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The role of biofilm in the development and dissemination of ubiquitous pathogens in drinking water distribution systems: an overview of surveillance, outbreaks, and prevention. World J Microbiol Biotechnol 2021; 37:36. [PMID: 33507414 DOI: 10.1007/s11274-021-03008-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 01/19/2021] [Indexed: 12/30/2022]
Abstract
A variety of pathogenic microorganisms can survive in the drinking water distribution systems (DWDS) by forming stable biofilms and, thus, continually disseminating their population through the system's dynamic water bodies. The ingestion of the pathogen-contaminated water could trigger a broad spectrum of illnesses and well-being-related obstacles. These waterborne diseases are a significant concern for babies, pregnant women, and significantly low-immune individuals. This review highlights the recent advances in understanding the microbiological aspects of drinking water quality, biofilm formation and its dynamics, health issues caused by the emerging microbes in biofilm, and approaches for biofilm investigation its prevention and suppression in DWDS.
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Savio D, Stadler P, Reischer GH, Demeter K, Linke RB, Blaschke AP, Mach RL, Kirschner AKT, Stadler H, Farnleitner AH. Spring Water of an Alpine Karst Aquifer Is Dominated by a Taxonomically Stable but Discharge-Responsive Bacterial Community. Front Microbiol 2019; 10:28. [PMID: 30828319 PMCID: PMC6385617 DOI: 10.3389/fmicb.2019.00028] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/09/2019] [Indexed: 11/13/2022] Open
Abstract
Alpine karst aquifers are important groundwater resources for the provision of drinking water all around the world. Yet, due to difficult accessibility and long-standing methodological limitations, the microbiology of these systems has long been understudied. The aim of the present study was to investigate the structure and dynamics of bacterial communities in spring water of an alpine limestone karst aquifer (LKAS2) under different hydrological conditions (base vs. event flow). The study was based on high-throughput 16S rRNA gene amplicon sequencing, study design and sample selection were guided by hydrology and pollution microbiology data. Spanning more than 27 months, our analyses revealed a taxonomically highly stable bacterial community, comprising high proportions of yet uncultivated bacteria in the suspended bacterial community fraction. Only the three candidate phyla Parcubacteria (OD1), Gracilibacteria (GN02), Doudnabacteria (SM2F11) together with Proteobacteria and Bacteroidetes contributed between 70.0 and 88.4% of total reads throughout the investigation period. A core-community of 300 OTUs consistently contributed between 37.6 and 56.3% of total reads, further supporting the hypothesis of a high temporal stability in the bacterial community in the spring water. Nonetheless, a detectable response in the bacterial community structure of the spring water was discernible during a high-discharge event. Sequence reads affiliated to the class Flavobacteriia clearly increased from a mean proportion of 2.3% during baseflow to a maximum of 12.7% during the early phase of the studied high-discharge event, suggesting direct impacts from changing hydrological conditions on the bacterial community structure in the spring water. This was further supported by an increase in species richness (Chao1) at higher discharge. The combination of these observations allowed the identification and characterization of three different discharge classes (Q1-Q3). In conclusion, we found a taxonomically stable bacterial community prevailing in spring waters from an alpine karst aquifer over the entire study period of more than 2 years. Clear response to changing discharge conditions could be detected for particular bacterial groups, whereas the most responsive group - bacteria affiliated to the class of Flavobacteriia - might harbor potential as a valuable natural indicator of "system disturbances" in karst aquifers.
