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Maksimović O, Bačnik K, Rivarez MPS, Vučurović A, Mehle N, Ravnikar M, Gutiérrez-Aguirre I, Kutnjak D. Virome analysis of irrigation water sources provides extensive insights into the diversity and distribution of plant viruses in agroecosystems. WATER RESEARCH 2024; 249:120712. [PMID: 38134622 DOI: 10.1016/j.watres.2023.120712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 12/24/2023]
Abstract
Plant viruses pose a significant threat to agriculture. Several are stable outside their hosts, can enter water bodies and remain infective for prolonged periods of time. Even though the quality of irrigation water is of increasing importance in the context of plant health, the presence of plant viruses in irrigation waters is understudied. In this study, we conducted a large-scale high-throughput sequencing (HTS)-based virome analysis of irrigation and surface water sources to obtain complete information about the abundance and diversity of plant viruses in such waters. We detected nucleic acids of plant viruses from 20 families, discovered several novel plant viruses from economically important taxa, like Tobamovirus and observed the influence of the water source on the present virome. By comparing viromes of water and surrounding plants, we observed presence of plant viruses in both compartments, especially in cases of large-scale outbreaks, such as that of tomato mosaic virus. Moreover, we demonstrated that water virome data can extensively inform us about the distribution and diversity of plant viruses for which only limited information is available from plants. Overall, the results of the study provided extensive insights into the virome of irrigation waters from the perspective of plant health. It also suggested that an HTS-based water virome surveillance system could be used to detect potential plant disease outbreaks and to survey the distribution and diversity of plant viruses in the ecosystem.
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Affiliation(s)
- Olivera Maksimović
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia; Jožef Stefan International Postgraduate School, Slovenia
| | - Katarina Bačnik
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia
| | - Mark Paul Selda Rivarez
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia; Department of Entomology and Plant Pathology, North Carolina State University, USA; College of Agriculture and Agri-Industries, Caraga State University, Philippines
| | - Ana Vučurović
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia
| | - Nataša Mehle
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia; School for Viticulture and Enology, University of Nova Gorica, Slovenia
| | - Maja Ravnikar
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia
| | | | - Denis Kutnjak
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia.
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Wang D, Shang J, Lin H, Liang J, Wang C, Sun Y, Bai Y, Qu J. Identifying ARG-carrying bacteriophages in a lake replenished by reclaimed water using deep learning techniques. WATER RESEARCH 2024; 248:120859. [PMID: 37976954 DOI: 10.1016/j.watres.2023.120859] [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: 06/16/2023] [Revised: 09/16/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
As important mobile genetic elements, phages support the spread of antibiotic resistance genes (ARGs). Previous analyses of metaviromes or metagenome-assembled genomes (MAGs) failed to assess the extent of ARGs transferred by phages, particularly in the generation of antibiotic pathogens. Therefore, we have developed a bioinformatic pipeline that utilizes deep learning techniques to identify ARG-carrying phages and predict their hosts, with a special focus on pathogens. Using this method, we discovered that the predominant types of ARGs carried by temperate phages in a typical landscape lake, which is fully replenished by reclaimed water, were related to multidrug resistance and β-lactam antibiotics. MAGs containing virulent factors (VFs) were predicted to serve as hosts for these ARG-carrying phages, which suggests that the phages may have the potential to transfer ARGs. In silico analysis showed a significant positive correlation between temperate phages and host pathogens (R = 0.503, p < 0.001), which was later confirmed by qPCR. Interestingly, these MAGs were found to be more abundant than those containing both ARGs and VFs, especially in December and March. Seasonal variations were observed in the abundance of phages harboring ARGs (from 5.62 % to 21.02 %) and chromosomes harboring ARGs (from 18.01 % to 30.94 %). In contrast, the abundance of plasmids harboring ARGs remained unchanged. In summary, this study leverages deep learning to analyze phage-transferred ARGs and demonstrates an alternative method to track the production of potential antibiotic-resistant pathogens by metagenomics that can be extended to microbiological risk assessment.
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Affiliation(s)
- Donglin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jiayu Shang
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Hui Lin
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jinsong Liang
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Chenchen Wang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Tianjin 300384, China
| | - Yanni Sun
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China.
| | - Yaohui Bai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Jiuhui Qu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, 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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Kuo HWD, Zure D, Lin CR. Occurrences of similar viral diversity in campus wastewater and reclaimed water of a university dormitory. CHEMOSPHERE 2023; 330:138713. [PMID: 37088208 DOI: 10.1016/j.chemosphere.2023.138713] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/10/2023] [Accepted: 04/15/2023] [Indexed: 05/03/2023]
Abstract
Water reuse from wastewater sources still remain some critical safety concerns associated with treacherous contaminants like pathogenic viruses. In this study, viral diversities in campus wastewater (CWW) and its reclaimed water (RCW) recycled for toilet flushing and garden irrigation of a university dormitory were assessed using metagenomic sequencing for acquisition of more background data. Results suggested majority (>80%) of gene sequences within assembled contigs predicted by open reading frame (ORF) finder were no-hit yet believed to be novel/unrevealed viral genomic information whereas hits matched bacteriophages (i.e., mainly Myoviridae, Podoviridae, and Siphoviridae families) were predominant in both CWW and RCW samples. Moreover, few pathogenic viruses (<1%) related to infections of human skin (e.g., Molluscum contagiosum virus, MCV), digestion system (e.g., hepatitis C virus, HCV), and gastrointestinal tract (e.g., human norovirus, HuNoV) were also noticed raising safety concerns about application of reclaimed waters. Low-affinity interactions of particular viral exterior proteins (e.g., envelope glycoproteins or spike proteins) for disinfectant ligand (e.g., chlorite) elucidated treatment limitations of current sewage processing systems even with membrane bioreactor and disinfectant contactor. Revolutionary disinfection approaches together with routine monitoring and new regulations are prerequisite to secure pathogen-correlated water quality for safer reuse of reclaimed waters.
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Affiliation(s)
- Hsion-Wen David Kuo
- Department of Environmental Science and Engineering, Tunghai University, Taiwan.
| | - Diaiti Zure
- Department of Environmental Science and Engineering, Tunghai University, Taiwan
| | - Chih-Rong Lin
- Department of Environmental Science and Engineering, Tunghai University, Taiwan
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Betancourt WQ. Waterborne Plant Viruses of Importance in Agriculture. Infect Dis (Lond) 2023. [DOI: 10.1007/978-1-0716-2463-0_1096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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Rashed MK, El-Senousy WM, Sayed ETAE, AlKhazindar M. Infectious Pepper Mild Mottle Virus and Human Adenoviruses as Viral Indices in Sewage and Water Samples. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:246-257. [PMID: 35713790 PMCID: PMC9458564 DOI: 10.1007/s12560-022-09525-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/27/2022] [Indexed: 05/14/2023]
Abstract
The objective of this study was to compare human adenoviruses (HAdVs) genome and infectivity, polyomaviruses (JC and BK) genome (JCPyVs) and (BKPyVs), Pepper Mild Mottle Virus (PMMoV) genome and infectivity, and infectious bacteriophages as viral indices for sewage and water samples. One hundred and forty-four samples were collected from inlets and outlets of water and wastewater treatment plants (WTPs), and WWTPs within Greater Cairo from October 2015 till March 2017. Two methods of viral concentration [Aluminium hydroxide (Al(OH)3) precipitation method and adsorption-elution technique followed by organic flocculation method] were compared to determine which of them was the best method to concentrate viruses from sewage and water. Although samples with only one litre volume were concentrated using Al(OH)3 precipitation method and the same samples with larger volumes (5-20 L) were concentrated using the adsorption-elution technique followed by the organic flocculation method, a non-significant difference was observed between the efficiency of the two methods in all types of samples except for the drinking water samples. Based on the qualitative prevalence of studied viruses in water and wastewater samples, the number of genome copies and infectious units in the same samples, resistance to treatment processes in water and wastewater treatment plants, higher frequency of both adenoviruses and PMMoV genomes as candidate viral indices in treated sewage and drinking water was observed. The problem of having a viral genome as indices of viral pollution is that it does not express the recent viral pollution because of the longer survivability of the viral genome than the infectious units in water and wastewater. Both infectious adenovirus and infectious phiX174 bacteriophage virus showed similar efficiencies as indices for viral pollution in drinking water and treated sewage samples. On the other hand, qualitative detection of infectious PMMoV failed to express efficiently the presence/absence of infectious enteric viruses in drinking water samples. Infectious adenoviruses and infectious bacteriophage phiX174 virus may be better candidates than adenoviruses genome, polyomaviruses genome, and PMMoV genome and infectivity as viral indices for water and wastewater.
