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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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Wan X, Li J, Wang S, Fan F, McLaughlin RW, Wang K, Wang D, Zheng J. Biogeographic patterns of potential pathogenic bacteria in the middle and lower reaches of the Yangtze River as well as its two adjoining lakes, China. Front Microbiol 2022; 13:972243. [PMID: 36118197 PMCID: PMC9479215 DOI: 10.3389/fmicb.2022.972243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022] Open
Abstract
Understanding the distribution patterns and shaping factors of bacterial pathogens in aquatic ecosystems, especially in natural waters, are critical to the control of pathogen transmission. In this study, using 16S rRNA gene amplicon sequencing, we explored the composition and biogeographic dynamics of potential bacterial pathogens in the middle and lower reaches of the Yangtze River, as well as its two vast adjoining lakes (Dongting Lake and Poyang Lake). The pathogen community belonged to 12 potential pathogenic groups, with “intracellular parasites,” “animal parasites or symbionts” and “human pathogens all” occupying 97.5% in total. The potential pathogen community covered seven phyla with Proteobacteria (69.8%) and Bacteroidetes (13.5%) the most predominant. In addition, 53 genera were identified with Legionella (15.2%) and Roseomonas (14.2%) the most dominant. The average relative abundance, alpha diversity and microbial composition of the potential bacterial pathogens exhibited significant biogeographical variations among the different sections. An in-depth analysis reflected that environmental variables significantly structured the potential bacterial pathogens, including water physiochemical properties (i.e., chlorophyll-a, total nitrogen and transparency), heavy metals (i.e., As and Ni), climate (i.e., air temperature) and land use type (i.e., waters). Compared to the overall bacterial community which was composed of both pathogenic and non-pathogenic bacteria, the pathogen community exhibited distinct microbial diversity patterns and shaping factors. This signifies the importance of different variables for shaping the pathogen community. This study represents one attempt to explore pathogen diversity patterns and their underlying drivers in the Yangtze River, which provides a foundation for the management of pathogenic bacteria.
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Affiliation(s)
- Xiaoling Wan
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jia Li
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shiyong Wang
- Changjiang Survey, Planning, Design and Research Co., Ltd., Wuhan, China
- Key Laboratory of Changjiang Regulation and Protection of Ministry of Water Resources, Wuhan, China
- *Correspondence: Shiyong Wang
| | - Fei Fan
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | | | - Kexiong Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ding Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jinsong Zheng
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Jinsong Zheng
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3
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Duffner C, Kublik S, Fösel B, Frostegård Å, Schloter M, Bakken L, Schulz S. Genotypic and phenotypic characterization of hydrogenotrophic denitrifiers. Environ Microbiol 2022; 24:1887-1901. [PMID: 35106904 DOI: 10.1111/1462-2920.15921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/30/2022]
Abstract
Stimulating litho-autotrophic denitrification in aquifers with hydrogen is a promising strategy to remove excess NO3 - , but it often entails accumulation of the cytotoxic intermediate NO2 - and the greenhouse gas N2 O. To explore if these high NO2 - and N2 O concentrations are caused by differences in the genomic composition, the regulation of gene transcription or the kinetics of the reductases involved, we isolated hydrogenotrophic denitrifiers from a polluted aquifer, performed whole-genome sequencing and investigated their phenotypes. We therefore assessed the kinetics of NO2 - , NO, N2 O, N2 and O2 as they depleted O2 and transitioned to denitrification with NO3 - as the only electron acceptor and hydrogen as the electron donor. Isolates with a complete denitrification pathway, although differing intermediate accumulation, were closely related to Dechloromonas denitrificans, Ferribacterium limneticum or Hydrogenophaga taeniospiralis. High NO2 - accumulation was associated with the reductases' kinetics. While available, electrons only flowed towards NO3 - in the narG-containing H. taeniospiralis but flowed concurrently to all denitrification intermediates in the napA-containing D. denitrificans and F. limneticum. The denitrification regulator RegAB, present in the napA strains, may further secure low intermediate accumulation. High N2 O accumulation only occurred during the transition to denitrification and is thus likely caused by delayed N2 O reductase expression.
