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Rishan ST, Kline RJ, Rahman MS. Exploitation of environmental DNA (eDNA) for ecotoxicological research: A critical review on eDNA metabarcoding in assessing marine pollution. CHEMOSPHERE 2024; 351:141238. [PMID: 38242519 DOI: 10.1016/j.chemosphere.2024.141238] [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: 07/04/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
The rise in worldwide population has led to a noticeable spike in the production, consumption, and transportation of energy and food, contributing to elevated environmental pollution. Marine pollution is a significant global environmental issue with ongoing challenges, including plastic waste, oil spills, chemical pollutants, and nutrient runoff, threatening marine ecosystems, biodiversity, and human health. Pollution detection and assessment are crucial to understanding the state of marine ecosystems. Conventional approaches to pollution evaluation usually represent laborious and prolonged physical and chemical assessments, constraining their efficacy and expansion. The latest advances in environmental DNA (eDNA) are valuable methods for the detection and surveillance of pollution in the environment, offering enhanced sensibility, efficacy, and involvement. Molecular approaches allow genetic information extraction from natural resources like water, soil, or air. The application of eDNA enables an expanded evaluation of the environmental condition by detecting both identified and unidentified organisms and contaminants. eDNA methods are valuable for assessing community compositions, providing indirect insights into the intensity and quality of marine pollution through their effects on ecological communities. While eDNA itself is not direct evidence of pollution, its analysis offers a sensitive tool for monitoring changes in biodiversity, serving as an indicator of environmental health and allowing for the indirect estimation of the impact and extent of marine pollution on ecosystems. This review explores the potential of eDNA metabarcoding techniques for detecting and identifying marine pollutants. This review also provides evidence for the efficacy of eDNA assessment in identifying a diverse array of marine pollution caused by oil spills, harmful algal blooms, heavy metals, ballast water, and microplastics. In this report, scientists can expand their knowledge and incorporate eDNA methodologies into ecotoxicological research.
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Affiliation(s)
- Sakib Tahmid Rishan
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | - Richard J Kline
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA; School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | - Md Saydur Rahman
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA; School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA.
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2
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Grimwood RM, Fortune-Kelly G, Holmes EC, Ingram T, Geoghegan JL. Host specificity shapes fish viromes across lakes on an isolated remote island. Virology 2023; 587:109884. [PMID: 37757732 DOI: 10.1016/j.virol.2023.109884] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/03/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Fish viromes often provide insights into the origin and evolution of viruses affecting tetrapods, including those associated with imporant human diseases. However, despite fish being the most diverse vertebrate group, their viruses are still understudied. We investigated the viromes of fish on Chatham Island (Rēkohu), a geographically isolated island housing 9% of New Zealand's threatened endemic fish species. Using metatranscriptomics, we analyzed samples from seven host species across 16 waterbodies. We identified 19 fish viruses, including 16 potentially novel species, expanding families such as the Coronaviridae, Hantaviridae, Poxviridae, and the recently proposed Tosoviridae. Surprisingly, virome composition was not influenced by the ecological factors measured and smelt (Retropinna retropinna) viromes were consistent across lakes despite differences in host life history, seawater influence, and community richness. Overall, fish viromes across Rēkohu were highly diverse and revealed a long history of co-divergence between host and virus despite their unique and geographically isolated ecosystem.
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Affiliation(s)
- Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | | | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Travis Ingram
- Department of Zoology, University of Otago, Dunedin, 9016, New Zealand
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand; Institute of Environmental Science and Research, Wellington, 5018, New Zealand.
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3
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Mehle N, Bačnik K, Bajde I, Brodarič J, Fox A, Gutiérrez-Aguirre I, Kitek M, Kutnjak D, Loh YL, Maksimović Carvalho Ferreira O, Ravnikar M, Vogel E, Vos C, Vučurović A. Tomato brown rugose fruit virus in aqueous environments - survival and significance of water-mediated transmission. FRONTIERS IN PLANT SCIENCE 2023; 14:1187920. [PMID: 37332729 PMCID: PMC10275568 DOI: 10.3389/fpls.2023.1187920] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023]
Abstract
Tomato brown rugose fruit virus (ToBRFV) has recently emerged as a major disease of tomatoes and peppers. ToBRFV is a seed- and contact-transmitted virus. In Slovenia, ToBRFV RNA was detected in samples of wastewater, river, and water used to irrigate plants. Even though the source of detected RNA could not be clearly established, this raised the question of the significance of the detection of ToBRFV in water samples and experimental studies were performed to address this question. The data presented here confirm that the release of virus particles from the roots of infected plants is a source of infectious ToBRFV particles in water and that the virus can remain infective up to four weeks in water stored at room temperature, while its RNA can be detected for much longer. These data also indicate that irrigation with ToBRFV-contaminated water can lead to plant infection. In addition, it has been shown that ToBRFV circulated in drain water in commercial tomato greenhouses from other European countries and that an outbreak of ToBRFV can be detected by regular monitoring of drain water. A simple method for concentrating ToBRFV from water samples and a comparison of the sensitivity of different methods, including the determination of the highest ToBRFV dilution still capable of infecting test plants, were also investigated. The results of our studies fill the knowledge gaps in the epidemiology and diagnosis of ToBRFV, by studying the role of water-mediated transmission, and provide a reliable risk assessment to identify critical points for monitoring and control.
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Affiliation(s)
- Nataša Mehle
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- School for Viticulture and Enology, University of Nova Gorica, Vipava, Slovenia
| | - Katarina Bačnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Irena Bajde
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Jakob Brodarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Adrian Fox
- Fera Science Ltd., York, United Kingdom
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Miha Kitek
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - Olivera Maksimović Carvalho Ferreira
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Elise Vogel
- Scientia Terrae Research Institute VZW, Sint-Katelijne-Waver, Belgium
- De Ceuster Meststoffen NV (DCM), Grobbendonk, Belgium
| | - Christine Vos
- Scientia Terrae Research Institute VZW, Sint-Katelijne-Waver, Belgium
| | - Ana Vučurović
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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4
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Laas P, Künnis-Beres K, Talas L, Tammert H, Kuprijanov I, Herlemann DPR, Kisand V. Bacterial communities in ballast tanks of cargo vessels - Shaped by salinity, treatment and the point of origin of the water but "hatch" its typical microbiome. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 324:116403. [PMID: 36352729 DOI: 10.1016/j.jenvman.2022.116403] [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: 07/27/2022] [Revised: 09/26/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Ballast water is a main vector of introduction of potentially harmful or pathogenic aquatic organisms. The development of genetic tools for ballast water monitoring has been underway and highlighted as a source for accurate and reliable data for decision making. We used 16S rRNA gene amplicon sequencing to analyze the microbial communities found in the ballast water of fifteen commercial ships routed through two Estonian ports. In parallel, samples from the port area were collected at the same time each ship visited. Fluorescence microscopy was utilized to assess the effectiveness of the treatment applied to ballast water. In addition, supplemental samples were collected from Hamburg Port (Germany) and a ballast tank decontamination system used at this port. The composition and diversity of bacterial communities varied greatly between obtained samples. The application of UV treatment did not demonstrate significant reduction in species richness estimates. The composition of microbial communities was significantly influenced by salinity, treatment (mainly untreated or UV treated) and the point of origin of the ballast water. Over a hundred potentially pathogenic bacterial taxa were found in relatively high abundance, including in ballast water that had received UV treatment. These shortcomings of stand-alone UV treatment of ballast water, especially when weak treatment is applied insufficiently, highlight the danger of possible harmful effects arising over time and the need for genetic tools for ballast water monitoring and management.
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Affiliation(s)
- Peeter Laas
- Institute of Technology, University of Tartu, Nooruse 1, Tartu, Estonia; Department of Marine Systems, Tallinn University of Technology, Akadeemia Tee 15a, Tallinn, Estonia
| | - Kai Künnis-Beres
- Department of Marine Systems, Tallinn University of Technology, Akadeemia Tee 15a, Tallinn, Estonia
| | - Liisi Talas
- Institute of Technology, University of Tartu, Nooruse 1, Tartu, Estonia
| | - Helen Tammert
- Institute of Technology, University of Tartu, Nooruse 1, Tartu, Estonia
| | - Ivan Kuprijanov
- Department of Marine Systems, Tallinn University of Technology, Akadeemia Tee 15a, Tallinn, Estonia
| | - Daniel P R Herlemann
- Estonian University of Life Sciences, Centre for Limnology, Vehendi, Elva, Tartu County, Estonia
| | - Veljo Kisand
- Institute of Technology, University of Tartu, Nooruse 1, Tartu, Estonia.
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Bassi C, Guerriero P, Pierantoni M, Callegari E, Sabbioni S. Novel Virus Identification through Metagenomics: A Systematic Review. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122048. [PMID: 36556413 PMCID: PMC9784588 DOI: 10.3390/life12122048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.
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Affiliation(s)
- Cristian Bassi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Paola Guerriero
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Marina Pierantoni
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Elisa Callegari
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Silvia Sabbioni
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Correspondence: ; Tel.: +39-053-245-5319
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Gu X, Yang Y, Mao F, Lee WL, Armas F, You F, Needham DM, Ng C, Chen H, Chandra F, Gin KY. A comparative study of flow cytometry-sorted communities and shotgun viral metagenomics in a Singapore municipal wastewater treatment plant. IMETA 2022; 1:e39. [PMID: 38868719 PMCID: PMC10989988 DOI: 10.1002/imt2.39] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/30/2022] [Accepted: 06/19/2022] [Indexed: 06/14/2024]
Abstract
Traditional or "bulk" viral enrichment and amplification methods used in viral metagenomics introduce unavoidable bias in viral diversity. This bias is due to shortcomings in existing viral enrichment methods and overshadowing by the more abundant viral populations. To reduce the complexity and improve the resolution of viral diversity, we developed a strategy coupling fluorescence-activated cell sorting (FACS) with random amplification and compared this to bulk metagenomics. This strategy was validated on both influent and effluent samples from a municipal wastewater treatment plant using the Modified Ludzack-Ettinger (MLE) process as the treatment method. We found that DNA and RNA communities generated using bulk samples were mostly different from those derived following FACS for both treatments before and after MLE. Before MLE treatment, FACS identified five viral families and 512 viral annotated contigs. Up to 43% of mapped reads were not detected in bulk samples. Nucleo-cytoplasmic large DNA viral families were enriched to a greater extent in the FACS-coupled subpopulations compared with bulk samples. FACS-coupled viromes captured a single-contig viral genome associated with Anabaena phage, which was not observed in bulk samples or in FACS-sorted samples after MLE. These short metagenomic reads, which were assembled into a high-quality draft genome of 46 kbp, were found to be highly dominant in one of the pre-MLE FACS annotated virome fractions (57.4%). Using bulk metagenomics, we identified that between Primary Settling Tank and Secondary Settling Tank viromes, Virgaviridae, Astroviridae, Parvoviridae, Picobirnaviridae, Nodaviridae, and Iridoviridae were susceptible to MLE treatment. In all, bulk and FACS-coupled metagenomics are complementary approaches that enable a more thorough understanding of the community structure of DNA and RNA viruses in complex environmental samples, of which the latter is critical for increasing the sensitivity of detection of viral signatures that would otherwise be lost through bulk viral metagenomics.
