1
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Hurst BN, Korajkic A, Pemberton A, McMinn BR. Improved virus concentration methods for wash waters from decontamination of permeable and non-permeable surfaces. J Virol Methods 2023; 322:114826. [PMID: 37778537 PMCID: PMC10841435 DOI: 10.1016/j.jviromet.2023.114826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
Surface decontamination is a method of using wash water to decontaminated surfaces preventing transmission of biological contaminants that can pose potential health risks to responders and the public. However, the risks associated with handling used wash water are largely unknown due to the lack of effective methodology to screen for pathogenic microorganisms present in these samples, especially viral pathogens. This study adapted the dead-end hollow-fiber ultrafiltration (D-HFUF) system to wash waters, including a separate procedure for recovering particle attached viruses. Simulated wash water was created using dechlorinated tap water containing a mild surfactant (0.05 % Tween 80). To determine virus recovery efficiencies, measured amounts of somatic and F+ coliphage were spiked into 2-liter volumes of wash water under the following scenarios: (1) wash water was amended with a measured amount of sterile river sediment with no sediment separation prior to filter concentration; or (2) sediment added to wash water was allowed to settle prior to filter concentrating clarified liquid portions, while precipitated sediment was subjected to viral extraction techniques to recover particle attached virus; and (3) the optimized method was deployed on non-porous and porous surfaces to simulate a decontamination clean-up event. Separation of sediment prior to D-HFUF significantly increased recovery of coliphages, (P = <0.0001) versus filtration of sediment and liquids simultaneously. A tryptic soy broth (TSB) elution solution was significantly more effective (P = ≤0.010) for recovery of both somatic and F+ coliphage, (108 ± 9 % and 92 ± 9 %, respectively), compared to elution buffers containing various surfactants (sodium hexametaphosphate, Tween 80) for recovering particle attached virus. Simulating a biocontaminate clean-up event (using the optimized sediment separation and elution protocol) resulted in coliphage recoveries of 75-96 % (permeable surface) and 71-92 % (non-permeable surface). This procedure can be used to effectively detect viruses in used wash waters aiding in reducing risks to human health during site decontamination.
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Affiliation(s)
- Brittany N Hurst
- Department of Environmental Health, University of Cincinnati College of Medicine, 3230 Eden Ave, Cincinnati, OH 45267, USA
| | - Asja Korajkic
- Office of Research and Development, United States Environmental Protection Laboratory, 26 West Martin Luther King Drive, Cincinnati, OH 45268 USA
| | - Adin Pemberton
- Office of Research and Development, United States Environmental Protection Laboratory, 26 West Martin Luther King Drive, Cincinnati, OH 45268 USA
| | - Brian R McMinn
- Office of Research and Development, United States Environmental Protection Laboratory, 26 West Martin Luther King Drive, Cincinnati, OH 45268 USA.
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2
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Harilanto AF, Christelle D, Philippe C, Bettarel Y. Viral life strategies in a heavily anthropized tropical lagoon. FEMS Microbiol Lett 2022; 369:6698716. [DOI: 10.1093/femsle/fnac091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Ecological traits of aquatic microorganisms have been poorly investigated in tropical latitudes, especially in lagoons, which are often subjected to strong anthropogenic influence, conducive to microbial development. In this study, we examined the abundance of both viral and bacterial communities, as well as their interactions (lytic and lysogenic infections) in the water and sediment of seven main stations of the Ebrié Lagoon (Ivory Coast) with contrasting levels of eutrophication. The highest bacterial and viral concentrations in both planktonic and benthic samples were found in the most eutrophicated stations, where viral lytic infections also exhibited their highest values. Conversely, the highest fractions of inducible lysogens were measured in the most oligotrophic stations, suggesting that these two main viral life strategies are mutually exclusive in this lagoon. Our findings also revealed the importance that nutrients (especially ammonium) play as drivers of the interactions between viruses and their bacterial hosts in tropical lagoons.
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Affiliation(s)
- Andrianjakarivony Felana Harilanto
- Microbes, Evolution, Phylogeny, and Infection (MEФI) , IHU - Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005, Marseille , France
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO) , 163 avenue de Luminy 13009, Marseille , France
| | - Desnues Christelle
- Microbes, Evolution, Phylogeny, and Infection (MEФI) , IHU - Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005, Marseille , France
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO) , 163 avenue de Luminy 13009, Marseille , France
| | - Cecchi Philippe
- MARBEC, Marine Biodiversity, Exploitation & Conservation, Univ. Montpellier , CNRS, Ifremer, IRD, 093 Place Eugène Bataillon 34090, Montpellier , France
| | - Yvan Bettarel
- MARBEC, Marine Biodiversity, Exploitation & Conservation, Univ. Montpellier , CNRS, Ifremer, IRD, 093 Place Eugène Bataillon 34090, Montpellier , France
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3
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Chu Y, Zhao Z, Cai L, Zhang G. Viral diversity and biogeochemical potential revealed in different prawn-culture sediments by virus-enriched metagenome analysis. ENVIRONMENTAL RESEARCH 2022; 210:112901. [PMID: 35227678 DOI: 10.1016/j.envres.2022.112901] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
As the most numerous biological entities on Earth, viruses affect the microbial dynamics, metabolism and biogeochemical cycles in the aquatic ecosystems. Viral diversity and functions in ocean have been relatively well studied, but our understanding of viruses in mariculture systems is limited. To fill this knowledge gap, we studied viral diversity and potential biogeochemical impacts of sediments from four different prawn-mariculture ecosystems (mono-culture of prawn and poly-culture of prawn with jellyfish, sea cucumber, and clam) using a metagenomic approach with prior virus-like particles (VLPs) separation. We found that the order Caudovirales was the predominant viral category and accounted for the most volume (78.39% of classified viruses). Sediment viruses were verified to have a high diversity by using the construct phylogenetic tree of terL gene, with three potential novel clades being identified. Meanwhile, compared with viruses inhabiting other ecosystems based on gene-sharing network, our results revealed that mariculture sediments harbored considerable unexplored viral diversity and that maricultural species were potentially important drivers of the viral community structure. Notably, viral auxiliary metabolic genes were identified and suggested that viruses influence carbon and sulfur cycling, as well as cofactors/vitamins and amino acid metabolism, which indirectly participate in biogeochemical cycling. Overall, our findings revealed the genomic diversity and ecological function of viral communities in prawn mariculture sediments, and suggested the role of viruses in microbial ecology and biogeochemistry.
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Affiliation(s)
- Yunmeng Chu
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, 361021, Fujian, China
| | - Zelong Zhao
- Shanghai BIOZERON Biotechnology Co., Ltd., Shanghai, 201800, China
| | - Lixi Cai
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, 361021, Fujian, China; Faculty of Basic Medicine, Putian University, Putian, 351100, Fujian, China
| | - Guangya Zhang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, 361021, Fujian, China.
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4
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Runa V, Wenk J, Bengtsson S, Jones BV, Lanham AB. Bacteriophages in Biological Wastewater Treatment Systems: Occurrence, Characterization, and Function. Front Microbiol 2021; 12:730071. [PMID: 34803947 PMCID: PMC8600467 DOI: 10.3389/fmicb.2021.730071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/25/2021] [Indexed: 12/20/2022] Open
Abstract
Phage bacteria interactions can affect structure, dynamics, and function of microbial communities. In the context of biological wastewater treatment (BWT), the presence of phages can alter the efficiency of the treatment process and influence the quality of the treated effluent. The active role of phages in BWT has been demonstrated, but many questions remain unanswered regarding the diversity of phages in these engineered environments, the dynamics of infection, the determination of bacterial hosts, and the impact of their activity in full-scale processes. A deeper understanding of the phage ecology in BWT can lead the improvement of process monitoring and control, promote higher influent quality, and potentiate the use of phages as biocontrol agents. In this review, we highlight suitable methods for studying phages in wastewater adapted from other research fields, provide a critical overview on the current state of knowledge on the effect of phages on structure and function of BWT bacterial communities, and highlight gaps, opportunities, and priority questions to be addressed in future research.
