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Listmann L, Peters C, Rahlff J, Esser SP, Schaum CE. Seasonality and Strain Specificity Drive Rapid Co-evolution in an Ostreococcus-Virus System from the Western Baltic Sea. MICROBIAL ECOLOGY 2023; 86:2414-2423. [PMID: 37268771 PMCID: PMC10640450 DOI: 10.1007/s00248-023-02243-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/16/2023] [Indexed: 06/04/2023]
Abstract
Marine viruses are a major driver of phytoplankton mortality and thereby influence biogeochemical cycling of carbon and other nutrients. Phytoplankton-targeting viruses are important components of ecosystem dynamics, but broad-scale experimental investigations of host-virus interactions remain scarce. Here, we investigated in detail a picophytoplankton (size 1 µm) host's responses to infections by species-specific viruses from distinct geographical regions and different sampling seasons. Specifically, we used Ostreococcus tauri and O. mediterraneus and their viruses (size ca. 100 nm). Ostreococcus sp. is globally distributed and, like other picoplankton species, play an important role in coastal ecosystems at certain times of the year. Further, Ostreococcus sp. is a model organism, and the Ostreococcus-virus system is well-known in marine biology. However, only few studies have researched its evolutionary biology and the implications thereof for ecosystem dynamics. The Ostreococcus strains used here stem from different regions of the Southwestern Baltic Sea that vary in salinity and temperature and were obtained during several cruises spanning different sampling seasons. Using an experimental cross-infection set-up, we explicitly confirm species and strain specificity in Ostreococcus sp. from the Baltic Sea. Moreover, we found that the timing of virus-host co-existence was a driver of infection patterns as well. In combination, these findings prove that host-virus co-evolution can be rapid in natural systems.
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Affiliation(s)
- Luisa Listmann
- Institute for Marine Ecosystem and Fisheries Science, University of Hamburg, Olbersweg 24, 22767, Hamburg, Germany.
- Centre for Earth System Science and Sustainability, 20146, Hamburg, Germany.
| | - Carina Peters
- Institute for Marine Ecosystem and Fisheries Science, University of Hamburg, Olbersweg 24, 22767, Hamburg, Germany
- Centre for Earth System Science and Sustainability, 20146, Hamburg, Germany
| | - Janina Rahlff
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Departement of Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39231, Kalmar, Sweden
| | - Sarah P Esser
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
| | - C-Elisa Schaum
- Institute for Marine Ecosystem and Fisheries Science, University of Hamburg, Olbersweg 24, 22767, Hamburg, Germany
- Centre for Earth System Science and Sustainability, 20146, Hamburg, Germany
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2
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Ha AD, Moniruzzaman M, Aylward FO. Assessing the biogeography of marine giant viruses in four oceanic transects. ISME COMMUNICATIONS 2023; 3:43. [PMID: 37120676 PMCID: PMC10148842 DOI: 10.1038/s43705-023-00252-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/01/2023]
Abstract
Viruses of the phylum Nucleocytoviricota are ubiquitous in ocean waters and play important roles in shaping the dynamics of marine ecosystems. In this study, we leveraged the bioGEOTRACES metagenomic dataset collected across the Atlantic and Pacific Oceans to investigate the biogeography of these viruses in marine environments. We identified 330 viral genomes, including 212 in the order Imitervirales and 54 in the order Algavirales. We found that most viruses appeared to be prevalent in shallow waters (<150 m), and that viruses of the Mesomimiviridae (Imitervirales) and Prasinoviridae (Algavirales) are by far the most abundant and diverse groups in our survey. Five mesomimiviruses and one prasinovirus are particularly widespread in oligotrophic waters; annotation of these genomes revealed common stress response systems, photosynthesis-associated genes, and oxidative stress modulation genes that may be key to their broad distribution in the pelagic ocean. We identified a latitudinal pattern in viral diversity in one cruise that traversed the North and South Atlantic Ocean, with viral diversity peaking at high latitudes of the northern hemisphere. Community analyses revealed three distinct Nucleocytoviricota communities across latitudes, categorized by latitudinal distance towards the equator. Our results contribute to the understanding of the biogeography of these viruses in marine systems.
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Affiliation(s)
- Anh D Ha
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA, 24061, USA
| | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA, 24061, USA.
- Center for Emerging, Zoonotic, and Arthropod-Borne Infectious Disease, Virginia Tech, Blacksburg, VA, 24061, USA.
