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Matos-Hernández ML, Samples R, Dyer G, Casimir Montán VM, Morales-Colón CA, Salvino JM, Montaner LJ, Cassel JA, Messick TE, Tietjen I, Caro-Diaz EJE. Metabolomic Analysis and Antiviral Screening of a Marine Algae Library Yield Jobosic Acid (2,5-Dimethyltetradecanoic Acid) as a Selective Inhibitor of SARS-CoV-2. JOURNAL OF NATURAL PRODUCTS 2024; 87:1513-1520. [PMID: 38781491 DOI: 10.1021/acs.jnatprod.3c01071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Current small-molecule-based SARS-CoV-2 treatments have limited global accessibility and pose the risk of inducing viral resistance. Therefore, a marine algae and cyanobacteria extract library was screened for natural products that could inhibit two well-defined and validated COVID-19 drug targets, disruption of the spike protein/ACE-2 interaction and the main protease (Mpro) of SARS-CoV-2. Following initial screening of 86 extracts, we performed an untargeted metabolomic analysis of 16 cyanobacterial extracts. This approach led to the isolation of an unusual saturated fatty acid, jobosic acid (2,5-dimethyltetradecanoic acid, 1). We confirmed that 1 demonstrated selective inhibitory activity toward both viral targets while retaining some activity against the spike-RBD/ACE-2 interaction of the SARS-CoV-2 omicron variant. To initially explore its structure-activity relationship (SAR), the methyl and benzyl ester derivatives of 1 were semisynthetically accessed and demonstrated acute loss of bioactivity in both SARS-CoV-2 biochemical assays. Our efforts have provided copious amounts of a fatty acid natural product that warrants further investigation in terms of SAR, unambiguous determination of its absolute configuration, and understanding of its specific mechanisms of action and binding site toward new therapeutic avenues for SARS-CoV-2 drug development.
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Affiliation(s)
- Marie L Matos-Hernández
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico 00935, United States
| | - Robert Samples
- Center for Mass Spectrometry, Smith College, Northampton, Massachusetts 01063, United States
| | - Grayce Dyer
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico 00935, United States
| | - Victoria M Casimir Montán
- Department of Chemistry, Natural Sciences College, University of Puerto Rico-Rio Piedras Campus, San Juan, Puerto Rico 00925, United States
| | - Chris A Morales-Colón
- Department of Chemistry, Natural Sciences College, University of Puerto Rico-Rio Piedras Campus, San Juan, Puerto Rico 00925, United States
| | - Joseph M Salvino
- The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Luis J Montaner
- The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Joel A Cassel
- The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Troy E Messick
- The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Ian Tietjen
- The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Eduardo J E Caro-Diaz
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico 00935, United States
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2
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Wang J, Li L, Lin S. Active viral infection during blooms of a dinoflagellate indicates dinoflagellate-viral co-adaptation. Appl Environ Microbiol 2023; 89:e0115623. [PMID: 37874280 PMCID: PMC10686096 DOI: 10.1128/aem.01156-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/06/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE This study represents the first that investigates in situ virus infection in dinoflagellate blooms. Our findings reveal highly similar viral assemblages that infected the bloom species Prorocentrum shikokuense and a co-adapted metabolic relationship between the host and the viruses in the blooms, which varied between the prolonged and the short-lived blooms of the same dinoflagellate species. These findings fill the gap in knowledge regarding the identity and behavior of viruses in a dinoflagellate bloom and shed light on what appears to be the complex mode of infection. The novel insight will be potentially valuable for fully understanding and modeling the role of viruses in regulating blooms of dinoflagellates and other algae.
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Affiliation(s)
- Jingtian Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
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3
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Murúa P, Garvetto A, Egan S, Gachon CMM. The Reemergence of Phycopathology: When Algal Biology Meets Ecology and Biosecurity. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:231-255. [PMID: 37253694 DOI: 10.1146/annurev-phyto-020620-120425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Viruses, bacteria, and eukaryotic symbionts interact with algae in a variety of ways to cause disease complexes, often shaping marine and freshwater ecosystems. The advent of phyconomy (a.k.a. seaweed agronomy) represents a need for a greater understanding of algal disease interactions, where underestimated cryptic diversity and lack of phycopathological basis are prospective constraints for algal domestication. Here, we highlight the limited yet increasing knowledge of algal pathogen biodiversity and the ecological interaction with their algal hosts. Finally, we discuss how ecology and cultivation experience contribute to and reinforce aquaculture practice, with the potential to reshape biosecurity policies of seaweed cultivation worldwide.
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Affiliation(s)
- Pedro Murúa
- Instituto de Acuicultura, Universidad Austral de Chile-Sede Puerto Montt, Los Lagos, Chile;
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
| | - Andrea Garvetto
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Tyrol, Austria
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Claire M M Gachon
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
- Muséum National d'Histoire Naturelle, CNRS, Paris, France
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4
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Roberts AJ, Suttle CA. Pathogens and Passengers: Roles for Crustacean Zooplankton Viruses in the Global Ocean. Microorganisms 2023; 11:microorganisms11041054. [PMID: 37110477 PMCID: PMC10142142 DOI: 10.3390/microorganisms11041054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Viruses infect all living organisms, but the viruses of most marine animals are largely unknown. Crustacean zooplankton are a functional lynchpin in marine food webs, but very few have been interrogated for their associated viruses despite the profound potential effects of viral infection. Nonetheless, it is clear that the diversity of viruses in crustacean zooplankton is enormous, including members of all realms of RNA viruses, as well as single- and double-stranded DNA viruses, in many cases representing deep branches of viral evolution. As there is clear evidence that many of these viruses infect and replicate in zooplankton species, we posit that viral infection is likely responsible for a significant portion of unexplained non-consumptive mortality in this group. In turn, this infection affects food webs and alters biogeochemical cycling. In addition to the direct impacts of infection, zooplankton can vector economically devastating viruses of finfish and other crustaceans. The dissemination of these viruses is facilitated by the movement of zooplankton vertically between epi- and mesopelagic communities through seasonal and diel vertical migration (DVM) and across long distances in ship ballast water. The large potential impact of viruses on crustacean zooplankton emphasises the need to clearly establish the relationships between specific viruses and the zooplankton they infect and investigate disease and mortality for these host-virus pairs. Such data will enable investigations into a link between viral infection and seasonal dynamics of host populations. We are only beginning to uncover the diversity and function of viruses associated with crustacean zooplankton.
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Affiliation(s)
- Alastair J Roberts
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Curtis A Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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5
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Klawonn I, Van den Wyngaert S, Iversen MH, Walles TJW, Flintrop CM, Cisternas-Novoa C, Nejstgaard JC, Kagami M, Grossart HP. Fungal parasitism on diatoms alters formation and bio-physical properties of sinking aggregates. Commun Biol 2023; 6:206. [PMID: 36810576 PMCID: PMC9944279 DOI: 10.1038/s42003-023-04453-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/10/2023] [Indexed: 02/24/2023] Open
Abstract
Phytoplankton forms the base of aquatic food webs and element cycling in diverse aquatic systems. The fate of phytoplankton-derived organic matter, however, often remains unresolved as it is controlled by complex, interlinked remineralization and sedimentation processes. We here investigate a rarely considered control mechanism on sinking organic matter fluxes: fungal parasites infecting phytoplankton. We demonstrate that bacterial colonization is promoted 3.5-fold on fungal-infected phytoplankton cells in comparison to non-infected cells in a cultured model pathosystem (diatom Synedra, fungal microparasite Zygophlyctis, and co-growing bacteria), and even ≥17-fold in field-sampled populations (Planktothrix, Synedra, and Fragilaria). Additional data obtained using the Synedra-Zygophlyctis model system reveals that fungal infections reduce the formation of aggregates. Moreover, carbon respiration is 2-fold higher and settling velocities are 11-48% lower for similar-sized fungal-infected vs. non-infected aggregates. Our data imply that parasites can effectively control the fate of phytoplankton-derived organic matter on a single-cell to single-aggregate scale, potentially enhancing remineralization and reducing sedimentation in freshwater and coastal systems.
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Affiliation(s)
- Isabell Klawonn
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany.
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), 18119, Rostock, Germany.
| | - Silke Van den Wyngaert
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Morten H Iversen
- Alfred Wegener Institute (AWI), Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
- Centre for Marine Environmental Sciences (MARUM) and University of Bremen, 28359, Bremen, Germany
| | - Tim J W Walles
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany
| | - Clara M Flintrop
- Alfred Wegener Institute (AWI), Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
- Centre for Marine Environmental Sciences (MARUM) and University of Bremen, 28359, Bremen, Germany
- The Inter-University Institute for Marine Sciences in Eilat, Eilat, 8810302, Israel
| | - Carolina Cisternas-Novoa
- Helmholtz Centre for Ocean Research (GEOMAR), 24148, Kiel, Germany
- Ocean Sciences Centre, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Jens C Nejstgaard
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany
| | - Maiko Kagami
- Faculty of Science, Toho University, Funabashi, Chiba, 274‑8510, Japan
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, 240‑8502, Japan
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, 14469, Potsdam, Germany
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6
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The Role of Chloroviruses as Possible Infectious Agents for Human Health: Putative Mechanisms of ATCV-1 Infection and Potential Routes of Transmission. Trop Med Infect Dis 2023; 8:tropicalmed8010040. [PMID: 36668947 PMCID: PMC9863483 DOI: 10.3390/tropicalmed8010040] [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: 11/15/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
The Chlorovirus genus of the Phycodnaviridae family includes large viruses with a double-stranded DNA genome. Chloroviruses are widely distributed in freshwater bodies around the world and have been isolated from freshwater sources in Europe, Asia, Australia, and North and South America. One representative of chloroviruses is Acanthocystis turfacea chlorella virus 1 (ATCV-1), which is hosted by Chlorella heliozoae. A few publications in the last ten years about the potential effects of ATCV-1 on the human brain sparked interest among specialists in the field of human infectious pathology. The goal of our viewpoint was to compile the scant research on the effects of ATCV-1 on the human body, to demonstrate the role of chloroviruses as new possible infectious agents for human health, and to indicate potential routes of virus transmission. We believe that ATCV-1 transmission routes remain unexplored. We also question whether chlorella-based nutritional supplements are dangerous for ATCV-1 infections. Further research will help to identify the routes of infection, the cell types in which ATCV-1 can persist, and the pathological mechanisms of the virus's effect on the human body.
