and Characterization in the Food Industry-A Review. Foods 2021; 10:3112. [PMID: 34945663 PMCID: PMC8701031 DOI: 10.3390/foods10123112] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022] Open
Abstract
As microbial contamination is persistent within the food and bioindustries and foodborne infections are still a significant cause of death, the detection, monitoring, and characterization of pathogens and spoilage microorganisms are of great importance. However, the current methods do not meet all relevant criteria. They either show (i) inadequate sensitivity, rapidity, and effectiveness; (ii) a high workload and time requirement; or (iii) difficulties in differentiating between viable and non-viable cells. Flow cytometry (FCM) represents an approach to overcome such limitations. Thus, this comprehensive literature review focuses on the potential of FCM and fluorescence in situ hybridization (FISH) for food and bioindustry applications. First, the principles of FCM and FISH and basic staining methods are discussed, and critical areas for microbial contamination, including abiotic and biotic surfaces, water, and air, are characterized. State-of-the-art non-specific FCM and specific FISH approaches are described, and their limitations are highlighted. One such limitation is the use of toxic and mutagenic fluorochromes and probes. Alternative staining and hybridization approaches are presented, along with other strategies to overcome the current challenges. Further research needs are outlined in order to make FCM and FISH even more suitable monitoring and detection tools for food quality and safety and environmental and clinical approaches.
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Affiliation(s)
- Elena Zand
- Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria;
| | - Antje Froehling
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Quality and Safety of Food and Feed, 14469 Potsdam, Germany; (A.F.); (O.S.)
| | - Christoph Schoenher
- Institute of Sanitary Engineering and Water Pollution Control, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (C.S.); (M.Z.-P.)
| | - Marija Zunabovic-Pichler
- Institute of Sanitary Engineering and Water Pollution Control, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (C.S.); (M.Z.-P.)
| | - Oliver Schlueter
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Quality and Safety of Food and Feed, 14469 Potsdam, Germany; (A.F.); (O.S.)
| | - Henry Jaeger
- Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria;
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20
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Predicting the Presence and Abundance of Bacterial Taxa in Environmental Communities through Flow Cytometric Fingerprinting. mSystems 2021; 6:e0055121. [PMID: 34546074 PMCID: PMC8547484 DOI: 10.1128/msystems.00551-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Microbiome management research and applications rely on temporally resolved measurements of community composition. Current technologies to assess community composition make use of either cultivation or sequencing of genomic material, which can become time-consuming and/or laborious in case high-throughput measurements are required. Here, using data from a shrimp hatchery as an economically relevant case study, we combined 16S rRNA gene amplicon sequencing and flow cytometry data to develop a computational workflow that allows the prediction of taxon abundances based on flow cytometry measurements. The first stage of our pipeline consists of a classifier to predict the presence or absence of the taxon of interest, with yielded an average accuracy of 88.13% ± 4.78% across the top 50 operational taxonomic units (OTUs) of our data set. In the second stage, this classifier was combined with a regression model to predict the relative abundances of the taxon of interest, which yielded an average R2 of 0.35 ± 0.24 across the top 50 OTUs of our data set. Application of the models to flow cytometry time series data showed that the generated models can predict the temporal dynamics of a large fraction of the investigated taxa. Using cell sorting, we validated that the model correctly associates taxa to regions in the cytometric fingerprint, where they are detected using 16S rRNA gene amplicon sequencing. Finally, we applied the approach of our pipeline to two other data sets of microbial ecosystems. This pipeline represents an addition to the expanding toolbox for flow cytometry-based monitoring of bacterial communities and complements the current plating- and marker gene-based methods. IMPORTANCE Monitoring of microbial community composition is crucial for both microbiome management research and applications. Existing technologies, such as plating and amplicon sequencing, can become laborious and expensive when high-throughput measurements are required. In recent years, flow cytometry-based measurements of community diversity have been shown to correlate well with those derived from 16S rRNA gene amplicon sequencing in several aquatic ecosystems, suggesting that there is a link between the taxonomic community composition and phenotypic properties as derived through flow cytometry. Here, we further integrated 16S rRNA gene amplicon sequencing and flow cytometry survey data in order to construct models that enable the prediction of both the presence and the abundances of individual bacterial taxa in mixed communities using flow cytometric fingerprinting. The developed pipeline holds great potential to be integrated into routine monitoring schemes and early warning systems for biotechnological applications.