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3
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Ha AD, Moniruzzaman M, Aylward FO. Assessing the biogeography of marine giant viruses in four oceanic transects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526306. [PMID: 36778472 PMCID: PMC9915497 DOI: 10.1101/2023.01.30.526306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Viruses of the phylum Nucleocytoviricota are ubiquitous in ocean waters and play important roles in shaping the dynamics of marine ecosystems. In this study, we leveraged the bioGEOTRACES metagenomic dataset collected across the Atlantic and Pacific Oceans to investigate the biogeography of these viruses in marine environments. We identified 330 viral genomes, including 212 in the order Imitervirales and 54 in the order Algavirales . We found that most viruses appeared to be prevalent in shallow waters (<150 meters), and that viruses of the Mesomimiviridae ( Imitervirales ) and Prasinoviridae ( Algavirales ) are by far the most abundant and diverse groups in our survey. Five mesomimiviruses and one prasinovirus are particularly widespread in oligotrophic waters; annotation of these genomes revealed common stress response systems, photosynthesis-associated genes, and oxidative stress modulation that may be key to their broad distribution in the pelagic ocean. We identified a latitudinal pattern in viral diversity in one cruise that traversed the North and South Atlantic Ocean, with viral diversity peaking at high latitudes of the northern hemisphere. Community analyses revealed three distinct Nucleocytoviricota communities across latitudes, categorized by latitudinal distance towards the equator. Our results contribute to the understanding of the biogeography of these viruses in marine systems.
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Affiliation(s)
- Anh D. Ha
- Department of Biological Sciences, Virginia Tech, Blacksburg VA, 24061
| | - Mohammad Moniruzzaman
- Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Coral Gables FL 33149
| | - Frank O. Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg VA, 24061
- Center for Emerging, Zoonotic, and Arthropod-Borne Infectious Disease, Virginia Tech, Blacksburg VA, 24061
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4
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Diversity and Evolution of Mamiellophyceae: Early-Diverging Phytoplanktonic Green Algae Containing Many Cosmopolitan Species. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10020240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The genomic revolution has bridged a gap in our knowledge about the diversity, biology and evolution of unicellular photosynthetic eukaryotes, which bear very few discriminating morphological features among species from the same genus. The high-quality genome resources available in the class Mamiellophyceae (Chlorophyta) have been paramount to estimate species diversity and screen available metagenomic data to assess the biogeography and ecological niches of different species on a global scale. Here we review the current knowledge about the diversity, ecology and evolution of the Mamiellophyceae and the large double-stranded DNA prasinoviruses infecting them, brought by the combination of genomic and metagenomic analyses, including 26 metabarcoding environmental studies, as well as the pan-oceanic GOS and the Tara Oceans expeditions.
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5
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Gann ER, Kang Y, Dyhrman ST, Gobler CJ, Wilhelm SW. Metatranscriptome Library Preparation Influences Analyses of Viral Community Activity During a Brown Tide Bloom. Front Microbiol 2021; 12:664189. [PMID: 34135876 PMCID: PMC8200674 DOI: 10.3389/fmicb.2021.664189] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/16/2021] [Indexed: 11/13/2022] Open
Abstract
There is growing interest in the use of metatranscriptomics to study virus community dynamics. We used RNA samples collected from harmful brown tides caused by the eukaryotic alga Aureococcus anophagefferens within New York (United States) estuaries and in the process observed how preprocessing of libraries by either selection for polyadenylation or reduction in ribosomal RNA (rRNA) influenced virus community analyses. As expected, more reads mapped to the A. anophagefferens genome in polyadenylation-selected libraries compared to the rRNA-reduced libraries, with reads mapped in each sample correlating to one another regardless of preprocessing of libraries. Yet, this trend was not seen for reads mapping to the Aureococcus anophagefferens Virus (AaV), where significantly more reads (approximately two orders of magnitude) were mapped to the AaV genome in the rRNA-reduced libraries. In the rRNA-reduced libraries, there was a strong and significant correlation between reads mappings to AaV and A. anophagefferens. Overall, polyadenylation-selected libraries produced fewer viral contigs, fewer reads mapped to viral contigs, and different proportions across viral realms and families, compared to their rRNA-reduced pairs. This study provides evidence that libraries generated by rRNA reduction and not selected for polyadenylation are more appropriate for quantitative characterization of viral communities in aquatic ecosystems by metatranscriptomics.
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Affiliation(s)
- Eric R Gann
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Yoonja Kang
- Department of Ocean Integrated Science, School of Marine Technology, Chonnam National University, Yeosu, South Korea
| | - Sonya T Dyhrman
- Biology and Paleo Environment Division, Lamont-Doherty Earth Observatory, Columbia University, New York, NY, United States.,Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
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Dong X, Sun S, Jia R, Xu L, Hou W, Lu N, Wang M, Zhao Q, Hou L. Effects of Sulfamethoxazole Exposure on the Growth, Antioxidant System of Chlorella vulgaris and Microcystis aeruginosa. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2020; 105:358-365. [PMID: 32740748 DOI: 10.1007/s00128-020-02952-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/24/2020] [Indexed: 06/11/2023]
Abstract
Sulfamethoxazole (SMZ) is a kind of sulfonamides antibiotic, which is widely used in human life. This study investigated the effects of SMZ on physiological and biochemical indexes of Chlorella vulgaris (C. vulgaris) and Microcystis aeruginosa (M. aeruginosa) for 35-day. The results showed that SMZ inhibited the growth and Chl-a content of C. vulgaris and M. aeruginosa, and growth inhibition rate was 8.06%-95.86%, Chl-a content decreased 2.44%-98.04%. SMZ resulting in increased SOD and CAT activity and destroyed the dynamic balance of antioxidant system. In addition, SMZ increased the content of malondialdehyde (MDA) in algae, destroyed the cell membrane to a certain extent, which was 1.8-7.3 folds higher than the control group. High concentration of SMZ can make algae cells exceed the limit of cell antioxidant capacity. Coupled with the serious damage of cell membrane, algae cells begin to appear a large number of death phenomenon.
