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Liu J, Zhao R, Feng J, Fu W, Cao L, Zhang J, Lei Y, Liang J, Lin L, Li X, Li B. Bacterial assembly and succession patterns in conventional and advanced drinking water systems: From source to tap. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134613. [PMID: 38788571 DOI: 10.1016/j.jhazmat.2024.134613] [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: 01/22/2024] [Revised: 05/01/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024]
Abstract
Bacteria are pivotal to drinking water treatment and public health. However, the mechanisms of bacterial assembly and their impact on species coexistence remain largely unexplored. This study explored the assembly and succession of bacterial communities in two full-scale drinking water systems over one year. We observed a decline in bacterial biomass, diversity, and co-occurrence network complexity along the treatment processes, except for the biological activated carbon filtration stage. The conventional plant showed higher bacterial diversity than the advanced plant, despite similar bacterial concentrations and better removal efficiency. The biological activated carbon filter exhibited high phylogenetic diversity, indicating enhanced bacterial metabolic functionality for organic matter removal. Chlorination inactivated most bacteria but favored some chlorination-resistant and potentially pathogenic species, such as Burkholderia, Bosea, Brevundimonas, and Acinetobacter. Moreover, the spatiotemporal dynamics of the bacterial continuum were primarily driven by stochastic processes, explaining more than 78% of the relative importance. The advanced plant's bacterial community was less influenced by dispersal limitation and more by homogeneous selection. The stochastic process regulated bacterial diversity and influenced the complexity of the species co-occurrence network. These findings deepen our understanding of microbial ecological mechanisms and species interactions, offering insights for enhancing hygienic safety in drinking water systems.
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Affiliation(s)
- Jie Liu
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Renxin Zhao
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Jie Feng
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Wenjie Fu
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Lijia Cao
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Jiayu Zhang
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Yusha Lei
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Jiajin Liang
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Lin Lin
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Xiaoyan Li
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Bing Li
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
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Molina CA, Quiroz-Moreno C, Jarrín-V P, Díaz M, Yugsi E, Pérez-Galarza J, Baldeón-Rojas L. Bacterial community assessment of drinking water and downstream distribution systems in highland localities of Ecuador. JOURNAL OF WATER AND HEALTH 2024; 22:536-549. [PMID: 38557569 DOI: 10.2166/wh.2024.290] [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: 09/22/2023] [Accepted: 01/23/2024] [Indexed: 04/04/2024]
Abstract
Bacterial communities in drinking water provide a gauge to measure quality and confer insights into public health. In contrast to urban systems, water treatment in rural areas is not adequately monitored and could become a health risk. We performed 16S rRNA amplicon sequencing to analyze the microbiome present in the water treatment plants at two rural communities, one city, and the downstream water for human consumption in schools and reservoirs in the Andean highlands of Ecuador. We tested the effect of water treatment on the diversity and composition of bacterial communities. A set of physicochemical variables in the sampled water was evaluated and correlated with the structure of the observed bacterial communities. Predominant bacteria in the analyzed communities belonged to Proteobacteria and Actinobacteria. The Sphingobium genus, a chlorine resistance group, was particularly abundant. Of health concern in drinking water reservoirs were Fusobacteriaceae, Lachnospiraceae, and Ruminococcaceae; these families are associated with human and poultry fecal contamination. We propose the latter families as relevant biomarkers for establishing local standards for the monitoring of potable water systems in highlands of Ecuador. Our assessment of bacterial community composition in water systems in the Ecuadorian highlands provides a technical background to inform management decisions.
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Affiliation(s)
- C Alfonso Molina
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Central del Ecuador, Cdla. Universitaria y Gaspar de Carvajal s/n., 170521 Quito, Ecuador; Instituto de Investigación en Zoonosis (CIZ), Universidad Central del Ecuador, Cdla. Universitaria y Gaspar de Carvajal s/n., 170521, Quito, Ecuador E-mail:
| | - Cristian Quiroz-Moreno
- Department of Horticulture and Crop Science, Ohio State University, 2021 Coffey Road, Columbus OH 43210
| | - Pablo Jarrín-V
- Laboratorio de Secuenciamiento de Ácidos Nucleicos, Dirección de Gestión de la Innovación, Instituto Nacional de Biodiversidad INABIO, Pje. Rumipamba N341 y Av. de los Shyris, Quito, Ecuador
| | - Magdalena Díaz
- Instituto de Investigación en Zoonosis (CIZ), Universidad Central del Ecuador, Cdla. Universitaria y Gaspar de Carvajal s/n., 170521, Quito, Ecuador; Facultad de Ingeniería Química, Universidad Central del Ecuador, Ritter s/n y Bolivia, 170521 Quito, Ecuador; Institute of Integrative Systems Biology (I2SysBio), University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), Carrer del Catedràtic Agustín Escardino Benlloch, 46980 Paterna, Valencia, Spain
| | - Elizabeth Yugsi
- Centro de Biotecnología 'Dr Daniel Alkalay Lowitt', Universidad Técnica Federico Santa María, General Bari 699, 2390136, Valparaíso, Chile
| | - Jorge Pérez-Galarza
- Facultad de Ciencias Médicas, Universidad Central del Ecuador, Iquique N14-121 y Sodiro, Quito, Ecuador; Instituto de Investigación en Biomedicina, Universidad Central del Ecuador, Capitán Giovanni Calles y Derby, Quito, Ecuador
| | - Lucy Baldeón-Rojas
- Facultad de Ciencias Médicas, Universidad Central del Ecuador, Iquique N14-121 y Sodiro, Quito, Ecuador; Instituto de Investigación en Biomedicina, Universidad Central del Ecuador, Capitán Giovanni Calles y Derby, Quito, Ecuador
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Ke Y, Sun W, Xue Y, Zhu Y, Yan S, Xie S. Effects of treatments and distribution on microbiome and antibiotic resistome from source to tap water in three Chinese geographical regions based on metagenome assembly. WATER RESEARCH 2024; 249:120894. [PMID: 38016224 DOI: 10.1016/j.watres.2023.120894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 10/23/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
Antibiotic resistance genes (ARGs) represent emerging environmental pollutants that present health risks. Drinking water supply systems (DWSSs), including sources to tap water, play crucial roles in the dissemination and propagation of ARGs. However, there was a paucity of knowledge on the relative abundance, diversity, mobility, and pathogenic hosts of ARGs in DWSSs from source to tap. Therefore, the effects of treatments and distributions on the microbial community and ARGs from three geographical regions (downstream areas of the Yellow, Yangtze, and Pearl Rivers) were elucidated in the present study. Treatment processes lowered the complexity of the microbial community network, whereas transportation increased it. The assembly mechanisms of the microbial community and antibiotic resistome were primarily driven by stochastic processes. Distribution greatly increased the contribution of stochastic processes. Multidrug ARGs (for example, multidrug transporter and adeJ) and bacitracin ARG (bacA) were the primary mobile ARGs in drinking water, as identified by the metagenomic assembly. Achromobacter xylosoxidans, Acinetobacter calcoaceticus, and Acinetobacter junii harbored diverse multidrug ARGs and mobile genetic elements (MGEs) (recombinases, integrases, and transposases) as potential pathogens and were abundant in the disinfected water. Environmental factors, including pH, chlorine, latitude, longitude, and temperature, influenced the ARG abundance by directly regulating the MGEs and microbial community diversity. This study provides critical information on the fate, mobility, host pathogenicity, and driving factors of ARGs in drinking water, which is conducive to ARG risk assessment and management to provide high-quality drinking water to consumers.
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Affiliation(s)
- Yanchu Ke
- School of Environment, Tsinghua University, Beijing 100084, China; State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Wenjun Sun
- School of Environment, Tsinghua University, Beijing 100084, China; Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou 215163, China.
| | - Yanei Xue
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Ying Zhu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Shuang Yan
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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4
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McKenney EA, Nichols LM, Alvarado S, Hardy S, Kemp K, Polmanteer R, Shoemaker A, Dunn RR. Sourdough starters exhibit similar succession patterns but develop flour-specific climax communities. PeerJ 2023; 11:e16163. [PMID: 37810791 PMCID: PMC10559884 DOI: 10.7717/peerj.16163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023] Open
Abstract
The microbial fermentation behind sourdough bread is among our oldest technologies, yet there are many opportunities for sourdough science to learn from traditional bakers. We analyzed 16S rRNA sequences in R to assess the bacterial community structure and performance of 40 starters grown from 10 types of flour over 14 days, and identified six distinct stages of succession. At each stage, bacterial taxa correlate with determinants of bread quality including pH, rise, and aromatic profile. Day 1 starter cultures were dominated by microorganisms commonly associated with plants and flour, and by aromas similar to toasted grain/cereal. Bacterial diversity peaked from days 2-6 as taxa shifted from opportunistic/generalist bacteria associated with flour inputs, toward specialized climax bacterial communities (days 10-14) characterized by acid-tolerant taxa and fruity (p < 3.03e-03), sour (p < 1.60e-01), and fermented (p < 1.47e-05) aromas. This collection of traits changes predictably through time, regardless of flour type, highlighting patterns of bacterial constraints and dynamics that are conserved across systems and scales. Yet, while sourdough climax communities exhibit similar markers of maturity (i.e., pH ≤ 4 and enriched in Lactobacillus (mean abundance 48.1%), Pediococcus (mean abundance 22.7%), and/or Gluconobacter (mean abundance 19.1%)), we also detected specific taxa and aromas associated with each type of flour. Our results address important ecological questions about the relationship between community structure and starter performance, and may enable bakers to deliberately select for specific sourdough starter and bread characteristics.