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Affiliation(s)
- Viviane Runa
- Centre for Sustainable and Circular Technologies, University of Bath, Bath, United Kingdom.,Department of Chemical Engineering, University of Bath, Bath, United Kingdom
| | - Jannis Wenk
- Department of Chemical Engineering, University of Bath, Bath, United Kingdom.,Water Innovation and Research Centre, University of Bath, Bath, United Kingdom
| | | | - Brian V Jones
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Ana B Lanham
- Centre for Sustainable and Circular Technologies, University of Bath, Bath, United Kingdom.,Department of Chemical Engineering, University of Bath, Bath, United Kingdom.,Water Innovation and Research Centre, University of Bath, Bath, United Kingdom
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5
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Orellana R, Arancibia A, Badilla L, Acosta J, Arancibia G, Escar R, Ferrada G, Seeger M. Ecophysiological Features Shape the Distribution of Prophages and CRISPR in Sulfate Reducing Prokaryotes. Microorganisms 2021; 9:microorganisms9050931. [PMID: 33925267 PMCID: PMC8146710 DOI: 10.3390/microorganisms9050931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/18/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022] Open
Abstract
Sulfate reducing prokaryotes (SRP) are a phylogenetically and physiologically diverse group of microorganisms that use sulfate as an electron acceptor. SRP have long been recognized as key players of the carbon and sulfur cycles, and more recently, they have been identified to play a relevant role as part of syntrophic and symbiotic relations and the human microbiome. Despite their environmental relevance, there is a poor understanding about the prevalence of prophages and CRISPR arrays and how their distribution and dynamic affect the ecological role of SRP. We addressed this question by analyzing the results of a comprehensive survey of prophages and CRISPR in a total of 91 genomes of SRP with several genotypic, phenotypic, and physiological traits, including genome size, cell volume, minimum doubling time, cell wall, and habitat, among others. Our analysis discovered 81 prophages in 51 strains, representing the 56% of the total evaluated strains. Prophages are non-uniformly distributed across the SRP phylogeny, where prophage-rich lineages belonged to Desulfovibrionaceae and Peptococcaceae. Furthermore, our study found 160 CRISPR arrays in 71 SRP, which is more abundant and widely spread than previously expected. Although there is no correlation between presence and abundance of prophages and CRISPR arrays at the strain level, our analysis showed that there is a directly proportional relation between cellular volumes and number of prophages per cell. This result suggests that there is an additional selective pressure for strains with smaller cells to get rid of foreign DNA, such as prophages, but not CRISPR, due to less availability of cellular resources. Analysis of the prophage genes encoding viral structural proteins reported that 44% of SRP prophages are classified as Myoviridae, and comparative analysis showed high level of homology, but not synteny, among prophages belonging to the Family Desulfovibrionaceae. We further recovered viral-like particles and structures that resemble outer membrane vesicles from D. vulgaris str. Hildenborough. The results of this study improved the current understanding of dynamic interactions between prophages and CRISPR with their hosts in both cultured and hitherto-uncultured SRP strains, and how their distribution affects the microbial community dynamics in several sulfidogenic natural and engineered environments.
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Affiliation(s)
- Roberto Orellana
- Laboratorio de Biología Celular y Ecofisiología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Leopoldo Carvallo 270, Valparaíso 2360001, Chile; (A.A.); (L.B.)
- Correspondence:
| | - Alejandra Arancibia
- Laboratorio de Biología Celular y Ecofisiología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Leopoldo Carvallo 270, Valparaíso 2360001, Chile; (A.A.); (L.B.)
| | - Leonardo Badilla
- Laboratorio de Biología Celular y Ecofisiología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Leopoldo Carvallo 270, Valparaíso 2360001, Chile; (A.A.); (L.B.)
| | - Jonathan Acosta
- Departamento de Estadística, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna 4860, Santiago 7820436, Chile;
| | - Gabriela Arancibia
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| | - Rodrigo Escar
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| | - Gustavo Ferrada
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
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6
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Sadeghi M, Tomaru Y, Ahola T. RNA Viruses in Aquatic Unicellular Eukaryotes. Viruses 2021; 13:v13030362. [PMID: 33668994 PMCID: PMC7996518 DOI: 10.3390/v13030362] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/05/2021] [Accepted: 02/22/2021] [Indexed: 12/24/2022] Open
Abstract
Increasing sequence information indicates that RNA viruses constitute a major fraction of marine virus assemblages. However, only 12 RNA virus species have been described, infecting known host species of marine single-celled eukaryotes. Eight of these use diatoms as hosts, while four are resident in dinoflagellate, raphidophyte, thraustochytrid, or prasinophyte species. Most of these belong to the order Picornavirales, while two are divergent and fall into the families Alvernaviridae and Reoviridae. However, a very recent study has suggested that there is extraordinary diversity in aquatic RNA viromes, describing thousands of viruses, many of which likely use protist hosts. Thus, RNA viruses are expected to play a major ecological role for marine unicellular eukaryotic hosts. In this review, we describe in detail what has to date been discovered concerning viruses with RNA genomes that infect aquatic unicellular eukaryotes.
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Affiliation(s)
- Mohammadreza Sadeghi
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland
- Correspondence: (M.S.); (T.A.)
| | - Yuji Tomaru
- Environment and Fisheries Applied Techniques Research Department, Fisheries Technology Institute, Fisheries Research and Education Agency, Hatsukaichi, Hiroshima 739-0452, Japan;
| | - Tero Ahola
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland
- Correspondence: (M.S.); (T.A.)
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7
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Host cell volume explains differences in the size of DsDNA viruses. Virus Res 2021; 295:198321. [PMID: 33515605 DOI: 10.1016/j.virusres.2021.198321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/19/2020] [Accepted: 01/23/2021] [Indexed: 11/23/2022]
Abstract
The nearly 3 orders of magnitude variation in size observed among double-stranded DNA viruses (dsDNA) has important ecological consequences, but the factors responsible for this variation remain poorly understood. Here we first evaluate if a relationship exists between the genome size of diverse dsDNA viruses and their hosts in single-celled organisms (prokaryotes and eukaryotes). We find that dsDNA genome size increases systematically, though less than proportionally, with host genome size. We next evaluate possible relationships between virus size, host size and burst size in an analysis that includes both single-celled and multicellular hosts where genome size and cell volume are not as highly correlated. Here we find that virus volume increases sublinearly with host cell volume (but not genome size) across species, and that virus burst volume (burst size * virus volume) increases with host cell volume. These findings suggest that the size and number of dsDNA viruses produced by a particular host may be constrained by the volume of the infected host cell. This may be useful for better understanding virus-host population dynamics, and ultimately, a better understanding of which viruses may infect which hosts (i.e., host specificity) and the likelihood of cross-species transmission events (i.e., host jumping).
