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Brown MR, Baptista JC, Lunn M, Swan DL, Smith SJ, Davenport RJ, Allen BD, Sloan WT, Curtis TP. Coupled virus - bacteria interactions and ecosystem function in an engineered microbial system. WATER RESEARCH 2019; 152:264-273. [PMID: 30682570 DOI: 10.1016/j.watres.2019.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
Viruses are thought to control bacterial abundance, affect community composition and influence ecosystem function in natural environments. Yet their dynamics have seldom been studied in engineered systems, or indeed in any system, for long periods of time. We measured virus abundance in a full-scale activated sludge plant every week for two years. Total bacteria and ammonia oxidising bacteria (AOB) abundances, bacterial community profiles, and a suite of environmental and operational parameters were also monitored. Mixed liquor virus abundance fluctuated over an order of magnitude (3.18 × 108-3.41 × 109 virus's mL-1) and that variation was statistically significantly associated with total bacterial and AOB abundance, community composition, and effluent concentrations of COD and NH4+- N and thus system function. This suggests viruses play a far more important role in the dynamics of activated sludge systems than previously realised and could be one of the key factors controlling bacterial abundance, community structure and functional stability and may cause reactors to fail. These findings are based on statistical associations, not mechanistic models. Nevertheless, viral associations with abiotic factors, such as pH, make physical sense, giving credence to these findings and highlighting the role that physical factors play in virus ecology. Further work is needed to identify and quantify specific bacteriophage and their hosts to enable us to develop mechanistic models of the ecology of viruses in wastewater treatment systems. However, since we have shown that viruses can be related to effluent quality and virus quantification is simple and cheap, practitioners would probably benefit from quantifying viruses now.
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Affiliation(s)
- M R Brown
- School of Engineering, Newcastle University, NE1 7RU, UK.
| | - J C Baptista
- School of Engineering, Newcastle University, NE1 7RU, UK
| | - M Lunn
- Department of Statistics, University of Oxford, OX1 3TG, UK
| | - D L Swan
- School of Engineering, Newcastle University, NE1 7RU, UK
| | - S J Smith
- School of Engineering, Newcastle University, NE1 7RU, UK
| | - R J Davenport
- School of Engineering, Newcastle University, NE1 7RU, UK
| | - B D Allen
- School of Engineering, Newcastle University, NE1 7RU, UK
| | - W T Sloan
- Department of Civil Engineering, University of Glasgow, G12 8LT, UK
| | - T P Curtis
- School of Engineering, Newcastle University, NE1 7RU, UK
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2
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Eissler Y, Gálvez MJ, Dorador C, Hengst M, Molina V. Active microbiome structure and its association with environmental factors and viruses at different aquatic sites of a high-altitude wetland. Microbiologyopen 2018; 8:e00667. [PMID: 30062777 PMCID: PMC6436485 DOI: 10.1002/mbo3.667] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/04/2018] [Accepted: 04/21/2018] [Indexed: 01/23/2023] Open
Abstract
Salar de Huasco is a high‐altitude wetland characterized by a highly diverse microbial life adapted to extreme climatic and environmental conditions. Our study aims to determine active microbial community structure changes within different aquatic sites and its relationship with environmental factors and viruses as potential drivers of diversification in different aquatic areas of this ecosystem. In this study, bacteria and archaea composition (16S rRNA subunit pyrolibraries) and picoplankton and viral abundance were determined at ponds, springs and lagoon sites of the wetland during wet and dry seasons (February and July 2012, respectively). In general, mixosaline waters (1,400–51,000 μS/cm) usually found in ponds and lagoon presented higher picoplanktonic abundances compared to freshwater (<800 μS/cm) spring sites, ranging from 1.07 × 105 to 1.83 × 107 cells/ml. Viral abundance and viral to picoplankton ratio (VPR) also presented greater values at ponds compared to spring sites, reaching up to 4.78 × 108 viruses‐like particles and up to 351 for VPR. In general, ponds hold a higher microbial diversity and complexity associated also with the presence of microbial mats compared with water sources or lagoon (Shannon index H′ 2.6–3.9 vs. <2.0). A greater richness of archaea was also detected in ponds characterized by functional groups such as known methanogens and ammonia oxidizers, and uncultured groups. In total, our results indicate that among the different aquatic sites of the wetland, ponds presented a great microbial community diversification associated to a higher top‐down control by viruses which may influence nutrient and greenhouse gases cycling.