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Affiliation(s)
- Mohammed Kamal Rashed
- Environmental Virology Lab, Water Pollution Research Department, Environmental and Climate Change Research Institute and Food-Borne Viruses Group, Centre of Excellence for Advanced Sciences, National Research Centre (NRC), 33 El-Buhouth Street, P. O. 12622, Dokki, Giza, Egypt
| | - Waled Morsy El-Senousy
- Environmental Virology Lab, Water Pollution Research Department, Environmental and Climate Change Research Institute and Food-Borne Viruses Group, Centre of Excellence for Advanced Sciences, National Research Centre (NRC), 33 El-Buhouth Street, P. O. 12622, Dokki, Giza, Egypt
| | | | - Maha AlKhazindar
- Botany and Microbiology Department, Faculty of Science, Cairo University, Cairo, Egypt
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7
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Rosario K, Van Bogaert N, López-Figueroa NB, Paliogiannis H, Kerr M, Breitbart M. Freshwater macrophytes harbor viruses representing all five major phyla of the RNA viral kingdom Orthornavirae. PeerJ 2022; 10:e13875. [PMID: 35990902 PMCID: PMC9390326 DOI: 10.7717/peerj.13875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/19/2022] [Indexed: 01/18/2023] Open
Abstract
Research on aquatic plant viruses is lagging behind that of their terrestrial counterparts. To address this knowledge gap, here we identified viruses associated with freshwater macrophytes, a taxonomically diverse group of aquatic phototrophs that are visible with the naked eye. We surveyed pooled macrophyte samples collected at four spring sites in Florida, USA through next generation sequencing of RNA extracted from purified viral particles. Sequencing efforts resulted in the detection of 156 freshwater macrophyte associated (FMA) viral contigs, 37 of which approximate complete genomes or segments. FMA viral contigs represent putative members from all five major phyla of the RNA viral kingdom Orthornavirae. Similar to viral types found in land plants, viral sequences identified in macrophytes were dominated by positive-sense RNA viruses. Over half of the FMA viral contigs were most similar to viruses reported from diverse hosts in aquatic environments, including phototrophs, invertebrates, and fungi. The detection of FMA viruses from orders dominated by plant viruses, namely Patatavirales and Tymovirales, indicate that members of these orders may thrive in aquatic hosts. PCR assays confirmed the presence of putative FMA plant viruses in asymptomatic vascular plants, indicating that viruses with persistent lifestyles are widespread in macrophytes. The detection of potato virus Y and oat blue dwarf virus in submerged macrophytes suggests that terrestrial plant viruses infect underwater plants and highlights a potential terrestrial-freshwater plant virus continuum. Defining the virome of unexplored macrophytes will improve our understanding of virus evolution in terrestrial and aquatic primary producers and reveal the potential ecological impacts of viral infection in macrophytes.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States
| | - Noémi Van Bogaert
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States,Present Address: FVPHouse, Berlare, Belgium
| | | | - Haris Paliogiannis
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States,Present Address: MIO-ECSDE, Athens, Greece
| | - Mason Kerr
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States
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8
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Diversity of CRESS DNA Viruses in Squamates Recapitulates Hosts Dietary and Environmental Sources of Exposure. Microbiol Spectr 2022; 10:e0078022. [PMID: 35616383 PMCID: PMC9241739 DOI: 10.1128/spectrum.00780-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses comprise viruses with covalently closed, circular, single-stranded DNA (ssDNA) genomes, and are considered the smallest known autonomously replicating, capsid-encoding animal pathogens. CRESS DNA viruses (phylum Cressdnaviricota) encompass several viral families including Circoviridae. Circoviruses are classified into two genera, Circovirus and Cyclovirus, and they are known to cause fatal diseases in birds and pigs. Circoviruses have also been identified in human stools, blood, and cerebrospinal fluid (CSF), as well as in various wild and domestic vertebrates, including reptiles. The synanthropic presence of Squamata reptiles has increased in the last century due to the anthropic pressure, which has shifted forested animal behavior to an urban and peri-urban adaptation. In this paper, we explored the diversity of CRESS DNA viruses in Squamata reptiles from different Italian areas representative of the Mediterranean basin. CRESS DNA viruses were detected in 31.7% (33/104) of sampled lizards and geckoes. Different CRESS DNA viruses likely reflected dietary composition or environmental contamination and included avian-like (n = 3), dog (n = 4), bat-like (n = 1), goat-like (n = 1), rodent-like (n = 4), and insect-like (n = 2) viruses. Rep sequences of at least two types of human-associated cycloviruses (CyV) were identified consistently, regardless of geographic location, namely, TN9-like (n = 11) and TN12-like (n = 6). A third human-associated CyV, TN25-like, was detected in a single sample. The complete genome of human-like CyVs, of a rodent-like, insect-like, and of a bat-like virus were generated. Collectively, the results recapitulate hosts dietary and environmental sources of exposure and may suggest unexpected ecological niches for some CRESS DNA viruses. IMPORTANCE CRESS DNA viruses are significant pathogens of birds and pigs and have been detected repeatedly in human samples (stools, serum, and cerebrospinal fluid), both from healthy individuals and from patients with neurological disease, eliciting in 2013 a risk assessment by the European Centre for Disease Prevention and Control (ECDC). Sequences of CRESS DNA viruses previously reported in humans (TN9, TN12, and TN25), and detected in different animal species (e.g., birds, dogs, and bats) were herein detected in fecal samples of synanthropic squamates (geckos and lizards). The complete genome sequence of six viruses was generated. This study extends the information on the genetic diversity and ecology of CRESS DNA viruses. Because geckos and lizards are synanthropic animals, a role in sustaining CRESS DNA virus circulation and increasing viral pressure in the environment is postulated.
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Zayed AA, Wainaina JM, Dominguez-Huerta G, Pelletier E, Guo J, Mohssen M, Tian F, Pratama AA, Bolduc B, Zablocki O, Cronin D, Solden L, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Ruscheweyh HJ, Salazar G, Shatoff E, Coordinators TO, Bundschuh R, Fredrick K, Kubatko LS, Chaffron S, Culley AI, Sunagawa S, Kuhn JH, Wincker P, Sullivan MB. Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome. Science 2022; 376:156-162. [PMID: 35389782 PMCID: PMC10990476 DOI: 10.1126/science.abm5847] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of the new phyla "Taraviricota," a missing link in early RNA virus evolution, and "Arctiviricota" are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.
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Affiliation(s)
- Ahmed A. Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - James M. Wainaina
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Guillermo Dominguez-Huerta
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Jiarong Guo
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Mohamed Mohssen
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
| | - Funing Tian
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Akbar Adjie Pratama
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Dylan Cronin
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Lindsey Solden
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Erwan Delage
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Nantes Université, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Corinne da Silva
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Elan Shatoff
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | | | - Ralf Bundschuh
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
- Division of Hematology, Department of Internal Medicine, Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Laura S. Kubatko
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
- Department of Statistics, Ohio State University, Columbus, OH 43210, USA
| | - Samuel Chaffron
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Nantes Université, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Alexander I. Culley
- Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA
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10
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Li R, Zhu L, Cui L, Zhu YG. Viral diversity and potential environmental risk in microplastic at watershed scale: Evidence from metagenomic analysis of plastisphere. ENVIRONMENT INTERNATIONAL 2022; 161:107146. [PMID: 35183943 DOI: 10.1016/j.envint.2022.107146] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/27/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Microplastics (MPs) have been considered as a new vector for the long-distance transport of pathogens in aquatic ecosystems. However, the composition of viral communities attached on MPs and their environmental risk are largely unknown. Here, we profiled the viral diversity and potential risk in five different MPs collected from the Beilun River based on metagenomic analysis. Nearly 2863 million raw reads were produced and assembled, and annotation resulted in the identification of 1719 different species of viruses in MPs. Viruses in polypropylene (PP) displayed the highest diversity, with about 250 specific viruses detected. Source tracking of viruses in MPs by the fast expectation-maximization microbial source tracking method (FEAST) demonstrated that viruses in upstream and downstream MPs are two major sources of viruses in estuary. Furthermore, the MP-type-dependent potential environmental risk of viruses was significant based on both antibiotic resistance genes (ARGs) and virulence factors (VFs) detected in viral metagenomes, and PP was confirmed with the highest potential environmental risk. This study reveals the high diversity and potential environmental risk of viruses in different MPs, and provides an important guidance for future environmental monitoring and understanding the potential risks associated with both viral transmission and MPs pollution.
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Affiliation(s)
- Ruilong Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Longji Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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11
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Prado T, Shubo T, Freitas L, Leomil L, Maranhão AG, Miagostovich MP. Virome in roof-harvested rainwater of a densely urbanized low-income region. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150778. [PMID: 34619218 DOI: 10.1016/j.scitotenv.2021.150778] [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: 06/28/2021] [Revised: 08/13/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
Rainwater harvesting has been considered an affordable practice to supplement the conventional sources of water supply for potable and non-potable uses worldwide. This study characterizes the viral community found in roof-harvested rainwater (RHRW) samples obtained under different rain volumes in a densely urbanized low-income region in Rio de Janeiro, Brazil. Three pilot-scale standardized metal-sheet roofs (same catchment area, material age, and slope - 3%) were installed in the study area aiming at obtaining more reliable and representative samples. Fifty-four samples were collected from six rainfall events from January to April 2019 and concentrated by the skimmed-milk flocculation method. Pools of different rainfall volumes were submitted to high throughput sequencing using the shotgun metagenomic approach. Sequencing was performed on NextSeq platform. Genomic analysis of the virus community revealed that most are RNA non-human viruses, including two main families: Dicistroviridae and Iflaviridae, recognized for infecting arthropods. Bacteriophages were also relatively abundant, with a predominance of DNA phages belonging to Microviridae and Siphoviridae families, showing percentages from 5.3 and 3.7% of the total viral hits present in these samples, respectively. Viral genomic RNA viruses (77%) predominated over DNA viruses (23%). Concerning number of viral species identified, a higher percentage was observed for plant viruses (12 families, 58%). Hepatitis A virus and human klassevirus 1 were detected among the established human pathogens, suggesting the need for RHRW treatment before it is considered for human consumption. Australian bat lyssavirus was also detected, emphasizing the importance of environmental monitoring facing emerging viruses. The results corroborate the influence of the surrounding area on the rainwater quality.
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Affiliation(s)
- Tatiana Prado
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation. Av. Brasil, 4365, Manguinhos CEP 21040-360, Rio de Janeiro, Brazil.
| | - Tatsuo Shubo
- Sergio Arouca Public Health National School, Oswaldo Cruz Foundation, Brazil
| | - Lucas Freitas
- Laboratory of Respiratory Virus and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Brazil
| | - Luciana Leomil
- SENAI Innovation Institute for Biosynthetics and Fibers, Technology Center for Chemical and Textile Industry, SENAI CETIQT - R: Fernando de Souza Barros, 120 - Cidade Universitária Ilha do Fundão, Rio de Janeiro CEP: 21941-857, RJ, Brazil
| | - Adriana Gonçalves Maranhão
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation. Av. Brasil, 4365, Manguinhos CEP 21040-360, Rio de Janeiro, Brazil
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation. Av. Brasil, 4365, Manguinhos CEP 21040-360, Rio de Janeiro, Brazil
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12
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Rothman JA, Loveless TB, Kapcia J, Adams ED, Steele JA, Zimmer-Faust AG, Langlois K, Wanless D, Griffith M, Mao L, Chokry J, Griffith JF, Whiteson KL. RNA Viromics of Southern California Wastewater and Detection of SARS-CoV-2 Single-Nucleotide Variants. Appl Environ Microbiol 2021; 87:e0144821. [PMID: 34550753 PMCID: PMC8579973 DOI: 10.1128/aem.01448-21] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/14/2021] [Indexed: 11/20/2022] Open
Abstract
Municipal wastewater provides an integrated sample of a diversity of human-associated microbes across a sewershed, including viruses. Wastewater-based epidemiology (WBE) is a promising strategy to detect pathogens and may serve as an early warning system for disease outbreaks. Notably, WBE has garnered substantial interest during the coronavirus disease 2019 (COVID-19) pandemic to track disease burden through analyses of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. Throughout the COVID-19 outbreak, tracking SARS-CoV-2 in wastewater has been an important tool for understanding the spread of the virus. Unlike traditional sequencing of SARS-CoV-2 isolated from clinical samples, which adds testing burden to the health care system, in this study, metatranscriptomics was used to sequence virus directly from wastewater. Here, we present a study in which we explored RNA viral diversity through sequencing 94 wastewater influent samples across seven wastewater treatment plants (WTPs), collected from August 2020 to January 2021, representing approximately 16 million people in Southern California. Enriched viral libraries identified a wide diversity of RNA viruses that differed between WTPs and over time, with detected viruses including coronaviruses, influenza A, and noroviruses. Furthermore, single-nucleotide variants (SNVs) of SARS-CoV-2 were identified in wastewater, and we measured proportions of overall virus and SNVs across several months. We detected several SNVs that are markers for clinically important SARS-CoV-2 variants along with SNVs of unknown function, prevalence, or epidemiological consequence. Our study shows the potential of WBE to detect viruses in wastewater and to track the diversity and spread of viral variants in urban and suburban locations, which may aid public health efforts to monitor disease outbreaks. IMPORTANCE Wastewater-based epidemiology (WBE) can detect pathogens across sewersheds, which represents the collective waste of human populations. As there is a wide diversity of RNA viruses in wastewater, monitoring the presence of these viruses is useful for public health, industry, and ecological studies. Specific to public health, WBE has proven valuable during the coronavirus disease 2019 (COVID-19) pandemic to track the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) without adding burden to health care systems. In this study, we used metatranscriptomics and reverse transcription-droplet digital PCR (RT-ddPCR) to assay RNA viruses across Southern California wastewater from August 2020 to January 2021, representing approximately 16 million people from Los Angeles, Orange, and San Diego counties. We found that SARS-CoV-2 quantification in wastewater correlates well with county-wide COVID-19 case data, and that we can detect SARS-CoV-2 single-nucleotide variants through sequencing. Likewise, wastewater treatment plants (WTPs) harbored different viromes, and we detected other human pathogens, such as noroviruses and adenoviruses, furthering our understanding of wastewater viral ecology.
