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Lopez-Simon J, Vila-Nistal M, Rosenova A, De Corte D, Baltar F, Martinez-Garcia M. Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles. Nat Commun 2023; 14:8295. [PMID: 38097581 PMCID: PMC10721903 DOI: 10.1038/s41467-023-44028-x] [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: 05/30/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023] Open
Abstract
Viruses play an important role in the marine ecosystem. However, our comprehension of viruses inhabiting the dark ocean, and in particular, under the Antarctic Ice Shelves, remains limited. Here, we mine single-cell genomic, transcriptomic, and metagenomic data to uncover the viral diversity, biogeography, activity, and their role as metabolic facilitators of microbes beneath the Ross Ice Shelf. This is the largest Antarctic ice shelf with a major impact on global carbon cycle. The viral community found in the cavity under the ice shelf mainly comprises endemic viruses adapted to polar and mesopelagic environments. The low abundance of genes related to lysogenic lifestyle (<3%) does not support a predominance of the Piggyback-the-Winner hypothesis, consistent with a low-productivity habitat. Our results indicate a viral community actively infecting key ammonium and sulfur-oxidizing chemolithoautotrophs (e.g. Nitrosopumilus spp, Thioglobus spp.), supporting a "kill-the-winner" dynamic. Based on genome analysis, these viruses carry specific auxiliary metabolic genes potentially involved in nitrogen, sulfur, and phosphorus acquisition. Altogether, the viruses under Antarctic ice shelves are putatively involved in programming the metabolism of ecologically relevant microbes that maintain primary production in these chemosynthetically-driven ecosystems, which have a major role in global nutrient cycles.
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Affiliation(s)
- Javier Lopez-Simon
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, 03690, Spain
| | - Marina Vila-Nistal
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, 03690, Spain
| | - Aleksandra Rosenova
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, 03690, Spain
| | - Daniele De Corte
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Ocean Technology and Engineering, National Oceanography Centre, Southampton, UK
| | - Federico Baltar
- Department of Functional & Evolutionary Ecology, University of Vienna, Djerassi-Platz 1, 1030, Vienna, Austria.
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, 03690, Spain.
- Instituto Multidisciplinar para el Estudio del Medio Ramon Margalef, University of Alicante, San Vicente del Raspeig, Alicante, 03690, Spain.
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2
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Vila-Nistal M, Maestre-Carballa L, Martinez-Hernández F, Martinez-Garcia M. Novel RNA viruses from the Atlantic Ocean: Ecogenomics, biogeography, and total virioplankton mass contribution from surface to the deep ocean. Environ Microbiol 2023; 25:3151-3160. [PMID: 37696769 DOI: 10.1111/1462-2920.16502] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/04/2023] [Indexed: 09/13/2023]
Abstract
Marine viruses play a major role in the energy and nutrient cycle and affect the evolution of their hosts. Despite their importance, there is still little knowledge about RNA viruses. Here, we have explored the Atlantic Ocean, from surface to deep (4.296 m), and used viromics and quantitative methods to unveil the genomics, biogeography, and the mass contribution of RNA viruses to the total viroplankton. A total of 2481 putative RNA viral contigs (>500 bp) and 107 larger bona fide RNA viral genomes (>2.5 kb) were identified; 88 of them representing novel viruses belonging mostly to two clades: Yangshan assemblage (sister clade to the class Alsuviricetes) and Nodaviridae. These viruses were highly endemic and locally abundant, with little or no presence in other oceans since only ≈15% of them were found in at least one of the Tara sampling metatranscriptomes. Quantitative data indicated that the abundance of RNA viruses in the surface and deep chlorophyll maximum zone was within ≈106 VLP/mL representing a potential contribution of 5.2%-24.4% to the total viroplankton community (DNA and RNA viruses), with DNA viruses being the predominant members (≈107 VLP/mL). However, for the deep sample, the observed trend was the opposite, although as further discussed, several biases should be considered. Together these results contribute to our understanding of the diversity, abundance, and distribution of RNA viruses in the oceans and provide a basis for further investigation into their ecological roles and biogeography.