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Affiliation(s)
- Domenico Savio
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria
| | - Philipp Stadler
- Centre for Water Resource Systems, TU Wien, Vienna, Austria
- Research Unit for Water Quality Management, Institute for Water Quality and Resource Management, TU Wien, Vienna, Austria
| | - Georg H. Reischer
- Molecular Diagnostics Group, Institute of Chemical, Environmental and Bioscience Engineering, Department of Agrobiotechnology, IFA-Tulln, TU Wien, Tulln an der Donau, Austria
- Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Katalin Demeter
- Centre for Water Resource Systems, TU Wien, Vienna, Austria
- Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Rita B. Linke
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria
- Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Alfred P. Blaschke
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria
- Institute of Hydraulic Engineering and Water Resources Management, TU Wien, Vienna, Austria
| | - Robert L. Mach
- Research Division of Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Alexander K. T. Kirschner
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria
- Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Hermann Stadler
- Department for Water Resources Management and Environmental Analytics, Institute for Water, Energy and Sustainability, Joanneum Research, Graz, Austria
| | - Andreas H. Farnleitner
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria
- Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
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Savio D, Stadler P, Reischer GH, Kirschner AK, Demeter K, Linke R, Blaschke AP, Sommer R, Szewzyk U, Wilhartitz IC, Mach RL, Stadler H, Farnleitner AH. Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management. WIRES. WATER 2018; 5:e1282. [PMID: 29780584 PMCID: PMC5947618 DOI: 10.1002/wat2.1282] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 01/25/2018] [Accepted: 01/26/2018] [Indexed: 06/08/2023]
Abstract
Over the past 15 years, pioneering interdisciplinary research has been performed on the microbiology of hydrogeologically well-defined alpine karst springs located in the Northern Calcareous Alps (NCA) of Austria. This article gives an overview on these activities and links them to other relevant research. Results from the NCA springs and comparable sites revealed that spring water harbors abundant natural microbial communities even in aquifers with high water residence times and the absence of immediate surface influence. Apparently, hydrogeology has a strong impact on the concentration and size of the observed microbes, and total cell counts (TCC) were suggested as a useful means for spring type classification. Measurement of microbial activities at the NCA springs revealed extremely low microbial growth rates in the base flow component of the studied spring waters and indicated the importance of biofilm-associated microbial activities in sediments and on rock surfaces. Based on genetic analysis, the autochthonous microbial endokarst community (AMEC) versus transient microbial endokarst community (TMEC) concept was proposed for the NCA springs, and further details within this overview article are given to prompt its future evaluation. In this regard, it is well known that during high-discharge situations, surface-associated microbes and nutrients such as from soil habitats or human settlements-potentially containing fecal-associated pathogens as the most critical water-quality hazard-may be rapidly flushed into vulnerable karst aquifers. In this context, a framework for the comprehensive analysis of microbial pollution has been proposed for the NCA springs to support the sustainable management of drinking water safety in accordance with recent World Health Organization guidelines. Near-real-time online water quality monitoring, microbial source tracking (MST) and MST-guided quantitative microbial-risk assessment (QMRA) are examples of the proposed analytical tools. In this context, this overview article also provides a short introduction to recently emerging methodologies in microbiological diagnostics to support reading for the practitioner. Finally, the article highlights future research and development needs. This article is categorized under: 1Engineering Water > Water, Health, and Sanitation2Science of Water > Water Extremes3Water and Life > Nature of Freshwater Ecosystems.
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Affiliation(s)
- Domenico Savio
- Division Water Quality and HealthDepartment Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health SciencesKrems a. d. DonauAustria
- Centre for Water Resource SystemsTechnische Universität WienViennaAustria
| | - Philipp Stadler
- Centre for Water Resource SystemsTechnische Universität WienViennaAustria
- Institute for Water Quality, Resource and Waste ManagementTechnische Universität WienViennaAustria
| | - Georg H. Reischer
- Institute of Chemical, Environmental & Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostics166/5/3, Technische Universität WienViennaAustria
- Interuniversity Cooperation Centre for Water and Health, www.waterandhealth.at
| | - Alexander K.T. Kirschner
- Interuniversity Cooperation Centre for Water and Health, www.waterandhealth.at
- Unit Water Hygiene, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| | - Katalin Demeter
- Centre for Water Resource SystemsTechnische Universität WienViennaAustria
- Institute of Chemical, Environmental & Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostics166/5/3, Technische Universität WienViennaAustria
| | - Rita Linke
- Institute of Chemical, Environmental & Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostics166/5/3, Technische Universität WienViennaAustria
- Interuniversity Cooperation Centre for Water and Health, www.waterandhealth.at
| | - Alfred P. Blaschke
- Centre for Water Resource SystemsTechnische Universität WienViennaAustria
- Interuniversity Cooperation Centre for Water and Health, www.waterandhealth.at
- Institute of Hydraulic Engineering and Water Resources ManagementTechnische Universität WienViennaAustria
| | - Regina Sommer
- Interuniversity Cooperation Centre for Water and Health, www.waterandhealth.at
- Unit Water Hygiene, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| | - Ulrich Szewzyk
- Department of Environmental TechnologyTechnical University of BerlinBerlinGermany