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7
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Bachy C, Baudoux AC. [Diversity and ecological importance of viruses in the marine environment]. Med Sci (Paris) 2022; 38:1008-1015. [PMID: 36692280 DOI: 10.1051/medsci/2022165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ocean is the largest reservoir of viruses on the planet with estimates of up to several billions per liter. These viruses represent a major driving force not only for the evolution and for structuring the microbial world, but also for the functioning and the balance of marine ecosystems. With the advances in high throughput sequencing techniques, we are beginning to uncover the diversity and the complexity of this marine virosphere. This review synthesizes milestones in the field of marine viral ecology, including the diversity of these fascinating microorganisms, their impact on microbial mortality and cycling of nutrients and energy in the ocean.
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Affiliation(s)
- Charles Bachy
- Sorbonne Université, CNRS, FR2424, Station biologique de Roscoff, Roscoff, 29680, France
| | - Anne-Claire Baudoux
- Sorbonne université, CNRS, Station biologique de Roscoff, Laboratoire adaptation et diversité en milieu marin, UMR7144, Roscoff, 29680, France
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8
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Farzad R, Ha AD, Aylward FO. Diversity and genomics of giant viruses in the North Pacific Subtropical Gyre. Front Microbiol 2022; 13:1021923. [PMID: 36504832 PMCID: PMC9732441 DOI: 10.3389/fmicb.2022.1021923] [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: 08/17/2022] [Accepted: 10/25/2022] [Indexed: 11/27/2022] Open
Abstract
Large double-stranded DNA viruses of the phylum Nucleocytoviricota, often referred to as "giant viruses," are ubiquitous members of marine ecosystems that are important agents of mortality for eukaryotic plankton. Although giant viruses are known to be prevalent in marine systems, their activities in oligotrophic ocean waters remain unclear. Oligotrophic gyres constitute the majority of the ocean and assessing viral activities in these regions is therefore critical for understanding overall marine microbial processes. In this study, we generated 11 metagenome-assembled genomes (MAGs) of giant viruses from samples previously collected from Station ALOHA in the North Pacific Subtropical Gyre. Phylogenetic analyses revealed that they belong to the orders Imitervirales (n = 6), Algavirales (n = 4), and Pimascovirales (n = 1). Genome sizes ranged from ~119-574 kbp, and several of the genomes encoded predicted TCA cycle components, cytoskeletal proteins, collagen, rhodopsins, and proteins potentially involved in other cellular processes. Comparison with other marine metagenomes revealed that several have broad distribution across ocean basins and represent abundant viral constituents of pelagic surface waters. Our work sheds light on the diversity of giant viruses present in oligotrophic ocean waters across the globe.
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Affiliation(s)
- Roxanna Farzad
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Anh D. Ha
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Frank O. Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States,Center for Emerging, Zoonotic, and Arthropod-Borne Infectious Disease, Virginia Tech, Blacksburg, VA, United States,*Correspondence: Frank O. Aylward,
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9
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Brahim Belhaouari D, Pires De Souza GA, Lamb DC, Kelly SL, Goldstone JV, Stegeman JJ, Colson P, La Scola B, Aherfi S. Metabolic arsenal of giant viruses: Host hijack or self-use? eLife 2022; 11:e78674. [PMID: 35801640 PMCID: PMC9270025 DOI: 10.7554/elife.78674] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/22/2022] [Indexed: 12/11/2022] Open
Abstract
Viruses generally are defined as lacking the fundamental properties of living organisms in that they do not harbor an energy metabolism system or protein synthesis machinery. However, the discovery of giant viruses of amoeba has fundamentally challenged this view because of their exceptional genome properties, particle sizes and encoding of the enzyme machinery for some steps of protein synthesis. Although giant viruses are not able to replicate autonomously and still require a host for their multiplication, numerous metabolic genes involved in energy production have been recently detected in giant virus genomes from many environments. These findings have further blurred the boundaries that separate viruses and living organisms. Herein, we summarize information concerning genes and proteins involved in cellular metabolic pathways and their orthologues that have, surprisingly, been discovered in giant viruses. The remarkable diversity of metabolic genes described in giant viruses include genes encoding enzymes involved in glycolysis, gluconeogenesis, tricarboxylic acid cycle, photosynthesis, and β-oxidation. These viral genes are thought to have been acquired from diverse biological sources through lateral gene transfer early in the evolution of Nucleo-Cytoplasmic Large DNA Viruses, or in some cases more recently. It was assumed that viruses are capable of hijacking host metabolic networks. But the giant virus auxiliary metabolic genes also may represent another form of host metabolism manipulation, by expanding the catalytic capabilities of the host cells especially in harsh environments, providing the infected host cells with a selective evolutionary advantage compared to non-infected cells and hence favoring the viral replication. However, the mechanism of these genes' functionality remains unclear to date.
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Affiliation(s)
- Djamal Brahim Belhaouari
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
| | - Gabriel Augusto Pires De Souza
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
| | - David C Lamb
- Faculty of Medicine, Health and Life Sciences, Institute of Life Science, Swansea UniversitySwanseaUnited Kingdom
| | - Steven L Kelly
- Faculty of Medicine, Health and Life Sciences, Institute of Life Science, Swansea UniversitySwanseaUnited Kingdom
| | - Jared V Goldstone
- Biology Department, Woods Hole Oceanographic InstitutionWoods HoleUnited States
| | - John J Stegeman
- Biology Department, Woods Hole Oceanographic InstitutionWoods HoleUnited States
| | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
- Assistance Publique - Hôpitaux de Marseille (AP-HM)MarseilleFrance
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
- Assistance Publique - Hôpitaux de Marseille (AP-HM)MarseilleFrance
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
- Assistance Publique - Hôpitaux de Marseille (AP-HM)MarseilleFrance
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10
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Flynn KJ, Mitra A, Wilson WH, Kimmance SA, Clark DR, Pelusi A, Polimene L. 'Boom-and-busted' dynamics of phytoplankton-virus interactions explain the paradox of the plankton. THE NEW PHYTOLOGIST 2022; 234:990-1002. [PMID: 35179778 PMCID: PMC9313554 DOI: 10.1111/nph.18042] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/04/2022] [Indexed: 05/13/2023]
Abstract
Rapid virus proliferation can exert a powerful control on phytoplankton host populations, playing a significant role in marine biogeochemistry and ecology. We explore how marine lytic viruses impact phytoplankton succession, affecting host and nonhost populations. Using an in silico food web we conducted simulation experiments under a range of different abiotic and biotic conditions, exploring virus-host-grazer interactions and manipulating competition, allometry, motility and cyst cycles. Virus-host and predator-prey interactions, and interactions with competitors, generate bloom dynamics with a pronounced 'boom-and-busted' dynamic (BBeD) which leads to the suppression of otherwise potentially successful phytoplankton species. The BBeD is less pronounced at low nutrient loading through distancing of phytoplankton hosts, while high sediment loading and high nonhost biomass decrease the abundance of viruses through adsorption. Larger hosts are inherently more distanced, but motility increases virus attack, while cyst cycles promote spatial and temporal distancing. Virus control of phytoplankton bloom development appears more important than virus-induced termination of those blooms. This affects plankton succession - not only the growth of species infected by the virus, but also those that compete for the same resources and are collectively subjected to common grazer control. The role of viruses in structuring plankton communities via BBeDs can thus provide an explanation for the paradox of the plankton.
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Affiliation(s)
- Kevin J. Flynn
- Plymouth Marine LaboratoryProspect Place, West HoePlymouthPL1 3DHUK
| | - Aditee Mitra
- School of Earth and Environmental SciencesCardiff UniversityCardiffCF10 3ATUK
| | - William H. Wilson
- Marine Biological Association of the UK, The LaboratoryCitadel HillPlymouthPL1 2PBUK
- School of Biological and Marine SciencesUniversity of PlymouthPL4 8AAUK
| | | | - Darren R. Clark
- Plymouth Marine LaboratoryProspect Place, West HoePlymouthPL1 3DHUK
| | - Angela Pelusi
- School of Earth and Environmental SciencesCardiff UniversityCardiffCF10 3ATUK
| | - Luca Polimene
- Plymouth Marine LaboratoryProspect Place, West HoePlymouthPL1 3DHUK
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11
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Zayed AA, Wainaina JM, Dominguez-Huerta G, Pelletier E, Guo J, Mohssen M, Tian F, Pratama AA, Bolduc B, Zablocki O, Cronin D, Solden L, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Ruscheweyh HJ, Salazar G, Shatoff E, Coordinators TO, Bundschuh R, Fredrick K, Kubatko LS, Chaffron S, Culley AI, Sunagawa S, Kuhn JH, Wincker P, Sullivan MB. Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome. Science 2022; 376:156-162. [PMID: 35389782 PMCID: PMC10990476 DOI: 10.1126/science.abm5847] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of the new phyla "Taraviricota," a missing link in early RNA virus evolution, and "Arctiviricota" are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.
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Affiliation(s)
- Ahmed A. Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - James M. Wainaina
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Guillermo Dominguez-Huerta
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Jiarong Guo
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Mohamed Mohssen
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
| | - Funing Tian
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Akbar Adjie Pratama
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Dylan Cronin
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Lindsey Solden
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Erwan Delage
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Nantes Université, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Corinne da Silva
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Elan Shatoff
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | | | - Ralf Bundschuh
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
- Division of Hematology, Department of Internal Medicine, Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Laura S. Kubatko
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
- Department of Statistics, Ohio State University, Columbus, OH 43210, USA
| | - Samuel Chaffron
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Nantes Université, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Alexander I. Culley
- Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA
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12
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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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13
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Retel C, Kowallik V, Becks L, Feulner PGD. Strong Selection and High Mutation Supply Characterize Experimental Chlorovirus Evolution. Virus Evol 2022; 8:veac003. [PMID: 35169490 PMCID: PMC8838748 DOI: 10.1093/ve/veac003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 11/24/2022] Open
Abstract
Characterizing how viruses evolve expands our understanding of the underlying fundamental processes, such as mutation, selection and drift. One group of viruses whose evolution has not yet been extensively studied is the Phycodnaviridae, a globally abundant family of aquatic large double-stranded (ds) DNA viruses. Here we studied the evolutionary change of Paramecium bursaria chlorella virus 1 during experimental coevolution with its algal host. We used pooled genome sequencing of six independently evolved populations to characterize genomic change over five time points. Across six experimental replicates involving either strong or weak demographic fluctuations, we found single nucleotide polymorphisms (SNPs) at sixty-seven sites. The occurrence of genetic variants was highly repeatable, with just two of the SNPs found in only a single experimental replicate. Three genes A122/123R, A140/145R and A540L showed an excess of variable sites, providing new information about potential targets of selection during Chlorella–Chlorovirus coevolution. Our data indicated that the studied populations were not mutation-limited and experienced strong positive selection. Our investigation highlighted relevant processes governing the evolution of aquatic large dsDNA viruses, which ultimately contributes to a better understanding of the functioning of natural aquatic ecosystems.