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Affiliation(s)
- Jason A. Rothman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
| | - Theresa B. Loveless
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, USA
| | - Joseph Kapcia
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
| | - Eric D. Adams
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
| | - Joshua A. Steele
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | | | - Kylie Langlois
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - David Wanless
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Madison Griffith
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Lucy Mao
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Jeffrey Chokry
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - John F. Griffith
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Katrine L. Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
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13
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Cui L, Li HZ, Yang K, Zhu LJ, Xu F, Zhu YG. Raman biosensor and molecular tools for integrated monitoring of pathogens and antimicrobial resistance in wastewater. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116415] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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14
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Le Gratiet T, Le Marechal C, Devaere M, Chemaly M, Woudstra C. Exploration of the Diversity of Clustered Regularly Interspaced Short Palindromic Repeats-Cas Systems in Clostridium novyi sensu lato. Front Microbiol 2021; 12:711413. [PMID: 34589070 PMCID: PMC8473940 DOI: 10.3389/fmicb.2021.711413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022] Open
Abstract
Classified as the genospecies Clostridium novyi sensu lato and distributed into four lineages (I-IV), Clostridium botulinum (group III), Clostridium novyi, and Clostridium haemolyticum are clostridial pathogens that cause animal diseases. Clostridium novyi sensu lato contains a large mobilome consisting of plasmids and circular bacteriophages. Here, we explored clustered regularly interspaced short palindromic repeats (CRISPR) arrays and their associated proteins (Cas) to shed light on the link between evolution of CRISPR-Cas systems and the plasmid and phage composition in a study of 58 Clostridium novyi sensu lato genomes. In 55 of these genomes, types I-B (complete or partial), I-D, II-C, III-B, III-D, or V-U CRISPR-Cas systems were detected in chromosomes as well as in mobile genetic elements (MGEs). Type I-B predominated (67.2%) and was the only CRISPR type detected in the Ia, III, and IV genomic lineages. Putative type V-U CRISPR Cas14a genes were detected in two different cases: next to partial type-IB CRISPR loci on the phage encoding the botulinum neurotoxin (BoNT) in lineage Ia and in 12 lineage II genomes, as part of a putative integrative element related to a phage-inducible chromosomal island (PICI). In the putative PICI, Cas14a was associated with CRISPR arrays and restriction modification (RM) systems as part of an accessory locus. This is the first time a PICI containing such locus has been detected in C. botulinum. Mobilome composition and dynamics were also investigated based on the contents of the CRISPR arrays and the study of spacers. A large proportion of identified protospacers (20.2%) originated from Clostridium novyi sensu lato (p1_Cst, p4_BKT015925, p6_Cst, CWou-2020a, p1_BKT015925, and p2_BKT015925), confirming active exchanges within this genospecies and the key importance of specific MGEs in Clostridium novyi sensu lato.
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Affiliation(s)
- Thibault Le Gratiet
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France.,UFR of Life Sciences and Environment, University of Rennes, Rennes, France
| | - Caroline Le Marechal
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
| | - Marie Devaere
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
| | - Marianne Chemaly
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
| | - Cédric Woudstra
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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15
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Liu G, Lu Y, Shi L, Kong J, Hu H, Liu W. Trace endotoxin in reclaimed water is only one of the risk sources in subchronic inhalation exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 285:117479. [PMID: 34090073 DOI: 10.1016/j.envpol.2021.117479] [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: 03/23/2021] [Revised: 05/12/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
Pulmonary injury and inflammation have been detected in cases of subchronic inhalation exposure to reclaimed water, but the mechanism remains unclear. Endotoxin has been verified as the key risk factor in acute inhalation exposure through the TLR4 (Toll-like receptor 4) signalling pathway. In long-term exposure, endotoxin may also be a risk factor in reclaimed water, but the contribution of other health risk factors should not be underestimated. Wild-type C57BL/6J and TLR4-signalling-pathway-defective mice were used in this study to assess the risk of subchronic inhalation exposure to reclaimed water. Two types of reclaimed water, i.e., secondary effluent and MBR (membrane bioreactor) effluent, were found to induce pulmonary injury and inflammation in the wild-type mice and Tlr4-/- mutants. However, when both mice were exposed to the same concentrations of pure endotoxin in reclaimed water, only the wild-type mice that were treated with high-dose endotoxin showed pulmonary injury. In summary, non-TLR4 signalling pathways are related to lung inflammation caused by long-term exposure to reclaimed water. It is highly possible that pollutants in addition to endotoxin in the reclaimed water can induce chronic inflammation in the lung.
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Affiliation(s)
- Gang Liu
- State Environment Protection Key Laboratory of Microorganism Application and Rish Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yun Lu
- State Environment Protection Key Laboratory of Microorganism Application and Rish Control, School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Liangliang Shi
- State Environment Protection Key Laboratory of Microorganism Application and Rish Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jiayang Kong
- State Environment Protection Key Laboratory of Microorganism Application and Rish Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Hongying Hu
- State Environment Protection Key Laboratory of Microorganism Application and Rish Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Wanli Liu
- School of Life Science, Tsinghua University, Beijing, 100084, China
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16
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NGS Techniques Reveal a High Diversity of RNA Viral Pathogens and Papillomaviruses in Fresh Produce and Irrigation Water. Foods 2021; 10:foods10081820. [PMID: 34441597 PMCID: PMC8394881 DOI: 10.3390/foods10081820] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/22/2021] [Accepted: 07/31/2021] [Indexed: 02/07/2023] Open
Abstract
Fresh fruits and vegetables are susceptible to microbial contamination at every stage of the food production chain, and as a potential source of pathogens, irrigation water quality is a critical factor. Next-generation sequencing (NGS) techniques have been flourishing and expanding to a wide variety of fields. However, their application in food safety remains insufficiently explored, and their sensitivity requires improvement. In this study, quantitative polymerase chain reaction (qPCR) assays showed low but frequent contamination of common circulating viral pathogens, which were found in 46.9% of samples of fresh produce: 6/12 lettuce samples, 4/12 strawberries samples, and 5/8 parsley samples. Furthermore, the application of two different NGS approaches, target enrichment sequencing (TES) for detecting viruses that infect vertebrates and amplicon deep sequencing (ADS), revealed a high diversity of viral pathogens, especially Norovirus (NoV) and Human Papillomavirus (HPV), in fresh produce and irrigation water. All NoV and HPV types found in fresh fruit and vegetable samples were also detected in irrigation water sources, indicating that these viruses are common circulating pathogens in the population and that irrigation water may be the most probable source of viral pathogens in food samples.
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17
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Near-Complete Genome Sequence of Ryegrass Mottle Virus from Irrigation Water in Ecuador. Microbiol Resour Announc 2021; 10:10/18/e00037-21. [PMID: 33958411 PMCID: PMC8103856 DOI: 10.1128/mra.00037-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
In this work, we report the near-complete genome sequence of Ryegrass mottle virus identified in irrigation water through next-generation sequencing and de novo assembly. The genome is 4,247 bp long, arranged in five open reading frames with a 5′ untranslated region (UTR) of 87 nucleotides and a 3′ UTR of 247 nucleotides. In this work, we report the near-complete genome sequence of ryegrass mottle virus identified in irrigation water through next-generation sequencing and de novo assembly. The genome is 4,247 bp long, arranged in five open reading frames with a 5′ untranslated region (UTR) of 87 nucleotides and a 3′ UTR of 247 nucleotides.
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18
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Wani GA, Khan MA, Dar MA, Shah MA, Reshi ZA. Next Generation High Throughput Sequencing to Assess Microbial Communities: An Application Based on Water Quality. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2021; 106:727-733. [PMID: 33774727 DOI: 10.1007/s00128-021-03195-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 03/13/2021] [Indexed: 06/12/2023]
Abstract
Traditional techniques to identify different contaminants (biological or chemical) in the waters are slow, laborious, and can require specialized expertise. Hence, the rapid determination of water quality using more sensitive and reliable metagenomic based approaches attains special importance. Metagenomics deals with the study of genetic material that is recovered from microbial communities present in environmental samples. In traditional techniques cultivation-based methodologies were used to describe the diversity of microorganisms in environmental samples. It has failed to function as a robust marker because of limited taxonomic and phylogenetic implications. In this backdrop, high-throughput DNA sequencing approaches have proven very powerful in microbial source tracking because of investigating the full variety of genome-based analysis such as microbial genetic diversity and population structure played by them. Next generation sequencing technologies can reveal a greater proportion of microbial communities that have not been reported earlier by traditional techniques. The present review highlights the shift from traditional techniques for the basic study of community composition to next-generation sequencing (NGS) platforms and their potential applications to the biomonitoring of water quality in relation to human health.
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Affiliation(s)
- Gowher A Wani
- Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190 006, India.
| | - Mohd Asgar Khan
- Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190 006, India
| | - Mudasir A Dar
- Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190 006, India
| | - Manzoor A Shah
- Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190 006, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190 006, India
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19
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Garner E, Davis BC, Milligan E, Blair MF, Keenum I, Maile-Moskowitz A, Pan J, Gnegy M, Liguori K, Gupta S, Prussin AJ, Marr LC, Heath LS, Vikesland PJ, Zhang L, Pruden A. Next generation sequencing approaches to evaluate water and wastewater quality. WATER RESEARCH 2021; 194:116907. [PMID: 33610927 DOI: 10.1016/j.watres.2021.116907] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/15/2021] [Accepted: 02/03/2021] [Indexed: 05/24/2023]
Abstract
The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.
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Affiliation(s)
- Emily Garner
- Wadsworth Department of Civil and Environmental Engineering, West Virginia University, 1306 Evansdale Drive, Morgantown, WV 26505, United States.
| | - Benjamin C Davis
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Erin Milligan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Matthew Forrest Blair
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ishi Keenum
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ayella Maile-Moskowitz
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Jin Pan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Mariah Gnegy
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Krista Liguori
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Suraj Gupta
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, United States
| | - Aaron J Prussin
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Linsey C Marr
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Peter J Vikesland
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Amy Pruden
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States.
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20
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Jafferali MH, Khatami K, Atasoy M, Birgersson M, Williams C, Cetecioglu Z. Benchmarking virus concentration methods for quantification of SARS-CoV-2 in raw wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 755:142939. [PMID: 33121776 PMCID: PMC7553858 DOI: 10.1016/j.scitotenv.2020.142939] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/04/2020] [Accepted: 10/04/2020] [Indexed: 05/17/2023]
Abstract
Wastewater-based epidemiology offers a cost-effective alternative to testing large populations for SARS-CoV-2 virus, and may potentially be used as an early warning system for SARS-CoV-2 pandemic spread. However, viruses are highly diluted in wastewater, and a validated method for their concentration and further processing, and suitable reference viruses, are the main needs to be established for reliable SARS-CoV-2 municipal wastewater detection. For this purpose, we collected wastewater from two European cities during the Covid-19 pandemic and evaluated the sensitivity of RT-qPCR detection of viral RNA after four concentration methods (two variants of ultrafiltration-based method and two adsorption and extraction-based methods). Further, we evaluated one external (bovine corona virus) and one internal (pepper mild mottle virus) reference virus. We found a consistently higher recovery of spiked virus using the modified ultrafiltration-based method. This method also had a significantly higher efficiency (p-value <0.01) for wastewater SARS-CoV-2 detection. The ultracentrifugation method was the only method that detected SARS-CoV-2 in the wastewater of both cities. The pepper mild mottle virus was found to function as a potentially suitable internal reference standard.
