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Toribio-Avedillo D, Gómez-Gómez C, Sala-Comorera L, Galofré B, Muniesa M. Adapted methods for monitoring influenza virus and respiratory syncytial virus in sludge and wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170636. [PMID: 38331285 DOI: 10.1016/j.scitotenv.2024.170636] [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: 11/30/2023] [Revised: 01/10/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
Wastewater-based surveillance constitutes a valuable methodology for the continuous monitoring of viral circulation, with the capacity to function as an early warning system. It holds particular significance in scenarios where respiratory viruses exhibit overlapping clinical presentations, as occurs with SARS-CoV-2, influenza virus (IV), and respiratory syncytial virus (RSV), and allows seasonal virus outbreaks to be distinguished from COVID-19 peaks. Furthermore, sewage sludge, given it harbors concentrated human waste from a large population, serves as a substantial reservoir for pathogen detection. To effectively integrate wastewater-based epidemiology into infectious disease surveillance, the detection methods employed in wastewater samples must be adapted to the distinct characteristics of sludge matrices. In this study, we adapted and applied protocols for the detection of IV and RSV in sewage sludge, comparing their performance with the results obtained in wastewater. To assess the efficiency of these protocols, sludge and wastewater samples were spiked with IV and RSV RNA, either free or incorporated in lentiviral particles. Samples were concentrated using the aluminum hydroxide adsorption-precipitation method before viral RNA extraction. Absolute virus quantification was carried out by RT-qPCR, including an internal control to monitor potential inhibitory factors. Recovery efficiencies for both free IV and RSV RNA were 60 % in sludge, and 75 % and 71 % respectively in wastewater, whereas the values for IV and RSV RNA in lentiviral particles were 16 % and 10 % in sludge and 21 % and 17 % in wastewater respectively. Additionally, the protocol enabled the quantification of naturally occurring IV and RSV in wastewater and sludge samples collected from two wastewater treatment plants during the winter months, thus affirming the efficacy of the employed methodologies.
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Affiliation(s)
- Daniel Toribio-Avedillo
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643 Annex, Floor 0, E-08028 Barcelona, Spain
| | - Clara Gómez-Gómez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643 Annex, Floor 0, E-08028 Barcelona, Spain
| | - Laura Sala-Comorera
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643 Annex, Floor 0, E-08028 Barcelona, Spain
| | - Belén Galofré
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain
| | - Maite Muniesa
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643 Annex, Floor 0, E-08028 Barcelona, Spain.
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2
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Lami R, Urios L, Molmeret M, Grimaud R. Quorum sensing in biofilms: a key mechanism to target in ecotoxicological studies. Crit Rev Microbiol 2023; 49:786-804. [PMID: 36334083 DOI: 10.1080/1040841x.2022.2142089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 10/18/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
Our environment is heavily contaminated by anthropogenic compounds, and this issue constitutes a significant threat to all life forms, including biofilm-forming microorganisms. Cell-cell interactions shape microbial community structures and functions, and pollutants that affect intercellular communications impact biofilm functions and ecological roles. There is a growing interest in environmental science fields for evaluating how anthropogenic pollutants impact cell-cell interactions. In this review, we synthesize existing literature that evaluates the impacts of quorum sensing (QS), which is a widespread density-dependent communication system occurring within many bacterial groups forming biofilms. First, we examine the perturbating effects of environmental contaminants on QS circuits; and our findings reveal that QS is an essential yet underexplored mechanism affected by pollutants. Second, our work highlights that QS is an unsuspected and key resistance mechanism that assists bacteria in dealing with environmental contamination (caused by metals or organic pollutants) and that favors bacterial growth in unfavourable environments. We emphasize the value of considering QS a critical mechanism for monitoring microbial responses in ecotoxicology. Ultimately, we determine that QS circuits constitute promising targets for innovative biotechnological approaches with major perspectives for applications in the field of environmental science.
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Affiliation(s)
- Raphaël Lami
- Sorbonne Université, USR3579, LBBM, Observatoire Océanologique, Banyuls-sur-Mer, France
- Centre National de la Recherche Scientifique, USR 3579, LBBM, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Laurent Urios
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Maëlle Molmeret
- Université de Toulon, Laboratoire MAPIEM, EA4323, Avenue de l'université, BP 20132, La Garde Cedex, France
| | - Régis Grimaud
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
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3
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Fan X, Ji M, Mu D, Zeng X, Tian Z, Sun K, Gao R, Liu Y, He X, Wu L, Li Q. Global diversity and biogeography of DNA viral communities in activated sludge systems. MICROBIOME 2023; 11:234. [PMID: 37865788 PMCID: PMC10589946 DOI: 10.1186/s40168-023-01672-1] [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: 05/12/2023] [Accepted: 09/21/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Activated sludge (AS) systems in wastewater treatment plants (WWTPs) harbor enormous viruses that regulate microbial metabolism and nutrient cycling, significantly influencing the stability of AS systems. However, our knowledge about the diversity of viral taxonomic groups and functional traits in global AS systems is still limited. To address this gap, we investigated the global diversity and biogeography of DNA viral communities in AS systems using 85,114 viral operational taxonomic units (vOTUs) recovered from 144 AS samples collected across 54 WWTPs from 13 different countries. RESULTS AS viral communities and their functional traits exhibited distance-decay relationship (DDR) at the global scale and latitudinal diversity gradient (LDG) from equator to mid-latitude. Furthermore, it was observed that AS viral community and functional gene structures were largely driven by the geographic factors and wastewater types, of which the geographic factors were more important. Carrying and disseminating auxiliary metabolic genes (AMGs) associated with the degradation of polysaccharides, sulfate reduction, denitrification, and organic phosphoester hydrolysis, as well as the lysis of crucial functional microbes that govern biogeochemical cycles were two major ways by which viruses could regulate AS functions. It was worth noting that our study revealed a high abundance of antibiotic resistance genes (ARGs) in viral genomes, suggesting that viruses were key reservoirs of ARGs in AS systems. CONCLUSIONS Our results demonstrated the highly diverse taxonomic groups and functional traits of viruses in AS systems. Viral lysis of host microbes and virus-mediated HGT can regulate the biogeochemical and nutrient cycles, thus affecting the performance of AS systems. These findings provide important insights into the viral diversity, function, and ecology in AS systems on a global scale. Video Abstract.
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Affiliation(s)
- Xiangyu Fan
- School of Biological Science and Technology, University of Jinan, Jinan, Shandong Province, China.
- Artificial Intelligence Institute, University of Jinan, Jinan, Shandong Province, China.
| | - Mengzhi Ji
- School of Biological Science and Technology, University of Jinan, Jinan, Shandong Province, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong Province, China
| | - Dashuai Mu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong Province, China
- Marine College, Shandong University, Weihai, Shandong Province, China
| | - Xianghe Zeng
- School of Biological Science and Technology, University of Jinan, Jinan, Shandong Province, China
| | - Zhen Tian
- Artificial Intelligence Institute, University of Jinan, Jinan, Shandong Province, China
| | - Kaili Sun
- School of Biological Science and Technology, University of Jinan, Jinan, Shandong Province, China
| | - Rongfeng Gao
- School of Biological Science and Technology, University of Jinan, Jinan, Shandong Province, China
| | - Yang Liu
- Artificial Intelligence Institute, University of Jinan, Jinan, Shandong Province, China
| | - Xinyuan He
- Artificial Intelligence Institute, University of Jinan, Jinan, Shandong Province, China
| | - Linwei Wu
- Institute of Ecology, Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, China.
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, Shandong Province, China.
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Ariyadasa S, Taylor W, Weaver L, McGill E, Billington C, Pattis I. Nonbacterial Microflora in Wastewater Treatment Plants: an Underappreciated Potential Source of Pathogens. Microbiol Spectr 2023; 11:e0048123. [PMID: 37222623 PMCID: PMC10269893 DOI: 10.1128/spectrum.00481-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023] Open
Abstract
Wastewater treatment plants (WWTPs) receive and treat large volumes of domestic, industrial, and urban wastewater containing pathogenic and nonpathogenic microorganisms, chemical compounds, heavy metals, and other potentially hazardous substances. WWTPs play an essential role in preserving human, animal, and environmental health by removing many of these toxic and infectious agents, particularly biological hazards. Wastewater contains complex consortiums of bacterial, viral, archaeal, and eukaryotic species, and while bacteria in WWTP have been extensively studied, the temporal and spatial distribution of nonbacterial microflora (viruses, archaea, and eukaryotes) is less understood. In this study, we analyzed the viral, archaeal, and eukaryotic microflora in wastewater throughout a treatment plant (raw influent, effluent, oxidation pond water, and oxidation pond sediment) in Aotearoa (New Zealand) using Illumina shotgun metagenomic sequencing. Our results suggest a similar trend across many taxa, with an increase in relative abundance in oxidation pond samples compared to influent and effluent samples, except for archaea, which had the opposite trend. Additionally, some microbial families, such as Podoviridae bacteriophages and Apicomplexa alveolates, appeared largely unaffected by the treatment process, with their relative abundance remaining stable throughout. Several groups encompassing pathogenic species, such as Leishmania, Plasmodium, Toxoplasma, Apicomplexa, Cryptococcus, Botrytis, and Ustilago, were identified. If present, these potentially pathogenic species could be a threat to human and animal health and agricultural productivity; therefore, further investigation is warranted. These nonbacterial pathogens should be considered when assessing the potential for vector transmission, distribution of biosolids to land, and discharge of treated wastewater to waterways or land. IMPORTANCE Nonbacterial microflora in wastewater remain understudied compared to their bacterial counterparts despite their importance in the wastewater treatment process. In this study, we report the temporal and spatial distributions of DNA viruses, archaea, protozoa, and fungi in raw wastewater influent, effluent, oxidation pond water, and oxidation pond sediments by using shotgun metagenomic sequencing. Our study indicated the presence of groups of nonbacterial taxa which encompass pathogenic species that may have potential to cause disease in humans, animals, and agricultural crops. We also observed higher alpha diversity in viruses, archaea, and fungi in effluent samples than in influent samples. This suggests that the resident microflora in the wastewater treatment plant may be making a greater contribution to the diversity of taxa observed in wastewater effluent than previously thought. This study provides important insights to better understand the potential human, animal, and environmental health impacts of discharged treated wastewater.
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Affiliation(s)
- Sujani Ariyadasa
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - William Taylor
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Louise Weaver
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Erin McGill
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Craig Billington
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Isabelle Pattis
- Institute of Environmental Science and Research, Christchurch, New Zealand
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5
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Cui H, Wang J, Cai X, Feng K, Xie GJ, Liu BF, Xing D. Chemical Pretreatments and Anaerobic Digestion Shape the Virome and Functional Microbiome in Fecal Sludge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:6008-6020. [PMID: 36996193 DOI: 10.1021/acs.est.2c09587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The decomposition and pathogen inactivation of fecal sludge (FS) are vitally important for safely managing onsite sanitation and protecting public and environmental health. However, the microbiome and virome assemblages in FS after chemical and biological treatments remain unclear. Here, we reported the differences in the solid reduction and microbiomes of FS subjected to potassium ferrate (PF), alkali (ALK), and sodium hypochlorite (NaClO) pretreatments and anaerobic digestion (AD). The PF and NaClO pretreatments enhanced FS hydrolysis and pathogen suppression, respectively; AD suppressed Gram-positive bacteria. Most of the viromes were those of bacteriophages, which were also shaped by chemical pretreatments and AD. Metatranscriptome analysis revealed distinct gene expression patterns between the PF- and ALK-pretreated FS and the subsequent AD. Differentially expressed gene profiles indicated that genes related to biological processes, molecular functions, and transcriptional regulators were upregulated in ALK-AD and PF-AD samples. These findings suggested that the effect of different treatment technologies on the viral diversity, pathogen abundance, and metabolic function of the core microbiome extends beyond FS decomposition and that the use of combined processes would provide possible alternatives for FS management in pandemic emergencies.