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Affiliation(s)
- Xiaoqiong Gu
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Yi Yang
- NUS Environmental Research InstituteNational University of SingaporeSingaporeSingapore
| | - Feijian Mao
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
| | - Wei Lin Lee
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Federica Armas
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Fang You
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
| | - David M. Needham
- Monterey Bay Aquarium Research InstituteMoss LandingCaliforniaUSA
- GEOMAR Helmholtz Centre for Ocean ResearchOcean EcoSystems Biology UnitKielGermany
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Charmaine Ng
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
| | - Hongjie Chen
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Franciscus Chandra
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
| | - Karina Yew‐Hoong Gin
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
- NUS Environmental Research InstituteNational University of SingaporeSingaporeSingapore
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Pagenkopp Lohan KM, Darling JA, Ruiz GM. International shipping as a potent vector for spreading marine parasites. DIVERS DISTRIB 2022; 28:1922-1933. [PMID: 38269301 PMCID: PMC10807284 DOI: 10.1111/ddi.13592] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/10/2022] [Indexed: 12/21/2022] Open
Abstract
Aim The global shipping fleet, the primary means of transporting goods among countries, also serves as a major dispersal mechanism for marine invasive species. To date, researchers have primarily focussed on the role of ships in transferring marine macrofauna, often overlooking transfers of associated parasites, which can have larger impacts on naïve host individuals and populations. Here, we re-examine three previously published metabarcode datasets targeting zooplankton and protists in ships' ballast water to assess the diversity of parasites across life stages arriving to three major US ports. Location Port of Hampton Roads in the Chesapeake Bay, Virginia; Ports of Texas City, Houston and Bayport in Galveston Bay, Texas; and Port of Valdez in Prince William Sound, Alaska. Methods We selected all known parasitic taxa, using sequences generated from the small subunit gene (SSU) from ribosomal RNA (rRNA) amplified from (1) zooplankton collected from plankton tows (35 and 80 μm datasets) and (2) eukaryotes collected from samples of ships' ballast water (3 μm dataset). Results In all three datasets, we found a broad range of parasitic taxa, including many protistan and metazoan parasites, that infect a wide range of hosts, from teleost fish to dinoflagellates. Parasite richness was highest in the 3 μm dataset and relatively uniform across arrival regions. Several parasite taxa were found in high relative abundance (based on number of sequences recovered) either in ships entering a single or across multiple regions. Main Conclusions The ubiquity, diversity and relative abundance of parasites detected demonstrate ships are a potent vector for spreading marine parasites across the world's oceans, potentially contributing to reported increases in outbreaks of marine diseases. Future research is urgently needed to evaluate the fate of parasites upon arrival and the efficacy of ballast water treatment systems to reduce future transfers and colonization.
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Affiliation(s)
| | - John A. Darling
- Center for Environmental Measurement and Modeling, United States Environmental Protection Agency, Durham, North Carolina, USA
| | - Gregory M. Ruiz
- Marine Invasions Research Laboratory, Smithsonian Environmental Research Center, Edgewater, Maryland, USA
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Nogueira WG, Gois BVA, Pinheiro KDC, Aragão ADO, Queiroz ALC, da Silva AL, Folador AC, Ramos RTJ. Viral Metagenomics Reveals Widely Diverse Viral Community of Freshwater Amazonian Lake. Front Public Health 2022; 10:869886. [PMID: 35548089 PMCID: PMC9081339 DOI: 10.3389/fpubh.2022.869886] [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: 02/05/2022] [Accepted: 03/24/2022] [Indexed: 11/28/2022] Open
Abstract
Despite the importance of understanding the ecology of freshwater viruses, there are not many studies on the subject compared to marine viruses. The microbiological interactions in these environments are still poorly known, especially between bacteriophages and their host bacteria and between cyanophages and cyanobacteria. Lake Bologna, Belém, capital of the Brazilian State of Pará, is a water source that supplies the city and its metropolitan region. However, it remains unexplored regarding the contents of its virome and viral diversity composition. Therefore, this work aims to explore the taxonomic diversity of DNA viruses in this lake, especially bacteriophages and cyanophages, since they can act as transducers of resistance genes and reporters of water quality for human consumption. We used metagenomic sequencing data generated by previous studies. We analyzed it at the taxonomic level using the tools Kraken2, Bracken, and Pavian; later, the data was assembled using Genome Detective, which performs the assembly of viruses. The results observed here suggest the existence of a widely diverse viral community and established microbial phage-regulated dynamics in Lake Bolonha. This work is the first ever to describe the virome of Lake Bolonha using a metagenomic approach based on high-throughput sequencing, as it contributes to the understanding of water-related public health concerns regarding the spreading of antibiotic resistance genes and population control of native bacteria and cyanobacteria.
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Affiliation(s)
| | | | | | - Andressa de Oliveira Aragão
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Brazil
| | | | - Artur Luiz da Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Brazil
| | - Adriana Carneiro Folador
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Brazil
| | - Rommel Thiago Jucá Ramos
- Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- *Correspondence: Rommel Thiago Jucá Ramos
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Lv B, Shi J, Li T, Ren L, Tian W, Lu X, Han Y, Cui Y, Jiang T. Deciphering the characterization, ecological function and assembly processes of bacterial communities in ship ballast water and sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:152721. [PMID: 34974026 DOI: 10.1016/j.scitotenv.2021.152721] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/10/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Various microorganisms are transported worldwide via the water and sediments inside ship ballast tanks. Nevertheless, the ecological functions and assembly processes of bacterial communities in ballast water and sediments remain poorly understood. Here, we investigated the bacterial composition, community assembly processes, and putative functions through analyses of 70 ballast water and sediment samples obtained from various ships. The results showed that the ballast sediments contained a higher diversity of bacterial communities, whereas the ballast water was characterized by the dominance of Proteobacteria. Both the composition and potential function structures of bacterial communities were clearly different between the ballast water and sediment samples. The ballast water exhibited an abundance of microorganisms that involved in sulfur oxidation, whereas the bacterial species associated with nitrogen metabolism were abundant in the sediments. Co-occurrence network analysis revealed that the communities in ballast sediment samples possessed more complex network structures with higher modularity and positive associations among bacterial populations. Stochastic processes, especially the dispersal limitation process played the most important influence in the assembly of the communities in ballast water. Meanwhile, the bacterial communities in the ballast sediments were primarily governed by the homogeneous selection of determinacy. The results from this study will help us understand the ecological processes related to the bacterial communities in the ballast tanks and provide a foundation for the management of ballast water and sediments.
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Affiliation(s)
- Baoyi Lv
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China.
| | - Jianhong Shi
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Tao Li
- China Waterborne Transport Research Institute, Beijing 100088, China
| | - Lili Ren
- China Waterborne Transport Research Institute, Beijing 100088, China
| | - Wen Tian
- Jiangyin Customs, Jiangyin 214400, China
| | - Xiaolan Lu
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
| | | | - Yuxue Cui
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Ting Jiang
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
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10
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Testerman T, Beka L, McClure EA, Reichley SR, King S, Welch TJ, Graf J. Detecting Flavobacterial Fish Pathogens in the Environment via High-Throughput Community Analysis. Appl Environ Microbiol 2022; 88:e0209221. [PMID: 34788066 PMCID: PMC8788675 DOI: 10.1128/aem.02092-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 11/09/2021] [Indexed: 11/20/2022] Open
Abstract
Diseases caused by the fish pathogens Flavobacterium columnare and Flavobacterium psychrophilum are major contributors of preventable losses in the aquaculture industry. The persistent and difficult-to-control infections caused by these bacteria make timely intervention and prophylactic elimination of pathogen reservoirs important measures to combat these disease-causing agents. In this study, we present two independent assays for detecting these pathogens in a range of environmental samples. Natural water samples were inoculated with F. columnare and F. psychrophilum over 5 orders of magnitude, and pathogen levels were detected using Illumina MiSeq sequencing and droplet digital PCR. Both detection methods accurately identified pathogen-positive samples and showed good agreement in quantifying each pathogen. Additionally, the real-world application of these approaches was demonstrated using environmental samples collected at a rainbow trout (Oncorhynchus mykiss) aquaculture facility. These results show that both methods can serve as useful tools for surveillance efforts in aquaculture facilities, where the early detection of these flavobacterial pathogens may direct preventative measures to reduce disease occurrence. IMPORTANCE Early detection of a deadly disease outbreak in a population can be the difference between mass mortality or mitigated effects. In the present study, we evaluated and compared two molecular techniques for detecting economically impactful aquaculture pathogens. We demonstrate that one of these techniques, 16S rRNA gene sequencing using Illumina MiSeq technology, provides the ability to accurately detect two freshwater fish pathogens, F. columnare and F. psychrophilum, while simultaneously profiling the native microbial community. The second technique, droplet digital PCR, is commonly used for pathogen detection, and the results obtained using the assays we designed with this method served to validate those obtained using the MiSeq method. These two methods offer distinct advantages. The MiSeq method pairs pathogen detection and microbial community profiling to answer immediate and long-term fish health concerns, while the droplet digital PCR method provides fast and highly sensitive detection that is useful for surveillance and rapid clinical responses.