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Affiliation(s)
- Xiaotong Dong
- School of Water Conservancy and Environment, University of Jinan, Jinan, 250022, People's Republic of China
- Shandong(Jinan) Water & Waste Water Monitoring Center, Jinan, 250101, People's Republic of China
| | - Shaohua Sun
- Shandong(Jinan) Water & Waste Water Monitoring Center, Jinan, 250101, People's Republic of China.
| | - Ruibao Jia
- Shandong(Jinan) Water & Waste Water Monitoring Center, Jinan, 250101, People's Republic of China
| | - Lirong Xu
- School of Water Conservancy and Environment, University of Jinan, Jinan, 250022, People's Republic of China
| | - Wei Hou
- Shandong(Jinan) Water & Waste Water Monitoring Center, Jinan, 250101, People's Republic of China
| | - Nannan Lu
- Shandong(Jinan) Water & Waste Water Monitoring Center, Jinan, 250101, People's Republic of China
| | - Mingquan Wang
- Shandong(Jinan) Water & Waste Water Monitoring Center, Jinan, 250101, People's Republic of China
| | - Qinghua Zhao
- Shandong(Jinan) Water & Waste Water Monitoring Center, Jinan, 250101, People's Republic of China
| | - Li'an Hou
- Institute for Logistic Science and Technology of the PLA Rocket Force, Beijing, 100011, People's Republic of China
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7
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Zimmerman AE, Bachy C, Ma X, Roux S, Jang HB, Sullivan MB, Waldbauer JR, Worden AZ. Closely related viruses of the marine picoeukaryotic alga Ostreococcus lucimarinus exhibit different ecological strategies. Environ Microbiol 2019; 21:2148-2170. [PMID: 30924271 PMCID: PMC6851583 DOI: 10.1111/1462-2920.14608] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/16/2019] [Accepted: 03/23/2019] [Indexed: 01/01/2023]
Abstract
In marine ecosystems, viruses are major disrupters of the direct flow of carbon and nutrients to higher trophic levels. Although the genetic diversity of several eukaryotic phytoplankton virus groups has been characterized, their infection dynamics are less understood, such that the physiological and ecological implications of their diversity remain unclear. We compared genomes and infection phenotypes of the two most closely related cultured phycodnaviruses infecting the widespread picoprasinophyte Ostreococcus lucimarinus under standard- (1.3 divisions per day) and limited-light (0.41 divisions per day) nutrient replete conditions. OlV7 infection caused early arrest of the host cell cycle, coinciding with a significantly higher proportion of infected cells than OlV1-amended treatments, regardless of host growth rate. OlV7 treatments showed a near-50-fold increase of progeny virions at the higher host growth rate, contrasting with OlV1's 16-fold increase. However, production of OlV7 virions was more sensitive than OlV1 production to reduced host growth rate, suggesting fitness trade-offs between infection efficiency and resilience to host physiology. Moreover, although organic matter released from OlV1- and OlV7-infected hosts had broadly similar chemical composition, some distinct molecular signatures were observed. Collectively, these results suggest that current views on viral relatedness through marker and core gene analyses underplay operational divergence and consequences for host ecology.
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Affiliation(s)
| | - Charles Bachy
- Monterey Bay Aquarium Research InstituteMoss LandingCAUSA
| | - Xiufeng Ma
- Department of the Geophysical SciencesUniversity of ChicagoChicagoILUSA
| | - Simon Roux
- Department of MicrobiologyEnvironmental and Geodetic Engineering, The Ohio State UniversityColumbusOHUSA
| | - Ho Bin Jang
- Department of MicrobiologyEnvironmental and Geodetic Engineering, The Ohio State UniversityColumbusOHUSA
- Department of CivilEnvironmental and Geodetic Engineering, The Ohio State UniversityColumbusOHUSA
| | - Matthew B. Sullivan
- Department of MicrobiologyEnvironmental and Geodetic Engineering, The Ohio State UniversityColumbusOHUSA
- Department of CivilEnvironmental and Geodetic Engineering, The Ohio State UniversityColumbusOHUSA
| | | | - Alexandra Z. Worden
- Monterey Bay Aquarium Research InstituteMoss LandingCAUSA
- Ocean EcoSystems Biology Unit, Marine Ecology DivisionGEOMAR Helmholtz Centre for Ocean Research KielKielDE
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8
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Abstract
Viruses infect all kingdoms of marine life from bacteria to whales. Viruses in the world's oceans play important roles in the mortality of phytoplankton, and as drivers of evolution and biogeochemical cycling. They shape host population abundance and distribution and can lead to the termination of algal blooms. As discoveries about this huge reservoir of genetic and biological diversity grow, our understanding of the major influences viruses exert in the global marine environment continues to expand. This chapter discusses the key discoveries that have been made to date about marine viruses and the current direction of this field of research.