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Affiliation(s)
- Han Cui
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jing Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xiaoyu Cai
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Kun Feng
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
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6
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Yuan L, Ju F. Potential Auxiliary Metabolic Capabilities and Activities Reveal Biochemical Impacts of Viruses in Municipal Wastewater Treatment Plants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:5485-5498. [PMID: 36947091 DOI: 10.1021/acs.est.2c07800] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Viruses influence biogeochemical cycles in oceans, freshwater, soil, and human gut through infection and by modulating virocell metabolism through virus-encoded auxiliary metabolic genes (vAMGs). However, the geographical distribution, potential metabolic function, and engineering significance of vAMGs in wastewater treatment plants (WWTPs) remain to be explored. Here, 752 single-contig viral genomes with high confidence, 510 of which belonged to Caudovirales, were recovered from the activated sludge metagenomes of 32 geographically distributed WWTPs. A total of 101 vAMGs involved in various metabolic pathways were identified, the most common of which were the queuosine biosynthesis genes folE, queD, and queE and the sulfur metabolism gene cysH. Phylogenetic analysis and virus-host relationship prediction revealed the probable evolutionary histories of vAMGs involved in carbon (acpP and prsA), nitrogen (amoC), sulfur (cysH), and phosphate (phoH) metabolism, which potentially mediate microbial carbon and nutrient cycling. Notably, 11 of the 38 (28.3%) vAMGs identified in the metagenomes with corresponding metatranscriptomes were transcriptionally expressed, implying an active functional state. This meta-analysis provides the first broad catalog of vAMGs in municipal WWTPs and how they may assist in the basic physiological reactions of their microbial hosts or nutrient cycling in the WWTPs, and therefore, may have important effects on the engineering of wastewater treatment processes.
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Affiliation(s)
- Ling Yuan
- Environmental Science and Engineering Department, Zhejiang University, Hangzhou 310012, Zhejiang, China
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, Zhejiang, China
- Environmental Microbiome and Biotechnology Laboratory (EMBLab), Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou 310030, Zhejiang, China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, Zhejiang, China
- Environmental Microbiome and Biotechnology Laboratory (EMBLab), Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou 310030, Zhejiang, China
- Research Center for Industries of the Future, Westlake University, Hangzhou 310030, Zhejiang, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
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7
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Liu R, Li Z, Han G, Cun S, Hou D, Yu Z, Xue K, Liu X. Microbial density-dependent viral dynamics and low activity of temperate phages in the activated sludge process. WATER RESEARCH 2023; 232:119709. [PMID: 36764107 DOI: 10.1016/j.watres.2023.119709] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/31/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
The ecological behavior of bacteriophages (phages), the most abundant biological entity in wastewater treatment systems, is poorly understood, especially that of temperate phages. Here, the temporal dynamics of lytic and temperate phages in a laboratory-scale activated sludge reactor with a sludge bulking issue was investigated using coupled sludge metagenomic and viromic analyses. The lysogenic fragments (prophages) identified were widely distributed in the reconstructed metagenome-assembled genomes (61.7%, n = 227). However, only 12.3% of the identified prophages experienced lysogenic-lytic switching, and the abundance contribution of prophages to free virus communities was only 0.02-0.3%, indicating low activity of temperate phages. Although the sludge community changed dramatically during reactor operation, no massive prophage induction events were detected. Statistical analyses showed strong correlations between sludge concentration and free virus and temperate phage communities, suggesting microbial density-dependent virus dynamics in the sludge microbiota.
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Affiliation(s)
- Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China; Binzhou Institute of Technology, Weiqiao-UCAS Science and Technology Park, Binzhou City, Shandong Province, China.
| | - Zong Li
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Ganghua Han
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Shujuan Cun
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Deyin Hou
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Xinchun Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China.
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8
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Expansion of Kuravirus-like Phage Sequences within the Past Decade, including Escherichia Phage YF01 from Japan, Prompt the Creation of Three New Genera. Viruses 2023; 15:v15020506. [PMID: 36851720 PMCID: PMC9965538 DOI: 10.3390/v15020506] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Bacteriophages, viruses that infect bacteria, are currently receiving significant attention amid an ever-growing global antibiotic resistance crisis. In tandem, a surge in the availability and affordability of next-generation and third-generation sequencing technologies has driven the deposition of a wealth of phage sequence data. Here, we have isolated a novel Escherichia phage, YF01, from a municipal wastewater treatment plant in Yokohama, Japan. We demonstrate that the YF01 phage shares a high similarity to a collection of thirty-five Escherichia and Shigella phages found in public databases, six of which have been previously classified into the Kuravirus genus by the International Committee on Taxonomy of Viruses (ICTV). Using modern phylogenetic approaches, we demonstrate that an expansion and reshaping of the current six-membered Kuravirus genus is required to accommodate all thirty-six member phages. Ultimately, we propose the creation of three additional genera, Vellorevirus, Jinjuvirus, and Yesanvirus, which will allow a more organized approach to the addition of future Kuravirus-like phages.
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9
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Zhang K, Zhang Y, Deng M, Wang P, Yue X, Wang P, Li W. Monthly dynamics of microbial communities and variation of nitrogen-cycling genes in an industrial-scale expanded granular sludge bed reactor. Front Microbiol 2023; 14:1125709. [PMID: 36876106 PMCID: PMC9978346 DOI: 10.3389/fmicb.2023.1125709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/18/2023] [Indexed: 02/18/2023] Open
Abstract
Introduction The expanded granular sludge bed (EGSB) is a major form of anaerobic digestion system during wastewater treatment. Yet, the dynamics of microbial and viral communities and members functioning in nitrogen cycling along with monthly changing physicochemical properties have not been well elucidated. Methods Here, by collecting the anaerobic activated sludge samples from a continuously operating industrial-scale EGSB reactor, we conducted 16S rRNA gene amplicon sequencing and metagenome sequencing to reveal the microbial community structure and variation with the ever-changing physicochemical properties along within a year. Results We observed a clear monthly variation of microbial community structures, while COD, the ratio of volatile suspended solids (VSS) to total suspended solids (TSS) (VSS/TSS ratio), and temperature were predominant factors in shaping community dissimilarities examined by generalized boosted regression modeling (GBM) analysis. Meanwhile, a significant correlation was found between the changing physicochemical properties and microbial communities (p <0.05). The alpha diversity (Chao1 and Shannon) was significantly higher (p <0.05) in both winter (December, January, and February) and autumn (September, October, and November) with higher organic loading rate (OLR), higher VSS/TSS ratio, and lower temperature, resulting higher biogas production and nutrition removal efficiency. Further, 18 key genes covering nitrate reduction, denitrification, nitrification, and nitrogen fixation pathways were discovered, the total abundance of which was significantly associated with the changing environmental factors (p <0.05). Among these pathways, the dissimilatory nitrate reduction to ammonia (DNRA) and denitrification had the higher abundance contributed by the top highly abundant genes narGH, nrfABCDH, and hcp. The COD, OLR, and temperature were primary factors in affecting DNRA and denitrification by GBM evaluation. Moreover, by metagenome binning, we found the DNRA populations mainly belonged to Proteobacteria, Planctomycetota, and Nitrospirae, while the denitrifying bacteria with complete denitrification performance were all Proteobacteria. Besides, we detected 3,360 non-redundant viral sequences with great novelty, in which Siphoviridae, Podoviridae, and Myoviridae were dominant viral families. Interestingly, viral communities likewise depicted clear monthly variation and had significant associations with the recovered populations (p <0.05). Discussion Our work highlights the monthly variation of microbial and viral communities during the continuous operation of EGSB affected by the predominant changing COD, OLR, and temperature, while DNRA and denitrification pathways dominated in this anaerobic system. The results also provide a theoretical basis for the optimization of the engineered system.
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Affiliation(s)
- Kun Zhang
- School of Eco-environment Technology, Guangdong Industry Polytechnic, Guangzhou, China
| | - Yanling Zhang
- School of Mechanics and Construction Engineering, Jinan University, Guangzhou, China
| | - Maocheng Deng
- School of Food and Bioengineering, Guangdong Industry Polytechnic, Guangzhou, China
| | - Pengcheng Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,China National Electric Apparatus Research Institute Co., Ltd., Guangzhou, China
| | - Xiu Yue
- School of Eco-environment Technology, Guangdong Industry Polytechnic, Guangzhou, China
| | - Pandeng Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wenjun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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10
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Tang X, Fan C, Zeng G, Zhong L, Li C, Ren X, Song B, Liu X. Phage-host interactions: The neglected part of biological wastewater treatment. WATER RESEARCH 2022; 226:119183. [PMID: 36244146 DOI: 10.1016/j.watres.2022.119183] [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: 07/02/2022] [Revised: 08/29/2022] [Accepted: 09/29/2022] [Indexed: 05/25/2023]
Abstract
In wastewater treatment plants (WWTPs), the stable operation of biological wastewater treatment is strongly dependent on the stability of associated microbiota. Bacteriophages (phages), viruses that specifically infect bacteria and archaea, are highly abundant and diverse in WWTPs. Although phages do not have known metabolic functions for themselves, they can shape functional microbiota via various phage-host interactions to impact biological wastewater treatment. However, the developments of phage-host interaction in WWTPs and their impact on biological wastewater treatment are overlooked. Here, we review the current knowledge regarding the phage-host interactions in biological wastewater treatment, mainly focusing on the characteristics of different phage populations, the phage-driven changes in functional microbiota, and the potential driving factors of phage-host interactions. We also discuss the efforts required further to understand and manipulate the phage-host interactions in biological wastewater treatment. Overall, this review advocates more attention to the phage dynamics in WWTPs.
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Affiliation(s)
- Xiang Tang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Changzheng Fan
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China.
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Linrui Zhong
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Chao Li
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China; Nova Skantek (Hunan) Environ Energy Co., Ltd., Changsha 410100, P.R. China
| | - Xiaoya Ren
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Biao Song
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Xigui Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
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11
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Modin O, Fuad N, Abadikhah M, I'Ons D, Ossiansson E, Gustavsson DJ, Edefell E, Suarez C, Persson F, Wilén BM. A relationship between phages and organic carbon in wastewater treatment plant effluents. WATER RESEARCH X 2022; 16:100146. [PMID: 35761925 PMCID: PMC9233278 DOI: 10.1016/j.wroa.2022.100146] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/27/2022] [Accepted: 06/15/2022] [Indexed: 06/10/2023]
Abstract
With stringent effluent requirements and the implementation of new processes for micropollutant removal, it is increasingly important for wastewater treatment plants (WWTPs) to understand the factors affecting effluent quality. Phages (viruses infecting prokaryotes) are abundant in the biological treatment processes. They can contribute to organic carbon in the treated effluent both because they are organic in nature and occur in the effluent and because they cause lysis of microorganisms. Today very little is known about the effects of phages on effluent quality. The goal of this study was, therefore, to determine the relationship between phages and organic carbon in WWTP effluents. We also examined the diversity, taxonomy, and host-association of DNA phages using metagenomics. Effluent samples were collected from four WWTPs treating municipal wastewater. Significant differences in both organic carbon and virus-like particle concentrations were observed between the plants and there was a linear relationship between the two parameters. The phage communities were diverse with many members being taxonomically unclassified. Putative hosts were dominated by bacteria known to be abundant in activated sludge systems such as Comamonadaceae. The composition of phages differed between the WWTPs, suggesting that local conditions shape the communities. Overall, our findings suggest that the abundance and composition of phages are related to effluent quality. Thus, there is a need for further research clarifying the association between phage dynamics and WWTP function.