| | - Inés C. Wilhartitz
- Department of Environmental MicrobiologyEawag, Swiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
| | - Robert L. Mach
- Institute of Chemical, Environmental & Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostics166/5/3, Technische Universität WienViennaAustria
| | - Hermann Stadler
- Department for Water Resources Management and Environmental AnalyticsInstitute for Water, Energy and Sustainability, Joanneum Research, GrazAustria
| | - Andreas H. Farnleitner
- Division Water Quality and HealthDepartment Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health SciencesKrems a. d. DonauAustria
- Institute of Chemical, Environmental & Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostics166/5/3, Technische Universität WienViennaAustria
- Interuniversity Cooperation Centre for Water and Health, www.waterandhealth.at
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A Keystone Methylobacterium Strain in Biofilm Formation in Drinking Water. WATER 2017. [DOI: 10.3390/w9100778] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Lesaulnier CC, Herbold CW, Pelikan C, Berry D, Gérard C, Le Coz X, Gagnot S, Niggemann J, Dittmar T, Singer GA, Loy A. Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters. MICROBIOME 2017; 5:126. [PMID: 28938908 PMCID: PMC5610417 DOI: 10.1186/s40168-017-0344-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 09/15/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND Non-carbonated natural mineral waters contain microorganisms that regularly grow after bottling despite low concentrations of dissolved organic matter (DOM). Yet, the compositions of bottled water microbiota and organic substrates that fuel microbial activity, and how both change after bottling, are still largely unknown. RESULTS We performed a multifaceted analysis of microbiota and DOM diversity in 12 natural mineral waters from six European countries. 16S rRNA gene-based analyses showed that less than 10 species-level operational taxonomic units (OTUs) dominated the bacterial communities in the water phase and associated with the bottle wall after a short phase of post-bottling growth. Members of the betaproteobacterial genera Curvibacter, Aquabacterium, and Polaromonas (Comamonadaceae) grew in most waters and represent ubiquitous, mesophilic, heterotrophic aerobes in bottled waters. Ultrahigh-resolution mass spectrometry of DOM in bottled waters and their corresponding source waters identified thousands of molecular formulae characteristic of mostly refractory, soil-derived DOM. CONCLUSIONS The bottle environment, including source water physicochemistry, selected for growth of a similar low-diversity microbiota across various bottled waters. Relative abundance changes of hundreds of multi-carbon molecules were related to growth of less than ten abundant OTUs. We thus speculate that individual bacteria cope with oligotrophic conditions by simultaneously consuming diverse DOM molecules.
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Affiliation(s)
- Celine C Lesaulnier
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Craig W Herbold
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Claus Pelikan
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - David Berry
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Cédric Gérard
- Nestec Ltd., Route du Jorat 57, CH-1000, Lausanne 26, Switzerland
| | - Xavier Le Coz
- Nestec Ltd., Route du Jorat 57, CH-1000, Lausanne 26, Switzerland
| | - Sophie Gagnot
- Nestec Ltd., Route du Jorat 57, CH-1000, Lausanne 26, Switzerland
| | - Jutta Niggemann
- University of Oldenburg, Institute for Chemistry and Biology of the Marine Environment, ICBM-MPI Bridging Group for Marine Geochemistry, Carl-von-Ossietzky-Straße 9-11, D-26129, Oldenburg, Germany
| | - Thorsten Dittmar
- University of Oldenburg, Institute for Chemistry and Biology of the Marine Environment, ICBM-MPI Bridging Group for Marine Geochemistry, Carl-von-Ossietzky-Straße 9-11, D-26129, Oldenburg, Germany
| | - Gabriel A Singer
- Department of Ecohydrology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, D-12587, Berlin, Germany
| | - Alexander Loy
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria.
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Riou V, Périot M, Biegala IC. Specificity Re-evaluation of Oligonucleotide Probes for the Detection of Marine Picoplankton by Tyramide Signal Amplification-Fluorescent In Situ Hybridization. Front Microbiol 2017; 8:854. [PMID: 28611732 PMCID: PMC5446981 DOI: 10.3389/fmicb.2017.00854] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/27/2017] [Indexed: 01/11/2023] Open
Abstract
Oligonucleotide probes are increasingly being used to characterize natural microbial assemblages by Tyramide Signal Amplification-Fluorescent in situ Hybridization (TSA-FISH, or CAtalysed Reporter Deposition CARD-FISH). In view of the fast-growing rRNA databases, we re-evaluated the in silico specificity of eleven bacterial and eukaryotic probes and competitor frequently used for the quantification of marine picoplankton. We performed tests on cell cultures to decrease the risk for non-specific hybridization, before they are used on environmental samples. The probes were confronted to recent databases and hybridization conditions were tested against target strains matching perfectly with the probes, and against the closest non-target strains presenting one to four mismatches. We increased the hybridization stringency from 55 to 65% formamide for the Eub338+EubII+EubIII probe mix to be specific to the Eubacteria domain. In addition, we found that recent changes in the Gammaproteobacteria classification decreased the specificity of Gam42a probe, and that the Roseo536R and Ros537 probes were not specific to, and missed part of the Roseobacter clade. Changes in stringency conditions were important for bacterial probes; these induced, respectively, a significant increase, in Eubacteria and Roseobacter and no significant changes in Gammaproteobacteria concentrations from the investigated natural environment. We confirmed the eukaryotic probes original conditions, and propose the Euk1209+NChlo01+Chlo02 probe mix to target the largest picoeukaryotic diversity. Experiences acquired through these investigations leads us to propose the use of seven steps protocol for complete FISH probe specificity check-up to improve data quality in environmental studies.