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Affiliation(s)
- Cas Retel
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Bio-geochemistry, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, Kastanienbaum 6047, Switzerland
- Division of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
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14
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Kim D, Lee J, Cho CH, Kim EJ, Bhattacharya D, Yoon HS. Group II intron and repeat-rich red algal mitochondrial genomes demonstrate the dynamic recent history of autocatalytic RNAs. BMC Biol 2022; 20:2. [PMID: 34996446 PMCID: PMC8742464 DOI: 10.1186/s12915-021-01200-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 11/29/2021] [Indexed: 11/10/2022] Open
Abstract
Background Group II introns are mobile genetic elements that can insert at specific target sequences, however, their origins are often challenging to reconstruct because of rapid sequence decay following invasion and spread into different sites. To advance understanding of group II intron spread, we studied the intron-rich mitochondrial genome (mitogenome) in the unicellular red alga, Porphyridium. Results Analysis of mitogenomes in three closely related species in this genus revealed they were 3–6-fold larger in size (56–132 kbp) than in other red algae, that have genomes of size 21–43 kbp. This discrepancy is explained by two factors, group II intron invasion and expansion of repeated sequences in large intergenic regions. Phylogenetic analysis demonstrates that many mitogenome group II intron families are specific to Porphyridium, whereas others are closely related to sequences in fungi and in the red alga-derived plastids of stramenopiles. Network analysis of intron-encoded proteins (IEPs) shows a clear link between plastid and mitochondrial IEPs in distantly related species, with both groups associated with prokaryotic sequences. Conclusion Our analysis of group II introns in Porphyridium mitogenomes demonstrates the dynamic nature of group II intron evolution, strongly supports the lateral movement of group II introns among diverse eukaryotes, and reveals their ability to proliferate, once integrated in mitochondrial DNA. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01200-3.
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Affiliation(s)
- Dongseok Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu, 41566, South Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Eun Jeung Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea.
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15
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Merges D, Dal Grande F, Greve C, Otte J, Schmitt I. Virus diversity in metagenomes of a lichen symbiosis (Umbilicaria phaea): complete viral genomes, putative hosts and elevational distributions. Environ Microbiol 2021; 23:6637-6650. [PMID: 34697892 DOI: 10.1111/1462-2920.15802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/01/2021] [Indexed: 11/28/2022]
Abstract
Viruses can play critical roles in symbioses by initiating horizontal gene transfer, affecting host phenotypes, or expanding their host's ecological niche. However, knowledge of viral diversity and distribution in symbiotic organisms remains elusive. Here we use deep-sequenced metagenomic DNA (PacBio Sequel II; two individuals), paired with a population genomics approach (Pool-seq; 11 populations, 550 individuals) to understand viral distributions in the lichen Umbilicaria phaea. We assess (i) viral diversity in lichen thalli, (ii) putative viral hosts (fungi, algae, bacteria) and (iii) viral distributions along two replicated elevation gradients. We identified five novel viruses, showing 28%-40% amino acid identity to known viruses. They tentatively belong to the families Caulimoviridae, Myoviridae, Podoviridae and Siphoviridae. Our analysis suggests that the Caulimovirus is associated with green algal photobionts (Trebouxia) of the lichen, and the remaining viruses with bacterial hosts. We did not detect viral sequences in the mycobiont. Caulimovirus abundance decreased with increasing elevation, a pattern reflected by a specific algal lineage hosting this virus. Bacteriophages showed population-specific patterns. Our work provides the first comprehensive insights into viruses associated with a lichen holobiont and suggests an interplay of viral hosts and environment in structuring viral distributions.
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Affiliation(s)
- Dominik Merges
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany.,Department of Biological Sciences, Goethe Universität Frankfurt, Frankfurt am Main, Germany
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16
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Mojica KDA, Behrenfeld MJ, Clay M, Brussaard CPD. Spring Accumulation Rates in North Atlantic Phytoplankton Communities Linked to Alterations in the Balance Between Division and Loss. Front Microbiol 2021; 12:706137. [PMID: 34504477 PMCID: PMC8422905 DOI: 10.3389/fmicb.2021.706137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/19/2021] [Indexed: 12/02/2022] Open
Abstract
For nearly a century, phytoplankton spring blooms have largely been explained in the context of abiotic factors regulating cellular division rates (e.g., mixed-layer light levels). However, the accumulation of new phytoplankton biomass represents a mismatch between phytoplankton division and mortality rates. The balance between division and loss, therefore, has important implications for marine food webs and biogeochemical cycles. A large fraction of phytoplankton mortality is due to the combination of microzooplankton grazing and viral lysis, however, broad scale simultaneous measurements of these mortality processes are scarce. We applied the modified dilution assay along a West-to-East diagonal transect in the North Atlantic during spring. Our results demonstrate positive accumulation rates with losses dominated by microzooplankton grazing. Considering the dynamic light environment phytoplankton experience in the mixed surface layer, particularly in the spring, we tested the potential for incubation light conditions to affect observed rates. Incubations acted as short-term 'light' perturbations experiments, in which deeply mixed communities are exposed to elevated light levels. These "light perturbations" increased phytoplankton division rates and resulted in proportional changes in phytoplankton biomass while having no significant effect on mortality rates. These results provide experimental evidence for the Disturbance-Recovery Hypothesis, supporting the tenet that biomass accumulation rates co-vary with the specific rate of change in division.
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Affiliation(s)
- Kristina D. A. Mojica
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Michael J. Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Megan Clay
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| | - Corina P. D. Brussaard
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
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17
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Sadeghi M, Tomaru Y, Ahola T. RNA Viruses in Aquatic Unicellular Eukaryotes. Viruses 2021; 13:v13030362. [PMID: 33668994 PMCID: PMC7996518 DOI: 10.3390/v13030362] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/05/2021] [Accepted: 02/22/2021] [Indexed: 12/24/2022] Open
Abstract
Increasing sequence information indicates that RNA viruses constitute a major fraction of marine virus assemblages. However, only 12 RNA virus species have been described, infecting known host species of marine single-celled eukaryotes. Eight of these use diatoms as hosts, while four are resident in dinoflagellate, raphidophyte, thraustochytrid, or prasinophyte species. Most of these belong to the order Picornavirales, while two are divergent and fall into the families Alvernaviridae and Reoviridae. However, a very recent study has suggested that there is extraordinary diversity in aquatic RNA viromes, describing thousands of viruses, many of which likely use protist hosts. Thus, RNA viruses are expected to play a major ecological role for marine unicellular eukaryotic hosts. In this review, we describe in detail what has to date been discovered concerning viruses with RNA genomes that infect aquatic unicellular eukaryotes.
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Affiliation(s)
- Mohammadreza Sadeghi
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland
- Correspondence: (M.S.); (T.A.)
| | - Yuji Tomaru
- Environment and Fisheries Applied Techniques Research Department, Fisheries Technology Institute, Fisheries Research and Education Agency, Hatsukaichi, Hiroshima 739-0452, Japan;
| | - Tero Ahola
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland
- Correspondence: (M.S.); (T.A.)
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18
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Pelusi A, De Luca P, Manfellotto F, Thamatrakoln K, Bidle KD, Montresor M. Virus-induced spore formation as a defense mechanism in marine diatoms. THE NEW PHYTOLOGIST 2021; 229:2251-2259. [PMID: 32978816 PMCID: PMC7894508 DOI: 10.1111/nph.16951] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/09/2020] [Indexed: 05/03/2023]
Abstract
Algal viruses are important contributors to carbon cycling, recycling nutrients and organic material through host lysis. Although viral infection has been described as a primary mechanism of phytoplankton mortality, little is known about host defense responses. We show that viral infection of the bloom-forming, planktonic diatom Chaetoceros socialis induces the mass formation of resting spores, a heavily silicified life cycle stage associated with carbon export due to rapid sinking. Although viral RNA was detected within spores, mature virions were not observed. 'Infected' spores were capable of germinating, but did not propagate or transmit infectious viruses. These results demonstrate that diatom spore formation is an effective defense strategy against viral-mediated mortality. They provide a possible mechanistic link between viral infection, bloom termination, and mass carbon export events and highlight an unappreciated role of viruses in regulating diatom life cycle transitions and ecological success.
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Affiliation(s)
- Angela Pelusi
- Department of Integrative Marine EcologyStazione Zoologica Anton DohrnVilla ComunaleNaples80121Italy
| | - Pasquale De Luca
- Research Infrastructures for Marine Biological ResourcesStazione Zoologica Anton DohrnVilla ComunaleNaples80121Italy
| | - Francesco Manfellotto
- Department of Integrative Marine EcologyStazione Zoologica Anton DohrnVilla ComunaleNaples80121Italy
| | | | - Kay D. Bidle
- Department of Marine and Coastal SciencesRutgers UniversityNew BrunswickNJ08901‐8520USA
| | - Marina Montresor
- Department of Integrative Marine EcologyStazione Zoologica Anton DohrnVilla ComunaleNaples80121Italy
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19
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Sun Z, Fu J, Li X, Blatchley ER, Zhou Z. Using Algal Virus Paramecium bursaria Chlorella Virus as a Human Adenovirus Surrogate for Validation of UV Treatment Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15507-15515. [PMID: 33166135 DOI: 10.1021/acs.est.0c06354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Adenovirus is among the most UV-resistant waterborne human pathogens. There is a need to identify nonpathogenic surrogates for adenovirus for the water treatment industry. In this study, the feasibility of using the algal virus Paramecium bursaria chlorella virus (PBCV-1) as an adenovirus surrogate for validation of UV reactors was evaluated. The UV dose-response behavior of PBCV-1 to monochromatic UV radiation at 254 nm and action spectrum for wavelengths ranging from 214 to 289 nm were measured. A culture-based infectivity assay was used to evaluate viral inactivation, and a quantitative PCR assay was used to quantify DNA damage. A UV254 dose of 150 mJ/cm2 resulted in roughly 5-log10 units of reduction of PBCV-1, which is similar to that of adenovirus. Furthermore, the inactivation action spectrum of PBCV-1 was similar to that of adenovirus between 214 and 289 nm. A simplified and inexpensive prepurification method was also developed to prepare PBCV-1 viral suspensions with similar inactivation behavior to purified PBCV-1. Overall, PBCV-1 appears to represent an appropriate adenovirus surrogate for UV system performance evaluation and illustrates the potential of using algal viruses as nonpathogenic, easy to culture, and readily available surrogates for human pathogens.