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Affiliation(s)
- Erin A. McKenney
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, United States
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina, United States
| | - Lauren M. Nichols
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, United States
| | - Samuel Alvarado
- Department of Biology, University of West Florida, Pensacola, Florida, United States
- Biotechnology Program, North Carolina State University, Biotechnology-based Sequencing-based Undergraduate Research Experience (BITSURE), Raleigh, North Carolina, United States
| | - Shannon Hardy
- The Exploris School, Raleigh, North Carolina, United States
| | - Kristen Kemp
- Moore Square Middle School, Raleigh, North Carolina, United States
| | | | | | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, United States
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5
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Hu Y, Cai J, Gong Y, Liu C, Jiang X, Tang X, Shao K, Gao G. The collapse and re-establishment of stability regulate the gradual transition of bacterial communities from macrophytes- to phytoplankton-dominated types in a large eutrophic lake. FEMS Microbiol Ecol 2023; 99:fiad074. [PMID: 37656870 DOI: 10.1093/femsec/fiad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 09/03/2023] Open
Abstract
Eutrophic lakes often exhibit two alternative types: macrophytes-dominated (MD) and phytoplankton-dominated (PD). However, the nature of bacterial community types that whether the transition from the MD to the PD types occurs in a gradual or abrupt manner remains hotly debated. Further, the theoretical recognition that stability regulates the transition of bacterial community types remains qualitative. To address these issues, we divided the transition of bacterial communities along a trophic gradient into 12 successional stages, ranging from the MD to the PD types. Results showed that 12 states were clustered into three distinct regimes: MD type, intermediate transitional type and PD type. Bacterial communities were not different between consecutive stages, suggesting that the transition of alternative types occurs in a continuous gradient. At the same time, the stability of bacterial communities was significantly lower in the intermediate type than in the MD or PD types, highlighting that the collapse and re-establishment of community stability regulate the transition. Further, our results showed that the high complexity of taxon interactions and strong stochastic processes disrupt the stability. Ultimately, this study enables deeper insights into understanding the alternative types of microbial communities in the view of community stability.
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Affiliation(s)
- Yang Hu
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jian Cai
- Xiangyang Polytechnic, Agriculture college, Hubei 441000, China
| | - Ying Gong
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Changqing Liu
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xingyu Jiang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Keqiang Shao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Guang Gao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
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6
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Lin TY, Liu WT. Validation of 16S rRNA gene sequencing and metagenomics for evaluating microbial immigration in a methanogenic bioreactor. WATER RESEARCH 2023; 243:120358. [PMID: 37481999 DOI: 10.1016/j.watres.2023.120358] [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: 03/05/2023] [Revised: 07/09/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023]
Abstract
To quantitatively evaluate the impact of microbial immigration from an upstream community on the microbial assembly of a downstream community, an ecological genomics (ecogenomics)-based mass balance (EGMB) model coupled with 16S rRNA gene sequencing was previously developed. In this study, a mock community was used to further validate the EGMB models and demonstrate the feasibility of using metagenome-based EGMB model to reveal both microbial activity and function. The mock community consisting of Aeromonas, Escherichia, and Pseudomonas was fed into a lab-scale methanogenic bioreactor together with dissolved organic substrate. Using qPCR, 16S rRNA gene, 16S rRNA gene copy number normalization (GCN), and metagenome, results showed highly comparable community profiles in the feed. In the bioreactor, Aeromonas and Pseudomonas exhibited negative growth rates throughout the experiment by all approaches. Escherichia's growth rate was negative by most biomarkers but was slightly positive by 16S rRNA gene. Still, all approaches showed a decreasing trend toward negative in the growth rate of Escherichia as reactor operation time increased. Uncultivated populations of phyla Desulfobacterota, Chloroflexi, Actinobacteriota, and Spirochaetota were observed to increase in abundance, suggesting their contribution in degrading the feed biomass. Based on metabolic reconstruction of metagenomes, these populations possessed functions of hydrolysis, fermentation, fatty acid degradation, or acetate oxidation. Overall results supported the application of both 16S rRNA gene- and metagenome-based EGMB models to measure the growth rate of microbes in the bioreactor, and the latter had advantage in providing insights into the microbial functions of uncultivated populations.
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Affiliation(s)
- Tzu-Yu Lin
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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7
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Li H, Feng M, Yu X. Qualitative and quantitative analysis of the effects of drinking water disinfection processes on eukaryotic microorganisms: A meta-analysis. CHEMOSPHERE 2023; 332:138839. [PMID: 37142108 DOI: 10.1016/j.chemosphere.2023.138839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/06/2023]
Abstract
The risk of eukaryotic microorganisms in drinking water treatment has not received sufficient attention. As the final step in ensuring drinking water quality, the effectiveness of disinfection in inactivating eukaryotic microorganisms remains to be qualitatively and quantitatively demonstrated. In this study, we conducted a meta-analysis using a mixed effects model and bootstrapping analysis to assess the effects of the disinfection process on eukaryotic microorganisms. The results revealed significant reduction of eukaryotic microorganisms in drinking water associated with the disinfection process. The estimated logarithmic reduction rates for chlorination, ozone, and UV disinfection were 1.74, 1.82 and 2.15 log, respectively, for all eukaryotic microorganisms. Analysis of relative abundance variation of eukaryotic microorganisms also indicated certain phyla and classes exhibited tolerance and competitive advantage during disinfection. This study provides qualitatively and quantitatively analysis on the influence of drinking water disinfection processes on eukaryotic microorganisms, and highlights the persistent risk of eukaryotic microbial contamination in drinking water even after disinfection, calling for further optimization of current conventional disinfection methods.
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Affiliation(s)
- Haoran Li
- College of the Environment & Ecology, Xiamen University, Xiamen, 361102, PR China
| | - Mingbao Feng
- College of the Environment & Ecology, Xiamen University, Xiamen, 361102, PR China
| | - Xin Yu
- College of the Environment & Ecology, Xiamen University, Xiamen, 361102, PR China.
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8
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Ke Y, Sun W, Jing Z, Zhu Y, Zhao Z, Xie S. Antibiotic resistome alteration along a full-scale drinking water supply system deciphered by metagenome assembly: Regulated by seasonality, mobile gene elements and antibiotic resistant gene hosts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 862:160887. [PMID: 36521611 DOI: 10.1016/j.scitotenv.2022.160887] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Both drinking water treatment processes and distribution can lead to antibiotic resistome variation, yet the variation of antibiotic resistome in the whole drinking water supply system (DWSS) combined with seasonality remains unknown. In this study, microbial community, antibiotic resistome, mobile genetic elements (MGEs) co-existing with antibiotic resistance genes (ARGs) and ARG hosts would be explored along a DWSS for four seasons with metagenome assembly. Multidrug and bacitracin ARGs were dominant ARGs in DWSS. Integrase, plasmids, recombinase and transposase were major MGEs co-existing with ARGs. Filtration and disinfection treatments could alter the ARG relative abundance, mainly via changing the abundance of ARG hosts (Limnohabitans and Polynucleobacter), which was influenced by water total organic carbon (TOC) content. When TOC was relatively high, filtration could proliferate ARGs via promoting antibiotic resistance bacteria (ARB) but chlorine dioxide could decrease ARGs via killing ARB. Filtration played an important role in controlling ARGs by reducing ARB when TOC was relatively low. The stimulation effect of disinfection on ARGs existed in more oligotrophic environment. Distribution could enrich ARGs in higher temperature by increasing MGEs co-occurring with ARGs and diversifying ARG hosts. MGEs co-occurring with ARGs became more abundant and diverse in disinfected water in warmer seasons. Microbial community was the most important factor determining the antibiotic resistome along a DWSS. These findings extend the knowledge about how and why water treatment processes and pipe distribution shape drinking water antibiotic resistome in different seasons.
