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Zhang Y, Zheng X, Yan W, Wang D, Chen X, Wang Y, Zhang T. Method evaluation for viruses in activated sludge: Concentration, sequencing, and identification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 955:176886. [PMID: 39419205 DOI: 10.1016/j.scitotenv.2024.176886] [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: 07/19/2024] [Revised: 10/09/2024] [Accepted: 10/10/2024] [Indexed: 10/19/2024]
Abstract
Activated sludge (AS) in wastewater treatment plants is one of the largest artificial microbial ecosystems on earth and it makes enormous contributions to human societies. Viruses are an important component in AS with a high abundance. However, their communities and functionalities have not been as widely explored as those of other microorganisms, such as bacteria. This gap is mainly due to technical challenges in effective viral concentration, extraction, and sequencing. In this study, we compared four kinds of concentration methods, two sequencing approaches, and four identification bioinformatic tools to evaluate the whole analysis workflow for viruses in AS. Results showed flocculation, filtration, and resuspension (FFR) could get the longest DNA lengths and ultracentrifugation obtained the highest DNA yields for viruses in AS. Based on the results of present study, FFR and tangential flow filtration with the membrane pore size of 100 kDa were most recommended to concentrate viruses in AS samples with huge volumes. Besides, different concentration methods could get different viral catalogs and thus multiple methods should be combined to get the whole picture of viruses in the system. In addition, geNomad was the most recommended identification tool for viruses in the present study and the long-read sequencing could improve the assembly statistics of viruses when compared with the short-read sequencing. For the 8192 viral operational taxonomic units in this study, 95.1 % of them were phages and belonged to the same lineage at the order level of Caudovirales. Virulent phages dominated the AS system and Pseudomonadota were the main host. Taken together, this study provides new insights into methods selection for virus research of AS.
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Affiliation(s)
- Yulin Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam, Road, Hong Kong, China
| | - Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam, Road, Hong Kong, China
| | - Weifu Yan
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam, Road, Hong Kong, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam, Road, Hong Kong, China
| | - Xi Chen
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam, Road, Hong Kong, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam, Road, Hong Kong, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam, Road, Hong Kong, China; School of Public Health, The University of Hong Kong, Pokfulam Road, Hong Kong, China; Macau Institute of Applied Research in Medicine and Health, Macau University of Science and Technology, Macao.
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2
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Combe M, Cherif E, Deremarque T, Rivera-Ingraham G, Seck-Thiam F, Justy F, Doudou JC, Carod JF, Carage T, Procureur A, Gozlan RE. Wastewater sequencing as a powerful tool to reveal SARS-CoV-2 variant introduction and spread in French Guiana, South America. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171645. [PMID: 38479523 DOI: 10.1016/j.scitotenv.2024.171645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/19/2024] [Accepted: 03/09/2024] [Indexed: 03/17/2024]
Abstract
The origin of introduction of a new pathogen in a country, the evolutionary dynamics of an epidemic within a country, and the role of cross-border areas on pathogen dynamics remain complex to disentangle and are often poorly understood. For instance, cross-border areas represent the ideal location for the sharing of viral variants between countries, with international air travel, land travel and waterways playing an important role in the cross-border spread of infectious diseases. Unfortunately, monitoring the point of entry and the evolutionary dynamics of viruses in space and time within local populations remain challenging. Here we tested the efficiency of wastewater-based epidemiology and genotyping in monitoring Covid-19 epidemiology and SARS-CoV-2 variant dynamics in French Guiana, a tropical country located in South America. Our results suggest that wastewater-based epidemiology and genotyping are powerful tools to monitor variant introduction and disease evolution within a tropical country but the inclusion of both clinical and wastewater samples could still improve our understanding of genetic diversity co-circulating. Wastewater sequencing also revealed the cryptic transmission of SARS-CoV-2 variants within the country. Interestingly, we found some amino acid changes specific to the variants co-circulating in French Guiana, suggesting a local evolution of the SARS-CoV-2 variants after their introduction. More importantly, our results showed that the proximity to bordering countries was not the origin of the emergence of the French Guianese B.1.160.25 variant, but rather that this variant emerged from an ancestor B.1.160 variant introduced by European air plane travelers, suggesting thus that air travel remains a significant risk for cross-border spread of infectious diseases. Overall, we suggest that wastewater-based epidemiology and genotyping provides a cost effective and non-invasive approach for pathogen monitoring and an early-warning tool for disease emergence and spread within a tropical country.
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Affiliation(s)
- Marine Combe
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, France.
