1
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Kuhlisch C, Shemi A, Barak-Gavish N, Schatz D, Vardi A. Algal blooms in the ocean: hot spots for chemically mediated microbial interactions. Nat Rev Microbiol 2024; 22:138-154. [PMID: 37833328 DOI: 10.1038/s41579-023-00975-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2023] [Indexed: 10/15/2023]
Abstract
The cycling of major nutrients in the ocean is affected by large-scale phytoplankton blooms, which are hot spots of microbial life. Diverse microbial interactions regulate bloom dynamics. At the single-cell level, interactions between microorganisms are mediated by small molecules in the chemical crosstalk that determines the type of interaction, ranging from mutualism to pathogenicity. Algae interact with viruses, bacteria, parasites, grazers and other algae to modulate algal cell fate, and these interactions are dependent on the environmental context. Recent advances in mass spectrometry and single-cell technologies have led to the discovery of a growing number of infochemicals - metabolites that convey information - revealing the ability of algal cells to govern biotic interactions in the ocean. The diversity of infochemicals seems to account for the specificity in cellular response during microbial communication. Given the immense impact of algal blooms on biogeochemical cycles and climate regulation, a major challenge is to elucidate how microscale interactions control the fate of carbon and the recycling of major elements in the ocean. In this Review, we discuss microbial interactions and the role of infochemicals in algal blooms. We further explore factors that can impact microbial interactions and the available tools to decipher them in the natural environment.
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Affiliation(s)
- Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Adva Shemi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Barak-Gavish
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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2
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Smith AN, Barton AD. Effects of dispersal and temperature variability on phytoplankton realized temperature niches. Ecol Evol 2024; 14:e10882. [PMID: 38327689 PMCID: PMC10847892 DOI: 10.1002/ece3.10882] [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: 04/12/2023] [Revised: 11/16/2023] [Accepted: 12/11/2023] [Indexed: 02/09/2024] Open
Abstract
Phytoplankton species exhibit fundamental temperature niches that drive observed species distributions linked to realized temperature niches. A recent analysis of field observations of Prochlorococcus showed that for all ecotypes, the realized niche was, on average, colder and wider than the fundamental niche. Using a simple trait-based metacommunity model that resolves fundamental temperature niches for a range of competing phytoplankton, we ask how dispersal and local temperature variability influence species distributions and diversity, and whether these processes help explain the observed discrepancies between fundamental and realized niches for Prochlorococcus. We find that, independently, both dispersal and temperature variability increase realized temperature niche widths and local diversity. The combined effects result in high diversity and realized temperature niches that are consistently wider than fundamental temperature niches. These results have broad implications for understanding the drivers of phytoplankton biogeography as well as for refining species distribution models used to project how climate change impacts phytoplankton distributions.
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Affiliation(s)
- Alaina N. Smith
- Scripps Institution of OceanographyUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Andrew D. Barton
- Scripps Institution of OceanographyUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of Ecology, Behavior and EvolutionUniversity of California San DiegoLa JollaCaliforniaUSA
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3
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Lievens EJP, Agarkova IV, Dunigan DD, Van Etten JL, Becks L. Efficient assays to quantify the life history traits of algal viruses. Appl Environ Microbiol 2023; 89:e0165923. [PMID: 38092674 PMCID: PMC10734466 DOI: 10.1128/aem.01659-23] [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: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 12/22/2023] Open
Abstract
IMPORTANCE Viruses play a crucial role in microbial ecosystems by liberating nutrients and regulating the growth of their hosts. These effects are governed by viral life history traits, i.e., by the traits determining viral reproduction and survival. Understanding these traits is essential to predicting viral effects, but measuring them is generally labor intensive. In this study, we present efficient methods to quantify the full life cycle of lytic viruses. We developed these methods for viruses infecting unicellular Chlorella algae but expect them to be applicable to other lytic viruses that can be quantified by flow cytometry. By making viral phenotypes accessible, our methods will support research into the diversity and ecological effects of microbial viruses.
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Affiliation(s)
- Eva J. P. Lievens
- Aquatic Ecology and Evolution Group, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Irina V. Agarkova
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - David D. Dunigan
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - James L. Van Etten
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Lutz Becks
- Aquatic Ecology and Evolution Group, Limnological Institute, University of Konstanz, Konstanz, Germany
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4
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Listmann L, Peters C, Rahlff J, Esser SP, Schaum CE. Seasonality and Strain Specificity Drive Rapid Co-evolution in an Ostreococcus-Virus System from the Western Baltic Sea. MICROBIAL ECOLOGY 2023; 86:2414-2423. [PMID: 37268771 PMCID: PMC10640450 DOI: 10.1007/s00248-023-02243-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/16/2023] [Indexed: 06/04/2023]
Abstract
Marine viruses are a major driver of phytoplankton mortality and thereby influence biogeochemical cycling of carbon and other nutrients. Phytoplankton-targeting viruses are important components of ecosystem dynamics, but broad-scale experimental investigations of host-virus interactions remain scarce. Here, we investigated in detail a picophytoplankton (size 1 µm) host's responses to infections by species-specific viruses from distinct geographical regions and different sampling seasons. Specifically, we used Ostreococcus tauri and O. mediterraneus and their viruses (size ca. 100 nm). Ostreococcus sp. is globally distributed and, like other picoplankton species, play an important role in coastal ecosystems at certain times of the year. Further, Ostreococcus sp. is a model organism, and the Ostreococcus-virus system is well-known in marine biology. However, only few studies have researched its evolutionary biology and the implications thereof for ecosystem dynamics. The Ostreococcus strains used here stem from different regions of the Southwestern Baltic Sea that vary in salinity and temperature and were obtained during several cruises spanning different sampling seasons. Using an experimental cross-infection set-up, we explicitly confirm species and strain specificity in Ostreococcus sp. from the Baltic Sea. Moreover, we found that the timing of virus-host co-existence was a driver of infection patterns as well. In combination, these findings prove that host-virus co-evolution can be rapid in natural systems.
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Affiliation(s)
- Luisa Listmann
- Institute for Marine Ecosystem and Fisheries Science, University of Hamburg, Olbersweg 24, 22767, Hamburg, Germany.