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Affiliation(s)
- Yanchu Ke
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; School of Environment, Tsinghua University, Beijing 100084, China
| | - Wenjun Sun
- School of Environment, Tsinghua University, Beijing 100084, China; Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou 215163, China.
| | - Zibo Jing
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yin Zhu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zhinan Zhao
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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Štiglić J, Ujević Bošnjak M, Héry M, Kurajica L, Kinsela AS, Casiot C, Capak K. Bacterial diversity across four drinking water distribution systems in Croatia: impacts of water management practices and disinfection by-products. FEMS Microbiol Ecol 2022; 99:fiac146. [PMID: 36473705 DOI: 10.1093/femsec/fiac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024] Open
Abstract
Several factors may impact bacterial diversity in drinking water distribution systems (DWDSs) including the origin of the raw water, the water treatment technologies, and the disinfection practices applied. 16S rRNA metabarcoding was used for the in-depth characterization of bacterial communities in the four studied Croatian DWDSs (A, B, C, D) two of which had residual disinfectant (A, B) and two were without (C, D), while only B utilized the conventional water treatment technology. Significantly higher diversity and species richness were evidenced in non-disinfected DWDSs (p<0.05) compared to disinfected DWDSs. The phylum Proteobacteria was the most abundant in all the DWDSs, being proportionately higher in non-disinfected systems (p<0.05). The most abundant genera in DWDS-A Mycobacterium and Sphingomonas both positively correlated, whereas Lactobacillus negatively correlated with the concentration of disinfection by-products (DBPs) as a sum of haloacetic acids (HAAs). Conversely, the genus Ralstonia positively correlated with the individual DBP dichloroacetic acid. These results indicate that genera Sphingomonas, Mycobacterium, Lactobacillus and Ralstonia could have an effect on promoting the formation of DBPs, in a similar manner to how negatively correlated taxa may influence their degradation.
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Affiliation(s)
- J Štiglić
- Croatian Institute of Public Health, Rockefellerova 7, 10000 Zagreb, Croatia
| | - M Ujević Bošnjak
- Croatian Institute of Public Health, Rockefellerova 7, 10000 Zagreb, Croatia
| | - M Héry
- HydroSciences Montpellier, University of Montpellier, CNRS, IRD, Montpellier, France
| | - L Kurajica
- Croatian Institute of Public Health, Rockefellerova 7, 10000 Zagreb, Croatia
| | - A S Kinsela
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - C Casiot
- HydroSciences Montpellier, University of Montpellier, CNRS, IRD, Montpellier, France
| | - K Capak
- Croatian Institute of Public Health, Rockefellerova 7, 10000 Zagreb, Croatia
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Entezari S, Al MA, Mostashari A, Ganjidoust H, Ayati B, Yang J. Microplastics in urban waters and its effects on microbial communities: a critical review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:88410-88431. [PMID: 36327084 DOI: 10.1007/s11356-022-23810-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Microplastic (MP) pollution is one of the emerging threats to the water and terrestrial environment, forcing a new environmental challenge due to the growing trend of plastic released into the environment. Synthetic and non-synthetic plastic components can be found in rivers, lakes/reservoirs, oceans, mountains, and even remote areas, such as the Arctic and Antarctic ice sheets. MPs' main challenge is identifying, measuring, and evaluating their impacts on environmental behaviors, such as carbon and nutrient cycles, water and wastewater microbiome, and the associated side effects. However, until now, no standardized methodical protocols have been proposed for comparing the results of studies in different environments, especially in urban water and wastewater. This review briefly discusses MPs' sources, fate, and transport in urban waters and explains methodological uncertainty. The effects of MPs on urban water microbiomes, including urban runoff, sewage wastewater, stagnant water in plumbing networks, etc., are also examined in depth. Furthermore, this study highlights the pathway of MPs and their transport vectors to different parts of ecosystems and human life, particularly through mediating microbial communities, antibiotic-resistant genes, and biogeochemical cycles. Overall, we have briefly highlighted the present research gaps, the lack of appropriate policy for evaluating microplastics and their interactions with urban water microbiomes, and possible future initiatives.
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Affiliation(s)
- Saber Entezari
- Environmental Engineering Division, Faculty of Civil & Env. Eng., TMU, Tehran, Iran
| | - Mamun Abdullah Al
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Amir Mostashari
- Environmental Engineering Division, Faculty of Civil & Env. Eng., TMU, Tehran, Iran
| | - Hossein Ganjidoust
- Environmental Engineering Division, Faculty of Civil & Env. Eng., TMU, Tehran, Iran.
| | - Bita Ayati
- Environmental Engineering Division, Faculty of Civil & Env. Eng., TMU, Tehran, Iran
| | - Jun Yang
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
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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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Vanhaecke T, Bretin O, Poirel M, Tap J. Drinking Water Source and Intake Are Associated with Distinct Gut Microbiota Signatures in US and UK Populations. J Nutr 2021; 152:171-182. [PMID: 34642755 PMCID: PMC8754568 DOI: 10.1093/jn/nxab312] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/28/2021] [Accepted: 08/25/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The microbiome of the digestive tract exerts fundamental roles in host physiology. Extrinsic factors including lifestyle and diet are widely recognized as key drivers of gut and oral microbiome compositions. Although drinking water is among the food items consumed in the largest amount, little is known about its potential impact on the microbiome. OBJECTIVES We explored the associations of plain drinking water source and intake with gut and oral microbiota compositions in a population-based cohort. METHODS Microbiota, health, lifestyle, and food intake data were extracted from the American Gut Project public database. Associations of drinking water source (bottled, tap, filtered, or well water) and intake with global microbiota composition were evaluated using linear and logistic models adjusted for anthropometric, diet, and lifestyle factors in 3413 and 3794 individuals, respectively (fecal samples; 56% female, median [IQR] age: 48 [36-59] y; median [IQR] BMI: 23.3 [20.9-26.3] kg/m2), and in 283 and 309 individuals, respectively (oral samples). RESULTS Drinking water source ranked among the key contributing factors explaining the gut microbiota variation, accounting for 13% [Faith's phylogenetic diversity (Faith's PD)] and 47% (Bray-Curtis dissimilarity) of the age effect size. Drinking water source was associated with differences in gut microbiota signatures, as revealed by β diversity analyses (P < 0.05; Bray-Curtis dissimilarity, weighted UniFrac distance). Subjects drinking mostly well water had higher fecal α diversity (P < 0.05; Faith's PD, observed amplicon sequence variants), higher Dorea, and lower Bacteroides, Odoribacter, and Streptococcus than the other groups. Low water drinkers also exhibited gut microbiota differences compared with high water drinkers (P < 0.05; Bray-Curtis dissimilarity, unweighted UniFrac distance) and a higher abundance of Campylobacter. No associations were found between oral microbiota composition and drinking water consumption. CONCLUSIONS Our results indicate that drinking water may be an important factor in shaping the human gut microbiome and that integrating drinking water source and intake as covariates in future microbiome analyses is warranted.
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Inkinen J, Siponen S, Jayaprakash B, Tiwari A, Hokajärvi AM, Pursiainen A, Ikonen J, Kauppinen A, Miettinen IT, Paananen J, Torvinen E, Kolehmainen M, Pitkänen T. Diverse and active archaea communities occur in non-disinfected drinking water systems-Less activity revealed in disinfected and hot water systems. WATER RESEARCH X 2021; 12:100101. [PMID: 34027378 PMCID: PMC8131914 DOI: 10.1016/j.wroa.2021.100101] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 05/25/2023]
Abstract
The knowledge about the members of active archaea communities in DWDS is limited. The current understanding is based on high-throughput 16S ribosomal RNA gene (DNA-based) amplicon sequencing that reveals the diversity of active, dormant, and dead members of the prokaryote (bacteria, archaea) communities. The sequencing primers optimized for bacteria community analysis may underestimate the share of the archaea community. This study characterized archaea communities at five full-scale drinking water distribution systems (DWDS), representing a variety of drinking water production units (A-E); A&B use artificially recharged non-disinfected groundwater (ARG), the other DWDS's supplied water disinfected by using ultraviolet (UV) light and chlorine compounds, C&D were surface waterworks and E was a ground waterworks. For the first time for archaea community analyses, this study employed the archaea-specific high-throughput sequencing primers for 16S ribosomal RNA (rRNA) as a target (reverse-transcribed cDNA; an RNA-based approach) in addition to the previously used 16S rRNA gene target (rDNA; a DNA-based approach) to reveal the active fraction of the archaea present in DWDS. The archaea community structure in varying environmental conditions in the water and biofilm of the five DWDSs were investigated by taking into consideration the system properties (cold or hot water system) and water age (distance from the treatment plants) in samples from each season of one year. The RNA-based archaea amplicon reads were obtained mostly from cold water samples from DWDSs (A-B) distributing water without disinfection where the DNA-based and RNA-based analysis created separate clusters in a weighted beta-diversity analysis. The season and location in DWDS A further affected the diversity of these archaea communities as was seen by different clusters in beta-diversity plots. The recovery of archaea reads was not adequate for analysis in any of the disinfected samples in DWDSs C-E or non-disinfected hot water in DWDSs A-B when utilizing RNA-based template. The metabolically active archaea community of DWDSs thus seemed to be effectively controlled by disinfection of water and in the hot water systems by the temperature. All biofilms regardless of DWDS showed lower species richness values (mainly Nitrososphaeria class) than non-disinfected water from DWDSs A-B where several archaea classes occurred (e.g. Woesearchaeia, Nitrososphaeria, Micrarchaeia, Methanomicrobia, Iairchaeia, Bathyarchaeia) indicating only part of the archaea members were able to survive in biofilms. Thus, Archaea has been shown as a significant part of normal DWDS biota, and their role especially in non-disinfected DWDS may be more important than previously considered.
