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Campostrini L, Proksch P, Jakwerth S, Farnleitner AH, Kirschner AKT. Introducing bacterial community turnover times to elucidate temporal and spatial hotspots of biological instability in a large Austrian drinking water distribution network. WATER RESEARCH 2024; 252:121188. [PMID: 38324987 DOI: 10.1016/j.watres.2024.121188] [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: 07/03/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 02/09/2024]
Abstract
Ensuring biological stability in drinking water distribution systems (DWDSs) is important to reduce the risk of aesthetic, operational and hygienic impairments of the distributed water. Drinking water after treatment often changes in quality during transport due to interactions with pipe-associated biofilms, temperature increases and disinfectant residual decay leading to potential biological instability. To comprehensively assess the potential for biological instability in a large chlorinated DWDS, a tool-box of bacterial biomass and activity parameters was applied, introducing bacterial community turnover times (BaCTT) as a direct, sensitive and easy-to-interpret quantitative parameter based on the combination of 3H-leucine incorporation with bacterial biomass. Using BaCTT, hotspots and periods of bacterial growth and potential biological instability could be identified in the DWDS that is fed by water with high bacterial growth potential. A de-coupling of biomass from activity parameters was observed, suggesting that bacterial biomass parameters depict seasonally fluctuating raw water quality rather than processes related to biological stability of the finished water in the DWDS. BaCTT, on the other hand, were significantly correlated to water age, disinfectant residual, temperature and a seasonal factor, indicating a higher potential of biological instability at more distant sampling sites and later in the year. As demonstrated, BaCTT is suggested as a novel, sensitive and very useful parameter for assessing the biological instability potential. However, additional studies in other DWDSs are needed to investigate the general applicability of BaCTT depending on water source, applied treatment processes, biofilm growth potential on different pipe materials, or size, age and complexity of the DWDS.
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Affiliation(s)
- Lena Campostrini
- Medical University of Vienna, Centre for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology - Water Microbiology, Kinderspitalgasse 15, Vienna A-1090, Austria; Interuniversity Cooperation Centre Water & Health, Austria
| | - Philipp Proksch
- University of Natural Resources and Life Sciences, Vienna, Institute of Sanitary Engineering and Water Pollution Control, Muthgasse 18, Vienna A-1190, Austria
| | - Stefan Jakwerth
- Medical University of Vienna, Centre for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology - Water Microbiology, Kinderspitalgasse 15, Vienna A-1090, Austria; Interuniversity Cooperation Centre Water & Health, Austria
| | - Andreas H Farnleitner
- Interuniversity Cooperation Centre Water & Health, Austria; Division Water Quality and Health, Karl Landsteiner University of Health Sciences, Dr. Karl Dorrek-Straße 30, Krems A-3500, Austria; Technische Universität Wien, Institute for Chemical, Environmental and Bioscience Engineering, Research Group Microbiology and Molecular Diagnostics 166/5/3, Gumpendorferstraße 1, Vienna A-1060, Austria
| | - Alexander K T Kirschner
- Medical University of Vienna, Centre for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology - Water Microbiology, Kinderspitalgasse 15, Vienna A-1090, Austria; Interuniversity Cooperation Centre Water & Health, Austria; Division Water Quality and Health, Karl Landsteiner University of Health Sciences, Dr. Karl Dorrek-Straße 30, Krems A-3500, Austria.
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2
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Fernández-Martínez M, Barquín J, Bonada N, Cantonati M, Churro C, Corbera J, Delgado C, Dulsat-Masvidal M, Garcia G, Margalef O, Pascual R, Peñuelas J, Preece C, Sabater F, Seiler H, Zamora-Marín JM, Romero E. Mediterranean springs: Keystone ecosystems and biodiversity refugia threatened by global change. GLOBAL CHANGE BIOLOGY 2024; 30:e16997. [PMID: 37937346 DOI: 10.1111/gcb.16997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/29/2023] [Accepted: 10/09/2023] [Indexed: 11/09/2023]
Abstract
Mediterranean spring ecosystems are unique habitats at the interface between surface water and groundwater. These ecosystems support a remarkable array of biodiversity and provide important ecological functions and ecosystem services. Spring ecosystems are influenced by abiotic, biotic, and anthropogenic factors such as the lithology of their draining aquifers, their climate, and the land use of their recharge area, all of which affect the water chemistry of the aquifer and the spring discharges. One of the most relevant characteristics of spring ecosystems is the temporal stability of environmental conditions, including physicochemical features of the spring water, across seasons and years. This stability allows a wide range of species to benefit from these ecosystems (particularly during dry periods), fostering an unusually high number of endemic species. However, global change poses important threats to these freshwater ecosystems. Changes in temperature, evapotranspiration, and precipitation patterns can alter the water balance and chemistry of spring water. Eutrophication due to agricultural practices and emergent pollutants, such as pharmaceuticals, personal care products, and pesticides, is also a growing concern for the preservation of spring biodiversity. Here, we provide a synthesis of the main characteristics and functioning of Mediterranean spring ecosystems. We then describe their ecological value and biodiversity patterns and highlight the main risks these ecosystems face. Moreover, we identify existing knowledge gaps to guide future research in order to fully uncover the hidden biodiversity within these habitats and understand the main drivers that govern them. Finally, we provide a brief summary of recommended actions that should be taken to effectively manage and preserve Mediterranean spring ecosystems for future generations. Even though studies on Mediterranean spring ecosystems are still scarce, our review shows there are sufficient data to conclude that their future viability as functional ecosystems is under severe threat.