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Affiliation(s)
- Zhe Sun
- Lyles School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jianing Fu
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Xing Li
- Lyles School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ernest R Blatchley
- Lyles School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907, United States
- Division of Environmental and Ecological Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhi Zhou
- Lyles School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907, United States
- Division of Environmental and Ecological Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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20
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Zabelskii D, Alekseev A, Kovalev K, Rankovic V, Balandin T, Soloviov D, Bratanov D, Savelyeva E, Podolyak E, Volkov D, Vaganova S, Astashkin R, Chizhov I, Yutin N, Rulev M, Popov A, Eria-Oliveira AS, Rokitskaya T, Mager T, Antonenko Y, Rosselli R, Armeev G, Shaitan K, Vivaudou M, Büldt G, Rogachev A, Rodriguez-Valera F, Kirpichnikov M, Moser T, Offenhäusser A, Willbold D, Koonin E, Bamberg E, Gordeliy V. Viral rhodopsins 1 are an unique family of light-gated cation channels. Nat Commun 2020; 11:5707. [PMID: 33177509 PMCID: PMC7659345 DOI: 10.1038/s41467-020-19457-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/07/2020] [Indexed: 11/09/2022] Open
Abstract
Phytoplankton is the base of the marine food chain as well as oxygen and carbon cycles and thus plays a global role in climate and ecology. Nucleocytoplasmic Large DNA Viruses that infect phytoplankton organisms and regulate the phytoplankton dynamics encompass genes of rhodopsins of two distinct families. Here, we present a functional and structural characterization of two proteins of viral rhodopsin group 1, OLPVR1 and VirChR1. Functional analysis of VirChR1 shows that it is a highly selective, Na+/K+-conducting channel and, in contrast to known cation channelrhodopsins, it is impermeable to Ca2+ ions. We show that, upon illumination, VirChR1 is able to drive neural firing. The 1.4 Å resolution structure of OLPVR1 reveals remarkable differences from the known channelrhodopsins and a unique ion-conducting pathway. Thus, viral rhodopsins 1 represent a unique, large group of light-gated channels (viral channelrhodopsins, VirChR1s). In nature, VirChR1s likely mediate phototaxis of algae enhancing the host anabolic processes to support virus reproduction, and therefore, might play a major role in global phytoplankton dynamics. Moreover, VirChR1s have unique potential for optogenetics as they lack possibly noxious Ca2+ permeability. Nucleocytoplasmic Large DNA Viruses (NCLDV) that infect algae encode two distinct families of microbial rhodopsins. Here, the authors characterise two proteins form the viral rhodopsin group 1 OLPVR1 and VirChR1, present the 1.4 Å crystal structure of OLPVR1 and show that viral rhodopsins 1 are light-gated cation channels.
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Affiliation(s)
- Dmitrii Zabelskii
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexey Alekseev
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Kirill Kovalev
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany.,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Vladan Rankovic
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany.,Auditory Neuroscience and Optogenetics Laboratory, German Primate Center, Göttingen, Germany
| | - Taras Balandin
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Dmytro Soloviov
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Joint Institute for Nuclear Research, Dubna, Russia.,Institute for Safety Problems of Nuclear Power Plants, NAS of Ukraine, Kyiv, 03680, Ukraine
| | - Dmitry Bratanov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ekaterina Savelyeva
- Institute of Biological Information Processing (IBI-3: Bioelectronics), Forschungszentrum Jülich GmbH, Jülich, Germany.,Laboratory of Functional Materials and Devices for Nanoelectronics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Center of Shared Research Facilities, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Elizaveta Podolyak
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Dmytro Volkov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Svetlana Vaganova
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Roman Astashkin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Igor Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Natalia Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Maksim Rulev
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,European Synchrotron Radiation Facility, Grenoble, France
| | | | - Ana-Sofia Eria-Oliveira
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Tatiana Rokitskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Thomas Mager
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Yuri Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Riccardo Rosselli
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain.,Department of Marine Microbiology and Biogeochemistry, Royal Netherland Institute for Sea Research (NIOZ), and Utrecht University, Den Burg, The Netherlands
| | - Grigoriy Armeev
- Biological Faculty, M. V. Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Konstantin Shaitan
- Biological Faculty, M. V. Lomonosov Moscow State University, Moscow, 119991, Russia.,N. N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Michel Vivaudou
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.,Laboratories of Excellence, Ion Channel Science and Therapeutics, 06560, Valbonne, France
| | - Georg Büldt
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Andrey Rogachev
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Joint Institute for Nuclear Research, Dubna, Russia
| | - Francisco Rodriguez-Valera
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | - Mikhail Kirpichnikov
- Biological Faculty, M. V. Lomonosov Moscow State University, Moscow, 119991, Russia.,M. M. Shemyakin-Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Tobias Moser
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany.,Auditory Neuroscience and Optogenetics Laboratory, German Primate Center, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Andreas Offenhäusser
- Institute of Biological Information Processing (IBI-3: Bioelectronics), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Eugene Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Ernst Bamberg
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Valentin Gordeliy
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany. .,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany. .,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia. .,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany. .,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
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21
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Pal M, Yesankar PJ, Dwivedi A, Qureshi A. Biotic control of harmful algal blooms (HABs): A brief review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 268:110687. [PMID: 32383649 DOI: 10.1016/j.jenvman.2020.110687] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 04/14/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
The water bodies, mainly coastal and lake, remain tainted worldwide, mostly because of the Cyanobacteria harbored in Harmful Algal Blooms (HABs). The main reason for the flourishing of blooms depends on the eutrophication. Blooms could be toxic as well as non-toxic, depending on the bloom-forming species. The blooms affect the water body, aquatic ecosystem and also dependents like human. A large number of organisms, including bacteria, viruses, fungi, fish and zooplankton have adverse effects on Cyanobacteria either through infection, predation or by the production of the algicidal compounds. It was reported, these microorganisms have species-specific interactions and hence differ in their interaction mechanism. The present review emphasises on the role of selected microbial species and the mechanism they follow for mitigation of HABs. Generally lab-scale entities were reported to involve lytic agents, like cyanobacteriolytic substances, released by bacteria. Cyanobacterial species release Cyanotoxins which may affect the water quality. Growing biotic factors in a large quantity and discharging it into the water-body needs excessive efficacy and economic requisite and hence the feasibility of extrapolation of the laboratory results in the field still finds promiscuity towards mitigation of HABs.
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Affiliation(s)
- Mili Pal
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; Environmental Biotechnology and Genomics Division (EBGD), CSIR - National Environmental Engineering Research Institute (CSIR-NEERI) Nehru Marg, Nagpur 440020, India
| | - Prerna J Yesankar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; Environmental Biotechnology and Genomics Division (EBGD), CSIR - National Environmental Engineering Research Institute (CSIR-NEERI) Nehru Marg, Nagpur 440020, India
| | - Ajay Dwivedi
- Environmental Impact and Sustainability Division, CSIR-NEERI, Nagpur, India
| | - Asifa Qureshi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; Environmental Biotechnology and Genomics Division (EBGD), CSIR - National Environmental Engineering Research Institute (CSIR-NEERI) Nehru Marg, Nagpur 440020, India.
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23
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Capsid Structure of a Marine Algal Virus of the Order Picornavirales. J Virol 2020; 94:JVI.01855-19. [PMID: 32024776 DOI: 10.1128/jvi.01855-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/29/2020] [Indexed: 12/17/2022] Open
Abstract
The order Picornavirales includes viruses that infect different kinds of eukaryotes and that share similar properties. The capsid proteins (CPs) of viruses in the order that infect unicellular organisms, such as algae, presumably possess certain characteristics that have changed little over the course of evolution, and thus these viruses may resemble the Picornavirales ancestor in some respects. Herein, we present the capsid structure of Chaetoceros tenuissimus RNA virus type II (CtenRNAV-II) determined using cryo-electron microscopy at a resolution of 3.1 Å, the first alga virus belonging to the family Marnaviridae of the order Picornavirales A structural comparison to related invertebrate and vertebrate viruses revealed a unique surface loop of the major CP VP1 that had not been observed previously, and further, revealed that another VP1 loop obscures the so-called canyon, which is a host-receptor binding site for many of the mammalian Picornavirales viruses. VP2 has an N-terminal tail, which has previously been reported as a primordial feature of Picornavirales viruses. The above-mentioned and other critical structural features provide new insights on three long-standing theories about Picornavirales: (i) the canyon hypothesis, (ii) the primordial VP2 domain swap, and (iii) the hypothesis that alga Picornavirales viruses could share characteristics with the Picornavirales ancestor.IMPORTANCE Identifying the acquired structural traits in virus capsids is important for elucidating what functions are essential among viruses that infect different hosts. The Picornavirales viruses infect a broad spectrum of hosts, ranging from unicellular algae to insects and mammals and include many human pathogens. Those viruses that infect unicellular protists, such as algae, are likely to have undergone fewer structural changes during the course of evolution compared to those viruses that infect multicellular eukaryotes and thus still share some characteristics with the Picornavirales ancestor. This article describes the first atomic capsid structure of an alga Marnavirus, CtenRNAV-II. A comparison to capsid structures of the related invertebrate and vertebrate viruses identified a number of structural traits that have been functionally acquired or lost during the course of evolution. These observations provide new insights on past theories on the viability and evolution of Picornavirales viruses.