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Keon MR, McKie MJ, Taylor-Edmonds L, Andrews RC. Evaluation of enzyme activity for monitoring biofiltration performance in drinking water treatment. WATER RESEARCH 2021; 205:117636. [PMID: 34555739 DOI: 10.1016/j.watres.2021.117636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 08/29/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Many water providers monitor adenosine triphosphate (ATP) as an indicator of biological acclimation of their biofilters; however, strong correlations between ATP concentration and filter performance (e.g., organic matter or disinfection by-product precursor removal) are not typically observed. As an alternative, this study evaluated the use of enzyme activity for monitoring biological processes within filters. Recent studies have proposed that enzyme activity may be used as an indicator of biofilter function as it provides a means to quantify biodegradation which may allow for a more accurate measure of degradation potential and to gain a better understanding of biofilter performance. Sampling was completed from full- and pilot-scale biofilters to assess impacts associated with pre-treatments, varying sources waters, as well as pre-treatment and operating conditions. Enzyme activity (carboxylic esterase, phosphatase, ß-glucosidase, α-glucosidase, ß-xylosidase, chitinase, and cellulase) and ATP were measured from the top 5 cm of biofilter media representative of typical full-scale sampling; water quality parameters included dissolved organic carbon (DOC) and disinfection by-products (DBPs): trihalomethane (THM) formation potential (FP), and haloacetic acid FP (HAA FP). Results confirmed that ATP was not a reliable monitoring tool for DOC and DBP FP reduction in biofilters. A strong relationship was observed between esterase activity and DOC reduction; chitinase activity significantly correlated to THM FP reduction for filters treating three different source waters and HAA FP reduction achieved by filters treating the same source water with a range of pre-treatment and backwash conditions. This study showed that enzyme activity may be appropriate for monitoring biological processes within drinking water filters and may act as a surrogate for the removal of organic compounds.
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Affiliation(s)
- Meaghan R Keon
- Department of Civil and Mineral Engineering, University of Toronto, 35 St. George St., Toronto, Ontario, M5S 1A4, Canada.
| | - Michael J McKie
- Department of Civil and Mineral Engineering, University of Toronto, 35 St. George St., Toronto, Ontario, M5S 1A4, Canada.
| | - Liz Taylor-Edmonds
- Department of Civil and Mineral Engineering, University of Toronto, 35 St. George St., Toronto, Ontario, M5S 1A4, Canada.
| | - Robert C Andrews
- Department of Civil and Mineral Engineering, University of Toronto, 35 St. George St., Toronto, Ontario, M5S 1A4, Canada.
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De Vrieze J, Heyer R, Props R, Van Meulebroek L, Gille K, Vanhaecke L, Benndorf D, Boon N. Triangulation of microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles. WATER RESEARCH 2021; 202:117422. [PMID: 34280807 DOI: 10.1016/j.watres.2021.117422] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/01/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
The anaerobic digestion microbiome has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a non-targeted holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods, i.e., amplicon sequencing, metaproteomics, metabolomics and cytomics, in their ability to characterise the full-scale anaerobic digestion microbiome. Cytometric fingerprinting through cytomics reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting by flow cytometry. Three different digester types, i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters, each reflected different operational parameters. The α-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, β-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method's features i.e., operational taxonomic units, metaproteins, metabolites, and cytometric traits, yielded certain similar features, yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, cytometric fingerprinting through flow cytometry is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium; Division of Soil and Water Management, Department of Earth and Environmental sciences, KU Leuven, Kasteelpark Arenberg 20, PO box 2411, B-3001, Leuven, Belgium; Bio- and Chemical Systems Technology, Reactor Engineering and Safety (CREaS), Department of Chemical Engineering, KU Leuven, Celestijnenlaan 200F, PO box 2424, B-3001, Leuven, Belgium.