- Centre for Earth System Science and Sustainability, 20146, Hamburg, Germany.
| | - Carina Peters
- Institute for Marine Ecosystem and Fisheries Science, University of Hamburg, Olbersweg 24, 22767, Hamburg, Germany
- Centre for Earth System Science and Sustainability, 20146, Hamburg, Germany
| | - Janina Rahlff
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Departement of Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39231, Kalmar, Sweden
| | - Sarah P Esser
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
| | - C-Elisa Schaum
- Institute for Marine Ecosystem and Fisheries Science, University of Hamburg, Olbersweg 24, 22767, Hamburg, Germany
- Centre for Earth System Science and Sustainability, 20146, Hamburg, Germany
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5
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Meng L, Delmont TO, Gaïa M, Pelletier E, Fernàndez-Guerra A, Chaffron S, Neches RY, Wu J, Kaneko H, Endo H, Ogata H. Genomic adaptation of giant viruses in polar oceans. Nat Commun 2023; 14:6233. [PMID: 37828003 PMCID: PMC10570341 DOI: 10.1038/s41467-023-41910-6] [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: 02/21/2023] [Accepted: 09/24/2023] [Indexed: 10/14/2023] Open
Abstract
Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of phyla Nucleocytoviricota and Mirusviricota are groups of eukaryote-infecting large and giant DNA viruses with genomes encoding a variety of functions. Here, by leveraging the Global Ocean Eukaryotic Viral database, we investigate the biogeography and functional repertoire of these viruses at a global scale. We first confirm the existence of an ecological barrier that clearly separates polar and nonpolar viral communities, and then demonstrate that temperature drives dramatic changes in the virus-host network at the polar-nonpolar boundary. Ancestral niche reconstruction suggests that adaptation of these viruses to polar conditions has occurred repeatedly over the course of evolution, with polar-adapted viruses in the modern ocean being scattered across their phylogeny. Numerous viral genes are specifically associated with polar adaptation, although most of their homologues are not identified as polar-adaptive genes in eukaryotes. These results suggest that giant viruses adapt to cold environments by changing their functional repertoire, and this viral evolutionary strategy is distinct from the polar adaptation strategy of their hosts.
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Affiliation(s)
- Lingjie Meng
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan
| | - Tom O Delmont
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, F-91057, Evry, France
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, F-75016, Paris, France
| | - Morgan Gaïa
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, F-91057, Evry, France
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, F-75016, Paris, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, F-91057, Evry, France
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, F-75016, Paris, France
| | - Antonio Fernàndez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Samuel Chaffron
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, F-75016, Paris, France
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Russell Y Neches
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan
| | - Junyi Wu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan
| | - Hiroto Kaneko
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan
| | - Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan.
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6
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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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7
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Tong D, Wang Y, Yu H, Shen H, Dahlgren RA, Xu J. Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil. THE ISME JOURNAL 2023:10.1038/s41396-023-01438-5. [PMID: 37248401 DOI: 10.1038/s41396-023-01438-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 05/13/2023] [Accepted: 05/22/2023] [Indexed: 05/31/2023]
Abstract
Viruses are critical for regulating microbial communities and biogeochemical processes affecting carbon/nutrient cycling. However, the role of soil phages in controlling microbial physiological traits and intrinsic dissolved organic matter (DOM) properties remains largely unknown. Herein, microcosm experiments with different soil phage concentrates (including no-added phages, inactive phages, and three dilutions of active phages) at two temperatures (15 °C and 25 °C) were conducted to disclose the nutrient and DOM dynamics associated with viral lysing. Results demonstrated three different phases of viral impacts on CO2 emission at both temperatures, and phages played a role in maintaining Q10 within bounds. At both temperatures, microbial nutrient limitations (especially P limitation) were alleviated by viral lysing as determined by extracellular enzyme activity (decreased Vangle with active phages). Additionally, the re-utilization of lysate-derived DOM by surviving microbes stimulated an increase of microbial metabolic efficiency and recalcitrant DOM components (e.g., SUV254, SUV260 and HIX). This research provides direct experimental evidence that the "viral shuttle" exists in soils, whereby soil phages increase recalcitrant DOM components. Our findings advance the understanding of viral controls on soil biogeochemical processes, and provide a new perspective for assessing whether soil phages provide a net "carbon sink" vs. "carbon source" in soils.
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Affiliation(s)
- Di Tong
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Youjing Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Haodan Yu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Haojie Shen
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Randy A Dahlgren
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China.
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8
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Diaz BP, Gallo F, Moore RH, Bidle KD. Virus infection of phytoplankton increases average molar mass and reduces hygroscopicity of aerosolized organic matter. Sci Rep 2023; 13:7361. [PMID: 37147322 PMCID: PMC10163044 DOI: 10.1038/s41598-023-33818-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 04/19/2023] [Indexed: 05/07/2023] Open
Abstract
Viral infection of phytoplankton is a pervasive mechanism of cell death and bloom termination, which leads to the production of dissolved and colloidal organic matter that can be aerosolized into the atmosphere. Earth-observing satellites can track the growth and death of phytoplankton blooms on weekly time scales but the impact of viral infection on the cloud forming potential of associated aerosols is largely unknown. Here, we determine the influence of viral-derived organic matter, purified viruses, and marine hydrogels on the cloud condensation nuclei activity of their aerosolized solutions, compared to organic exudates from healthy phytoplankton. Dissolved organic material derived from exponentially growing and infected cells of well-characterized eukaryotic phytoplankton host-virus systems, including viruses from diatoms, coccolithophores and chlorophytes, was concentrated, desalted, and nebulized to form aerosol particles composed of primarily of organic matter. Aerosols from infected phytoplankton cultures resulted in an increase in critical activation diameter and average molar mass in three out of five combinations evaluated, along with a decrease in organic kappa (hygroscopicity) compared to healthy cultures and seawater controls. The infected samples also displayed evidence of increased surface tension depression at realistic cloud water vapor supersaturations. Amending the samples with xanthan gum to simulate marine hydrogels increased variability in organic kappa and surface tension in aerosols with high organic to salt ratios. Our findings suggest that the pulses of increased dissolved organic matter associated with viral infection in surface waters may increase the molar mass of dissolved organic compounds relative to surface waters occupied by healthy phytoplankton or low phytoplankton biomass.
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Affiliation(s)
- Ben P Diaz
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, USA
| | - Francesca Gallo
- NASA Langley Research Center, Hampton, VA, USA
- NASA Postdoctoral Program, Oak Ridge Associated Universities, Oak Ridge, TN, USA
| | | | - Kay D Bidle
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, USA.