| | - Emira Cherif
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, France
| | | | - Georgina Rivera-Ingraham
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, France; Centre IRD de Cayenne, Guyane Française, France
| | | | | | | | - Jean-François Carod
- Laboratoire et Pôle Appui aux Fonctions Cliniques, Centre Hospitalier de l'Ouest Guyanais (CHOG), 97320 Saint-Laurent du Maroni, Guyane Française, France
| | - Thierry Carage
- Laboratoire de Biologie Médicale Carage de Kourou, 6 avenue Leopold Heder, 97310 Kourou, Guyane Française, France
| | - Angélique Procureur
- Laboratoire de Biologie Médicale Carage de Kourou, 6 avenue Leopold Heder, 97310 Kourou, Guyane Française, France
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3
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Bichet MC, Gardette M, Das Neves B, Challant J, Erbs A, Roman V, Robin M, La Carbona S, Gantzer C, Boudaud N, Bertrand I. A new understanding of somatic coliphages belonging to the Microviridae family in urban wastewater. WATER RESEARCH 2024; 249:120916. [PMID: 38043350 DOI: 10.1016/j.watres.2023.120916] [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: 09/06/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
Somatic coliphages (SC) and F-specific RNA coliphages (FRNAPH) have been included in regulations or guidelines by several developed countries as a way of monitoring water safety and the microbiological quality of shellfish harvesting waters. SC are highly diverse in their morphology, size and genome. The Microviridae family contains three genera of phages (Alphatrevirus, Gequatrovirus, and Sinsheimervirus), all having a capsid of similar morphology (icosahedral) and size (25-30 nm in diameter) to that of common pathogenic enteric viruses. Three PCR assays specific for each genus of Microviridae were designed to study these phages in raw and treated wastewater (WW) in order to gain knowledge about the diversity and prevalence of Microviridae among SC, as well as their inactivation and removal during WW treatments. Among the four wastewater treatment plants (WWTPs) monitored here, two WWTPs applied disinfection by UV light as tertiary treatment. First, we noticed that Microviridae represented 10 to 30 % of infectious SC in both raw and treated WW. Microviridae appeared to behave in the same way as all SC during these WW treatments. As expected, the highest inactivation, at least 4 log10, was achieved for infectious Microviridae and SC in both WWTPs using UV disinfection. PCR assays showed that the highest removal of Microviridae reached about 4 log10, but the phage removal can vary greatly between WWTPs using similar treatments. This work forms the basis for a broader evaluation of Microviridae as a viral indicator of water treatment efficiency and WW reuse.
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Affiliation(s)
- Marion C Bichet
- Food Safety Department, ACTALIA, Saint-Lô F-50000, France; Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France
| | - Marion Gardette
- Food Safety Department, ACTALIA, Saint-Lô F-50000, France; Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France
| | | | - Julie Challant
- Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France
| | - Anaïs Erbs
- Food Safety Department, ACTALIA, Saint-Lô F-50000, France; Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France
| | - Véronica Roman
- Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France
| | - Maëlle Robin
- Food Safety Department, ACTALIA, Saint-Lô F-50000, France
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Shuai X, Zhou Z, Ba X, Lin Y, Lin Z, Liu Z, Yu X, Zhou J, Zeng G, Ge Z, Chen H. Bacteriophages: Vectors of or weapons against the transmission of antibiotic resistance genes in hospital wastewater systems? WATER RESEARCH 2024; 248:120833. [PMID: 37952327 DOI: 10.1016/j.watres.2023.120833] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/26/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023]
Abstract
Antimicrobial resistance poses a serious threat to human health and is responsible for the death of millions of people annually. Hospital wastewater is an important hotspot for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). However, little is known about the relationship between phages and ARGs in hospital wastewater systems (HWS). In the present study, the viral diversity of 12 HWSs using data from public metagenomic databases was investigated. Viruses were widely found in both the influent and effluent of each HWS. A total of 45 unique ARGs were carried by 85 viral contigs, which accounted for only 0.14% of the total viral populations, implying that ARGs were not commonly present in phages. Three efflux pump genes were identified as shared between phages and bacterial genomes. However, the predominant types of ARGs in HWS such as aminoglycoside- and beta-lactam-resistance genes were rarely found in phages. Based on CRISPR spacer and tRNA matches, interactions between 171 viral contigs and 60 antibiotic-resistant genomes were predicted, including interactions involving phages and vancomycin-resistant Enterococcus_B faecium or beta-lactam-resistant Klebsiella pneumoniae. More than half (56.1%) of these viral contigs indicated lytic and none of them carried ARGs. As the vOTUs in this study had few ARGs and were primarily lytic, HWS may be a valuable source for phage discovery. Future studies will be able to experimentally validate these sequence-based results to confirm the suitability of HWS phages for pathogen control measures in wastewater.
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Affiliation(s)
- Xinyi Shuai
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhenchao Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Yanhan Lin
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zejun Lin
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhe Liu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xi Yu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinyu Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Guangshu Zeng
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ziye Ge
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hong Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; International Cooperation Base of Environmental Pollution and Ecological Health, Science and Technology Agency of Zhejiang, Zhejiang University, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
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5
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Sabatino R, Sbaffi T, Sivalingam P, Corno G, Fontaneto D, Di Cesare A. Bacteriophages limitedly contribute to the antimicrobial resistome of microbial communities in wastewater treatment plants. Microbiol Spectr 2023; 11:e0110123. [PMID: 37724865 PMCID: PMC10580818 DOI: 10.1128/spectrum.01101-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/26/2023] [Indexed: 09/21/2023] Open
Abstract
Bacteriophages are known as players in the transmission of antimicrobial resistance genes (ARGs) by horizontal gene transfer. In this study, we characterized the bacteriophage community and the associated ARGs to estimate the potential for phages to spread ARGs in aquatic ecosystems analyzing the intra- and extracellular DNA isolated from two wastewater treatment plants (WWTPs) by shotgun metagenomics. We compared the phage antimicrobial resistome with the bacterial resistome and investigated the effect of the final disinfection treatment on the phage community and its resistome. Phage community was mainly composed by Siphoviridae and other members of the order Caudovirales. The final disinfection only marginally affected the composition of the phage community, and it was not possible to measure its effect on the antimicrobial resistome. Indeed, only three phage metagenome-assembled genomes (pMAGs) annotated as Siphoviridae, Padoviridae, and Myoviridae were positive for putative ARGs. Among the detected ARGs, i.e., dfrB6, rpoB mutants, and EF-Tu mutants, the first one was not annotated in the bacterial MAGs. Overall, these results demonstrate that bacteriophages limitedly contribute to the whole antimicrobial resistome. However, in order to obtain a comprehensive understanding of the antimicrobial resistome within a microbial community, the role of bacteriophages needs to be investigated. IMPORTANCE WWTPs are considered hotspots for the spread of ARGs by horizontal gene transfer. In this study, we evaluated the phage composition and the associated antimicrobial resistome by shotgun metagenomics of samples collected before and after the final disinfection treatment. Only a few bacteriophages carried ARGs. However, since one of the detected genes was not found in the bacterial metagenome-assembled genomes, it is necessary to investigate the phage community in order to gain a comprehensive overview of the antimicrobial resistome. This investigation could help assess the potential threats to human health.