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Affiliation(s)
- M Fernández-Martínez
- CREAF, Campus de Bellaterra (UAB), Cerdanyola del Vallès, Spain
- Delegació de la Serralada Litoral Central - ICHN, Mataró, Spain
- Department of Evolutionary Biology, Ecology and Environmental Sciences (BEECA-UB), University of Barcelona, Barcelona, Spain
| | - J Barquín
- Instituto de Hidráulica Ambiental de la Universidad de Cantabria (IHCantabria), Santander, Spain
| | - N Bonada
- Freshwater Ecology, Hydrology and Management Research Group (FEHM), Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), University of Barcelona, Barcelona, Spain
| | - M Cantonati
- BIOME Lab, Department of Biological, Geological and Environmental Sciences - BiGeA, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - C Churro
- Laboratory of Virology and Molecular Biology and Laboratory of Phytoplankton, Department of the Sea and Marine Resources, Portuguese Institute for the Sea and Atmosphere (IPMA), Lisbon, Portugal
- Blue Biotechnology and Ecotoxicology (BBE), CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
| | - J Corbera
- Delegació de la Serralada Litoral Central - ICHN, Mataró, Spain
| | - C Delgado
- Departamento de Ecoloxía e Bioloxía Animal, Facultade de Ciencias, Universidade de Vigo, Vigo, Spain
| | - M Dulsat-Masvidal
- IDAEA-CSIC, Institute of Environmental Assessment and Water Research, Barcelona, Spain
| | - G Garcia
- BioSciCat, The Catalan Society of Sciences for the Conservation of Biodiversity, Tarragona, Spain
| | - O Margalef
- CREAF, Campus de Bellaterra (UAB), Cerdanyola del Vallès, Spain
- Departament de Dinàmica de la Terra i de l'Oceà, GRC RISKNAT, UB-Geomodels, Facultat de Ciències de la Terra, University of Barcelona, Barcelona, Spain
| | - R Pascual
- BioSciCat, The Catalan Society of Sciences for the Conservation of Biodiversity, Tarragona, Spain
| | - J Peñuelas
- CREAF, Campus de Bellaterra (UAB), Cerdanyola del Vallès, Spain
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Barcelona, Spain
| | - C Preece
- Institute of Agrifood Research and Technology (IRTA), Sustainability in Biosystems Programme, Barcelona, Spain
| | - F Sabater
- CREAF, Campus de Bellaterra (UAB), Cerdanyola del Vallès, Spain
- Delegació de la Serralada Litoral Central - ICHN, Mataró, Spain
- Department of Evolutionary Biology, Ecology and Environmental Sciences (BEECA-UB), University of Barcelona, Barcelona, Spain
| | - H Seiler
- Vegetation Ecology, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - J M Zamora-Marín
- Department of Applied Biology, Centro de Investigación e Innovación Agroalimentaria (CIAGRO-UMH), Miguel Hernández University of Elche, Elche, Spain
| | - E Romero
- CREAF, Campus de Bellaterra (UAB), Cerdanyola del Vallès, Spain
- Department of Evolutionary Biology, Ecology and Environmental Sciences (BEECA-UB), University of Barcelona, Barcelona, Spain
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3
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Szekeres E, Baricz A, Cristea A, Levei EA, Stupar Z, Brad T, Kenesz M, Moldovan OT, Banciu HL. Karst spring microbiome: Diversity, core taxa, and community response to pathogens and antibiotic resistance gene contamination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165133. [PMID: 37364839 DOI: 10.1016/j.scitotenv.2023.165133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/19/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Karst aquifers are important water resources for drinking water supplies worldwide. Although they are susceptible to anthropogenic contamination due to their high permeability, there is a lack of detailed knowledge on the stable core microbiome and how contamination may affect these communities. In this study, eight karst springs (distributed across three different regions in Romania) were sampled seasonally for one year. The core microbiota was analysed by 16S rRNA gene amplicon sequencing. To identify bacteria carrying antibiotic resistance genes and mobile genetic elements, an innovative method was applied, consisting of high-throughput antibiotic resistance gene quantification performed on potential pathogen colonies cultivated on Compact Dry™ plates. A taxonomically stable bacterial community consisting of Pseudomonadota, Bacteroidota, and Actinomycetota was revealed. Core analysis reaffirmed these results and revealed primarily freshwater-dwelling, psychrophilic/psychrotolerant species affiliated to Rhodoferax, Flavobacterium, and Pseudomonas genera. Both sequencing and cultivation methods indicated that more than half of the springs were contaminated with faecal bacteria and pathogens. These samples contained high levels of sulfonamide, macrolide, lincosamide and streptogramins B, and trimethoprim resistance genes spread primarily by transposase and insertion sequences. Differential abundance analysis found Synergistota, Mycoplasmatota, and Chlamydiota as suitable candidates for pollution monitoring in karst springs. This is the first study highlighting the applicability of a combined approach based on high-throughput SmartChip™ antibiotic resistance gene quantification and Compact Dry™ pathogen cultivation for estimating microbial contaminants in karst springs and other challenging low biomass environments.