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8
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Courtier‐Orgogozo V, Danchin A, Gouyon P, Boëte C. Evaluating the probability of CRISPR-based gene drive contaminating another species. Evol Appl 2020; 13:1888-1905. [PMID: 32908593 PMCID: PMC7463340 DOI: 10.1111/eva.12939] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/03/2020] [Accepted: 02/07/2020] [Indexed: 12/27/2022] Open
Abstract
The probability D that a given clustered regularly interspaced short palindromic repeats (CRISPR)-based gene drive element contaminates another, nontarget species can be estimated by the following Drive Risk Assessment Quantitative Estimate (DRAQUE) Equation: D = h y b + t r a n s f × e x p r e s s × c u t × f l a n k × i m m u n e × n o n e x t i n c t with hyb = probability of hybridization between the target species and a nontarget species; transf = probability of horizontal transfer of a piece of DNA containing the gene drive cassette from the target species to a nontarget species (with no hybridization); express = probability that the Cas9 and guide RNA genes are expressed; cut = probability that the CRISPR-guide RNA recognizes and cuts at a DNA site in the new host; flank = probability that the gene drive cassette inserts at the cut site; immune = probability that the immune system does not reject Cas9-expressing cells; nonextinct = probability of invasion of the drive within the population. We discuss and estimate each of the seven parameters of the equation, with particular emphasis on possible transfers within insects, and between rodents and humans. We conclude from current data that the probability of a gene drive cassette to contaminate another species is not insignificant. We propose strategies to reduce this risk and call for more work on estimating all the parameters of the formula.
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Affiliation(s)
| | - Antoine Danchin
- Institut Cochin INSERM U1016 – CNRS UMR8104 – Université Paris DescartesParisFrance
| | - Pierre‐Henri Gouyon
- Institut de Systématique, Évolution, BiodiversitéMuséum National d'Histoire NaturelleCNRSSorbonne UniversitéEPHEUAParisFrance
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9
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Roy K, Ghosh D, DeBruyn JM, Dasgupta T, Wommack KE, Liang X, Wagner RE, Radosevich M. Temporal Dynamics of Soil Virus and Bacterial Populations in Agricultural and Early Plant Successional Soils. Front Microbiol 2020; 11:1494. [PMID: 32733413 PMCID: PMC7358527 DOI: 10.3389/fmicb.2020.01494] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022] Open
Abstract
As reported in many aquatic environments, recent studies in terrestrial ecosystems implicate a role for viruses in shaping the structure, function, and evolution of prokaryotic soil communities. However, given the heterogeneity of soil and the physical constraints (i.e., pore-scale hydrology and solid-phase adsorption of phage and host cells) on the mobility of viruses and bacteria, phage-host interactions likely differ from those in aquatic systems. In this study, temporal changes in the population dynamics of viruses and bacteria in soils under different land management practices were examined. The results showed that bacterial abundance was significantly and positively correlated to both virus and inducible prophage abundance. Bacterial and viral abundance were also correlated with soil organic carbon and nitrogen content as well as with C:N ratio. The seasonal variability in viral abundance increased with soil organic carbon content. The prokaryotic community structure was influenced more by land use than by seasonal variation though considerable variation was evident in the early plant successional and grassland sites. The free extracellular viral communities were also separated by land use, and the forest soil viral assemblage exhibiting the most seasonal variability was more distinct from the other sites. Viral assemblages from the agricultural soils exhibited the least seasonal variability. Similar patterns were observed for inducible prophage viral assemblages. Seasonal variability of viral assemblages was greater in mitomycin-C (mitC) induced prophages than in extracellular viruses irrespective of land use and management. Taken together, the data suggest that soil viral production and decay are likely balanced but there was clear evidence that the structure of viral assemblages is influenced by land use and by season.
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Affiliation(s)
- Krishnakali Roy
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Dhritiman Ghosh
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - K Eric Wommack
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, United States
| | - Xiaolong Liang
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Regan E Wagner
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
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10
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Wei M, Xu K. New Insights Into the Virus-to-Prokaryote Ratio (VPR) in Marine Sediments. Front Microbiol 2020; 11:1102. [PMID: 32547525 PMCID: PMC7272709 DOI: 10.3389/fmicb.2020.01102] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 05/04/2020] [Indexed: 11/13/2022] Open
Abstract
The virus-to-prokaryote ratio (VPR), which reflects the numerical dominance of viruses over their hosts, has been proposed as a proxy for assessing the relationship between viruses and prokaryotes. Previous studies showed that VPR values fluctuate over six orders of magnitude within and across various benthic ecosystems, with an average value of approximately 10. We hypothesize that this high VPR value is largely due to the inaccurate enumeration of viruses and prokaryotes (e.g., centrifugation treatments may lead to a three-fourfold overestimation of VPR). In this study, we evaluated the impact of processing methods on the determination of VPR values. Using an optimized procedure, we investigated the marine benthic VPR at 31 sites, from intertidal zones through continental shelves to abyssal plains, and assessed its monthly variation in two contrasting intertidal habitats (muddy-sand and sandy). By compiling 135 VPR data points of surface sediments from 37 publications, we reveal the effect of centrifugation on published VPR values and describe the spatial distribution of VPR values on a larger scale based on reliable data. The results showed that the commonly used centrifugation method may result in an overestimation of VPR values that are approximately one order of magnitude higher than those obtained using the dilution method, while other processing steps had a limited impact on the VPR. Our analysis indicates that the benthic VPR value is low and less varied across temporal and spatial scales, fluctuating mostly within 10, and the average VPR is approximately 2 in both marine and freshwater habitats. An insignificant seasonal pattern in the VPR was observed in the intertidal zone, with lower VPR values occurring at high temperatures. The VPR spatial distribution was primarily associated with sediment phaeophytin a, suggesting that the trophic conditions of the upper water column and the sedimentation of organic matter to the bottom are the key factors affecting VPR values. The mean VPR in benthic habitats is approximately one order of magnitude lower and much less varied than that observed in pelagic habitats, indicating that the virus-host relationship and the ecological function of viruses in the two ecosystems may be very different.
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Affiliation(s)
- Miao Wei
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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11
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Colombet J, Robin A, Sime-Ngando T. Genotypic, size and morphological diversity of virioplankton in a deep oligomesotrophic freshwater lake (Lac Pavin, France). J Environ Sci (China) 2017; 53:48-59. [PMID: 28372760 DOI: 10.1016/j.jes.2016.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 05/02/2016] [Accepted: 05/05/2016] [Indexed: 06/07/2023]
Abstract
We examined changes in morphological and genomic diversities of viruses by means of transmission electronic microscopy and pulsed field gel electrophoresis (PFGE) over a nine-month period (April-December 2005) at four different depths in the oligomesotrophic Lac Pavin. We found that the majority of viruses in this lake belonged to the family of Siphoviridae or were untailed, with capsid sizes ranging from 30 to 60nm, and exhibited genome sizes ranging from 15 to 45kb. On average, 12 different genotypes dominated each of the PFGE fingerprints. The highest genomic viral richness was recorded in summer (mean=14 bands per PFGE fingerprint) and in the epilimnion (mean=13 bands per PFGE fingerprint). Among the physico-chemical and biological variables considered, the availability of the hosts appeared to be the main factor regulating the variations in the viral diversity.