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Affiliation(s)
- Oskar Modin
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Nafis Fuad
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Department of Civil and Environmental Engineering, University of Connecticut, USA
| | - Marie Abadikhah
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | | | - Elin Ossiansson
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- VA SYD, P.O. Box 191, Malmö SE-2021, Sweden
| | - David J.I. Gustavsson
- VA SYD, P.O. Box 191, Malmö SE-2021, Sweden
- Sweden Water Research, c/o Ideon Science Park, Scheelevägen 15, Lund SE-223 70, Sweden
| | - Ellen Edefell
- Sweden Water Research, c/o Ideon Science Park, Scheelevägen 15, Lund SE-223 70, Sweden
- Department of Chemical Engineering, Lund University, PO Box 124, Lund SE-221 00, Sweden
| | - Carolina Suarez
- Division of Water Resources Engineering, Faculty of Engineering LTH, Lund University, Box 118, Lund SE-221 00, Sweden
| | - Frank Persson
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Britt-Marie Wilén
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
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12
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Petrovski S, Batinovic S, Rose JJ, Seviour RJ. Biological control of problem bacterial populations causing foaming in activated sludge wastewater treatment plants - phage therapy and beyond. Lett Appl Microbiol 2022; 75:776-784. [PMID: 35598184 DOI: 10.1111/lam.13742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022]
Abstract
The production of a stable foam on the surfaces of reactors is a global operating problem in activated sludge plants. In many cases these foams are stabilized by hydrophobic members of the Mycolata, a group of Actinobacteria whose outer membranes contains long chain hydroxylated mycolic acids. There is currently no single strategy which works for all foams. One attractive approach is to use lytic bacteriophages specific for the foam stabilizing Mycolata population. Such phages are present in activated sludge mixed liquor, and can be recovered readily from it. However, no phage has been recovered which lyses Gordonia amarae and Gordonia pseudoamarae, probably the most common foaming Mycolata members. Whole genome sequencing revealed that both G. amarae and G. pseudoamarae from plants around the world are particularly well endowed with genes encoding anti-viral defence mechanisms. However, both these populations were lysed rapidly by a parasitic nanobacterium isolated from a plant in Australia. This organism, a member of the Saccharibacteria was also effective against many other Mycolata, thus providing a potential agent for control of foams stabilized by them.
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Affiliation(s)
- Steve Petrovski
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, 3086, Victoria, Australia
| | - Steven Batinovic
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, 3086, Victoria, Australia
| | - Jayson Ja Rose
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, 3086, Victoria, Australia
| | - Robert J Seviour
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, 3086, Victoria, Australia
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13
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Abdeldayem OM, Dabbish AM, Habashy MM, Mostafa MK, Elhefnawy M, Amin L, Al-Sakkari EG, Ragab A, Rene ER. Viral outbreaks detection and surveillance using wastewater-based epidemiology, viral air sampling, and machine learning techniques: A comprehensive review and outlook. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 803:149834. [PMID: 34525746 PMCID: PMC8379898 DOI: 10.1016/j.scitotenv.2021.149834] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/05/2021] [Accepted: 08/18/2021] [Indexed: 05/06/2023]
Abstract
A viral outbreak is a global challenge that affects public health and safety. The coronavirus disease 2019 (COVID-19) has been spreading globally, affecting millions of people worldwide, and led to significant loss of lives and deterioration of the global economy. The current adverse effects caused by the COVID-19 pandemic demands finding new detection methods for future viral outbreaks. The environment's transmission pathways include and are not limited to air, surface water, and wastewater environments. The wastewater surveillance, known as wastewater-based epidemiology (WBE), can potentially monitor viral outbreaks and provide a complementary clinical testing method. Another investigated outbreak surveillance technique that has not been yet implemented in a sufficient number of studies is the surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in the air. Artificial intelligence (AI) and its related machine learning (ML) and deep learning (DL) technologies are currently emerging techniques for detecting viral outbreaks using global data. To date, there are no reports that illustrate the potential of using WBE with AI to detect viral outbreaks. This study investigates the transmission pathways of SARS-CoV-2 in the environment and provides current updates on the surveillance of viral outbreaks using WBE, viral air sampling, and AI. It also proposes a novel framework based on an ensemble of ML and DL algorithms to provide a beneficial supportive tool for decision-makers. The framework exploits available data from reliable sources to discover meaningful insights and knowledge that allows researchers and practitioners to build efficient methods and protocols that accurately monitor and detect viral outbreaks. The proposed framework could provide early detection of viruses, forecast risk maps and vulnerable areas, and estimate the number of infected citizens.
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Affiliation(s)
- Omar M Abdeldayem
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands.
| | - Areeg M Dabbish
- Biotechnology Graduate Program, Biology Department, School of Science and Engineering, The American University in Cairo, New Cairo 11835, Egypt
| | - Mahmoud M Habashy
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands
| | - Mohamed K Mostafa
- Faculty of Engineering and Technology, Badr University in Cairo (BUC), Cairo 11829, Egypt
| | - Mohamed Elhefnawy
- CanmetENERGY, 1615 Lionel-Boulet Blvd, P.O. Box 4800, Varennes, Québec J3X 1P7, Canada; Department of Mathematics and Industrial Engineering, Polytechnique Montréal 2500 Chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada
| | - Lobna Amin
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands; Department of Built Environment, Aalto University, PO Box 15200, FI-00076, Aalto, Finland
| | - Eslam G Al-Sakkari
- Chemical Engineering Department, Cairo University, Cairo University Road, 12613 Giza, Egypt
| | - Ahmed Ragab
- CanmetENERGY, 1615 Lionel-Boulet Blvd, P.O. Box 4800, Varennes, Québec J3X 1P7, Canada; Department of Mathematics and Industrial Engineering, Polytechnique Montréal 2500 Chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada; Faculty of Electronic Engineering, Menoufia University, 32952, Menouf, Egypt
| | - Eldon R Rene
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands
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14
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Runa V, Wenk J, Bengtsson S, Jones BV, Lanham AB. Bacteriophages in Biological Wastewater Treatment Systems: Occurrence, Characterization, and Function. Front Microbiol 2021; 12:730071. [PMID: 34803947 PMCID: PMC8600467 DOI: 10.3389/fmicb.2021.730071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/25/2021] [Indexed: 12/20/2022] Open
Abstract
Phage bacteria interactions can affect structure, dynamics, and function of microbial communities. In the context of biological wastewater treatment (BWT), the presence of phages can alter the efficiency of the treatment process and influence the quality of the treated effluent. The active role of phages in BWT has been demonstrated, but many questions remain unanswered regarding the diversity of phages in these engineered environments, the dynamics of infection, the determination of bacterial hosts, and the impact of their activity in full-scale processes. A deeper understanding of the phage ecology in BWT can lead the improvement of process monitoring and control, promote higher influent quality, and potentiate the use of phages as biocontrol agents. In this review, we highlight suitable methods for studying phages in wastewater adapted from other research fields, provide a critical overview on the current state of knowledge on the effect of phages on structure and function of BWT bacterial communities, and highlight gaps, opportunities, and priority questions to be addressed in future research.
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Affiliation(s)
- Viviane Runa
- Centre for Sustainable and Circular Technologies, University of Bath, Bath, United Kingdom.,Department of Chemical Engineering, University of Bath, Bath, United Kingdom
| | - Jannis Wenk
- Department of Chemical Engineering, University of Bath, Bath, United Kingdom.,Water Innovation and Research Centre, University of Bath, Bath, United Kingdom
| | | | - Brian V Jones
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Ana B Lanham
- Centre for Sustainable and Circular Technologies, University of Bath, Bath, United Kingdom.,Department of Chemical Engineering, University of Bath, Bath, United Kingdom.,Water Innovation and Research Centre, University of Bath, Bath, United Kingdom
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15
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Chen Y, Wang Y, Paez-Espino D, Polz MF, Zhang T. Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants. Nat Commun 2021; 12:5398. [PMID: 34518545 PMCID: PMC8438041 DOI: 10.1038/s41467-021-25678-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/24/2021] [Indexed: 11/09/2022] Open
Abstract
As one of the largest biotechnological applications, activated sludge (AS) systems in wastewater treatment plants (WWTPs) harbor enormous viruses, with 10-1,000-fold higher concentrations than in natural environments. However, the compositional variation and host-connections of AS viruses remain poorly explored. Here, we report a catalogue of ~50,000 prokaryotic viruses from six WWTPs, increasing the number of described viral species of AS by 23-fold, and showing the very high viral diversity which is largely unknown (98.4-99.6% of total viral contigs). Most viral genera are represented in more than one AS system with 53 identified across all. Viral infection widely spans 8 archaeal and 58 bacterial phyla, linking viruses with aerobic/anaerobic heterotrophs, and other functional microorganisms controlling nitrogen/phosphorous removal. Notably, Mycobacterium, notorious for causing AS foaming, is associated with 402 viral genera. Our findings expand the current AS virus catalogue and provide reference for the phage treatment to control undesired microorganisms in WWTPs.
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Affiliation(s)
- Yiqiang Chen
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - David Paez-Espino
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China.
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16
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Du B, Wang Q, Yang Q, Wang R, Yuan W, Yan L. Responses of bacterial and bacteriophage communities to long-term exposure to antimicrobial agents in wastewater treatment systems. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125486. [PMID: 33676244 DOI: 10.1016/j.jhazmat.2021.125486] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/05/2021] [Accepted: 02/19/2021] [Indexed: 06/12/2023]
Abstract
The occurrence of antibacterial agents has received increasing concern due to their possible threats to human health. However, the effects of antibacterial residues on the evolution and dynamics between bacteria and bacteriophages in wastewater treatment systems have seldom been researched. Especially for phages, little is known about their response to antimicrobial exposure. In this study, two identical anoxic-aerobic wastewater treatment systems were established to evaluate the responses of bacterial and phage communities to long-term exposure to antimicrobial agents. The results indicated simultaneous exposure to combined antimicrobials significantly inhibited (p < 0.05) the abundance of phages and bacteria. Metagenomic sequencing analysis indicated the community of bacteria and phages changed greatly at the genus level due to combined antibacterial exposure. Additionally, long-term exposure to antimicrobial agents promoted the attachment of receptor-binding protein genes to Klebsiella, Escherichia and Salmonella (which were all members of Enterobacteriaceae). Compared to that in the control system, the numbers of receptor-binding protein genes on their possible phages (such as Lambdalikevirus and P2likevirus) were also obviously higher when the microorganisms were exposed to antimicrobials. The results are helpful to understanding the microbial communities and tracking the relationship of phage-bacterial host systems, especially under the pressure of antimicrobial exposure.