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Affiliation(s)
- Edina Szekeres
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania; Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, Cluj-Napoca, Romania; National Institute of Research and Development for Biological Sciences, Institute of Biological Research, Cluj-Napoca, Romania
| | - Andreea Baricz
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania; Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Adorján Cristea
- Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, Cluj-Napoca, Romania; Department of Taxonomy and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Erika Andrea Levei
- INCDO-INOE 2000, Research Institute for Analytical Instrumentation, Cluj-Napoca, Romania
| | - Zamfira Stupar
- INCDO-INOE 2000, Research Institute for Analytical Instrumentation, Cluj-Napoca, Romania
| | - Traian Brad
- Department of Cluj-Napoca, Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
| | - Marius Kenesz
- Department of Cluj-Napoca, Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
| | - Oana Teodora Moldovan
- Department of Cluj-Napoca, Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
| | - Horia Leonard Banciu
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania; Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, Cluj-Napoca, Romania.
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4
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Gupta A, Dutt V, Sharma N, Kajale S, Bhatt A, Shafi S, Azhar E, Zumla A, Sharma A. Examining the microbial composition of natural springs in Bhaderwah, Jammu and Kashmir, India. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:949. [PMID: 37450062 DOI: 10.1007/s10661-023-11507-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/10/2023] [Indexed: 07/18/2023]
Abstract
Natural springs are the main source of water supply for domestic and agricultural use for humans living in the mountainous regions of Asia. Increasing anthropogenic activities with associated waste load, coupled with inadequate sanitation, and contamination of natural water resources and the environment are emerging as important public health issues. We performed a prospective microbiological and physicochemical investigation of water samples from seven distinct natural springs situated at an altitude of 1615 m in the Bhaderwah region of Jammu and Kashmir, India. Bacterial groups belonging to opportunistic pathogens such as members of Moraxellaceae (Acinetobacter), Arcobacteraceae (Pseudoarcobacter), Pseudomonadaceae (Pseudomonas), Oxalobacteraceae (Massilia), and Flavobacteriaceae (Flavobacterium) were observed. The total coliform test indicated an intermediate level of risk of fecal contamination of the springs, except for one site. Through a questionnaire-based survey of the local population, we discovered that around 40% of participants had suffered from waterborne diseases including typhoid (~14%) and diarrhea (~11%). Our data suggests that increased surveillance of fecal contamination and heterotrophic opportunistic pathogens is needed to enhance water quality and reduce health risks for people living in mountainous regions.
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Affiliation(s)
- Abhishek Gupta
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Vandana Dutt
- Institute of Mountain Environment, University of Jammu, Bhaderwah Campus, Jammu and Kashmir, India
| | - Neeraj Sharma
- Institute of Mountain Environment, University of Jammu, Bhaderwah Campus, Jammu and Kashmir, India.
| | - Swapnil Kajale
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Arun Bhatt
- GB Pant Institute of Engineering and Technology, Garhwal, Uttarakhand, India
| | - Shuja Shafi
- Mass Gatherings and Global Health Network, London, UK
| | - Esam Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, and Medical Laboratory Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Alimuddin Zumla
- Division of Infection and Immunity, NIHR Biomedical Research Centre, UCL Hospitals NHS Foundation Trust, University College London, London, UK
| | - Avinash Sharma
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India.
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5
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Retter A, Haas JC, Birk S, Stumpp C, Hausmann B, Griebler C, Karwautz C. From the Mountain to the Valley: Drivers of Groundwater Prokaryotic Communities along an Alpine River Corridor. Microorganisms 2023; 11:microorganisms11030779. [PMID: 36985351 PMCID: PMC10055094 DOI: 10.3390/microorganisms11030779] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/08/2023] [Accepted: 03/11/2023] [Indexed: 03/19/2023] Open
Abstract
Rivers are the “tip of the iceberg”, with the underlying groundwater being the unseen freshwater majority. Microbial community composition and the dynamics of shallow groundwater ecosystems are thus crucial, due to their potential impact on ecosystem processes and functioning. In early summer and late autumn, samples of river water from 14 stations and groundwater from 45 wells were analyzed along a 300 km transect of the Mur River valley, from the Austrian alps to the flats at the Slovenian border. The active and total prokaryotic communities were characterized using high-throughput gene amplicon sequencing. Key physico-chemical parameters and stress indicators were recorded. The dataset was used to challenge ecological concepts and assembly processes in shallow aquifers. The groundwater microbiome is analyzed regarding its composition, change with land use, and difference to the river. Community composition and species turnover differed significantly. At high altitudes, dispersal limitation was the main driver of groundwater community assembly, whereas in the lowland, homogeneous selection explained the larger share. Land use was a key determinant of the groundwater microbiome composition. The alpine region was more diverse and richer in prokaryotic taxa, with some early diverging archaeal lineages being highly abundant. This dataset shows a longitudinal change in prokaryotic communities that is dependent on regional differences affected by geomorphology and land use.