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Affiliation(s)
- Jonathan Colombet
- Laboratory Microorganisms: Genome and Environment, Clermont University Blaise Pascal, UMR CNRS 6023, 24 avenue des Landais, BP 80026, F-63171 Aubière, France.
| | - Agnès Robin
- CIRAD, UMR Eco&Sols, 2 place Viala, 34060 Montpellier Cedex 1, France
| | - Télesphore Sime-Ngando
- Laboratory Microorganisms: Genome and Environment, Clermont University Blaise Pascal, UMR CNRS 6023, 24 avenue des Landais, BP 80026, F-63171 Aubière, France
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12
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Hassard F, Gwyther CL, Farkas K, Andrews A, Jones V, Cox B, Brett H, Jones DL, McDonald JE, Malham SK. Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments-a Review. Front Microbiol 2016; 7:1692. [PMID: 27847499 PMCID: PMC5088438 DOI: 10.3389/fmicb.2016.01692] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/10/2016] [Indexed: 11/26/2022] Open
Abstract
The long term survival of fecal indicator organisms (FIOs) and human pathogenic microorganisms in sediments is important from a water quality, human health and ecological perspective. Typically, both bacteria and viruses strongly associate with particulate matter present in freshwater, estuarine and marine environments. This association tends to be stronger in finer textured sediments and is strongly influenced by the type and quantity of clay minerals and organic matter present. Binding to particle surfaces promotes the persistence of bacteria in the environment by offering physical and chemical protection from biotic and abiotic stresses. How bacterial and viral viability and pathogenicity is influenced by surface attachment requires further study. Typically, long-term association with surfaces including sediments induces bacteria to enter a viable-but-non-culturable (VBNC) state. Inherent methodological challenges of quantifying VBNC bacteria may lead to the frequent under-reporting of their abundance in sediments. The implications of this in a quantitative risk assessment context remain unclear. Similarly, sediments can harbor significant amounts of enteric viruses, however, the factors regulating their persistence remains poorly understood. Quantification of viruses in sediment remains problematic due to our poor ability to recover intact viral particles from sediment surfaces (typically <10%), our inability to distinguish between infective and damaged (non-infective) viral particles, aggregation of viral particles, and inhibition during qPCR. This suggests that the true viral titre in sediments may be being vastly underestimated. In turn, this is limiting our ability to understand the fate and transport of viruses in sediments. Model systems (e.g., human cell culture) are also lacking for some key viruses, preventing our ability to evaluate the infectivity of viruses recovered from sediments (e.g., norovirus). The release of particle-bound bacteria and viruses into the water column during sediment resuspension also represents a risk to water quality. In conclusion, our poor process level understanding of viral/bacterial-sediment interactions combined with methodological challenges is limiting the accurate source apportionment and quantitative microbial risk assessment for pathogenic organisms associated with sediments in aquatic environments.
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Affiliation(s)
| | - Ceri L. Gwyther
- Department of Engineering and Innovation, Open UniversityMilton Keynes, UK
| | - Kata Farkas
- School of Environment, Natural Resources and Geography, Bangor UniversityBangor, UK
| | | | | | | | | | - Davey L. Jones
- School of Environment, Natural Resources and Geography, Bangor UniversityBangor, UK
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13
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Vuillemin A, Friese A, Alawi M, Henny C, Nomosatryo S, Wagner D, Crowe SA, Kallmeyer J. Geomicrobiological Features of Ferruginous Sediments from Lake Towuti, Indonesia. Front Microbiol 2016; 7:1007. [PMID: 27446046 PMCID: PMC4928248 DOI: 10.3389/fmicb.2016.01007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/13/2016] [Indexed: 11/23/2022] Open
Abstract
Lake Towuti is a tectonic basin, surrounded by ultramafic rocks. Lateritic soils form through weathering and deliver abundant iron (oxy)hydroxides but very little sulfate to the lake and its sediment. To characterize the sediment biogeochemistry, we collected cores at three sites with increasing water depth and decreasing bottom water oxygen concentrations. Microbial cell densities were highest at the shallow site-a feature we attribute to the availability of labile organic matter (OM) and the higher abundance of electron acceptors due to oxic bottom water conditions. At the two other sites, OM degradation and reduction processes below the oxycline led to partial electron acceptor depletion. Genetic information preserved in the sediment as extracellular DNA (eDNA) provided information on aerobic and anaerobic heterotrophs related to Nitrospirae, Chloroflexi, and Thermoplasmatales. These taxa apparently played a significant role in the degradation of sinking OM. However, eDNA concentrations rapidly decreased with core depth. Despite very low sulfate concentrations, sulfate-reducing bacteria were present and viable in sediments at all three sites, as confirmed by measurement of potential sulfate reduction rates. Microbial community fingerprinting supported the presence of taxa related to Deltaproteobacteria and Firmicutes with demonstrated capacity for iron and sulfate reduction. Concomitantly, sequences of Ruminococcaceae, Clostridiales, and Methanomicrobiales indicated potential for fermentative hydrogen and methane production. Such first insights into ferruginous sediments showed that microbial populations perform successive metabolisms related to sulfur, iron, and methane. In theory, iron reduction could reoxidize reduced sulfur compounds and desorb OM from iron minerals to allow remineralization to methane. Overall, we found that biogeochemical processes in the sediments can be linked to redox differences in the bottom waters of the three sites, like oxidant concentrations and the supply of labile OM. At the scale of the lacustrine record, our geomicrobiological study should provide a means to link the extant subsurface biosphere to past environments.
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Affiliation(s)
- Aurèle Vuillemin
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Potsdam Germany
| | - André Friese
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Potsdam Germany
| | - Mashal Alawi
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Potsdam Germany
| | - Cynthia Henny
- Research Center for Limnology, Indonesian Institute of Sciences Cibinong, Indonesia
| | - Sulung Nomosatryo
- Research Center for Limnology, Indonesian Institute of Sciences Cibinong, Indonesia
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Potsdam Germany
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British ColumbiaVancouver, BC, Canada; Department of Earth, Ocean, and Atmospheric Sciences, University of British ColumbiaVancouver, BC, Canada
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Potsdam Germany
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14
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Danchin A. Nature or manufacture: What should we fear most? C R Biol 2016; 339:329-35. [PMID: 27260497 DOI: 10.1016/j.crvi.2016.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 03/19/2016] [Accepted: 03/19/2016] [Indexed: 11/27/2022]
Abstract
Of very ancient descent, domestication switched the outcome of natural selection to that due to human design. A widespread fancy is that man-created contraptions develop dangerously on their own because of their Promethean essence. This assumes implicitly-how difficult is it to refrain from thinking that we are the sawyers of nature!-that their crafted powers would dominate the autonomy resulting from billions of years of evolution. Yet artifice depends on the skills of its creator, so that it is when coming close to nature that danger surfaces. Invasive species are natural, and the havoc they create is here to call for some modesty in the appraisal of our endeavours. The farther away, the less dangerous. Being distant from man, engineered plants are considerably less harmful than animal constructs, especially those that are close to man and meant for medical use. This reality contrasts with popular belief. In this misconception lies the danger, magnified by the present demographic explosion of the invasive species Homo sapiens, which develops artificial environments that provide progressively less room for life to evolve.
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Affiliation(s)
- Antoine Danchin
- Institute of Cardiometabolism and Nutrition (ICAN), hôpital de la Pitié-Salpêtrière, 47, boulevard de l'Hôpital, 75013 Paris, France.