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Affiliation(s)
- Jenni Inkinen
- Finnish Institute for Health and Welfare, Department of Health Security, P.O. Box 95, FI-70701 Kuopio, Finland
- University of Eastern Finland, Institute of Biomedicine, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Sallamaari Siponen
- Finnish Institute for Health and Welfare, Department of Health Security, P.O. Box 95, FI-70701 Kuopio, Finland
- University of Eastern Finland, Department of Environmental and Biological Sciences, P.O. Box, 1627, FI-70211 Kuopio, Finland
| | | | - Ananda Tiwari
- Finnish Institute for Health and Welfare, Department of Health Security, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Anna-Maria Hokajärvi
- Finnish Institute for Health and Welfare, Department of Health Security, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Anna Pursiainen
- Finnish Institute for Health and Welfare, Department of Health Security, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Jenni Ikonen
- Finnish Institute for Health and Welfare, Department of Health Security, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Ari Kauppinen
- Finnish Institute for Health and Welfare, Department of Health Security, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Ilkka T. Miettinen
- Finnish Institute for Health and Welfare, Department of Health Security, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Jussi Paananen
- University of Eastern Finland, Institute of Biomedicine, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Eila Torvinen
- University of Eastern Finland, Department of Environmental and Biological Sciences, P.O. Box, 1627, FI-70211 Kuopio, Finland
| | - Mikko Kolehmainen
- University of Eastern Finland, Department of Environmental and Biological Sciences, P.O. Box, 1627, FI-70211 Kuopio, Finland
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Department of Health Security, P.O. Box 95, FI-70701 Kuopio, Finland
- University of Helsinki, Faculty of Veterinary Medicine, Dept. Food Hygiene and Environmental Health, Finland
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14
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Zhou W, Li W, Chen J, Zhou Y, Wei Z, Gong L. Microbial diversity in full-scale water supply systems through sequencing technology: a review. RSC Adv 2021; 11:25484-25496. [PMID: 35478887 PMCID: PMC9037190 DOI: 10.1039/d1ra03680g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/10/2021] [Indexed: 01/07/2023] Open
Abstract
The prevalence of microorganisms in full-scale water supply systems raises concerns about their pathogenicity and threats to public health. Clean tap water is essential for public health safety. The conditions of the water treatment process from the source water to tap water, including source water quality, water treatment processes, the drinking water distribution system (DWDS), and building water supply systems (BWSSs) in buildings, greatly influence the bacterial community in tap water. Given the importance of drinking water biosafety, the study of microbial diversity from source water to tap water is essential. With the development of molecular biology methods and bioinformatics in recent years, sequencing technology has been applied to study bacterial communities in full-scale water supply systems. In this paper, changes in the bacterial community and the influence of each treatment stage on microbial diversity in full-scale water supply systems are classified and analyzed. Microbial traceability analysis and control are discussed, and suggestions for future drinking water biosafety research and its prospects are proposed.
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Affiliation(s)
- Wei Zhou
- College of Environmental Science and Engineering, Tongji University Shanghai 200092 China .,State Key Laboratory of Pollution Control and Resource Reuse, Tongji University Shanghai 200092 China
| | - Weiying Li
- College of Environmental Science and Engineering, Tongji University Shanghai 200092 China .,State Key Laboratory of Pollution Control and Resource Reuse, Tongji University Shanghai 200092 China
| | - Jiping Chen
- College of Environmental Science and Engineering, Tongji University Shanghai 200092 China
| | - Yu Zhou
- College of Environmental Science and Engineering, Tongji University Shanghai 200092 China
| | - Zhongqing Wei
- Fuzhou Water Affairs Investment Development Co., Ltd. Fuzhou 350000 Fujian China
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15
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Bruno A, Sandionigi A, Magnani D, Bernasconi M, Pannuzzo B, Consolandi C, Camboni T, Labra M, Casiraghi M. Different Effects of Mineral Versus Vegetal Granular Activated Carbon Filters on the Microbial Community Composition of a Drinking Water Treatment Plant. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.615513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Drinking water quality and safety is strictly regulated and constantly monitored, but little is known about the microorganisms inhabiting drinking water treatment plants (DWTPs). This lack of knowledge prevents optimization of designs and operational controls. Here we investigated the drinking water microbial community harbored by a groundwater-derived DWTP, involving mineral and vegetal granular activated carbon filters (GACs). We used 16S rRNA gene sequencing to analyze water microbiome variations through the potabilization process, considering (i) different GAC materials and (ii) time from GAC regeneration. Our results revealed the predominance of Cand. Patescibacteria, uncultivable bacteria with limited metabolic capacities and small genomes, from source to downstream water. Microbial communities clustered per sampling date, with the noteworthy exception of groundwater samples. If the groundwater microbiome showed no significant variations over time, the community structure of water downstream GACs (both mineral and vegetal) seemed to be affected by time from GAC regeneration. Looking at a finer scale, different GAC material affected microbiome assembly over time with significant variation in the relative abundances of specific taxa. The significance of our research is in identifying the environmental microorganisms intrinsic of deep groundwater and the community shift after the perturbations induced by potabilization processes. Which microorganisms colonize different GACs and become abundant after GACs regeneration and over time is a first step toward advanced control of microbial communities, improving drinking water safety and management of operational costs.
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16
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Shi D, Ma H, Miao J, Liu W, Yang D, Qiu Z, Shen Z, Yin J, Yang Z, Wang H, Li H, Chen Z, Li J, Jin M. Levels of human Rotaviruses and Noroviruses GII in urban rivers running through the city mirror their infection prevalence in populations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142203. [PMID: 32920413 PMCID: PMC7470703 DOI: 10.1016/j.scitotenv.2020.142203] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/02/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
Enteric viruses exposed to water pose a huge threat to global public health and can lead to waterborne disease outbreaks. A sudden increase in enteric viruses in some water matrices also underpins the prevalence of corresponding waterborne diseases in communities over the same time period. However, few efforts have been focused on water matrices whose viral pollution may best reflect the clinical prevalence in communities. Here, a one-year surveillance of human enteric viruses including Enteroviruses (EnVs), Rotaviruses (HRVs), Astroviruses (AstVs), Noroviruses GII (HuNoVsGII) and Mastadenoviruses (HAdVs) in four representative water matrices: an urban river (UR) running through city, effluent from Wastewater Treatment Plant (EW), raw water for Urban Water Treatment Plant (RW), and tap water (TW) were performed by qPCR. The relationship between the virus detection frequency at each site and their prevalence in clinical PCR assay was further analyzed. We found that the detection frequencies of HRVs, HuNoVsGII, and AstVs in stools peaked in winter, while EnVs peaked in autumn. No EnVs occurred in EW, RW, or TW, but HuNoVsGII and AstVs occurred intensively in winter. For UR, all types of enteric viruses could be detected and the levels of acute gastroenteritis viruses (HRVs, HuNoVsGII, AstVs, and HAdVs) were highest in autumn or winter, whereas EnVs peaked in summer. In terms of correlation analyses, only HRVs and HuNoVsGII levels in UR showed a strong positive correlation with their prevalence in clinical stool samples. This study indicated that HRVs and HuNoVsGII levels in URs may mirror the local virus prevalence, thereby implying the possibility of revealing their local epidemiology by monitoring them in the URs.
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Affiliation(s)
- Danyang Shi
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin Institute of Environmental & Operational Medicine, No.1, Dali Road, Tianjin 300050, China
| | - Hui Ma
- Department of Clinical Laboratory, Tianjin Children's Hospital, No. 238, Longyan Road, Tianjin 300134, China
| | - Jing Miao
- Department of Public Health, Shanxi University of Chinese Medicine, Xianyang 712046, China
| | - Weili Liu
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin Institute of Environmental & Operational Medicine, No.1, Dali Road, Tianjin 300050, China
| | - Dong Yang
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin Institute of Environmental & Operational Medicine, No.1, Dali Road, Tianjin 300050, China
| | - Zhigang Qiu
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin Institute of Environmental & Operational Medicine, No.1, Dali Road, Tianjin 300050, China
| | - Zhiqiang Shen
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin Institute of Environmental & Operational Medicine, No.1, Dali Road, Tianjin 300050, China
| | - Jing Yin
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin Institute of Environmental & Operational Medicine, No.1, Dali Road, Tianjin 300050, China
| | - Zhongwei Yang
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin Institute of Environmental & Operational Medicine, No.1, Dali Road, Tianjin 300050, China
| | - Huaran Wang
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin Institute of Environmental & Operational Medicine, No.1, Dali Road, Tianjin 300050, China
| | - Haibei Li
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin Institute of Environmental & Operational Medicine, No.1, Dali Road, Tianjin 300050, China
| | - Zhengshan Chen
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin Institute of Environmental & Operational Medicine, No.1, Dali Road, Tianjin 300050, China
| | - Junwen Li
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin Institute of Environmental & Operational Medicine, No.1, Dali Road, Tianjin 300050, China.
| | - Min Jin
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin Institute of Environmental & Operational Medicine, No.1, Dali Road, Tianjin 300050, China.