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Affiliation(s)
- Virginie Riou
- Centre National de la Recherche Scientifique, Mediterranean Institute of Oceanography - Institut de Recherche pour le Développement, Aix Marseille Université - Université de ToulonMarseille, France
| | - Marine Périot
- Centre National de la Recherche Scientifique, Mediterranean Institute of Oceanography - Institut de Recherche pour le Développement, Aix Marseille Université - Université de ToulonMarseille, France
| | - Isabelle C Biegala
- Centre National de la Recherche Scientifique, Mediterranean Institute of Oceanography - Institut de Recherche pour le Développement, Aix Marseille Université - Université de ToulonMarseille, France
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Aguayo P, González P, Campos V, Maugeri TL, Papale M, Gugliandolo C, Martinez MA. Comparison of Prokaryotic Diversity in Cold, Oligotrophic Remote Lakes of Chilean Patagonia. Curr Microbiol 2017; 74:598-613. [PMID: 28265709 DOI: 10.1007/s00284-017-1209-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 01/31/2017] [Indexed: 11/26/2022]
Abstract
The prokaryotic abundance and diversity in three cold, oligotrophic Patagonian lakes (Témpanos, Las Torres and Mercedes) in the northern region Aysén (Chile) were compared in winter and summer using 16S rRNA fluorescence in situ hybridization and PCR-denaturing gradient gel electrophoresis technique. Prokaryotic abundances, numerically dominated by Bacteria, were quite similar in the three lakes, but higher in sediments than in waters, and they were also higher in summer than in winter. The relative contribution of Archaea was greater in waters than in sediments, and in winter rather than in summer. Despite the phylogenetic analysis indicated that most sequences were affiliated to a few taxonomic groups, mainly referred to Proteobacteria (consisting of Beta-, Alpha- and Gammaproteobacteria) and Euryarchaeota (mainly related to uncultured methanogens), their relative abundances differed in each sample, resulting in different bacterial and archaeal assemblages. In winter, the abundance of the dominant bacterial phylotypes were mainly regulated by the increasing levels of total organic carbon in waters. Archaeal abundance and richness appeared mostly influenced by pH in winter and total nitrogen content in summer. The prokaryotic community composition at Témpanos lake, located most northerly and closer to a glacier, greatly differed in respect to the other two lakes. In this lake was detected the highest bacterial diversity, being Betaproteobacteria the most abundant group, whereas Alphaproteobacteria were distinctive of Mercedes. Archaeal community associated with sediments was mainly represent by members related to the order of Methanosarcinales at Mercedes and Las Torres lakes, and by Crenarchaeota at Témpanos lake. Our results indicate that the proximity to the glacier and the seasonality shape the composition of the prokaryotic communities in these remote lakes. These results may be used as baseline information to follow the microbial community responses to potential global changes and to anthropogenic impacts.
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Affiliation(s)
- Paulina Aguayo
- Department of Microbiology, Laboratory of Basic Microbiology and Bioremedation, University of Concepción, Concepción, Chile
- Research Centre for Extreme Environments and Extremophiles, Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres, 31, 98166, Messina, Italy
| | - Paulina González
- Department of Microbiology, Laboratory of Basic Microbiology and Bioremedation, University of Concepción, Concepción, Chile
| | - Víctor Campos
- Research Centre for Extreme Environments and Extremophiles, Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres, 31, 98166, Messina, Italy
- Department of Microbiology, Laboratory of Environmental Microbiology, University of Concepción, Concepción, Chile
| | - Teresa L Maugeri
- Research Centre for Extreme Environments and Extremophiles, Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres, 31, 98166, Messina, Italy
| | - Maria Papale
- Research Centre for Extreme Environments and Extremophiles, Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres, 31, 98166, Messina, Italy
| | - Concetta Gugliandolo
- Research Centre for Extreme Environments and Extremophiles, Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres, 31, 98166, Messina, Italy.