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Affiliation(s)
- Clara Duffner
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Bärbel Fösel
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Michael Schloter
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Lars Bakken
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
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Kagemasa S, Kuroda K, Nakai R, Li YY, Kubota K. Diversity of <i>Candidatus</i> Patescibacteria in Activated Sludge Revealed by a Size-Fractionation Approach. Microbes Environ 2022; 37. [PMID: 35676047 PMCID: PMC9530733 DOI: 10.1264/jsme2.me22027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Uncultivated members of Candidatus Patescibacteria are commonly found in activated sludge treating sewage and are widely distributed in wastewater treatment plants in different regions and countries. However, the phylogenetic diversity of Ca. Patescibacteria is difficult to examine because of their low relative abundance in the environment. Since Ca. Patescibacteria members have small cell sizes, we herein collected small microorganisms from activated sludge using a filtration-based size-fractionation approach (i.e., 0.45–0.22 μm and 0.22–0.1 μm fractions). Fractionated samples were characterized using 16S rRNA gene amplicon and shotgun metagenomic sequence analyses. The amplicon analysis revealed that the relative abundance of Ca. Patescibacteria increased to 73.5% and 52.5% in the 0.45–0.22 μm and 0.22–0.1 μm fraction samples, respectively, from 5.8% in the unfractionated sample. The members recovered from the two size-fractionated samples included Ca. Saccharimonadia, Ca. Gracilibacteria, Ca. Paceibacteria, Ca. Microgenomatia, class-level uncultured lineage ABY1, Ca. Berkelbacteria, WS6 (Ca. Dojkabacteria), and WWE3, with Ca. Saccharimonadia being predominant in both fraction samples. The number of operational taxonomic units belonging to Ca. Patescibacteria was approximately 6-fold higher in the size-fractionated samples than in the unfractionated sample. The shotgun metagenomic analysis of the 0.45–0.22 μm fractioned sample enabled the reconstruction of 24 high-quality patescibacterial bins. The bins obtained were classified into diverse clades at the family and genus levels, some of which were rarely detected in previous activated sludge studies. Collectively, the present results suggest that the overall diversity of Ca. Patescibacteria inhabiting activated sludge is higher than previously expected.
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Affiliation(s)
- Shuka Kagemasa
- Department of Civil and Environmental Engineering, Tohoku University
| | - Kyohei Kuroda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Tohoku University
| | - Kengo Kubota
- Department of Frontier Sciences for Advanced Environment, Tohoku University
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Cameron ES, Schmidt PJ, Tremblay BJM, Emelko MB, Müller KM. Enhancing diversity analysis by repeatedly rarefying next generation sequencing data describing microbial communities. Sci Rep 2021; 11:22302. [PMID: 34785722 PMCID: PMC8595385 DOI: 10.1038/s41598-021-01636-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
Amplicon sequencing has revolutionized our ability to study DNA collected from environmental samples by providing a rapid and sensitive technique for microbial community analysis that eliminates the challenges associated with lab cultivation and taxonomic identification through microscopy. In water resources management, it can be especially useful to evaluate ecosystem shifts in response to natural and anthropogenic landscape disturbances to signal potential water quality concerns, such as the detection of toxic cyanobacteria or pathogenic bacteria. Amplicon sequencing data consist of discrete counts of sequence reads, the sum of which is the library size. Groups of samples typically have different library sizes that are not representative of biological variation; library size normalization is required to meaningfully compare diversity between them. Rarefaction is a widely used normalization technique that involves the random subsampling of sequences from the initial sample library to a selected normalized library size. This process is often dismissed as statistically invalid because subsampling effectively discards a portion of the observed sequences, yet it remains prevalent in practice and the suitability of rarefying, relative to many other normalization approaches, for diversity analysis has been argued. Here, repeated rarefying is proposed as a tool to normalize library sizes for diversity analyses. This enables (i) proportionate representation of all observed sequences and (ii) characterization of the random variation introduced to diversity analyses by rarefying to a smaller library size shared by all samples. While many deterministic data transformations are not tailored to produce equal library sizes, repeatedly rarefying reflects the probabilistic process by which amplicon sequencing data are obtained as a representation of the amplified source microbial community. Specifically, it evaluates which data might have been obtained if a particular sample's library size had been smaller and allows graphical representation of the effects of this library size normalization process upon diversity analysis results.
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Affiliation(s)
- Ellen S Cameron
- Department of Biology, University of Waterloo, 200 University Ave. W, Waterloo, ON, N2L 3G1, Canada
| | - Philip J Schmidt
- Department of Civil and Environmental Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON, N2L 3G1, Canada
| | - Benjamin J-M Tremblay
- Department of Biology, University of Waterloo, 200 University Ave. W, Waterloo, ON, N2L 3G1, Canada
| | - Monica B Emelko
- Department of Civil and Environmental Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON, N2L 3G1, Canada
| | - Kirsten M Müller
- Department of Biology, University of Waterloo, 200 University Ave. W, Waterloo, ON, N2L 3G1, Canada.
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