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Affiliation(s)
- Bingbing Du
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu 476000, China
| | - Qiang Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang 453007, China
| | - Qingxiang Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang 453007, China.
| | - Ruifei Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang 453007, China
| | - Wei Yuan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Luyu Yan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
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17
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Bacteriophage ecology in biological wastewater treatment systems. Appl Microbiol Biotechnol 2021; 105:5299-5307. [PMID: 34181033 DOI: 10.1007/s00253-021-11414-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/12/2022]
Abstract
Biological wastewater treatment (BWT) is currently the most widely applied approach for treating wastewater. The performance of BWT systems depends on the complex microbial communities they support. Although bacteriophages (phages), which are the viruses that infect prokaryotes, are recognized as the most abundant life entities, understanding of their ecological roles in BWT systems remains limited. Here, we review recent progress in phage-associated researches in BWT systems, including the interactions between phage and host, polyvalent phages, the influence of phage activity on BWT performance, and the potential applications of phage-based control for sludge bulking/foaming and pathogens. The challenges and perspectives of phage ecology are also outlined, which are expected to provide implications for future research and applications.Key points• Phage-host interactions in BWT systems are summarized• Impacts of phage activities on BWT performance• Potential applications of phages in BWT systems.
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18
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Park DS, Park JH. Characteristics of Bacteriophage Isolates and Expression of Shiga Toxin Genes Transferred to Non Shiga Toxin-Producing E. coli by Transduction. J Microbiol Biotechnol 2021; 31:710-716. [PMID: 33782222 PMCID: PMC9705938 DOI: 10.4014/jmb.2102.02040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 12/15/2022]
Abstract
A risk analysis of Shiga toxin (Stx)-encoding bacteriophage was carried out by confirming the transduction phage to non-Stx-producing Escherichia coli (STEC) and subsequent expression of the Shiga toxin genes. The virulence factor stx1 was identified in five phages, and both stx1 and stx2 were found in four phages from a total of 19 phage isolates with seven non-O157 STEC strains. The four phages, designated as φNOEC41, φNOEC46, φNOEC47, and φNOEC49, belonged morphologically to the Myoviridae family. The stabilities of these phages to temperature, pH, ethanol, and NaClO were high with some variabilities among the phages. The infection of five non-STEC strains by nine Stx-encoding phages occurred at a rate of approximately 40%. Non-STEC strains were transduced by Stx-encoding phage to become lysogenic strains, and seven convertant strains had stx1 and/or stx2 genes. Only the stx1 gene was transferred to the receptor strains without any deletion. Gene expression of a convertant having both stx1 and stx2 genes was confirmed to be up to 32 times higher for Stx1 in 6% NaCl osmotic media and twice for Stx2 in 4% NaCl media, compared with expression in low-salt environments. Therefore, a new risk might arise from the transfer of pathogenic genes from Stx-encoding phages to otherwise harmless hosts. Without adequate sterilization of food exposed to various environments, there is a possibility that the toxicity of the phages might increase.
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Affiliation(s)
- Da-Som Park
- Department of Food Science and Biotechnology, College of BioNano Technology, Gachon University, Seongnam 13120, Republic of Korea
| | - Jong-Hyun Park
- Department of Food Science and Biotechnology, College of BioNano Technology, Gachon University, Seongnam 13120, Republic of Korea,Corresponding author Phone: +82-31-750-5523 Fax: +82-31-750-5283 E-mail:
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19
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Bar-Or I, Yaniv K, Shagan M, Ozer E, Weil M, Indenbaum V, Elul M, Erster O, Mendelson E, Mannasse B, Shirazi R, Kramarsky-Winter E, Nir O, Abu-Ali H, Ronen Z, Rinott E, Lewis YE, Friedler E, Bitkover E, Paitan Y, Berchenko Y, Kushmaro A. Regressing SARS-CoV-2 Sewage Measurements Onto COVID-19 Burden in the Population: A Proof-of-Concept for Quantitative Environmental Surveillance. Front Public Health 2021. [PMID: 35047467 DOI: 10.1101/2020.04.26.20073569] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus, a member of the coronavirus family of respiratory viruses that includes severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and the Middle East respiratory syndrome (MERS). It has had an acute and dramatic impact on health care systems, economies, and societies of affected countries during the past 8 months. Widespread testing and tracing efforts are being employed in many countries in attempts to contain and mitigate this pandemic. Recent data has indicated that fecal shedding of SARS-CoV-2 is common and that the virus RNA can be detected in wastewater. This indicates that wastewater monitoring may provide a potentially efficient tool for the epidemiological surveillance of SARS-CoV-2 infection in large populations at relevant scales. In particular, this provides important means of (i) estimating the extent of outbreaks and their spatial distributions, based primarily on in-sewer measurements, (ii) managing the early-warning system quantitatively and efficiently, and (iii) verifying disease elimination. Here we report different virus concentration methods using polyethylene glycol (PEG), alum, or filtration techniques as well as different RNA extraction methodologies, providing important insights regarding the detection of SARS-CoV-2 RNA in sewage. Virus RNA particles were detected in wastewater in several geographic locations in Israel. In addition, a correlation of virus RNA concentration to morbidity was detected in Bnei-Barak city during April 2020. This study presents a proof of concept for the use of direct raw sewage-associated virus data, during the pandemic in the country as a potential epidemiological tool.
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Affiliation(s)
- Itay Bar-Or
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Karin Yaniv
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Marilou Shagan
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Eden Ozer
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Merav Weil
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Victoria Indenbaum
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Michal Elul
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Oran Erster
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Ella Mendelson
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Batya Mannasse
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Rachel Shirazi
- Central Virology Lab, Ministry of Health, Sheba Medical Center, Jerusalem, Israel
| | - Esti Kramarsky-Winter
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Oded Nir
- Zuckerberg Institute for Water Research (ZIWR), Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker, Israel
| | - Hala Abu-Ali
- Zuckerberg Institute for Water Research (ZIWR), Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker, Israel
| | - Zeev Ronen
- Zuckerberg Institute for Water Research (ZIWR), Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker, Israel
| | - Ehud Rinott
- Maccabi Healthcare Services, Tel-Aviv, Israel
| | - Yair E Lewis
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Eran Friedler
- Faculty of Civil and Environmental Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Eden Bitkover
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Yossi Paitan
- Clinical Microbiology Laboratory, Meir Medical Center, Kfar Saba, Israel
| | - Yakir Berchenko
- Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The Ilse Katz Center for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
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20
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Corpuz MVA, Buonerba A, Vigliotta G, Zarra T, Ballesteros F, Campiglia P, Belgiorno V, Korshin G, Naddeo V. Viruses in wastewater: occurrence, abundance and detection methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 745:140910. [PMID: 32758747 PMCID: PMC7368910 DOI: 10.1016/j.scitotenv.2020.140910] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 04/14/2023]
Abstract
This paper presents an updated and comprehensive review on the different methods used for detection and quantification of viruses in wastewater treatment systems. The analysis of viability of viruses in wastewater and sludge is another thrust of this review. Recent studies have mostly focused on determining the abundance and diversity of viruses in wastewater influents, in samples from primary, secondary, and tertiary treatment stages, and in final effluents. A few studies have also examined the occurrence and diversity of viruses in raw and digested sludge samples. Recent efforts to improve efficiency of virus detection and quantification methods in the complex wastewater and sludge matrices are highlighted in this review. A summary and a detailed comparison of the pre-treatment methods that have been utilized for wastewater and sludge samples are also presented. The role of metagenomics or sequencing analysis in monitoring wastewater systems to predict disease outbreaks, to conduct public health surveillance, to assess the efficiency of existing treatment systems in virus removal, and to re-evaluate current regulations regarding pathogenic viruses in wastewater is discussed in this paper. Challenges and future perspectives in the detection of viruses, including emerging and newly emerged viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), in wastewater systems are discussed in this review.
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Affiliation(s)
- Mary Vermi Aizza Corpuz
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines.
| | - Antonio Buonerba
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| | - Giovanni Vigliotta
- Laboratory of Microbiology, University of Salerno, 84084 Fisciano, Italy.
| | - Tiziano Zarra
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| | - Florencio Ballesteros
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines; Department of Chemical Engineering, College of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines.
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy.
| | - Vincenzo Belgiorno
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| | - Gregory Korshin
- Department of Civil and Environmental Engineering, University of Washington, Box 352700, Seattle, WA 98105-2700, United States.
| | - Vincenzo Naddeo
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
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21
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de Leeuw M, Baron M, Ben David O, Kushmaro A. Molecular Insights into Bacteriophage Evolution toward Its Host. Viruses 2020; 12:E1132. [PMID: 33036277 PMCID: PMC7599783 DOI: 10.3390/v12101132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages (phages), viruses that infect bacteria, are considered to be highly host-specific. To add to the knowledge about the evolution and development of bacteriophage speciation toward its host, we conducted a 21-day experiment with the broad host-range bacteriophage Aquamicrobium phage P14. We incubated the phage, which was previously isolated and enriched with the Alphaproteobacteria Aquamicrobium H14, with the Betaproteobacteria Alcaligenaceae H5. During the experiment, we observed an increase in the phage's predation efficacy towards Alcaligenaceae H5. Furthermore, genome analysis and the comparison of the bacteriophage's whole genome indicated that rather than being scattered evenly along the genome, mutations occur in specific regions. In total, 67% of the mutations with a frequency higher than 30% were located in genes that encode tail proteins, which are essential for host recognition and attachment. As control, we incubated the phage with the Alphaproteobacteria Aquamicrobium H8. In both experiments, most of the mutations appeared in the gene encoding the tail fiber protein. However, mutations in the gene encoding the tail tubular protein B were only observed when the phage was incubated with Alcaligenaceae H5. This highlights the phage's tail as a key player in its adaptation to different hosts. We conclude that mutations in the phage's genome were mainly located in tail-related regions. Further investigation is needed to fully characterize the adaptation mechanisms of the Aquamicrobium phage P14.
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Affiliation(s)
- Marina de Leeuw
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 8410501, Israel; (M.d.L.); (M.B.); (O.B.D.)
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Maayan Baron
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 8410501, Israel; (M.d.L.); (M.B.); (O.B.D.)
| | - Oshrit Ben David
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 8410501, Israel; (M.d.L.); (M.B.); (O.B.D.)
| | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 8410501, Israel; (M.d.L.); (M.B.); (O.B.D.)
- The Ilse Katz Center for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be’er Sheva 8410501, Israel
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22
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Michael-Kordatou I, Karaolia P, Fatta-Kassinos D. Sewage analysis as a tool for the COVID-19 pandemic response and management: the urgent need for optimised protocols for SARS-CoV-2 detection and quantification. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2020. [PMID: 32834990 DOI: 10.1016/j.jece:2020.104306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
COVID-19 is an ongoing global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of July 29th 2020, more than 16,6 million cases have been reported in more than 188 countries/territories, leading to more than 659000 deaths. One of the main challenges facing health authorities has been testing for the virus on a sufficiently comprehensive scale. The pandemic has been an impetus for the wastewater community as it has inspired scientists to look to wastewater to help fill in the gap of measuring the prevalence of SARS-CoV-2 within a given community. Testing the wastewater may serve as an early warning system allowing timely interventions. Although viral shedding varies among individuals and over the course of their infection, the sewage system can blend these variations into an average that represents the wider studied community. The urgent need has led to a lack of coherent reporting of data regarding the analysis, as these huge and remarkable efforts by the wastewater scientific community were made in a very short time. Important information on the analytical approach is often lacking, while there is still no optimisation of the methodology, including sampling, sample storage and concentration, RNA extraction and detection/quantification. This review aims at identifying the main issues for consideration, relating to the development of validated methodological protocols for the virus quantitative analysis in wastewater. Their inclusion will enable the methodological optimisation of SARS-CoV-2 wastewater analyses, transforming the wastewater infrastructure into a source of useful information for the health sector.