| | - Miguel A Martinez
- Department of Microbiology, Laboratory of Basic Microbiology and Bioremedation, University of Concepción, Concepción, Chile
- Research Centre for Extreme Environments and Extremophiles, Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres, 31, 98166, Messina, Italy
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Vierheilig J, Savio D, Ley RE, Mach RL, Farnleitner AH, Reischer GH. Potential applications of next generation DNA sequencing of 16S rRNA gene amplicons in microbial water quality monitoring. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2015; 72:1962-72. [PMID: 26606090 PMCID: PMC4884447 DOI: 10.2166/wst.2015.407] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The applicability of next generation DNA sequencing (NGS) methods for water quality assessment has so far not been broadly investigated. This study set out to evaluate the potential of an NGS-based approach in a complex catchment with importance for drinking water abstraction. In this multi-compartment investigation, total bacterial communities in water, faeces, soil, and sediment samples were investigated by 454 pyrosequencing of bacterial 16S rRNA gene amplicons to assess the capabilities of this NGS method for (i) the development and evaluation of environmental molecular diagnostics, (ii) direct screening of the bulk bacterial communities, and (iii) the detection of faecal pollution in water. Results indicate that NGS methods can highlight potential target populations for diagnostics and will prove useful for the evaluation of existing and the development of novel DNA-based detection methods in the field of water microbiology. The used approach allowed unveiling of dominant bacterial populations but failed to detect populations with low abundances such as faecal indicators in surface waters. In combination with metadata, NGS data will also allow the identification of drivers of bacterial community composition during water treatment and distribution, highlighting the power of this approach for monitoring of bacterial regrowth and contamination in technical systems.
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Affiliation(s)
- J Vierheilig
- Research Group Environmental Microbiology and Molecular Ecology, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorfer Straße 1a, A-1060 Vienna, Austria E-mail: ; Centre for Water Resource Systems (CWRS), Vienna University of Technology, Karlsplatz 13/222, A-1040 Vienna, Austria; Present address: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
| | - D Savio
- Research Group Environmental Microbiology and Molecular Ecology, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorfer Straße 1a, A-1060 Vienna, Austria E-mail: ; Centre for Water Resource Systems (CWRS), Vienna University of Technology, Karlsplatz 13/222, A-1040 Vienna, Austria
| | - R E Ley
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - R L Mach
- Gene Technology Group, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorfer Straße 1a, A-1060 Vienna, Austria
| | - A H Farnleitner
- Research Group Environmental Microbiology and Molecular Ecology, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorfer Straße 1a, A-1060 Vienna, Austria E-mail: ; Interuniversity Cooperation Centre Water & Health, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorfer Straße 1a, A-1060 Vienna, Austria
| | - G H Reischer
- Research Group Environmental Microbiology and Molecular Ecology, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorfer Straße 1a, A-1060 Vienna, Austria E-mail: ; Interuniversity Cooperation Centre Water & Health, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorfer Straße 1a, A-1060 Vienna, Austria
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Douterelo I, Boxall JB, Deines P, Sekar R, Fish KE, Biggs CA. Methodological approaches for studying the microbial ecology of drinking water distribution systems. WATER RESEARCH 2014; 65:134-156. [PMID: 25105587 DOI: 10.1016/j.watres.2014.07.008] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 06/08/2014] [Accepted: 07/04/2014] [Indexed: 06/03/2023]
Abstract
The study of the microbial ecology of drinking water distribution systems (DWDS) has traditionally been based on culturing organisms from bulk water samples. The development and application of molecular methods has supplied new tools for examining the microbial diversity and activity of environmental samples, yielding new insights into the microbial community and its diversity within these engineered ecosystems. In this review, the currently available methods and emerging approaches for characterising microbial communities, including both planktonic and biofilm ways of life, are critically evaluated. The study of biofilms is considered particularly important as it plays a critical role in the processes and interactions occurring at the pipe wall and bulk water interface. The advantages, limitations and usefulness of methods that can be used to detect and assess microbial abundance, community composition and function are discussed in a DWDS context. This review will assist hydraulic engineers and microbial ecologists in choosing the most appropriate tools to assess drinking water microbiology and related aspects.