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Affiliation(s)
- Yoanna Eissler
- Facultad de Ciencias, Centro de Investigación y Gestión de Recursos Naturales, Instituto de Química y Bioquímica, Universidad de Valparaíso, Valparaíso, Chile
| | - María-Jesús Gálvez
- Programa de Biodiversidad and Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Observatorio de Ecología Microbiana, Universidad de Playa Ancha, Valparaíso, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology and Bioengineering, Santiago, Chile
| | - Martha Hengst
- Centre for Biotechnology and Bioengineering, Santiago, Chile.,Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta, Chile
| | - Verónica Molina
- Programa de Biodiversidad and Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Observatorio de Ecología Microbiana, Universidad de Playa Ancha, Valparaíso, Chile
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3
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Knowles B, Bailey B, Boling L, Breitbart M, Cobián-Güemes A, Del Campo J, Edwards R, Felts B, Grasis J, Haas AF, Katira P, Kelly LW, Luque A, Nulton J, Paul L, Peters G, Robinett N, Sandin S, Segall A, Silveira C, Youle M, Rohwer F. Variability and host density independence in inductions-based estimates of environmental lysogeny. Nat Microbiol 2017; 2:17064. [PMID: 28452987 DOI: 10.1038/nmicrobiol.2017.64] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/22/2017] [Indexed: 11/09/2022]
Abstract
Temperate bacterial viruses (phages) may enter a symbiosis with their host cell, forming a unit called a lysogen. Infection and viral replication are disassociated in lysogens until an induction event such as DNA damage occurs, triggering viral-mediated lysis. The lysogen-lytic viral reproduction switch is central to viral ecology, with diverse ecosystem impacts. It has been argued that lysogeny is favoured in phages at low host densities. This paradigm is based on the fraction of chemically inducible cells (FCIC) lysogeny proxy determined using DNA-damaging mitomycin C inductions. Contrary to the established paradigm, a survey of 39 inductions publications found FCIC to be highly variable and pervasively insensitive to bacterial host density at global, within-environment and within-study levels. Attempts to determine the source(s) of variability highlighted the inherent complications in using the FCIC proxy in mixed communities, including dissociation between rates of lysogeny and FCIC values. Ultimately, FCIC studies do not provide robust measures of lysogeny or consistent evidence of either positive or negative host density dependence to the lytic-lysogenic switch. Other metrics are therefore needed to understand the drivers of the lytic-lysogenic decision in viral communities and to test models of the host density-dependent viral lytic-lysogenic switch.
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Affiliation(s)
- Ben Knowles
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Barbara Bailey
- Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Lance Boling
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Mya Breitbart
- College of Marine Science, University of South Florida, 140 Seventh Avenue South, St Petersburg, Florida 33701, USA
| | - Ana Cobián-Güemes
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Javier Del Campo
- Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Rob Edwards
- Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.,Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Ben Felts
- Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Juris Grasis
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Andreas F Haas
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Parag Katira
- Department of Mechanical Engineering, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Linda Wegley Kelly
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Antoni Luque
- Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.,Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Jim Nulton
- Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Lauren Paul
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Gregory Peters
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Nate Robinett
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Stuart Sandin
- Scripps Institution of Oceanography, University of California San Diego, 950 Gilman Drive, California 92903, USA
| | - Anca Segall
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Cynthia Silveira
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | | | - Forest Rohwer
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
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Pradeep Ram AS, Colombet J, Perriere F, Thouvenot A, Sime-Ngando T. Viral Regulation of Prokaryotic Carbon Metabolism in a Hypereutrophic Freshwater Reservoir Ecosystem (Villerest, France). Front Microbiol 2016; 7:81. [PMID: 26903963 PMCID: PMC4746248 DOI: 10.3389/fmicb.2016.00081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/18/2016] [Indexed: 01/27/2023] Open
Abstract
The current consensus concerning the viral regulation of prokaryotic carbon metabolism is less well-studied, compared to substrate availability. We explored the seasonal and vertical distribution of viruses and its relative influence on prokaryotic carbon metabolism in a hypereutrophic reservoir, Lake Villerest (France). Flow cytometry and transmission electron microscopy (TEM) analyses to determine viral abundance (VA; range = 6.1–63.5 × 107 ml-1) and viral infection rates of prokaryotes (range = 5.3–32%) respectively suggested that both the parameters varied more significantly with depths than with seasons. Prokaryotic growth efficiency (PGE, considered as a proxy of prokaryotic carbon metabolism) calculated from prokaryotic production and respiration measurements (PGE = prokaryotic production/[prokaryotic production + prokaryotic respiration] × 100) varied from 14 to 80% across seasons and depths. Viruses through selective lyses had antagonistic impacts on PGE by regulating key prokaryotic metabolic processes (i.e., production and respiration). Higher viral lysis accompanied by higher respiration rates and lower PGE in the summer (mean = 22.9 ± 10.3%) than other seasons (mean = 59.1 ± 18.6%), led to significant loss of carbon through bacterial-viral loop and shifted the reservoir system to net heterotrophy. Our data therefore suggests that the putative adverse impact of viruses on the growth efficiency of the prokaryotic community can have strong implications on nutrient flux patterns and on the overall ecosystem metabolism in anthropogenic dominated aquatic systems such as Lake Villerest.