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15
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Long AM, Short SM. Seasonal determinations of algal virus decay rates reveal overwintering in a temperate freshwater pond. ISME JOURNAL 2016; 10:1602-12. [PMID: 26943625 DOI: 10.1038/ismej.2015.240] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 10/30/2015] [Accepted: 11/18/2015] [Indexed: 11/09/2022]
Abstract
To address questions about algal virus persistence (i.e., continued existence) in the environment, rates of decay of infectivity for two viruses that infect Chlorella-like algae, ATCV-1 and CVM-1, and a virus that infects the prymnesiophyte Chrysochromulina parva, CpV-BQ1, were estimated from in situ incubations in a temperate, seasonally frozen pond. A series of experiments were conducted to estimate rates of decay of infectivity in all four seasons with incubations lasting 21 days in spring, summer and autumn, and 126 days in winter. Decay rates observed across this study were relatively low compared with previous estimates obtained for other algal viruses, and ranged from 0.012 to 11% h(-1). Overall, the virus CpV-BQ1 decayed most rapidly whereas ATCV-1 decayed most slowly, but for all viruses the highest decay rates were observed during the summer and the lowest were observed during the winter. Furthermore, the winter incubations revealed the ability of each virus to overwinter under ice as ATCV-1, CVM-1 and CpV-BQ1 retained up to 48%, 19% and 9% of their infectivity after 126 days, respectively. The observed resilience of algal viruses in a seasonally frozen freshwater pond provides a mechanism that can support the maintenance of viral seed banks in nature. However, the high rates of decay observed in the summer demonstrate that virus survival and therefore environmental persistence can be subject to seasonal bottlenecks.
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Affiliation(s)
- Andrew M Long
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Steven M Short
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
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16
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Williamson KE, Harris JV, Green JC, Rahman F, Chambers RM. Stormwater runoff drives viral community composition changes in inland freshwaters. Front Microbiol 2014; 5:105. [PMID: 24672520 PMCID: PMC3954104 DOI: 10.3389/fmicb.2014.00105] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 02/27/2014] [Indexed: 11/30/2022] Open
Abstract
Storm events impact freshwater microbial communities by transporting terrestrial viruses and other microbes to freshwater systems, and by potentially resuspending microbes from bottom sediments. The magnitude of these impacts on freshwater ecosystems is unknown and largely unexplored. Field studies carried out at two discrete sites in coastal Virginia (USA) were used to characterize the viral load carried by runoff and to test the hypothesis that terrestrial viruses introduced through stormwater runoff change the composition of freshwater microbial communities. Field data gathered from an agricultural watershed indicated that primary runoff can contain viral densities approximating those of receiving waters. Furthermore, viruses attached to suspended colloids made up a large fraction of the total load, particularly in early stages of the storm. At a second field site (stormwater retention pond), RAPD-PCR profiling showed that the viral community of the pond changed dramatically over the course of two intense storms while relatively little change was observed over similar time scales in the absence of disturbance. Comparisons of planktonic and particle-associated viral communities revealed two completely distinct communities, suggesting that particle-associated viruses represent a potentially large and overlooked portion of aquatic viral abundance and diversity. Our findings show that stormwater runoff can quickly change the composition of freshwater microbial communities. Based on these findings, increased storms in the coastal mid-Atlantic region predicted by most climate change models will likely have important impacts on the structure and function of local freshwater microbial communities.
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Affiliation(s)
- Kurt E Williamson
- Department of Biology, The College of William and Mary Williamsburg, VA, USA
| | - Jamie V Harris
- Department of Biology, The College of William and Mary Williamsburg, VA, USA
| | - Jasmin C Green
- Department of Biology, The College of William and Mary Williamsburg, VA, USA
| | - Faraz Rahman
- Department of Biology, The College of William and Mary Williamsburg, VA, USA
| | - Randolph M Chambers
- Department of Biology, The College of William and Mary Williamsburg, VA, USA
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17
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Zhong X, Ram ASP, Colombet J, Jacquet S. Variations in abundance, genome size, morphology, and functional role of the virioplankton in Lakes Annecy and Bourget over a 1-year period. MICROBIAL ECOLOGY 2014; 67:66-82. [PMID: 24253662 DOI: 10.1007/s00248-013-0320-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 10/24/2013] [Indexed: 06/02/2023]
Abstract
We sampled the surface waters (2-50 m) of two deep peri-alpine lakes over a 1-year period in order to examine (1) the abundance, vertical distribution, genome size, and morphology structures of the virioplankton; (2) the virus-mediated bacterial mortality; and (3) the specific genome size range of double-stranded DNA (dsDNA) phytoplankton viruses. Virus-like particle (VLP) concentrations varied between 4.16 × 10(7) (January) and 2.08 × 10(8) part mL(-1) (May) in Lake Bourget and between 2.7 × 10(7) (June) and 8.39 × 10(7) part mL(-1) (November) in Lake Annecy. Our flow cytometry analysis revealed at least three viral groups (referred to as virus-like particles 1, 2, and 3) that exhibited distinctive dynamics suggestive of different host types. Phage-induced bacterial mortality varied between 6.1% (June) and 33.2% (October) in Lake Bourget and between 7.4% (June) and 52.6% (November) in Lake Annecy, suggesting that viral lysis may be a key cause of mortality of the bacterioplankton. Virioplankton genome size ranged from 27 to 486 kb in Lake Bourget, while it reached 620 kb in Lake Annecy for which larger genome sizes were recorded. Our analysis of pulsed field gel electrophoresis bands using different PCR primers targeting both cyanophages and algal viruses showed that (1) dsDNA viruses infecting phytoplankton may range from 65 to 486 kb, and (2) both cyanophage and algal "diversity" were higher in Lake Annecy. Lakes Annecy and Bourget also differed regarding the proportions of both viral families (with the dominance of myoviruses vs. podoviruses) and infected bacterial morphotypes (short rods vs. elongated rods), in each of these lakes, respectively. Overall, our results reveal that (1) viruses displayed distinct temporal and vertical distribution, dynamics, community structure in terms of genome size and morphology, and viral activity in the two lakes; (2) the Myoviridae seemed to be the main cause of bacterial mortality in both lakes and this group seemed to be related to VLP2; and (3) phytoplankton viruses may have a broader range of genome size than previously thought. This study adds to growing evidence that viruses are diverse and play a significant role in freshwater microbial dynamics and more globally lake functioning. It highlights the importance of further considering this biological compartment for a better understanding of plankton ecology in peri-alpine lakes.
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Affiliation(s)
- Xu Zhong
- INRA, UMR 042 CARRTEL, 75 Avenue de Corzent, 74203, Thonon-les-Bains cx, France
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18
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Ganesh A, Lin J. Waterborne human pathogenic viruses of public health concern. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2013; 23:544-64. [PMID: 23432800 DOI: 10.1080/09603123.2013.769205] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In recent years, the impending impact of waterborne pathogens on human health has become a growing concern. Drinking water and recreational exposure to polluted water have shown to be linked to viral infections, since viruses are shed in extremely high numbers in the faeces and vomit of infected individuals and are routinely introduced into the water environment. All of the identified pathogenic viruses that pose a significant public health threat in the water environment are transmitted via the faecal-oral route. This group, are collectively known as enteric viruses, and their possible health effects include gastroenteritis, paralysis, meningitis, hepatitis, respiratory illness and diarrhoea. This review addresses both past and recent investigations into viral contamination of surface waters, with emphasis on six types of potential waterborne human pathogenic viruses. In addition, the viral associated illnesses are outlined with reference to their pathogenesis and routes of transmission.