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Affiliation(s)
- Todd Testerman
- University of Connecticut, Department of Molecular and Cell Biology, Storrs, Connecticut, USA
| | - Lidia Beka
- University of Connecticut, Department of Molecular and Cell Biology, Storrs, Connecticut, USA
| | - Emily Ann McClure
- University of Connecticut, Department of Molecular and Cell Biology, Storrs, Connecticut, USA
| | | | | | - Timothy J. Welch
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service/U.S. Department of Agriculture, Kearneysville, West Virginia, USA
| | - Joerg Graf
- University of Connecticut, Department of Molecular and Cell Biology, Storrs, Connecticut, USA
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Lu J, Yang S, Zhang X, Tang X, Zhang J, Wang X, Wang H, Shen Q, Zhang W. Metagenomic Analysis of Viral Community in the Yangtze River Expands Known Eukaryotic and Prokaryotic Virus Diversity in Freshwater. Virol Sin 2022; 37:60-69. [PMID: 35234628 PMCID: PMC8922420 DOI: 10.1016/j.virs.2022.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/03/2021] [Indexed: 11/16/2022] Open
Abstract
Viruses in aquatic ecosystems are characterized by extraordinary abundance and diversity. Thus far, there have been limited studies focused on viral communities in river water systems. Here, we investigated the virome of the Yangtze River Delta using viral metagenomic analysis. The compositions of viral communities from six sampling sites were analyzed and compared. By using library construction and next generation sequencing, contigs and singlet reads similar to viral sequences were classified into 17 viral families, including nine dsDNA viral families, four ssDNA viral families and four RNA viral families. Statistical analysis using Friedman test suggested that there was no significant difference among the six sampling sites (P > 0.05). The viromes in this study were all dominated by the order Caudovirales, and a group of Freshwater phage uvFW species were particularly prevalent among all the samples. The virome from Nanjing presented a unique pattern of viral community composition with a relatively high abundance of family Parvoviridae. Phylogenetic analyses based on virus hallmark genes showed that the Caudovirales order and CRESS-DNA viruses presented high genetic diversity, while viruses in the Microviridae and Parvoviridae families and the Riboviria realm were relatively conservative. Our study provides the first insight into viral community composition in large river ecosystem, revealing the diversity and stability of river water virome, contributing to the proper utilization of freshwater resource. First insight into viral community composition in large river ecosystem. Virus hallmark genes present both diverse and conservative characteristics. The composition of viral communities is similar on the whole. Slight regional variation of virome is existed in individual areas.
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12
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Rosenau NA, Gignoux-Wolfsohn S, Everett RA, Miller AW, Minton MS, Ruiz GM. Considering Commercial Vessels as Potential Vectors of Stony Coral Tissue Loss Disease. FRONTIERS IN MARINE SCIENCE 2021; 8:1-8. [PMID: 35685121 PMCID: PMC9175181 DOI: 10.3389/fmars.2021.709764] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Stony coral tissue loss disease (SCTLD) is a troubling new disease that is spreading rapidly across the greater Caribbean region, but the etiological agent(s) and the mechanisms(s) of spread are both unknown. First detected off the coast of Miami, Florida, major ocean currents alone do not explain the pattern of spread, with outbreaks occurring across geographically disjunct and distant locations. This has raised concerns by researchers and resource managers that commercial vessels may contribute as vectors to spread of the disease. Despite existing regulatory and management strategies intended to limit coastal marine invasion risks, the efficacy of these measures is still unresolved for ship-borne microorganisms, and disease transport via ballast water and hull biofouling are under examination given the high ship traffic in the region. Here, to help inform the discussion of ships as possible vectors of SCTLD, we provide an overview of the current state of knowledge about ships and their potential to transfer organisms in the greater Caribbean, focusing in particular on ballast water, and outline a set of recommendations for future research.
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Affiliation(s)
- Nicholas A. Rosenau
- Ocean and Coastal Management Branch, Office of Wetlands, Oceans, and Watersheds, United States Environmental Protection Agency, Washington, DC, United States
| | | | - Richard A. Everett
- United States Coast Guard, Office of Operating and Environmental Standards, Washington, DC, United States
| | - A. Whitman Miller
- Smithsonian Environmental Research Center, Edgewater, MD, United States
| | - Mark S. Minton
- Smithsonian Environmental Research Center, Edgewater, MD, United States
| | - Gregory M. Ruiz
- Smithsonian Environmental Research Center, Edgewater, MD, United States
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13
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Soleimani F, Taherkhani R, Dobaradaran S, Spitz J, Saeedi R. Molecular detection of E. coli and Vibrio cholerae in ballast water of commercial ships: a primary study along the Persian Gulf. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2021; 19:457-463. [PMID: 34150249 PMCID: PMC8172682 DOI: 10.1007/s40201-021-00618-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/15/2020] [Accepted: 01/18/2021] [Indexed: 05/15/2023]
Abstract
PURPOSE Ballast water is one of the most important ways for the transfer of aquatic organisms such as Escherichia coli (E. coli) and Vibrio cholerae. The aim of this study was to investigate Mdh gene of E. coli and the OmpW gene of Vibrio cholerae bacteria by PCR technique in the ballast water of commercial ships entering Bushehr port along the Persian Gulf. METHODS In this study, 34 samples of ballast water entered Bushehr port were studied by using culture and PCR methods to determine Mdh gene of E. coli and OmpW gene of Vibrio cholerae. Genomic DNA of bacterial strains was extracted and PCR was performed by using specific primers of E. coli and Vibrio cholerae. RESULTS The specific Mdh gene of E. coli was detected in 4 ballast water samples and the positive samples were analyzed by antisera methods for E. coli O157:H7. Results of antisera showed that there were 3 positive samples of O157:H7 serotype. The results of the PCR technique showed that the OmpW gene of Vibrio cholerae was negative for all positive culture samples. CONCLUSIONS Further studies are highly recommended to monitor other aquatic organisms in ballast water to protect the marine environment.
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Affiliation(s)
- Farshid Soleimani
- Systems Environmental Health and Energy Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Boostan 19 Alley, Imam Khomeini Street, Bushehr, Iran
| | - Reza Taherkhani
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Sina Dobaradaran
- Systems Environmental Health and Energy Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Boostan 19 Alley, Imam Khomeini Street, Bushehr, Iran
- Department of Environmental Health Engineering, Faculty of Health, Bushehr University of Medical Sciences, Bushehr, Iran
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, Essen, Germany
| | - Jörg Spitz
- Akademie für menschliche Medizin GmbH, Krauskopfallee 27, 65388 Schlangenbad, Germany
| | - Reza Saeedi
- Workplace Health Promotion Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Health, Safety and Environment, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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14
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Towards the Optimization of eDNA/eRNA Sampling Technologies for Marine Biosecurity Surveillance. WATER 2021. [DOI: 10.3390/w13081113] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The field of eDNA is growing exponentially in response to the need for detecting rare and invasive species for management and conservation decisions. Developing technologies and standard protocols within the biosecurity sector must address myriad challenges associated with marine environments, including salinity, temperature, advective and deposition processes, hydrochemistry and pH, and contaminating agents. These approaches must also provide a robust framework that meets the need for biosecurity management decisions regarding threats to human health, environmental resources, and economic interests, especially in areas with limited clean-laboratory resources and experienced personnel. This contribution aims to facilitate dialogue and innovation within this sector by reviewing current approaches for sample collection, post-sampling capture and concentration of eDNA, preservation, and extraction, all through a biosecurity monitoring lens.
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15
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Zhang Y, Li Z, Guo X, Liu G, Zhang S. Potentiometric Sensor Based on Carbon Paste Electrode for Monitoring Total Residual Chlorine in Electrolytically-Treated Ballast Water. SENSORS (BASEL, SWITZERLAND) 2021; 21:E350. [PMID: 33430170 PMCID: PMC7825626 DOI: 10.3390/s21020350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/30/2020] [Accepted: 01/02/2021] [Indexed: 11/18/2022]
Abstract
A new potentiometric sensor based on modified carbon paste electrode (CPE) was prepared for the sensitive and selective detection of total residual chlorine (TRC) in simulated electrolytically-treated ballast water (BW). The modified CPE was prepared using ferrocene (Fc) as the sensing species and paraffin oil as the binder. It is revealed that the addition of Fc can significantly shorten the response time and improve the reproducibility, selectivity, and stability of the sensor. The open circuit potential of the Fc-CPE is in linear proportion to the logarithm of TRC within the TRC concentration range from 1 mg∙dm-3 to 15 mg∙dm-3. In addition, the Fc-CPE sensor exhibits good selectivity to TRC over a wide concentration range of the possible co-exiting interference ions in seawater. The Fc-CPE electrode can be used as a convenient and reliable sensor for the continuous monitoring of TRC during the electrolytic treatment of BW.
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Affiliation(s)
- Yaning Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China;
| | - Zhihui Li
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; (Z.L.); (X.G.); (G.L.)
| | - Xiaotong Guo
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; (Z.L.); (X.G.); (G.L.)
| | - Guangzhou Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; (Z.L.); (X.G.); (G.L.)
| | - Shuyong Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; (Z.L.); (X.G.); (G.L.)
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16
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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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17
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Lv B, Cui Y, Tian W, Wei H, Chen Q, Liu B, Zhang D, Xie B. Vessel transport of antibiotic resistance genes across oceans and its implications for ballast water management. CHEMOSPHERE 2020; 253:126697. [PMID: 32298915 DOI: 10.1016/j.chemosphere.2020.126697] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
The emergence and spread of antibiotic resistance are major threats to ecosystems and human health. Transoceanic channels (e.g., ship ballast water) can transfer harmful aquatic organisms across geographically isolated waters. However, the occurrence of antibiotic resistance genes (ARGs) in ship ballast water and their relationship with microbial communities and environmental factors remain unknown. In this study, ballast water from 28 vessels sailing to Shanghai and Jiangyin (China) were collected, and the ARGs in these water samples were investigated. Considerable levels of ARGs and integrase of the class-I integrons (intI1) were detected in all ballast water samples. sul1 and tetQ were the most and least abundant ARGs in ballast water samples, respectively. The ARGs were strongly correlated with those of the 16S rRNA and intI1 genes. Ballast water exchange can reduce the absolute abundance of some kinds of ARGs while increasing the relative abundance of several ARGs (e.g., mefA, mexF, strB, sul1, and tetQ). Moreover, the bacterial hosts of ARGs were generally different in the unexchanged ballast water (UEBW) and exchanged ballast water (EBW). In particular, Leisingera and unclassified_Erythrobacteraceae were the main ARGs-associated genera in the EBW, while Pseudohongiella, Cycloclasticus, OM43_clade, norank_f_Rhodospirillaceae, and norank_f_Rhodobacteraceae were the dominant ARGs hosts in the UEBW. Overall, ship ballast water is an effective moving carrier for the global transference of ARGs, and its sufficient management is required for mitigating ARGs propagation across oceans.