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Affiliation(s)
- Raffaella Sabatino
- Molecular Ecology Group (MEG), National Research Council of Italy – Water Research Institute (CNR-IRSA), Verbania, Italy
| | - Tomasa Sbaffi
- Molecular Ecology Group (MEG), National Research Council of Italy – Water Research Institute (CNR-IRSA), Verbania, Italy
| | - Periyasamy Sivalingam
- Molecular Ecology Group (MEG), National Research Council of Italy – Water Research Institute (CNR-IRSA), Verbania, Italy
| | - Gianluca Corno
- Molecular Ecology Group (MEG), National Research Council of Italy – Water Research Institute (CNR-IRSA), Verbania, Italy
| | - Diego Fontaneto
- Molecular Ecology Group (MEG), National Research Council of Italy – Water Research Institute (CNR-IRSA), Verbania, Italy
| | - Andrea Di Cesare
- Molecular Ecology Group (MEG), National Research Council of Italy – Water Research Institute (CNR-IRSA), Verbania, Italy
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6
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Flores-Vargas G, Korber DR, Bergsveinson J. Sub-MIC antibiotics influence the microbiome, resistome and structure of riverine biofilm communities. Front Microbiol 2023; 14:1194952. [PMID: 37593545 PMCID: PMC10427767 DOI: 10.3389/fmicb.2023.1194952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/17/2023] [Indexed: 08/19/2023] Open
Abstract
The effects of sub-minimum inhibitory concentrations (sub-MICs) of antibiotics on aquatic environments is not yet fully understood. Here, we explore these effects by employing a replicated microcosm system fed with river water where biofilm communities were continuously exposed over an eight-week period to sub-MIC exposure (1/10, 1/50, and 1/100 MIC) to a mix of common antibiotics (ciprofloxacin, streptomycin, and oxytetracycline). Biofilms were examined using a structure-function approach entailing microscopy and metagenomic techniques, revealing details on the microbiome, resistome, virulome, and functional prediction. A comparison of three commonly used microbiome and resistome databases was also performed. Differences in biofilm architecture were observed between sub-MIC antibiotic treatments, with an overall reduction of extracellular polymeric substances and autotroph (algal and cyanobacteria) and protozoan biomass, particularly at the 1/10 sub-MIC condition. While metagenomic analyses demonstrated that microbial diversity was lowest at the sub-MIC 1/10 antibiotic treatment, resistome diversity was highest at sub-MIC 1/50. This study also notes the importance of benchmarking analysis tools and careful selection of reference databases, given the disparity in detected antimicrobial resistance genes (ARGs) identity and abundance across methods. Ultimately, the most detected ARGs in sub-MICs exposed biofilms were those that conferred resistance to aminoglycosides, tetracyclines, β-lactams, sulfonamides, and trimethoprim. Co-occurrence of microbiome and resistome features consistently showed a relationship between Proteobacteria genera and aminoglycoside ARGs. Our results support the hypothesis that constant exposure to sub-MICs antibiotics facilitate the transmission and promote prevalence of antibiotic resistance in riverine biofilms communities, and additionally shift overall microbial community metabolic function.
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Affiliation(s)
| | - Darren R. Korber
- Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jordyn Bergsveinson
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Saskatoon, SK, Canada
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Farkas K, Williams R, Alex-Sanders N, Grimsley JMS, Pântea I, Wade MJ, Woodhall N, Jones DL. Wastewater-based monitoring of SARS-CoV-2 at UK airports and its potential role in international public health surveillance. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001346. [PMID: 36963000 PMCID: PMC10021541 DOI: 10.1371/journal.pgph.0001346] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/24/2022] [Indexed: 01/20/2023]
Abstract
It is well established that air travel plays a key role in the global spread of many enteric and respiratory diseases, including COVID-19. Even with travel restrictions (e.g. mask wearing, negative COVID-19 test prior to departure), SARS-CoV-2 may be transmitted by asymptomatic or pre-symptomatic individuals carrying the virus. Due to the limitation of current clinical surveillance approaches, complementary methods need to be developed to allow estimation of the frequency of SARS-CoV-2 entry across international borders. Wastewater-based epidemiology (WBE) represents one such approach, allowing the unbiased sampling of SARS-CoV-2 carriage by passenger cohorts entering via airports. In this study, we monitored sewage in samples from terminals (n = 150) and aircraft (n = 32) at three major international airports in the UK for 1-3 weeks in March 2022. As the raw samples were more turbid than typical municipal wastewater, we used beef extract treatment followed by polyethylene glycol (PEG) precipitation to concentrate viruses, followed by reverse transcription quantitative PCR (RT-qPCR) for the detection of SARS-CoV-2 and a faecal indicator virus, crAssphage. All samples taken from sewers at the arrival terminals of Heathrow and Bristol airports, and 85% of samples taken from sites at Edinburgh airport, were positive for SARS-CoV-2. This suggests a high COVID-19 prevalence among passengers and/or airport staff members. Samples derived from aircraft also showed 93% SARS-CoV-2 positivity. No difference in viral prevalence was found before and after COVID-19 travel restrictions were lifted. Our results suggest that WBE is a useful tool for monitoring the global transfer rate of human pathogens and other disease-causing agents across international borders and should form part of wider international efforts to monitor and contain the spread of future disease outbreaks.