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24
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Van Etten JL, Agarkova IV, Dunigan DD. Chloroviruses. Viruses 2019; 12:E20. [PMID: 31878033 PMCID: PMC7019647 DOI: 10.3390/v12010020] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 12/20/2022] Open
Abstract
Chloroviruses are large dsDNA, plaque-forming viruses that infect certain chlorella-like green algae; the algae are normally mutualistic endosymbionts of protists and metazoans and are often referred to as zoochlorellae. The viruses are ubiquitous in inland aqueous environments throughout the world and occasionally single types reach titers of thousands of plaque-forming units per ml of native water. The viruses are icosahedral in shape with a spike structure located at one of the vertices. They contain an internal membrane that is required for infectivity. The viral genomes are 290 to 370 kb in size, which encode up to 16 tRNAs and 330 to ~415 proteins, including many not previously seen in viruses. Examples include genes encoding DNA restriction and modification enzymes, hyaluronan and chitin biosynthetic enzymes, polyamine biosynthetic enzymes, ion channel and transport proteins, and enzymes involved in the glycan synthesis of the virus major capsid glycoproteins. The proteins encoded by many of these viruses are often the smallest or among the smallest proteins of their class. Consequently, some of the viral proteins are the subject of intensive biochemical and structural investigation.
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Affiliation(s)
- James L. Van Etten
- Department of Plant Pathology, Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA; (I.V.A.); (D.D.D.)
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25
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French RK, Holmes EC. An Ecosystems Perspective on Virus Evolution and Emergence. Trends Microbiol 2019; 28:165-175. [PMID: 31744665 DOI: 10.1016/j.tim.2019.10.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/19/2019] [Accepted: 10/21/2019] [Indexed: 12/18/2022]
Abstract
Understanding the emergence of pathogenic viruses has dominated studies of virus evolution. However, new metagenomic studies imply that relatively few of an immense number of viruses may lead to overt disease. This suggests a change in emphasis, from viruses as habitual pathogens to integral components of ecosystems. Here we show how viruses alter interactions between host individuals, populations, and ecosystems, impacting ecosystem health, resilience, and function, and how host ecology in turn impacts viral abundance and diversity. Moving to an ecosystems perspective will put virus evolution and disease emergence in its true context, and enhance our understanding of ecological processes.
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Affiliation(s)
- Rebecca K French
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
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26
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Gran-Stadniczeñko S, Krabberød AK, Sandaa RA, Yau S, Egge E, Edvardsen B. Seasonal Dynamics of Algae-Infecting Viruses and Their Inferred Interactions with Protists. Viruses 2019; 11:v11111043. [PMID: 31717498 PMCID: PMC6893440 DOI: 10.3390/v11111043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/06/2019] [Accepted: 11/08/2019] [Indexed: 11/28/2022] Open
Abstract
Viruses are a highly abundant, dynamic, and diverse component of planktonic communities that have key roles in marine ecosystems. We aimed to reveal the diversity and dynamics of marine large dsDNA viruses infecting algae in the Northern Skagerrak, South Norway through the year by metabarcoding, targeting the major capsid protein (MCP) and its correlation to protist diversity and dynamics. Metabarcoding results demonstrated a high diversity of algal viruses compared to previous metabarcoding surveys in Norwegian coastal waters. We obtained 313 putative algal virus operational taxonomic units (vOTUs), all classified by phylogenetic analyses to either the Phycodnaviridae or Mimiviridae families, most of them in clades without any cultured or environmental reference sequences. The viral community showed a clear temporal variation, with some vOTUs persisting for several months. The results indicate co-occurrences between abundant viruses and potential hosts during long periods. This study gives new insights into the virus-algal host dynamics and provides a baseline for future studies of algal virus diversity and temporal dynamics.
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Affiliation(s)
- Sandra Gran-Stadniczeñko
- Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway; (A.K.K.); (E.E.); (B.E.)
- Correspondence: ; Tel.: +47-22-85-70-38
| | - Anders K. Krabberød
- Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway; (A.K.K.); (E.E.); (B.E.)
| | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, 5020 Bergen, Norway;
| | - Sheree Yau
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), 08003 Barcelona, Spain;
| | - Elianne Egge
- Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway; (A.K.K.); (E.E.); (B.E.)
| | - Bente Edvardsen
- Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway; (A.K.K.); (E.E.); (B.E.)
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27
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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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28
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Bell TAS, Sen-Kilic E, Felföldi T, Vasas G, Fields MW, Peyton BM. Microbial community changes during a toxic cyanobacterial bloom in an alkaline Hungarian lake. Antonie Van Leeuwenhoek 2018; 111:2425-2440. [PMID: 30069722 DOI: 10.1007/s10482-018-1132-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 07/13/2018] [Indexed: 01/28/2023]
Abstract
The Carpathian Basin is a lowland plain located mainly in Hungary. Due to the nature of the bedrock, alluvial deposits, and a bowl shape, many lakes and ponds of the area are characterized by high alkalinity. In this study, we characterized temporal changes in eukaryal and bacterial community dynamics with high throughput sequencing and relate the changes to environmental conditions in Lake Velence located in Fejér county, Hungary. The sampled Lake Velence microbial populations (algal and bacterial) were analyzed to identify potential correlations with other community members and environmental parameters at six timepoints over 6 weeks in the Spring of 2012. Correlations between community members suggest a positive relationship between certain algal and bacterial populations (e.g. Chlamydomondaceae with Actinobacteria and Acidobacteria), while other correlations allude to changes in these relationships over time. During the study, high nitrogen availability may have favored non-nitrogen fixing cyanobacteria, such as the toxin-producing Microcystis aeruginosa, and the eutrophic effect may have been exacerbated by high phosphorus availability as well as the high calcium and magnesium content of the Carpathian Basin bedrock, potentially fostering exopolymer production and cell aggregation. Cyanobacterial bloom formation could have a negative environmental impact on other community members and potentially affect overall water quality as well as recreational activities. To our knowledge, this is the first prediction for relationships between photoautotrophic eukaryotes and bacteria from an alkaline, Hungarian lake.
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Affiliation(s)
- Tisza A S Bell
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA.
- Genome Core and Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
| | - Emel Sen-Kilic
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - Tamás Felföldi
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Gabor Vasas
- Department of Botany, University of Debrecen, Debrecen, Hungary
| | - Matthew W Fields
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
- Energy Research Institute, Montana State University, Bozeman, MT, USA
| | - Brent M Peyton
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Energy Research Institute, Montana State University, Bozeman, MT, USA.
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA.
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29
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Communities of Phytoplankton Viruses across the Transition Zone of the St. Lawrence Estuary. Viruses 2018; 10:v10120672. [PMID: 30486388 PMCID: PMC6316209 DOI: 10.3390/v10120672] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 01/26/2023] Open
Abstract
The St. Lawrence hydrographic system includes freshwater, brackish, and marine habitats, and is the largest waterway in North America by volume. The food-webs in these habitats are ultimately dependent on phytoplankton. Viral lysis is believed to be responsible for a major part of phytoplankton mortality. To better understand their role, we characterized the diversity and distribution of two viral taxa infecting phytoplankton: the picornaviruses and phycodnaviruses. Our study focused on the estuary transition zone, which is an important nursery for invertebrates and fishes. Both viral taxa were investigated by PCR amplification of conserved molecular markers and next-generation sequencing at six sites, ranging from freshwater to marine. Our results revealed few shared viral phylotypes between saltwater and freshwater sites. Salinity appeared to be the primary determinant of viral community composition. Moreover, our analysis indicated that the viruses identified in this region of the St. Lawrence diverge from classified viruses and homologous published environmental virotypes. These results suggest that DNA and RNA viruses infecting phytoplankton are likely active in the estuary transition zone, and that this region harbors its own unique viral assemblages.
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30
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Zhang QY, Gui JF. Diversity, evolutionary contribution and ecological roles of aquatic viruses. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1486-1502. [DOI: 10.1007/s11427-018-9414-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/26/2018] [Indexed: 01/21/2023]
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31
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Wagstaff BA, Rejzek M, Field RA. Identification of a Kdn biosynthesis pathway in the haptophyte Prymnesium parvum suggests widespread sialic acid biosynthesis among microalgae. J Biol Chem 2018; 293:16277-16290. [PMID: 30171074 PMCID: PMC6200933 DOI: 10.1074/jbc.ra118.004921] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/31/2018] [Indexed: 01/08/2023] Open
Abstract
Sialic acids are a family of more than 50 structurally distinct acidic sugars on the surface of all vertebrate cells where they terminate glycan chains and are exposed to many interactions with the surrounding environment. In particular, sialic acids play important roles in cell-cell and host-pathogen interactions. The sialic acids or related nonulosonic acids have been observed in Deuterostome lineages, Eubacteria, and Archaea but are notably absent from plants. However, the structurally related C8 acidic sugar 3-deoxy-d-manno-2-octulosonic acid (Kdo) is present in Gram-negative bacteria and plants as a component of bacterial lipopolysaccharide and pectic rhamnogalacturonan II in the plant cell wall. Until recently, sialic acids were not thought to occur in algae, but as in plants, Kdo has been observed in algae. Here, we report the de novo biosynthesis of the deaminated sialic acid, 3-deoxy-d-glycero-d-galacto-2-nonulosonic acid (Kdn), in the toxin-producing microalga Prymnesium parvum Using biochemical methods, we show that this alga contains CMP-Kdn and identified and recombinantly expressed the P. parvum genes encoding Kdn-9-P synthetase and CMP-Kdn synthetase enzymes that convert mannose-6-P to CMP-Kdn. Bioinformatics analysis revealed sequences related to those of the two P. parvum enzymes, suggesting that sialic acid biosynthesis is likely more widespread among microalgae than previously thought and that this acidic sugar may play a role in host-pathogen interactions involving microalgae. Our findings provide evidence that P. parvum has the biosynthetic machinery for de novo production of the deaminated sialic acid Kdn and that sialic acid biosynthesis may be common among microalgae.