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Affiliation(s)
- Baoyi Lv
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China; Key Laboratory for Urban and Ecological Restoration of Shanghai, School of Ecology and Environmental Sciences, East China Normal University, Shanghai 200241, China.
| | - Yuxue Cui
- Key Laboratory for Urban and Ecological Restoration of Shanghai, School of Ecology and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Wen Tian
- Jiangyin Customs, Jiangyin 214400, China
| | - Huawei Wei
- Key Laboratory for Urban and Ecological Restoration of Shanghai, School of Ecology and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Qihao Chen
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Bingli Liu
- Jiangyin Customs, Jiangyin 214400, China
| | - Di Zhang
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China; International Joint Research Center for Persistent Toxic Substances (IJRC-PTS), Shanghai Maritime University, Shanghai, 201306, China
| | - Bing Xie
- Key Laboratory for Urban and Ecological Restoration of Shanghai, School of Ecology and Environmental Sciences, East China Normal University, Shanghai 200241, China
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18
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Haas CN. Quantitative Microbial Risk Assessment and Molecular Biology: Paths to Integration. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:8539-8546. [PMID: 32539352 DOI: 10.1021/acs.est.0c00664] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Quantitative microbial risk assessment (QMRA) has now been in use for over 35 years and has formed the basis for developing criteria for ensuring public health related to water, food, and remediation, to name a few areas. The initial data for QMRA (both in exposure assessment and in dose response assessment) came from measurements using assays for viability, such as plate counts, plaque assays, or animal infectivity. With the increasing use of molecular methods for the measurement of microorganisms in the environment, it has become important to assess how to use such data to estimate infectious disease risks. The limitations to the use of such data and needs to resolve the limitations will be addressed.
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Affiliation(s)
- Charles N Haas
- Department of Civil, Architectural & Environmental Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
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19
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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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20
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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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21
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Cantrell DL, Groner ML, Ben-Horin T, Grant J, Revie CW. Modeling Pathogen Dispersal in Marine Fish and Shellfish. Trends Parasitol 2020; 36:239-249. [PMID: 32037136 DOI: 10.1016/j.pt.2019.12.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/19/2019] [Accepted: 12/25/2019] [Indexed: 12/12/2022]
Abstract
In marine ecosystems, oceanographic processes often govern host contacts with infectious agents. Consequently, many approaches developed to quantify pathogen dispersal in terrestrial ecosystems have limited use in the marine context. Recent applications in marine disease modeling demonstrate that physical oceanographic models coupled with biological models of infectious agents can characterize dispersal networks of pathogens in marine ecosystems. Biophysical modeling has been used over the past two decades to model larval dispersion but has only recently been utilized in marine epidemiology. In this review, we describe how biophysical models function and how they can be used to measure connectivity of infectious agents between sites, test hypotheses regarding pathogen dispersal, and quantify patterns of pathogen spread, focusing on fish and shellfish pathogens.
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Affiliation(s)
- Danielle L Cantrell
- Health Management Department, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada.
| | - Maya L Groner
- Prince William Sound Science Center, Cordova, AK, USA; Affiliate, US Geological Survey, Western Fisheries Research Center, Seattle, WA, USA
| | - Tal Ben-Horin
- Department of Fisheries, Animal and Veterinary Science, College of the Environment and Life Science, University of Rhode Island, Kingston, RI, USA; Center for Marine Science and Technology, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Morehead City, NC, USA
| | - Jon Grant
- Oceanography Department, Dalhousie University, Halifax, NS, Canada
| | - Crawford W Revie
- Health Management Department, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada; Department of Computer and Information Sciences, University of Strathclyde, Glasgow, UK
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22
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Zolfo M, Pinto F, Asnicar F, Manghi P, Tett A, Bushman FD, Segata N. Detecting contamination in viromes using ViromeQC. Nat Biotechnol 2020; 37:1408-1412. [PMID: 31748692 DOI: 10.1038/s41587-019-0334-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Adrian Tett
- Department CIBIO, University of Trento, Trento, Italy
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
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23
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Kaszab E, Doszpoly A, Lanave G, Verma A, Bányai K, Malik YS, Marton S. Metagenomics revealing new virus species in farm and pet animals and aquaculture. GENOMICS AND BIOTECHNOLOGICAL ADVANCES IN VETERINARY, POULTRY, AND FISHERIES 2020. [PMCID: PMC7149329 DOI: 10.1016/b978-0-12-816352-8.00002-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Viral metagenomics is slowly taking over the traditional and widely used molecular techniques for the investigation of pathogenic viruses responsible for illness and inflicting great economic burden on the farm animal industry. Owing to the continued improvements in sequencing technologies and the dramatic reduction of per base costs of sequencing the use of next generation sequencing have been key factors in this progress. Discoveries linked to viral metagenomics are expected to be beneficial to the field of veterinary medicine starting from the development of better diagnostic assays to the design of new subunit vaccines with minimal investments. With these achievements the research has taken a giant leap even toward the better healthcare of animals and, as a result, the animal sector could be growing at an unprecedented pace.
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24
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Ji P, Aw TG, Van Bonn W, Rose JB. Evaluation of a portable nanopore-based sequencer for detection of viruses in water. J Virol Methods 2019; 278:113805. [PMID: 31891731 DOI: 10.1016/j.jviromet.2019.113805] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 12/20/2022]
Abstract
The newly emerged nanopore sequencing technology such as MinION™ allows for real-time detection of long DNA/RNA fragments on a portable device, yet few have examined its performance for environmental viromes. Here we seeded one RNA virus bacteriophage MS2 and one DNA virus bacteriophage PhiX174 into 10 L well water at three levels ranging from 1 to 21,100 plaque-forming units (PFU)/mL. Two workflows were established to maximize the number of sequencing reads of RNA and DNA viruses using MinION™. With dead-end ultrafiltration, PEG precipitation, and random amplification, MinION™ was capable of detecting MS2 at 155 PFU/mL and PhiX174 at 1-2 PFU/mL. While the DNA workflow only detected PhiX174, the RNA workflow detected both MS2 and PhiX174. The virus concentration, or relative abundance of viral nucleic acids in total nucleic acids, is critical to the proportion of viral reads in sequencing results. Our findings also highlight the importance of including control samples in sequencing runs for environmental water samples with low virus abundance.
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Affiliation(s)
- Pan Ji
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - William Van Bonn
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA; A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, Chicago, IL 60605, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA.
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Global Comparison of the Bacterial Communities of Bilge Water, Boat Surfaces, and External Port Water. Appl Environ Microbiol 2019; 85:AEM.01804-19. [PMID: 31585994 DOI: 10.1128/aem.01804-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/16/2019] [Indexed: 01/07/2023] Open
Abstract
In the past, ballast water has been a key vector in the ship-mediated dispersal of invasive species. Here, we evaluate the potential for port microorganisms to enter and colonize the hull and bilge water of ships. Due to the small size and ubiquitous nature of bacteria, they also have the potential to be spread through hull fouling and bilge water discharge. The goal of this study was to identify the extent to which the boat microbial community is shaped by the microbial community in the port water where the boat spends most of its time. Here, we compared the microbial communities of the hull and bilge compartments of 20 boats to those of the port water in 20 different ports in five regions around the world. We found that there was a significant difference in microbial diversity between boat and port microbial communities. Despite these differences, we found that Cyanobacteria were present at high abundances in the bilge water of most vessels. Due to the limited light in the bilge, the presence of Cyanobacteria suggests that port microorganisms can enter the bilge. Using source-tracking software, we found that, on average, 40% of the bilge and 52% of the hull microbial communities were derived from water. These findings suggest that the bilge of a vessel contains a diverse microbial community that is influenced by the port microbial community and has the potential to serve as an underappreciated vector for dispersal of life.IMPORTANCE Invasive species have been a worldwide problem for many years. However, the potential for microorganisms to become invasive is relatively underexplored. As the tools to study bacterial communities become more affordable, we are able to perform large-scale studies and examine bacterial communities in higher resolution than was previously practical. This study looked at the potential for bacteria to colonize both boat surfaces and bilge water. We describe the bacterial communities on boats in 20 shipping ports in five regions around the world, describing how these microorganisms were similar to microorganisms found in port water. This suggests that the water influences the bacterial community of a boat and that microorganisms living on a boat could be moved from place to place when the boat travels.
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Rey A, Carney KJ, Quinones LE, Pagenkopp Lohan KM, Ruiz GM, Basurko OC, Rodríguez-Ezpeleta N. Environmental DNA Metabarcoding: A Promising Tool for Ballast Water Monitoring. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:11849-11859. [PMID: 31545591 DOI: 10.1021/acs.est.9b01855] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nonindigenous species are introduced worldwide with ballast water (BW). To prevent further introductions, oceanic BW exchange and BW treatment systems are utilized, but their performance needs to be evaluated. To that aim, characterizing BW communities is essential but usually relies on exhaustive sampling and morphological taxonomic identification, which does not always allow fine-scale taxonomic resolution. Through the analysis of BW samples from 11 vessels arriving to the Chesapeake Bay (USA), we evaluated the potential of environmental DNA (eDNA) metabarcoding for BW monitoring by assessing whether the impact of BW management type could be identified, analyzing the influence of BW sampling access locations on communities, and comparing the accuracy of eDNA for taxonomic assignment and identification of nonindigenous taxa. We found that (1) different sampling access locations of the same tank resulted in different communities, (2) communities from treated and exchanged BW differ, (3) signals of source port and of ocean exchange are observed, (4) eDNA metabarcoding results in more diversity than morphological taxonomy, and (5) the nonindigenous copepod Oithona davisae, not reported before in the Chesapeake Bay, is detected. Overall, this study highlights the potential of eDNA metabarcoding for BW monitoring, but more comprehensive sampling will be needed to optimize the approach.