| | - Robert Heyer
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Ruben Props
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Lieven Van Meulebroek
- Laboratory of Chemical Analysis, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Karen Gille
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Lynn Vanhaecke
- Laboratory of Chemical Analysis, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106, Magdeburg, Germany; Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany; Microbiology, Anhalt University of Applied Sciences, Bernburger Straße 55, 06354, Köthen, Germany
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
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Favere J, Waegenaar F, Boon N, De Gusseme B. Online microbial monitoring of drinking water: How do different techniques respond to contaminations in practice? WATER RESEARCH 2021; 202:117387. [PMID: 34243050 DOI: 10.1016/j.watres.2021.117387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Safeguarding the microbial water quality remains a challenge for drinking water utilities, and because of population growth and climate change, new issues arise regularly. To overcome these problems, biostable drinking water production and water reuse will become increasingly important. In this respect, high-resolution online microbial monitoring during treatment and distribution could prove essential. Here, we present the first scientific and practical comparison of multiple online microbial monitoring techniques in which six commercially available devices were set up in a full-scale drinking water production plant. Both the devices' response towards operational changes and contaminations, as well as their detection limit for different contaminations were evaluated and compared. During normal operation, all devices were able to detect abrupt operational changes such as backwashing of activated carbon filters and interruption of the production process in a fast and sensitive way. To benchmark their response to contaminations, the calculation of a dynamic baseline for sensitive separation between noise and events is proposed. In order of sensitivity, enzymatic analysis, ATP measurement, and flow cytometric fingerprinting were the most performant for detection of rain- and groundwater contaminations (0.01 - 0.1 v%). On the other hand, optical classification and flow cytometric cell counts showed to be more robust techniques, requiring less maintenance and providing direct information about the cell concentration, even though they were still more sensitive than plate counting. The choice for a certain technology will thus depend on the type of application and is a balance between sensitivity, price and maintenance. All things considered, a combination of several devices and use of advanced data analysis such as fingerprinting may be of added value. In general, the strategic implementation of online microbial monitoring as early-warning system will allow for intensive quality control by high-frequency sampling as well as a short event response timeframe.
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Affiliation(s)
- Jorien Favere
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium; Centre for Advanced Process Technology for Urban Resource Recovery (CAPTURE), P.O., Frieda Saeysstraat 1, B-9000 Gent, Belgium
| | - Fien Waegenaar
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium; Centre for Advanced Process Technology for Urban Resource Recovery (CAPTURE), P.O., Frieda Saeysstraat 1, B-9000 Gent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium; Centre for Advanced Process Technology for Urban Resource Recovery (CAPTURE), P.O., Frieda Saeysstraat 1, B-9000 Gent, Belgium
| | - Bart De Gusseme
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium; Centre for Advanced Process Technology for Urban Resource Recovery (CAPTURE), P.O., Frieda Saeysstraat 1, B-9000 Gent, Belgium.