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Affiliation(s)
- I Michael-Kordatou
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, CY-1678, Nicosia, Cyprus
| | - P Karaolia
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, CY-1678, Nicosia, Cyprus
| | - D Fatta-Kassinos
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, CY-1678, Nicosia, Cyprus
- Department of Civil and Environmental Engineering, University of Cyprus, P.O. Box 20537, CY-1678, Nicosia, Cyprus
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23
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Michael-Kordatou I, Karaolia P, Fatta-Kassinos D. Sewage analysis as a tool for the COVID-19 pandemic response and management: the urgent need for optimised protocols for SARS-CoV-2 detection and quantification. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2020; 8:104306. [PMID: 32834990 PMCID: PMC7384408 DOI: 10.1016/j.jece.2020.104306] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 05/02/2023]
Abstract
COVID-19 is an ongoing global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of July 29th 2020, more than 16,6 million cases have been reported in more than 188 countries/territories, leading to more than 659000 deaths. One of the main challenges facing health authorities has been testing for the virus on a sufficiently comprehensive scale. The pandemic has been an impetus for the wastewater community as it has inspired scientists to look to wastewater to help fill in the gap of measuring the prevalence of SARS-CoV-2 within a given community. Testing the wastewater may serve as an early warning system allowing timely interventions. Although viral shedding varies among individuals and over the course of their infection, the sewage system can blend these variations into an average that represents the wider studied community. The urgent need has led to a lack of coherent reporting of data regarding the analysis, as these huge and remarkable efforts by the wastewater scientific community were made in a very short time. Important information on the analytical approach is often lacking, while there is still no optimisation of the methodology, including sampling, sample storage and concentration, RNA extraction and detection/quantification. This review aims at identifying the main issues for consideration, relating to the development of validated methodological protocols for the virus quantitative analysis in wastewater. Their inclusion will enable the methodological optimisation of SARS-CoV-2 wastewater analyses, transforming the wastewater infrastructure into a source of useful information for the health sector.
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Affiliation(s)
- I Michael-Kordatou
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, CY-1678, Nicosia, Cyprus
| | - P Karaolia
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, CY-1678, Nicosia, Cyprus
| | - D Fatta-Kassinos
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, CY-1678, Nicosia, Cyprus
- Department of Civil and Environmental Engineering, University of Cyprus, P.O. Box 20537, CY-1678, Nicosia, Cyprus
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24
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de Jonge PA, von Meijenfeldt FB, Costa AR, Nobrega FL, Brouns SJ, Dutilh BE. Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts. iScience 2020; 23:101439. [PMID: 32823052 PMCID: PMC7452251 DOI: 10.1016/j.isci.2020.101439] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/23/2020] [Accepted: 08/03/2020] [Indexed: 01/08/2023] Open
Abstract
An important viromics challenge is associating bacteriophages to hosts. To address this, we developed adsorption sequencing (AdsorpSeq), a readily implementable method to measure phages that are preferentially adsorbed to specific host cell envelopes. AdsorpSeq thus captures the key initial infection cycle step. Phages are added to cell envelopes, adsorbed phages are isolated through gel electrophoresis, after which adsorbed phage DNA is sequenced and compared with the full virome. Here, we show that AdsorpSeq allows for separation of phages based on receptor-adsorbing capabilities. Next, we applied AdsorpSeq to identify phages in a wastewater virome that adsorb to cell envelopes of nine bacteria, including important pathogens. We detected 26 adsorbed phages including common and rare members of the virome, a minority being related to previously characterized phages. We conclude that AdsorpSeq is an effective new tool for rapid characterization of environmental phage adsorption, with a proof-of-principle application to Gram-negative host cell envelopes.
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Affiliation(s)
- Patrick A. de Jonge
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, 3584 CH Utrecht, the Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands
| | | | - Ana Rita Costa
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands
| | - Franklin L. Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands
| | - Stan J.J. Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands
| | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, 3584 CH Utrecht, the Netherlands
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25
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Hu XR, Han MF, Wang C, Yang NY, Wang YC, Duan EH, Hsi HC, Deng JG. A short review of bioaerosol emissions from gas bioreactors: Health threats, influencing factors and control technologies. CHEMOSPHERE 2020; 253:126737. [PMID: 32302908 PMCID: PMC7142688 DOI: 10.1016/j.chemosphere.2020.126737] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 04/02/2020] [Accepted: 04/04/2020] [Indexed: 05/20/2023]
Abstract
Bioaerosols have widely been a concern due to their potential harm to human health caused by the carrying and spreading of harmful microorganisms. Biofiltration has been generally used as a green and effective technology for processing VOCs. However, bioaerosols can be emitted into the atmosphere as secondary pollutants from the biofiltration process. This review presents an overview of bioaerosol emissions from gas bioreactors. The mechanism of bioaerosols production and the effect of biofiltration on bioaerosol emissions were analyzed. The results showed that the bioaerosol emission concentrations were generally exceeded 104 CFU m-3, which would damage to human health. Biomass, inlet gas velocity, moisture content, temperature, and some other factors have significant influences on bioaerosol emissions. Moreover, as a result of the analysis done herein, different inactivation technologies and microbial immobilization of bioaerosols were proposed and evaluated as a potential solution for reducing bioaerosols emissions. The purpose of this paper is to make more people realize the importance of controlling the emissions of bioaerosols in the biofiltration process and to make the treatment of VOCs by biotechnology more environmentally friendly. Additionally, the present work intends to increase people's awareness in regards to the control of bioaerosols, including microbial fragment present in bioaerosols.
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Affiliation(s)
- Xu-Rui Hu
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China; Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, 300072, China; School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang, Hebei, 050018, China
| | - Meng-Fei Han
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China; Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, 300072, China; School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang, Hebei, 050018, China
| | - Can Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China; Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, 300072, China.
| | - Nan-Yang Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China; Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, 300072, China
| | - Yong-Chao Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China; Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, 300072, China
| | - Er-Hong Duan
- School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang, Hebei, 050018, China.
| | - Hsing-Cheng Hsi
- Graduate Institute of Environmental Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 106, Taiwan
| | - Ji-Guang Deng
- College of Environmental and Energy Engineering, Beijing University of Technology, Beijing, 100124, China
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26
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Abstract
Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment. Bacteriophages are abundant members of all microbiomes studied to date, influencing microbial communities through interactions with their bacterial hosts. Despite their functional importance and ubiquity, phages have been underexplored in urban environments compared to their bacterial counterparts. We profiled the viral communities in New York City (NYC) wastewater using metagenomic data collected in November 2014 from 14 wastewater treatment plants. We show that phages accounted for the largest viral component of the sewage samples and that specific virus communities were associated with local environmental conditions within boroughs. The vast majority of the virus sequences had no homology matches in public databases, forming an average of 1,700 unique virus clusters (putative genera). These new clusters contribute to elucidating the overwhelming proportion of data that frequently goes unidentified in viral metagenomic studies. We assigned potential hosts to these phages, which appear to infect a wide range of bacterial genera, often outside their presumed host. We determined that infection networks form a modular-nested pattern, indicating that phages include a range of host specificities, from generalists to specialists, with most interactions organized into distinct groups. We identified genes in viral contigs involved in carbon and sulfur cycling, suggesting functional importance of viruses in circulating pathways and gene functions in the wastewater environment. In addition, we identified virophage genes as well as a nearly complete novel virophage genome. These findings provide an understanding of phage abundance and diversity in NYC wastewater, previously uncharacterized, and further examine geographic patterns of phage-host association in urban environments. IMPORTANCE Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment.
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27
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Cheng X, Delanka-Pedige HMK, Munasinghe-Arachchige SP, Abeysiriwardana-Arachchige ISA, Smith GB, Nirmalakhandan N, Zhang Y. Removal of antibiotic resistance genes in an algal-based wastewater treatment system employing Galdieria sulphuraria: A comparative study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 711:134435. [PMID: 31810689 PMCID: PMC6992497 DOI: 10.1016/j.scitotenv.2019.134435] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 05/04/2023]
Abstract
In this study, we compared removal of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in two wastewater treatment systems fed with the same primary effluent: a conventional wastewater treatment system (consisting of a trickling filter followed by an activated sludge process) versus an algal-based system, employing an extremophilic alga, Galdieria sulphuraria. Our results demonstrated that the algal system can reduce concentrations of erythromycin- and sulfamethoxazole-resistant bacteria in the effluent more effectively than the conventional treatment system. A decreasing trend of total bacteria and ARGs was observed in both the treatment systems. However, the relative ratio of most ARGs (qnrA, qnrB, qnrS, sul1) and intI1 in the surviving bacteria increased in the conventional system; whereas, the algal system reduced more of the relative abundance of qnrA, qnrS, tetW and intⅠ1 in the surviving bacteria. The role of bacteriophages in horizontal gene transfer (HGT) of ARGs in the two systems was indicated by a positive correlation between ARG absolute abundance in bacteriophage and ARG relative abundance in the bacteria. Four of the five detectable genes (qnrS, tetW, sul1 and intI1) were significantly reduced in the algal system in bacteriophage phase which signified a decrease in phage-mediated ARG transfer in the algal system. Results of this study demonstrate the feasibility of the algal-based wastewater treatment system in decreasing ARGs and ARB and in minimizing the spread of antibiotic resistance to the environment.
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Affiliation(s)
- Xiaoxiao Cheng
- Civil Engineering Department, New Mexico State University, Las Cruces, NM 88003, USA
| | | | | | | | - Geoffrey B Smith
- Biology Department, New Mexico State University, Las Cruces, NM 88003, USA
| | | | - Yanyan Zhang
- Civil Engineering Department, New Mexico State University, Las Cruces, NM 88003, USA.
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28
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Petrovich ML, Ben Maamar S, Hartmann EM, Murphy BT, Poretsky RS, Wells GF. Viral composition and context in metagenomes from biofilm and suspended growth municipal wastewater treatment plants. Microb Biotechnol 2019; 12:1324-1336. [PMID: 31410982 PMCID: PMC6801142 DOI: 10.1111/1751-7915.13464] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/05/2019] [Indexed: 11/30/2022] Open
Abstract
Wastewater treatment plants (WWTPs) contain high density and diversity of viruses which can significantly impact microbial communities in aquatic systems. While previous studies have investigated viruses in WWTP samples that have been specifically concentrated for viruses and filtered to exclude bacteria, little is known about viral communities associated with bacterial communities throughout wastewater treatment systems. Additionally, differences in viral composition between attached and suspended growth wastewater treatment bioprocesses are not well characterized. Here, shotgun metagenomics was used to analyse wastewater and biomass from transects through two full-scale WWTPs for viral composition and associations with bacterial hosts. One WWTP used a suspended growth activated sludge bioreactor and the other used a biofilm reactor (trickling filter). Myoviridae, Podoviridae and Siphoviridae were the dominant viral families throughout both WWTPs, which are all from the order Caudovirales. Beta diversity analysis of viral sequences showed that samples clustered significantly both by plant and by specific sampling location. For each WWTP, the overall bacterial community structure was significantly different than community structure of bacterial taxa associated with viral sequences. These findings highlight viral community composition in transects through different WWTPs and provide context for dsDNA viral sequences in bacterial communities from these systems.