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Affiliation(s)
- Marina Vila-Nistal
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies (IMEM), University of Alicante, Alicante, Spain
| | - Lucia Maestre-Carballa
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies (IMEM), University of Alicante, Alicante, Spain
| | | | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies (IMEM), University of Alicante, Alicante, Spain
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3
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Han F, Zhang Y, Song N, Gao T. TLR pathway signaling molecules in burbot (Lota lota): molecular characterization, basal expression, and their response to Poly(I:C). FISH & SHELLFISH IMMUNOLOGY 2023; 140:108939. [PMID: 37451526 DOI: 10.1016/j.fsi.2023.108939] [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: 05/12/2023] [Revised: 06/19/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Burbot (Lota lota), a fish species of economic and ecological significance found across northern hemisphere freshwater ecosystems, was the focus of this study. We characterized 19 Toll-like receptor (TLR) genes in burbot, tracing their expression patterns following pathogen exposure. TLR genes, crucial to the innate immune system, including TLR13-1/2/3, TLR2/2-2/2-3/2-4/2-5, and TLR22a/22b/22c/22d, were discovered to be tandemly repeated, signifying an evolution in the fish's immune system. Notably, different TLR subfamilies displayed tissue-specific expressions, with TLR1 primarily in spleen and head kidney, TLR13 in head kidney, trunk kidney, and heart, TLR22 in trunk kidney and liver, and TLR3 and TLR9 predominantly in spleen and head kidney, but also in trunk kidney. Further, we investigated the response of TLR genes in burbot to pathogen exposure using qRT-PCR. This involved measuring mRNA expressions of identified TLR genes in spleen and liver tissues after injecting Poly(I:C) to simulate a double-stranded RNA viral infection. The results revealed a time and tissue-specific expression pattern. Specifically, LoTLR3 reached peak expression in the spleen 12 h post-injection, declining thereafter, while TLR2 subfamily members only began expressing after 24 h. In the liver, activation of the TLR3-IRF7 and TLR3-IRF3 signaling pathways was noted. Integrating these results with transcriptomic data illuminated the pivotal role of TLR genes in the burbot's immune response. Such findings are vital in shaping future disease prevention and treatment strategies.
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Affiliation(s)
- Fei Han
- Fishery College, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Yuan Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, 510301, China
| | - Na Song
- Fishery College, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Tianxiang Gao
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316022, China.
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4
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Dominguez-Huerta G, Wainaina JM, Zayed AA, Culley AI, Kuhn JH, Sullivan MB. The RNA virosphere: How big and diverse is it? Environ Microbiol 2023; 25:209-215. [PMID: 36511833 PMCID: PMC9852017 DOI: 10.1111/1462-2920.16312] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022]
Affiliation(s)
- Guillermo Dominguez-Huerta
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA.,Center of Microbiome Science, Ohio State University, Columbus, Ohio, USA
| | - James M Wainaina
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA.,Center of Microbiome Science, Ohio State University, Columbus, Ohio, USA
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA.,Center of Microbiome Science, Ohio State University, Columbus, Ohio, USA
| | - Alexander I Culley
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA.,Center of Microbiome Science, Ohio State University, Columbus, Ohio, USA.,Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, Ohio, USA
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5