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9
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Gsell AS, Biere A, de Boer W, de Bruijn I, Eichhorn G, Frenken T, Geisen S, van der Jeugd H, Mason-Jones K, Meisner A, Thakur MP, van Donk E, Zwart MP, Van de Waal DB. Environmental refuges from disease in host-parasite interactions under global change. Ecology 2023; 104:e4001. [PMID: 36799146 DOI: 10.1002/ecy.4001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/04/2022] [Accepted: 12/08/2022] [Indexed: 02/18/2023]
Abstract
The physiological performance of organisms depends on their environmental context, resulting in performance-response curves along environmental gradients. Parasite performance-response curves are generally expected to be broader than those of their hosts due to shorter generation times and hence faster adaptation. However, certain environmental conditions may limit parasite performance more than that of the host, thereby providing an environmental refuge from disease. Thermal disease refuges have been extensively studied in response to climate warming, but other environmental factors may also provide environmental disease refuges which, in turn, respond to global change. Here, we (1) showcase laboratory and natural examples of refuges from parasites along various environmental gradients, and (2) provide hypotheses on how global environmental change may affect these refuges. We strive to synthesize knowledge on potential environmental disease refuges along different environmental gradients including salinity and nutrients, in both natural and food-production systems. Although scaling up from single host-parasite relationships along one environmental gradient to their interaction outcome in the full complexity of natural environments remains difficult, integrating host and parasite performance-response can serve to formulate testable hypotheses about the variability in parasitism outcomes and the occurrence of environmental disease refuges under current and future environmental conditions.
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Affiliation(s)
- Alena S Gsell
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Ecosystem Research Department, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Arjen Biere
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Soil Biology Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Irene de Bruijn
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Koppert, Berkel en Rodenrijs, The Netherlands
| | - Götz Eichhorn
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Centre for Avian Migration and Demography, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Thijs Frenken
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Great Lakes Institute for Environmental Research (GLIER), University of Windsor, Windsor, Ontario, Canada
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Department of Nematology, Wageningen University and Research, Wageningen, The Netherlands
| | - Henk van der Jeugd
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Centre for Avian Migration and Demography, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Kyle Mason-Jones
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Annelein Meisner
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Wageningen University & Research, Wageningen Research, Wageningen, The Netherlands.,Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
| | - Madhav P Thakur
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Terrestrial Ecology Group, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Ellen van Donk
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Mark P Zwart
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Dedmer B Van de Waal
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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10
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Wang S, Yu S, Zhao X, Zhao X, Mason-Jones K, Zhu Z, Redmile-Gordon M, Li Y, Chen J, Kuzyakov Y, Ge T. Experimental evidence for the impact of phages on mineralization of soil-derived dissolved organic matter under different temperature regimes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157517. [PMID: 35872205 DOI: 10.1016/j.scitotenv.2022.157517] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/08/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
Microbial mineralization of dissolved organic matter (DOM) plays an important role in regulating C and nutrient cycling. Viruses are the most abundant biological agents on Earth, but their effect on the density and activity of soil microorganisms and, consequently, on mineralization of DOM under different temperatures remains poorly understood. To assess the impact of viruses on DOM mineralization, we added soil phage concentrate (active vs. inactive phage control) to four DOM extracts containing inoculated microbial communities and incubated them at 18 °C and 23 °C for 32 days. Infection with active phages generally decreased DOM mineralization at day one and showed accelerated DOM mineralization later (especially from day 5 to 15) compared to that with the inactivated phages. Overall, phage infection increased the microbially driven CO2 release. Notably, while higher temperature increased the total CO2 release, the cumulative CO2 release induced by phage infection (difference between active phages and inactivated control) was not affected. However, higher temperatures advanced the response time of the phages but shortening its active period. Our findings suggest that bacterial predation by phages can significantly affect soil DOM mineralization. Therefore, higher temperatures may accelerate host-phage interactions and thus, the duration of C recycling.
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Affiliation(s)
- Shuang Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Senxiang Yu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Xiaoyan Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Xiaolei Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Kyle Mason-Jones
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Zhenke Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Marc Redmile-Gordon
- Department of Environmental Horticulture, Royal Horticultural Society, Wisley GU23 6QB, UK
| | - Yong Li
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Göttingen, 37077 Göttingen, Germany
| | - Tida Ge
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
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11
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Marine viruses and climate change: Virioplankton, the carbon cycle, and our future ocean. Adv Virus Res 2022. [DOI: 10.1016/bs.aivir.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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12
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Xu D, Wang H, Han D, Chen A, Niu Y. Phytoplankton community structural reshaping as response to the thermal effect of cooling water discharged from power plant. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 285:117517. [PMID: 34380219 DOI: 10.1016/j.envpol.2021.117517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/24/2021] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
The increase of water temperature caused by the thermal effect of cooling water discharged from power plants has become a major environmental problem, especially its influence on phytoplankton community. The change of water temperature usually reshapes the structure of phytoplankton community. A research combining phytoplankton community and thermal discharge of power plants was conducted to identify the potential influences. Results indicated the average annual water temperature of the reservoir increased gradually by 5-11 °C because of the thermal discharge. Through annual diversity analysis, 139 species or taxa from 6 phyla (i.e., Bacillariophyta, Chlorophyta, Cyanobacteria, Euglenophyta, Dinoflagellata, and Cryptophyta) were found in different sampling sites, among which Bacillariophyta was the dominant community. Preliminary experimental results revealed the increasing temperature completely reshaped the phytoplankton community structure, especially during the cold season, and this was confirmed by the results of redundancy analysis. In addition, lots of thermophilic genera (i.e., Synedra, Nitzschia, and Navicula) were detected at sampling station 1 (Spt1) and sampling station 2 (Spt2) where the effect of thermal discharge was the most obvious. The increase in biomass and cell count of Bacillariophyta was the result of thermal effect, especially in cold season. Besides, consequences also revealed some environmental parameters (i.e., dissolved oxygen concentration, chlorophyll a concentration, and transparency) were affected by the thermal discharge. Chlorophyll a concentration exhibited a slow rising trend while dissolved oxygen concentration and transparency gradually decreased.