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Affiliation(s)
- Angia Sriram Pradeep Ram
- UMR CNRS 6023, Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal Aubière, France
| | - Jonathan Colombet
- UMR CNRS 6023, Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal Aubière, France
| | - Fanny Perriere
- UMR CNRS 6023, Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal Aubière, France
| | | | - Télesphore Sime-Ngando
- UMR CNRS 6023, Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal Aubière, France
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Pradeep Ram AS, Colombet J, Perriere F, Thouvenot A, Sime-Ngando T. Viral and grazer regulation of prokaryotic growth efficiency in temperate freshwater pelagic environments. FEMS Microbiol Ecol 2015; 91:1-12. [PMID: 25764557 DOI: 10.1093/femsec/fiv002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In aquatic systems, limited data exists on the impact of mortality forces such as viral lysis and flagellate grazing when seeking to explain factors regulating prokaryotic metabolism. We explored the relative influence of top-down factors (viral lysis and heterotrophic nanoflagellate grazing) on prokaryotic mortality and their subsequent impact on their community metabolism in the euphotic zone of 21 temperate freshwater lakes located in the French Massif Central. Prokaryotic growth efficiency (PGE, index of prokaryotic community metabolism) determined from prokaryotic production and respiration measurements varied from 5 to 74% across the lakes. Viral and potential grazer-induced mortality of prokaryotes had contrasting impact on PGE. Potential flagellate grazing was found to enhance PGE whereas viral lysis had antagonistic impacts on PGE. The average PGE value in the grazing and viral lysis dominated lake water samples was 35.4% (±15.2%) and 17.2% (±8.1%), respectively. Selective viral lysis or flagellate grazing on prokaryotes together with the nature of contrasted substrates released through mortality processes can perhaps explain for the observed variation and differences in PGE among the studied lakes. The influences of such specific top-down processes on PGE can have strong implications on the carbon and nutrient fluxes in freshwater pelagic environments.
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Affiliation(s)
- A S Pradeep Ram
- Laboratoire Microorganismes : Génome et Environnement, UMR CNRS 6023, Clermont Université, Université Blaise Pascal, BP 80026, 63171 Aubière Cedex, France
| | - Jonathan Colombet
- Laboratoire Microorganismes : Génome et Environnement, UMR CNRS 6023, Clermont Université, Université Blaise Pascal, BP 80026, 63171 Aubière Cedex, France
| | - Fanny Perriere
- Laboratoire Microorganismes : Génome et Environnement, UMR CNRS 6023, Clermont Université, Université Blaise Pascal, BP 80026, 63171 Aubière Cedex, France
| | - Antoine Thouvenot
- Athos Environnement, Université Blaise Pascal, BP 80026, 63171 Aubière Cedex, France
| | - Telesphore Sime-Ngando
- Laboratoire Microorganismes : Génome et Environnement, UMR CNRS 6023, Clermont Université, Université Blaise Pascal, BP 80026, 63171 Aubière Cedex, France
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Sime-Ngando T. Environmental bacteriophages: viruses of microbes in aquatic ecosystems. Front Microbiol 2014; 5:355. [PMID: 25104950 PMCID: PMC4109441 DOI: 10.3389/fmicb.2014.00355] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 06/25/2014] [Indexed: 11/29/2022] Open
Abstract
Since the discovery 2–3 decades ago that viruses of microbes are abundant in marine ecosystems, viral ecology has grown increasingly to reach the status of a full scientific discipline in environmental sciences. A dedicated ISVM society, the International Society for Viruses of Microorganisms, (http://www.isvm.org/) was recently launched. Increasing studies in viral ecology are sources of novel knowledge related to the biodiversity of living things, the functioning of ecosystems, and the evolution of the cellular world. This is because viruses are perhaps the most diverse, abundant, and ubiquitous biological entities in the biosphere, although local environmental conditions enrich for certain viral types through selective pressure. They exhibit various lifestyles that intimately depend on the deep-cellular mechanisms, and are ultimately replicated by members of all three domains of cellular life (Bacteria, Eukarya, Archaea), as well as by giant viruses of some eukaryotic cells. This establishes viral parasites as microbial killers but also as cell partners or metabolic manipulators in microbial ecology. The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e., phages) in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology.
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Affiliation(s)
- Télesphore Sime-Ngando
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Clermont Université Blaise Pascal Aubière, France
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