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Differential Effects of Viruses on the Growth Efficiency of Freshwater Bacterioplankton in Eutrophic Relative to Non-Eutrophic Lakes. Microorganisms 2023; 11:microorganisms11020384. [PMID: 36838349 PMCID: PMC9966266 DOI: 10.3390/microorganisms11020384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/04/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
In aquatic environments, the consensus of viral impact on bacterial carbon metabolism with the nutrient environment as an important axis is limited. Henceforth, we explored the viral regulation of carbon-based bacterial growth efficiency (BGE) in a set of freshwater systems from French Massif Central, which were broadly classified based on two trophic statuses: eutrophic and non-eutrophic lakes. Comparative analysis showed that microbial abundances (viruses and bacteria) were 3-fold higher in eutrophic compared with non-eutrophic lakes, and so were bacterial production and viral lytic infection. The observed variability in BGE (10-60%) was explained by the uncoupling between bacterial respiration and production. Viruses through selective lysis of susceptible host communities had an antagonistic impact on BGE in the eutrophic lakes, whereas the release of substrates via viral shunt exerted a synergistic influence on the carbon metabolism of non-targeted host populations in non-eutrophic lakes. The decisive effect of the two individual processes (i.e., lysis and substrate release) on BGE was supported by regressions of bacterial abundance as a function of bacterial production, which is considered as a proxy of top-down processes. The role of viruses through their negative impact via mortality and positive impact via substrate supply can eventually have implications on carbon transfer through bacterioplankton in freshwaters.
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2
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Wang X, Howe S, Deng F, Zhao J. Current Applications of Absolute Bacterial Quantification in Microbiome Studies and Decision-Making Regarding Different Biological Questions. Microorganisms 2021; 9:1797. [PMID: 34576694 PMCID: PMC8467167 DOI: 10.3390/microorganisms9091797] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/16/2021] [Accepted: 08/21/2021] [Indexed: 11/17/2022] Open
Abstract
High throughput sequencing has emerged as one of the most important techniques for characterizing microbial dynamics and revealing bacteria and host interactions. However, data interpretation using this technique is mainly based on relative abundance and ignores total bacteria load. In certain cases, absolute abundance is more important than compositional relative data, and interpretation of microbiota data based solely on relative abundance can be misleading. The available approaches for absolute quantification are highly diverse and challenging, especially for quantification in differing biological situations, such as distinguishing between live and dead cells, quantification of specific taxa, enumeration of low biomass samples, large sample size feasibility, and the detection of various other cellular features. In this review, we first illustrate the importance of integrating absolute abundance into microbiome data interpretation. Second, we briefly discuss the most widely used cell-based and molecular-based bacterial load quantification methods, including fluorescence spectroscopy, flow cytometry, 16S qPCR, 16S qRT-PCR, ddPCR, and reference spike-in. Last, we present a specific decision-making scheme for absolute quantification methods based on different biological questions and some of the latest quantitative methods and procedure modifications.
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Affiliation(s)
- Xiaofan Wang
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Samantha Howe
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Feilong Deng
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
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3
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Pradeep Ram AS, Keshri J, Sime-Ngando T. Differential impact of top-down and bottom-up forces in structuring freshwater bacterial communities. FEMS Microbiol Ecol 2020; 96:5700279. [PMID: 31922543 DOI: 10.1093/femsec/fiaa005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/09/2020] [Indexed: 01/21/2023] Open
Abstract
Limited data exist on the simultaneous impact of bottom-up (nutrients) and top-down (viruses and heterotrophic nanoflagellates) forces in shaping freshwater bacterial communities. In our laboratory microcosms, nutrient additions (organic and inorganic) and viral reduction approach led to the proliferation of high nucleic acid (HNA) bacterial subpopulation without an increase in phage abundance. High viral-mediated bacterial lysis in the presence of nanoflagellates yielded high proportion of low nucleic acid bacterial subpopulation. 16S rRNA gene sequence analysis indicated that members of classes Proteobacteria and Bacteroidetes evoked differential responses to nutrients and mortality forces, thereby resulting in differences (P < 0.001) in bacterial community composition and diversity, as observed from analysis of similarities and UniFrac analysis. Bacterial species richness (Chao) and diversity (Shannon) index was significantly higher (P < 0.001) in the presence of both the top-down factors and viruses alone, whereas lower host diversity was observed under nutrient relaxation of growth-limiting substrates due to the explosive growth of opportunistic HNA bacterial subpopulation. Our results are in agreement with the theoretical model of 'killing the winner', where the availability of growth-limiting substrates can act as a stimulating factor for host community composition while top-down forces can operate in the control of host diversity.