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Affiliation(s)
- Duo Xu
- College of Civil and Architectural Engineering, North China University of Science and Technology, Tangshan, PR China; College of Natural Resources and Environment, Northwest A&F University, Yangling, PR China
| | - Hao Wang
- College of Civil and Architectural Engineering, North China University of Science and Technology, Tangshan, PR China
| | - Dongyun Han
- College of Chemical Engineering, North China University of Science and Technology, Tangshan, PR China.
| | - Aiting Chen
- School of Chemical and Environmental Engineering, China University of Mining and Technology Beijing, Beijing, PR China
| | - Yunxia Niu
- College of Civil and Architectural Engineering, North China University of Science and Technology, Tangshan, PR China
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13
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DeLong JP, Al-Sammak MA, Al-Ameeli ZT, Dunigan DD, Edwards KF, Fuhrmann JJ, Gleghorn JP, Li H, Haramoto K, Harrison AO, Marston MF, Moore RM, Polson SW, Ferrell BD, Salsbery ME, Schvarcz CR, Shirazi J, Steward GF, Van Etten JL, Wommack KE. Towards an integrative view of virus phenotypes. Nat Rev Microbiol 2021; 20:83-94. [PMID: 34522049 DOI: 10.1038/s41579-021-00612-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2021] [Indexed: 12/25/2022]
Abstract
Understanding how phenotypes emerge from genotypes is a foundational goal in biology. As challenging as this task is when considering cellular life, it is further complicated in the case of viruses. During replication, a virus as a discrete entity (the virion) disappears and manifests itself as a metabolic amalgam between the virus and the host (the virocell). Identifying traits that unambiguously constitute a virus's phenotype is straightforward for the virion, less so for the virocell. Here, we present a framework for categorizing virus phenotypes that encompasses both virion and virocell stages and considers functional and performance traits of viruses in the context of fitness. Such an integrated view of virus phenotype is necessary for comprehensive interpretation of viral genome sequences and will advance our understanding of viral evolution and ecology.
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Affiliation(s)
- John P DeLong
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Maitham A Al-Sammak
- Tropical Biological Research Unit, College of Science, University of Baghdad, Baghdad, Iraq.,Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Zeina T Al-Ameeli
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA.,Medical Technical Institutes, Middle Technical University, Baghdad, Iraq
| | - David D Dunigan
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA.,Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Kyle F Edwards
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Jeffry J Fuhrmann
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.,Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Jason P Gleghorn
- Department of Biological Sciences, University of Delaware, Newark, DE, USA.,Department of Biomedical Engineering, University of Delaware, Newark, DE, USA
| | - Hanqun Li
- Department of Biological Sciences, University of Delaware, Newark, DE, USA.,Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Kona Haramoto
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.,Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Amelia O Harrison
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.,Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Marcia F Marston
- Department of Biology and Marine Biology, Roger Williams University, Bristol, RI, USA
| | - Ryan M Moore
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Shawn W Polson
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.,Department of Biological Sciences, University of Delaware, Newark, DE, USA.,Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Barbra D Ferrell
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Miranda E Salsbery
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | - Jasmine Shirazi
- Department of Biomedical Engineering, University of Delaware, Newark, DE, USA
| | - Grieg F Steward
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - James L Van Etten
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA.,Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - K Eric Wommack
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA. .,Department of Biological Sciences, University of Delaware, Newark, DE, USA. .,Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
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14
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Ahamedemujtaba V, Atheena PV, Bhat AI, Krishnamurthy KS, Srinivasan V. Symptoms of piper yellow mottle virus in black pepper as influenced by temperature and relative humidity. Virusdisease 2021; 32:305-313. [PMID: 34423100 DOI: 10.1007/s13337-021-00686-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/26/2021] [Indexed: 11/26/2022] Open
Abstract
Masking of symptoms in winter and their re-appearance in black pepper (Piper nigrum L.) infected with piper yellow mottle virus (PYMoV) in summer is common, especially on new flushes that appear after pre-monsoon showers. Plants of nineteen cultivars of black pepper infected with PYMoV but without any visible symptoms were grown in a polyhouse under natural conditions and in a greenhouse under controlled conditions from January 2019 to January 2020. The number of plants expressing symptoms in the polyhouse increased gradually from 1% during the 3rd standard meteorological week (SMW) (16 January) to 41% during the 21st SMW (22 May), when the afternoon temperature was 30-40 °C and relative humidity (RH) was 75-93%, but began declining thereafter until the 53rd SMW (1 January), when the afternoon temperature was 30-36 °C and RH was 65-86%. The proportion of plants expressing symptoms varied with the cultivar. However, in the greenhouse, in which temperature and RH were maintained at approximately 26 °C and 80%, respectively, not more than 2% of the plants expressed symptoms. The number of symptomatic plants was positively correlated to maximum temperature (T Max) and maximum relative humidity (RH Max) in the afternoon. Based on this observation, a model for predicting the percentage of symptomatic plants was developed using stepwise regression analysis. Plants at the two sites did not differ significantly in the concentration of virus (virus titre) but differed significantly in the content of total carbohydrates, lipid peroxidase, and phenols. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-021-00686-3.
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Affiliation(s)
- V Ahamedemujtaba
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala 673 012 India
| | - P V Atheena
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala 673 012 India
| | - A I Bhat
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala 673 012 India
| | - K S Krishnamurthy
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala 673 012 India
| | - V Srinivasan
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala 673 012 India
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15
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Demory D, Weitz JS, Baudoux AC, Touzeau S, Simon N, Rabouille S, Sciandra A, Bernard O. A thermal trade-off between viral production and degradation drives virus-phytoplankton population dynamics. Ecol Lett 2021; 24:1133-1144. [PMID: 33877734 DOI: 10.1111/ele.13722] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/24/2020] [Accepted: 02/11/2021] [Indexed: 12/13/2022]
Abstract
Marine viruses interact with microbial hosts in dynamic environments shaped by variation in abiotic factors, including temperature. However, the impacts of temperature on viral infection of phytoplankton are not well understood. Here we coupled mathematical modelling with experiments to explore the effect of temperature on virus-phytoplankton interactions. Our model shows the negative consequences of high temperatures on infection and suggests a temperature-dependent threshold between viral production and degradation. Modelling long-term dynamics in environments with different average temperatures revealed the potential for long-term host-virus coexistence, epidemic free or habitat loss states. We generalised our model to variation in global sea surface temperatures corresponding to present and future seas and show that climate change may differentially influence virus-host dynamics depending on the virus-host pair. Temperature-dependent changes in the infectivity of virus particles may lead to shifts in virus-host habitats in warmer oceans, analogous to projected changes in the habitats of macro-, microorganisms and pathogens.