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Affiliation(s)
- Isabel Douterelo
- Pennine Water Group, Department of Civil and Structural Engineering, The University of Sheffield, UK.
| | - Joby B Boxall
- Pennine Water Group, Department of Civil and Structural Engineering, The University of Sheffield, UK
| | - Peter Deines
- Institute of Natural and Mathematical Sciences, Massey University, New Zealand
| | - Raju Sekar
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, China
| | - Katherine E Fish
- Pennine Water Group, Department of Civil and Structural Engineering, The University of Sheffield, UK
| | - Catherine A Biggs
- Department of Chemical and Biological Engineering, The University of Sheffield, UK
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Homonnay ZG, Török G, Makk J, Brumbauer A, Major É, Márialigeti K, Tóth E. Bacterial communities in the collection and chlorinated distribution sections of a drinking water system in Budapest, Hungary. J Basic Microbiol 2014; 54:729-38. [DOI: 10.1002/jobm.201300960] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/20/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Zalán G. Homonnay
- Department of Microbiology; Eötvös Loránd University; Budapest Hungary
| | - György Török
- Department of Microbiology; Eötvös Loránd University; Budapest Hungary
| | - Judit Makk
- Department of Microbiology; Eötvös Loránd University; Budapest Hungary
| | - Anikó Brumbauer
- Water Quality and Environmental Protection Department; Waterworks of Budapest; Budapest Hungary
| | - Éva Major
- Water Quality and Environmental Protection Department; Waterworks of Budapest; Budapest Hungary
| | | | - Erika Tóth
- Department of Microbiology; Eötvös Loránd University; Budapest Hungary
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11
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França L, Lopéz-Lopéz A, Rosselló-Móra R, da Costa MS. Microbial diversity and dynamics of a groundwater and a still bottled natural mineral water. Environ Microbiol 2014; 17:577-93. [DOI: 10.1111/1462-2920.12430] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 02/12/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Luís França
- Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
| | - Arantxa Lopéz-Lopéz
- Marine Microbiology Group; IMEDEA (CSIC-UIB); Esporles Balearic Islands Spain
| | - Ramon Rosselló-Móra
- Marine Microbiology Group; IMEDEA (CSIC-UIB); Esporles Balearic Islands Spain
| | - Milton S. da Costa
- Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
- Department of Life Sciences; University of Coimbra; Coimbra Portugal
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12
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Matturro B, Tandoi V, Rossetti S. Different activity levels of Dehalococcoides mccartyi revealed by FISH and CARD-FISH under non-steady and pseudo-steady state conditions. N Biotechnol 2013; 30:756-62. [DOI: 10.1016/j.nbt.2013.07.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 07/16/2013] [Accepted: 07/23/2013] [Indexed: 11/15/2022]
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13
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Williamson WM, Close ME, Leonard MM, Webber JB, Lin S. Groundwater biofilm dynamics grown in situ along a nutrient gradient. GROUND WATER 2012; 50:690-703. [PMID: 22220932 DOI: 10.1111/j.1745-6584.2011.00904.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This paper describes the in situ response of groundwater biofilms in an alluvial gravel aquifer system on the Canterbury Plains, New Zealand. Biofilms were developed on aquifer gravel, encased in fine mesh bags and suspended in protective columns in monitoring wells for at least 20 weeks. Four sites were selected in the same groundwater system where previous analyses indicated a gradient of increasing nitrate down the hydraulic gradient from Sites 1 to 4. Measurements during the current study classified the groundwater as oligotrophic. Biofilm responses to the nutrient gradients were assessed using bioassays, with biomass determined using protein and cellular and nucleic acid staining and biofilm activity using enzyme assays for lipid, carbohydrate, phosphate metabolism, and cell viability. In general, biofilm activity decreased as nitrate levels increased from Sites 1 to 4, with the opposite relationship for carbon and phosphorus concentrations. These results showed that the groundwater system supported biofilm growth and that the upper catchment supported efficient and productive biofilms (high ratio of activity per unit biomass).
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Affiliation(s)
- Wendy M Williamson
- Institute of Environmental Science & Research Ltd, Christchurch Science Centre, P.O. Box 29-181, Christchurch 8540, New Zealand.