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Gabrielli M, Turolla A, Antonelli M. Bacterial dynamics in drinking water distribution systems and flow cytometry monitoring scheme optimization. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 286:112151. [PMID: 33609931 DOI: 10.1016/j.jenvman.2021.112151] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
Water biostability is desired within drinking water distribution systems (DWDSs) to limit microbiologically-related operational, aesthetic and, eventually, health-related issues. However, variations in microbiological quality can take place both spatially along DWDS pipelines and temporally at single locations due to biofilm detachment, water quality seasonality and other processes. In this study, long- and short-term trends of bacterial concentration and community structure were investigated in a secondary branch of an unchlorinated DWDS for several months using high-frequency flow cytometry (FCM) and traditional laboratory monitoring campaigns. Long-term trends of bacterial concentrations and community structures were likely caused by changes in the water physical-chemical quality (i.e. pH and conductivity). Short-term daily pattern, instead, resulted in significant variations between the bacterial concentrations and community structures at different hours, likely due to biofilm detachment and loose deposits resuspension related to changes in the local water flow. These patterns, however, showed broad variations and did not persist during the entire monitoring campaign presumably due to the stochasticity of local instantaneous demand and seasonal changes in water consumption. During periods without sensible long-term trends, the sampling hours explain a comparable or larger fraction of the bacterial community diversity compared to dates. The variations observed with FCM were poorly or not detected by traditional laboratory analyses, as the correlation between the two were rather weak, highlighting the limited information provided by traditional approaches. On the other hand, FCM data correlated with water pH and conductivity, underlining the relation between physical-chemical and microbiological water quality. Such results suggest that the advanced control of the physical-chemical water quality could minimize the microbiological water quality variations. Moreover, monitoring campaign planning should take into account the sampling time to reduce the noise caused by daily fluctuations and/or assess the overall quality variations. Finally, as monitoring costs are one of the barriers which prevent a more widespread use of FCM, a monitoring scheme optimization strategy was developed. Such strategy employs the data from an initial high-frequency sampling period to select the sampling hours which maximize the observed variations of bacterial concentration and community composition.
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Affiliation(s)
- Marco Gabrielli
- Politecnico di Milano, Department of Civil and Environmental Engineering (DICA), Piazza Leonardo da Vinci 32, Milano, 20133, Italy
| | - Andrea Turolla
- Politecnico di Milano, Department of Civil and Environmental Engineering (DICA), Piazza Leonardo da Vinci 32, Milano, 20133, Italy
| | - Manuela Antonelli
- Politecnico di Milano, Department of Civil and Environmental Engineering (DICA), Piazza Leonardo da Vinci 32, Milano, 20133, Italy.
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Abstract
Flow cytometry is an important technology for the study of microbial communities. It grants the ability to rapidly generate phenotypic single-cell data that are both quantitative, multivariate and of high temporal resolution. The complexity and amount of data necessitate an objective and streamlined data processing workflow that extends beyond commercial instrument software. No full overview of the necessary steps regarding the computational analysis of microbial flow cytometry data currently exists. In this review, we provide an overview of the full data analysis pipeline, ranging from measurement to data interpretation, tailored toward studies in microbial ecology. At every step, we highlight computational methods that are potentially useful, for which we provide a short nontechnical description. We place this overview in the context of a number of open challenges to the field and offer further motivation for the use of standardized flow cytometry in microbial ecology research.
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Affiliation(s)
| | - Ruben Props
- Center for Microbial Ecology & Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Dynamic Hydraulics in a Drinking Water Distribution System Influence Suspended Particles and Turbidity, But Not Microbiology. WATER 2021. [DOI: 10.3390/w13010109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Spatial and short-term temporal changes in water quality as a result of water age and fluctuating hydraulic conditions were investigated in a drinking water distribution system. Online measurements of total and intracellular adenosine tri-phosphate (ATP), total and intact cell concentrations measured with flow cytometry (FCM), turbidity, and particle counts were performed over five weeks at five subsequent locations of the distribution system. The high number of parallel FCM and ATP measurements revealed the combined effect of water age and final disinfection on spatial changes in microbiology in the system. The results underlined that regular daily dynamics in flow velocities are normal and inevitable in drinking water distribution systems, and significantly impact particle counts and turbidity. However, hydraulic conditions had no detectable impact on the concentration of suspended microbial cells. A weak correlation between flow velocity and ATP concentrations suggests incidental resuspension of particle-bound bacteria, presumably caused by either biofilm detachment or resuspension from sediment when flow velocities increase. The highly dynamic hydraulic conditions highlight the value of online monitoring tools for the meaningful description of short-term dynamics (day-scale) in drinking water distribution systems.
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