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Affiliation(s)
- David Demory
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anne-Claire Baudoux
- Sorbonne Université, CNRS, UMR 7144 - Ecology of Marine Plankton, Station Biologique de Roscoff, Roscoff, 29860, France
| | - Suzanne Touzeau
- Université Côte d'Azur, INRIA, INRAE, CNRS, Sorbonne Université, BIOCORE, Sophia Antipolis, 06902, France.,Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Natalie Simon
- Sorbonne Université, CNRS, UMR 7144 - Ecology of Marine Plankton, Station Biologique de Roscoff, Roscoff, 29860, France
| | - Sophie Rabouille
- Sorbonne Université, CNRS, UMR 7621 - Laboratoire d'Océanographie Microbienne, Banyuls-sur-Mer, 66650, France
| | - Antoine Sciandra
- Sorbonne Université, CNRS, UMR 7093 - Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, 06230, France
| | - Olivier Bernard
- Université Côte d'Azur, INRIA, INRAE, CNRS, Sorbonne Université, BIOCORE, Sophia Antipolis, 06902, France
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16
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Thiroux S, Dupont S, Nesbø CL, Bienvenu N, Krupovic M, L'Haridon S, Marie D, Forterre P, Godfroy A, Geslin C. The first head-tailed virus, MFTV1, infecting hyperthermophilic methanogenic deep-sea archaea. Environ Microbiol 2020; 23:3614-3626. [PMID: 33022088 DOI: 10.1111/1462-2920.15271] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/20/2020] [Accepted: 10/03/2020] [Indexed: 11/27/2022]
Abstract
Deep-sea hydrothermal vents are inhabited by complex communities of microbes and their viruses. Despite the importance of viruses in controlling the diversity, adaptation and evolution of their microbial hosts, to date, only eight bacterial and two archaeal viruses isolated from abyssal ecosystems have been described. Thus, our efforts focused on gaining new insights into viruses associated with deep-sea autotrophic archaea. Here, we provide the first evidence of an infection of hyperthermophilic methanogenic archaea by a head-tailed virus, Methanocaldococcus fervens tailed virus 1 (MFTV1). MFTV1 has an isometric head of 50 nm in diameter and a 150 nm-long non-contractile tail. Virions are released continuously without causing a sudden drop in host growth. MFTV1 infects Methanocaldococcus species and is the first hyperthermophilic head-tailed virus described thus far. The viral genome is a double-stranded linear DNA of 31 kb. Interestingly, our results suggest potential strategies adopted by the plasmid pMEFER01, carried by M. fervens, to spread horizontally in hyperthermophilic methanogens. The data presented here open a new window of understanding on how the abyssal mobilome interacts with hyperthermophilic marine archaea.
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Affiliation(s)
- Sarah Thiroux
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Samuel Dupont
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Camilla L Nesbø
- Biozone, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G2R3, 12, Canada
| | - Nadège Bienvenu
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, 75015, France
| | - Stéphane L'Haridon
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Dominique Marie
- UPMC Univ Paris 06, INSU-CNRS, UMR 7144, Station Biologique de Roscoff, Sorbonne University, Roscoff, 29680, France
| | - Patrick Forterre
- Archaeal Virology Unit, Institut Pasteur, Paris, 75015, France.,Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS., Gif-sur-Yvette, 91198, France
| | - Anne Godfroy
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Claire Geslin
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
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17
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Abdulrahman Ashy R, Agustí S. Low Host Abundance and High Temperature Determine Switching from Lytic to Lysogenic Cycles in Planktonic Microbial Communities in a Tropical Sea (Red Sea). Viruses 2020; 12:v12070761. [PMID: 32679656 PMCID: PMC7411798 DOI: 10.3390/v12070761] [Citation(s) in RCA: 7] [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: 04/16/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 12/26/2022] Open
Abstract
The lytic and lysogenic life cycles of marine phages are influenced by environmental conditions such as solar radiation, temperature, and host abundance. Temperature can regulate phage infection, but its role is difficult to discern in oligotrophic waters where there is typically low host abundance and high temperatures. Here, we study the temporal variability of viral dynamics and the occurrence of lysogeny using mitomycin C in a eutrophic coastal lagoon in the oligotrophic Red Sea, which showed strong seasonality in terms of temperature (22.1–33.3 °C) and large phytoplankton blooms. Viral abundances ranged from 2.2 × 106 to 1.5 × 107 viruses mL−1 and were closely related to chlorophyll a (chl a) concentration. Observed high virus-to-bacterium ratio (VBR) (4–79; 16 ± 4 (SE)) suggests that phages exerted a tight control of their hosts as indicated by the significant decrease in bacterial abundance with increasing virus concentration. Heterotrophic bacterial abundance also showed a significant decrease with increasing temperature. However, viral abundance was not related to temperature changes and the interaction of water temperature, suggesting an indirect effect of temperature on decreased host abundance, which was observed at the end of the summertime. From the estimated burst size (BS), we observed lysogeny (undetectable to 29.1%) at low percentages of 5.0% ± 1.2 (SE) in half of the incubations with mitomycin C, while it increased to 23.9% ± 2.8 (SE) when the host abundance decreased. The results suggest that lytic phages predominate, switching to a moderate proportion of temperate phages when the host abundance reduces.
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Affiliation(s)
- Ruba Abdulrahman Ashy
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, University of Jeddah, Jeddah 23445, Saudi Arabia
- Correspondence: or (R.A.A.); (S.A.)
| | - Susana Agustí
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
- Correspondence: or (R.A.A.); (S.A.)
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18
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Lin Z, Chen B, Zhao L. Fluorescence-based bioassays with dose-response curve and relative potency in measuring algicidal virulence of Bacillus sp. B1 exudates against Heterosigma akashiwo. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 724:137691. [PMID: 32247969 DOI: 10.1016/j.scitotenv.2020.137691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/14/2020] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
This study demonstrated a Bacillus strain, B1, which was isolated from Pearl river estuary, China, and extracted extracellular algicidal compounds (EACs), exhibited algicidal effects against H. akashiwo upon fertilization experiments (>90% growth inhibition when exposed to 10% volume concentration of EACs within 96 h). Here we evaluated the feasibility of fluorescence-based bioassays (auto or stained fluorescence detected from on PAM fluorometry and flow cytometry) in quantifying algicidal potency of EACs released from Bacillus sp. B1 on H. akashiwo. Esterase activity and maximum photosystem II quantum yield (Fv/Fm) inhibition were used as sensitive endpoints in the bioassays. Logarithmic dose-response curve (DRC) based on three-parameters log-logistic model was applied to derived effective EACs concentrations (ECy, y being typically 10%, 50% or 90% of maximal effect) and relative potency (RP) was used to compare esterase activity and Fv/Fm inhibition sensitivities in dose-dependent manner. Esterase activity inhibition was more sensitive when exposed to low-dose EACs (RP10, fv/fm = 0.57 ± 0.01 < 1), conversely, Fv/Fm inhibition was accepted as a sensitive parameter when H. akashiwo exposed to higher-EACs doses. The fluorescence-based bioassays with dose-response curve and relative potency will help to assess bacterial virulence against H. akashiwo and its physiological mechanistic studies, and may be applicable for further insights into the role and influence of bacteria producing bioactive compounds in harmful algae blooms and shaping marine ecosystems.