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17
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Jalili F, Trigui H, Guerra Maldonado JF, Dorner S, Zamyadi A, Shapiro BJ, Terrat Y, Fortin N, Sauvé S, Prévost M. Can Cyanobacterial Diversity in the Source Predict the Diversity in Sludge and the Risk of Toxin Release in a Drinking Water Treatment Plant? Toxins (Basel) 2021; 13:toxins13010025. [PMID: 33401450 PMCID: PMC7823770 DOI: 10.3390/toxins13010025] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 02/05/2023] Open
Abstract
Conventional processes (coagulation, flocculation, sedimentation, and filtration) are widely used in drinking water treatment plants and are considered a good treatment strategy to eliminate cyanobacterial cells and cell-bound cyanotoxins. The diversity of cyanobacteria was investigated using taxonomic cell counts and shotgun metagenomics over two seasons in a drinking water treatment plant before, during, and after the bloom. Changes in the community structure over time at the phylum, genus, and species levels were monitored in samples retrieved from raw water (RW), sludge in the holding tank (ST), and sludge supernatant (SST). Aphanothece clathrata brevis, Microcystis aeruginosa, Dolichospermum spiroides
, and Chroococcus minimus were predominant species detected in RW by taxonomic cell counts. Shotgun metagenomics revealed that Proteobacteria was the predominant phylum in RW before and after the cyanobacterial bloom. Taxonomic cell counts and shotgun metagenomic showed that the Dolichospermum bloom occurred inside the plant. Cyanobacteria and Bacteroidetes were the major bacterial phyla during the bloom. Shotgun metagenomics also showed that Synechococcus, Microcystis
, and Dolichospermum were the predominant detected cyanobacterial genera in the samples. Conventional treatment removed more than 92% of cyanobacterial cells but led to cell accumulation in the sludge up to 31 times more than in the RW influx. Coagulation/sedimentation selectively removed more than 96% of Microcystis and Dolichospermum. Cyanobacterial community in the sludge varied from raw water to sludge during sludge storage (1-13 days). This variation was due to the selective removal of coagulation/sedimentation as well as the accumulation of captured cells over the period of storage time. However, the prediction of the cyanobacterial community composition in the SST remained a challenge. Among nutrient parameters, orthophosphate availability was related to community profile in RW samples, whereas communities in ST were influenced by total nitrogen, Kjeldahl nitrogen (N- Kjeldahl), total and particulate phosphorous, and total organic carbon (TOC). No trend was observed on the impact of nutrients on SST communities. This study profiled new health-related, environmental, and technical challenges for the production of drinking water due to the complex fate of cyanobacteria in cyanobacteria-laden sludge and supernatant.
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Affiliation(s)
- Farhad Jalili
- Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montréal, QC H3C 3A7, Canada; (H.T.); (J.F.G.M.); (S.D.); (M.P.)
- Correspondence:
| | - Hana Trigui
- Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montréal, QC H3C 3A7, Canada; (H.T.); (J.F.G.M.); (S.D.); (M.P.)
| | - Juan Francisco Guerra Maldonado
- Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montréal, QC H3C 3A7, Canada; (H.T.); (J.F.G.M.); (S.D.); (M.P.)
| | - Sarah Dorner
- Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montréal, QC H3C 3A7, Canada; (H.T.); (J.F.G.M.); (S.D.); (M.P.)
| | - Arash Zamyadi
- Water Research Australia, Adelaide SA 5001, Australia;
| | - B. Jesse Shapiro
- Department of Biological Sciences, University of Montréal, Montréal, QC H2V 0B3, Canada; (B.J.S.); (Y.T.)
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
- McGill Genome Center, McGill University, Montréal, QC H3A 0G1, Canada
| | - Yves Terrat
- Department of Biological Sciences, University of Montréal, Montréal, QC H2V 0B3, Canada; (B.J.S.); (Y.T.)
| | - Nathalie Fortin
- National Research Council Canada, Energy, Mining and Environment, Montréal, QC H4P 2R2, Canada;
| | - Sébastien Sauvé
- Department of Chemistry, University of Montréal, Montréal, QC H3C 3J7, Canada;
| | - Michèle Prévost
- Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montréal, QC H3C 3A7, Canada; (H.T.); (J.F.G.M.); (S.D.); (M.P.)
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Kumar Awasthi M, Ravindran B, Sarsaiya S, Chen H, Wainaina S, Singh E, Liu T, Kumar S, Pandey A, Singh L, Zhang Z. Metagenomics for taxonomy profiling: tools and approaches. Bioengineered 2020; 11:356-374. [PMID: 32149573 PMCID: PMC7161568 DOI: 10.1080/21655979.2020.1736238] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/25/2022] Open
Abstract
The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about specific genes, microbial communities and its metabolic pathways. More specific drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this 'targeted based metagenomics' approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.
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Affiliation(s)
- Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
- Swedish Centre for Resource Recovery, University of Borås, Borås, Sweden
| | - B. Ravindran
- Department of Environmental Energy and Engineering, Kyonggi University Youngtong-Gu, Suwon, South Korea
| | - Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Hongyu Chen
- Institute of Biology, Freie Universität Berlin Altensteinstr, Berlin, Germany
| | - Steven Wainaina
- Swedish Centre for Resource Recovery, University of Borås, Borås, Sweden
| | - Ekta Singh
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Tao Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Sunil Kumar
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Ashok Pandey
- Centre for Innovation and Translational Research CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Lal Singh
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
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Mei R, Liu WT. Quantifying the contribution of microbial immigration in engineered water systems. MICROBIOME 2019; 7:144. [PMID: 31694700 PMCID: PMC6836541 DOI: 10.1186/s40168-019-0760-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/17/2019] [Indexed: 05/03/2023]
Abstract
Immigration is a process that can influence the assembly of microbial communities in natural and engineered environments. However, it remains challenging to quantitatively evaluate the contribution of this process to the microbial diversity and function in the receiving ecosystems. Currently used methods, i.e., counting shared microbial species, microbial source tracking, and neutral community model, rely on abundance profile to reveal the extent of overlapping between the upstream and downstream communities. Thus, they cannot suggest the quantitative contribution of immigrants to the downstream community function because activities of individual immigrants are not considered after entering the receiving environment. This limitation can be overcome by using an approach that couples a mass balance model with high-throughput DNA sequencing, i.e., ecogenomics-based mass balance. It calculates the net growth rate of individual microbial immigrants and partitions the entire community into active populations that contribute to the community function and inactive ones that carry minimal function. Linking activities of immigrants to their abundance further provides quantification of the contribution from an upstream environment to the downstream community. Considering only active populations can improve the accuracy of identifying key environmental parameters dictating process performance using methods such as machine learning.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL USA
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Jia S, Wu J, Ye L, Zhao F, Li T, Zhang XX. Metagenomic assembly provides a deep insight into the antibiotic resistome alteration induced by drinking water chlorination and its correlations with bacterial host changes. JOURNAL OF HAZARDOUS MATERIALS 2019; 379:120841. [PMID: 31279312 DOI: 10.1016/j.jhazmat.2019.120841] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 04/09/2019] [Accepted: 06/26/2019] [Indexed: 05/21/2023]
Abstract
Chlorination can contribute to the enrichment of specific antibiotic resistance genes (ARGs) in drinking water, but the underlying molecular ecological mechanisms remain unknown, which may hinder the assessment and control of the resulting health risks. In this study, metagenomic assembly and Resfams annotation were used to profile the co-occurrence patterns of ARGs, mobile genetic elements (MGEs) and their bacterial hosts, as well as the correlations of potential pathogens with the antibiotic resistome, in a full-scale drinking water treatment and transportation system. Seven ARG types involved in different resistance mechanisms occurred in drinking water and chlorination enhanced the total abundance of the ARGs (p < 0.05). The ARGs encoding resistance-nodulation-cell division and ATP-binding cassette antibiotic efflux pumps predominated in all the samples and were primarily responsible for the ARG accumulation. After chlorination, the ARGs were primarily carried by predominant Sphingomonas, Polaromonas, Hyphomicrobium, Acidovorax, Pseudomonas and Fluviicola. Further, enrichment of the bacterial hosts and MGEs greatly contributed to alteration of the antibiotic resistome. Pseudomonas alcaligenes, carrying multiple ARGs, was identified as a potential pathogen in the chlorinated drinking water. These findings provide novel insights into the host-ARG relationship and the mechanism underlying the resistome alteration during drinking water chlorination.