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Affiliation(s)
- Morgan L. Petrovich
- Department of Civil and Environmental EngineeringNorthwestern University2145 Sheridan Rd., Tech A236EvanstonIL60208USA
| | - Sarah Ben Maamar
- Department of Civil and Environmental EngineeringNorthwestern University2145 Sheridan Rd., Tech A236EvanstonIL60208USA
| | - Erica M. Hartmann
- Department of Civil and Environmental EngineeringNorthwestern University2145 Sheridan Rd., Tech A236EvanstonIL60208USA
| | - Brian T. Murphy
- Department of Medicinal Chemistry and PharmacognosyUniversity of Illinois at Chicago900 S. Ashland Ave, MBRB Room 3120; MC 870ChicagoIL60607USA
| | - Rachel S. Poretsky
- Department of Biological SciencesUniversity of Illinois at Chicago950 S. Halsted Street, SEL 4100ChicagoIL60607USA
| | - George F. Wells
- Department of Civil and Environmental EngineeringNorthwestern University2145 Sheridan Rd., Tech A236EvanstonIL60208USA
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Batinovic S, Wassef F, Knowler SA, Rice DTF, Stanton CR, Rose J, Tucci J, Nittami T, Vinh A, Drummond GR, Sobey CG, Chan HT, Seviour RJ, Petrovski S, Franks AE. Bacteriophages in Natural and Artificial Environments. Pathogens 2019; 8:pathogens8030100. [PMID: 31336985 PMCID: PMC6789717 DOI: 10.3390/pathogens8030100] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 02/07/2023] Open
Abstract
Bacteriophages (phages) are biological entities that have attracted a great deal of attention in recent years. They have been reported as the most abundant biological entities on the planet and their ability to impact the composition of bacterial communities is of great interest. In this review, we aim to explore where phages exist in natural and artificial environments and how they impact communities. The natural environment in this review will focus on the human body, soils, and the marine environment. In these naturally occurring environments there is an abundance of phages suggesting a role in the maintenance of bacterial community homeostasis. The artificial environment focuses on wastewater treatment plants, industrial processes, followed by pharmaceutical formulations. As in natural environments, the existence of bacteria in manmade wastewater treatment plants and industrial processes inevitably attracts phages. The presence of phages in these environments can inhibit the bacteria required for efficient water treatment or food production. Alternatively, they can have a positive impact by eliminating recalcitrant organisms. Finally, we conclude by describing how phages can be manipulated or formulated into pharmaceutical products in the laboratory for use in natural or artificial environments.
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Affiliation(s)
- Steven Batinovic
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Flavia Wassef
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Sarah A Knowler
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Daniel T F Rice
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Cassandra R Stanton
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Jayson Rose
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Joseph Tucci
- Department of Pharmacy & Biomedical Sciences, La Trobe University, Bendigo, VIC 3550, Australia
| | - Tadashi Nittami
- Division of Materials Science and Chemical Engineering, Yokohama National University, Yokohama 240-8501, Japan
| | - Antony Vinh
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Grant R Drummond
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Christopher G Sobey
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Hiu Tat Chan
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Robert J Seviour
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Steve Petrovski
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia.
| | - Ashley E Franks
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
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30
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Brown MR, Baptista JC, Lunn M, Swan DL, Smith SJ, Davenport RJ, Allen BD, Sloan WT, Curtis TP. Coupled virus - bacteria interactions and ecosystem function in an engineered microbial system. WATER RESEARCH 2019; 152:264-273. [PMID: 30682570 DOI: 10.1016/j.watres.2019.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
Viruses are thought to control bacterial abundance, affect community composition and influence ecosystem function in natural environments. Yet their dynamics have seldom been studied in engineered systems, or indeed in any system, for long periods of time. We measured virus abundance in a full-scale activated sludge plant every week for two years. Total bacteria and ammonia oxidising bacteria (AOB) abundances, bacterial community profiles, and a suite of environmental and operational parameters were also monitored. Mixed liquor virus abundance fluctuated over an order of magnitude (3.18 × 108-3.41 × 109 virus's mL-1) and that variation was statistically significantly associated with total bacterial and AOB abundance, community composition, and effluent concentrations of COD and NH4+- N and thus system function. This suggests viruses play a far more important role in the dynamics of activated sludge systems than previously realised and could be one of the key factors controlling bacterial abundance, community structure and functional stability and may cause reactors to fail. These findings are based on statistical associations, not mechanistic models. Nevertheless, viral associations with abiotic factors, such as pH, make physical sense, giving credence to these findings and highlighting the role that physical factors play in virus ecology. Further work is needed to identify and quantify specific bacteriophage and their hosts to enable us to develop mechanistic models of the ecology of viruses in wastewater treatment systems. However, since we have shown that viruses can be related to effluent quality and virus quantification is simple and cheap, practitioners would probably benefit from quantifying viruses now.
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Affiliation(s)
- M R Brown
- School of Engineering, Newcastle University, NE1 7RU, UK.
| | - J C Baptista
- School of Engineering, Newcastle University, NE1 7RU, UK
| | - M Lunn
- Department of Statistics, University of Oxford, OX1 3TG, UK
| | - D L Swan
- School of Engineering, Newcastle University, NE1 7RU, UK
| | - S J Smith
- School of Engineering, Newcastle University, NE1 7RU, UK
| | - R J Davenport
- School of Engineering, Newcastle University, NE1 7RU, UK
| | - B D Allen
- School of Engineering, Newcastle University, NE1 7RU, UK
| | - W T Sloan
- Department of Civil Engineering, University of Glasgow, G12 8LT, UK
| | - T P Curtis
- School of Engineering, Newcastle University, NE1 7RU, UK
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García-Aljaro C, Blanch AR, Campos C, Jofre J, Lucena F. Pathogens, faecal indicators and human-specific microbial source-tracking markers in sewage. J Appl Microbiol 2019; 126:701-717. [PMID: 30244503 DOI: 10.1111/jam.14112] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/12/2018] [Accepted: 09/18/2018] [Indexed: 02/06/2023]
Abstract
The objective of this review is to assess the current state of knowledge of pathogens, general faecal indicators and human-specific microbial source tracking markers in sewage. Most of the microbes present in sewage are from the microbiota of the human gut, including pathogens. Bacteria and viruses are the most abundant groups of microbes in the human gut microbiota. Most reports on this topic show that raw sewage microbiological profiles reflect the human gut microbiota. Human and animal faeces share many commensal microbes as well as pathogens. Faecal-orally transmitted pathogens constitute a serious public health problem that can be minimized through sanitation. Assessing both the sanitation processes and the contribution of sewage to the faecal contamination of water bodies requires knowledge of the content of pathogens in sewage, microbes indicating general faecal contamination and microbes that are only present in human faecal remains, which are known as the human-specific microbial source-tracking (MST) markers. Detection of pathogens would be the ideal option for managing sanitation and determining the microbiological quality of waters contaminated by sewage; but at present, this is neither practical nor feasible in routine testing. Traditionally, faecal indicator bacteria have been used as surrogate indicators of general faecal residues. However, in many water management circumstances, it becomes necessary to detect both the origin of faecal contamination, for which MST is paramount, and live micro-organisms, for which molecular methods are not suitable. The presence and concentrations of pathogens, general faecal indicators and human-specific MST markers most frequently reported in different areas of the world are summarized in this review.
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Affiliation(s)
- C García-Aljaro
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain.,The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - A R Blanch
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain.,The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - C Campos
- Departamento de Microbiología, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - J Jofre
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain.,The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - F Lucena
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain.,The Water Research Institute, University of Barcelona, Barcelona, Spain
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Zhang QY, Gui JF. Diversity, evolutionary contribution and ecological roles of aquatic viruses. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1486-1502. [DOI: 10.1007/s11427-018-9414-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/26/2018] [Indexed: 01/21/2023]
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Wang Q, Zeng X, Yang Q, Yang C. Identification of a bacteriophage from an environmental multidrug-resistant E. coli isolate and its function in horizontal transfer of ARGs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 639:617-623. [PMID: 29803035 DOI: 10.1016/j.scitotenv.2018.05.213] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/08/2018] [Accepted: 05/17/2018] [Indexed: 06/08/2023]
Abstract
Horizontal transfer of ARGs was generally considered to be mediated by three methods - transformation, conjugation and transduction through phages - during which the contribution of bacteriophages to gene transfer in the environment is unclear or even questioned. In this study, a multiple-antibiotic-resistant Escherichia coli strain and its phage (YZ1) were isolated from a municipal wastewater treatment system. The results of the morphological and genomic analyses of phage YZ1 showed that it is a member of the T7 viral genus in the subfamily Autographivirinae. Its genome is similar to that of the E. coli phage K1F in both organization and sequence and does not encode ARGs. However, 28 paired reads in the raw sequencing data aligned to ARGs, including those promoting β-lactam, aminoglycoside, and fluoroquinolone resistance, among others. Quantitative PCR showed that ARGs were present in bacteriophage DNA (approximately 103 copies/mL) and were also detected in the bacterial host DNA. The results suggested that while infrequent, some ARG-carrying transducing phages were presumably generated by erroneous packaging during infection of antibiotic-resistant bacteria, which may create the possibility of horizontal transfer of ARGs.
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Affiliation(s)
- Qiang Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Key Laboratory for Microorganisms and Functional Molecules (Henan Normal University), University of Henan Province, Xinxiang 453007, China
| | - Xiangpeng Zeng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Qingxiang Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Key Laboratory for Microorganisms and Functional Molecules (Henan Normal University), University of Henan Province, Xinxiang 453007, China.
| | - Chuanzhen Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
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Wang Y, Jiang X, Liu L, Li B, Zhang T. High-Resolution Temporal and Spatial Patterns of Virome in Wastewater Treatment Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:10337-10346. [PMID: 30148618 DOI: 10.1021/acs.est.8b03446] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Wastewater treatment plants (WWTPs) are considered reservoirs of viruses, but the diversity and dynamic changes of viruses are not well understood. In this study, we recovered 8478 metagenomic viral contigs (mVCs; >5 kb) from two WWTPs (Shatin, 2806; Shek Wu Hui, 5672) in Hong Kong. Approximately 60% of the mVCs were poorly covered (<35% of genes in identified mVCs) by the current NCBI and IMG/VR viral databases. The temporal profile of the newly identified mVCs among 98 Shatin AS samples collected monthly (for approximately 9 years) revealed the presence of periodic dynamics at an interval of approximately one year (341 days). The spatial distribution pattern of the virome in the wastewater treatment systems showed that shared viral clusters (viral populations categorized based on shared gene content and network analysis) can be globally found among similar samples of wastewater treatment systems, indicating the presence of core viral communities among geographically isolated wastewater treatment systems. These results not only supplemented the current virome database of engineered systems but also, to some extent, expanded the understanding of long-term cyclical development and spatial distributions of viral communities in wastewater treatment systems.