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Affiliation(s)
- Atheesha Ganesh
- a Discipline of Microbiology, School of Life Sciences , University of KwaZulu-Natal (Westville) , Durban , South Africa
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19
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Matteson AR, Rowe JM, Ponsero AJ, Pimentel TM, Boyd PW, Wilhelm SW. High abundances of cyanomyoviruses in marine ecosystems demonstrate ecological relevance. FEMS Microbiol Ecol 2013; 84:223-34. [PMID: 23240688 DOI: 10.1111/1574-6941.12060] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 09/11/2012] [Accepted: 12/03/2012] [Indexed: 12/01/2022] Open
Abstract
The distribution of cyanomyoviruses was estimated using a quantitative PCR (qPCR) approach that targeted the g20 gene as a proxy for phage. Samples were collected spatially during a > 3000 km transect through the Sargasso Sea and temporally during a gyre-constrained phytoplankton bloom within the southern Pacific Ocean. Cyanomyovirus abundances were lower in the Sargasso Sea than in the southern Pacific Ocean, ranging from 2.75 × 10(3) to 5.15 × 10(4) mL(-1) and correlating with the abundance of their potential hosts (Prochlorococcus and Synechococcus). Cyanomyovirus abundance in the southern Pacific Ocean (east of New Zealand) followed Synechococcus host populations in the system: this included a decrease in g20 gene copies (from 4.3 × 10(5) to 9.6 × 10(3) mL(-1) ) following the demise of a Synechococcus bloom. When compared with direct counts of viruses, observations suggest that the cyanomyoviruses comprised 0.5 to >25% of the total virus community. We estimated daily lysis rates of 0.2-46% of the standing stock of Synechococcus in the Pacific Ocean compared with c. < 1.0% in the Sargasso Sea. In total, our observations confirm this family of viruses is abundant in marine systems and that they are an important source of cyanobacterial mortality.
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Affiliation(s)
- Audrey R Matteson
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996-0845, USA
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20
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Forterre P, Soler N, Krupovic M, Marguet E, Ackermann HW. Fake virus particles generated by fluorescence microscopy. Trends Microbiol 2012; 21:1-5. [PMID: 23140888 DOI: 10.1016/j.tim.2012.10.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 10/10/2012] [Accepted: 10/10/2012] [Indexed: 01/07/2023]
Abstract
Many laboratories are actively studying the abundance and roles of viruses in natural ecosystems. In these studies, the presence and number of viral particles is usually determined using fluorescent dyes. However, DNA associated with membrane-derived vesicles (MVs), gene transfer agents (GTAs), or cell debris can produce fluorescent dots that can be confused with viral particles. We suspect that fluorescence counting can lead to overestimation of virus numbers and even suggest the presence of viruses when there are none. Future studies in environmental virology should acknowledge this point and consider how to bypass this problem. Besides trying to improve discrimination between virions and MVs, we suggest adopting less holistic approaches, focusing on the detection of known virus groups and the isolation of new viruses from a broader range of hosts.
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Affiliation(s)
- Patrick Forterre
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS UMR 8621, 91405 Orsay Cedex, France.
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21
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Manrique JM, Calvo AY, Jones LR. Phylogenetic analysis of Ostreococcus virus sequences from the Patagonian Coast. Virus Genes 2012; 45:316-26. [PMID: 22674355 DOI: 10.1007/s11262-012-0762-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Accepted: 05/11/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Julieta M Manrique
- Division of Molecular Biology, Estación de Fotobiología Playa Unión, CC 15 (9103), Playa Unión, Rawson, Chubut, Argentina
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22
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Unexpected and novel putative viruses in the sediments of a deep-dark permanently anoxic freshwater habitat. ISME JOURNAL 2012; 6:2119-27. [PMID: 22648129 DOI: 10.1038/ismej.2012.49] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Morphological diversity, abundance and community structure of viruses were examined in the deep and anoxic sediments of the volcanic Lake Pavin (France). The sediment core, encompassing 130 years of sedimentation, was subsampled every centimeter. High viral abundances were recorded and correlated to prokaryotic densities. Abundances of viruses and prokaryotes decreased with the depth, contrasting the pattern of virus-to-prokaryote ratio. According to fingerprint analyses, the community structure of viruses, bacteria and archaea gradually changed, and communities of the surface (0-10 cm) could be discriminated from those of the intermediate (11-27 cm) and deep (28-40 cm) sediment layers. Viral morphotypes similar to virions of ubiquitous dsDNA viruses of bacteria were observed. Exceptional morphotypes, previously never reported in freshwater systems, were also detected. Some of these resembled dsDNA viruses of hyperthermophilic and hyperhalophilic archaea. Moreover, unusual types of spherical and cubic virus-like particles (VLPs) were observed. Infected prokaryotic cells were detected in the whole sediment core, and their vertical distribution correlated with both viral and prokaryotic abundances. Pleomorphic ellipsoid VLPs were visible in filamentous cells tentatively identified as representatives of the archaeal genus Methanosaeta, a major group of methane producers on earth.
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23
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Crotty FV, Adl SM, Blackshaw RP, Murray PJ. Protozoan pulses unveil their pivotal position within the soil food web. MICROBIAL ECOLOGY 2012; 63:905-918. [PMID: 21990016 DOI: 10.3354/ame01485] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 08/11/2011] [Indexed: 05/21/2023]
Abstract
Protozoa are one of the most abundant groups of bacterivores within the soil and are responsible for mineralisation of bacterial biomass, having a large impact on C and N cycling. Little is known of their contribution to soil nutrient transfers or the identity of their consumers. Here, for the first time indigenous flagellates and ciliates, enriched to 83 atom% for (13)C and 10 atom% for (15)N, were introduced to soil cores from two different land managements, grassland and woodland with the same soil type, to trace the flow of protozoan C and N through the soil food web. Nematodes, Collembola, earthworms and insect larvae obtained the greatest amounts of C and N of protozoan origin, either through direct consumption or uptake of biomass post-cell death. Our results show that changes in management, affect the functioning of the soil food web and the utilisation of protozoa as a food source.
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Affiliation(s)
- Felicity V Crotty
- Sustainable Soil and Grassland Systems, Rothamsted Research, North Wyke, Okehampton, Devon, UK.
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24
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Bouvy M, Combe M, Bettarel Y, Dupuy C, Rochelle-Newall E, Charpy L. Uncoupled viral and bacterial distributions in coral reef waters of Tuamotu Archipelago (French Polynesia). MARINE POLLUTION BULLETIN 2012; 65:506-515. [PMID: 22284701 DOI: 10.1016/j.marpolbul.2012.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 01/02/2012] [Accepted: 01/03/2012] [Indexed: 05/31/2023]
Abstract
This study examined the distribution of virioplankton and bacterioplankton in two coral reef systems (Ahe and Takaroa atolls) in the Tuamotu Archipelago, in comparison with the surrounding oligotrophic ocean. Mean concentrations of 4.8×10(5) and 6.2×10(5) cells ml(-1) for bacteria and 8.1×10(6) and 4.3×10(6) VLP(virus-like particle) ml(-1) were recorded in Ahe and Takaroa lagoons, respectively. Chlorophyll-a concentrations and dissolved organic matter were higher in Ahe whereas (3)H thymidine incorporation rates were higher in Takaroa. First data on lytic and lysogenic strategies of phages in coral reef environments were discussed in this paper. The fraction of visibly infected cells by viruses was negligible regardless of the lagoon station (mean=0.15%). However, the fraction of lysogenic cells ranged between 2.5% and 88.9%. Our results suggest that the distribution patterns of virioplankton are apparently not coupled to the spatial dynamics of the bacterioplankton communities.
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Affiliation(s)
- Marc Bouvy
- UMR 5119, ECOSYM - Ecologie des systèmes marins côtiers (UM2, CNRS, IRD, Ifremer, UM1), Université Montpellier 2, Place Eugène Bataillon, Case 093, 34095 Montpellier Cedex 5, France.