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Affiliation(s)
- Ben A Wagstaff
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Martin Rejzek
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Robert A Field
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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32
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Johns CT, Grubb AR, Nissimov JI, Natale F, Knapp V, Mui A, Fredricks HF, Van Mooy BAS, Bidle KD. The mutual interplay between calcification and coccolithovirus infection. Environ Microbiol 2018; 21:1896-1915. [PMID: 30043404 PMCID: PMC7379532 DOI: 10.1111/1462-2920.14362] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 06/15/2018] [Accepted: 07/11/2018] [Indexed: 11/30/2022]
Abstract
Two prominent characteristics of marine coccolithophores are their secretion of coccoliths and their susceptibility to infection by coccolithoviruses (EhVs), both of which display variation among cells in culture and in natural populations. We examined the impact of calcification on infection by challenging a variety of Emiliania huxleyi strains at different calcification states with EhVs of different virulence. Reduced cellular calcification was associated with increased infection and EhV production, even though calcified cells and associated coccoliths had significantly higher adsorption coefficients than non-calcified (naked) cells. Sialic acid glycosphingolipids, molecules thought to mediate EhV infection, were generally more abundant in calcified cells and enriched in purified, sorted coccoliths, suggesting a biochemical link between calcification and adsorption rates. In turn, viable EhVs impacted cellular calcification absent of lysis by inducing dramatic shifts in optical side scatter signals and a massive release of detached coccoliths in a subpopulation of cells, which could be triggered by resuspension of healthy, calcified host cells in an EhV-free, 'induced media'. Our findings show that calcification is a key component of the E. huxleyi-EhV arms race and an aspect that is critical both to the modelling of these host-virus interactions in the ocean and interpreting their impact on the global carbon cycle.
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Affiliation(s)
- Christopher T Johns
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Austin R Grubb
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Jozef I Nissimov
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Frank Natale
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Viki Knapp
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA.,University of South Carolina, Honors College, Columbia, SC, 29208, USA
| | - Alwin Mui
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Helen F Fredricks
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Benjamin A S Van Mooy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Kay D Bidle
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
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Viruses of Eukaryotic Algae: Diversity, Methods for Detection, and Future Directions. Viruses 2018; 10:v10090487. [PMID: 30208617 PMCID: PMC6165237 DOI: 10.3390/v10090487] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/04/2018] [Accepted: 09/07/2018] [Indexed: 11/16/2022] Open
Abstract
The scope for ecological studies of eukaryotic algal viruses has greatly improved with the development of molecular and bioinformatic approaches that do not require algal cultures. Here, we review the history and perceived future opportunities for research on eukaryotic algal viruses. We begin with a summary of the 65 eukaryotic algal viruses that are presently in culture collections, with emphasis on shared evolutionary traits (e.g., conserved core genes) of each known viral type. We then describe how core genes have been used to enable molecular detection of viruses in the environment, ranging from PCR-based amplification to community scale "-omics" approaches. Special attention is given to recent studies that have employed network-analyses of -omics data to predict virus-host relationships, from which a general bioinformatics pipeline is described for this type of approach. Finally, we conclude with acknowledgement of how the field of aquatic virology is adapting to these advances, and highlight the need to properly characterize new virus-host systems that may be isolated using preliminary molecular surveys. Researchers can approach this work using lessons learned from the Chlorella virus system, which is not only the best characterized algal-virus system, but is also responsible for much of the foundation in the field of aquatic virology.
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Horas EL, Theodosiou L, Becks L. Why Are Algal Viruses Not Always Successful? Viruses 2018; 10:v10090474. [PMID: 30189587 PMCID: PMC6165140 DOI: 10.3390/v10090474] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/31/2018] [Accepted: 09/02/2018] [Indexed: 12/14/2022] Open
Abstract
Algal viruses are considered to be key players in structuring microbial communities and biogeochemical cycles due to their abundance and diversity within aquatic systems. Their high reproduction rates and short generation times make them extremely successful, often with immediate and strong effects for their hosts and thus in biological and abiotic environments. There are, however, conditions that decrease their reproduction rates and make them unsuccessful with no or little immediate effects. Here, we review the factors that lower viral success and divide them into intrinsic—when they are related to the life cycle traits of the virus—and extrinsic factors—when they are external to the virus and related to their environment. Identifying whether and how algal viruses adapt to disadvantageous conditions will allow us to better understand their role in aquatic systems. We propose important research directions such as experimental evolution or the resurrection of extinct viruses to disentangle the conditions that make them unsuccessful and the effects these have on their surroundings.
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Affiliation(s)
- Elena L Horas
- Community Dynamics Group, Max-Planck for Evolutionary Biology, 24306 Plön, Germany.
- Limnology-Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, 78464 Konstanz, Germany.
| | - Loukas Theodosiou
- Community Dynamics Group, Max-Planck for Evolutionary Biology, 24306 Plön, Germany.
- Department of Microbial Population Biology, Max-Planck for Evolutionary Biology, 24306 Plön, Germany.
| | - Lutz Becks
- Community Dynamics Group, Max-Planck for Evolutionary Biology, 24306 Plön, Germany.
- Limnology-Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, 78464 Konstanz, Germany.
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Yau S, Caravello G, Fonvieille N, Desgranges É, Moreau H, Grimsley N. Rapidity of Genomic Adaptations to Prasinovirus Infection in a Marine Microalga. Viruses 2018; 10:v10080441. [PMID: 30126244 PMCID: PMC6116238 DOI: 10.3390/v10080441] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/16/2018] [Accepted: 08/17/2018] [Indexed: 12/19/2022] Open
Abstract
Prasinoviruses are large dsDNA viruses commonly found in aquatic systems worldwide, where they can infect and lyse unicellular prasinophyte algae such as Ostreococcus. Host susceptibility is virus strain-specific, but resistance of susceptible Ostreococcus tauri strains to a virulent virus arises frequently. In clonal resistant lines that re-grow, viruses are usually present for many generations, and genes clustered on chromosome 19 show physical rearrangements and differential expression. Here, we investigated changes occurring during the first two weeks after inoculation of the prasinovirus OtV5. By serial dilutions of cultures at the time of inoculation, we estimated the frequency of resistant cells arising in virus-challenged O. tauri cultures to be 10-3⁻10-4 of the inoculated population. Re-growing resistant cells were detectable by flow cytometry 3 days post-inoculation (dpi), visible re-greening of cultures occurred by 6 dpi, and karyotypic changes were visually detectable at 8 dpi. Resistant cell lines showed a modified spectrum of host-virus specificities and much lower levels of OtV5 adsorption.
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Affiliation(s)
- Sheree Yau
- Integrative Biology of Marine Organisms Laboratory (BIOM), CNRS UMR7232, 66650 Banuyls-sur-Mer, France.
- Sorbonne University, OOB, Avenue de Pierre Fabre, 66650 Banyuls-sur-Mer, France.
| | - Gaëtan Caravello
- Integrative Biology of Marine Organisms Laboratory (BIOM), CNRS UMR7232, 66650 Banuyls-sur-Mer, France.
- Sorbonne University, OOB, Avenue de Pierre Fabre, 66650 Banyuls-sur-Mer, France.
| | - Nadège Fonvieille
- Integrative Biology of Marine Organisms Laboratory (BIOM), CNRS UMR7232, 66650 Banuyls-sur-Mer, France.
- Sorbonne University, OOB, Avenue de Pierre Fabre, 66650 Banyuls-sur-Mer, France.
| | - Élodie Desgranges
- Integrative Biology of Marine Organisms Laboratory (BIOM), CNRS UMR7232, 66650 Banuyls-sur-Mer, France.
- Sorbonne University, OOB, Avenue de Pierre Fabre, 66650 Banyuls-sur-Mer, France.
| | - Hervé Moreau
- Integrative Biology of Marine Organisms Laboratory (BIOM), CNRS UMR7232, 66650 Banuyls-sur-Mer, France.
- Sorbonne University, OOB, Avenue de Pierre Fabre, 66650 Banyuls-sur-Mer, France.
| | - Nigel Grimsley
- Integrative Biology of Marine Organisms Laboratory (BIOM), CNRS UMR7232, 66650 Banuyls-sur-Mer, France.
- Sorbonne University, OOB, Avenue de Pierre Fabre, 66650 Banyuls-sur-Mer, France.
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Guillory WX, Onyshchenko A, Ruck EC, Parks M, Nakov T, Wickett NJ, Alverson AJ. Recurrent Loss, Horizontal Transfer, and the Obscure Origins of Mitochondrial Introns in Diatoms (Bacillariophyta). Genome Biol Evol 2018; 10:1504-1515. [PMID: 29850800 PMCID: PMC6007386 DOI: 10.1093/gbe/evy103] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2018] [Indexed: 01/23/2023] Open
Abstract
We sequenced mitochondrial genomes from five diverse diatoms (Toxarium undulatum, Psammoneis japonica, Eunotia naegelii, Cylindrotheca closterium, and Nitzschia sp.), chosen to fill important phylogenetic gaps and help us characterize broadscale patterns of mitochondrial genome evolution in diatoms. Although gene content was strongly conserved, intron content varied widely across species. The vast majority of introns were of group II type and were located in the cox1 or rnl genes. Although recurrent intron loss appears to be the principal underlying cause of the sporadic distributions of mitochondrial introns across diatoms, phylogenetic analyses showed that intron distributions superficially consistent with a recurrent-loss model were sometimes more complicated, implicating horizontal transfer as a likely mechanism of intron acquisition as well. It was not clear, however, whether diatoms were the donors or recipients of horizontally transferred introns, highlighting a general challenge in resolving the evolutionary histories of many diatom mitochondrial introns. Although some of these histories may become clearer as more genomes are sampled, high rates of intron loss suggest that the origins of many diatom mitochondrial introns are likely to remain unclear.