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Affiliation(s)
- Kata Farkas
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, United Kingdom
| | - Rachel Williams
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Natasha Alex-Sanders
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Jasmine M. S. Grimsley
- Data, Analytics, and Surveillance Group, UK Health Security Agency, London, United Kingdom
- The London Data Company, London, United Kingdom
| | - Igor Pântea
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Matthew J. Wade
- Data, Analytics, and Surveillance Group, UK Health Security Agency, London, United Kingdom
- School of Engineering, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Nick Woodhall
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Davey L. Jones
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
- Food Futures Institute, Murdoch University, Murdoch, Australia
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8
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Metagenomic insights into taxonomic, functional diversity and inhibitors of microbial biofilms. Microbiol Res 2022; 265:127207. [DOI: 10.1016/j.micres.2022.127207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/17/2022] [Accepted: 09/18/2022] [Indexed: 11/21/2022]
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Gagné MJ, Savard T, Brassard J. Interactions Between Infectious Foodborne Viruses and Bacterial Biofilms Formed on Different Food Contact Surfaces. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:267-279. [PMID: 36030359 PMCID: PMC9458689 DOI: 10.1007/s12560-022-09534-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Bacterial biofilms contribute to contamination, spoilage, persistence, and hygiene failure in the food industry, but relatively little is known about the behavior of foodborne viruses evolving in the complex communities that make up biofilm. The aim of this study was to evaluate the association between enteric viruses and biofilms on food contact surfaces. Formed biofilms of mono- and multispecies cultures were prepared on glass, stainless steel, and polystyrene coupons and 105 pfu/ml of murine norovirus, rotavirus, and hepatitis A virus were added and incubated for 15 min, 90 min, and 24 h. The data obtained clearly demonstrate that the presence of biofilms generally influences the adhesion of enteric viruses to different surfaces. Many significant increases in attachment rates were observed, particularly with rotavirus whose rate of viral infectious particles increased 7000 times in the presence of Pseudomonas fluorescens on polystyrene after 24 h of incubation and with hepatitis A virus, which seems to have an affinity for the biofilms formed by lactic acid bacteria. Murine norovirus seems to be the least influenced by the presence of biofilms with few significant increases. However, the different factors surrounding this association are unknown and seem to vary according to the viruses, the environmental conditions, and the composition of the biofilm.
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Affiliation(s)
- Marie-Josée Gagné
- Agriculture and Agri-Food Canada, Saint-Hyacinthe Research and Development Centre, 3600 Casavant Boulevard West, Saint-Hyacinthe, QC, J2S 8E3, Canada
| | - Tony Savard
- Agriculture and Agri-Food Canada, Saint-Hyacinthe Research and Development Centre, 3600 Casavant Boulevard West, Saint-Hyacinthe, QC, J2S 8E3, Canada
| | - Julie Brassard
- Agriculture and Agri-Food Canada, Saint-Hyacinthe Research and Development Centre, 3600 Casavant Boulevard West, Saint-Hyacinthe, QC, J2S 8E3, Canada.
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10
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Salih H, Karaynir A, Yalcin M, Oryasin E, Holyavkin C, Basbulbul G, Bozdogan B. Metagenomic analysis of wastewater phageome from a University Hospital in Turkey. Arch Microbiol 2022; 204:353. [DOI: 10.1007/s00203-022-02962-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/08/2022] [Indexed: 12/15/2022]
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Jankowski P, Gan J, Le T, McKennitt M, Garcia A, Yanaç K, Yuan Q, Uyaguari-Diaz M. Metagenomic community composition and resistome analysis in a full-scale cold climate wastewater treatment plant. ENVIRONMENTAL MICROBIOME 2022; 17:3. [PMID: 35033203 PMCID: PMC8760730 DOI: 10.1186/s40793-022-00398-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Wastewater treatment plants are an essential part of maintaining the health and safety of the general public. However, they are also an anthropogenic source of antibiotic resistance genes. In this study, we characterized the resistome, the distribution of classes 1-3 integron-integrase genes (intI1, intI2, and intI3) as mobile genetic element biomarkers, and the bacterial and phage community compositions in the North End Sewage Treatment