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Affiliation(s)
- Karen D Weynberg
- School of Chemistry & Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia.
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Weynberg KD, Allen MJ, Wilson WH. Marine Prasinoviruses and Their Tiny Plankton Hosts: A Review. Viruses 2017; 9:E43. [PMID: 28294997 PMCID: PMC5371798 DOI: 10.3390/v9030043] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/04/2017] [Accepted: 03/08/2017] [Indexed: 12/29/2022] Open
Abstract
Viruses play a crucial role in the marine environment, promoting nutrient recycling and biogeochemical cycling and driving evolutionary processes. Tiny marine phytoplankton called prasinophytes are ubiquitous and significant contributors to global primary production and biomass. A number of viruses (known as prasinoviruses) that infect these important primary producers have been isolated and characterised over the past decade. Here we review the current body of knowledge about prasinoviruses and their interactions with their algal hosts. Several genes, including those encoding for glycosyltransferases, methyltransferases and amino acid synthesis enzymes, which have never been identified in viruses of eukaryotes previously, have been detected in prasinovirus genomes. The host organisms are also intriguing; most recently, an immunity chromosome used by a prasinophyte in response to viral infection was discovered. In light of such recent, novel discoveries, we discuss why the cellular simplicity of prasinophytes makes for appealing model host organism-virus systems to facilitate focused and detailed investigations into the dynamics of marine viruses and their intimate associations with host species. We encourage the adoption of the prasinophyte Ostreococcus and its associated viruses as a model host-virus system for examination of cellular and molecular processes in the marine environment.
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Affiliation(s)
- Karen D Weynberg
- Australian Institute of Marine Science, PMB 3, Townsville, Queensland 4810, Australia.
| | - Michael J Allen
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK.
| | - William H Wilson
- Sir Alister Hardy Foundation for Ocean Science, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK.
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10
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Clerissi C, Desdevises Y, Romac S, Audic S, de Vargas C, Acinas SG, Casotti R, Poulain J, Wincker P, Hingamp P, Ogata H, Grimsley N. Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:979-989. [PMID: 26472079 DOI: 10.1111/1758-2229.12345] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 10/08/2015] [Accepted: 10/08/2015] [Indexed: 06/05/2023]
Abstract
High-throughput sequencing of Prasinovirus DNA polymerase and host green algal (Mamiellophyceae) ribosomal RNA genes was used to analyse the diversity and distribution of these taxa over a ∼10 000 km latitudinal section of the Indian Ocean. New viral and host groups were identified among the different trophic conditions observed, and highlighted that although unknown prasinoviruses are diverse, the cosmopolitan algal genera Bathycoccus, Micromonas and Ostreococcus represent a large proportion of the host diversity. While Prasinovirus communities were correlated to both the geography and the environment, host communities were not, perhaps because the genetic marker used lacked sufficient resolution. Nevertheless, analysis of single environmental variables showed that eutrophic conditions strongly influence the distributions of both hosts and viruses. Moreover, these communities were not correlated, in their composition or specific richness. These observations could result from antagonistic dynamics, such as that illustrated in a prey-predator model, and/or because hosts might be under a complex set of selective pressures. Both of these reasons must be considered to interpret environmental surveys of viruses and hosts, because covariation does not always imply interaction.