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Affiliation(s)
- Yulin Wang
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong
| | - Xiaotao Jiang
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong
| | - Lei Liu
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong
| | - Bing Li
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong
- Division of Energy and Environment , Graduate School at Shenzhen, Tsinghua University , Shenzhen , 518055 , China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong
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Haramoto E, Kitajima M, Hata A, Torrey JR, Masago Y, Sano D, Katayama H. A review on recent progress in the detection methods and prevalence of human enteric viruses in water. WATER RESEARCH 2018; 135:168-186. [PMID: 29471200 DOI: 10.1016/j.watres.2018.02.004] [Citation(s) in RCA: 235] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 05/17/2023]
Abstract
Waterborne human enteric viruses, such as noroviruses and adenoviruses, are excreted in the feces of infected individuals and transmitted via the fecal-oral route including contaminated food and water. Since viruses are normally present at low concentrations in aquatic environments, they should be concentrated into smaller volumes prior to downstream molecular biological applications, such as quantitative polymerase chain reaction (qPCR). This review describes recent progress made in the development of concentration and detection methods of human enteric viruses in water, and discusses their applications for providing a better understanding of the prevalence of the viruses in various types of water worldwide. Maximum concentrations of human enteric viruses in water that have been reported in previous studies are summarized to assess viral abundances in aquatic environments. Some descriptions are also available on recent applications of sequencing analyses used to determine the genetic diversity of viral genomes in water samples, including those of novel viruses. Furthermore, the importance and significance of utilizing appropriate process controls during viral analyses are discussed, and three types of process controls are considered: whole process controls, molecular process controls, and (reverse transcription (RT)-)qPCR controls. Although no standards have been established for acceptable values of virus recovery and/or extraction-(RT-)qPCR efficiency, use of at least one of these appropriate control types is highly recommended for more accurate interpretation of observed data.
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Affiliation(s)
- Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan.
| | - Akihiko Hata
- Integrated Research System for Sustainability Science, Institutes for Advanced Study, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.
| | - Jason R Torrey
- School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
| | - Yoshifumi Masago
- Institute for the Advanced Study of Sustainability, United Nations University, 5-53-70 Jingumae, Shibuya-ku, Tokyo 150-8925, Japan.
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
| | - Hiroyuki Katayama
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Vietnam Japan University, Luu Huu Phuoc Road, My Dinh 1 Ward, Nam Tu Liem District, Ha Noi, Vietnam.
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Reducing inherent biases introduced during DNA viral metagenome analyses of municipal wastewater. PLoS One 2018; 13:e0195350. [PMID: 29614100 PMCID: PMC5882159 DOI: 10.1371/journal.pone.0195350] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/20/2018] [Indexed: 01/21/2023] Open
Abstract
Metagenomics is a powerful tool for characterizing viral composition within environmental samples, but sample and molecular processing steps can bias the estimation of viral community structure. The objective of this study is to understand the inherent variability introduced when conducting viral metagenomic analyses of wastewater and provide a bioinformatic strategy to accurately analyze sequences for viral community analyses. A standard approach using a combination of ultrafiltration, membrane filtration, and DNase treatment, and multiple displacement amplification (MDA) produced DNA preparations without any bacterial derived genes. Results showed recoveries in wastewater matrix ranged between 60–100%. A bias towards small single stranded DNA (ssDNA; polyomavirus) virus types vs larger double stranded DNA (dsDNA; adenovirus) viruses was also observed with a total estimated recovery of small circular viruses to be as much as 173-fold higher. Notably, ssDNA abundance decreased with sample dilution while large dsDNA genomes (e.g., Caudovirales) initially increased in abundance with dilution before gradually decreasing with further dilution in wastewater samples. The present study revealed the inherent biases associated with different components of viral metagenomic methods applied to wastewater. Overall, these results provide a well-characterized approach for effectively conducting viral metagenomics analysis of wastewater and reveal that dilution can effectively mitigate MDA bias.
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Fan N, Qi R, Yang M. Isolation and characterization of a virulent bacteriophage infecting Acinetobacter johnsonii from activated sludge. Res Microbiol 2017; 168:472-481. [DOI: 10.1016/j.resmic.2017.01.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/17/2017] [Accepted: 01/31/2017] [Indexed: 11/26/2022]
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38
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Zhang J, Gao Q, Zhang Q, Wang T, Yue H, Wu L, Shi J, Qin Z, Zhou J, Zuo J, Yang Y. Bacteriophage-prokaryote dynamics and interaction within anaerobic digestion processes across time and space. MICROBIOME 2017; 5:57. [PMID: 28569210 PMCID: PMC5452288 DOI: 10.1186/s40168-017-0272-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/28/2017] [Indexed: 05/15/2023]
Abstract
BACKGROUND Bacteriophage-prokaryote dynamics and interaction are believed to be important in governing microbiome composition and ecosystem functions, yet our limited knowledge of the spatial and temporal variation in phage and prokaryotic community compositions precludes accurate assessment of their roles and impacts. Anaerobic digesters are ideal model systems to examine phage-host interaction, owing to easy access, stable operation, nutrient-rich environment, and consequently enormous numbers of phages and prokaryotic cells. RESULTS Equipped with high-throughput, cutting-edge environmental genomics techniques, we examined phage and prokaryotic community composition of four anaerobic digesters in full-scale wastewater treatment plants across China. Despite the relatively stable process performance in biogas production, phage and prokaryotic groups fluctuated monthly over a year of study period, showing significant correlations between those two groups at the α- and β-diversity levels. Strikingly, phages explained 40.6% of total variations of the prokaryotic community composition, much higher than the explanatory power by abiotic factors (14.5%). Consequently, phages were significantly (P < 0.010) linked to parameters related to process performance including biogas production and volatile solid concentrations. Association network analyses showed phage-prokaryote pairs were shallowly conserved since they were detected only within small viral clades. CONCLUSIONS Those results collectively demonstrate phages as a major biotic factor in controlling prokaryotic composition and process performance. Therefore, phages may play a larger role in shaping prokaryotic community dynamics and process performance of anaerobic digesters than currently appreciated.
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Affiliation(s)
- Junyu Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 10084, China
| | - Qun Gao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 10084, China
| | - Qiuting Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 10084, China
| | - Tengxu Wang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 10084, China
| | - Haowei Yue
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 10084, China
| | - Linwei Wu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 10084, China
| | - Jason Shi
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Ziyan Qin
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 10084, China
| | - Jizhong Zhou
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 10084, China
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
- Earth and Environmental Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94270, USA
| | - Jiane Zuo
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 10084, China.
| | - Yunfeng Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 10084, China.
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Genome Analysis of a Novel Broad Host Range Proteobacteria Phage Isolated from a Bioreactor Treating Industrial Wastewater. Genes (Basel) 2017; 8:genes8010040. [PMID: 28106814 PMCID: PMC5295034 DOI: 10.3390/genes8010040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 12/27/2016] [Accepted: 01/11/2017] [Indexed: 01/18/2023] Open
Abstract
Bacteriophages are viruses that infect bacteria, and consequently they have a major impact on the development of a microbial population. In this study, the genome of a novel broad host range bacteriophage, Aquamicrobium phage P14, isolated from a wastewater treatment plant, was analyzed. The Aquamicrobium phage P14 was found to infect members of different Proteobacteria classes (Alphaproteobacteria and Betaproteobacteria). This phage contains a 40,551 bp long genome and 60% of its genes had blastx hits. Furthermore, the bacteriophage was found to share more than 50% of its genes with several podoviruses and has the same gene order as other polyvalent bacteriophages. The results obtained in this study led to the conclusion that indeed general features of the genome of the Aquamicrobium phage P14 are shared with other broad host range bacteriophages, however further analysis of the genome is needed in order to identify the specific mechanisms which enable the bacteriophage to infect both Alphaproteobacteria and Betaproteobacteria.
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40
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Motlagh AM, Bhattacharjee AS, Goel R. Microbiological study of bacteriophage induction in the presence of chemical stress factors in enhanced biological phosphorus removal (EBPR). WATER RESEARCH 2015; 81:1-14. [PMID: 26024959 DOI: 10.1016/j.watres.2015.04.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 04/10/2015] [Accepted: 04/11/2015] [Indexed: 06/04/2023]
Abstract
Polyphosphate accumulating organisms (PAOs) are responsible for carrying the enhanced biological phosphorus removal (EBPR). Although the EBPR process is well studied, the failure of EBPR performance at both laboratory and full-scale plants has revealed a lack of knowledge about the ecological and microbiological aspects of EBPR processes. Bacteriophages are viruses that infect bacteria as their sole host. Bacteriophage infection of polyphosphate accumulating organisms (PAOs) has not been considered as a main contributor to biological phosphorus removal upsets. This study examined the effects of different stress factors on the dynamics of bacteriophages and the corresponding effects on the phosphorus removal performance in a lab-scale EBPR system. The results showed that copper (heavy metal), cyanide (toxic chemical), and ciprofloxacin (antibiotic), as three different anthropogenic stress factors, can induce phages integrated onto bacterial genomes (i.e. prophages) in an enriched EBPR sequencing batch reactor, resulting in a decrease in the polyphosphate kinase gene ppk1 clades copy number, phosphorus accumulation capacity, and phosphorus removal performance. This study opens opportunities for further research on the effects of bacteriophages in nutrient cycles both in controlled systems such as wastewater treatment plants and natural ecosystems.
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Affiliation(s)
- Amir Mohaghegh Motlagh
- Department of Civil and Environmental Engineering, University of Utah, 110 S Central Campus Drive, Salt Lake City, UT 84112, USA
| | - Ananda S Bhattacharjee
- Department of Civil and Environmental Engineering, University of Utah, 110 S Central Campus Drive, Salt Lake City, UT 84112, USA
| | - Ramesh Goel
- Department of Civil and Environmental Engineering, University of Utah, 110 S Central Campus Drive, Salt Lake City, UT 84112, USA.
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41
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Brown MR, Camézuli S, Davenport RJ, Petelenz-Kurdziel E, Øvreås L, Curtis TP. Flow cytometric quantification of viruses in activated sludge. WATER RESEARCH 2015; 68:414-22. [PMID: 25462748 DOI: 10.1016/j.watres.2014.10.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 09/22/2014] [Accepted: 10/08/2014] [Indexed: 05/21/2023]
Abstract
Viruses may play a critical role in the microbial dynamics of activated sludge systems; however the difficulty of their quantification makes long term and large scale studies costly, timely and challenging. Thus a flow cytometric protocol was optimised and employed to determine virus abundance in activated sludge samples. The best flow cytometry signature and highest virus count was obtained by separating the indigenous floc-associated viruses using Tween 80 and sodium pyrophosphate, diluting the sample with Tris-EDTA and staining with SYBR Green II. Using the optimised protocol viral concentrations from 25 activated sludge plants were determined, with average concentrations of 2.35 × 10⁹ mL⁻¹ observed. Direct counts by transmission electron microscopy were highly correlated with flow cytometric counts (p = <0.05 and r² = 0.77), with concentrations from both quantification methods comparable at the order of magnitude level. The high counting efficiency, ease of preparation and rapidity and reproducibility of analysis makes flow cytometric quantification of viruses in activated sludge ideal for routine investigation and thus invaluable in unravelling the complexity of phage host interactions in such systems.
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Affiliation(s)
- M R Brown
- School of Civil Engineering and Geosciences, Newcastle University, NE1 7RU, UK.