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Affiliation(s)
- Shuyu Jia
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Jialu Wu
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Fuzheng Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Tong Li
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China.
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21
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Kantor RS, Miller SE, Nelson KL. The Water Microbiome Through a Pilot Scale Advanced Treatment Facility for Direct Potable Reuse. Front Microbiol 2019; 10:993. [PMID: 31139160 PMCID: PMC6517601 DOI: 10.3389/fmicb.2019.00993] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 04/18/2019] [Indexed: 01/01/2023] Open
Abstract
Advanced treatment facilities for potable water reuse of wastewater are designed to achieve high removal levels of specific pathogens, as well as many other constituents. However, changes to the microbial community throughout treatment, storage, and distribution of this water have not been well characterized. We applied high-throughput amplicon sequencing, read-based, assembly-based, and genome-resolved metagenomics, and flow cytometry to investigate the microbial communities present in a pilot-scale advanced water treatment facility. Advanced treatment of secondary-treated wastewater consisted of ozonation, chloramination, microfiltration, reverse osmosis (RO), advanced oxidation (UV/H2O2), granular activated carbon (GAC) filtration, and chlorination. Treated water was fed into bench-scale simulated distribution systems (SDS). Cell counts and microbial diversity in bulk water decreased until GAC filtration, and the bacterial communities were significantly different following each treatment step. Bacteria grew within GAC media and contributed to a consistent microbial community in the filtrate, which included members of the Rhizobiales and Mycobacteriaceae. After chlorination, some of the GAC filtrate community was maintained within the SDS, and community shifts were associated with stagnation. Putative antibiotic resistance genes and potential opportunistic pathogens were identified before RO and after advanced oxidation, although few if any members of the wastewater microbial community passed through these treatment steps. These findings can contribute to improved design of advanced treatment trains and management of microbial communities in post-treatment steps.
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Affiliation(s)
- Rose S Kantor
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, United States.,Engineering Research Center for Re-inventing the Nation's Urban Water Infrastructure, Berkeley, CA, United States
| | - Scott E Miller
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, United States.,Engineering Research Center for Re-inventing the Nation's Urban Water Infrastructure, Berkeley, CA, United States
| | - Kara L Nelson
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, United States.,Engineering Research Center for Re-inventing the Nation's Urban Water Infrastructure, Berkeley, CA, United States
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22
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Setty K, Loret JF, Courtois S, Hammer CC, Hartemann P, Lafforgue M, Litrico X, Manasfi T, Medema G, Shaheen M, Tesson V, Bartram J. Faster and safer: Research priorities in water and health. Int J Hyg Environ Health 2019; 222:593-606. [PMID: 30910612 PMCID: PMC6545151 DOI: 10.1016/j.ijheh.2019.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 11/22/2022]
Abstract
The United Nations' Sustainable Development Goals initiated in 2016 reiterated the need for safe water and healthy lives across the globe. The tenth anniversary meeting of the International Water and Health Seminar in 2018 brought together experts, students, and practitioners, setting the stage for development of an inclusive and evidence-based research agenda on water and health. Data collection relied on a nominal group technique gathering perceived research priorities as well as underlying drivers and adaptation needs. Under a common driver of public health protection, primary research priorities included the socioeconomy of water, risk assessment and management, and improved monitoring methods and intelligence. Adaptations stemming from these drivers included translating existing knowledge to providing safe and timely services to support the diversity of human water needs. Our findings present a comprehensive agenda of topics at the forefront of water and health research. This information can frame and inform collective efforts of water and health researchers over the coming decades, contributing to improved water services, public health, and socioeconomic outcomes.
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Affiliation(s)
- Karen Setty
- The Water Institute at University of North Carolina at Chapel Hill, Department of Environmental Sciences and Engineering, 166 Rosenau Hall, CB #7431, Chapel Hill, NC, 27599-7431, USA.
| | - Jean-Francois Loret
- Suez, Centre International de Recherche sur l'Eau et l'Environnement (CIRSEE), 38 rue du President Wilson, 78230, Le Pecq, France.
| | - Sophie Courtois
- Suez, Centre International de Recherche sur l'Eau et l'Environnement (CIRSEE), 38 rue du President Wilson, 78230, Le Pecq, France.
| | - Charlotte Christiane Hammer
- Norwich Medical School, University of East Anglia Faculty of Medicine and Health Sciences, Norwich, NR4 7TJ, UK.
| | - Philippe Hartemann
- Université de Lorraine, Faculté de Médecine, EA 7298, ERAMBO, DESP, Vandœuvre-lès-Nancy, France.
| | - Michel Lafforgue
- Suez Consulting, Le Bruyère 2000 - Bâtiment 1, Zone du Millénaire, 650 Rue Henri Becquerel, CS79542, 34961, Montpellier Cedex 2, France.
| | - Xavier Litrico
- Suez, Tour CB21, 16 Place de l'Iris, 92040, Paris La Defense Cedex, France.
| | - Tarek Manasfi
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600, Dübendorf, Switzerland.
| | - Gertjan Medema
- KWR Watercycle Research Institute, Groningenhaven 7, 3433, PE, Nieuwegein, the Netherlands; Delft University of Technology, Stevinweg 1, 2628 CN, Delft, the Netherlands.
| | - Mohamed Shaheen
- School of Public Health, University of Alberta, 3-300 Edmonton Clinic Health Academy, 11405 - 87 Ave, Edmonton, AB T6G 1C9, Canada.
| | - Vincent Tesson
- French National Institute for Agricultural Research (INRA), UMR 1114 EMMAH, 228 route de l'Aérodrome, CS 40 509, 84914, Avignon Cedex 9, France.
| | - Jamie Bartram
- The Water Institute at University of North Carolina at Chapel Hill, Department of Environmental Sciences and Engineering, 166 Rosenau Hall, CB #7431, Chapel Hill, NC, 27599-7431, USA.
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Perrin Y, Bouchon D, Delafont V, Moulin L, Héchard Y. Microbiome of drinking water: A full-scale spatio-temporal study to monitor water quality in the Paris distribution system. WATER RESEARCH 2019; 149:375-385. [PMID: 30471533 DOI: 10.1016/j.watres.2018.11.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/25/2018] [Accepted: 11/05/2018] [Indexed: 05/22/2023]
Abstract
The microbiological water quality of drinking water distribution system (DWDS) is of primary importance for human health. High-throughput sequencing has gained more and more attention in the last decade to describe this microbial diversity in water networks. However, there are few studies describing this approach on large drinking water distribution systems and for extended periods of time. To fill this gap and observe the potential subtle variation in microbiota of a water network through time and space, we aimed to apply high-throughput sequencing of the 16S rRNA gene approach to characterize bacterial communities of the Paris' DWDS over a one-year period. In this study, the Paris network, composed of four different DWDSs, was sampled at 31 sites, each month for one year. The sampling campaign was one of the largest described so far (n = 368) and the importance of key spatio-temporal and physico-chemical parameters was investigated. Overall, 1321 taxa were identified within the Paris network, although only fifteen of them were found in high relative abundance (>1%) in all samples. Two genera, Phreatobacter and Hyphomicrobium were dominant. The whole bacterial diversity was not significantly affected between the four DWDSs (spatial parameter) and by physico-chemical parameters. However, the bacterial diversity was slightly modified over the one-year period (temporal parameter) as we were able to observe DWDS microbiome perturbations, presumably linked to a preceding flood event. Comparison of high-throughput sequencing of the 16S rRNA gene amplicons vs. cultivation-based techniques showed that only 1.8% of bacterial diversity was recovered through cultivation. High throughput sequencing has made it possible to monitor DWDS more accurately than conventional methods by describing the whole diversity and detecting slight fluctuations in bacterial communities. This method would be further used to supervise drinking water networks, to follow any perturbations due to internals events (such as treatments) or external events (such as flooding).
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Affiliation(s)
- Yoann Perrin
- Laboratoire Ecologie et Biologie des Interactions, Equipes Microbiologie de l'Eau, et., Ecologie, Evolution, Symbiose, Université de Poitiers, UMR CNRS 7267, F-86073, Poitiers, France; Eau de Paris, Direction de la Recherche et du Développement pour la Qualité de l'Eau, R&D Biologie, 33, Avenue Jean Jaurès, F-94200, Ivry sur Seine, France
| | - Didier Bouchon
- Laboratoire Ecologie et Biologie des Interactions, Equipes Microbiologie de l'Eau, et., Ecologie, Evolution, Symbiose, Université de Poitiers, UMR CNRS 7267, F-86073, Poitiers, France
| | - Vincent Delafont
- Laboratoire Ecologie et Biologie des Interactions, Equipes Microbiologie de l'Eau, et., Ecologie, Evolution, Symbiose, Université de Poitiers, UMR CNRS 7267, F-86073, Poitiers, France
| | - Laurent Moulin
- Eau de Paris, Direction de la Recherche et du Développement pour la Qualité de l'Eau, R&D Biologie, 33, Avenue Jean Jaurès, F-94200, Ivry sur Seine, France.
| | - Yann Héchard
- Laboratoire Ecologie et Biologie des Interactions, Equipes Microbiologie de l'Eau, et., Ecologie, Evolution, Symbiose, Université de Poitiers, UMR CNRS 7267, F-86073, Poitiers, France.