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Affiliation(s)
- Mohammed Hakim Jafferali
- Department of Protein Science, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Kasra Khatami
- Department of Chemical Engineering, KTH Royal Institute of Technology, SE-100 44, Sweden
| | - Merve Atasoy
- Department of Chemical Engineering, KTH Royal Institute of Technology, SE-100 44, Sweden
| | - Madeleine Birgersson
- Department of Protein Science, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Cecilia Williams
- Department of Protein Science, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Zeynep Cetecioglu
- Department of Chemical Engineering, KTH Royal Institute of Technology, SE-100 44, Sweden.
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21
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Zhang G, Guan Y, Zhao R, Feng J, Huang J, Ma L, Li B. Metagenomic and network analyses decipher profiles and co-occurrence patterns of antibiotic resistome and bacterial taxa in the reclaimed wastewater distribution system. JOURNAL OF HAZARDOUS MATERIALS 2020; 400:123170. [PMID: 32590136 DOI: 10.1016/j.jhazmat.2020.123170] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 06/02/2020] [Accepted: 06/07/2020] [Indexed: 05/08/2023]
Abstract
Metagenomic and network analyses were applied to decipher the profiles and co-occurrence of resistome and microbial taxa in the reclaimed wastewater distribution system, including reclaimed wastewater and two types of biofilms, i.e., surface layer biofilms and inner layer biofilms. The effects of chlorination, UV irradiation and no disinfection treatment on ARG relative abundance and composition were systemically investigated. The reclaimed wastewater possesses more diverse and abundant ARGs than biofilms and total ARG relative abundance followed the order of reclaimed wastewater samples > surface layer biofilms > inner layer biofilms. Multidrug, bacitracin, sulfonamide, aminoglycoside, beta-lactam, and macrolide-lincosamide-streptogramin resistance genes were the six most dominant ARG types and their sum accounted for 90.1 %-96.0 % of the total ARG relative abundance in different samples. Beta-lactam resistance gene was the discriminative ARG type for reclaimed wastewater. Bacitracin resistance gene and bacA were the discriminative ARG type and subtype for biofilms. Chlorination significantly reduced ARG relative abundance in the reclaimed wastewater. Nevertheless, it could not reduce ARG relative abundance in biofilms. Regarding to the total ARG profiles, there were no obvious increasing or decreasing trends over time during one year period. Co-occurrence results revealed twenty-six genera were deduced as the potential hosts of twenty-two ARG subtypes.
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Affiliation(s)
- Guijuan Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing, China
| | - Yuntao Guan
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing, China
| | - Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Jie Feng
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Jin Huang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Liping Ma
- Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
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22
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Miyani B, McCall C, Xagoraraki I. High abundance of human herpesvirus 8 in wastewater from a large urban area. J Appl Microbiol 2020; 130:1402-1411. [PMID: 33058412 DOI: 10.1111/jam.14895] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/18/2020] [Accepted: 10/07/2020] [Indexed: 11/28/2022]
Abstract
AIMS This study assesses the diversity and abundance of Human Herpesviruses (HHVs) in the influent of an urban wastewater treatment plant using shotgun sequencing, metagenomic analysis and qPCR. METHODS AND RESULTS Influent wastewater samples were collected from the three interceptors that serve the City of Detroit and Wayne, Macomb and Oakland counties between November 2017 to February 2018. The samples were subjected to a series of processes to concentrate viruses which were further sequenced and amplified using qPCR. All nine types of HHV were detected in wastewater. Human Herpesvirus 8 (HHV-8), known as Kaposi's sarcoma herpesvirus, which is only prevalent in 5-10% of USA population, was found to be the most abundant followed by HHV-3 or Varicella-zoster virus. CONCLUSIONS The high abundance of HHV-8 in the Detroit metropolitan area may be attributed to the HIV-AIDS outbreak that was ongoing in Detroit during the sampling period. SIGNIFICANCE AND IMPACT OF THE STUDY The approach described in this paper can be used to establish a baseline of viruses secreted by the community as a whole. Sudden changes in the baseline would identify changes in community health and immunity.
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Affiliation(s)
- B Miyani
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - C McCall
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - I Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
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23
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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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24
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Jebri S, Rahmani F, Hmaied F. Bacteriophages as antibiotic resistance genes carriers in agro-food systems. J Appl Microbiol 2020; 130:688-698. [PMID: 32916015 DOI: 10.1111/jam.14851] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/04/2020] [Indexed: 12/14/2022]
Abstract
Antibiotic resistance genes (ARGs) are a global health concern. Antibiotic resistance occurs naturally, but misuse of antibiotics in humans and animals is accelerating the process of antibiotic resistance emergency, which has been aggravated by exposure to molecules of antibiotics present in clinical and agricultural settings and the engagement of many countries in water reuse especially in Middle East and North Africa region. Bacteriophages have the potential to be significant actors in ARGs transmission through the transduction process. These viruses have been detected along with ARGs in non impacted habitats and in anthropogenic impacted environments like wastewater, reclaimed water and manure amended soil as well as minimally processed food and ready to eat vegetables. The ubiquity of bacteriophages and their persistence in the environment raises concern about their involvement in ARGs transmission among different biomes and the generation of pathogenic-resistant bacteria that pose a great threat to human health. The aim of this review is to give an overview of the potential role of bacteriophages in the dissemination and the transfer of ARGs to pathogens in food production and processing and the consequent contribution to antibiotic resistance transmission through faecal oral route carrying ARGs to our dishes.
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Affiliation(s)
- S Jebri
- Laboratoire de Biotechnologies et Technologie Nucléaire (LR16CNSTN01), Centre National des Sciences et Technologie Nucléaire, Sidi Thabet, Tunisia
| | - F Rahmani
- Laboratoire de Biotechnologies et Technologie Nucléaire (LR16CNSTN01), Centre National des Sciences et Technologie Nucléaire, Sidi Thabet, Tunisia
| | - F Hmaied
- Laboratoire de Biotechnologies et Technologie Nucléaire (LR16CNSTN01), Centre National des Sciences et Technologie Nucléaire, Sidi Thabet, Tunisia
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25
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Profile of the Spatial Distribution Patterns of the Human and Bacteriophage Virome in a Wastewater Treatment Plant Located in the South of Spain. WATER 2020. [DOI: 10.3390/w12082316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In wastewater treatment plants, most microbial characterization has focused on bacterial, archaeal, and fungal populations. Due to the difficult isolation, quantification, and identification of viruses, only a limited number of virome studies associated with wastewater treatment plants have been carried out. However, the virus populations play an important role in the microbial dynamics in wastewater treatment systems and the biosafety of effluents. In this work, the viral members present in influent wastewater, mixed liquor (aerobic bioreactor), excess sludge, and effluent water of a conventional activated sludge system for the treatment of urban wastewater were identified. Viral members were observed by transmission electron microscopy and studied through next-generation sequencing studies. The results showed the dominance of bacteriophages in the viral community in all samples, with the dominant viral phylotype classified as Escherichia coli O157 typing phage 7. Moreover, different human viruses, such as Cynomolgus cytomegalovirus and Gammaherpesvirus, were also detected.
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26
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Abstract
Many biological contaminants are disseminated through water, and their occurrence has potential detrimental impacts on public and environmental health. Conventional monitoring tools rely on cultivation and are not robust in addressing modern water quality concerns. This review proposes metagenomics as a means to provide a rapid, nontargeted assessment of biological contaminants in water. When further coupled with appropriate methods (e.g., quantitative PCR and flow cytometry) and bioinformatic tools, metagenomics can provide information concerning both the abundance and diversity of biological contaminants in reclaimed waters. Further correlation between the metagenomic-derived data of selected contaminants and the measurable parameters of water quality can also aid in devising strategies to alleviate undesirable water quality. Here, we review metagenomic approaches (i.e., both sequencing platforms and bioinformatic tools) and studies that demonstrated their use for reclaimed-water quality monitoring. We also provide recommendations on areas of improvement that will allow metagenomics to significantly impact how the water industry performs reclaimed-water quality monitoring in the future.
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Affiliation(s)
- Pei-Ying Hong
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - David Mantilla-Calderon
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Changzhi Wang
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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27
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Yukgehnaish K, Kumar P, Sivachandran P, Marimuthu K, Arshad A, Paray BA, Arockiaraj J. Gut microbiota metagenomics in aquaculture: factors influencing gut microbiome and its physiological role in fish. REVIEWS IN AQUACULTURE 2020; 12:1903-1927. [DOI: 10.1111/raq.12416] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/03/2020] [Indexed: 10/16/2023]
Abstract
AbstractFish gut microbiome confers various effects to the host fish; this includes overall size, metabolism, feeding behaviour and immune response in the fish. The emergence of antimicrobial‐resistant (AMR) bacteria and hard to cure fish diseases warrant the possible utilization of gut microbes that exhibits a positive effect on the fish and thus lead to the usage of these microbes as probiotics. The widespread and systematic use of antibiotics has led to severe biological and ecological problems, especially the development of antibiotic resistance that affects the gut microbiota of aquatic organisms. Probiotics are proposed as an effective and environmentally friendly alternative to antibiotics, known as beneficial microbes. At the same time, prebiotics are considered beneficial to the host's health and growth by decreasing the prevalence of intestinal pathogens and/or changing the development of bacterial metabolites related to health. Uprise of sequencing technology and the development of intricate bioinformatics tools has provided a way to study these gut microbes through metagenomic analysis. From various metagenomic studies, ample of information was obtained; such information includes the effect of the gut microbiome on the physiology of fish, gut microbe composition of different fish, factors affecting the gut microbial composition of the fish and the immunological effect of gut microbes in fish; such this information related to the fish gut microbiome, their function and their importance in aquaculture is discussed in this review.