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Affiliation(s)
- Zehong Lin
- School of Environment, Jinan University, Panyu Campus, Guangzhou, Guangdong 511443, China
| | - Binbin Chen
- School of Environment, Jinan University, Panyu Campus, Guangzhou, Guangdong 511443, China
| | - Ling Zhao
- School of Environment, Jinan University, Panyu Campus, Guangzhou, Guangdong 511443, China.
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19
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Novel Protocol for Estimating Viruses Specifically Infecting the Marine Planktonic Diatoms. DIVERSITY 2020. [DOI: 10.3390/d12060225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Since their discovery, at least 15 diatom viruses have been isolated and characterised using a culture method with two cycles of extinction dilution. However, the method is time consuming and laborious, and it isolates only the most dominant virus in a water sample. Recent studies have suggested inter-species host specificity of diatom viruses. Here, we describe a new protocol to estimate previously unrecognised host-virus relationships. Host cell cultures after inoculation of natural sediment pore water samples were obtained before complete lysis. The proliferated viral genomes in the host cells were amplified using degenerate primer pairs targeting protein replication regions of single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA) viruses, and then sequenced. Diverse ssRNA virus types within known diatom virus group were detected from inoculated Chaetoceros tenuissimus and C. setoensis cells. A previously unknown ssDNA virus type was detected in inoculated C. tenuissimus cells, but not in C. setoensis cells. Despite the possible protocol biases, for example non-specific adsorptions of virions onto the host cells, the present method helps to estimate the viruses infectious to a single host species. Further improvements to this protocol targeting the proliferated viral genomes might reveal unexpected diatom–virus ecological relationships.
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20
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Linking Light-Dependent Life History Traits with Population Dynamics for Prochlorococcus and Cyanophage. mSystems 2020; 5:5/2/e00586-19. [PMID: 32234774 PMCID: PMC7112961 DOI: 10.1128/msystems.00586-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Prochlorococcus cyanobacteria grow in diurnal rhythms driven by diel cycles. Their ecology depends on light, nutrients, and top-down mortality processes, including lysis by viruses. Cyanophage, viruses that infect cyanobacteria, are also impacted by light. For example, the extracellular viability and intracellular infection kinetics of some cyanophage vary between light and dark conditions. Nonetheless, it remains unclear whether light-dependent viral life history traits scale up to influence population-level dynamics. Here, we examined the impact of diel forcing on both cellular- and population-scale dynamics in multiple Prochlorococcus-phage systems. To do so, we developed a light-driven population model, including both cellular growth and viral infection dynamics. We then tested the model against measurements of experimental infection dynamics with diel forcing to examine the extent to which population level changes in both viral and host abundances could be explained by light-dependent life history traits. Model-data integration reveals that light-dependent adsorption can improve fits to population dynamics for some virus-host pairs. However, light-dependent variation alone does not fully explain realized host and virus population dynamics. Instead, we show evidence consistent with lysis saturation at relatively high virus-to-cell ratios. Altogether, our study represents a quantitative approach to integrate mechanistic models to reconcile Prochlorococcus-virus dynamics spanning cellular-to-population scales.IMPORTANCE The cyanobacterium Prochlorococcus is an essential member of global ocean ecosystems. Light rhythms drive Prochlorococcus photosynthesis, ecology, and interactions with potentially lethal viruses. At present, the impact of light on Prochlorococcus-virus interactions is not well understood. Here, we analyzed Prochlorococcus and virus population dynamics with a light-driven population model and compared our results with experimental data. Our approach revealed that light profoundly drives both cellular- and population-level dynamics for some host-virus systems. However, we also found that additional mechanisms, including lysis saturation, are required to explain observed host-virus dynamics at the population scale. This study provides the basis for future work to understand the intertwined fates of Prochlorococcus and associated viruses in the surface ocean.
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21
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Zimmerman AE, Howard-Varona C, Needham DM, John SG, Worden AZ, Sullivan MB, Waldbauer JR, Coleman ML. Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. Nat Rev Microbiol 2019; 18:21-34. [PMID: 31690825 DOI: 10.1038/s41579-019-0270-x] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2019] [Indexed: 12/23/2022]
Abstract
Ecosystems are controlled by 'bottom-up' (resources) and 'top-down' (predation) forces. Viral infection is now recognized as a ubiquitous top-down control of microbial growth across ecosystems but, at the same time, cell death by viral predation influences, and is influenced by, resource availability. In this Review, we discuss recent advances in understanding the biogeochemical impact of viruses, focusing on how metabolic reprogramming of host cells during lytic viral infection alters the flow of energy and nutrients in aquatic ecosystems. Our synthesis revealed several emerging themes. First, viral infection transforms host metabolism, in part through virus-encoded metabolic genes; the functions performed by these genes appear to alleviate energetic and biosynthetic bottlenecks to viral production. Second, viral infection depends on the physiological state of the host cell and on environmental conditions, which are challenging to replicate in the laboratory. Last, metabolic reprogramming of infected cells and viral lysis alter nutrient cycling and carbon export in the oceans, although the net impacts remain uncertain. This Review highlights the need for understanding viral infection dynamics in realistic physiological and environmental contexts to better predict their biogeochemical consequences.
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Affiliation(s)
- Amy E Zimmerman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | | | - David M Needham
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Seth G John
- Department of Earth Science, University of Southern California, Los Angeles, CA, USA
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, USA.,Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA
| | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA.
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22
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Padfield D, Castledine M, Buckling A. Temperature-dependent changes to host-parasite interactions alter the thermal performance of a bacterial host. ISME JOURNAL 2019; 14:389-398. [PMID: 31628440 DOI: 10.1038/s41396-019-0526-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/18/2019] [Accepted: 09/22/2019] [Indexed: 01/26/2023]
Abstract
Thermal performance curves (TPCs) are used to predict changes in species interactions, and hence, range shifts, disease dynamics and community composition, under forecasted climate change. Species interactions might in turn affect TPCs. Here, we investigate how temperature-dependent changes in a microbial host-parasite interaction (the bacterium Pseudomonas fluorescens, and its lytic bacteriophage, SBW[Formula: see text]) changes the host TPC and the ecological and evolutionary mechanisms underlying these changes. The bacteriophage had a narrower thermal tolerance for infection, with their critical thermal maximum ~6 °C lower than those at which the bacteria still had high growth. Consequently, in the presence of phage, the host TPC changed, resulting in a lower maximum growth rate. These changes were not just driven by differences in thermal tolerance, with temperature-dependent costs of evolved resistance also playing a major role: the largest cost of resistance occurred at the temperature at which bacteria grew best in the absence of phage. Our work highlights how ecological and evolutionary mechanisms can alter the effect of a parasite on host thermal performance, even over very short timescales.