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24
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Delafont V, Perrin Y, Bouchon D, Moulin L, Héchard Y. Targeted Metagenomics of Microbial Diversity in Free-Living Amoebae and Water Samples. Methods Mol Biol 2019; 1921:421-428. [PMID: 30694507 DOI: 10.1007/978-1-4939-9048-1_26] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The presence of Legionella spp. in natural and man-made water systems is a great public health concern and heavily depends on the presence of free-living amoebae. Taking advantage of the development and affordability of next-generation sequencing technology, we present here a method to characterize the whole bacterial community directly from water samples, as well as from isolated free-living amoebae.
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Affiliation(s)
- Vincent Delafont
- Laboratoire Ecologie et Biologie des Interactions, Equipes "Microbiologie de l'Eau" et "Ecologie, Evolution, Symbiose", Université de Poitiers, UMR CNRS 7267, Poitiers, France
| | - Yoann Perrin
- Laboratoire Ecologie et Biologie des Interactions, Equipes "Microbiologie de l'Eau" et "Ecologie, Evolution, Symbiose", Université de Poitiers, UMR CNRS 7267, Poitiers, France
- Eau de Paris, Direction de la Recherche et du Développement pour la Qualité de l'Eau, R&D Biologie, Ivry sur Seine, France
| | - Didier Bouchon
- Laboratoire Ecologie et Biologie des Interactions, Equipes "Microbiologie de l'Eau" et "Ecologie, Evolution, Symbiose", Université de Poitiers, UMR CNRS 7267, Poitiers, France
| | - Laurent Moulin
- Eau de Paris, Direction de la Recherche et du Développement pour la Qualité de l'Eau, R&D Biologie, Ivry sur Seine, France
| | - Yann Héchard
- Laboratoire Ecologie et Biologie des Interactions, Equipes "Microbiologie de l'Eau" et "Ecologie, Evolution, Symbiose", Université de Poitiers, UMR CNRS 7267, Poitiers, France.
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25
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Wang H, Xu J, Tang W, Li H, Xia S, Zhao J, Zhang W, Yang Y. Removal Efficacy of Opportunistic Pathogens and Bacterial Community Dynamics in Two Drinking Water Treatment Trains. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1804436. [PMID: 30536542 DOI: 10.1002/smll.201804436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/16/2018] [Indexed: 06/09/2023]
Abstract
Drinking water treatment processes (DWTPs) impact pathogen colonization and microbial communities in finished water; however, their efficacies against opportunistic pathogens are not fully understood. In this study, the effects of treatment steps on the removal of Legionella spp., Legionella pneumophila, nontuberculous mycobacteria, Mycobacterium avium, and two amoeba hosts (Vermamoeba vermiformis, Acanthamoeba) are evaluated in two parallel trains of DWTPs equipped with different pretreatment units. Quantitative polymerase chain reaction analysis demonstrates significantly reduced numbers of total bacteria, Legionella, and mycobacteria during ozonation, followed by a rebound in granular activated carbon (GAC) filtration, whereas sand filtration exerts an overarching effect in removing microorganisms in both treatment trains. V. vermiformis is more prevalent in biofilm (34%) than water samples (7.7%), while Acanthamoeba is not found in the two trains of DWTPs. Illumina sequencing of bacterial 16S rRNA genes reveals significant community shifts at different treatment steps, as well as distinct bacterial community structures in water and biofilm samples in parallel units (e.g., ozonation, GAC, sand filtration) between the two trains (analysis of similarities (ANOSIM), p < 0.05), implying the potential influence of different pretreatment steps in shaping the downstream microbiome. Overall, the results provide insights to mitigation of opportunistic pathogens and engineer approaches for managing bacterial communities in DWTPs.
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Affiliation(s)
- Hong Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Jiajiong Xu
- Shanghai Municipal Engineering Design Institute (Group) CO., LTD, Shanghai, 200092, China
| | - Wei Tang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Huan Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Siqing Xia
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Jianfu Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Weixian Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Yang Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, 200433, China
- Institute for Advanced Study, Tongji University, 1239 Siping Road, Shanghai, 200430, China
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26
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Liu J, Zhao R, Zhang J, Zhang G, Yu K, Li X, Li B. Occurrence and Fate of Ultramicrobacteria in a Full-Scale Drinking Water Treatment Plant. Front Microbiol 2018; 9:2922. [PMID: 30568635 PMCID: PMC6290093 DOI: 10.3389/fmicb.2018.02922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/14/2018] [Indexed: 12/23/2022] Open
Abstract
Ultramicrobacteria (UMB) are omnipresent and numerically dominate in freshwater, as microbes can present in drinking water systems, however, the UMB communities that occur and their removal behaviors remain poorly characterized in drinking water treatment plants (DWTPs). To gain insights into these issues, we profiled bacterial cell density, community structure and functions of UMB and their counterpart large bacteria (LB) using flow cytometry and filtration paired with 16S rRNA gene high-throughput sequencing in a full-scale DWTP. Contrary to the reduction of bacterial density and diversity, the proportion of UMB in the total bacteria community increased as the drinking water treatment process progressed, and biological activated carbon facilitated bacterial growth. Moreover, UMB were less diverse than LB, and their community structure and predicted functions were significantly different. In the DWTP, UMB indicator taxa were mainly affiliated with α/β/γ-Proteobacteria, Deinococcus-Thermus, Firmicutes, Acidobacteria, and Dependentiae. In particular, the exclusive clustering of UMB at the phylum level, e.g., Parcubacteria, Elusimicrobia, and Saccharibacteria, confirmed the fact that the ultra-small size of UMB is a naturally and evolutionarily conserved trait. Additionally, the streamlined genome could be connected to UMB, such as candidate phyla radiation (CPR) bacteria, following a symbiotic or parasitic lifestyle, which then leads to the observed high connectedness, i.e., non-random intra-taxa co-occurrence patterns within UMB. Functional prediction analysis revealed that environmental information processing and DNA replication and repair likely contribute to the higher resistance of UMB to drinking water treatment processes in comparison to LB. Overall, the study provides valuable insights into the occurrence and fate of UMB regarding community structure, phylogenetic characteristics and potential functions in a full-scale DWTP, and it is a useful reference for beneficial manipulation of the drinking water microbiome.
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Affiliation(s)
- Jie Liu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Jiayu Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Guijuan Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Xiaoyan Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
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27
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Fiedler CJ, Schönher C, Proksch P, Kerschbaumer DJ, Mayr E, Zunabovic-Pichler M, Domig KJ, Perfler R. Assessment of Microbial Community Dynamics in River Bank Filtrate Using High-Throughput Sequencing and Flow Cytometry. Front Microbiol 2018; 9:2887. [PMID: 30555435 PMCID: PMC6281747 DOI: 10.3389/fmicb.2018.02887] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/12/2018] [Indexed: 11/13/2022] Open
Abstract
Surface-groundwater interactions play an important role in microbial community compositions of river bank filtrates. Surface water contaminations deriving from environmental influences are attenuated by biogeochemical processes in the hyporheic zone, which are essential for providing clean and high-quality drinking water in abstraction wells. Characterizing the flow regime of surface water into the groundwater body can provide substantial information on water quality, but complex hydraulic dynamics make predictions difficult. Thus, a bottom up approach using microbial community shifting patterns as an overall outcome of dynamic water characteristics could provide more detailed information on the influences that affect groundwater quality. The combination of high-throughput sequencing data together with flow cytometric measurements of total cell counts reveals absolute abundances among taxa, thus enhancing interpretation of bacterial dynamics. 16S rRNA high-throughput sequencing of 55 samples among six wells in a well field in Austria that is influenced by river bank filtrate within a time period of 3 months has revealed both, clear differences as well as strong similarity in microbiome compositions between wells and dates. A significant community shift from April to May occurred in four of six wells, suggesting that surface water flow regimes do affect these wells stronger than others. Triplicate sampling and subsequent sequencing of wells at different dates proved the method to be reproducible. Flow cytometric measurements of total cells indicate microbial shifts due to increased cell counts and emphasize the rise of allochthonous microorganisms. Typical freshwater bacterial lineages (Verrucomicrobia, Bacteroidetes, Actinobacteria, Cyanobacteria, Armatimonadetes) were identified as most increasing phyla during community shifts. The changes are most likely a result of increased water abstraction in the wells together with constant river water levels rather than rain events. The results provide important knowledge for future implementations of well utilization in dependency of the nearby Danube River water levels and can help drawing conclusions about the influence of surface water in the groundwater such that hygienically save and clean drinking water with a stable microbial community can be provided.