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42
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Characterization of the morphology and genome of an Escherichia coli podovirus. Arch Virol 2014; 159:3249-56. [PMID: 25163858 DOI: 10.1007/s00705-014-2189-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 07/18/2014] [Indexed: 01/20/2023]
Abstract
Escherichia coli is an important opportunistic pathogen. It can cause sepsis and severe infection. The application of lytic bacteriophages to treat infectious diseases is an alternative to antibiotics. A lytic Escherichia coli phage, designated IME-EC2, was isolated from hospital sewage. Transmission electron microscopy revealed that IME-EC2 to be a member of the family Podoviridae. It had a 60-nm head and a 15-nm tail. Here, we present the complete genome sequence of this phage, which consists of 41,510 bp with an overall G+C content of 59.2 %. A total of 60 coding sequences (CDS) were identified, and the phage genome does not contain any tRNA genes. Forty percent of the unknown CDSs are unique to IME-EC2. This phage does not show significant similarity to other phages at the DNA level, which suggests that IME-EC2 could be a novel phage. One of the unique features identified in the IME-EC2 genome was a gene coding for a putative colanic-acid-degrading protein, which could allow the phage to degrade bacterial capsule and biofilms. Another unique feature is that IME-EC2 does not contain a terminase small subunit, which suggests that this phage may have a unique packaging mechanism. The present work provides novel information on phages and shows that this lytic phage or its products could be exploited to destroy bacterial biofilms and pathogenic E. coli.
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Calero-Cáceres W, Melgarejo A, Colomer-Lluch M, Stoll C, Lucena F, Jofre J, Muniesa M. Sludge as a potential important source of antibiotic resistance genes in both the bacterial and bacteriophage fractions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:7602-11. [PMID: 24873655 DOI: 10.1021/es501851s] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The emergence and prevalence of antibiotic resistance genes (ARGs) in the environment is a serious global health concern. ARGs found in bacteria can become mobilized in bacteriophage particles in the environment. Sludge derived from secondary treatment in wastewater treatment plants (WWTPs) constitutes a concentrated pool of bacteria and phages that are removed during the treatment process. This study evaluates the prevalence of ARGs in the bacterial and phage fractions of anaerobic digested sludge; five ARGs (blaTEM, blaCTX-M, qnrA, qnrS, and sul1) are quantified by qPCR. Comparison between the wastewater and sludge revealed a shift in the prevalence of ARGs (blaTEM and sul1 became more prevalent in sludge), suggesting there is a change in the bacterial and phage populations from wastewater to those selected during the secondary treatment and the later anaerobic mesophilic digestion of the sludge. ARGs densities were higher in the bacterial than in the phage fraction, with high densities in both fractions; particularly for blaTEM and sul1 (5 and 8 log10 gene copies (GC)/g, respectively, in bacterial DNA; 5.5 and 4.4 log10 GC/g, respectively, in phage DNA). These results question the potential agricultural uses of treated sludge, as it could contribute to the spread of ARGs in the environment and have an impact on the bacterial communities of the receiving ecosystem.
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Affiliation(s)
- William Calero-Cáceres
- Department of Microbiology, University of Barcelona , Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain
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Muniesa M, Colomer-Lluch M, Jofre J. Potential impact of environmental bacteriophages in spreading antibiotic resistance genes. Future Microbiol 2013; 8:739-51. [PMID: 23701331 DOI: 10.2217/fmb.13.32] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The idea that bacteriophage transduction plays a role in the horizontal transfer of antibiotic resistance genes is gaining momentum. Such transduction might be vital in horizontal transfer from environmental to human body-associated biomes and here we review many lines of evidence supporting this notion. It is well accepted that bacteriophages are the most abundant entities in most environments, where they have been shown to be quite persistent. This fact, together with the ability of many phages to infect bacteria belonging to different taxa, makes them suitable vehicles for gene transfer. Metagenomic studies confirm that substantial percentages of the bacteriophage particles present in most environments contain bacterial genes, including mobile genetic elements and antibiotic resistance genes. When specific genes of resistance to antibiotics are detected by real-time PCR in the bacteriophage populations of different environments, only tenfold lower numbers of these genes are observed, compared with those found in the corresponding bacterial populations. In addition, the antibiotic resistance genes from these bacteriophages are functional and generate resistance to the bacteria when these genes are transfected. Finally, reports about the transduction of antibiotic resistance genes are on the increase.
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Affiliation(s)
- Maite Muniesa
- Department of Microbiology, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain
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Satoh H, Oshima K, Suda W, Ranasinghe P, Li N, Gunawardana EGW, Hattori M, Mino T. Bacterial population dynamics in a laboratory activated sludge reactor monitored by pyrosequencing of 16S rRNA. Microbes Environ 2012; 28:65-70. [PMID: 23100021 PMCID: PMC4070689 DOI: 10.1264/jsme2.me12115] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The microbial population in a laboratory activated sludge reactor was monitored for 245 d at 75 time points by pyrosequencing of 16S rRNA. Synthetic wastewater was used as the influent, and the reactor was operated under the same conditions throughout the experiment. The behaviors of different bacterial operational taxonomic units (OTUs) were observed. Multiple OTUs showed periodic propagation and recession. One of the OTUs showed sharp recession, which suggests that cells in the OTU were selectively killed. The behaviors of different phylogenetic lineages of Candidatus ‘Accumulibacter phosphatis’ were also visualized. It was clearly demonstrated that pyrosequencing with barcoded primers is a very effective tool to clarify the dynamics of the bacterial population in activated sludge.
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Affiliation(s)
- Hiroyasu Satoh
- Department of Socio-cultural and Environmental Studies, The University of Tokyo, Tokyo, Japan.
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46
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Zhang Y, Hu Z. Combined treatment ofPseudomonas aeruginosabiofilms with bacteriophages and chlorine. Biotechnol Bioeng 2012; 110:286-95. [DOI: 10.1002/bit.24630] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 07/14/2012] [Accepted: 07/26/2012] [Indexed: 11/12/2022]
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Otawa K, Hirakata Y, Kaku M, Nakai Y. Bacteriophage control of vancomycin-resistant enterococci in cattle compost. J Appl Microbiol 2012; 113:499-507. [PMID: 22702478 DOI: 10.1111/j.1365-2672.2012.05361.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 05/31/2012] [Accepted: 06/09/2012] [Indexed: 11/26/2022]
Abstract
AIMS To isolate bacteriophage that infects vancomycin-resistant enterococci (VRE) and to investigate the ability of this phage to diminish VRE number in vitro and in experimentally VRE-inoculated compost. METHODS AND RESULTS We sampled 106 solid or water samples, including 101 bovine faecal samples; lytic phage named Vrep-5 was isolated from one bovine faecal sample by plaque assay using the clinical VRE isolate FN1 (Enterococcus faecium). Vrep-5 generated clear plaques 1 mm in diameter and exhibited characteristics of the family Myoviridae A1, with a spherical head (122 ± 16 nm) and a contractile tail (152 ± 17 nm long). Vrep-5 lysed other bacterial strains, including Enterococcus faecalis. Inoculation of vrep-5 into 0.5 g unsterilized compost experimentally inoculated with FN1 at the multiplicity of infection of 1500 (8.8 × 10(4) CFU g(-1) VRE and 1.3 × 10(8) PFU g(-1) vrep-5) led to a decrease of >3 log(10) in VRE abundance compared with the untreated control after 24 h of incubation. CONCLUSIONS The data show that bacteriophage vrep-5 is effective in the rapid reduction in VRE colonization in compost. SIGNIFICANCE AND IMPACT OF THE STUDY The present study gives valuable new knowledge in the fight against VRE in the animal production.
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Affiliation(s)
- K Otawa
- Laboratory of Sustainable Environmental Biology, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
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Tamaki H, Zhang R, Angly FE, Nakamura S, Hong PY, Yasunaga T, Kamagata Y, Liu WT. Metagenomic analysis of DNA viruses in a wastewater treatment plant in tropical climate. Environ Microbiol 2011; 14:441-52. [PMID: 22040222 DOI: 10.1111/j.1462-2920.2011.02630.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Viruses have been detected in the different stages of wastewater treatment plants (WWTPs) at concentrations of 10(8) -10(10) ml(-1) of virus-like particles (VLPs), 10-1000 times higher than in natural aquatic environments, suggesting that WWTPs can be considered as an important reservoir and source of viruses. This study revealed novel diversity and function with the DNA viral communities in the influent, activated sludge, anaerobic digester, and effluent of a domestic WWTP using metagenomics. WWTP was a very specific environment, with less than 5% of the > 936 000 metagenomic sequences obtained (∼70-119 Mbp per sample) similar to sequences present in other environmental viromes. Many viruses found in the WWTP were novel, resulting in only < 5-20% of the reads being phylogenetically or functionally assigned. DNA metabolism was observed as the most abundant function with DNA methylase detected at levels 4.2-fold higher than other published viromes, while carbohydrate and amino acids metabolisms were 3.7- and 4.2-fold less abundant respectively. These specific aspects of the WWTP community functions are likely due to high biomass concentration, turnover rate and microbial activity in WWTPs, and likely include mechanisms that help viruses increase their infectivity. Among ∼500 genotypes estimated in individual WWTP viromes, > 82% were shared. These data suggested that VLPs of most viral types could be present between 1 and 30 days in the process before they were discharged. Viruses in WWTP and the discharged ones can have potential impacts on the functioning of the wastewater treatment system and on the dynamics of microbial community in the surrounding aquatic environments respectively.
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Affiliation(s)
- Hideyuki Tamaki
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Avenue, Urbana, IL 61801, USA
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Hao X, Wang Q, Cao Y, van Loosdrecht MCM. Evaluating sludge minimization caused by predation and viral infection based on the extended activated sludge model No. 2d. WATER RESEARCH 2011; 45:5130-5140. [PMID: 21821271 DOI: 10.1016/j.watres.2011.07.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 07/11/2011] [Accepted: 07/12/2011] [Indexed: 05/31/2023]
Abstract
The Activated Sludge Model No. 2d (ASM2d) was extended to incorporate the processes of both predation and viral infection. The extended model was used to evaluate the contributions of predation and viral infection to sludge minimization in a sequencing batch reactor (SBR) system enriching polyphosphate-accumulating organisms (PAOs). Three individual decay processes formulated according to the general model rules were used in the extended model. The model was firstly calibrated and validated by different experimental results. It was used to evaluate the potential extent of predation and viral infection on sludge minimization. Simulations indicate that predation contributes roughly two times more to sludge minimization than viral infection in the SBR system enriching PAOs. The sensitivity analyses of the selected key parameters reveal that there are thresholds on both predation and viral infection rates, if they are too large a minimal sludge retention time is obtained and the effluent quality is deteriorating. Due to the thresholds, the contributions of predation and viral infection to sludge minimization are limited to a maximal extent of about 21% and 9%, respectively. However, it should be noted that the parameters concerning predation and viral infection were not calibrated separately by independent experiment in our study due to the lack of an effective method, especially for the parameters regarding viral infection. Therefore, it is essential to better evaluate these parameters in the future.
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Affiliation(s)
- Xiaodi Hao
- Key Laboratory of Urban Stormwater System and Water Environment/R & D Centre for Sustainable Environmental Biotechnology, Beijing University of Civil Engineering and Architecture, Ministry of Education, 1 Zhanlanguan Road, Xicheng District, Beijing 100044, PR China.
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Vázquez-Rodríguez GA, Beltrán-Hernández RI, Coronel-Olivares C, Rols JL. Standardization of activated sludge for biodegradation tests. Anal Bioanal Chem 2011; 401:1127-37. [DOI: 10.1007/s00216-011-5212-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 06/23/2011] [Accepted: 06/24/2011] [Indexed: 11/28/2022]
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