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Affiliation(s)
| | - Praveen Kumar
- SRM Research Institute SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Parimannan Sivachandran
- Faculty of Applied Sciences Centre of Excellence for Omics-Driven Computational Biodiscovery (CO MBio) AIMST University Bedong Malaysia
- Faculty of Science School of Life and Environmental Sciences Engineering and Built Environment Deakin University, Waurn Ponds Campus Geelong Australia
| | - Kasi Marimuthu
- Department of Biotechnology AIMST University Semeling Kedah Darul Aman Malaysia
| | - Aziz Arshad
- International Institute of Aquaculture and Aquatic Sciences (I-AQUAS) Universiti Putra Malaysia Serdang Negeri Sembilan Malaysia
- Department of Aquaculture Faculty of Agriculture Universiti Putra Malaysia Serdang Selangor Malaysia
- Laboratory of Marine Biotechnology Institute of Bioscience Universiti Putra Malaysia Serdang Selangor Darul Ehsan Malaysia
| | - Bilal Ahmad Paray
- Department of Zoology College of Science King Saud University Riyadh Saudi Arabia
| | - Jesu Arockiaraj
- SRM Research Institute SRM Institute of Science and Technology Chennai Tamil Nadu India
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28
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Inoue K, Asami T, Shibata T, Furumai H, Katayama H. Spatial and temporal profiles of enteric viruses in the coastal waters of Tokyo Bay during and after a series of rainfall events. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138502. [PMID: 32335450 DOI: 10.1016/j.scitotenv.2020.138502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/04/2020] [Accepted: 04/04/2020] [Indexed: 05/09/2023]
Abstract
Recreational activities in coastal waters that are polluted by enteric viruses can result in gastroenteritis etc. In this study, the pollution profiles of enteric viruses were examined in the coastal area of Tokyo Bay, Japan, by collecting 57 water samples from three different depths (0.5 m, 3.0 m, and 5.0 m) during and after a series of heavy rainfall events. Vertically spatial and temporal changes in the concentrations of NoV genogroup I (GI) and genogroup II (GII), pepper mild mottle virus (PMMoV), and Aichi virus (AiV) were determined using quantitative reverse transcription-polymerase chain reaction, while those of the bacterial indicator, Escherichia coli, and F-specific RNA bacteriophages (FRNA phages) were monitored using culture methods. PMMoV was highly abundant (1.4 × 104-6.8 × 106 genome copies/L), whereas the concentrations of the other enteric viruses were relatively low (AiV, 1.3 × 102-2.9 × 104; GI, 2.9 × 10-5.6 × 103; GII, 2.5 × 10-1.2 × 104 genome copies/L). All of the viruses showed lower fluctuations in concentration than E. coli, which increased up to 460-fold after the rainfall event and then decreased over the subsequent two weeks. The maximum vertical difference in E. coli concentration was observed immediately after the rainfall. The E. coli reached the surface and then gradually spread down, whereas the virus concentrations exhibited few fluctuations due to the remaining effects of the previous combined sewer overflows. These findings indicate that viruses have a relatively long retention period over fecal indicator bacteria in this coastal area.
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Affiliation(s)
- Kentaro Inoue
- Department of Urban Engineering, The University of Tokyo, Tokyo, Japan
| | - Tatsuya Asami
- Department of Urban Engineering, The University of Tokyo, Tokyo, Japan
| | - Tomoyo Shibata
- Department of Urban Engineering, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Furumai
- Department of Urban Engineering, The University of Tokyo, Tokyo, Japan; Research Center for Water Environment Technology, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Katayama
- Department of Urban Engineering, The University of Tokyo, Tokyo, Japan.
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29
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Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome. Nat Microbiol 2020; 5:1262-1270. [PMID: 32690954 PMCID: PMC7508674 DOI: 10.1038/s41564-020-0755-4] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 06/16/2020] [Indexed: 12/26/2022]
Abstract
RNA viruses in aquatic environments remain poorly studied. Here, we analysed the RNA virome from approximately 10 l water from Yangshan Deep-Water Harbour near the Yangtze River estuary in China and identified more than 4,500 distinct RNA viruses, doubling the previously known set of viruses. Phylogenomic analysis identified several major lineages, roughly, at the taxonomic ranks of class, order and family. The 719-member-strong Yangshan virus assemblage is the sister clade to the expansive class Alsuviricetes and consists of viruses with simple genomes that typically encode only RNA-dependent RNA polymerase (RdRP), capping enzyme and capsid protein. Several clades within the Yangshan assemblage independently evolved domain permutation in the RdRP. Another previously unknown clade shares ancestry with Potyviridae, the largest known plant virus family. The ‘Aquatic picorna-like viruses/Marnaviridae’ clade was greatly expanded, with more than 800 added viruses. Several RdRP-linked protein domains not previously detected in any RNA viruses were identified, such as the small ubiquitin-like modifier (SUMO) domain, phospholipase A2 and PrsW-family protease domain. Multiple viruses utilize alternative genetic codes implying protist (especially ciliate) hosts. The results reveal a vast RNA virome that includes many previously unknown groups. However, phylogenetic analysis of the RdRPs supports the previously established five-branch structure of the RNA virus evolutionary tree, with no additional phyla. Metagenomic analysis of a single RNA virome from the Yangshan Deep-Water Harbour in China enabled the recovery of more than 4,500 distinct RNA viruses, doubling the known set of RNA viruses to date, and provided insights into their biology.
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30
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Bačnik K, Kutnjak D, Pecman A, Mehle N, Tušek Žnidarič M, Gutiérrez Aguirre I, Ravnikar M. Viromics and infectivity analysis reveal the release of infective plant viruses from wastewater into the environment. WATER RESEARCH 2020; 177:115628. [PMID: 32299020 DOI: 10.1016/j.watres.2020.115628] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 05/06/2023]
Abstract
Viruses represent one of the most important threats to agriculture. Several viral families include highly stable pathogens, which remain infective and can be transported long distances in water. The diversity of plant viruses in wastewater remains understudied; however, their potential impact is increasing with the increased irrigation usage of reclaimed wastewater. To determine the abundance, diversity and biological relevance of plant viruses in wastewater influents and effluents we applied an optimized virus concentration method followed by high-throughput sequencing and infectivity assays. We detected representatives of 47 plant virus species, including emerging crop threats. We also demonstrated infectivity for pathogenic and economically relevant plant viruses from the genus Tobamovirus (family Virgaviridae), which remain infective even after conventional wastewater treatment. These results demonstrate the potential of metagenomics to capture the diversity of plant viruses circulating in the environment and expose the potential risk of the uncontrolled use of reclaimed water for irrigation.
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Affiliation(s)
- Katarina Bačnik
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Denis Kutnjak
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Anja Pecman
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Nataša Mehle
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Ion Gutiérrez Aguirre
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Maja Ravnikar
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia; University of Nova Gorica, Vipavska cesta, 5000, Nova Gorica, Slovenia.
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31
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Rivadulla E, Romalde JL. A Comprehensive Review on Human Aichi Virus. Virol Sin 2020; 35:501-516. [PMID: 32342286 PMCID: PMC7223127 DOI: 10.1007/s12250-020-00222-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 02/28/2020] [Indexed: 12/16/2022] Open
Abstract
Although norovirus, rotavirus, adenovirus and Astrovirus are considered the most important viral agents transmitted by food and water, in recent years other viruses, such as Aichi virus (AiV), have emerged as responsible for gastroenteritis outbreaks associated with different foods. AiV belongs to the genus Kobuvirus of the family Picornaviridae. It is a virus with icosahedral morphology that presents a single stranded RNA genome with positive sense (8280 nucleotides) and a poly (A) chain. AiV was first detected from clinical samples and in recent years has been involved in acute gastroenteritis outbreaks from different world regions. Furthermore, several studies conducted in Japan, Germany, France, Tunisia and Spain showed a high prevalence of AiV antibodies in adults (between 80% and 99%), which is indicative of a large exposure to this virus. The aim of this review is to bring together all the discovered information about the emerging pathogen human Aichi virus (AiV), discussing the possibles routes of transmission, new detection techniques and future research. Although AiV is responsible for a low percentage of gastroenteritis outbreaks, the high seroprevalence shown by human populations indicates an evident role as an enteric agent. The low percentage of AiV detection could be explained by the fact that the pathogen is more associated to subclinical infections. Further studies will be needed to clarify the real impact of AiV in human health and its importance as a causative gastroenteritis agent worldwide.
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Affiliation(s)
- Enrique Rivadulla
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago, Spain
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago, Spain.
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32
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Petrovich ML, Zilberman A, Kaplan A, Eliraz GR, Wang Y, Langenfeld K, Duhaime M, Wigginton K, Poretsky R, Avisar D, Wells GF. Microbial and Viral Communities and Their Antibiotic Resistance Genes Throughout a Hospital Wastewater Treatment System. Front Microbiol 2020; 11:153. [PMID: 32140141 PMCID: PMC7042388 DOI: 10.3389/fmicb.2020.00153] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 01/22/2020] [Indexed: 11/16/2022] Open
Abstract
Antibiotic resistance poses a serious threat to global public health, and antibiotic resistance determinants can enter natural aquatic systems through discharge of wastewater effluents. Hospital wastewater in particular is expected to contain high abundances of antibiotic resistance genes (ARGs) compared to municipal wastewater because it contains human enteric bacteria that may include antibiotic-resistant organisms originating from hospital patients, and can also have high concentrations of antibiotics and antimicrobials relative to municipal wastewater. Viruses also play an important role in wastewater treatment systems since they can influence the bacterial community composition through killing bacteria, facilitating transduction of genetic material between organisms, and modifying the chromosomal content of bacteria as prophages. However, little is known about the fate and connections between ARGs, viruses, and their associated bacteria in hospital wastewater systems. To address this knowledge gap, we characterized the composition and persistence of ARGs, dsDNA viruses, and bacteria from influent to effluent in a pilot-scale hospital wastewater treatment system in Israel using shotgun metagenomics. Results showed that ARGs, including genes conferring resistance to antibiotics of high clinical relevance, were detected in all sampling locations throughout the pilot-scale system, with only 16% overall depletion of ARGs per genome equivalent between influent and effluent. The most common classes of ARGs detected throughout the system conferred resistance to aminoglycoside, cephalosporin, macrolide, penam, and tetracycline antibiotics. A greater proportion of total ARGs were associated with plasmid-associated genes in effluent compared to in influent. No strong associations between viral sequences and ARGs were identified in viral metagenomes from the system, suggesting that phage may not be a significant vector for ARG transfer in this system. The majority of viruses in the pilot-scale system belonged to the families Myoviridae, Podoviridae, and Siphoviridae. Gammaproteobacteria was the dominant class of bacteria harboring ARGs and the most common putative viral host in all samples, followed by Bacilli and Betaproteobacteria. In the total bacterial community, the dominant class was Betaproteobacteria for each sample. Overall, we found that a variety of different types of ARGs and viruses were persistent throughout this hospital wastewater treatment system, which can be released to the environment through effluent discharge.
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Affiliation(s)
- Morgan L Petrovich
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
| | - Adi Zilberman
- The Water Research Center, School of The Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Aviv Kaplan
- The Water Research Center, School of The Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Gefen R Eliraz
- The Water Research Center, School of The Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yubo Wang
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
| | - Kathryn Langenfeld
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Melissa Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
| | - Krista Wigginton
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Rachel Poretsky
- Department of Biological Sciences, The University of Illinois at Chicago, Chicago, IL, United States
| | - Dror Avisar
- The Water Research Center, School of The Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - George F Wells
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
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A multiplex RT-PCR assay for the simultaneous detection of prevalent viruses infecting pepper (Capsicum annuum L.). J Virol Methods 2020; 278:113838. [PMID: 32061842 DOI: 10.1016/j.jviromet.2020.113838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 11/23/2022]
Abstract
The aim of this work was to create an easy, fast and sensitive method for the simultaneous detection of the most frequent viruses known to infect pepper (Capsicum annuum L.) crops. A multiplex RT-PCR assay was developed that successfully achieved this aim. Using specifically designed primer pairs, the assay could simultaneously amplify the genomes of members of the two subgroups (I and II) of cucumber mosaic virus (CMV), two tobamoviruses, tobacco mosaic virus (TMV) and pepper mild mottle virus (PMMoV), potato virus Y (PVY), and tomato spotted wilt virus (TSWV) in a single assay. The multiplex RT-PCR assay was found to be a sensitive diagnostic tool for the detection of the viruses from the leaves and fruits of naturally infected pepper plants. This assay would provide prompt disease status information for pepper breeders.