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Affiliation(s)
- Alice Retter
- Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Wien, Austria
| | | | - Steffen Birk
- Institute of Earth Sciences, NAWI Graz Geocenter, University of Graz, 8010 Graz, Austria
| | - Christine Stumpp
- Institute of Soil Physics and Rural Water Management, University of Natural Resources and Life Sciences (BOKU), 1180 Wien, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1030 Wien, Austria
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Wien, Austria
| | - Christian Griebler
- Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Wien, Austria
| | - Clemens Karwautz
- Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Wien, Austria
- Correspondence:
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6
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Vucinic L, O'Connell D, Dubber D, Coxon C, Gill L. Multiple fluorescence approaches to identify rapid changes in microbial indicators at karst springs. JOURNAL OF CONTAMINANT HYDROLOGY 2023; 254:104129. [PMID: 36634484 DOI: 10.1016/j.jconhyd.2022.104129] [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: 05/24/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Karst springs are globally important for drinking water supply but are often also exceptionally vulnerable to contamination. Such springs usually exhibit strong variation in microbial water quality in sharp response to rainfall events, thus, posing a health hazard to consumers of water supplied from these sources. The rapid detection of such changes is extremely important as well as being able to establish a link to the sources of such pollution, so that appropriate measures can be taken both in terms of immediate protection of human health and the management of karst aquifers. In this study, a fluorescence-based multi-parameter approach was trialed in order to evaluate which methods can be used to monitor rainfall-induced rapid changes in microbial water quality at karst springs, as well as determine whether such changes can be linked to sources of human effluent contamination. The results from three monitoring periods at two karst springs revealed marked responses to rainfall events for all of the microbial parameters measured. Total cell count (TCC) measurements using flow cytometry (FCM) showed very strong positive correlations with the more conventionally monitored faecal indicator bacteria (FIB) and total coliforms (TC), indicating that such a fluorescence-based and cultivation-independent technique can be very useful to indicate rapid changes in microbial water quality at karst springs. Furthermore, very strong positive correlations were also found between tryptophan-like fluorescence (TLF) measurements and concentrations of all monitored microbial parameters, again demonstrating that such a fluorescence-based approach can also be useful for detecting rapid changes in concentrations of traditional faecal indicators. Interestingly, it was found that fluorescent whitening compounds (FWCs) signals do not necessarily follow temporal variations of microbial indicators. However, the frequency of detection of positive FWCs signals may still reveal useful information about the overall magnitude of human wastewater effluent impacts on karst aquifer systems.
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Affiliation(s)
- Luka Vucinic
- Department of Civil, Structural and Environmental Engineering, University of Dublin, Trinity College, Dublin, Ireland.
| | - David O'Connell
- Department of Civil, Structural and Environmental Engineering, University of Dublin, Trinity College, Dublin, Ireland
| | - Donata Dubber
- Department of Civil, Structural and Environmental Engineering, University of Dublin, Trinity College, Dublin, Ireland
| | - Catherine Coxon
- Department of Geology, Trinity Centre for the Environment, University of Dublin, Trinity College, Dublin, Ireland
| | - Laurence Gill
- Department of Civil, Structural and Environmental Engineering, University of Dublin, Trinity College, Dublin, Ireland
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7
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Michaelis C, Grohmann E. Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms. Antibiotics (Basel) 2023; 12:antibiotics12020328. [PMID: 36830238 PMCID: PMC9952180 DOI: 10.3390/antibiotics12020328] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Most bacteria attach to biotic or abiotic surfaces and are embedded in a complex matrix which is known as biofilm. Biofilm formation is especially worrisome in clinical settings as it hinders the treatment of infections with antibiotics due to the facilitated acquisition of antibiotic resistance genes (ARGs). Environmental settings are now considered as pivotal for driving biofilm formation, biofilm-mediated antibiotic resistance development and dissemination. Several studies have demonstrated that environmental biofilms can be hotspots for the dissemination of ARGs. These genes can be encoded on mobile genetic elements (MGEs) such as conjugative and mobilizable plasmids or integrative and conjugative elements (ICEs). ARGs can be rapidly transferred through horizontal gene transfer (HGT) which has been shown to occur more frequently in biofilms than in planktonic cultures. Biofilm models are promising tools to mimic natural biofilms to study the dissemination of ARGs via HGT. This review summarizes the state-of-the-art of biofilm studies and the techniques that visualize the three main HGT mechanisms in biofilms: transformation, transduction, and conjugation.
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8
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Pedron R, Esposito A, Cozza W, Paolazzi M, Cristofolini M, Segata N, Jousson O. Microbiome characterization of alpine water springs for human consumption reveals site- and usage-specific microbial signatures. Front Microbiol 2022; 13:946460. [PMID: 36274724 PMCID: PMC9581249 DOI: 10.3389/fmicb.2022.946460] [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: 05/17/2022] [Accepted: 09/12/2022] [Indexed: 11/26/2022] Open
Abstract
The microbiome of water springs is gaining increasing interest, especially in water intended for human consumption. However, the knowledge about large-scale patterns in water springs microbiome is still incomplete. The presence of bacteria in water sources used for human consumption is a major concern for health authorities; nonetheless, the standard microbiological quality checks are focused only on pathogenic species and total microbial load. Using 16S rRNA high throughput sequencing, we characterized the microbiome from 38 water springs in Trentino (Northern Italy) for 2 consecutive years in order to gain precious insights on the microbiome composition of these unexplored yet hardly exploited environments. The microbiological studies were integrated with standard measurements of physico-chemical parameters performed by the Provincial Office for Environmental Monitoring in order to highlight some of the dynamics influencing the microbial communities of these waters. We found that alpha diversity showed consistent patterns of variation overtime, and showed a strong positive correlation with the water nitrate concentration and negatively with fixed residue, electrical conductivity, and calcium concentration. Surprisingly, alpha diversity did not show any significant correlation with neither pH nor temperature. We found that despite their remarkable stability, different water springs display different coefficients of variation in alpha diversity, and that springs used for similar purposes showed similar microbiomes. Furthermore, the springs could be grouped according to the number of shared species into three major groups: low, mid, and high number of shared taxa, and those three groups of springs were consistent with the spring usage. Species belonging to the phyla Planctomycetes and Verrucomicrobia were prevalent and at relatively high abundance in springs classified as low number of shared species, whereas the phylum Lentisphaerae and the Candidate Phyla radiation were prevalent at higher abundance in the mineral and potable springs. The present study constitutes an example for standard water spring monitoring integrated with microbial community composition on a regional scale, and provides information which could be useful in the design and application of future water management policies in Trentino.