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14
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Rapid and sensitive quantification of Vibrio cholerae and Vibrio mimicus cells in water samples by use of catalyzed reporter deposition fluorescence in situ hybridization combined with solid-phase cytometry. Appl Environ Microbiol 2012; 78:7369-75. [PMID: 22885749 DOI: 10.1128/aem.02190-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new protocol for rapid, specific, and sensitive cell-based quantification of Vibrio cholerae/Vibrio mimicus in water samples was developed. The protocol is based on catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) in combination with solid-phase cytometry. For pure cultures, we were able to quantify down to 6 V. cholerae cells on one membrane with a relative precision of 39% and down to 12 cells with a relative precision of 17% after hybridization with the horseradish peroxidase (HRP)-labeled probe Vchomim1276 (specific for V. cholerae and V. mimicus) and signal amplification. The corresponding position of the probe on the 16S rRNA is highly accessible even when labeled with HRP. For the first time, we were also able to successfully quantify V. cholerae/V. mimicus via solid-phase cytometry in extremely turbid environmental water samples collected in Austria. Cell numbers ranged from 4.5 × 10(1) cells ml(-1) in the large saline lake Neusiedler See to 5.6 × 10(4) cells ml(-1) in an extremely turbid shallow soda lake situated nearby. We therefore suggest CARD-FISH in combination with solid-phase cytometry as a powerful tool to quantify V. cholerae/V. mimicus in ecological studies as well as for risk assessment and monitoring programs.
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15
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Kirschner A, Rameder A, Schrammel B, Indra A, Farnleitner A, Sommer R. Development of a new CARD-FISH protocol for quantification of Legionella pneumophila and its application in two hospital cooling towers. J Appl Microbiol 2012; 112:1244-56. [DOI: 10.1111/j.1365-2672.2012.05289.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Kirschner AKT, Schauer S, Steinberger B, Wilhartitz I, Grim CJ, Huq A, Colwell RR, Herzig A, Sommer R. Interaction of Vibrio cholerae non-O1/non-O139 with copepods, cladocerans and competing bacteria in the large alkaline lake Neusiedler See, Austria. MICROBIAL ECOLOGY 2011; 61:496-506. [PMID: 21049271 PMCID: PMC3072514 DOI: 10.1007/s00248-010-9764-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 10/16/2010] [Indexed: 05/30/2023]
Abstract
Vibrio cholerae is a human pathogen and natural inhabitant of aquatic environments. Serogroups O1/O139 have been associated with epidemic cholera, while non-O1/non-O139 serogroups usually cause human disease other than classical cholera. V. cholerae non-O1/non-O139 from the Neusiedler See, a large Central European lake, have caused ear and wound infections, including one case of fatal septicaemia. Recent investigations demonstrated rapid planktonic growth of V. cholerae non-O1/non-O139 and correlation with zooplankton biomass. The aim of this study was to elucidate the interaction of autochthonous V. cholerae with two dominant crustacean zooplankton species in the lake and investigate the influence of the natural bacterial community on this interaction. An existing data set was evaluated for statistical relationships between zooplankton species and V. cholerae and co-culture experiments were performed in the laboratory. A new fluorescence in situ hybridisation protocol was applied for quantification of V. cholerae non-O1/non-O139 cells, which significantly reduced analysis time. The experiments clearly demonstrated a significant relationship of autochthonous V. cholerae non-O1/non-O139 with cladocerans by promoting growth of V. cholerae non-O1/non-O139 in the water and on the surfaces of the cladocerans. In contrast, copepods had a negative effect on the growth of V. cholerae non-O1/non-O139 via competing bacteria from their surfaces. Thus, beside other known factors, biofilm formation by V. cholerae on crustacean zooplankton appears to be zooplankton taxon specific and may be controlled by the natural bacterial community.
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Affiliation(s)
- Alexander K T Kirschner
- Institute for Hygiene and Applied Immunology, Water Hygiene, Medical University of Vienna, Wien, Austria.
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17
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Longnecker K, Lomas MW, Van Mooy BAS. Abundance and diversity of heterotrophic bacterial cells assimilating phosphate in the subtropical North Atlantic Ocean. Environ Microbiol 2011; 12:2773-82. [PMID: 20545744 DOI: 10.1111/j.1462-2920.2010.02247.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microorganisms play key roles in the cycles of carbon and nutrients in the ocean, and identifying the extent to which specific taxa contribute to these cycles will establish their ecological function. We examined the use of (33)P-phosphate to identify heterotrophic bacteria actively involved in the cycling of phosphate, an essential inorganic nutrient. Seawater from the sub-tropical North Atlantic Ocean was incubated with (33)P-phosphate and analysed by microautoradiography to determine the proportion and diversity of the bacterial community-assimilating phosphate. Complementary incubations using (3)H-leucine and (3)H-thymidine were also conducted. We found that a higher proportion of total heterotrophic bacterial cells in surface water samples assimilated phosphate compared with leucine or thymidine. Bacteria from all of the phylogenetic groups we identified by CARD-FISH were able to assimilate phosphate, although the abundances of cells within each group did not scale directly with the number found to assimilate phosphate. Furthermore, a significantly higher proportion of Alphaproteobacteria, Gammaproteobacteria and Cytophaga-like cells assimilated phosphate compared with leucine or thymidine. Our results suggest that a greater proportion of bacterial cells in surface waters are actively participating in the biogeochemical cycling of phosphorus, and possibly other elements, than is currently estimated through the use of (3)H-leucine or (3)H-thymidine.