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Diverse RNA Viruses Associated with Diatom, Eustigmatophyte, Dinoflagellate, and Rhodophyte Microalgae Cultures. J Virol 2022; 96:e0078322. [PMID: 36190242 PMCID: PMC9599419 DOI: 10.1128/jvi.00783-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Unicellular microalgae are of immense ecological importance with growing commercial potential in industries such as renewable energy, food, and pharmacology. Viral infections can have a profound impact on the growth and evolution of their hosts. However, very little is known of the diversity within, and the effect of, unicellular microalgal RNA viruses. In addition, identifying RNA viruses in these organisms that could have originated more than a billion years ago constitutes a robust data set to dissect molecular events and address fundamental questions in virus evolution. We assessed the diversity of RNA viruses in eight microalgal cultures, including representatives from the diatom, eustigmatophyte, dinoflagellate, red algae, and euglenid groups. Using metatranscriptomic sequencing combined with bioinformatic approaches optimized to detect highly divergent RNA viruses, we identified 10 RNA virus sequences, with nine constituting new viral species. Most of the newly identified RNA viruses belonged to the double-stranded Totiviridae, Endornaviridae, and Partitiviridae, greatly expanding the reported host range for these families. Two new species belonging to the single-stranded RNA viral clade Marnaviridae, commonly associated with microalgal hosts, were also identified. This study highlights that a substantial diversity of RNA viruses likely exists undetected within the unicellular microalgae. It also highlights the necessity for RNA viral characterization and for investigation of the effects of viral infections on microalgal physiology, biology, and growth, considering their environmental and industrial roles. IMPORTANCE Our knowledge of the diversity of RNA viruses infecting microbial algae-the microalgae-is minimal. However, describing the RNA viruses infecting these organisms is of primary importance at both the ecological and economic scales because of the fundamental roles these organisms play in aquatic environments and their growing value across a range of industrial fields. Using metatranscriptomic sequencing, we aimed to reveal the RNA viruses present in cultures of eight microalgae species belonging to the diatom, dinoflagellate, eustigmatophyte, rhodophyte, and euglena major clades of algae. Accordingly, we identified 10 new divergent RNA virus species belonging to RNA virus families as diverse as the double-stranded Totiviridae, Endornaviridae, and Partitiviridae and the single-stranded Marnaviridae. By expanding the known diversity of RNA viruses infecting unicellular eukaryotes, this study contributes to a better understanding of the early evolution of the virosphere and will inform the use of microalgae in industrial applications.
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6
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Zell R, Groth M, Selinka L, Selinka HC. Picorna-Like Viruses of the Havel River, Germany. Front Microbiol 2022; 13:865287. [PMID: 35444619 PMCID: PMC9013969 DOI: 10.3389/fmicb.2022.865287] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
To improve the understanding of the virome diversity of riverine ecosystems in metropolitan areas, a metagenome analysis was performed with water collected in June 2018 from the river Havel in Berlin, Germany. After enrichment of virus particles and RNA extraction, paired-end Illumina sequencing was conducted and assignment to virus groups and families was performed. This paper focuses on picorna-like viruses, the most diverse and abundant group of viruses with impact on human, animal, and environmental health. Here, we describe altogether 166 viral sequences ranging in size from 1 to 11.5 kb. The 71 almost complete genomes are comprised of one candidate iflavirus, one picornavirus, two polycipiviruses, 27 marnaviruses, 27 dicistro-like viruses, and 13 untypeable viruses. Many partial picorna-like virus sequences up to 10.2 kb were also investigated. The sequences of the Havel picorna-like viruses represent genomes of seven of eight so far known Picornavirales families. Detection of numerous distantly related dicistroviruses suggests the existence of additional, yet unexplored virus groups with dicistronic genomes, including few viruses with unusual genome layout. Of special interest is a clade of dicistronic viruses with capsid protein-encoding sequences at the 5′-end of the genome. Also, monocistronic viruses with similarity of their polymerase and capsid proteins to those of dicistroviruses are interesting. A second protein with NTP-binding site present in the polyprotein of solinviviruses and related viruses needs further attention. The results underline the importance to study the viromes of fluvial ecosystems. So far acknowledged marnaviruses have been isolated from marine organisms. However, the present study and available sequence data suggest that rivers and limnic habitats are relevant ecosystems with circulation of marnaviruses as well as a plethora of unknown picorna-like viruses.