Plant in Winnipeg, Manitoba. Samples were collected from raw sewage, returned activated sludge, final effluent, and dewatered sludge. A total of 28 bacterial and viral metagenomes were sequenced over two seasons, fall and winter. Integron-integrase genes, the 16S rRNA gene, and the coliform beta-glucuronidase gene were also quantified during this time period. RESULTS Bacterial classes observed above 1% relative abundance in all treatments were Actinobacteria (39.24% ± 0.25%), Beta-proteobacteria (23.99% ± 0.16%), Gamma-proteobacteria (11.06% ± 0.09%), and Alpha-proteobacteria (9.18 ± 0.04%). Families within the Caudovirales order: Siphoviridae (48.69% ± 0.10%), Podoviridae (23.99% ± 0.07%), and Myoviridae (19.94% ± 0.09%) were the dominant phage observed throughout the NESTP. The most abundant bacterial genera (in terms of average percent relative abundance) in influent, returned activated sludge, final effluent, and sludge, respectively, includes Mycobacterium (37.4%, 18.3%, 46.1%, and 7.7%), Acidovorax (8.9%, 10.8%, 5.4%, and 1.3%), and Polaromonas (2.5%, 3.3%, 1.4%, and 0.4%). The most abundant class of antibiotic resistance in bacterial samples was tetracycline resistance (17.86% ± 0.03%) followed by peptide antibiotics (14.24% ± 0.03%), and macrolides (10.63% ± 0.02%). Similarly, the phage samples contained a higher prevalence of macrolide (30.12% ± 0.30%), peptide antibiotic (10.78% ± 0.13%), and tetracycline (8.69% ± 0.11%) resistance. In addition, intI1 was the most abundant integron-integrase gene throughout treatment (1.14 × 104 gene copies/mL) followed by intI3 (4.97 × 103 gene copies/mL) while intI2 abundance remained low (6.4 × 101 gene copies/mL). CONCLUSIONS Wastewater treatment successfully reduced the abundance of bacteria, DNA phage and antibiotic resistance genes although many antibiotic resistance genes remained in effluent and biosolids. The presence of integron-integrase genes throughout treatment and in effluent suggests that antibiotic resistance genes could be actively disseminating resistance between both environmental and pathogenic bacteria.
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Affiliation(s)
- Paul Jankowski
- Department of Microbiology, University of Manitoba, 45 Chancellors Circle, Buller Building, Winnipeg, MB, R3T 2N2, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Jaydon Gan
- Department of Microbiology, University of Manitoba, 45 Chancellors Circle, Buller Building, Winnipeg, MB, R3T 2N2, Canada
| | - Tri Le
- Department of Microbiology, University of Manitoba, 45 Chancellors Circle, Buller Building, Winnipeg, MB, R3T 2N2, Canada
| | - Michaela McKennitt
- Clayton H. Riddell Faculty of Environment, Earth, and Resources, University of Manitoba, Winnipeg, MB, Canada
- Institute of the Environment, University of Ottawa, Ottawa, ON, Canada
| | - Audrey Garcia
- Department of Microbiology, University of Manitoba, 45 Chancellors Circle, Buller Building, Winnipeg, MB, R3T 2N2, Canada
| | - Kadir Yanaç
- Department of Civil Engineering, University of Manitoba, Winnipeg, MB, Canada
| | - Qiuyan Yuan
- Department of Civil Engineering, University of Manitoba, Winnipeg, MB, Canada
| | - Miguel Uyaguari-Diaz
- Department of Microbiology, University of Manitoba, 45 Chancellors Circle, Buller Building, Winnipeg, MB, R3T 2N2, Canada.
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12
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Runa V, Wenk J, Bengtsson S, Jones BV, Lanham AB. Bacteriophages in Biological Wastewater Treatment Systems: Occurrence, Characterization, and Function. Front Microbiol 2021; 12:730071. [PMID: 34803947 PMCID: PMC8600467 DOI: 10.3389/fmicb.2021.730071] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/25/2021] [Indexed: 12/20/2022] Open
Abstract
Phage bacteria interactions can affect structure, dynamics, and function of microbial communities. In the context of biological wastewater treatment (BWT), the presence of phages can alter the efficiency of the treatment process and influence the quality of the treated effluent. The active role of phages in BWT has been demonstrated, but many questions remain unanswered regarding the diversity of phages in these engineered environments, the dynamics of infection, the determination of bacterial hosts, and the impact of their activity in full-scale processes. A deeper understanding of the phage ecology in BWT can lead the improvement of process monitoring and control, promote higher influent quality, and potentiate the use of phages as biocontrol agents. In this review, we highlight suitable methods for studying phages in wastewater adapted from other research fields, provide a critical overview on the current state of knowledge on the effect of phages on structure and function of BWT bacterial communities, and highlight gaps, opportunities, and priority questions to be addressed in future research.