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Affiliation(s)
- Krista Longnecker
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, MA 02543, USA
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18
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Wilhartitz IC, Kirschner AKT, Stadler H, Herndl GJ, Dietzel M, Latal C, Mach RL, Farnleitner AH. Heterotrophic prokaryotic production in ultraoligotrophic alpine karst aquifers and ecological implications. FEMS Microbiol Ecol 2009; 68:287-99. [PMID: 19490127 DOI: 10.1111/j.1574-6941.2009.00679.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Spring waters from alpine karst aquifers are important drinking water resources. To investigate in situ heterotrophic prokaryotic production and its controlling factors, two different alpine karst springs were studied over two annual cycles. Heterotrophic production in spring water, as determined by [(3)H]leucine incorporation, was extremely low ranging from 0.06 to 6.83 pmol C L(-1) h(-1) (DKAS1, dolomitic-karst-spring) and from 0.50 to 75.6 pmol C L(-1) h(-1) (LKAS2, limestone-karst-spring). Microautoradiography combined with catalyzed reporter deposition-FISH showed that only about 7% of the picoplankton community took up [(3)H]leucine, resulting in generation times of 3-684 days. Principal component analysis, applying hydrological, chemical and biological parameters demonstrated that planktonic heterotrophic production in LKAS2 was governed by the respective hydrological conditions, whereas variations in DKAS1 changed seemingly independent from discharge. Measurements in sediments recovered from LKAS2, DKAS1 and similar alpine karst aquifers (n=12) revealed a 10(6)-fold higher heterotrophic production (average 19 micromol C dm(-3) h(-1)) with significantly lower generation times as compared with the planktonic fraction, highlighting the potential of surface-associated communities to add to self-purification processes. Estimates of the microbially mediated CO(2) in this compartment indicated a possible contribution to karstification.
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Affiliation(s)
- Inés C Wilhartitz
- Department for Applied Biochemistry and Gene Technology, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
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Assessment of the diversity, abundance, and ecological distribution of members of candidate division SR1 reveals a high level of phylogenetic diversity but limited morphotypic diversity. Appl Environ Microbiol 2009; 75:4139-48. [PMID: 19395567 DOI: 10.1128/aem.00137-09] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We used a combination of 16S rRNA gene clone library surveys, quantitative PCR (qPCR) analysis, and fluorescent in situ hybridization to investigate the diversity, abundance, and distribution of members of candidate division SR1 in multiple habitats. Using SR1-specific 16S rRNA gene primers, we identified multiple novel SR1 lineages in four different anaerobic environments: sediments from Zodletone Spring, a sulfide- and sulfur-rich spring in southwestern Oklahoma; inner layers of microbial mats obtained from Sperm Pool, a high-temperature, low-pH pool (55 degrees C, pH 2.5) in Yellowstone National Park; fresh bovine ruminal contents; and anaerobic freshwater pond sediments (Duck Pond) in Norman, Oklahoma. qPCR analysis indicated that SR1 members constitute a small fraction (<0.01%) of the microbial communities in Duck Pond and ruminal samples but constitute a significant fraction (11.6 and 48.7%) of the total number of bacterial 16S rRNA genes in Zodletone Spring and the inner layers of Sperm Pool microbial mat samples, respectively. By using SR1-specific fluorescent probes, filamentous cells were identified as the sole SR1 morphotype in all environments examined, with the exception of Sperm Pool, where a second bacillus morphotype was also identified. Using a full-cycle 16S rRNA approach, we show that each of these two morphotypes corresponds to a specific phylogenetic lineage identified in the Sperm Pool clone library. This work greatly expands the intralineage phylogenetic diversity within candidate division SR1 and provides valuable quantification and visualization tools that could be used for investigating the ecological roles, dynamics, and genomics of this as-yet-uncultured bacterial phylum.
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