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Affiliation(s)
- Roland Zell
- Section of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Marco Groth
- CF DNA Sequencing, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Lukas Selinka
- Section of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Hans-Christoph Selinka
- Section II 1.4 Microbiological Risks, Department of Environmental Hygiene, German Environment Agency, Berlin, Germany
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7
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Zayed AA, Wainaina JM, Dominguez-Huerta G, Pelletier E, Guo J, Mohssen M, Tian F, Pratama AA, Bolduc B, Zablocki O, Cronin D, Solden L, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Ruscheweyh HJ, Salazar G, Shatoff E, Coordinators TO, Bundschuh R, Fredrick K, Kubatko LS, Chaffron S, Culley AI, Sunagawa S, Kuhn JH, Wincker P, Sullivan MB. Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome. Science 2022; 376:156-162. [PMID: 35389782 PMCID: PMC10990476 DOI: 10.1126/science.abm5847] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of the new phyla "Taraviricota," a missing link in early RNA virus evolution, and "Arctiviricota" are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.
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Affiliation(s)
- Ahmed A. Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - James M. Wainaina
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Guillermo Dominguez-Huerta
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Jiarong Guo
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Mohamed Mohssen
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
| | - Funing Tian
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Akbar Adjie Pratama
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Dylan Cronin
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Lindsey Solden
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Erwan Delage
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Nantes Université, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Corinne da Silva
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Elan Shatoff
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | | | - Ralf Bundschuh
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
- Division of Hematology, Department of Internal Medicine, Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Laura S. Kubatko
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
- Department of Statistics, Ohio State University, Columbus, OH 43210, USA
| | - Samuel Chaffron
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Nantes Université, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Alexander I. Culley
- Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA
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8
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RNA Viruses in Aquatic Ecosystems through the Lens of Ecological Genomics and Transcriptomics. Viruses 2022; 14:v14040702. [PMID: 35458432 PMCID: PMC9029791 DOI: 10.3390/v14040702] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 02/04/2023] Open
Abstract
Massive amounts of data from nucleic acid sequencing have changed our perspective about diversity and dynamics of marine viral communities. Here, we summarize recent metatranscriptomic and metaviromic studies targeting predominantly RNA viral communities. The analysis of RNA viromes reaffirms the abundance of lytic (+) ssRNA viruses of the order Picornavirales, but also reveals other (+) ssRNA viruses, including RNA bacteriophages, as important constituents of extracellular RNA viral communities. Sequencing of dsRNA suggests unknown diversity of dsRNA viruses. Environmental metatranscriptomes capture the dynamics of ssDNA, dsDNA, ssRNA, and dsRNA viruses simultaneously, unravelling the full complexity of viral dynamics in the marine environment. RNA viruses are prevalent in large size fractions of environmental metatranscriptomes, actively infect marine unicellular eukaryotes larger than 3 µm, and can outnumber bacteriophages during phytoplankton blooms. DNA and RNA viruses change abundance on hourly timescales, implying viral control on a daily temporal basis. Metatranscriptomes of cultured protists host a diverse community of ssRNA and dsRNA viruses, often with multipartite genomes and possibly persistent intracellular lifestyles. We posit that RNA viral communities might be more diverse and complex than formerly anticipated and that the influence they exert on community composition and global carbon flows in aquatic ecosystems may be underestimated.
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9
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Solomon C, Hewson I. Putative Invertebrate, Plant, and Wastewater Derived ssRNA Viruses in Plankton of the Anthropogenically Impacted Anacostia River, District of Columbia, USA. Microbes Environ 2022; 37:ME21070. [PMID: 35264468 PMCID: PMC9763036 DOI: 10.1264/jsme2.me21070] [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] [Indexed: 01/05/2023] Open
Abstract
The Anacostia River is a highly impacted watershed in the Northeastern United States which experiences combined sewage outfall in downstream waters. We examined the composition of RNA viruses at three sites in the river using viral metagenomics. Viromes had well represented Picornaviruses, Tombusviruses, Wolframviruses, Nodaviruses, with fewer Tobamoviruses, Sobemoviruses, and Densoviruses (ssDNA). Phylogenetic ana-lyses of detected viruses provide evidence for putatively autochthonous and allochthonous invertebrate, plant, and vertebrate host origin. The number of viral genomes matching Ribovaria increased downstream, and assemblages were most disparate between distant sites, suggesting impacts of the combined sewage overflows at these sites. Additionally, we recovered a densovirus genome fragment which was highly similar to the Clinch ambidensovirus 1, which has been attributed to mass mortality of freshwater mussels in Northeastern America. Taken together, these data suggest that RNA viromes of the Anacostia River reflect autochthonous production of virus particles by benthic metazoan and plants, and inputs from terrestrial habitats including sewage.