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Affiliation(s)
- Daniel Padfield
- College of Life and Environmental Sciences, Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9EZ, UK.
| | - Meaghan Castledine
- College of Life and Environmental Sciences, Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9EZ, UK
| | - Angus Buckling
- College of Life and Environmental Sciences, Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9EZ, UK
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23
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Needham DM, Poirier C, Hehenberger E, Jiménez V, Swalwell JE, Santoro AE, Worden AZ. Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190086. [PMID: 31587639 PMCID: PMC6792449 DOI: 10.1098/rstb.2019.0086] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Giant viruses have remarkable genomic repertoires—blurring the line with cellular life—and act as top–down controls of eukaryotic plankton. However, to date only six cultured giant virus genomes are available from the pelagic ocean. We used at-sea flow cytometry with staining and sorting designed to target wild predatory eukaryotes, followed by DNA sequencing and assembly, to recover novel giant viruses from the Pacific Ocean. We retrieved four ‘PacV’ partial genomes that range from 421 to 1605 Kb, with 13 contigs on average, including the largest marine viral genomic assembly reported to date. Phylogenetic analyses indicate that three of the new viruses span a clade with deep-branching members of giant Mimiviridae, incorporating the Cafeteria roenbergensis virus, the uncultivated terrestrial Faunusvirus, one PacV from a choanoflagellate and two PacV with unclear hosts. The fourth virus, oPacV-421, is phylogenetically related to viruses that infect haptophyte algae. About half the predicted proteins in each PacV have no matches in NCBI nr (e-value < 10−5), totalling 1735 previously unknown proteins; the closest affiliations of the other proteins were evenly distributed across eukaryotes, prokaryotes and viruses of eukaryotes. The PacVs encode many translational proteins and two encode eukaryotic-like proteins from the Rh family of the ammonium transporter superfamily, likely influencing the uptake of nitrogen during infection. cPacV-1605 encodes a microbial viral rhodopsin (VirR) and the biosynthesis pathway for the required chromophore, the second finding of a choanoflagellate-associated virus that encodes these genes. In co-collected metatranscriptomes, 85% of cPacV-1605 genes were expressed, with capsids, heat shock proteins and proteases among the most highly expressed. Based on orthologue presence–absence patterns across the PacVs and other eukaryotic viruses, we posit the observed viral groupings are connected to host lifestyles as heterotrophs or phototrophs. This article is part of a discussion meeting issue ‘Single cell ecology’.
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Affiliation(s)
- David M Needham
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Camille Poirier
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA.,Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24105, Germany
| | - Elisabeth Hehenberger
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA.,Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24105, Germany
| | - Valeria Jiménez
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Jarred E Swalwell
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA.,School of Oceanography, University of Washington, Box 357940, Seattle, WA 98195, USA
| | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA.,Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24105, Germany
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24
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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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25
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Piedade GJ, Wesdorp EM, Montenegro-Borbolla E, Maat DS, Brussaard CPD. Influence of Irradiance and Temperature on the Virus MpoV-45T Infecting the Arctic Picophytoplankter Micromonas polaris. Viruses 2018; 10:E676. [PMID: 30501060 PMCID: PMC6316886 DOI: 10.3390/v10120676] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/18/2018] [Accepted: 11/27/2018] [Indexed: 11/23/2022] Open
Abstract
Arctic marine ecosystems are currently undergoing rapid changes in temperature and light availability. Picophytoplankton, such as Micromonas polaris, are predicted to benefit from such changes. However, little is known about how these environmental changes affect the viruses that exert a strong mortality pressure on these small but omnipresent algae. Here we report on one-step infection experiments, combined with measurements of host physiology and viability, with 2 strains of M. polaris and the virus MpoV-45T under 3 light intensities (5, 60 and 160 μmol quanta m-2 s-1), 2 light period regimes (16:8 and 24:0 h light:dark cycle) and 2 temperatures (3 and 7 °C). Our results show that low light intensity (16:8 h light:dark) delayed the decline in photosynthetic efficiency and cell lysis, while decreasing burst size by 46%. In contrast, continuous light (24:0 h light:dark) shortened the latent period by 5 h for all light intensities, and even increased the maximum virus production rate and burst size under low light (by 157 and 69%, respectively). Higher temperature (7 °C vs 3 °C) led to earlier cell lysis and increased burst size (by 19%), except for the low light conditions. These findings demonstrate the ecological importance of light in combination with temperature as a controlling factor for Arctic phytoplankton host and virus dynamics seasonally, even more so in the light of global warming.
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Affiliation(s)
- Gonçalo J Piedade
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands.
- Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94248, 1090 GE Amsterdam, The Netherlands.
| | - Ella M Wesdorp
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands.
- Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94248, 1090 GE Amsterdam, The Netherlands.
| | - Elena Montenegro-Borbolla
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands.
- Department of Systems Biology, Spanish National Center for Biotechnology (CNB), Calle Darwin, 3, 28049 Madrid, Spain.
| | - Douwe S Maat
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands.
| | - Corina P D Brussaard
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands.
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26
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Bachy C, Charlesworth CJ, Chan AM, Finke JF, Wong CH, Wei CL, Sudek S, Coleman ML, Suttle CA, Worden AZ. Transcriptional responses of the marine green alga Micromonas pusilla and an infecting prasinovirus under different phosphate conditions. Environ Microbiol 2018; 20:2898-2912. [PMID: 29749714 DOI: 10.1111/1462-2920.14273] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 04/06/2018] [Accepted: 05/07/2018] [Indexed: 12/12/2022]
Abstract
Prasinophytes are widespread marine algae for which responses to nutrient limitation and viral infection are not well understood. We studied the picoprasinophyte, Micromonas pusilla, grown under phosphate-replete (0.65 ± 0.07 d-1 ) and 10-fold lower (low)-phosphate (0.11 ± 0.04 d-1 ) conditions, and infected by the phycodnavirus MpV-SP1. Expression of 17% of Micromonas genes in uninfected cells differed by >1.5-fold (q < 0.01) between nutrient conditions, with genes for P-metabolism and the uniquely-enriched Sel1-like repeat (SLR) family having higher relative transcript abundances, while phospholipid-synthesis genes were lower in low-P than P-replete. Approximately 70% (P-replete) and 30% (low-P) of cells were lysed 24 h post-infection, and expression of ≤5.8% of host genes changed relative to uninfected treatments. Host genes for CAZymes and glycolysis were activated by infection, supporting importance in viral production, which was significantly lower in slower growing (low-P) hosts. All MpV-SP1 genes were expressed, and our analyses suggest responses to differing host-phosphate backgrounds involve few viral genes, while the temporal program of infection involves many more, and is largely independent of host-phosphate background. Our study (i) identifies genes previously unassociated with nutrient acclimation or viral infection, (ii) provides insights into the temporal program of prasinovirus gene expression by hosts and (iii) establishes cell biological aspects of an ecologically important host-prasinovirus system that differ from other marine algal-virus systems.