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Affiliation(s)
- Anaïs Rey
- Marine Research Division , AZTI , Sukarrieta , Spain
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Bytesnikova Z, Richtera L, Smerkova K, Adam V. Graphene oxide as a tool for antibiotic-resistant gene removal: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:20148-20163. [PMID: 31115815 DOI: 10.1007/s11356-019-05283-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 04/17/2019] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
Environmental pollutants, including antibiotics (ATBs), have become an increasingly common health hazard in the last several decades. Overdose and abuse of ATBs led to the emergence of antibiotic-resistant genes (ARGs), which represent a serious health threat. Moreover, water bodies and reservoirs are places where a wide range of bacterial species with ARGs originate, owing to the strong selective pressure from presence of ATB residues. In this regard, graphene oxide (GO) has been utilised in several fields including remediation of the environment. In this review, we present a brief overview of resistant genes of frequently used ATBs, their occurrence in the environment and their behaviour. Further, we discussed the factors influencing the binding of nucleic acids and the response of ARGs to GO, including the presence of salts in the water environment or water pH, because of intrinsic properties of GO of not only binding to nucleic acids but also catalysing their decomposition. This would be helpful in designing new types of water treatment facilities.
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Affiliation(s)
- Zuzana Bytesnikova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00, Brno, Czech Republic
| | - Lukas Richtera
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czech Republic.
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00, Brno, Czech Republic.
| | - Kristyna Smerkova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00, Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00, Brno, Czech Republic
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Hess-Erga OK, Moreno-Andrés J, Enger Ø, Vadstein O. Microorganisms in ballast water: Disinfection, community dynamics, and implications for management. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 657:704-716. [PMID: 30677936 DOI: 10.1016/j.scitotenv.2018.12.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 11/30/2018] [Accepted: 12/01/2018] [Indexed: 06/09/2023]
Abstract
Increasing concerns have accelerated the development of international regulations and methods for ballast water management to limit the introduction of non-indigenous species. The transport of microorganisms with ballast water has received scientific attention in recent years. However, few studies have focused on the importance of organisms smaller than 10 μm in diameter. In this work, we review the effects of ballast water transport, disinfection, and the release of microorganisms on ecosystem processes with a special focus on heterotrophic bacteria. It is important to evaluate both direct and indirect effects of ballast water treatment systems, such as the generation of easily degradable substrates and the subsequent regrowth of heterotrophic microorganisms in ballast tanks. Disinfection of water can alter the composition of bacterial communities through selective recolonization in the ballast water or the recipient water, and thereby affects bacterial driven functions that are important for the marine food web. Dissolved organic matter quality and quantity and the ecosystem status of the treated water can also be affected by the disinfection method used. These side effects of disinfection should be further investigated in a broader context and in different scales (laboratory studies, large-scale facilities, and on the ships).
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Affiliation(s)
- Ole-Kristian Hess-Erga
- NTNU Norwegian University of Science and Technology, Department of Biotechnology and Food Science, 7491 Trondheim, Norway
| | - Javier Moreno-Andrés
- Department of Environmental Technologies, University of Cádiz, INMAR-Marine Research Institute, Camepus Universitario Puerto Real, 11510 Puerto Real, Cádiz, Spain
| | - Øivind Enger
- Sarsia Seed AS, Postboks 7150, 5020 Bergen, Norway
| | - Olav Vadstein
- NTNU Norwegian University of Science and Technology, Department of Biotechnology and Food Science, 7491 Trondheim, Norway.
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Gerhard WA, Gunsch CK. Metabarcoding and machine learning analysis of environmental DNA in ballast water arriving to hub ports. ENVIRONMENT INTERNATIONAL 2019; 124:312-319. [PMID: 30660844 DOI: 10.1016/j.envint.2018.12.038] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
Abstract
While ballast water has long been linked to the global transport of invasive species, little is known about its microbiome. Herein, we used 16S rRNA gene sequencing and metabarcoding to perform the most comprehensive microbiological survey of ballast water arriving to hub ports to date. In total, we characterized 41 ballast, 20 harbor, and 6 open ocean water samples from four world ports (Shanghai, China; Singapore; Durban, South Africa; Los Angeles, California). In addition, we cultured Enterococcus and E. coli to evaluate adherence to International Maritime Organization standards for ballast discharge. Five of the 41 vessels - all of which were loaded in China - did not comply with standards for at least one indicator organism. Dominant bacterial taxa of ballast water at the class level were Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia. Ballast water samples were composed of significantly lower proportions of Oxyphotobacteria than either ocean or harbor samples. Linear discriminant analysis (LDA) effect size (LEfSe) and machine learning were used to identify and test potential biomarkers for classifying sample types (ocean, harbor, ballast). Eight candidate biomarkers were used to achieve 81% (k nearest neighbors) to 88% (random forest) classification accuracy. Further research of these biomarkers could aid the development of techniques to rapidly assess ballast water origin.
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Affiliation(s)
- William A Gerhard
- Duke University, Department of Civil and Environmental Engineering, 121 Hudson Hall, Durham, NC 27708-0287, United States
| | - Claudia K Gunsch
- Duke University, Department of Civil and Environmental Engineering, 121 Hudson Hall, Durham, NC 27708-0287, United States.
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Hwang J, Park SY, Lee S, Lee TK. High diversity and potential translocation of DNA viruses in ballast water. MARINE POLLUTION BULLETIN 2018; 137:449-455. [PMID: 30503454 DOI: 10.1016/j.marpolbul.2018.10.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 09/07/2018] [Accepted: 10/24/2018] [Indexed: 05/22/2023]
Abstract
Ballast water is a common vector for the transport of invasive species to new marine and aquatic environments. We used a metagenomics approach to examine the composition and diversity of viral communities in ballast water from ships originating in Mexico, Saudi Arabia, New York, and Panama, and in water from the port of their destination in Busan, Korea. Myoviridae was the most abundant virus family in ballast water, followed Podoviridae and Siphoviridae. We also identified viruses that infect invertebrates, amoebas, and algae in ballast water and in the Busan port water. Interestingly, there were several viruses that infect humans or other animals (Swinepox virus, Raccoonpox virus, Suid herpesvirus, and Human endogenous retrovirus) in the samples from New York and Panama. In addition, there were giant viruses in all the ballast water samples, especially, identified Megavirus chilensis in New York and Panama, and Pandoravirus salinus in Mexico and Saudi Arabia. These results provide detailed descriptions of the characteristics of the viruses present in ballast water, document significant viral diversity, and indicate the potential translocation of viruses via ballast water.
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Affiliation(s)
- Jinik Hwang
- South Sea Environment Research Department, Korea Institute of Ocean Science and Technology, Geoje 53201, Republic of Korea; Marine Ecology and Resource Convergence Center, AICT, Suwon, 16229, Republic of Korea
| | - So Yun Park
- South Sea Environment Research Department, Korea Institute of Ocean Science and Technology, Geoje 53201, Republic of Korea
| | - Sukchan Lee
- Department of Genetic Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Taek-Kyun Lee
- South Sea Environment Research Department, Korea Institute of Ocean Science and Technology, Geoje 53201, Republic of Korea.
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Lv B, Cui Y, Tian W, Li J, Xie B, Yin F. Abundances and profiles of antibiotic resistance genes as well as co-occurrences with human bacterial pathogens in ship ballast tank sediments from a shipyard in Jiangsu Province, China. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 157:169-175. [PMID: 29621708 DOI: 10.1016/j.ecoenv.2018.03.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 03/18/2018] [Accepted: 03/23/2018] [Indexed: 06/08/2023]
Abstract
Ship ballasting operations may transfer harmful aquatic organisms across global ocean. This study aims to reveal the occurrences and abundances of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs) in ballast tank sediments. Nine samples were collected and respectively analyzed by real-time quantitative PCR and high-throughput sequencing technologies. Ten ARGs (aadA1, blaCTX-M, blaTEM, ermB, mefA, strB, sul1, sul2, tetM, and tetQ) and the Class-I integron gene (intI1) were highly prevalent (105-109 gene copies/g) in ballast tank sediments. The sul1 was the most abundant ARG with the concentration of 108-109 copies/g and intI1 was much more abundant than the ARGs in ballast tank sediments. The strong positive correlations between intI1 and ARGs (blaCTX-M, sul1, sul2 and tetM) indicated the potential spread of ARGs via horizontal gene transfer. In ballast tank sediments, 44 bacterial species were identified as HBPs and accounted for 0.13-21.46% of the total bacterial population although the three indicator pathogenic microbes (Vibrio cholerae, Escherichia coli, and Enterococci) proposed by the International Maritime Organization were not detected. Pseudomonas pseudoalcaligenes, Enterococcus hirae, Shigella sonnei and Bacillus anthracis were the dominant pathogens in ballast tank sediments. Zn and P in sediments had positive effects on the ARGs. Network analysis results indicated that sul1 and sul2 genes existed in several bacterial pathogens. Ballast tank sediments could be regarded as a carrier for the migration of ARGs. It is important to manage ballast tank sediments reasonably in order to prevent the dissemination of ARGs and bacterial pathogens.
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Affiliation(s)
- Baoyi Lv
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China; International Joint Research Center for Persistent Toxic Substances (IJRC-PTS), Shanghai Maritime University, Shanghai 201306, China.
| | - Yuxue Cui
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai 200241, China
| | - Wen Tian
- Jiangyin Entry-Exit Inspection and Quarantine Bureau, Jiangyin 214442, China
| | - Jing Li
- Jiangyin Entry-Exit Inspection and Quarantine Bureau, Jiangyin 214442, China
| | - Bing Xie
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai 200241, China
| | - Fang Yin
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China; International Joint Research Center for Persistent Toxic Substances (IJRC-PTS), Shanghai Maritime University, Shanghai 201306, China
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Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes. Viruses 2018; 10:v10080429. [PMID: 30110939 PMCID: PMC6115975 DOI: 10.3390/v10080429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.