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Affiliation(s)
- A S Pradeep Ram
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, 63178 Aubière Cedex, France
| | - J Keshri
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, 63178 Aubière Cedex, France
| | - T Sime-Ngando
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, 63178 Aubière Cedex, France
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4
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Arkhipova K, Skvortsov T, Quinn JP, McGrath JW, Allen CC, Dutilh BE, McElarney Y, Kulakov LA. Temporal dynamics of uncultured viruses: a new dimension in viral diversity. ISME JOURNAL 2017; 12:199-211. [PMID: 29027998 DOI: 10.1038/ismej.2017.157] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/26/2017] [Accepted: 08/22/2017] [Indexed: 11/09/2022]
Abstract
Recent work has vastly expanded the known viral genomic sequence space, but the seasonal dynamics of viral populations at the genome level remain unexplored. Here we followed the viral community in a freshwater lake for 1 year using genome-resolved viral metagenomics, combined with detailed analyses of the viral community structure, associated bacterial populations and environmental variables. We reconstructed 8950 complete and partial viral genomes, the majority of which were not persistent in the lake throughout the year, but instead continuously succeeded each other. Temporal analysis of 732 viral genus-level clusters demonstrated that one-fifth were undetectable at specific periods of the year. Based on host predictions for a subset of reconstructed viral genomes, we for the first time reveal three distinct patterns of host-pathogen dynamics, where the viruses may peak before, during or after the peak in their host's abundance, providing new possibilities for modelling of their interactions. Time series metagenomics opens up a new dimension in viral profiling, which is essential to understand the full scale of viral diversity and evolution, and the ecological roles of these important factors in the global ecosystem.
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Affiliation(s)
- Ksenia Arkhipova
- School of Biological Sciences, The Queen's University of Belfast, Belfast, UK.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Timofey Skvortsov
- School of Biological Sciences, The Queen's University of Belfast, Belfast, UK.,Institute for Global Food Security, The Queen's University of Belfast, Belfast, UK
| | - John P Quinn
- School of Biological Sciences, The Queen's University of Belfast, Belfast, UK
| | - John W McGrath
- School of Biological Sciences, The Queen's University of Belfast, Belfast, UK.,Institute for Global Food Security, The Queen's University of Belfast, Belfast, UK
| | - Christopher Cr Allen
- School of Biological Sciences, The Queen's University of Belfast, Belfast, UK.,Institute for Global Food Security, The Queen's University of Belfast, Belfast, UK
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | | | - Leonid A Kulakov
- School of Biological Sciences, The Queen's University of Belfast, Belfast, UK
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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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Parikka KJ, Le Romancer M, Wauters N, Jacquet S. Deciphering the virus-to-prokaryote ratio (VPR): insights into virus-host relationships in a variety of ecosystems. Biol Rev Camb Philos Soc 2016; 92:1081-1100. [DOI: 10.1111/brv.12271] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 02/18/2016] [Accepted: 03/01/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Kaarle J. Parikka
- Laboratory of Microbiology of Extreme Environments; lnstitut Universitaire Européen de la Mer; Plouzané 29280 France
- LabMCT, Belgian Department of Defense; Queen Astrid Military Hospital; Brussels 1120 Belgium
| | - Marc Le Romancer
- Laboratory of Microbiology of Extreme Environments; lnstitut Universitaire Européen de la Mer; Plouzané 29280 France
| | - Nina Wauters
- Biological Evolution and Ecology; Université Libre de Bruxelles; Brussels 1050 Belgium
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Liu J, Hao Z, Ma L, Ji Y, Bartlam M, Wang Y. Spatio-Temporal Variations of High and Low Nucleic Acid Content Bacteria in an Exorheic River. PLoS One 2016; 11:e0153678. [PMID: 27082986 PMCID: PMC4833404 DOI: 10.1371/journal.pone.0153678] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 04/01/2016] [Indexed: 11/30/2022] Open
Abstract