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Affiliation(s)
- Charles Bachy
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Christina J Charlesworth
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Amy M Chan
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jan F Finke
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Chee-Hong Wong
- Lawrence Berkeley National Laboratory, Sequencing Technology Group, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Chia-Lin Wei
- Lawrence Berkeley National Laboratory, Sequencing Technology Group, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Curtis A Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, M5G 1Z8, Canada.,Departments of Botany, and Microbiology & Immunology, and Institute of Oceans & Fisheries, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA.,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, M5G 1Z8, Canada
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27
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Prasinovirus Attack of Ostreococcus Is Furtive by Day but Savage by Night. J Virol 2018; 92:JVI.01703-17. [PMID: 29187539 PMCID: PMC5790953 DOI: 10.1128/jvi.01703-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/09/2017] [Indexed: 12/12/2022] Open
Abstract
Prasinoviruses are large DNA viruses that infect diverse genera of green microalgae worldwide in aquatic ecosystems, but molecular knowledge of their life cycles is lacking. Several complete genomes of both these viruses and their marine algal hosts are now available and have been used to show the pervasive presence of these species in microbial metagenomes. We have analyzed the life cycle of Ostreococcus tauri virus 5 (OtV5), a lytic virus, using transcriptome sequencing (RNA-Seq) from 12 time points of healthy or infected Ostreococcus tauri cells over a day/night cycle in culture. In the day, viral gene transcription remained low while host nitrogen metabolism gene transcription was initially strongly repressed for two successive time points before being induced for 8 h, but during the night, viral transcription increased steeply while host nitrogen metabolism genes were repressed and many host functions that are normally reduced in the dark appeared to be compensated either by genes expressed from the virus or by increased expression of a subset of 4.4% of the host's genes. Some host cells underwent lysis progressively during the night, but a larger proportion were lysed the following morning. Our data suggest that the life cycles of algal viruses mirror the diurnal rhythms of their hosts.IMPORTANCE Prasinoviruses are common in marine environments, and although several complete genomes of these viruses and their hosts have been characterized, little is known about their life cycles. Here we analyze in detail the transcriptional changes occurring over a 27-h-long experiment in a natural diurnal rhythm, in which the growth of host cells is to some extent synchronized, so that host DNA replication occurs late in the day or early in the night and cell division occurs during the night. Surprisingly, viral transcription remains quiescent over the daytime, when the most energy (from light) is available, but during the night viral transcription activates, accompanied by expression of a few host genes that are probably required by the virus. Although our experiment was accomplished in the lab, cyclical changes have been documented in host transcription in the ocean. Our observations may thus be relevant for eukaryotic phytoplankton in natural environments.
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28
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Maat DS, Biggs T, Evans C, van Bleijswijk JDL, van der Wel NN, Dutilh BE, Brussaard CPD. Characterization and Temperature Dependence of Arctic Micromonas polaris Viruses. Viruses 2017; 9:v9060134. [PMID: 28574420 PMCID: PMC5490811 DOI: 10.3390/v9060134] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 05/24/2017] [Accepted: 05/25/2017] [Indexed: 11/16/2022] Open
Abstract
Global climate change-induced warming of the Artic seas is predicted to shift the phytoplankton community towards dominance of smaller-sized species due to global warming. Yet, little is known about their viral mortality agents despite the ecological importance of viruses regulating phytoplankton host dynamics and diversity. Here we report the isolation and basic characterization of four prasinoviruses infectious to the common Arctic picophytoplankter Micromonas. We furthermore assessed how temperature influenced viral infectivity and production. Phylogenetic analysis indicated that the putative double-stranded DNA (dsDNA) Micromonas polaris viruses (MpoVs) are prasinoviruses (Phycodnaviridae) of approximately 120 nm in particle size. One MpoV showed intrinsic differences to the other three viruses, i.e., larger genome size (205 ± 2 vs. 191 ± 3 Kb), broader host range, and longer latent period (39 vs. 18 h). Temperature increase shortened the latent periods (up to 50%), increased the burst size (up to 40%), and affected viral infectivity. However, the variability in response to temperature was high for the different viruses and host strains assessed, likely affecting the Arctic picoeukaryote community structure both in the short term (seasonal cycles) and long term (global warming).
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Affiliation(s)
- Douwe S Maat
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands.
| | - Tristan Biggs
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands.
| | - Claire Evans
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands.
- Ocean Biogeochemistry & Ecosystems Research Group, National Oceanography Centre, Southampton, European Way, Southampton SO14 3ZH, UK.
| | - Judith D L van Bleijswijk
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands.
| | - Nicole N van der Wel
- Electron Microscopy Center Amsterdam, Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands.
| | - Corina P D Brussaard
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands.
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29
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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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30
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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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31
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Emerging Interaction Patterns in the Emiliania huxleyi-EhV System. Viruses 2017; 9:v9030061. [PMID: 28327527 PMCID: PMC5371816 DOI: 10.3390/v9030061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 01/25/2023] Open
Abstract
Viruses are thought to be fundamental in driving microbial diversity in the oceanic planktonic realm. That role and associated emerging infection patterns remain particularly elusive for eukaryotic phytoplankton and their viruses. Here we used a vast number of strains from the model system Emiliania huxleyi/Emiliania huxleyi Virus to quantify parameters such as growth rate (µ), resistance (R), and viral production (Vp) capacities. Algal and viral abundances were monitored by flow cytometry during 72-h incubation experiments. The results pointed out higher viral production capacity in generalist EhV strains, and the virus-host infection network showed a strong co-evolution pattern between E. huxleyi and EhV populations. The existence of a trade-off between resistance and growth capacities was not confirmed.
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