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Occurrence of Traditional and Alternative Fecal Indicators in Tropical Urban Environments under Different Land Use Patterns. Appl Environ Microbiol 2018; 84:AEM.00287-18. [PMID: 29776926 DOI: 10.1128/aem.00287-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/09/2018] [Indexed: 11/20/2022] Open
Abstract
This study evaluated the geospatial distribution of fecal indicator bacteria (FIB) (i.e., Escherichia coli, Enterococcus spp.) and the alternative fecal indicator pepper mild mottle virus (PMMoV) in tropical freshwater environments under different land use patterns. Results show that the occurrence and concentration of microbial fecal indicators were higher for urban than for parkland-dominated areas, consistent with land use weightage. Significant positive correlations with traditional FIB indicate that PMMoV is a suitable indicator of fecal contamination in tropical catchments waters (0.549 ≤ rho ≤ 0.612; P < 0.01). PMMoV exhibited a strong significant correlation with land use weightage (rho = 0.728; P < 0.01) compared to traditional FIB (rho = 0.583; P < 0.01). In addition, chemical tracers were also added to evaluate the potential relationships with microbial fecal indicators. The relationships between diverse variables (e.g., environmental parameters, land use coverage, and chemical tracers) and the occurrence of FIB and PMMoV were evaluated. By using stepwise multiple linear regression (MLR), the empirical experimental models substantiate the impact of land use patterns and anthropogenic activities on microbial water quality, and the output results of the empirical models may be able to predict the sources and transportation of human fecal pollution or sewage contamination. In addition, the high correlation between PMMoV data obtained from quantitative real-time PCR (qPCR) and viral metagenomics data supports the possibility of using viral metagenomics to relatively quantify specific microbial indicators for monitoring microbial water quality (0.588 ≤ rho ≤ 0.879; P < 0.05).IMPORTANCE The results of this study may support the hypothesis of using PMMoV as an alternative indicator of human fecal contamination in tropical surface waters from the perspective of land use patterns. The predictive result of the occurrence of human fecal indicators with high accuracy may reflect the source and transportation of human fecal pollution, which are directly related to the risk to human health, and thereafter, steps can be taken to mitigate these risks.
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Gu X, Tay QXM, Te SH, Saeidi N, Goh SG, Kushmaro A, Thompson JR, Gin KYH. Geospatial distribution of viromes in tropical freshwater ecosystems. WATER RESEARCH 2018; 137:220-232. [PMID: 29550725 PMCID: PMC7112100 DOI: 10.1016/j.watres.2018.03.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/02/2018] [Accepted: 03/07/2018] [Indexed: 05/05/2023]
Abstract
This study seeks to understand the general distribution of virome abundance and diversity in tropical freshwater ecosystems in Singapore and the geospatial distribution of the virome under different landuse patterns. Correlations between diversity, environmental parameters and land use patterns were analyzed and significant correlations were highlighted. Overall, the majority (65.5%) of the annotated virome belonged to bacteriophages. The percentage of Caudovirales was higher in reservoirs whereas the percentages of Dicistroviridae, Microviridae and Circoviridae were higher in tributaries. Reservoirs showed a higher Shannon-index virome diversity compared to upstream tributaries. Land use (urbanized, agriculture and parkland areas) influenced the characteristics of the virome distribution pattern. Dicistroviridae and Microviridae were enriched in urbanized tributaries while Mimiviridae, Phycodnaviridae, Siphoviridae and Podoviridae were enriched in parkland reservoirs. Several sequences closely related to the emerging zoonotic virus, cyclovirus, and the human-related virus (human picobirnavirus), were also detected. In addition, the relative abundance of PMMoV (pepper mild mottle virus) sequences was significantly correlated with RT-qPCR measurements (0.588 < r < 0.879, p < 0.05). This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems.
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Affiliation(s)
- Xiaoqiong Gu
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | | | - Shu Harn Te
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | - Nazanin Saeidi
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | - Shin Giek Goh
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | - Ariel Kushmaro
- School of Material Science and Engineering, Nanyang Technological University, 637819, Singapore
| | | | - Karina Yew-Hoong Gin
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore.
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The Geographic Structure of Viruses in the Cuatro Ciénegas Basin, a Unique Oasis in Northern Mexico, Reveals a Highly Diverse Population on a Small Geographic Scale. Appl Environ Microbiol 2018; 84:AEM.00465-18. [PMID: 29625974 DOI: 10.1128/aem.00465-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/21/2018] [Indexed: 12/28/2022] Open
Abstract
The Cuatro Ciénegas Basin (CCB) is located in the Chihuahuan desert in the Mexican state of Coahuila; it has been characterized as a site with high biological diversity despite its extreme oligotrophic conditions. It has the greatest number of endemic species in North America, containing abundant living microbialites (including stromatolites and microbial mats) and diverse microbial communities. With the hypothesis that this high biodiversity and the geographic structure should be reflected in the virome, the viral communities in 11 different locations of three drainage systems, Churince, La Becerra, and Pozas Rojas, and in the intestinal contents of 3 different fish species, were analyzed for both eukaryotic and prokaryotic RNA and DNA viruses using next-generation sequencing methods. Double-stranded DNA (dsDNA) virus families were the most abundant (72.5% of reads), followed by single-stranded DNA (ssDNA) viruses (2.9%) and ssRNA and dsRNA virus families (0.5%). Thirteen families had dsDNA genomes, five had ssDNA, three had dsRNA, and 16 had ssRNA. A highly diverse viral community was found, with an ample range of hosts and a strong geographical structure, with very even distributions and signals of endemicity in the phylogenetic trees from several different virus families. The majority of viruses found were bacteriophages but eukaryotic viruses were also frequent, and the large diversity of viruses related to algae were a surprise, since algae are not evident in the previously analyzed aquatic systems of this ecosystem. Animal viruses were also frequently found, showing the large diversity of aquatic animals in this oasis, where plants, protozoa, and archaea are rare.IMPORTANCE In this study, we tested whether the high biodiversity and geographic structure of CCB is reflected in its virome. CCB is an extraordinarily biodiverse oasis in the Chihuahuan desert, where a previous virome study suggested that viruses had followed the marine ancestry of the marine bacteria and, as a result of their long isolation, became endemic to the site. In this study, which includes a larger sequencing coverage and water samples from other sites within the valley, we confirmed the high virus biodiversity and uniqueness as well as the strong biogeographical diversification of the CCB. In addition, we also analyzed fish intestinal contents, finding that each fish species eats different prey and, as a result, presents different viral compositions even if they coexist in the same pond. These facts highlight the high and novel virus diversity of CCB and its "lost world" status.
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Abstract
Viruses represent the most abundant and diverse of the biological entities in environmental waters, including the seas and probably also freshwater systems. They are important players in ecological networks in waters and influence global biochemical cycling and community composition dynamics. Among the many diverse viruses from terrestrial environments found in environmental waters, some are plant, animal, and/or human pathogens. The majority of pathogenic viral species found in waters are very stable and can survive outside host cells for long periods. The occurrence of such viruses in environmental waters has raised concerns because of the confirmation of the infectivity of waterborne viruses even at very low concentrations. This chapter focuses mainly on the survival of human, animal, and plant pathogenic viruses in aqueous environments, the possibility of their water-mediated transmission, the ecological implications of viruses in water, the methods adapted for detecting such viruses, and how to minimize the risk of viruses spreading through water.
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Darling JA, Frederick RM. Nucleic acids-based tools for ballast water surveillance, monitoring, and research. JOURNAL OF SEA RESEARCH 2018; 133:43-52. [PMID: 30147432 PMCID: PMC6104837 DOI: 10.1016/j.seares.2017.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Understanding the risks of biological invasion posed by ballast water-whether in the context of compliance testing, routine monitoring, or basic research-is fundamentally an exercise in biodiversity assessment, and as such should take advantage of the best tools available for tackling that problem. The past several decades have seen growing application of genetic methods for the study of biodiversity, driven in large part by dramatic technological advances in nucleic acids analysis. Monitoring approaches based on such methods have the potential to increase dramatically sampling throughput for biodiversity assessments, and to improve on the sensitivity, specificity, and taxonomic accuracy of traditional approaches. The application of targeted detection tools (largely focused on PCR but increasingly incorporating novel probe-based methodologies) has led to a paradigm shift in rare species monitoring, and such tools have already been applied for early detection in the context of ballast water surveillance. Rapid improvements in community profiling approaches based on high throughput sequencing (HTS) could similarly impact broader efforts to catalogue biodiversity present in ballast tanks, and could provide novel opportunities to better understand the risks of biotic exchange posed by ballast water transport-and the effectiveness of attempts to mitigate those risks. These various approaches still face considerable challenges to effective implementation, depending on particular management or research needs. Compliance testing, for instance, remains dependent on accurate quantification of viable target organisms; while tools based on RNA detection show promise in this context, the demands of such testing require considerable additional investment in methods development. In general surveillance and research contexts, both targeted and community-based approaches are still limited by various factors: quantification remains a challenge (especially for taxa in larger size classes), gaps in nucleic acids reference databases are still considerable, uncertainties in taxonomic assignment methods persist, and many applications have not yet matured sufficiently to offer standardized methods capable of meeting rigorous quality assurance standards. Nevertheless, the potential value of these tools, their growing utilization in biodiversity monitoring, and the rapid methodological advances over the past decade all suggest that they should be seriously considered for inclusion in the ballast water surveillance toolkit.
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Affiliation(s)
- John A. Darling
- National Exposure Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Raymond M. Frederick
- National Risk Management Research Laboratory, U.S. Environmental Protection Agency, Edison, NJ, USA
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Ng C, Goh SG, Saeidi N, Gerhard WA, Gunsch CK, Gin KYH. Occurrence of Vibrio species, beta-lactam resistant Vibrio species, and indicator bacteria in ballast and port waters of a tropical harbor. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 610-611:651-656. [PMID: 28822933 DOI: 10.1016/j.scitotenv.2017.08.099] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/10/2017] [Accepted: 08/10/2017] [Indexed: 06/07/2023]
Abstract
Ballast water discharges are potential sources for the spread of invasive and pathogenic aquatic organisms. Ballast waters from six ships docked in the Port of Singapore were tested to determine if indictor organisms fell within proposed standards for ballast water discharge according to regulation D-2 of the Ballast Water Management Convention (BWMC) guidelines. Vibrio species were cultured on media supplemented with beta-lactam antibiotics to determine the presence of antibiotic resistant Vibrio species in the ballast waters of these vessels. Indicator organisms were quantified using culture media Colilert-18 and Enterolert in ballast waters of six ships docked in a tropical harbor, with uptake from different geographical locations. Of the six ships, one had ballast water originating from the Persian Gulf, another from the East China Sea, and four from the South China Sea. Two of the six ships which carried ballast waters from the East China Sea and the South China Sea did not meet the D-2 stipulated requirements of the Ballast Water Management Convention for indicator organisms with Enterococci values more than three times higher than the acceptable limit of <100CFU/100mL. Using the most-probable-number-PCR (MPN-PCR) method for Vibrio species detection, non-toxigenic species of V. cholerae (2 MPN/100mL), Vibrio vulnificus (>110 MPN/100mL), and Vibrio parahaemolyticus (2 to >110 MPN/100mL) were detected in at least one of six ballast water samples. Using thiosulfate-citrate-bile salts-sucrose agar (TCBS) supplemented with beta-lactam antibiotics (meropenem, ceftazidime), 11 different Vibrio species, exhibiting resistance to beta-lactam antibiotics were isolated; with Vibrio campbellii (44%) and Vibrio alginolyticus (15%) the most detected antibiotic resistant Vibrio species. A practical approach of prioritized screening of high-risk vessels should be conducted to ensure that the water quality meets D-2 standards prior to discharge.