Bacteria with high nucleic acid (HNA) and low nucleic acid (LNA) content are commonly observed in aquatic environments. To date, limited knowledge is available on their temporal and spatial variations in freshwater environments. Here an investigation of HNA and LNA bacterial abundance and their flow cytometric characteristics was conducted in an exorheic river (Haihe River, Northern China) over a one year period covering September (autumn) 2011, December (winter) 2011, April (spring) 2012, and July (summer) 2012. The results showed that LNA and HNA bacteria contributed similarly to the total bacterial abundance on both the spatial and temporal scale. The variability of HNA on abundance, fluorescence intensity (FL1) and side scatter (SSC) were more sensitive to environmental factors than that of LNA bacteria. Meanwhile, the relative distance of SSC between HNA and LNA was more variable than that of FL1. Multivariate analysis further demonstrated that the influence of geographical distance (reflected by the salinity gradient along river to ocean) and temporal changes (as temperature variation due to seasonal succession) on the patterns of LNA and HNA were stronger than the effects of nutrient conditions. Furthermore, the results demonstrated that the distribution of LNA and HNA bacteria, including the abundance, FL1 and SSC, was controlled by different variables. The results suggested that LNA and HNA bacteria might play different ecological roles in the exorheic river.
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Affiliation(s)
- Jie Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, Tianjin, China
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong, China
| | - Zhenyu Hao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Lili Ma
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, Tianjin, China
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, Sichuan, China
| | - Yurui Ji
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- College of Life Sciences, Nankai University, Tianjin, China
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, China
- * E-mail:
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8
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Bettarel Y, Motegi C, Weinbauer MG, Mari X. Colonization and release processes of viruses and prokaryotes on artificial marine macroaggregates. FEMS Microbiol Lett 2015; 363:fnv216. [DOI: 10.1093/femsle/fnv216] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2015] [Indexed: 11/12/2022] Open
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9
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Krupovic M, Forterre P. Single-stranded DNA viruses employ a variety of mechanisms for integration into host genomes. Ann N Y Acad Sci 2015; 1341:41-53. [PMID: 25675979 DOI: 10.1111/nyas.12675] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Single-stranded DNA (ssDNA) viruses are widespread in the environment and include economically, medically, and ecologically important pathogens. Recently, it has been discovered that ssDNA virus genomes are also prevalent in the chromosomes of their bacterial, archaeal, and eukaryotic hosts. Sequences originating from viruses of the families Parvoviridae, Circoviridae, and Geminiviridae are particularly widespread in the genomes of eukaryotes, where they are often fossilized as endogenous viral elements. ssDNA viruses have evolved diverse mechanisms to invade cellular genomes, and these principally vary between viruses infecting bacteria/archaea and eukaryotes. Filamentous bacteriophages (Inoviridae) use at least three major mechanisms of integration. Some of these phages encode integrases of serine or tyrosine recombinase superfamilies, while others utilize DDE transposases of the IS3, IS30, or IS110/IS492 families, whereas some inoviruses, and possibly certain members of the Microviridae, hijack the host XerCD recombination machinery. By contrast, eukaryotic viruses for integration rely on the endonuclease activity of their rolling-circle replication-initiation proteins, mimicking the mechanisms used by some bacterial transposons. Certain bacterial and eukaryotic ssDNA viruses have embraced a transposon-like means of propagation, with occasionally dramatic effects on host genome evolution. Here, we review the diversity of experimentally verified and hypothetical mechanisms of genome integration employed by ssDNA viruses, and consider the evolutionary implications of these processes, particularly in the emergence of novel virus groups.
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Affiliation(s)
- Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Paris, France
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10
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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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