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Lewis E, Hudson JA, Cook N, Barnes JD, Haynes E. Next-generation sequencing as a screening tool for foodborne pathogens in fresh produce. J Microbiol Methods 2020; 171:105840. [PMID: 31945388 DOI: 10.1016/j.mimet.2020.105840] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/10/2020] [Accepted: 01/10/2020] [Indexed: 01/10/2023]
Abstract
Next generation sequencing (NGS) approaches are increasingly applied to tracing microbial contaminants entering the food chain due to NGS' untargeted nature and ability to investigate non-culturable (and/or difficult to culture) organisms while yielding genomic information about the microbiota. So far, a plethora of microbes has been shown to be associated with fresh produce, but few studies have utilised NGS to identify contamination with human pathogens. This study aims to establish the limit of detection (LoD) for Salmonella and phage MS2 (a Norovirus surrogate) contamination of fresh produce employing NGS approaches on the Illumina MiSeq: 16S amplicon-sequencing, and RNA-seq, using ScriptSeq (Illumina) and NEBNext (New England BioLabs) kits. ScriptSeq proved the most sensitive approach; delivering an LoD of 104 CFU reaction-1 (Colony Forming Units) for Salmonella and 105 PFU reaction-1 (Plaque Forming Units) for phage MS2. Use of the NEBNext kit resulted in detection of Salmonella at 106 CFU reaction-1 and phage MS2 at 107 PFU reaction-1. 16S amplicon-sequencing yielded a similar LoD of 105 CFU reaction-1 for Salmonella but could not detect MS2. The tested NGS methodologies, in combination with bioinformatics approaches applied, proved less sensitive than conventional microbial detection approaches.
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Affiliation(s)
- E Lewis
- IAFRI, Newcastle University, Newcastle upon Tyne, UK; Fera, National Agrifood Innovation Campus, Sand Hutton, York, UK.
| | | | - N Cook
- Jorvik Food Safety Services, York, UK
| | - J D Barnes
- IAFRI, Newcastle University, Newcastle upon Tyne, UK
| | - E Haynes
- Fera, National Agrifood Innovation Campus, Sand Hutton, York, UK
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Wang H, Kjellberg I, Sikora P, Rydberg H, Lindh M, Bergstedt O, Norder H. Hepatitis E virus genotype 3 strains and a plethora of other viruses detected in raw and still in tap water. WATER RESEARCH 2020; 168:115141. [PMID: 31590036 DOI: 10.1016/j.watres.2019.115141] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/24/2019] [Accepted: 09/29/2019] [Indexed: 06/10/2023]
Abstract
In this study, next generation sequencing was used to explore the virome in 20L up to 10,000L water from different purification steps at two Swedish drinking water treatment plants (DWTPs), and in tap water. One DWTP used ultrafiltration (UF) with 20 nm pores, the other UV light treatment after conventional treatment of the water. Viruses belonging to 26 different families were detected in raw water, in which 6-9 times more sequence reads were found for phages than for known environmental, plant or vertebrate viruses. The total number of viral reads was reduced more than 4-log10 after UF and 3-log10 over UV treatment. However, for some viruses the reduction was 3.5-log10 after UF, as for hepatitis E virus (HEV), which was also detected in tap water, with sequences similar to those in raw water and after treatment. This indicates that HEV had passed through the treatment and entered into the supply network. However, the viability of the viruses is unknown. In tap water 10-130 International Units of HEV RNA/mL were identified, which is a comparable low amount of virus. The risk of getting infected through consumption of tap water is probably negligible, but needs to be investigated. The HEV strains in the waters belonged to subtypes HEV3a and HEV3c/i, which is associated with unknown source of infection in humans infected in Sweden. None of these subtypes are common among pigs or wild boar, the major reservoirs for HEV, indicating that water may play a role in transmitting this virus. The results indicate that monitoring small fecal/oral transmitted viruses in DWTPs may be considered, especially during community outbreaks, to prevent potential transmission by tap water.
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Affiliation(s)
- Hao Wang
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden
| | | | - Per Sikora
- Department of Pathology and Genetics, Institute of Biomedicine at Sahlgrenska Academy, University of Gothenburg, 41345, Gothenburg, Sweden; Clinical Genomics Gothenburg, SciLife Labs, Gothenburg, Sweden
| | | | - Magnus Lindh
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Infectious Diseases, Gothenburg, Sweden
| | - Olof Bergstedt
- Göteborgs Stad Kretslopp och vatten, Gothenburg, Sweden; City of Gothenburg and DRICKS Chalmers University of Technology, Gothenburg, Sweden
| | - Heléne Norder
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Infectious Diseases, Gothenburg, Sweden.
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Metagenomic analysis of viruses, bacteria and protozoa in irrigation water. Int J Hyg Environ Health 2019; 224:113440. [PMID: 31978735 DOI: 10.1016/j.ijheh.2019.113440] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 12/17/2019] [Accepted: 12/20/2019] [Indexed: 12/27/2022]
Abstract
Viruses (e.g., noroviruses and hepatitis A and E virus), bacteria (e.g., Salmonella spp. and pathogenic Escherichia coli) and protozoa (e.g., Cryptosporidium parvum and Giardia intestinalis) are well-known contributors to food-borne illnesses linked to contaminated fresh produce. As agricultural irrigation increases the total amount of water used annually, reclaimed water is a good alternative to reduce dependency on conventional irrigation water sources. European guidelines have established acceptable concentrations of certain pathogens and/or indicators in irrigation water, depending on the irrigation system used and the irrigated crop. However, the incidences of food-borne infections are known to be underestimated and all the different pathogens contributing to these infections are not known. Next-generation sequencing (NGS) enables the determination of the viral, bacterial and protozoan populations present in a water sample, providing an opportunity to detect emerging pathogens and develop improved tools for monitoring the quality of irrigation water. This is a descriptive study of the virome, bacteriome and parasitome present in different irrigation water sources. We applied the same concentration method for all the studied samples and specific metagenomic approaches to characterize both DNA and RNA viruses, bacteria and protozoa. In general, most of the known viral species corresponded to plant viruses and bacteriophages. Viral diversity in river water varied over the year, with higher bacteriophage prevalences during the autumn and winter. Reservoir water contained Enterobacter cloacae, an opportunistic human pathogen and an indicator of fecal contamination, as well as Naegleria australiensis and Naegleria clarki. Hepatitis E virus and Naegleria fowleri, emerging human pathogens, were detected in groundwater. Reclaimed water produced in a constructed wetland system presented a virome and bacteriome that resembled those of freshwater samples (river and reservoir water). Viral, bacterial and protozoan pathogens were occasionally detected in the different irrigation water sources included in this study, justifying the use of improved NGS techniques to get a comprehensive evaluation of microbial species and potential environmental health hazards associated to irrigation water.
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Deng S, Yan X, Zhu Q, Liao C. The utilization of reclaimed water: Possible risks arising from waterborne contaminants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:113020. [PMID: 31421574 DOI: 10.1016/j.envpol.2019.113020] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 07/11/2019] [Accepted: 08/04/2019] [Indexed: 05/04/2023]
Abstract
Increasing interest of seeking substitutable water resources accrues from shortage of freshwater. One of the options considered is reclaimed water (also designated as recycled water) that has been widely used in daily life. Although reclaimed water can serve as a feasible reliever of water pressure, attention about its technologies and potential risks is growing in the meantime. Most established wastewater treatment plants (WWTPs) predate many new contaminants, which means treatment processes cannot ensure to dislodge certain contaminants completely from origin water. Furthermore, a wide range of factors, such as seasons and influent variations, affect occurrence and concentration of reclaimed water-borne contaminants, making research about quality of reclaimed water especially significant. Many reclaimed water-borne contaminants, including biological and chemical contaminants, are toxic to human health, and complex wastewater matrix may aggravate water quality of concern. The widespread use of reclaimed water continues to be a concern on agriculture, ecological environment and human health. This study aims to: 1) provide a critical review about occurrence and profiles of diverse contaminants in the treated reclaimed water, 2) discuss the possibility to avoid the secondary pollution in reuse of reclaimed water, and 3) reveal the prospective consequences of using reclaimed water on agriculture, ecological environment and human health.
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Affiliation(s)
- Shenxi Deng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueting Yan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingqing Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunyang Liao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Environment and Health, Jianghan University, Wuhan, Hubei 430056, China.
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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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Robledo-Mahón T, Silva-Castro GA, Kuhar U, Jamnikar-Ciglenečki U, Barlič-Maganja D, Aranda E, Calvo C. Effect of Composting Under Semipermeable Film on the Sewage Sludge Virome. MICROBIAL ECOLOGY 2019; 78:895-903. [PMID: 31037376 DOI: 10.1007/s00248-019-01365-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/18/2019] [Indexed: 05/15/2023]
Abstract
The addition of compost from sewage sludge to soils represents a sustainable option from an environmental and economic point of view, which involves the valorisation of these wastes. However, before their use as a soil amendment, compost has to reach the quality levels according to the normative, including microbial parameters. Viruses are not included in this regulation and they can produce agricultural problems and human diseases if the compost is not well sanitised. In this study, we carried out the analysis of the viral populations during a composting process with sewage sludge at an industrial scale, using semipermeable cover technology. Viral community was characterised by the presence of plant viruses and bacteriophages of enteric bacteria. The phytopathogen viruses were the group with the highest relative abundance in the sewage sludge sample and at 70 days of the composting process. The diversity of bacterial viruses and their specificity, with respect to the more abundant bacterial taxa throughout the process, highlights the importance of the interrelations between viral and bacterial communities in the control of pathogenic communities. These results suggest the possibility of using them as a tool to predict the effectiveness of the process.
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Affiliation(s)
- Tatiana Robledo-Mahón
- Institute of Water Research, Department of Microbiology, University of Granada, Ramón y Cajal 4, 18071, Granada, Spain
- Department of Microbiology, Pharmacy Faculty, University of Granada, Campus de Cartuja s/n, Ramón y Cajal 4, 18071, Granada, Spain
| | - Gloria Andrea Silva-Castro
- Institute of Water Research, Department of Microbiology, University of Granada, Ramón y Cajal 4, 18071, Granada, Spain
- Department of Microbiology, Pharmacy Faculty, University of Granada, Campus de Cartuja s/n, Ramón y Cajal 4, 18071, Granada, Spain
| | - Urška Kuhar
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000, Ljubljana, Slovenia
| | - Urška Jamnikar-Ciglenečki
- Institute of Food safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000, Ljubljana, Slovenia
| | - Darja Barlič-Maganja
- Faculty of Health Sciences, University of Primorska, Polje 42, 6310, Izola, Slovenia
| | - Elisabet Aranda
- Institute of Water Research, Department of Microbiology, University of Granada, Ramón y Cajal 4, 18071, Granada, Spain
- Department of Microbiology, Pharmacy Faculty, University of Granada, Campus de Cartuja s/n, Ramón y Cajal 4, 18071, Granada, Spain
| | - Concepción Calvo
- Institute of Water Research, Department of Microbiology, University of Granada, Ramón y Cajal 4, 18071, Granada, Spain.