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Affiliation(s)
- Renato Pedron
- Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento, Italy
| | - Alfonso Esposito
- International Centre for Genetic Engineering and Biotechnology – ICGEB, Trieste, Italy
| | - William Cozza
- Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento, Italy
| | - Massimo Paolazzi
- Agenzia provinciale per la protezione dell'ambiente – APPA, Trento, Italy
| | | | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento, Italy
| | - Olivier Jousson
- Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento, Italy
- *Correspondence: Olivier Jousson,
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9
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Ebner JN, Wyss MK, Ritz D, von Fumetti S. Effects of thermal acclimation on the proteome of the planarian Crenobia alpina from an alpine freshwater spring. J Exp Biol 2022; 225:276068. [PMID: 35875852 PMCID: PMC9440759 DOI: 10.1242/jeb.244218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/18/2022] [Indexed: 11/25/2022]
Abstract
Species' acclimation capacity and their ability to maintain molecular homeostasis outside ideal temperature ranges will partly predict their success following climate change-induced thermal regime shifts. Theory predicts that ectothermic organisms from thermally stable environments have muted plasticity, and that these species may be particularly vulnerable to temperature increases. Whether such species retained or lost acclimation capacity remains largely unknown. We studied proteome changes in the planarian Crenobia alpina, a prominent member of cold-stable alpine habitats that is considered to be a cold-adapted stenotherm. We found that the species' critical thermal maximum (CTmax) is above its experienced habitat temperatures and that different populations exhibit differential CTmax acclimation capacity, whereby an alpine population showed reduced plasticity. In a separate experiment, we acclimated C. alpina individuals from the alpine population to 8, 11, 14 or 17°C over the course of 168 h and compared their comprehensively annotated proteomes. Network analyses of 3399 proteins and protein set enrichment showed that while the species' proteome is overall stable across these temperatures, protein sets functioning in oxidative stress response, mitochondria, protein synthesis and turnover are lower in abundance following warm acclimation. Proteins associated with an unfolded protein response, ciliogenesis, tissue damage repair, development and the innate immune system were higher in abundance following warm acclimation. Our findings suggest that this species has not suffered DNA decay (e.g. loss of heat-shock proteins) during evolution in a cold-stable environment and has retained plasticity in response to elevated temperatures, challenging the notion that stable environments necessarily result in muted plasticity. Summary: The proteome of an alpine Crenobia alpina population shows plasticity in response to acclimation to warmer temperatures.
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Affiliation(s)
- Joshua Niklas Ebner
- 1 Spring Ecology Research Group, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Mirjam Kathrin Wyss
- 1 Spring Ecology Research Group, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Danilo Ritz
- 2 Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Stefanie von Fumetti
- 1 Spring Ecology Research Group, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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10
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Vucinic L, O’Connell D, Teixeira R, Coxon C, Gill L. Flow Cytometry and Fecal Indicator Bacteria Analyses for Fingerprinting Microbial Pollution in Karst Aquifer Systems. WATER RESOURCES RESEARCH 2022; 58:e2021WR029840. [PMID: 35859924 PMCID: PMC9285701 DOI: 10.1029/2021wr029840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/23/2022] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Microbial pollution of aquifers is a persistent water quality problem globally which poses significant risks to public health. Karst aquifer systems are exceptionally vulnerable to pollution from fecal contamination sources as a result of rapid recharge of water from the surface via discrete pathways linked to highly conductive, solutionally enlarged conduits alongside strong aquifer heterogeneity. Consequently, rapid changes in microbial water quality, which are difficult to monitor with expensive and time-consuming conventional microbiological methods, are a major concern in karst environments. This study examined flow cytometric (FCM) fingerprinting of bacterial cells in groundwater together with fecal indicator bacteria (FIB) at nine separate karst springs of varying catchment size over a 14 month period in order to assess whether such a technique can provide faster and more descriptive information about microbial pollution through such karst aquifer systems. Moreover, the data have also been evaluated with respect to the potential of using turbidity as an easy-to-measure proxy indicator of microbial pollution in a novel way. We argue that FCM provides additional data from which enhanced insights into fecal pollution sources and its fate and transport in such karst catchments can be gained. We also present valuable new information on the potential and limitations of turbidity as an indicator of fecal groundwater contamination in karst. FCM has the potential to become a more widely used tool in the field of contaminant hydrogeology.