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Affiliation(s)
- Caroline Solomon
- School of Science, Technology, Accessibility, Mathematics and Public Health, Gallaudet University, 800 Florida Ave NE, Washington, DC 20002 USA
| | - Ian Hewson
- Department of Microbiology, Cornell University, Wing Hall 403, Ithaca NY 14853 USA, Corresponding author. E-mail: ; Tel: +1–607–255–0151; Fax: +1–607–255–3904
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10
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Lu J, Yang S, Zhang X, Tang X, Zhang J, Wang X, Wang H, Shen Q, Zhang W. Metagenomic Analysis of Viral Community in the Yangtze River Expands Known Eukaryotic and Prokaryotic Virus Diversity in Freshwater. Virol Sin 2022; 37:60-69. [PMID: 35234628 PMCID: PMC8922420 DOI: 10.1016/j.virs.2022.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/03/2021] [Indexed: 11/16/2022] Open
Abstract
Viruses in aquatic ecosystems are characterized by extraordinary abundance and diversity. Thus far, there have been limited studies focused on viral communities in river water systems. Here, we investigated the virome of the Yangtze River Delta using viral metagenomic analysis. The compositions of viral communities from six sampling sites were analyzed and compared. By using library construction and next generation sequencing, contigs and singlet reads similar to viral sequences were classified into 17 viral families, including nine dsDNA viral families, four ssDNA viral families and four RNA viral families. Statistical analysis using Friedman test suggested that there was no significant difference among the six sampling sites (P > 0.05). The viromes in this study were all dominated by the order Caudovirales, and a group of Freshwater phage uvFW species were particularly prevalent among all the samples. The virome from Nanjing presented a unique pattern of viral community composition with a relatively high abundance of family Parvoviridae. Phylogenetic analyses based on virus hallmark genes showed that the Caudovirales order and CRESS-DNA viruses presented high genetic diversity, while viruses in the Microviridae and Parvoviridae families and the Riboviria realm were relatively conservative. Our study provides the first insight into viral community composition in large river ecosystem, revealing the diversity and stability of river water virome, contributing to the proper utilization of freshwater resource. First insight into viral community composition in large river ecosystem. Virus hallmark genes present both diverse and conservative characteristics. The composition of viral communities is similar on the whole. Slight regional variation of virome is existed in individual areas.
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11
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Abstract
Although the knowledge about biological systems has advanced exponentially in recent decades, it is surprising to realize that the very definition of Life keeps presenting theoretical challenges. Even if several lines of reasoning seek to identify the essence of life phenomenon, most of these thoughts contain fundamental problem in their basic conceptual structure. Most concepts fail to identify either necessary or sufficient features to define life. Here, we analyzed the main conceptual frameworks regarding theoretical aspects that have been supporting the most accepted concepts of life, such as (i) the physical, (ii) the cellular and (iii) the molecular approaches. Based on an ontological analysis, we propose that Life should not be positioned under the ontological category of Matter. Yet, life should be better understood under the top-level ontology of "Process". Exercising an epistemological approach, we propose that the essential characteristic that pervades each and every living being is the presence of organic codes. Therefore, we explore theories in biosemiotics and code biology in order to propose a clear concept of life as a macrocode composed by multiple inter-related coding layers. This way, as life is a sort of metaphysical process of encoding, the living beings became the molecular materialization of that process. From the proposed concept, we show that the evolutionary process is a fundamental characteristic for life's maintenance but it is not necessary to define life, as many organisms are clearly alive but they do not participate in the evolutionary process (such as infertile hybrids). The current proposition opens a fertile field of debate in astrobiology, epistemology, biosemiotics, code biology and robotics.