- Department of Microbiology, Pharmacy Faculty, University of Granada, Campus de Cartuja s/n, Ramón y Cajal 4, 18071, Granada, Spain.
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Becker DJ, Washburne AD, Faust CL, Pulliam JRC, Mordecai EA, Lloyd-Smith JO, Plowright RK. Dynamic and integrative approaches to understanding pathogen spillover. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190014. [PMID: 31401959 PMCID: PMC6711302 DOI: 10.1098/rstb.2019.0014] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2019] [Indexed: 12/23/2022] Open
Affiliation(s)
- Daniel J. Becker
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Alex D. Washburne
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Christina L. Faust
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Juliet R. C. Pulliam
- South African Centre for Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | | | - James O. Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Raina K. Plowright
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
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Malik YS, Verma AK, Kumar N, Touil N, Karthik K, Tiwari R, Bora DP, Dhama K, Ghosh S, Hemida MG, Abdel-Moneim AS, Bányai K, Vlasova AN, Kobayashi N, Singh RK. Advances in Diagnostic Approaches for Viral Etiologies of Diarrhea: From the Lab to the Field. Front Microbiol 2019; 10:1957. [PMID: 31608017 PMCID: PMC6758846 DOI: 10.3389/fmicb.2019.01957] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/08/2019] [Indexed: 12/25/2022] Open
Abstract
The applications of correct diagnostic approaches play a decisive role in timely containment of infectious diseases spread and mitigation of public health risks. Nevertheless, there is a need to update the diagnostics regularly to capture the new, emergent, and highly divergent viruses. Acute gastroenteritis of viral origin has been identified as a significant cause of mortality across the globe, with the more serious consequences seen at the extremes of age groups (young and elderly) and immune-compromised individuals. Therefore, significant advancements and efforts have been put in the development of enteric virus diagnostics to meet the WHO ASSURED criteria as a benchmark over the years. The Enzyme-Linked Immunosorbent (ELISA) and Polymerase Chain Reaction (PCR) are the basic assays that provided the platform for development of several efficient diagnostics such as real-time RT-PCR, loop-mediated isothermal amplification (LAMP), polymerase spiral reaction (PSR), biosensors, microarrays and next generation sequencing. Herein, we describe and discuss the applications of these advanced technologies in context to enteric virus detection by delineating their features, advantages and limitations.
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Affiliation(s)
- Yashpal Singh Malik
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Atul Kumar Verma
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Naveen Kumar
- ICAR-National Institute of High Security Animal Diseases, OIE Reference Laboratory for Avian Influenza, Bhopal, India
| | - Nadia Touil
- Laboratoire de Biosécurité et de Recherche, Hôpital Militaire d’Instruction Mohammed V, Rabat, Morocco
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology & Immunology, College of Veterinary Sciences, DUVASU, Mathura, India
| | - Durlav Prasad Bora
- Department of Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati, India
| | - Kuldeep Dhama
- Division of Pathology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Souvik Ghosh
- Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Maged Gomaa Hemida
- Department of Microbiology and Parasitology, College of Veterinary Medicine, King Faisal University, Al-Hufuf, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Ahmed S. Abdel-Moneim
- Department of Microbiology, College of Medicine, Taif University, Taif, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Beni Suef University, Beni Suef, Egypt
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anastasia N. Vlasova
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, CFAES, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | | | - Raj Kumar Singh
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
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Rapid assessment of viral water quality using a novel recombinase polymerase amplification test for human adenovirus. Appl Microbiol Biotechnol 2019; 103:8115-8125. [PMID: 31435714 DOI: 10.1007/s00253-019-10077-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 06/28/2019] [Accepted: 07/31/2019] [Indexed: 10/26/2022]
Abstract
Sensitive and rapid methods for determining viral contamination of water are critical, since illness can be caused by low numbers of viruses and bacterial indicators do not adequately predict viral loads. We developed novel rapid assays for detecting the viral water quality indicator human adenovirus (HAdV). A simple 15-min recombinase polymerase amplification step followed by a 5-min lateral flow detection is used. Species-specific assays were developed to discriminate HAdV A, B, C and F, and combined into a multiplex test (Ad-FAC). Species-specific assays enabled detection of 10-50 copies of the HAdV plasmid. Sample testing using methods optimised for wastewater analysis indicated the Ad-FAC assay showed 100% sensitivity and 100% specificity when compared with HAdV qPCR, with a detection limit as low as 50 gene copies. This is the first study to demonstrate the use of RPA for detecting enteric viruses in water samples, to assess virological water quality. The ability to rapidly detect enteric virus contamination of water could assist in more effective management of water safety and better protection of public health.
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Chopyk J, Kulkarni P, Nasko DJ, Bradshaw R, Kniel KE, Chiu P, Sharma M, Sapkota AR. Zero-valent iron sand filtration reduces concentrations of virus-like particles and modifies virome community composition in reclaimed water used for agricultural irrigation. BMC Res Notes 2019; 12:223. [PMID: 30975220 PMCID: PMC6458639 DOI: 10.1186/s13104-019-4251-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 04/03/2019] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVE Zero-valent iron sand filtration can remove multiple contaminants, including some types of pathogenic bacteria, from contaminated water. However, its efficacy at removing complex viral populations, such as those found in reclaimed water used for agricultural irrigation, has not been fully evaluated. Therefore, this study utilized metagenomic sequencing and epifluorescent microscopy to enumerate and characterize viral populations found in reclaimed water and zero-valent iron-sand filtered reclaimed water sampled three times during a larger greenhouse study. RESULTS Zero-valent iron-sand filtered reclaimed water samples had significantly less virus-like particles than reclaimed water samples at all collection dates, with the reclaimed water averaging between 108 and 109 and the zero-valent iron-sand filtered reclaimed water averaging between 106 and 107 virus-like particles per mL. In addition, for both sample types, viral metagenomes (viromes) were dominated by bacteriophages of the order Caudovirales, largely Siphoviridae, and genes related to DNA metabolism. However, the proportion of sequences homologous to bacteria, as well as the abundance of genes possibly originating from a bacterial host, was higher in the viromes of zero-valent iron-sand filtered reclaimed water samples. Overall, zero-valent iron-sand filtered reclaimed water had a lower total concentration of virus-like particles and a different virome community composition compared to unfiltered reclaimed water.
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Affiliation(s)
- Jessica Chopyk
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, School of Public Health Building (255), 4200 Valley Drive, Room 2234P, College Park, MD, 20742, USA
| | - Prachi Kulkarni
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, School of Public Health Building (255), 4200 Valley Drive, Room 2234P, College Park, MD, 20742, USA
| | - Daniel J Nasko
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
| | - Rhodel Bradshaw
- United States Department of Agriculture, Agricultural Research Service, Environmental and Microbial Food Safety Laboratory, Beltsville, MD, 20705, USA
| | - Kalmia E Kniel
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Pei Chiu
- Department of Civil and Environmental Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Manan Sharma
- United States Department of Agriculture, Agricultural Research Service, Environmental and Microbial Food Safety Laboratory, Beltsville, MD, 20705, USA
| | - Amy R Sapkota
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, School of Public Health Building (255), 4200 Valley Drive, Room 2234P, College Park, MD, 20742, USA.
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Abstract
Very little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new viruses discovered in this study are representative of the most abundant family of marine RNA viruses, the Marnaviridae, and expand our view of the diversity of this important group. Overall, our data and analyses provide a foundation for interpreting marine RNA virus diversity and evolution. RNA viruses, particularly genetically diverse members of the Picornavirales, are widespread and abundant in the ocean. Gene surveys suggest that there are spatial and temporal patterns in the composition of RNA virus assemblages, but data on their diversity and genetic variability in different oceanographic settings are limited. Here, we show that specific RNA virus genomes have widespread geographic distributions and that the dominant genotypes are under purifying selection. Genomes from three previously unknown picorna-like viruses (BC-1, -2, and -3) assembled from a coastal site in British Columbia, Canada, as well as marine RNA viruses JP-A, JP-B, and Heterosigma akashiwo RNA virus exhibited different biogeographical patterns. Thus, biotic factors such as host specificity and viral life cycle, and not just abiotic processes such as dispersal, affect marine RNA virus distribution. Sequence differences relative to reference genomes imply that virus quasispecies are under purifying selection, with synonymous single-nucleotide variations dominating in genomes from geographically distinct regions resulting in conservation of amino acid sequences. Conversely, sequences from coastal South Africa that mapped to marine RNA virus JP-A exhibited more nonsynonymous mutations, probably representing amino acid changes that accumulated over a longer separation. This biogeographical analysis of marine RNA viruses demonstrates that purifying selection is occurring across oceanographic provinces. These data add to the spectrum of known marine RNA virus genomes, show the importance of dispersal and purifying selection for these viruses, and indicate that closely related RNA viruses are pathogens of eukaryotic microbes across oceans. IMPORTANCE Very little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new viruses discovered in this study are representative of the most abundant family of marine RNA viruses, the Marnaviridae, and expand our view of the diversity of this important group. Overall, our data and analyses provide a foundation for interpreting marine RNA virus diversity and evolution.
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Hwangbo M, Claycomb EC, Liu Y, Alivio TEG, Banerjee S, Chu KH. Effectiveness of zinc oxide-assisted photocatalysis for concerned constituents in reclaimed wastewater: 1,4-Dioxane, trihalomethanes, antibiotics, antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 649:1189-1197. [PMID: 30308890 PMCID: PMC7263876 DOI: 10.1016/j.scitotenv.2018.08.360] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 08/03/2018] [Accepted: 08/25/2018] [Indexed: 05/28/2023]
Abstract
Microbial and emerging chemical contaminants are unwanted constituents in reclaimed wastewater, due to the health concerns of using the water for agricultural irrigation, aquifer recharges, and potable water. Removal of these contaminants is required but it is currently challenging, given that there is no simple treatment technology to effectively remove the mixture of these contaminants. This study examined the effectiveness of ZnO-assisted photocatalytic degradation of several constituents, including 1,4-dioxane, trihalomethanes (THMs), triclosan (TCS), triclocarban (TCC), antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs), under low intensity of UV exposure. E. coli with an ARGs-carrying circular plasmid (pUC19) was used as a model antibiotic resistant bacterium. Our results show that commercial zinc oxide (C-ZnO) assisted photodegradation of 1,4-dioxane, and dehalogenation of THMs, TCS, and TCC, while tetrapodal zinc oxide (T-ZnO) enhanced the dehalogenation of TCS and TCC. Additionally, T-ZnO assisted the photocatalytic inactivation of the E. coli within 6 h and caused structural changes in the plasmid DNA (pUC19) with additional UV exposure, resulting in non-functional AGR-containing plasmids. These results also suggest that higher UV dose is required not only to inactivate ARB but also to damage ARGs in the ARB in order to decrease risks in promoting ARB population in the environment. Overall, our results implicated that, under low UV intensity, ZnO-assisted photocatalysis is a promising alternative to simultaneously remove biological and emerging chemical contaminants in treated wastewater for safe reuse.