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Affiliation(s)
- Camille Clerissi
- Observatoire Océanologique, Sorbonne Universités, UPMC Univ Paris 06, Avenue du Fontaulé, 66650, Banyuls-sur-Mer, France
- Biologie Intégrative des Organismes Marins, CNRS, UMR 7232, Avenue du Fontaulé, 66650, Banyuls-sur-Mer, France
| | - Yves Desdevises
- Observatoire Océanologique, Sorbonne Universités, UPMC Univ Paris 06, Avenue du Fontaulé, 66650, Banyuls-sur-Mer, France
- Biologie Intégrative des Organismes Marins, CNRS, UMR 7232, Avenue du Fontaulé, 66650, Banyuls-sur-Mer, France
| | - Sarah Romac
- Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
- Equipe Evolution du Plancton et Paleo-Ocean, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Stéphane Audic
- Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
- Equipe Evolution du Plancton et Paleo-Ocean, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Colomban de Vargas
- Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
- Equipe Evolution du Plancton et Paleo-Ocean, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Science (ICM), CSIC, Pg Marítim de la Barceloneta 37-49, Barcelona, Spain
| | - Raffaella Casotti
- Stazione Zoologica, Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Julie Poulain
- CEA, Institut de Génomique, Génoscope, 2 Rue Gaston Crémieux, BP5706, Evry, 91057, France
| | - Patrick Wincker
- CEA, Institut de Génomique, Génoscope, 2 Rue Gaston Crémieux, BP5706, Evry, 91057, France
| | - Pascal Hingamp
- CNRS, Université Aix-Marseille, Laboratoire Information Génomique et Structurale (UMR 7256), Mediterranean Institute of Microbiology (FR 3479), 13288, Marseille, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Kyoto, 611-0011, Japan
| | - Nigel Grimsley
- Observatoire Océanologique, Sorbonne Universités, UPMC Univ Paris 06, Avenue du Fontaulé, 66650, Banyuls-sur-Mer, France
- Biologie Intégrative des Organismes Marins, CNRS, UMR 7232, Avenue du Fontaulé, 66650, Banyuls-sur-Mer, France
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11
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Diversity of Viruses Infecting the Green Microalga Ostreococcus lucimarinus. J Virol 2015; 89:5812-21. [PMID: 25787287 DOI: 10.1128/jvi.00246-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 03/06/2015] [Indexed: 01/10/2023] Open
Abstract
UNLABELLED The functional diversity of eukaryotic viruses infecting a single host strain from seawater samples originating from distant marine locations is unknown. To estimate this diversity, we used lysis plaque assays to detect viruses that infect the widespread species Ostreococcus lucimarinus, which is found in coastal and mesotrophic systems, and O. tauri, which was isolated from coastal and lagoon sites from the northwest Mediterranean Sea. Detection of viral lytic activities against O. tauri was not observed using seawater from most sites, except those close to the area where the host strain was isolated. In contrast, the more cosmopolitan O. lucimarinus species recovered viruses from locations in the Atlantic and Pacific Oceans and the Mediterranean Sea. Six new O. lucimarinus viruses (OlVs) then were characterized and their genomes sequenced. Two subgroups of OlVs were distinguished based on their genetic distances and on the inversion of a central 32-kb-long DNA fragment, but overall their genomes displayed a high level of synteny. The two groups did not correspond to proximity of isolation sites, and the phylogenetic distance between these subgroups was higher than the distances observed among viruses infecting O. tauri. Our study demonstrates that viruses originating from very distant sites are able to infect the same algal host strain and can be more diverse than those infecting different species of the same genus. Finally, distinctive features and evolutionary distances between these different viral subgroups does not appear to be linked to biogeography of the viral isolates. IMPORTANCE Marine eukaryotic phytoplankton virus diversity has yet to be addressed, and more specifically, it is unclear whether diversity is connected to geographical distance and whether differential infection and lysis patterns exist among such viruses that infect the same host strain. Here, we assessed the genetic distance of geographically segregated viruses that infect the ubiquitous green microalga Ostreococcus. This study provides the first glimpse into the diversity of predicted gene functions in Ostreococcus viruses originating from distant sites and provides new insights into potential host distributions and restrictions in the world oceans.
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12
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Clerissi C, Grimsley N, Subirana L, Maria E, Oriol L, Ogata H, Moreau H, Desdevises Y. Prasinovirus distribution in the Northwest Mediterranean Sea is affected by the environment and particularly by phosphate availability. Virology 2014; 466-467:146-57. [PMID: 25109909 DOI: 10.1016/j.virol.2014.07.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 05/13/2014] [Accepted: 07/08/2014] [Indexed: 10/24/2022]
Abstract
Numerous seawater lagoons punctuate the southern coastline of France. Exchanges of seawater between these lagoons and the open sea are limited by narrow channels connecting them. Lagoon salinities vary according to evaporation and to the volume of freshwater arriving from influent streams, whose nutrients also promote the growth of algae. We compared Prasinovirus communities, whose replication is supported by microscopic green algae, in four lagoons and at a coastal sampling site. Using high-throughput sequencing of DNA from a giant virus-specific marker gene, we show that the environmental conditions significantly affect the types of detectable viruses across samples. In spatial comparisons between 5 different sampling sites, higher levels of phosphates, nitrates, nitrites, ammonium and silicates tend to increase viral community richness independently of geographical distances between the sampling sites. Finally, comparisons of Prasinovirus communities at 2 sampling sites over a period of 10 months highlighted seasonal effects and the preponderant nature of phosphate concentrations in constraining viral distribution.