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Affiliation(s)
- Wilson X Guillory
- Department of Biological Sciences, University of Arkansas
- Department of Zoology, Southern Illinois University, Carbondale, IL
| | | | | | - Matthew Parks
- Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, Illinois
| | - Teofil Nakov
- Department of Biological Sciences, University of Arkansas
| | - Norman J Wickett
- Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, Illinois
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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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Moniruzzaman M, Gann ER, Wilhelm SW. Infection by a Giant Virus (AaV) Induces Widespread Physiological Reprogramming in Aureococcus anophagefferens CCMP1984 - A Harmful Bloom Algae. Front Microbiol 2018; 9:752. [PMID: 29725322 PMCID: PMC5917014 DOI: 10.3389/fmicb.2018.00752] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/03/2018] [Indexed: 01/05/2023] Open
Abstract
While viruses with distinct phylogenetic origins and different nucleic acid types can infect and lyse eukaryotic phytoplankton, “giant” dsDNA viruses have been found to be associated with important ecological processes, including the collapse of algal blooms. However, the molecular aspects of giant virus–host interactions remain largely unknown. Aureococcus anophagefferens virus (AaV), a giant virus in the Mimiviridae clade, is known to play a critical role in regulating the fate of brown tide blooms caused by the pelagophyte Aureococcus anophagefferens. To understand the physiological response of A. anophagefferens CCMP1984 upon AaV infection, we studied the transcriptomic landscape of this host–virus pair over an entire infection cycle using a RNA-sequencing approach. A massive transcriptional response of the host was evident as early as 5 min post-infection, with modulation of specific processes likely related to both host defense mechanism(s) and viral takeover of the cell. Infected Aureococcus showed a relative suppression of host-cell transcripts associated with photosynthesis, cytoskeleton formation, fatty acid, and carbohydrate biosynthesis. In contrast, host cell processes related to protein synthesis, polyamine biosynthesis, cellular respiration, transcription, and RNA processing were overrepresented compared to the healthy cultures at different stages of the infection cycle. A large number of redox active host-selenoproteins were overexpressed, which suggested that viral replication and assembly progresses in a highly oxidative environment. The majority (99.2%) of annotated AaV genes were expressed at some point during the infection cycle and demonstrated a clear temporal–expression pattern and an increasing relative expression for the majority of the genes through the time course. We detected a putative early promoter motif for AaV, which was highly similar to the early promoter elements of two other Mimiviridae members, indicating some degree of evolutionary conservation of gene regulation within this clade. This large-scale transcriptome study provides insights into the Aureococcus cells infected by a giant virus and establishes a foundation to test hypotheses regarding metabolic and regulatory processes critical for AaV and other Mimiviridae members.
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Affiliation(s)
- Mohammad Moniruzzaman
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA, United States
| | - Eric R Gann
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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Using agro-industrial wastes for the cultivation of microalgae and duckweeds: Contamination risks and biomass safety concerns. Biotechnol Adv 2018; 36:1238-1254. [PMID: 29673973 PMCID: PMC7125918 DOI: 10.1016/j.biotechadv.2018.04.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 04/12/2018] [Accepted: 04/12/2018] [Indexed: 12/17/2022]
Abstract
Aquatic organisms, such as microalgae (Chlorella, Arthrospira (Spirulina), Tetrasselmis, Dunalliela etc.) and duckweed (Lemna spp., Wolffia spp. etc.) are a potential source for the production of protein-rich biomass and for numerous other high-value compounds (fatty acids, pigments, vitamins etc.). Their cultivation using agro-industrial wastes and wastewater (WaW) is of particular interest in the context of a circular economy, not only for recycling valuable nutrients but also for reducing the requirements for fresh water for the production of biomass. Recovery and recycling of nutrients is an unavoidable long-term approach for securing future food and feed production. Agro-industrial WaW are rich in nutrients and have been widely considered as a potential nutrient source for the cultivation of microalgae/duckweed. However, they commonly contain various hazardous contaminants, which could potentially taint the produced biomass, raising various concerns about the safety of their consumption. Herein, an overview of the most important contaminants, including heavy metals and metalloids, pathogens (bacteria, viruses, parasites etc.), and xenobiotics (hormones, antibiotics, parasiticides etc.) is given. It is concluded that pretreatment and processing of WaW is a requisite step for the removal of several contaminants. Among the various technologies, anaerobic digestion (AD) is widely used in practice and offers a technologically mature approach for WaW treatment. During AD, various organic and biological contaminants are significantly removed. Further removal of contaminants could be achieved by post-treatment and processing of digestates (solid/liquid separation, dilution etc.) to further decrease the concentration of contaminants. Moreover, during cultivation an additional removal may occur through various mechanisms, such as precipitation, degradation, and biotransformation. Since many jurisdictions regulate the presence of various contaminants in feed or food setting strict safety monitoring processes, it would be of particular interest to initiate a multi-disciplinary discussion whether agro-industrial WaW ought to be used to cultivate microalgae/duckweed for feed or food production and identify most feasible options for doing this safely. Based on the current body of knowledge it is estimated that AD and post-treatment of WaW can lower significantly the risks associated with heavy metals and pathogens, but it is yet unclear to what extent this is the case for certain persistent xenobiotics.
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Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton. Proc Natl Acad Sci U S A 2017; 114:E7489-E7498. [PMID: 28827361 DOI: 10.1073/pnas.1708097114] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytoplankton community structure is shaped by both bottom-up factors, such as nutrient availability, and top-down processes, such as predation. Here we show that marine viruses can blur these distinctions, being able to amend how host cells acquire nutrients from their environment while also predating and lysing their algal hosts. Viral genomes often encode genes derived from their host. These genes may allow the virus to manipulate host metabolism to improve viral fitness. We identify in the genome of a phytoplankton virus, which infects the small green alga Ostreococcus tauri, a host-derived ammonium transporter. This gene is transcribed during infection and when expressed in yeast mutants the viral protein is located to the plasma membrane and rescues growth when cultured with ammonium as the sole nitrogen source. We also show that viral infection alters the nature of nitrogen compound uptake of host cells, by both increasing substrate affinity and allowing the host to access diverse nitrogen sources. This is important because the availability of nitrogen often limits phytoplankton growth. Collectively, these data show that a virus can acquire genes encoding nutrient transporters from a host genome and that expression of the viral gene can alter the nutrient uptake behavior of host cells. These results have implications for understanding how viruses manipulate the physiology and ecology of phytoplankton, influence marine nutrient cycles, and act as vectors for horizontal gene transfer.
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Novel chaperonins are prevalent in the virioplankton and demonstrate links to viral biology and ecology. ISME JOURNAL 2017; 11:2479-2491. [PMID: 28731469 PMCID: PMC5649160 DOI: 10.1038/ismej.2017.102] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 04/26/2017] [Accepted: 05/06/2017] [Indexed: 12/18/2022]
Abstract
Chaperonins are protein-folding machinery found in all cellular life. Chaperonin genes have been documented within a few viruses, yet, surprisingly, analysis of metagenome sequence data indicated that chaperonin-carrying viruses are common and geographically widespread in marine ecosystems. Also unexpected was the discovery of viral chaperonin sequences related to thermosome proteins of archaea, indicating the presence of virioplankton populations infecting marine archaeal hosts. Virioplankton large subunit chaperonin sequences (GroELs) were divergent from bacterial sequences, indicating that viruses have carried this gene over long evolutionary time. Analysis of viral metagenome contigs indicated that: the order of large and small subunit genes was linked to the phylogeny of GroEL; both lytic and temperate phages may carry group I chaperonin genes; and viruses carrying a GroEL gene likely have large double-stranded DNA (dsDNA) genomes (>70 kb). Given these connections, it is likely that chaperonins are critical to the biology and ecology of virioplankton populations that carry these genes. Moreover, these discoveries raise the intriguing possibility that viral chaperonins may more broadly alter the structure and function of viral and cellular proteins in infected host cells.
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Moniruzzaman M, Wurch LL, Alexander H, Dyhrman ST, Gobler CJ, Wilhelm SW. Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics. Nat Commun 2017; 8:16054. [PMID: 28656958 PMCID: PMC5493757 DOI: 10.1038/ncomms16054] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/16/2017] [Indexed: 01/12/2023] Open
Abstract
Establishing virus–host relationships has historically relied on culture-dependent approaches. Here we report on the use of marine metatranscriptomics to probe virus–host relationships. Statistical co-occurrence analyses of dsDNA, ssRNA and dsRNA viral markers of polyadenylation-selected RNA sequences from microbial communities dominated by Aureococcus anophagefferens (Quantuck Bay, NY), and diatoms (Narragansett Bay, RI) show active infections by diverse giant viruses (NCLDVs) associated with algal and nonalgal hosts. Ongoing infections of A. anophagefferens by a known Mimiviridae (AaV) occur during bloom peak and decline. Bloom decline is also accompanied by increased activity of viruses other than AaV, including (+) ssRNA viruses. In Narragansett Bay, increased temporal resolution reveals active NCLDVs with both ‘boom-and-bust’ and ‘steady-state infection’-like ecologies that include known as well as novel virus–host interactions. Our approach offers a method for screening active viral infections and develops links between viruses and their potential hosts in situ. Our observations further demonstrate that previously unknown virus–host relationships in marine systems are abundant. Viruses are partners in ecosystem ecology, yet their study has been primarily limited to laboratory models virus-host or derived from metagenomics. Here, Moniruzzaman et al. use metatranscriptomics to resolve interactions between giant viruses and single-celled eukaryotic hosts.
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Affiliation(s)
- Mohammad Moniruzzaman
- Department of Microbiology, The University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Louie L Wurch
- Department of Biology, James Madison University, Harrisonburg, Virginia 22807, USA
| | - Harriet Alexander
- Department of Earth and Environmental Science and Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York 10964, USA
| | - Sonya T Dyhrman
- Department of Earth and Environmental Science and Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York 10964, USA
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794, USA
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Tennessee 37996, USA
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Seasonal Dynamics of Haptophytes and dsDNA Algal Viruses Suggest Complex Virus-Host Relationship. Viruses 2017; 9:v9040084. [PMID: 28425942 PMCID: PMC5408690 DOI: 10.3390/v9040084] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/06/2017] [Accepted: 04/13/2017] [Indexed: 01/06/2023] Open
Abstract
Viruses influence the ecology and diversity of phytoplankton in the ocean. Most studies of phytoplankton host-virus interactions have focused on bloom-forming species like Emiliania huxleyi or Phaeocystis spp. The role of viruses infecting phytoplankton that do not form conspicuous blooms have received less attention. Here we explore the dynamics of phytoplankton and algal viruses over several sequential seasons, with a focus on the ubiquitous and diverse phytoplankton division Haptophyta, and their double-stranded DNA viruses, potentially with the capacity to infect the haptophytes. Viral and phytoplankton abundance and diversity showed recurrent seasonal changes, mainly explained by hydrographic conditions. By 454 tag-sequencing we revealed 93 unique haptophyte operational taxonomic units (OTUs), with seasonal changes in abundance. Sixty-one unique viral OTUs, representing Megaviridae and Phycodnaviridae, showed only distant relationship with currently isolated algal viruses. Haptophyte and virus community composition and diversity varied substantially throughout the year, but in an uncoordinated manner. A minority of the viral OTUs were highly abundant at specific time-points, indicating a boom-bust relationship with their host. Most of the viral OTUs were very persistent, which may represent viruses that coexist with their hosts, or able to exploit several host species.