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Affiliation(s)
- Luka Vucinic
- Department of Civil, Structural and Environmental EngineeringUniversity of DublinTrinity CollegeDublinIreland
| | - David O’Connell
- Department of Civil, Structural and Environmental EngineeringUniversity of DublinTrinity CollegeDublinIreland
| | - Rui Teixeira
- Department of Civil, Structural and Environmental EngineeringUniversity of DublinTrinity CollegeDublinIreland
| | - Catherine Coxon
- Department of Geology and Trinity Centre for the EnvironmentUniversity of DublinTrinity CollegeDublinIreland
| | - Laurence Gill
- Department of Civil, Structural and Environmental EngineeringUniversity of DublinTrinity CollegeDublinIreland
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11
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Bourrain M, Suzuki MT, Calvez A, West NJ, Lions J, Lebaron P. In-depth prospection of Avène Thermal Spring Water reveals an uncommon and stable microbial community. J Eur Acad Dermatol Venereol 2021; 34 Suppl 5:8-14. [PMID: 32870559 DOI: 10.1111/jdv.16599] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/24/2020] [Accepted: 04/30/2020] [Indexed: 01/04/2023]
Abstract
BACKGROUND Avène Thermal Spring Water (TSW) exhibits therapeutic properties in the treatment of skin pathologies. Arising from a dolomitic aquifer system, its physico-chemical properties are well-established and its bacteriological quality regularly monitored. The microbiota of this aquifer have been characterized. OBJECTIVES We aimed to describe the structure of the bacterial community inhabiting the deep aquifer and to examine its dynamics over time. METHODS The Avène TSW was collected at the catchment point and filtered through 0.1 µm pore size filters. The sampling was carried out every 3 months to generate a 4-year time series. The DNA extracted from filters was analysed using high-throughput 16S rRNA gene amplicon sequencing, and the microorganisms and their contribution were characterized by the taxonomic assignment of sequence variants generated from each sample. RESULTS Bacteria were distributed into 39 phyla. Nitrospirae and Proteobacteria were the most prevalent, accounting for 38% and 23% of the total community on average, respectively. A stable pattern was observed throughout the study. A few bacterial species were always detected, forming a core community of likely chemolithoautotrophic organisms which might use energy sources and nutrients produced from water-bedrock interactions. Most of the species were distantly related to organisms described to date. CONCLUSIONS Avène TSW provided by the deep aquifer system harbours a unique microbial community, shaped by the physico-chemical characteristics of the deep environment. Its remarkable stability over time has revealed a high level of confinement of the water resource.
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Affiliation(s)
- M Bourrain
- Pierre Fabre Dermo-Cosmétique R&D Center, Toulouse, France
| | - M T Suzuki
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, Observatoire Océanologique, Banyuls-sur-mer, France
| | - A Calvez
- Pierre Fabre Dermo-Cosmétique R&D Center, Toulouse, France
| | - N J West
- Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls, Banyuls-sur-mer, France
| | - J Lions
- Pierre Fabre Dermo-Cosmétique R&D Center, Toulouse, France
| | - P Lebaron
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, Observatoire Océanologique, Banyuls-sur-mer, France
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12
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Chik AHS, Emelko MB, Anderson WB, O'Sullivan KE, Savio D, Farnleitner AH, Blaschke AP, Schijven JF. Evaluation of groundwater bacterial community composition to inform waterborne pathogen vulnerability assessments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 743:140472. [PMID: 32758810 DOI: 10.1016/j.scitotenv.2020.140472] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/05/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Microbial water quality evaluations are essential for determining the vulnerability of subsurface drinking water sources to fecal pathogen intrusion. Rather than directly monitor waterborne pathogens using culture- or enumeration-based techniques, the potential of assessing bacterial community using 16S rRNA gene amplicon sequencing to support these evaluations was investigated. A framework for analyzing 16S rRNA gene amplicon sequencing results featuring negative-binomial generalized linear models is demonstrated, and applied to bacterial taxa sequences in purge water samples collected from a shallow, highly aerobic, unconfined aquifer. Bacterial taxa relevant as indicators of fecal source and surface connectivity were examined using this approach. Observed sequences of Escherichia, a genus suggestive of fecal source, were consistently detected but not confirmed by culture-based methods. On the other hand, episodic appearance of anaerobic taxa sequences in this highly aerobic environment, namely Clostridia and Bacteroides, warrants further investigation as potential indicators of fecal contamination. Betaproteobacteria sequences varied significantly on a seasonal basis, and therefore may be linked to understanding surface-water groundwater interactions at this site. However, sequences that are often encountered in surface water bodies (Cyanobacteria and Flavobacteriia) were notably absent or present at very low levels, suggesting that microbial transport from surface-derived sources may be rather limited. This work demonstrates the utility of 16S rRNA gene amplicon sequencing for contextualizing and complementing conventional microbial techniques, allowing for hypotheses about source and transport processes to be tested and refined.
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Affiliation(s)
- Alex H S Chik
- Utrecht University, Domplein 29, 3512 JE Utrecht, Netherlands; TU Wien, Karlsplatz 13, 1040 Vienna, Austria; University of Waterloo, 200 University Ave. W., Waterloo, Ontario N2L 3G1, Canada.
| | - Monica B Emelko
- University of Waterloo, 200 University Ave. W., Waterloo, Ontario N2L 3G1, Canada
| | - William B Anderson
- University of Waterloo, 200 University Ave. W., Waterloo, Ontario N2L 3G1, Canada
| | - Kaitlyn E O'Sullivan
- University of Waterloo, 200 University Ave. W., Waterloo, Ontario N2L 3G1, Canada
| | - Domenico Savio
- Karl Landsteiner University of Health Sciences, Dr.-Karl-Dorrek-Straße 30, 3500 Krems an der Donau, Austria; TU Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria.
| | - Andreas H Farnleitner
- Karl Landsteiner University of Health Sciences, Dr.-Karl-Dorrek-Straße 30, 3500 Krems an der Donau, Austria; TU Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria.