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Affiliation(s)
- Camille Clerissi
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7232, Biologie Intégrative des Organismes Marin, Observatoire Océanologique, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France; Sorbonne Universités, CNRS, UMR 7232, Observatoire Océanologique, Biologie Intégrative des Organismes Marins, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France
| | - Nigel Grimsley
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7232, Biologie Intégrative des Organismes Marin, Observatoire Océanologique, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France; Sorbonne Universités, CNRS, UMR 7232, Observatoire Océanologique, Biologie Intégrative des Organismes Marins, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France.
| | - Lucie Subirana
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7232, Biologie Intégrative des Organismes Marin, Observatoire Océanologique, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France; Sorbonne Universités, CNRS, UMR 7232, Observatoire Océanologique, Biologie Intégrative des Organismes Marins, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France
| | - Eric Maria
- Sorbonne Universités, UPMC Univ Paris 06, UMS 2348, Observatoire Océanologique, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France
| | - Louise Oriol
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7621, Laboratoire d׳Océanographie Microbienne, Observatoire Océanologique, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France; Sorbonne Universités, CNRS, UMR 7621, Observatoire Océanologique, Laboratoire d׳Océanographie Microbienne, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hervé Moreau
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7232, Biologie Intégrative des Organismes Marin, Observatoire Océanologique, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France; Sorbonne Universités, CNRS, UMR 7232, Observatoire Océanologique, Biologie Intégrative des Organismes Marins, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France
| | - Yves Desdevises
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7232, Biologie Intégrative des Organismes Marin, Observatoire Océanologique, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France; Sorbonne Universités, CNRS, UMR 7232, Observatoire Océanologique, Biologie Intégrative des Organismes Marins, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France
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13
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Bellec L, Clerissi C, Edern R, Foulon E, Simon N, Grimsley N, Desdevises Y. Cophylogenetic interactions between marine viruses and eukaryotic picophytoplankton. BMC Evol Biol 2014; 14:59. [PMID: 24669847 PMCID: PMC3983898 DOI: 10.1186/1471-2148-14-59] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 03/20/2014] [Indexed: 01/10/2023] Open
Abstract
Background Numerous studies have investigated cospeciation (or cophylogeny) in various host-symbiont systems, and different patterns were inferred, from strict cospeciation where symbiont phylogeny mirrors host phylogeny, to complete absence of correspondence between trees. The degree of cospeciation is generally linked to the level of host specificity in the symbiont species and the opportunity they have to switch hosts. In this study, we investigated cophylogeny for the first time in a microalgae-virus association in the open sea, where symbionts are believed to be highly host-specific but have wide opportunities to switch hosts. We studied prasinovirus-Mamiellales associations using 51 different viral strains infecting 22 host strains, selected from the characterisation and experimental testing of the specificities of 313 virus strains on 26 host strains. Results All virus strains were restricted to their host genus, and most were species-specific, but some of them were able to infect different host species within a genus. Phylogenetic trees were reconstructed for viruses and their hosts, and their congruence was assessed based on these trees and the specificity data using different cophylogenetic methods, a topology-based approach, Jane, and a global congruence method, ParaFit. We found significant congruence between virus and host trees, but with a putatively complex evolutionary history. Conclusions Mechanisms other than true cospeciation, such as host-switching, might explain a part of the data. It has been observed in a previous study on the same taxa that the genomic divergence between host pairs is larger than between their viruses. It implies that if cospeciation predominates in this algae-virus system, this would support the hypothesis that prasinoviruses evolve more slowly than their microalgal hosts, whereas host switching would imply that these viruses speciated more recently than the divergence of their host genera.
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Affiliation(s)
| | | | | | | | | | | | - Yves Desdevises
- Integrative Biology of Marine Organisms, Observatoire Océanologique, Sorbonne Universités, UPMC Univ Paris 06, UMR 7232, F-66650 Banyuls-sur-Mer, France.
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14
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Unveiling of the diversity of Prasinoviruses (Phycodnaviridae) in marine samples by using high-throughput sequencing analyses of PCR-amplified DNA polymerase and major capsid protein genes. Appl Environ Microbiol 2014; 80:3150-60. [PMID: 24632251 DOI: 10.1128/aem.00123-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viruses strongly influence the ecology and evolution of their eukaryotic hosts in the marine environment, but little is known about their diversity and distribution. Prasinoviruses infect an abundant and widespread class of phytoplankton, the Mamiellophyceae, and thereby exert a specific and important role in microbial ecosystems. However, molecular tools to specifically identify this viral genus in environmental samples are still lacking. We developed two primer sets, designed for use with polymerase chain reactions and 454 pyrosequencing technologies, to target two conserved genes, encoding the DNA polymerase (PolB gene) and the major capsid protein (MCP gene). While only one copy of the PolB gene is present in Prasinovirus genomes, there are at least seven paralogs for MCP, the copy we named number 6 being shared with other eukaryotic alga-infecting viruses. Primer sets for PolB and MCP6 were thus designed and tested on 6 samples from the Tara Oceans project. The results suggest that the MCP6 amplicons show greater richness but that PolB gave a wider coverage of Prasinovirus diversity. As a consequence, we recommend use of the PolB primer set, which will certainly reveal exciting new insights about the diversity and distribution of prasinoviruses at the community scale.