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Affiliation(s)
- Viviane Runa
- Centre for Sustainable and Circular Technologies, University of Bath, Bath, United Kingdom.,Department of Chemical Engineering, University of Bath, Bath, United Kingdom
| | - Jannis Wenk
- Department of Chemical Engineering, University of Bath, Bath, United Kingdom.,Water Innovation and Research Centre, University of Bath, Bath, United Kingdom
| | | | - Brian V Jones
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Ana B Lanham
- Centre for Sustainable and Circular Technologies, University of Bath, Bath, United Kingdom.,Department of Chemical Engineering, University of Bath, Bath, United Kingdom.,Water Innovation and Research Centre, University of Bath, Bath, United Kingdom
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13
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Selvarajan R, Sibanda T, Pandian J, Mearns K. Taxonomic and Functional Distribution of Bacterial Communities in Domestic and Hospital Wastewater System: Implications for Public and Environmental Health. Antibiotics (Basel) 2021; 10:antibiotics10091059. [PMID: 34572642 PMCID: PMC8470611 DOI: 10.3390/antibiotics10091059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 11/17/2022] Open
Abstract
The discharge of untreated hospital and domestic wastewater into receiving water bodies is still a prevalent practice in developing countries. Unfortunately, because of an ever-increasing population of people who are perennially under medication, these wastewaters contain residues of antibiotics and other antimicrobials as well as microbial shedding, the direct and indirect effects of which include the dissemination of antibiotic resistance genes and an increase in the evolution of antibiotic-resistant bacteria that pose a threat to public and environmental health. This study assessed the taxonomic and functional profiles of bacterial communities, as well as the antibiotic concentrations in untreated domestic wastewater (DWW) and hospital wastewater (HWW), using high-throughput sequencing analysis and solid-phase extraction coupled to Ultra-high-performance liquid chromatography Mass Spectrometry (UHPLC–MS/MS) analysis, respectively. The physicochemical qualities of both wastewater systems were also determined. The mean concentration of antibiotics and the concentrations of Cl−, F− and PO43 were higher in HWW samples than in DWW samples. The phylum Firmicutes was dominant in DWW with a sequence coverage of 59.61% while Proteobacteria was dominant in HWW samples with a sequence coverage of 86.32%. At genus level, the genus Exiguobacterium (20.65%) and Roseomonas (67.41%) were predominant in DWW and HWW samples, respectively. Several pathogenic or opportunistic bacterial genera were detected in HWW (Enterococcus, Pseudomonas and Vibrio) and DWW (Clostridium, Klebsiella, Corynebacterium, Bordetella, Staphylocccus and Rhodococcus) samples. Functional prediction analysis indicated the presence of beta-lactam resistance, cationic antimicrobial peptide (CAMP) resistance and vancomycin resistance genes in HWW samples. The presence of these antibiotic resistance genes and cassettes were positively correlated with the presence of pathogens. These findings show the risk posed to public and environmental health by the discharge of untreated domestic and hospital wastewaters into environmental water bodies.
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Affiliation(s)
- Ramganesh Selvarajan
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, UNISA, Florida 1709, South Africa;
- Correspondence:
| | - Timothy Sibanda
- Department of Biochemistry, Microbiology and Biotechnology, University of Namibia, Mandume Ndemufayo Ave, Pionierspark, Windhoek 13301, Namibia;
| | - Jeevan Pandian
- P.G and Research Department of Microbiology, J.J College of Arts and Science (Autonomous), Pudukkottai 622422, Tamil Nadu, India;
| | - Kevin Mearns
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, UNISA, Florida 1709, South Africa;
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14
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Langenfeld K, Chin K, Roy A, Wigginton K, Duhaime MB. Comparison of ultrafiltration and iron chloride flocculation in the preparation of aquatic viromes from contrasting sample types. PeerJ 2021; 9:e11111. [PMID: 33996275 PMCID: PMC8106395 DOI: 10.7717/peerj.11111] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/23/2021] [Indexed: 12/24/2022] Open
Abstract
Viral metagenomes (viromes) are a valuable untargeted tool for studying viral diversity and the central roles viruses play in host disease, ecology, and evolution. Establishing effective methods to concentrate and purify viral genomes prior to sequencing is essential for high quality viromes. Using virus spike-and-recovery experiments, we stepwise compared two common approaches for virus concentration, ultrafiltration and iron chloride flocculation, across diverse matrices: wastewater influent, wastewater secondary effluent, river water, and seawater. Viral DNA was purified by removing cellular DNA via chloroform cell lysis, filtration, and enzymatic degradation of extra-viral DNA. We found that viral genomes were concentrated 1-2 orders of magnitude more with ultrafiltration than iron chloride flocculation for all matrices and resulted in higher quality DNA suitable for amplification-free and long-read sequencing. Given its widespread use and utility as an inexpensive field method for virome sampling, we nonetheless sought to optimize iron flocculation. We found viruses were best concentrated in seawater with five-fold higher iron concentrations than the standard used, inhibition of DNase activity reduced purification effectiveness, and five-fold more iron was needed to flocculate viruses from freshwater than seawater—critical knowledge for those seeking to apply this broadly used method to freshwater virome samples. Overall, our results demonstrated that ultrafiltration and purification performed better than iron chloride flocculation and purification in the tested matrices. Given that the method performance depended on the solids content and salinity of the samples, we suggest spike-and-recovery experiments be applied when concentrating and purifying sample types that diverge from those tested here.
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Affiliation(s)
- Kathryn Langenfeld
- Department of Civil and Environmental Engineering, University of Michigan - Ann Arbor, Ann Arbor, MI, United States of America
| | - Kaitlyn Chin
- Department of Civil and Environmental Engineering, University of Michigan - Ann Arbor, Ann Arbor, MI, United States of America
| | - Ariel Roy
- Department of Civil and Environmental Engineering, University of Michigan - Ann Arbor, Ann Arbor, MI, United States of America
| | - Krista Wigginton
- Department of Civil and Environmental Engineering, University of Michigan - Ann Arbor, Ann Arbor, MI, United States of America
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan - Ann Arbor, Ann Arbor, MI, United States of America
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15
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Tian L, Wang L. Multi-omics analysis reveals structure and function of biofilm microbial communities in a pre-denitrification biofilter. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143908. [PMID: 33316516 DOI: 10.1016/j.scitotenv.2020.143908] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
The highly complex microbial communities in biofilm play crucial roles in the pollutant removal performance of wastewater treatment plants (WWTPs). In the present study, using multi-omics analysis, we studied microbial structure, key enzymes, functional traits, and key metabolic pathways of pre-denitrification biofilter in an urban WWTP in China. The analysis results of metagenomic and metaproteomic showed that Betaproteobacteria and Flavobacteriia were dominant in biofilms. The integrated metagenomic and metaproteomic data showed that the expression of nitrogen metabolism genes was high, and the high proportion of denitrification module indicating that denitrification was the main nitrogen removal pathway. The most abundant denitrifying bacterial genera were: Dechloromonas, Acidovorax, Bosea, Polaromonas, and Chryseobacterium. And microorganisms with denitrification potential may not be able to denitrify in the actual operation of the filter. The integrated analysis of metaproteomic and metabolomic showed that there was a correlation between biofilm microorganisms and metabolites. Metabolomic analysis indicated that metabolic profiles of biofilms varied with layer height. This study provides the first detailed microbial communities and metabolic profiles in a full-scale pre-denitrification biofilter and clarifies the mechanism of denitrification.