| | | | - Jack F Schijven
- Utrecht University, Domplein 29, 3512 JE Utrecht, Netherlands
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13
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Hofmann R, Uhl J, Hertkorn N, Griebler C. Linkage Between Dissolved Organic Matter Transformation, Bacterial Carbon Production, and Diversity in a Shallow Oligotrophic Aquifer: Results From Flow-Through Sediment Microcosm Experiments. Front Microbiol 2020; 11:543567. [PMID: 33250862 PMCID: PMC7674671 DOI: 10.3389/fmicb.2020.543567] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 09/10/2020] [Indexed: 11/24/2022] Open
Abstract
Aquifers are important reservoirs for organic carbon. A fundamental understanding of the role of groundwater ecosystems in carbon cycling, however, is still missing. Using sediment flow-through microcosms, long-term (171d) experiments were conducted to test two scenarios. First, aquifer sediment microbial communities received dissolved organic matter (DOM) at low concentration and typical to groundwater in terms of composition (DOM-1x). Second, sediments received an elevated concentration of DOM originating from soil (DOM-5x). Changes in DOM composition were analyzed via NMR and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Carbon production, physiological adaptations and biodiversity of groundwater, and sediment prokaryotic communities were monitored by total cell counts, substrate use arrays, and deep amplicon sequencing. The experiments showed that groundwater microbial communities do not react very fast to the sudden availability of labile organic carbon from soil in terms of carbon degradation and biomass production. It took days to weeks for incoming DOM being efficiently degraded and pronounced cell production occurred. Once conditioned, the DOM-1x supplied sediments mineralized 294(±230) μgC L−1sed d−1, 10-times less than the DOM-5x fed sediment communities [2.9(±1.1) mgC L−1sed d−1]. However, the overall biomass carbon production was hardly different in the two treatments with 13.7(±4.8) μgC L−1sed d−1 and 14.3(±3.5) μgC L−1sed d−1, respectively, hinting at a significantly lower carbon use efficiency with higher DOM availability. However, the molecularly more diverse DOM from soil fostered a higher bacterial diversity. Taking the irregular inputs of labile DOM into account, shallow aquifers are assumed to have a low resilience. Lacking a highly active and responsive microbial community, oligotrophic aquifers are at high risk of contamination with organic chemicals.
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Affiliation(s)
- Roland Hofmann
- Institute of Groundwater Ecology, Helmholtz Center Munich, Neuherberg, Germany
| | - Jenny Uhl
- Research Unit Analytical Biogeochemistry, Helmholtz Center Munich, Neuherberg, Germany
| | - Norbert Hertkorn
- Research Unit Analytical Biogeochemistry, Helmholtz Center Munich, Neuherberg, Germany
| | - Christian Griebler
- Institute of Groundwater Ecology, Helmholtz Center Munich, Neuherberg, Germany.,Division of Limnology, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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14
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Kongprajug A, Chyerochana N, Mongkolsuk S, Sirikanchana K. Effect of Quantitative Polymerase Chain Reaction Data Analysis Using Sample Amplification Efficiency on Microbial Source Tracking Assay Performance and Source Attribution. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:8232-8244. [PMID: 32484662 DOI: 10.1021/acs.est.0c01559] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The widely used microbial source tracking (MST) technique, quantitative polymerase chain reaction (qPCR), quantifies host-specific gene abundance in polluted water to identify and prioritize contamination sources. This study characterized the effects of a qPCR data analysis using the sample PCR efficiencies (the LinRegPCR model) on gene abundance and compared them with the standard curve-based method (the mixed model). Five qPCR assays were evaluated: the universal GenBac3, human-specific HF183/BFDrev and CPQ_056, swine-specific Pig-2-Bac, and cattle-specific Bac3qPCR assays. The LinRegPCR model increased the low-copy amplification, especially in the HF183/BFDrev assay, thus lowering the specificity to 0.34. Up to 1.41 log10 copies/g and 0.41 log10 copies/100 mL differences were observed for composite fecal and sewage samples (n = 147) by the LinRegPCR approach, corresponding to an 18.2% increase and 6.4% decrease, respectively. Freshwater samples (n = 48) demonstrated a maximum of 1.95 log10 copies/100 mL difference between the two models. Identical attributing sources by both models were shown in 54.55% of environmental samples; meanwhile, the LinRegPCR approach improved the inability to identify sources by the mixed model in 29.55% of the samples. This study emphasizes the need for a standardized data analysis protocol for qPCR MST assays for interlaboratory consistency and comparability.
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Affiliation(s)
- Akechai Kongprajug
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
| | - Natcha Chyerochana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok 10400, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok 10400, Thailand
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15
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Xiang S, Wang X, Ma W, Liu X, Zhang B, Huang F, Liu F, Guan X. Response of microbial communities of karst river water to antibiotics and microbial source tracking for antibiotics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 706:135730. [PMID: 31791761 DOI: 10.1016/j.scitotenv.2019.135730] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
In southwestern China, karst river water is the main source of water for humans. As emerging pollutants, antibiotics have contaminated karst river water in some areas for a long time. Microbiota is highly susceptible to environmental changes, and can be used in tracing the source of antibiotics in complex systems such as karst water. Ten karst river water samples were collected along the river flow. The diversity and structure of the microbial community were analyzed together with environmental factors through correlation analysis, the random forest algorithm and co-occurrence network analysis. At genus level, Arcobacter was significantly positively correlated with the antibiotics, indicating that Arcobacter and antibiotics probably came from the same source. Based on co-occurrence network analysis between microbes, the microbial community was divided into eight modules, and the relative abundance of three modules was significantly correlated with antibiotics. The co-occurrence networks between bacteria and antibiotic resistance genes (ARGs) showed that pathogenic bacteria potentially carried multiple ARGs. This could increase the disease risk to humans and disease transmission in the study area. When river water flowed underground, the concentration of antibiotics decreased for the two underground river outlet sites, but abundance of bacteria and ARGs increased. Microbial source tracking studies showed that contamination was derived from humans rather than livestock. The ranking importance of prediction for antibiotics in this study area from random forest follows: specific bacteria Arcobacter > ARGs > ecological clusters. This study will be helpful in identifying the effect of antibiotics discharge on the microbial community, improving evaluation of antibiotics' risks and contaminants source tracking.