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15
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Michely S, Toulza E, Subirana L, John U, Cognat V, Maréchal-Drouard L, Grimsley N, Moreau H, Piganeau G. Evolution of codon usage in the smallest photosynthetic eukaryotes and their giant viruses. Genome Biol Evol 2013; 5:848-59. [PMID: 23563969 PMCID: PMC3673656 DOI: 10.1093/gbe/evt053] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Prasinoviruses are among the largest viruses (>200 kb) and encode several hundreds of
protein coding genes, including most genes of the DNA replication machinery and several
genes involved in transcription and translation, as well as transfer RNAs (tRNAs). They
can infect and lyse small eukaryotic planktonic marine green algae, thereby affecting
global algal population dynamics. Here, we investigate the causes of codon usage bias
(CUB) in one prasinovirus, OtV5, and its host Ostreococcus tauri, during
a viral infection using microarray expression data. We show that 1) CUB in the host and in
the viral genes increases with expression levels and 2) optimal codons use those tRNAs
encoded by the most abundant host tRNA genes, supporting the notion of translational
optimization by natural selection. We find evidence that viral tRNA genes complement the
host tRNA pool for those viral amino acids whose host tRNAs are in short supply. We
further discuss the coevolution of CUB in hosts and prasinoviruses by comparing optimal
codons in three evolutionary diverged host–virus-specific pairs whose complete
genome sequences are known.
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Affiliation(s)
- Stephanie Michely
- UPMC Univ Paris 06, UMR7232, BIOM, Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
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16
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Manrique JM, Jones LR. Genetic data generated from virus-host complexes obtained by membrane co-immobilization are equivalent to data obtained from tangential filtrate virus concentrates and virus cultures. Virus Genes 2013; 48:160-7. [PMID: 24166738 DOI: 10.1007/s11262-013-0999-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 10/16/2013] [Indexed: 10/26/2022]
Abstract
The sieving and immobilization of virus-host complexes using impact filtration (aka membrane co-immobilization or MCI) is a novel approach to the study of plankton viruses. One of the most interesting characteristics of the method is the possibility of generating data on potential viral hosts without the need of culturing hosts cells. MCI has demonstrated to be useful for studying viruses of picoalgae, but studies comparing data generated by MCI to data obtained by other techniques are lacking. In this work, Ostreococcus virus (OV) and Ostreococcus sp. sequences generated from virus-host complexes obtained by MCI were compared to sequences obtained from tangential filtration (TF) concentrates and virus cultures (VC). Statistical parsimony, phylogenetic analyses, pairwise distance comparisons, and analysis of molecular variance showed that the viral and host sequences obtained by the three methods were highly related to each other, indicating that MCI, TF, and VC produce equivalent results. Minor differences were observed among viral sequences obtained from VC and TF concentrates as well as among host sequences generated from VC and MCI. As discussed in the body of the paper, the divergence observed for cultured cells could be due to selective pressures exerted by culture conditions, whereas the correlate observed for the corresponding viral sequences could obey to a hitchhiking effect.
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Affiliation(s)
- J M Manrique
- Laboratory of Virology and Molecular Genetics, Faculty of Natural Sciences, Trelew seat, National University of Patagonia "San Juan Bosco", Av. 9 de Julio 25, 9100, Trelew, Chubut, Argentina
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17
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Clerissi C, Grimsley N, Desdevises Y. GENETIC EXCHANGES OF INTEINS BETWEENPRASINOVIRUSES(PHYCODNAVIRIDAE). Evolution 2012; 67:18-33. [DOI: 10.1111/j.1558-5646.2012.01738.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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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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19
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Abstract
Because viruses of eukaryotic algae are incredibly diverse, sweeping generalizations about their ecology are rare. These obligate parasites infect a range of algae and their diversity can be illustrated by considering that isolates range from small particles with ssRNA genomes to much larger particles with 560 kb dsDNA genomes. Molecular research has also provided clues about the extent of their diversity especially considering that genetic signatures of algal viruses in the environment rarely match cultivated viruses. One general concept in algal virus ecology that has emerged is that algal viruses are very host specific and most infect only certain strains of their hosts; with the exception of viruses of brown algae, evidence for interspecies infectivity is lacking. Although some host-virus systems behave with boom-bust oscillations, complex patterns of intraspecies infectivity can lead to host-virus coexistence obfuscating the role of viruses in host population dynamics. Within the framework of population dynamics, host density dependence is an important phenomenon that influences virus abundances in nature. Variable burst sizes of different viruses also influence their abundances and permit speculations about different life strategies, but as exceptions are common in algal virus ecology, life strategy generalizations may not be broadly applicable. Gaps in knowledge of virus seasonality and persistence are beginning to close and investigations of environmental reservoirs and virus resilience may answer questions about virus inter-annual recurrences. Studies of algal mortality have shown that viruses are often important agents of mortality reinforcing notions about their ecological relevance, while observations of the surprising ways viruses interact with their hosts highlight the immaturity of our understanding. Considering that just two decades ago algal viruses were hardly acknowledged, recent progress affords the optimistic perspective that future studies will provide keys to unlocking our understanding of algal virus ecology specifically, and aquatic ecosystems generally.