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Affiliation(s)
- Lu Tian
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Lin Wang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.
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16
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Mohan SV, Hemalatha M, Kopperi H, Ranjith I, Kumar AK. SARS-CoV-2 in environmental perspective: Occurrence, persistence, surveillance, inactivation and challenges. CHEMICAL ENGINEERING JOURNAL (LAUSANNE, SWITZERLAND : 1996) 2021; 405:126893. [PMID: 32901196 PMCID: PMC7471803 DOI: 10.1016/j.cej.2020.126893] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 05/03/2023]
Abstract
The unprecedented global spread of the severe acute respiratory syndrome (SARS) caused by SARS-CoV-2 is depicting the distressing pandemic consequence on human health, economy as well as ecosystem services. So far novel coronavirus (CoV) outbreaks were associated with SARS-CoV-2 (2019), middle east respiratory syndrome coronavirus (MERS-CoV, 2012), and SARS-CoV-1 (2003) events. CoV relates to the enveloped family of Betacoronavirus (βCoV) with positive-sense single-stranded RNA (+ssRNA). Knowing well the persistence, transmission, and spread of SARS-CoV-2 through proximity, the faecal-oral route is now emerging as a major environmental concern to community transmission. The replication and persistence of CoV in the gastrointestinal (GI) tract and shedding through stools is indicating a potential transmission route to the environment settings. Despite of the evidence, based on fewer reports on SARS-CoV-2 occurrence and persistence in wastewater/sewage/water, the transmission of the infective virus to the community is yet to be established. In this realm, this communication attempted to review the possible influx route of the enteric enveloped viral transmission in the environmental settings with reference to its occurrence, persistence, detection, and inactivation based on the published literature so far. The possibilities of airborne transmission through enteric virus-laden aerosols, environmental factors that may influence the viral transmission, and disinfection methods (conventional and emerging) as well as the inactivation mechanism with reference to the enveloped virus were reviewed. The need for wastewater epidemiology (WBE) studies for surveillance as well as for early warning signal was elaborated. This communication will provide a basis to understand the SARS-CoV-2 as well as other viruses in the context of the environmental engineering perspective to design effective strategies to counter the enteric virus transmission and also serves as a working paper for researchers, policy makers and regulators.
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Key Words
- (h+), Photoholes
- +ssRNA, Positive Sense Single-Stranded RNA
- A-WWTS, Algal-WWTS
- ACE2, Angiotensin-converting enzyme 2
- AH, Absolute Humidity
- AOPs, Advanced Oxidation Processes
- ASP, Activate Sludge Process
- Aerosols
- BCoV, Bovine Enteric Coronavirus)
- BSL, Biosafety Level
- BVDV1, Bovine Viral Diarrhea Virus Type 1
- BVDV2, Bovine Viral Diarrhea Virus Type 2
- BoRv, Bovine Rotavirus Group A
- CCA, Carbon Covered Alumina
- CNT, Carbon Nanotubes
- COVID-19
- COVID-19, Coronavirus Disease 2019
- CRFK, Crandell Reese feline kidney cell line (CRFK)
- CVE, Coxsackievirus B5
- ClO2, Chlorine dioxide
- Cl−, Chlorine
- Cys, Cysteine
- DBP, Disinfection by-products
- DBT, L2 and Delayed Brain Tumor Cell Cultures
- DMEM, Dulbecco’s Modified Eagle Medium
- DNA, deoxyribose nucleic acid
- Disinfection
- E gene, Envelope protein gene
- EV, Echovirus 11
- Enteric virus
- Enveloped virus
- FC, Free Chlorine
- FFP3, Filtering Face Piece
- FIPV, Feline infectious peritonitis virus
- GI, Gastrointestinal tract
- H2O2, Hydrogen Peroxide
- H3N2, InfluenzaA
- H6N2, Avian influenza virus
- HAV, Hepatitis A virus (HAV)
- HAdV, Human Adenovirus
- HCoV, Human CoV
- HEV, Hepatitis E virus
- HKU1, Human CoV1
- ICC-PCR, Integrated Cell Culture with PCR
- JCV, JCV polyomavirus
- MALDI-TOF MS, Mass Spectrometry
- MBR, Membrane Bioreactor (MBR)
- MERS-CoV, Middle East Respiratory Syndrome Coronavirus
- MHV, Murine hepatitis virus
- MNV-1, Murine Norovirus
- MWCNTs, Multiwalled Carbon Nanotubes
- Met, Methionine
- N gene, Nucleocapsid protein gene
- NCoV, Novel coronavirus
- NGS, Next generation sequencing
- NTP, Non-Thermal Plasma
- O2, Singlet Oxygen
- O3, Ozone
- ORF, Open Reading Frame
- PAA, Para Acetic Acid
- PCR, Polymerase Chain Reaction
- PEC, Photoelectrocatalytical
- PEG, Polyethylene Glycol
- PFU, Plaque Forming Unit
- PMMoV, Pepper Mild Mottle Virus
- PMR, Photocatalytic Membrane Reactors
- PPE, Personal Protective Equipment
- PTAF, Photocatalytic Titanium Apatite Filter
- PV-1, Polivirus-1
- PV-3, Poliovirus 3
- PVDF, Polyvinylidene Fluoride
- Qβ, bacteriophages
- RH, Relative Humidity
- RNA, Ribose nucleic acid
- RONS, Reactive Oxygen and/or Nitrogen Species
- RT-PCR, Real Time Polymerase Chain Reaction
- RVA, Rotaviruses A
- SARS-CoV-1, Severe Acute Respiratory Syndrome Coronavirus 1
- SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2
- SBR, Sequential Batch Reactor
- SODIS, Solar water disinfection
- STP, Sewage Treatment Plant
- Sewage
- T90, First order reaction time required for completion of 90%
- T99.9, First order reaction time required for completion of 99.9%
- TGEV, Porcine Coronavirus Transmissible Gastroenteritis Virus
- TGEV, Transmissible Gastroenteritis
- Trp, Tryptophan
- Tyr, Tyrosine
- US-EPA, United States Environmental Protection Agency
- UV, Ultraviolet
- WBE, Wastewater-Based Epidemiology
- WWT, Wastewater Treatment
- WWTPs, Wastewater Treatment Plants
- dPCR, Digital PCR
- ds, Double Stranded
- dsDNA, Double Stranded DNA
- log10, logarithm with base 10
- qRT-PCR, quantitative RT-PCR
- ss, Single Stranded
- ssDNA, Single Stranded DNA
- ssRNA, Single Stranded RNA
- αCoV, Alphacoronavirus
- βCoV, Betacoronavirus
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Affiliation(s)
- S Venkata Mohan
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Technology (CSIR-IICT) Campus, Hyderabad 500007, India
| | - Manupati Hemalatha
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Technology (CSIR-IICT) Campus, Hyderabad 500007, India
| | - Harishankar Kopperi
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
| | - I Ranjith
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
| | - A Kiran Kumar
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
- CSIR-Indian Institute of Chemical Technology (CSIR-IICT) Dispensary, Hyderabad 500007, India
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17
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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: 3.8] [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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18
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Yang Y, Zhang Y, Cápiro NL, Yan J. Genomic Characteristics Distinguish Geographically Distributed Dehalococcoidia. Front Microbiol 2020; 11:546063. [PMID: 33013780 PMCID: PMC7506110 DOI: 10.3389/fmicb.2020.546063] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/12/2020] [Indexed: 12/13/2022] Open
Abstract
Dehalococcoidia (Dia) class microorganisms are frequently found in various pristine and contaminated environments. Metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) studies have substantially improved the understanding of Dia microbial ecology and evolution; however, an updated thorough investigation on the genomic and evolutionary characteristics of Dia microorganisms distributed in geographically distinct environments has not been implemented. In this study, we analyzed available genomic data to unravel Dia evolutionary and metabolic traits. Based on the phylogeny of 16S rRNA genes retrieved from sixty-seven genomes, Dia microorganisms can be categorized into three groups, the terrestrial cluster that contains all Dehalococcoides and Dehalogenimonas strains, the marine cluster I, and the marine cluster II. These results reveal that a higher ratio of horizontally transferred genetic materials was found in the Dia marine clusters compared to that of the Dia terrestrial cluster. Pangenome analysis further suggests that Dia microorganisms have evolved cluster-specific enzymes (e.g., dehalogenase in terrestrial Dia, sulfite reductase in marine Dia) and biosynthesis capabilities (e.g., siroheme biosynthesis in marine Dia). Marine Dia microorganisms are likely adapted to versatile metabolisms for energy conservation besides organohalide respiration. The genomic differences between marine and terrestrial Dia may suggest distinct functions and roles in element cycling (e.g., carbon, sulfur, chlorine), which require interdisciplinary approaches to unravel the physiology and evolution of Dia in various environments.
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Affiliation(s)
- Yi Yang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Yaozhi Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Natalie L Cápiro
- Department of Civil and Environmental Engineering, Auburn University, Auburn, AL, United States
| | - Jun Yan
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
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19
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Siles JA, Michán C. Bacteria, archae, fungi and viruses: it takes a community to eliminate waste. Microb Biotechnol 2020; 13:892-894. [PMID: 31701639 PMCID: PMC7264746 DOI: 10.1111/1751-7915.13503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 11/28/2022] Open
Abstract
Importance of the microbiota communities for improving the efficiency in Waste Water Treatment Plants.
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Affiliation(s)
- José Angel Siles
- Departamento de Química Inorgánica e Ingeniería QuímicaUniversidad de CórdobaCampus Universitario de Rabanales, edificio Marie Curie C‐3, planta baja14071CórdobaSpain
| | - Carmen Michán
- Departamento de Bioquímica y Biología MolecularUniversidad de Córdoba Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa C‐6, 2ª Planta14071CórdobaSpain
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