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Ruiz E, Baudoux AC, Simon N, Sandaa RA, Thingstad TF, Pagarete A. Micromonas versus virus: New experimental insights challenge viral impact. Environ Microbiol 2017; 19:2068-2076. [DOI: 10.1111/1462-2920.13733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 03/13/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Eliana Ruiz
- Department of Biology; University of Bergen; Bergen Norway
| | - Anne-Claire Baudoux
- CNRS, UMR 7144 (Adaptation et Diversité en Milieu Marin), Station Biologique de Roscoff; Sorbonne Universités; UPMC Univ Paris 06 Roscoff 29680 France
| | - Nathalie Simon
- CNRS, UMR 7144 (Adaptation et Diversité en Milieu Marin), Station Biologique de Roscoff; Sorbonne Universités; UPMC Univ Paris 06 Roscoff 29680 France
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Wilhelm SW, Bird JT, Bonifer KS, Calfee BC, Chen T, Coy SR, Gainer PJ, Gann ER, Heatherly HT, Lee J, Liang X, Liu J, Armes AC, Moniruzzaman M, Rice JH, Stough JMA, Tams RN, Williams EP, LeCleir GR. A Student's Guide to Giant Viruses Infecting Small Eukaryotes: From Acanthamoeba to Zooxanthellae. Viruses 2017; 9:E46. [PMID: 28304329 PMCID: PMC5371801 DOI: 10.3390/v9030046] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/07/2017] [Accepted: 03/09/2017] [Indexed: 12/15/2022] Open
Abstract
The discovery of infectious particles that challenge conventional thoughts concerning "what is a virus" has led to the evolution a new field of study in the past decade. Here, we review knowledge and information concerning "giant viruses", with a focus not only on some of the best studied systems, but also provide an effort to illuminate systems yet to be better resolved. We conclude by demonstrating that there is an abundance of new host-virus systems that fall into this "giant" category, demonstrating that this field of inquiry presents great opportunities for future research.
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Affiliation(s)
- Steven W Wilhelm
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Jordan T Bird
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Kyle S Bonifer
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Benjamin C Calfee
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Tian Chen
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Samantha R Coy
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - P Jackson Gainer
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Eric R Gann
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Huston T Heatherly
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Jasper Lee
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Xiaolong Liang
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Jiang Liu
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - April C Armes
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Mohammad Moniruzzaman
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - J Hunter Rice
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Joshua M A Stough
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Robert N Tams
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Evan P Williams
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Gary R LeCleir
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
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46
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Wagstaff BA, Vladu IC, Barclay JE, Schroeder DC, Malin G, Field RA. Isolation and Characterization of a Double Stranded DNA Megavirus Infecting the Toxin-Producing Haptophyte Prymnesium parvum. Viruses 2017; 9:v9030040. [PMID: 28282930 PMCID: PMC5371795 DOI: 10.3390/v9030040] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 02/22/2017] [Accepted: 02/27/2017] [Indexed: 01/31/2023] Open
Abstract
Prymnesium parvum is a toxin-producing haptophyte that causes harmful algal blooms globally, leading to large-scale fish kills that have severe ecological and economic implications. For the model haptophyte, Emiliania huxleyi, it has been shown that large dsDNA viruses play an important role in regulating blooms and therefore biogeochemical cycling, but much less work has been done looking at viruses that infect P. parvum, or the role that these viruses may play in regulating harmful algal blooms. In this study, we report the isolation and characterization of a lytic nucleo-cytoplasmic large DNA virus (NCLDV) collected from the site of a harmful P. parvum bloom. In subsequent experiments, this virus was shown to infect cultures of Prymnesium sp. and showed phylogenetic similarity to the extended Megaviridae family of algal viruses.
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Affiliation(s)
- Ben A Wagstaff
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Iulia C Vladu
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - J Elaine Barclay
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | | | - Gill Malin
- Centre for Ocean and Atmospheric Studies, School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window. Viruses 2017; 9:v9010017. [PMID: 28117696 PMCID: PMC5294986 DOI: 10.3390/v9010017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/13/2017] [Accepted: 01/13/2017] [Indexed: 12/16/2022] Open
Abstract
The nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes. Recent studies showed that certain eukaryotes contain fragments of NCLDV DNA integrated in their genome, when surprisingly many of these organisms were not previously shown to be infected by NCLDVs. We performed an update survey of NCLDV genes hidden in eukaryotic sequences to measure the incidence of this phenomenon in common public sequence databases. A total of 66 eukaryotic genomic or transcriptomic datasets-many of which are from algae and aquatic protists-contained at least one of the five most consistently conserved NCLDV core genes. Phylogenetic study of the eukaryotic NCLDV-like sequences identified putative new members of already recognized viral families, as well as members of as yet unknown viral clades. Genomic evidence suggested that most of these sequences resulted from viral DNA integrations rather than contaminating viruses. Furthermore, the nature of the inserted viral genes helped predicting original functional capacities of the donor viruses. These insights confirm that genomic insertions of NCLDV DNA are common in eukaryotes and can be exploited to delineate the contours of NCLDV biodiversity.
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Maumus F, Blanc G. Study of Gene Trafficking between Acanthamoeba and Giant Viruses Suggests an Undiscovered Family of Amoeba-Infecting Viruses. Genome Biol Evol 2016; 8:3351-3363. [PMID: 27811174 PMCID: PMC5203793 DOI: 10.1093/gbe/evw260] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2016] [Indexed: 01/10/2023] Open
Abstract
The nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes. Recent studies showed that certain unicellular eukaryotes contain fragments of NCLDV DNA integrated in their genome, when surprisingly many of these organisms were not previously shown to be infected by NCLDVs. These findings prompted us to search the genome of Acanthamoeba castellanii strain Neff (Neff), one of the most prolific hosts in the discovery of giant NCLDVs, for possible DNA inserts of viral origin. We report the identification of 267 markers of lateral gene transfer with viruses, approximately half of which are clustered in Neff genome regions of viral origins, transcriptionally inactive or exhibit nucleotide-composition signatures suggestive of a foreign origin. The integrated viral genes had diverse origin among relatives of viruses that infect Neff, including Mollivirus, Pandoravirus, Marseillevirus, Pithovirus, and Mimivirus However, phylogenetic analysis suggests the existence of a yet-undiscovered family of amoeba-infecting NCLDV in addition to the five already characterized. The active transcription of some apparently anciently integrated virus-like genes suggests that some viral genes might have been domesticated during the amoeba evolution. These insights confirm that genomic insertion of NCLDV DNA is a common theme in eukaryotes. This gene flow contributed fertilizing the eukaryotic gene repertoire and participated in the occurrence of orphan genes, a long standing issue in genomics. Search for viral inserts in eukaryotic genomes followed by environmental screening of the original viruses should be used to isolate radically new NCLDVs.
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Affiliation(s)
| | - Guillaume Blanc
- Structural and Genomic Information Laboratory (IGS), Aix-Marseille Université, CNRS UMR (IMM FR 3479), Marseille, France
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Higashi A, Fujitani Y, Nakayama N, Tani A, Ueki S. Selective growth promotion of bloom-forming raphidophyte Heterosigma akashiwo by a marine bacterial strain. HARMFUL ALGAE 2016; 60:150-156. [PMID: 28073558 DOI: 10.1016/j.hal.2016.11.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/28/2016] [Accepted: 11/14/2016] [Indexed: 06/06/2023]
Abstract
Algal bloom is typically caused by aberrant propagation of a single species, resulting in its predomination in the local population. While environmental factors including temperature and eutrophication are linked to bloom, the precise mechanism of its formation process is still obscure. Here, we isolated a bacterial strain that promotes growth of Heterosigma akashiwo, a Raphidophyceae that causes harmful algal blooms. Based on 16S rRNA gene sequence, the strain was identified as Altererythrobacter ishigakiensis, a member of the class Alphaproteobacteria. When added to culture, this strain facilitated growth of H. akashiwo and increased its cell culture yield significantly. Importantly, this strain did not affect the growth of other raphidophytes, Chattonella ovate and C. antiqua, indicating that it promotes growth of H. akashiwo in a species-specific manner. We also found that, in co-culture, H. akashiwo suppressed the growth of C. ovate. When A. ishigakiensis was added to the mixed culture, H. akashiwo growth was facilitated while C. ovate propagation was markedly suppressed, indicating that the presence of the bacterium enhances the dominance of H. akashiwo over C. ovate. This is the first example of selective growth promotion of H. akashiwo by a marine bacterium, and may exemplify importance of symbiotic bacterium on algal bloom forming process in general.
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Affiliation(s)
- Aiko Higashi
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Yoshiko Fujitani
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Natsuko Nakayama
- National Research and Development Agency, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
| | - Akio Tani
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Shoko Ueki
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan.
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Quispe CF, Sonderman O, Seng A, Rasmussen B, Weber G, Mueller C, Dunigan DD, Van Etten JL. Three-year survey of abundance, prevalence and genetic diversity of chlorovirus populations in a small urban lake. Arch Virol 2016; 161:1839-47. [PMID: 27068168 DOI: 10.1007/s00705-016-2853-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/30/2016] [Indexed: 11/28/2022]
Abstract
Inland water environments cover about 2.5 percent of our planet and harbor huge numbers of known and still unknown microorganisms. In this report, we examined water samples for the abundance, prevalence, and genetic diversity of a group of infectious viruses (chloroviruses) that infect symbiotic chlorella-like green algae. Samples were collected on a weekly basis for a period of 24 to 36 months from a recreational freshwater lake in Lincoln, Nebraska, and assayed for infectious viruses by plaque assay. The numbers of infectious virus particles were both host- and site-dependent. The consistent fluctuations in numbers of viruses suggest their impact as key factors in shaping microbial community structures in the water surface. Even in low-viral-abundance months, infectious chlorovirus populations were maintained, suggesting either that the viruses are very stable or that there is ongoing viral production in natural hosts.
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Affiliation(s)
- Cristian F Quispe
- Department of Plant Pathology, Plant Science Hall, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
- School of Biological Science, Manter Hall, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
| | - Olivia Sonderman
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Anya Seng
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Brenna Rasmussen
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Garrett Weber
- Department of Plant Pathology, Plant Science Hall, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Claire Mueller
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - David D Dunigan
- Department of Plant Pathology, Plant Science Hall, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - James L Van Etten
- Department of Plant Pathology, Plant Science Hall, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
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