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Affiliation(s)
- Charmaine Ng
- National University of Singapore, Department of Civil and Environmental Engineering, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | - Shin Giek Goh
- National University of Singapore, Department of Civil and Environmental Engineering, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | - Nazanin Saeidi
- National University of Singapore, Department of Civil and Environmental Engineering, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | - William A Gerhard
- Duke University, Department of Civil and Environmental Engineering, 100 Hudson Hall, Durham, NC 27708-0287, United States
| | - Claudia K Gunsch
- Duke University, Department of Civil and Environmental Engineering, 100 Hudson Hall, Durham, NC 27708-0287, United States
| | - Karina Yew Hoong Gin
- National University of Singapore, Department of Civil and Environmental Engineering, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore; NUS Environmental Research Institute (NERI), Engineering Drive 1, T-lab Building, #02-01, 117576, Singapore.
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Lv B, Cui Y, Tian W, Feng D. Composition and influencing factors of bacterial communities in ballast tank sediments: Implications for ballast water and sediment management. MARINE ENVIRONMENTAL RESEARCH 2017; 132:14-22. [PMID: 29046225 DOI: 10.1016/j.marenvres.2017.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 10/08/2017] [Accepted: 10/08/2017] [Indexed: 06/07/2023]
Abstract
This study aims to reveal the composition and influencing factors of bacterial communities in ballast tank sediments. Nine samples were collected and their 16S rRNA gene sequences were analyzed by high-throughput sequencing. The analysis results showed the Shannon index in ballast tank sediments was in the range of 5.27-6.35, which was significantly higher than that in ballast water. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi and Proteobacteria were the dominant phyla and accounted for approximately 80% of all 16S rRNA gene sequences of the samples. Besides, the high contents of sulfate reducing bacteria (SRB) and sulfur oxidizing bacteria were detected in sediments, indicating that the corrosion of metal caused by SRB might occur in ballast tank. In addition, the trace of human fecal bacteria and candidate pathogens were also detected in ballast tank sediments, and these undesirable microbes reduced the effect of ballast water exchange. Furthermore, C and N had significant effects on the bacterial community composition in ballast tank sediments. In conclusion, our findings suggest that the proper management and disposal of the ballast tank sediments should be considered in order to reduce the negative impact and ecological risks related to ballast water and sediments.
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Affiliation(s)
- Baoyi Lv
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China.
| | - Yuxue Cui
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai 200241, China
| | - Wen Tian
- Jiangyin Entry-Exit Inspection and Quarantine Bureau, Jiangyin 214442, China
| | - Daolun Feng
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
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40
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Orosco FL, Lluisma AO. Variation in virome diversity in wild populations of Penaeus monodon (Fabricius 1798) with emphasis on pathogenic viruses. Virusdisease 2017; 28:262-271. [PMID: 29291212 DOI: 10.1007/s13337-017-0389-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/20/2017] [Indexed: 11/28/2022] Open
Abstract
Marine animals typically harbor a community of viruses, a number of which are known to cause diseases. In shrimp aquaculture, viral pathogens are the principal causes of major economic losses. However, the composition of the viral load of shrimps in wild population is poorly known. In this study, we explored the viral diversity in the microbiome of wild Penaeus monodon collected from six sites in the Philippines, with a view to detecting pathogenic forms. We employed a metagenomic approach via particle-associated nucleic acid isolation, sequence-independent single primer amplification, and pyrosequencing. Virome analysis of shrimp samples from different sites revealed distinct virome profiles, and hence significant differences in diversity, among the various sites based on number of OTUs, Shannon-Weaver Index, and Inverse Simpson Index. Sequences of key shrimp pathogens were detected such as the white spot syndrome virus (WSSV), and Penaeus stylirostris densovirus (PstDV). However, the patterns of distribution of the pathogenic viruses varied; whereas WSSV was found only in three out of six sites and PstDV were found in all but one site. The results also revealed shrimp-associated viruses that have not yet been observed in P. monodon such as avian virus-like, insect virus-like, plankton virus-like and bacteriophage-like sequences. Despite the diverse array of viruses detected in the study, a large proportion remains unidentified (i.e., similarity to sequences in the database was lower than the threshold required for definitive identification), and therefore could represent unexplored virus sequences and viral genomes in the environment.
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Affiliation(s)
- Fredmoore L Orosco
- Marine Genomics and Molecular Genetics Laboratory, Marine Science Institute, University of the Philippines - Diliman, 1101 Quezon City, Philippines.,Institute of Biology, University of the Philippines - Diliman, 1101 Quezon City, Philippines
| | - Arturo O Lluisma
- Marine Genomics and Molecular Genetics Laboratory, Marine Science Institute, University of the Philippines - Diliman, 1101 Quezon City, Philippines
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41
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Nkili-Meyong AA, Bigarré L, Labouba I, Vallaeys T, Avarre JC, Berthet N. Contribution of Next-Generation Sequencing to Aquatic and Fish Virology. Intervirology 2017; 59:285-300. [PMID: 28668959 DOI: 10.1159/000477808] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 05/27/2017] [Indexed: 12/13/2022] Open
Abstract
The recent technological advances in nucleic acid sequencing, called next-generation sequencing (NGS), have revolutionized the field of genomics and have also influenced viral research. Aquatic viruses, and especially those infecting fish, have also greatly benefited from NGS technologies, which provide a huge amount of molecular information at a low cost in a relatively short period of time. Here, we review the use of the current high-throughput sequencing platforms with a special focus on the associated challenges (regarding sample preparation and bioinformatics) in their applications to the field of aquatic virology, especially for: (i) discovering novel viruses that may be associated with fish mortalities, (ii) elucidating the mechanisms of pathogenesis, and finally (iii) studying the molecular epidemiology of these pathogens.
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Affiliation(s)
- Andriniaina Andy Nkili-Meyong
- Département Zoonoses et Maladies Emergentes, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
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Kim Y, Van Bonn W, Aw TG, Rose JB. Aquarium Viromes: Viromes of Human-Managed Aquatic Systems. Front Microbiol 2017; 8:1231. [PMID: 28713358 PMCID: PMC5492393 DOI: 10.3389/fmicb.2017.01231] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/19/2017] [Indexed: 11/13/2022] Open
Abstract
An aquarium ecosystem is home to many animal species providing conditions similar to native aquatic habitats but under highly controlled management. With a growing interest in understanding the interaction of microbiomes and resident animal health within aquarium environments, we undertook a metagenomic survey of viromes in seven aquarium systems with differing physicochemical and resident animal profiles. Our results show that a diverse array of viruses was represented in aquarium viromes, many of which were widespread in different aquarium systems (27 common viral families in all of the aquarium systems). Most viromes were dominated by DNA phages of the order Caudovirales as commonly found in other aquatic environments with average relative abundance greater than 64%. The composition and structure of aquarium viromes were associated with controlled system parameters, including nitrate, salinity, and temperature as well as resident animal profiles, indicating the close interaction of viromes with aquarium management practices. Furthermore, finding human associated viruses in a touch exhibit suggested that exposure of aquarium systems to human contact may lead to introduction of human cutaneous viruses into aquaria. This is consistent with the high abundance of skin microflora on the palms of healthy individuals and their detection in recreational waters, such as swimming pools. Lastly, assessment of antibiotic resistance genes (ARGs) in aquarium viromes revealed a unique signature of ARGs in different aquarium systems with trimethoprim being the most common. This is the first study to provide vital information on viromes and their unique relationships with management practices in a human-built and controlled aquarium environment.
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Affiliation(s)
- Yiseul Kim
- Department of Fisheries and Wildlife, Michigan State University, East LansingMI, United States.,National Institute of Agricultural Sciences, Rural Development AdministrationWanju, South Korea
| | - William Van Bonn
- Department of Fisheries and Wildlife, Michigan State University, East LansingMI, United States.,A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, ChicagoIL, United States
| | - Tiong G Aw
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New OrleansLA, United States
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, East LansingMI, United States
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Pagenkopp Lohan KM, Fleischer RC, Carney KJ, Holzer KK, Ruiz GM. Molecular characterisation of protistan species and communities in ships’ ballast water across three U.S. coasts. DIVERS DISTRIB 2017. [DOI: 10.1111/ddi.12550] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Katrina M. Pagenkopp Lohan
- Marine Invasions Laboratory Smithsonian Environmental Research Center Edgewater MD USA
- Center for Conservation Genomics Smithsonian Conservation Biology Institute National Zoological Park Washington DC USA
| | - Robert C. Fleischer
- Center for Conservation Genomics Smithsonian Conservation Biology Institute National Zoological Park Washington DC USA
| | - Katharine J. Carney
- Marine Invasions Laboratory Smithsonian Environmental Research Center Edgewater MD USA
| | - Kimberly K. Holzer
- Marine Invasions Laboratory Smithsonian Environmental Research Center Edgewater MD USA
| | - Gregory M. Ruiz
- Marine Invasions Laboratory Smithsonian Environmental Research Center Edgewater MD USA
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44
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Widespread and enduring demographic collapse of invasive common carp (Cyprinus carpio) in the Upper Mississippi River System. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1405-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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45
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O'Brien E, Munir M, Marsh T, Heran M, Lesage G, Tarabara VV, Xagoraraki I. Diversity of DNA viruses in effluents of membrane bioreactors in Traverse City, MI (USA) and La Grande Motte (France). WATER RESEARCH 2017; 111:338-345. [PMID: 28107747 DOI: 10.1016/j.watres.2017.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 01/03/2017] [Accepted: 01/06/2017] [Indexed: 05/03/2023]
Abstract
This study assesses diversity of DNA viruses in the effluents of two membrane bioreactor (MBR) wastewater treatment plants (WWTPs): an MBR in the United States and an MBR in France. Viral diversity of these effluents is compared to that of a conventional activated sludge WWTP in the U.S. Diversity analysis indicates Herpesvirales to be the most abundant order of potentially pathogenic human DNA viruses in wastewater treated effluent in all utilities. Other potentially pathogenic human viruses detected include Adenoviridae, Parvoviridae, and Polyomaviridae. Bacteriophage order Caudovirales comprises the majority of DNA virus sequences in the effluent of all utilities. The choice of treatment process (MBR versus activated sludge reactor) utilized had no impact on effluent DNA viral diversity. In contrast, the type of disinfection applied had an impact on the viral diversity present in the effluent.