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Affiliation(s)
- Steven M Short
- Department of Biology, University of Toronto Mississauga, Mississauga, Canada.
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Prasinoviruses of the marine green alga Ostreococcus tauri are mainly species specific. J Virol 2012; 86:4611-9. [PMID: 22318150 DOI: 10.1128/jvi.07221-11] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Prasinoviruses infecting unicellular green algae in the order Mamiellales (class Mamiellophyceae) are commonly found in coastal marine waters where their host species frequently abound. We tested 40 Ostreococcus tauri viruses on 13 independently isolated wild-type O. tauri strains, 4 wild-type O. lucimarinus strains, 1 Ostreococcus sp. ("Ostreococcus mediterraneus") clade D strain, and 1 representative species of each of two other related species of Mamiellales, Bathycoccus prasinos and Micromonas pusilla. Thirty-four out of 40 viruses infected only O. tauri, 5 could infect one other species of the Ostreococcus genus, and 1 infected two other Ostreococcus spp., but none of them infected the other genera. We observed that the overall susceptibility pattern of Ostreococcus strains to viruses was related to the size of two host chromosomes known to show intraspecific size variations, that genetically related viruses tended to infect the same host strains, and that viruses carrying inteins were strictly strain specific. Comparison of two complete O. tauri virus proteomes revealed at least three predicted proteins to be candidate viral specificity determinants.
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21
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Bellec L, Grimsley N, Derelle E, Moreau H, Desdevises Y. Abundance, spatial distribution and genetic diversity of Ostreococcus tauri viruses in two different environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2010; 2:313-21. [PMID: 23766083 DOI: 10.1111/j.1758-2229.2010.00138.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Although large DNA viruses of eukaryotic algae represent a major force in shaping populations of plankton, knowledge about them is often limited to their overall diversity, abundance, and the flux of their constituent matter between ecosystem compartments. In order to gain insight about the genetics and structure of such populations, we used an easily cultivable model unicellular algal species, Ostreococcus tauri (Prasinophyceae), to monitor and compare populations of viruses in different marine environments. The abundance of O. tauri viruses showed very large temporal fluctuations, but remarkably was more than two orders of magnitude higher in lagoons than in coastal waters. We analysed 161 individual viruses found after plating out for lysis plaques on the host during a time series of water samplings. The haplotypes of viruses infecting our host strain were determined by sequence analysis of the partial DNA polymerase gene, permitting a spatiotemporal analysis of their population structure. We found 48 haplotypes, only the two most abundant ones being shared among all of the three study sites (lagoon, coastal and offshore), supporting the hypothesis that there is great diversity among the viruses infecting one host strain. However, our data suggest that the population structure differ between lagoons and coastal sea.
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Affiliation(s)
- Laure Bellec
- UPMC Univ Paris 06 and CNRS, UMR 7621, Observatoire océanologique, 66650, Banyuls-sur-Mer, France
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22
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DaPalma T, Doonan BP, Trager NM, Kasman LM. A systematic approach to virus-virus interactions. Virus Res 2010; 149:1-9. [PMID: 20093154 PMCID: PMC7172858 DOI: 10.1016/j.virusres.2010.01.002] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2009] [Revised: 01/02/2010] [Accepted: 01/06/2010] [Indexed: 02/02/2023]
Abstract
A virus–virus interaction is a measurable difference in the course of infection of one virus as a result of a concurrent or prior infection by a different species or strain of virus. Many such interactions have been discovered by chance, yet they have rarely been studied systematically. Increasing evidence suggests that virus–virus interactions are common and may be critical to understanding viral pathogenesis in natural hosts. In this review we propose a system for classifying virus–virus interactions by organizing them into three main categories: (1) direct interactions of viral genes or gene products, (2) indirect interactions that result from alterations in the host environment, and (3) immunological interactions. We have so far identified 15 subtypes of interaction and assigned each to one of these categories. It is anticipated that this framework will provide for a more systematic approach to investigating virus–virus interactions, both at the cellular and organismal levels.
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Affiliation(s)
- T DaPalma
- Dept. of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425, United States
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