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Affiliation(s)
- Christina J Fiedler
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christoph Schönher
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Philipp Proksch
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| | - David Johannes Kerschbaumer
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Ernest Mayr
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Marija Zunabovic-Pichler
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Konrad J Domig
- Laboratory of Food Microbiology and Hygiene, Institute of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Reinhard Perfler
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
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28
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Props R, Rubbens P, Besmer M, Buysschaert B, Sigrist J, Weilenmann H, Waegeman W, Boon N, Hammes F. Detection of microbial disturbances in a drinking water microbial community through continuous acquisition and advanced analysis of flow cytometry data. WATER RESEARCH 2018; 145:73-82. [PMID: 30121434 DOI: 10.1016/j.watres.2018.08.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 07/26/2018] [Accepted: 08/06/2018] [Indexed: 06/08/2023]
Abstract
Detecting disturbances in microbial communities is an important aspect of managing natural and engineered microbial communities. Here, we implemented a custom-built continuous staining device in combination with real-time flow cytometry (RT-FCM) data acquisition, which, combined with advanced FCM fingerprinting methods, presents a powerful new approach to track and quantify disturbances in aquatic microbial communities. Through this new approach we were able to resolve various natural community and single-species microbial contaminations in a flow-through drinking water reactor. Next to conventional FCM metrics, we applied metrics from a recently developed fingerprinting technique in order to gain additional insight into the microbial dynamics during these contamination events. Importantly, we found that multiple community FCM metrics based on different statistical approaches were required to fully characterize all contaminations. Furthermore we found that for accurate cell concentration measurements and accurate inference from the FCM metrics (coefficient of variation ≤ 5%), at least 1000 cells should be measured, which makes the achievable temporal resolution a function of the prevalent bacterial concentration in the system-of-interest. The integrated RT-FCM acquisition and analysis approach presented herein provides a considerable improvement in the temporal resolution by which microbial disturbances can be observed and simultaneously provides a multi-faceted toolset to characterize such disturbances.
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Affiliation(s)
- Ruben Props
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Peter Rubbens
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Michael Besmer
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Ueberlandstrasse 133, CH-8600, Duebendorf, Switzerland; Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
| | - Benjamin Buysschaert
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Jurg Sigrist
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Ueberlandstrasse 133, CH-8600, Duebendorf, Switzerland
| | - Hansueli Weilenmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Ueberlandstrasse 133, CH-8600, Duebendorf, Switzerland
| | - Willem Waegeman
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Frederik Hammes
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Ueberlandstrasse 133, CH-8600, Duebendorf, Switzerland.
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29
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Bruno A, Sandionigi A, Bernasconi M, Panio A, Labra M, Casiraghi M. Changes in the Drinking Water Microbiome: Effects of Water Treatments Along the Flow of Two Drinking Water Treatment Plants in a Urbanized Area, Milan (Italy). Front Microbiol 2018; 9:2557. [PMID: 30429832 PMCID: PMC6220058 DOI: 10.3389/fmicb.2018.02557] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/08/2018] [Indexed: 11/13/2022] Open
Abstract
While safe and of high quality, drinking water can host an astounding biodiversity of microorganisms, dismantling the belief of its "biological simplicity." During the very few years, we are witnessing an exponential growth in scientific publications, exploring the ecology hidden in drinking water treatment plants (DWTPs) and drinking water distribution system (DWDS). We focused on what happens to the microbial communities from source water (groundwater) throughout the main steps of the potabilization process of a DWTP, located in an urbanized area in Northern Italy. Samples were processed by a stringent water filtration to retain even the smallest environmental bacteria and then analyzed with High-Throughput DNA Sequencing (HTS) techniques. We showed that carbon filters harbored a microbial community seeding and shaping water microbiota downstream, introducing a significant variation on incoming (groundwater) microbial community. Chlorination did not instantly affect the altered microbiota. We were also able to correctly predict (through machine learning analysis) samples belonging to groundwater (overall accuracy was 0.71), but the assignation was not reliable with carbon filter samples, which were incorrectly predicted as chlorination samples. The presence and abundance of specific microorganisms allowed us to hypothesize their role as indicators. In particular, Candidatus Adlerbacteria (Parcubacteria), together with microorganisms belonging to Alphaproteobacteria and Gammaproteobacteria, characterized treated water, but not raw water. An exception, confirming our hypothesis, is given by the samples downstream the filters renewal, which had a composition resembling groundwater. Volatility analysis illustrated how carbon filters represented an ecosystem that is stable over time, probably bearing the environmental conditions that promote the survival and growth of this peculiar microbial community.
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Affiliation(s)
- Antonia Bruno
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Anna Sandionigi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | | | - Antonella Panio
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Massimo Labra
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- Bicocca cEnter of Science and Technology for FOOD, University of Milano-Bicocca, Milan, Italy
| | - Maurizio Casiraghi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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Xu H, Pei H, Jin Y, Ma C, Wang Y, Sun J, Li H. High-throughput sequencing reveals microbial communities in drinking water treatment sludge from six geographically distributed plants, including potentially toxic cyanobacteria and pathogens. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 634:769-779. [PMID: 29653422 DOI: 10.1016/j.scitotenv.2018.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 04/01/2018] [Accepted: 04/01/2018] [Indexed: 05/20/2023]
Abstract
The microbial community structures of drinking water treatment sludge (DWTS) generated for raw water (RW) from different locations and with different source types - including river water, lake water and reservoir water -were investigated using high-throughput sequencing. Because the unit operations in the six DWTPs were similar, community composition in fresh sludge may be determined by microbial community in the corresponding RW. Although Proteobacteria, Cyanobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, and Planctomycetes were the dominant phyla among the six DWTS samples, no single phylum exhibited similar abundance across all the samples, owing to differences in total phosphorus, chemical oxygen demand, Al, Fe, and chloride in RW. Three genera of potentially toxic cyanobacteria (Planktothrix, Microcystis and Cylindrospermopsis), and four potential pathogens (Escherichia coli, Bacteroides ovatus, Prevotella copri and Rickettsia) were found in sludge samples. Because proliferation of potentially toxic cyanobacteria and Rickettsia in RW was mainly affected by nutrients, while growth of Escherichia coli, Bacteroides ovatus and Prevotella copri in RW may be influenced by Fe, control of nutrients and Fe in RW is essential to decrease toxic cyanobacteria and pathogens in DWTS.
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Affiliation(s)
- Hangzhou Xu
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
| | - Haiyan Pei
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China; Provincial Engineering Center on Environmental Science and Technology, Jinan 250061, China.
| | - Yan Jin
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
| | - Chunxia Ma
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
| | - Yuting Wang
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
| | - Jiongming Sun
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
| | - Hongmin Li
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
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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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32
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Zhang Y, Kitajima M, Whittle AJ, Liu WT. Benefits of Genomic Insights and CRISPR-Cas Signatures to Monitor Potential Pathogens across Drinking Water Production and Distribution Systems. Front Microbiol 2017; 8:2036. [PMID: 29097994 PMCID: PMC5654357 DOI: 10.3389/fmicb.2017.02036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/05/2017] [Indexed: 11/22/2022] Open
Abstract
The occurrence of pathogenic bacteria in drinking water distribution systems (DWDSs) is a major health concern, and our current understanding is mostly related to pathogenic species such as Legionella pneumophila and Mycobacterium avium but not to bacterial species closely related to them. In this study, genomic-based approaches were used to characterize pathogen-related species in relation to their abundance, diversity, potential pathogenicity, genetic exchange, and distribution across an urban drinking water system. Nine draft genomes recovered from 10 metagenomes were identified as Legionella (4 draft genomes), Mycobacterium (3 draft genomes), Parachlamydia (1 draft genome), and Leptospira (1 draft genome). The pathogenicity potential of these genomes was examined by the presence/absence of virulence machinery, including genes belonging to Type III, IV, and VII secretion systems and their effectors. Several virulence factors known to pathogenic species were detected with these retrieved draft genomes except the Leptospira-related genome. Identical clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins (CRISPR-Cas) genetic signatures were observed in two draft genomes recovered at different stages of the studied system, suggesting that the spacers in CRISPR-Cas could potentially be used as a biomarker in the monitoring of Legionella related strains at an evolutionary scale of several years across different drinking water production and distribution systems. Overall, metagenomics approach was an effective and complementary tool of culturing techniques to gain insights into the pathogenic characteristics and the CRISPR-Cas signatures of pathogen-related species in DWDSs.
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Affiliation(s)
- Ya Zhang
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Andrew J Whittle
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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