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Affiliation(s)
- Evan O'Brien
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA
| | - Mariya Munir
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA
| | - Terence Marsh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48823, USA
| | - Marc Heran
- Institut Européen des Membranes, IEM, UMR-5635, Université de Montpellier, ENSCM, CNRS, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - Geoffroy Lesage
- Institut Européen des Membranes, IEM, UMR-5635, Université de Montpellier, ENSCM, CNRS, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - Volodymyr V Tarabara
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA.
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46
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van Aerle R, Santos EM. Advances in the application of high-throughput sequencing in invertebrate virology. J Invertebr Pathol 2017; 147:145-156. [PMID: 28249815 DOI: 10.1016/j.jip.2017.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 10/20/2022]
Abstract
Over the last decade, advances in high-throughput sequencing technologies have revolutionised biological research, making it possible for DNA/RNA sequencing of any organism of interest to be undertaken. Sequencing approaches are now routinely used in the detection and characterisation of (novel) viruses, investigation of host-pathogen interactions, and effective development of disease treatment strategies. For the sequencing and identification of viruses of interest, metagenomics approaches using infected host tissue are frequently used, as it is not always possible to culture and isolate these pathogens. High-throughput sequencing can also be used to investigate host-pathogen interactions by investigating (temporal) transcriptomic responses of both the host and virus, potentially leading to the discovery of novel opportunities for treatment and drug targets. In addition, viruses in environmental samples (e.g. water or soil samples) can be identified using eDNA/metagenomics approaches. The promise that recent developments in sequencing brings to the field of invertebrate virology are not devoid of technical challenges, including the need for better laboratory and bioinformatics strategies to sequence and assemble virus genomes within complex tissue or environmental samples, and the difficulties associated with the annotation of the large number of novel viruses being discovered.
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Affiliation(s)
- R van Aerle
- Centre for Environment, Fisheries, and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, UK.
| | - E M Santos
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
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47
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Lymperopoulou DS, Dobbs FC. Bacterial Diversity in Ships' Ballast Water, Ballast-Water Exchange, and Implications for Ship-Mediated Dispersal of Microorganisms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:1962-1972. [PMID: 28135081 DOI: 10.1021/acs.est.6b03108] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Using next-generation DNA sequencing of the 16S rRNA gene, we analyzed the composition and diversity of bacterial assemblages in ballast water from tanks of 17 commercial ships arriving to Hampton Roads, Virginia (USA) following voyages in the North Atlantic Ocean. Amplicon sequencing analysis showed the heterogeneous assemblages were (1) dominated by Alpha- and Gammaproteobacteria, Bacteroidetes, and unclassified Bacteria; (2) temporally distinct (June vs August/September); and (3) highly fidelitous among replicate samples. Whether tanks were exchanged at sea or not, their bacterial assemblages differed from those of local, coastal water. Compositional data suggested at-sea exchange did not fully flush coastal Bacteria from all tanks; there were several instances of a genetic geographic signal. Quantitative PCR yielded no Escherichia coli and few instances of Vibrio species. Salinity, but not ballast-water age or temperature, contributed significantly to bacterial diversity. Whether anthropogenic mixing of marine Bacteria restructures their biogeography remains to be tested.
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Affiliation(s)
- Despoina S Lymperopoulou
- Department of Plant and Microbial Biology, University of California-Berkeley , 331 Koshland Hall, Berkeley, California 94720, United States
| | - Fred C Dobbs
- Department of Ocean, Earth and Atmospheric Sciences, Old Dominion University , 4600 Elkhorn Avenue, Norfolk, Virginia 23529, United States
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48
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Darling JA, Galil BS, Carvalho GR, Rius M, Viard F, Piraino S. Recommendations for developing and applying genetic tools to assess and manage biological invasions in marine ecosystems. MARINE POLICY 2017; 85:56-64. [PMID: 29681680 PMCID: PMC5909192 DOI: 10.1016/j.marpol.2017.08.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The European Union's Marine Strategy Framework Directive (MSFD) aims to adopt integrated ecosystem management approaches to achieve or maintain "Good Environmental Status" for marine waters, habitats and resources, including mitigation of the negative effects of non-indigenous species (NIS). The Directive further seeks to promote broadly standardized monitoring efforts and assessment of temporal trends in marine ecosystem condition, incorporating metrics describing the distribution and impacts of NIS. Accomplishing these goals will require application of advanced tools for NIS surveillance and risk assessment, particularly given known challenges associated with surveying and monitoring with traditional methods. In the past decade, a host of methods based on nucleic acids (DNA and RNA) analysis have been developed or advanced that promise to dramatically enhance capacity in assessing and managing NIS. However, ensuring that these rapidly evolving approaches remain accessible and responsive to the needs of resource managers remains a challenge. This paper provides recommendations for future development of these genetic tools for assessment and management of NIS in marine systems, within the context of the explicit requirements of the MSFD. Issues considered include technological innovation, methodological standardization, data sharing and collaboration, and the critical importance of shared foundational resources, particularly integrated taxonomic expertise. Though the recommendations offered here are not exhaustive, they provide a basis for future intentional (and international) collaborative development of a genetic toolkit for NIS research, capable of fulfilling the immediate and long term goals of marine ecosystem and resource conservation.
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Affiliation(s)
- John A. Darling
- National Exposure Research Laboratory, United States Environmental
Protection Agency, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711,
USA
- Corresponding author.
(J.A. Darling)
| | - Bella S. Galil
- The Steinhardt Museum of Natural History, Israel National Center for
Biodiversity Studies, Tel Aviv University, Tel Aviv 6997801, Israel
| | | | - Marc Rius
- Ocean and Earth Science, National Oceanography Centre, University of
Southampton, UK
- Centre for Ecological Genomics and Wildlife Conservation, University
of Johannesburg, South Africa
| | - Frédérique Viard
- Sorbonne Université, Université Paris 06, CNRS, UMR
7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff,
France
| | - Stefano Piraino
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali,
Università del Salento, Lecce, Italy
- Consorzio Nazionale Interuniversitario per le Scienze del Mare
(CoNISMa), Roma, Italy
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49
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Munang'andu HM. Environmental Viral Metagenomics Analyses in Aquaculture: Applications in Epidemiology and Disease Control. Front Microbiol 2016; 7:1986. [PMID: 28018317 PMCID: PMC5155513 DOI: 10.3389/fmicb.2016.01986] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/28/2016] [Indexed: 11/17/2022] Open
Abstract
Studies on the epidemiology of viral diseases in aquaculture have for a long time depended on isolation of viruses from infected aquatic organisms. The role of aquatic environments in the epidemiology of viral diseases in aquaculture has not been extensively expounded mainly because of the lack of appropriate tools for environmental studies on aquatic viruses. However, the upcoming of metagenomics analyses opens great avenues in which environmental samples can be used to study the epidemiology of viral diseases outside their host species. Hence, in this review I have shown that epidemiological factors that influence the composition of viruses in different aquatic environments include ecological factors, anthropogenic activities and stocking densities of cultured organisms based on environmental metagenomics studies carried out this far. Ballast water transportation and global trade of aquatic organisms are the most common virus dispersal process identified this far. In terms of disease control for outdoor aquaculture systems, baseline data on viruses found in different environments intended for aquaculture use can be obtained to enable the design of effective disease control strategies. And as such, high-risk areas having a high specter of pathogenic viruses can be identified as an early warning system. As for the control of viral diseases for indoor recirculation aquaculture systems (RAS), the most effective disinfection methods able to eliminate pathogenic viruses from water used in RAS can be identified. Overall, the synopsis I have put forth in this review shows that environmental samples can be used to study the epidemiology of viral diseases in aquaculture using viral metagenomics analysis as an overture for the design of rational disease control strategies.
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Affiliation(s)
- Hetron M Munang'andu
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences Oslo, Norway
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50
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Liu L, Chu X, Chen P, Xiao Y, Hu J. Effects of water quality on inactivation and repair of Microcystis viridis and Tetraselmis suecica following medium-pressure UV irradiation. CHEMOSPHERE 2016; 163:209-216. [PMID: 27529385 DOI: 10.1016/j.chemosphere.2016.08.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/14/2016] [Accepted: 08/04/2016] [Indexed: 06/06/2023]
Abstract
The transfer of invasive organisms by ballast-water discharge has become a growing concern. UV treatment has become an attractive ballast water treatment technology due to its effectiveness, no harmful disinfection byproducts and easiness to handle. Two robust algae strains Microcystis viridis and Tetraselmis suecica were selected as indicator organisms to determine efficiency of medium-pressure (MP) UV-treatment on ballast water. Inactivation and potential repair of these two algae strains following MP UV irradiation were assessed under various turbidity, total organic carbon (TOC) and salinity conditions. The investigated range of UV doses was from 25 to 500 mJ/cm(2). For M. viridis, results indicated that disinfection efficiency was negatively correlated with all of these three factors at low doses (25-200 mJ/cm(2)). Photoreactivation and dark repair were promoted at high TOC levels (6-15 mg/L) with about 6-25% higher repair levels compared with those in distilled water, whereas no significant impacts were identified for turbidity and salinity on both of the photoreactivation and dark repair. For T. suecica, increased turbidity and TOC levels both hindered the performance of UV irradiation at high doses (200-500 mJ/cm(2)). Suppressive effects on photoreactivation and dark repair were consistently observed with changes of all of the three factors. In conclusion, generally these three factors resulted in repressive effects on UV disinfection efficiency, and TOC played a more significant role in the levels of reactivation than the other two. The responses of T. suecica to these three factors were more sensitive than M. viridis.
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Affiliation(s)
- Lei Liu
- Department of Civil & Environmental Engineering, National University of Singapore, Singapore 117576, Singapore; School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Xiaona Chu
- Department of Civil & Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Pengyu Chen
- Department of Civil & Environmental Engineering, National University of Singapore, Singapore 117576, Singapore; School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yan Xiao
- Department of Civil & Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Jiangyong Hu
- Department of Civil & Environmental Engineering, National University of Singapore, Singapore 117576, Singapore.
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