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Affiliation(s)
- Shizheng Xiang
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing 100083, China
| | - Xusheng Wang
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing 100083, China
| | - Wen Ma
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing 100083, China
| | - Xiaoping Liu
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing 100083, China
| | - Biao Zhang
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing 100083, China
| | - Fuyang Huang
- Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences (Beijing), Beijing 100083, China
| | - Fei Liu
- Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences (Beijing), Beijing 100083, China
| | - Xiangyu Guan
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing 100083, China; Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences (Beijing), Beijing 100083, China.
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16
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Yu S, He R, Song A, Huang Y, Jin Z, Liang Y, Li Q, Wang X, Müller WEG, Cao J. Spatial and temporal dynamics of bacterioplankton community composition in a subtropical dammed karst river of southwestern China. Microbiologyopen 2019; 8:e00849. [PMID: 31058472 PMCID: PMC6741127 DOI: 10.1002/mbo3.849] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 12/03/2022] Open
Abstract
River damming influences the hydro‐physicochemical variations in karst water; however, such disruption in bacterioplankton communities has seldom been studied. Here, three sampling sites (city‐river section, reservoir area, and outflow area) of the Ca2+–Mg2+–HCO3−–SO42− water type in the dammed Liu River were selected to investigate the bacterioplankton community composition as identified by high‐throughput 16S rRNA gene sequencing. In the dammed Liu River, thermal regimes have been altered, which has resulted in considerable spatial‐temporal differences in total dissolved solids (TDSs), oxidation‐reduction potential (Eh), dissolved oxygen (DO), and pH and in a different microenvironment for bacterioplankton. Among the dominant bacterioplankton phyla, Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria account for 38.99%–87.24%, 3.75%–36.55%, 4.77%–38.90%, and 0%–14.44% of the total reads (mean relative frequency), respectively. Bacterioplankton communities are dominated by Brevundimonas, Novosphingobium, Zymomonas, the Actinobacteria hgcIclade, the CL500‐29 marine group, Sediminibacterium, Flavobacterium, Pseudarcicella, Cloacibacterium, and Prochlorococcus. Their abundances covary with spatial‐temporal variations in hydro‐physicochemical factors, as also demonstrated by beta diversity analyses. In addition, temperature plays a pivotal role in maintaining bacterioplankton biodiversity and hydro‐physicochemical variations. This result also highlights the concept that ecological niches for aquatic bacteria in dammed karst rivers do not accidentally occur but are the result of a suite of environmental forces. In addition, bacterioplankton can alter the aquatic carbon/nitrogen cycle and contribute to karst river metabolism.
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Affiliation(s)
- Shi Yu
- Key Laboratory of Karst Dynamics, MLR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China.,International Research Center on Karst under the Auspices of UNESCO, Guilin, China
| | - Ruoxue He
- Key Laboratory of Karst Dynamics, MLR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China.,International Research Center on Karst under the Auspices of UNESCO, Guilin, China.,Chengdu Technological University, Chengdu, China
| | - Ang Song
- Key Laboratory of Karst Dynamics, MLR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China.,International Research Center on Karst under the Auspices of UNESCO, Guilin, China
| | - Yadan Huang
- Graduate School of Guilin Medical University, Guilin, China
| | - Zhenjiang Jin
- Environmental Science and Engineering College, Guilin University of Technology, Guilin, China
| | - Yueming Liang
- Key Laboratory of Karst Dynamics, MLR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China.,International Research Center on Karst under the Auspices of UNESCO, Guilin, China
| | - Qiang Li
- Key Laboratory of Karst Dynamics, MLR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China.,International Research Center on Karst under the Auspices of UNESCO, Guilin, China
| | - Xiaohong Wang
- ERC Advanced Investigator Grant Research Group at Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Werner E G Müller
- ERC Advanced Investigator Grant Research Group at Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Jianhua Cao
- Key Laboratory of Karst Dynamics, MLR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China.,International Research Center on Karst under the Auspices of UNESCO, Guilin, China
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17
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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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18
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Targeted 16S rRNA amplicon analysis reveals the diversity of bacterial communities in carwash effluents. Int Microbiol 2018; 22:181-189. [PMID: 30810982 DOI: 10.1007/s10123-018-00038-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 09/18/2018] [Accepted: 10/16/2018] [Indexed: 10/28/2022]
Abstract
This study aimed to analyze the bacterial diversity in carwash effluents and to determine their potential for use in microbial degradation of environmental contaminants. Nine carwash effluent samples were collected for physicochemical and bacterial community diversity analysis using multi-digital probes and 16S rRNA gene amplicon sequencing respectively. The pH of all effluent samples was neutral to slightly alkaline. Oil and grease concentrations ranged from 15.3 to 49.7 mg/L. 16S gene amplicon sequencing of the nine samples produced 45,934-sequence reads, which translated to 13 bacterial phyla, 26 classes, and 43 genera. The most dominant phyla were Proteobacteria, Bacteroidetes, Firmicutes, and Fusobacteria. Canonical correspondence analysis (CCA) showed that the distribution of the phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Verrucomicrobia was influenced by the presence of oil and grease, total petroleum hydrocarbons-gasoline range organics (GRO-TPH), and metals species (Pb, Cu, and Zn). The dominant bacterial genera found in the present study were previously proven to biodegrade hydrocarbons, and their presence in carwash effluents could bode well for in situ natural bioremediation of these contaminated sites.
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