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25
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Williamson KE, Helton RR, Wommack KE. Bias in bacteriophage morphological classification by transmission electron microscopy due to breakage or loss of tail structures. Microsc Res Tech 2011; 75:452-7. [PMID: 21919126 DOI: 10.1002/jemt.21077] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 07/30/2011] [Indexed: 11/06/2022]
Abstract
Virtually every study that has used transmission electron microscopy (TEM) to estimate viral diversity has acknowledged that loss of phage tails during sample preparation may have biased the results. However, the magnitude of this potential bias has yet to be constrained. To characterize biases in virus morphological diversity due to tail loss, six phage strains representing the order Caudovirales were inoculated into sterile sediments and soils. Phage particles were then extracted using standard methods. Morphologies of extracted phage particles were compared to those of unmanipulated control samples to determine the extent of tail breakage incurred by extraction procedures. Podoviruses exhibited the smallest frequency of tail loss during extraction (1.2-14%), myoviruses were moderately susceptible to tail breakage (15-40%), and siphoviruses were highly susceptible (32-76%). Thus, TEM assessments of viral diversity in soils or sediments by distribution of tail morphologies may be biased toward podoviruses and virions lacking tails, while simultaneously underestimating the abundance of siphoviruses. However, since the majority of viral capsids observed under TEM were intact, estimates of viral diversity based on the distribution of capsid diameters may provide a more reliable basis for morphological comparisons within and across ecosystems.
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Affiliation(s)
- Kurt E Williamson
- Department of Biology, College of William and Mary, Williamsburg, Virginia 23186, USA.
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26
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Thomas R, Berdjeb L, Sime-Ngando T, Jacquet S. Viral abundance, production, decay rates and life strategies (lysogeny versus lysis) in Lake Bourget (France). Environ Microbiol 2010; 13:616-30. [PMID: 21054737 DOI: 10.1111/j.1462-2920.2010.02364.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We have investigated the ecology of viruses in Lake Bourget (France) from January to August 2008. Data were analysed for viral and bacterial abundance and production, viral decay, frequency of lysogenic cells, the contribution of bacteriophages to prokaryotic mortality and their potential influence on nutrient dynamics. Analyses and experiments were conducted on samples from the epilimnion (2 m) and the hypolimnion (50 m), taken at the reference site of the lake. The abundance of virus-like particles (VLP) varied from 3.4 × 10⁷to 8.2 × 10⁷ VLP ml⁻¹; with the highest numbers and virus-to-bacterium ratio (VBR = 69) recorded in winter. Viral production varied from 3.2 × 10⁴ VLP ml⁻¹ h⁻¹ (July) to 2 × 10⁶ VLP ml⁻¹ h⁻¹ (February and April), and production was lower in the hypolimnion. Viral decay rate reached 0.12-0.15 day⁻¹, and this parameter varied greatly with sampling date and methodology (i.e. KCN versus filtration). Using transmission electron microscopy (TEM) analysis, viral lysis was responsible for 0% (January) to 71% (February) of bacterial mortality, while viral lysis varied between 0% (April) and 53% (January) per day when using a modified dilution approach. Calculated from viral production and burst size, the virus-induced bacterial mortality varied between 0% (January) and 68% (August). A weak relationship was found between the two first methods (TEM versus dilution approach). Interestingly, flow cytometry analysis performed on the dilution experiment samples revealed that the viral impact was mostly on high DNA content bacterial cells whereas grazing, varying between 8.3% (June) and 75.4% (April), was reflected in both HDNA and LDNA cells equally. The lysogenic fraction varied between 0% (spring/summer) and 62% (winter) of total bacterial abundance, and increased slightly with increasing amounts of mitomycin C added. High percentages of lysogenic cells were recorded when bacterial abundance and activity were the lowest. The calculated release of carbon and phosphorus from viral lysis reached up to 56.5 µgC l⁻¹ day⁻¹ (assuming 20 fgC cell⁻¹) and 1.4 µgP l⁻¹ day⁻¹ (assuming 0.5 fgP cell⁻¹), respectively, which may represent a significant fraction of bacterioplankton nutrient demand. This study provides new evidence of the quantitative and functional importance of the virioplankton in the functioning of microbial food webs in peri-alpine lakes. It also highlights methodologically dependent results.
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Affiliation(s)
- Rozenn Thomas
- INRA, UMR 42 CARRTEL, Station d'Hydrobiologie Lacustre, Thonon-les-Bains, France
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Holmfeldt K, Titelman J, Riemann L. Virus production and lysate recycling in different sub-basins of the northern Baltic Sea. MICROBIAL ECOLOGY 2010; 60:572-580. [PMID: 20407893 DOI: 10.1007/s00248-010-9668-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 03/26/2010] [Indexed: 05/29/2023]
Abstract
In the Gulf of Bothnia, northern Baltic Sea, a large freshwater inflow creates north-southerly gradients in physico-chemical and biological factors across the two sub-basins, the Bothnian Bay (BB) and the Bothnian Sea. In particular, the sub-basins differ in nutrient limitation (nitrogen vs. phosphorus; P). Since viruses are rich in P, and virus production is commonly connected with bacterial abundance and growth, we hypothesized that the role of viral lysis differs between the sub-basins. Thus, we examined virus production and the potential importance of lysate recycling in surface waters along a transect in the Gulf of Bothnia. Surprisingly, virus production and total P were negatively correlated. In the BB, virus production rates were double those elsewhere in the system, although bacterial abundance and production were the lowest. In the BB, virus-mediated cell lysates could account for 70-180% and 100-250% of the bacterial carbon and P demand, respectively, while only 4-15% and 8-21% at the other stations. Low concentrations of dissolved DNA (D-DNA) with a high proportion of encapsulated DNA (viruses) in the BB suggested rapid turnover and high uptake of free DNA. The correlation of D-DNA and total P indicates that D-DNA is a particularly important nutrient source in the P-limited BB. Our study demonstrates large and counterintuitive differences in virus-mediated recycling of carbon and nutrients in two basins of the Gulf of Bothnia, which differ in microbial community composition and nutrient limitation.
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Affiliation(s)
- Karin Holmfeldt
- Department of Natural Sciences, Linneaus University, SE-39182 Kalmar, Sweden.
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Stanhope SA. Occupancy modeling, maximum contig size probabilities and designing metagenomics experiments. PLoS One 2010; 5:e11652. [PMID: 20686599 PMCID: PMC2912229 DOI: 10.1371/journal.pone.0011652] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Accepted: 06/22/2010] [Indexed: 11/19/2022] Open
Abstract
Mathematical aspects of coverage and gaps in genome assembly have received substantial attention by bioinformaticians. Typical problems under consideration suppose that reads can be experimentally obtained from a single genome and that the number of reads will be set to cover a large percentage of that genome at a desired depth. In metagenomics experiments genomes from multiple species are simultaneously analyzed and obtaining large numbers of reads per genome is unlikely. We propose the probability of obtaining at least one contig of a desired minimum size from each novel genome in the pool without restriction based on depth of coverage as a metric for metagenomic experimental design. We derive an approximation to the distribution of maximum contig size for single genome assemblies using relatively few reads. This approximation is verified in simulation studies and applied to a number of different metagenomic experimental design problems, ranging in difficulty from detecting a single novel genome in a pool of known species to detecting each of a random number of novel genomes collectively sized and with abundances corresponding to given distributions in a single pool.
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Affiliation(s)
- Stephen A Stanhope
- Biological Sciences Division, University of Chicago, Chicago, Illinois, United States of America.