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Affiliation(s)
- Myung Hwangbo
- Zachry Department of Civil Engineering, Texas A&M University, College Station, TX 77843-3136, USA
| | - Everett Caleb Claycomb
- Department of Petroleum Engineering, Texas A&M University, College Station, TX 77843-3116, USA
| | - Yina Liu
- Geochemical and Environmental Research Group, Texas A&M University, College Station, TX 77843-3136, USA
| | - Theodore E G Alivio
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3012, USA; Department of Materials Science and Engineering, Texas A&M University, College Station, TX 77843-3003, USA
| | - Sarbajit Banerjee
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3012, USA; Department of Materials Science and Engineering, Texas A&M University, College Station, TX 77843-3003, USA
| | - Kung-Hui Chu
- Zachry Department of Civil Engineering, Texas A&M University, College Station, TX 77843-3136, USA.
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Arsenieff L, Simon N, Rigaut-Jalabert F, Le Gall F, Chaffron S, Corre E, Com E, Bigeard E, Baudoux AC. First Viruses Infecting the Marine Diatom Guinardia delicatula. Front Microbiol 2019; 9:3235. [PMID: 30687251 PMCID: PMC6334475 DOI: 10.3389/fmicb.2018.03235] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/12/2018] [Indexed: 11/17/2022] Open
Abstract
The marine diatom Guinardia delicatula is a cosmopolitan species that dominates seasonal blooms in the English Channel and the North Sea. Several eukaryotic parasites are known to induce the mortality of this species. Here, we report the isolation and characterization of the first viruses that infect G. delicatula. Viruses were isolated from the Western English Channel (SOMLIT-Astan station) during the late summer bloom decline of G. delicatula. A combination of laboratory approaches revealed that these lytic viruses (GdelRNAV) are small tailless particles of 35–38 nm in diameter that replicate in the host cytoplasm where both unordered particles and crystalline arrays are formed. GdelRNAV display a linear single-stranded RNA genome of ~9 kb, including two open reading frames encoding for replication and structural polyproteins. Phylogenetic relationships based on the RNA-dependent-RNA-polymerase gene marker showed that GdelRNAV are new members of the Bacillarnavirus, a monophyletic genus belonging to the order Picornavirales. GdelRNAV are specific to several strains of G. delicatula. They were rapidly and largely produced (<12 h, 9.34 × 104 virions per host cell). Our analysis points out the host's variable viral susceptibilities during the early exponential growth phase. Interestingly, we consistently failed to isolate viruses during spring and early summer while G. delicatula developed important blooms. While our study suggests that viruses do contribute to the decline of G. delicatula's late summer bloom, they may not be the primary mortality agents during the remaining blooms at SOMLIT-Astan. Future studies should focus on the relative contribution of the viral and eukaryotic pathogens to the control of Guinardia's blooms to understand the fate of these prominent organisms in marine systems.
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Affiliation(s)
- Laure Arsenieff
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
| | - Nathalie Simon
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
| | - Fabienne Rigaut-Jalabert
- Sorbonne Université, CNRS Fédération de Recherche FR2424 - Station Biologique de Roscoff, Roscoff, France
| | - Florence Le Gall
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
| | - Samuel Chaffron
- Laboratoire des Sciences du Numérique de Nantes (LS2N), CNRS UMR 6004 - Université de Nantes, Nantes, France
| | - Erwan Corre
- Sorbonne Université, CNRS Fédération de Recherche FR2424 - Station Biologique de Roscoff, Roscoff, France
| | - Emmanuelle Com
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France.,Protim, Univ Rennes, Rennes, France
| | - Estelle Bigeard
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
| | - Anne-Claire Baudoux
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
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Hata A, Hanamoto S, Ihara M, Shirasaka Y, Yamashita N, Tanaka H. Comprehensive Study on Enteric Viruses and Indicators in Surface Water in Kyoto, Japan, During 2014-2015 Season. FOOD AND ENVIRONMENTAL VIROLOGY 2018; 10:353-364. [PMID: 30151619 DOI: 10.1007/s12560-018-9355-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/23/2018] [Indexed: 06/08/2023]
Abstract
Certain enteric viruses that are present in the water environment are potential risk factors of waterborne infections. To better understand the impact of viruses in water, both enteric viruses and their potential indicators should be comparatively investigated. In this study, occurrences of GI- and GII-noroviruses (NoVs), sapovirus (SaV), rotavirus (RoV), Aichi virus 1 (AiV-1), enterovirus (EV), and pepper mild mottle virus (PMMoV) were quantitatively determined in surface water samples in Japan. Additionally, the genotype distribution of GI- and GII-NoVs was determined using a next-generation amplicon sequencing. PMMoV was the most abundant virus regardless of season and location, indicating its usefulness as an indicator for the viral contamination of water. Other potential indicators, AiV and EV, were less abundant than GII-NoV. Viruses other than PMMoV showed seasonality, i.e., EV and other viruses (NoVs, SaV, RoV, and AiV-1) became prevalent during summer and winter, respectively. SaV showed a relatively high abundance at a location that was affected by untreated wastewater. Regarding NoV genotypes, GI.1, GI.2, GI.4, GI.5, GI.6, GII.3, GII.4, GII.6, and GII.17 were found from the surface water samples. GII.4 and GII.17 seemed to have contributed to the high abundance of GII-NoV in the samples. Interestingly, GII.17 strains became prevalent in the water samples before becoming prevalent among gastroenteritis patients in Japan. These findings provide further insights into the properties of viruses as contaminants in the water environment.
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Affiliation(s)
- Akihiko Hata
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan.
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Seiya Hanamoto
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
- Water Quality Research Team, Public Works Research Institute, 1-6 Minamihara, Tsukuba, Ibaraki, 305-8516, Japan
| | - Masaru Ihara
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
| | - Yuya Shirasaka
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
| | - Naoyuki Yamashita
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
- Course of Rural Engineering, Department of Science and Technology for Biological Resources and Environment, Faculty of Agriculture, Graduate School of Agriculture Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
| | - Hiroaki Tanaka
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
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Symonds EM, Nguyen KH, Harwood VJ, Breitbart M. Pepper mild mottle virus: A plant pathogen with a greater purpose in (waste)water treatment development and public health management. WATER RESEARCH 2018; 144:1-12. [PMID: 30005176 PMCID: PMC6162155 DOI: 10.1016/j.watres.2018.06.066] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/26/2018] [Accepted: 06/28/2018] [Indexed: 05/06/2023]
Abstract
An enteric virus surrogate and reliable domestic wastewater tracer is needed to manage microbial quality of food and water as (waste)water reuse becomes more prevalent in response to population growth, urbanization, and climate change. Pepper mild mottle virus (PMMoV), a plant pathogen found at high concentrations in domestic wastewater, is a promising surrogate for enteric viruses that has been incorporated into over 29 water- and food-related microbial quality and technology investigations around the world. This review consolidates the available literature from across disciplines to provide guidance on the utility of PMMoV as either an enteric virus surrogate and/or domestic wastewater marker in various situations. Synthesis of the available research supports PMMoV as a useful enteric virus process indicator since its high concentrations in source water allow for identifying the extent of virus log-reductions in field, pilot, and full-scale (waste)water treatment systems. PMMoV reduction levels during many forms of wastewater treatment were less than or equal to the reduction of other viruses, suggesting this virus can serve as an enteric virus surrogate when evaluating new treatment technologies. PMMoV excels as an index virus for enteric viruses in environmental waters exposed to untreated domestic wastewater because it was detected more frequently and in higher concentrations than other human viruses in groundwater (72.2%) and surface waters (freshwater, 94.5% and coastal, 72.2%), with pathogen co-detection rates as high as 72.3%. Additionally, PMMoV is an important microbial source tracking marker, most appropriately associated with untreated domestic wastewater, where its pooled-specificity is 90% and pooled-sensitivity is 100%, as opposed to human feces where its pooled-sensitivity is only 11.3%. A limited number of studies have also suggested that PMMoV may be a useful index virus for enteric viruses in monitoring the microbial quality of fresh produce and shellfish, but further research is needed on these topics. Finally, future work is needed to fill in knowledge gaps regarding PMMoV's global specificity and sensitivity.
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Affiliation(s)
- E M Symonds
- University of South Florida, College of Marine Science, 140 7th Avenue South, St. Petersburg, FL, USA.
| | - Karena H Nguyen
- University of South Florida, Department of Integrative Biology, 4202 E. Fowler Avenue, Tampa, FL, USA.
| | - V J Harwood
- University of South Florida, Department of Integrative Biology, 4202 E. Fowler Avenue, Tampa, FL, USA.
| | - M Breitbart
- University of South Florida, College of Marine Science, 140 7th Avenue South, St. Petersburg, FL, USA.
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Genetic and functional diversity of double-stranded DNA viruses in a tropical monsoonal estuary, India. Sci Rep 2018; 8:16036. [PMID: 30375431 PMCID: PMC6207776 DOI: 10.1038/s41598-018-34332-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/04/2018] [Indexed: 11/08/2022] Open
Abstract
The present study illustrates the genetic diversity of four uncultured viral communities from the surface waters of Cochin Estuary (CE), India. Viral diversity inferred using Illumina HiSeq paired-end sequencing using a linker-amplified shotgun library (LASL) revealed different double-stranded DNA (dsDNA) viral communities. The water samples were collected from four stations PR1, PR2, PR3, and PR4, during the pre-monsoon (PRM) season. Analysis of virus families indicated that the Myoviridae was the most common viral community in the CE followed by Siphoviridae and Podoviridae. There were significant (p < 0.05) spatial variations in the relative abundance of dominant families in response to the salinity regimes. The relative abundance of Myoviridae and Podoviridae were high in the euryhaline region and Siphoviridae in the mesohaline region of the estuary. The predominant phage type in CE was phages that infected Synechococcus. The viral proteins were found to be involved in major functional activities such as ATP binding, DNA binding, and DNA replication. The study highlights the genetic diversity of dsDNA viral communities and their functional protein predictions from a highly productive estuarine system. Further, the metavirome data generated in this study will enhance the repertoire of publicly available dataset and advance our understanding of estuarine viral ecology.
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50
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Colombo S, Arioli S, Gargari G, Neri E, Della Scala G, Mora D. Characterization of airborne viromes in cheese production plants. J Appl Microbiol 2018; 125:1444-1454. [DOI: 10.1111/jam.14046] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/28/2018] [Accepted: 07/05/2018] [Indexed: 12/29/2022]
Affiliation(s)
- S. Colombo
- Department of Food, Environmental and Nutritional Sciences; University of Milan; Milan Italy
| | - S. Arioli
- Department of Food, Environmental and Nutritional Sciences; University of Milan; Milan Italy
| | - G. Gargari
- Department of Food, Environmental and Nutritional Sciences; University of Milan; Milan Italy
| | - E. Neri
- Department of Food, Environmental and Nutritional Sciences; University of Milan; Milan Italy
| | - G. Della Scala
- Department of Food, Environmental and Nutritional Sciences; University of Milan; Milan Italy
| | - D. Mora
- Department of Food, Environmental and Nutritional Sciences; University of Milan; Milan Italy
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