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Säwström C, Ask J, Karlsson J. Viruses in subarctic lakes and their impact on benthic and pelagic bacteria. FEMS Microbiol Ecol 2009; 70:471-82. [PMID: 19732143 DOI: 10.1111/j.1574-6941.2009.00760.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Virus-bacterium interactions were investigated in the pelagic and benthic habitats in a set of lakes along an altitudinal gradient in the subarctic northern Sweden. Viral and bacterial abundances showed a significant variation between the lakes, with the highest benthic microbial abundances recorded in a high-altitude lake [993 m above sea level (a.s.l.)], whereas the highest pelagic microbial abundances were found in a low-altitude lake (270 m a.s.l.). In the pelagic habitat, there was also a distinct difference in microbial abundances between the summer-autumn and the winter sampling occasion. A positive relationship was noted between viruses and bacteria in both the pelagic and the benthic habitats. Visibly virus-infected bacterial cells were uncommon in the pelagic habitat and undetectable in the benthos. Both lytic and lysogenic pelagic viral production rates were undetectable or low; thus, a possible explanation for the relative high viral abundances found in the water column could be an allochthonous input of viruses or release of sediment-derived viruses. Overall, our results provide novel information about the relevance of viruses in the subarctic region and indicate that viruses play only a minor role in the nutrient and carbon cycling in the microbial communities of subarctic lakes.
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Affiliation(s)
- Christin Säwström
- Department of Ecology and Environmental Science, Climate Impacts Research Centre (CIRC), Umeå University, Abisko, Sweden.
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Abstract
In this review, available data on the structure (diversity, abundance, biomass) and functional imprints (bacteriolysis, lysogeny, gene transfers, regulation of prokaryotic diversity) of natural viruses in the context of food webs in aquatic microbial ecology, and the related biogeochemical cycles, are summarized. Viruses are the most abundant, and probably the most diverse, biological entities in aquatic ecosystems and in the biosphere (i.e., viriosphere). Aquatic viruses typically exceed 107 particles/mL in mesotrophic conditions, the majority being represented by phages without tails and by tailed-phages such as members of the family Siphoviridae. Both types of phages have a small capsid and a small genome size, which is considered an evolutionary adaptation to planktonic life. Their contribution to microbial mortality is significant. There is strong evidence that phages exert a significant pressure on the community structure and diversity and on the diversification of potential hosts, mainly through two major pathways: biogeochemical catalysis from lysis products and horizontal gene transfers. In turn, phages are sensitive to environmental factors, both in terms of integrity and of infectivity. Some phages contain typical viral genes that code for biological functions of interest, such as photosynthesis. In general, development in viral ecology is a source of new knowledge for the scientific community in the domain of environmental sciences, but also in the context of evolutionary biology of living cellular organisms, the obligatory hosts for viruses. For example, the recent discovery of a giant virus that becomes ill through infection by another virus (i.e., a viriophage) is fuelling debate about whether viruses are alive. Finally, future research directions are identified in the context of general aquatic ecology, including ecological researches on cyanophages and other phytoplanktonic phages as a priority, primarily in freshwater lakes.
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Phylogenetic analysis indicates evolutionary diversity and environmental segregation of marine podovirus DNA polymerase gene sequences. Appl Environ Microbiol 2009; 75:3634-40. [PMID: 19363063 DOI: 10.1128/aem.02317-08] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The distribution of viral genotypes in the ocean and their evolutionary relatedness remain poorly constrained. This paper presents data on the genetic diversity and evolutionary relationships of 1.2-kb DNA polymerase (pol) gene fragments from podoviruses. A newly designed set of PCR primers was used to amplify DNA directly from coastal sediment and water samples collected from inlets adjacent to the Strait of Georgia, British Columbia, Canada, and from the northeastern Gulf of Mexico. Restriction fragment length polymorphism analysis of 160 cloned PCR products revealed 29 distinct operational taxonomic units (OTUs), with OTUs within a site typically being more similar than those among sites. Phylogenetic analysis of the DNA pol gene fragments demonstrated high similarity between some environmental sequences and sequences from the marine podoviruses roseophage SIO1 and cyanophage P60, while others were not closely related to sequences from cultured phages. Interrogation of the CAMERA database for sequences from metagenomics data demonstrated that the amplified sequences were representative of the diversity of podovirus pol sequences found in marine samples. Our results indicate high genetic diversity within marine podovirus communities within a small geographic region and demonstrate that the diversity of environmental polymerase gene sequences for podoviruses is far more extensive than previously recognized.
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Riemann L, Holmfeldt K, Titelman J. Importance of viral lysis and dissolved DNA for bacterioplankton activity in a P-limited estuary, Northern Baltic Sea. MICROBIAL ECOLOGY 2009; 57:286-294. [PMID: 18670729 DOI: 10.1007/s00248-008-9429-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2008] [Revised: 07/01/2008] [Accepted: 07/07/2008] [Indexed: 05/26/2023]
Abstract
Through lysis of bacterioplankton cells, viruses mediate an important, but poorly understood, pathway of carbon and nutrients from the particulate to the dissolved form. Via this activity, nutrient-rich cell lysates may become available to noninfected cells and support significant growth. However, the nutritional value of lysates for noninfected bacteria presumably depends on the prevailing nutrient limitation. In the present study, we examined dynamics of dissolved DNA (D-DNA) and viruses along a transect in the phosphorus (P)-limited Ore Estuary, northern Baltic Sea. We found that viruses were an important mortality factor for bacterioplankton and that their activity mediated a significant recycling of carbon and especially of P. Uptake of dissolved DNA accounted for up to 70% of the bacterioplankton P demand, and about a quarter of the D-DNA pool was supplied through viral lysis of bacterial cells. Generally, the importance of viral lysates and uptake of D-DNA was highest at the estuarine and offshore stations and was positively correlated with P limitation measured as alkaline phosphatase activity. Our results highlight the importance of viral activity for the internal recycling of principal nutrients and pinpoints D-DNA as a particularly relevant compound in microbial P dynamics.
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Affiliation(s)
- Lasse Riemann
- Department of Natural Sciences, Kalmar University, 39182, Kalmar, Sweden.
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Shen C, Phanikumar MS, Fong TT, Aslam I, McElmurry SP, Molloy SL, Rose JB. Evaluating bacteriophage P22 as a tracer in a complex surface water system: the Grand River, Michigan. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2008; 42:2426-31. [PMID: 18504976 DOI: 10.1021/es702317t] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Viruses are important pathogens in both marine and fresh water environments. There is a strong interest in using bacteriophages as tracers because of their role as model viruses, since dissolved chemical tracers may not adequately describe the behavior of viruses that are suspended colloids. Despite a large number of studies that examined the transport of bacteriophages in the subsurface environment, few studies examined phage transport in large and complex surface water systems. In this paper we report the results of a dual tracer study on a 40 km reach of the Grand River, the longest river in Michigan, and we examine the performance of bacteriophage P22 relative to a chemical tracer (Rhodamine WT). Our analysis based on the transient storage (TS) model indicated that P22 can be successfully used as a tracer in complex surface water environments. Estimated P22 inactivation rates were found to be in the range 0.27-0.57 per day (0.12-0.25 log10 per day). The highest inactivation rate was found in a reach with high suspended solids concentration, relatively low dissolved organic carbon content, and sediment with high clay content. Estimated TS model parameters for both tracers were found to be consistent with surficial geology and land use patterns. Maximum storage zone sizes for the two tracers were found in different river reaches, indicating that different processes contributed to TS within the same reach for the two tracers. This model can be used to examine the arrival times and concentrations of human viral pathogens released from untreated sewage at recreational areas.
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Affiliation(s)
- Chaopeng Shen
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan 48824, USA
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