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12
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Chase EE, Monteil-Bouchard S, Gobet A, Andrianjakarivony FH, Desnues C, Blanc G. A High Rate Algal Pond Hosting a Dynamic Community of RNA Viruses. Viruses 2021; 13:2163. [PMID: 34834969 PMCID: PMC8619904 DOI: 10.3390/v13112163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 12/16/2022] Open
Abstract
Despite a surge of RNA virome sequencing in recent years, there are still many RNA viruses to uncover-as indicated by the relevance of viral dark matter to RNA virome studies (i.e., putative viruses that do not match to taxonomically identified viruses). This study explores a unique site, a high-rate algal pond (HRAP), for culturing industrially microalgae, to elucidate new RNA viruses. The importance of viral-host interactions in aquatic systems are well documented, and the ever-expanding microalgae industry is no exception. As the industry becomes a more important source of sustainable plastic manufacturing, a producer of cosmetic pigments and alternative protein sources, and a means of CO2 remediation in the face of climate change, studying microalgal viruses becomes a vital practice for proactive management of microalgae cultures at the industrial level. This study provides evidence of RNA microalgal viruses persisting in a CO2 remediation pilot project HRAP and uncovers the diversity of the RNA virosphere contained within it. Evidence shows that family Marnaviridae is cultured in the basin, alongside other potential microalgal infecting viruses (e.g., family Narnaviridae, family Totitiviridae, and family Yueviridae). Finally, we demonstrate that the RNA viral diversity of the HRAP is temporally dynamic across two successive culturing seasons.
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Affiliation(s)
- Emily E. Chase
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d’Océanologie, 163 Avenue de Luminy, 13009 Marseille, France; (S.M.-B.); (F.H.A.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Sonia Monteil-Bouchard
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d’Océanologie, 163 Avenue de Luminy, 13009 Marseille, France; (S.M.-B.); (F.H.A.)
| | - Angélique Gobet
- MARBEC University Montpellier, CNRS, Ifremer, IRD, 34203 Sète, France;
| | - Felana H. Andrianjakarivony
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d’Océanologie, 163 Avenue de Luminy, 13009 Marseille, France; (S.M.-B.); (F.H.A.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Christelle Desnues
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d’Océanologie, 163 Avenue de Luminy, 13009 Marseille, France; (S.M.-B.); (F.H.A.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Guillaume Blanc
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d’Océanologie, 163 Avenue de Luminy, 13009 Marseille, France; (S.M.-B.); (F.H.A.)
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Zhou H, Chen P, Zhang M, Chen J, Fang J, Li X. Revealing the Viral Community in the Hadal Sediment of the New Britain Trench. Genes (Basel) 2021; 12:genes12070990. [PMID: 34209474 PMCID: PMC8306916 DOI: 10.3390/genes12070990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 12/24/2022] Open
Abstract
Marine viruses are widely distributed and influence matter and energy transformation in ecosystems by modulating hosts’ metabolism. The hadal trenches represent the deepest marine habitat on Earth, for which the viral communities and related biogeochemical functions are least explored and poorly understood. Here, using the sediment samples (8720 m below sea level) collected from the New Britain Trench (NBT), we investigated the viral community, diversity, and genetic potentials in the hadal sediment habitat for the first time by deep shotgun metagenomic sequencing. We found the NBT sediment viral community was dominated by Siphoviridae, Myoviridae, Podoviridae, Mimiviridae, and Phycodnaviridae, which belong to the dsDNA viruses. However, the large majority of them remained uncharacterized. We found the hadal sediment virome had some common components by comparing the hadal sediment viruses with those of hadal aquatic habitats and those of bathypelagic and terrestrial habitats. It was also distinctive in community structure and had many novel viral clusters not associated with the other habitual virome included in our analyses. Further phylogenetic analysis on its Caudovirales showed novel diversities, including new clades specially evolved in the hadal sediment habitat. Annotation of the NBT sediment viruses indicated the viruses might influence microbial hydrocarbon biodegradation and carbon and sulfur cycling via metabolic augmentation through auxiliary metabolic genes (AMGs). Our study filled in the knowledge gaps on the virome of the hadal sediment habitats and provided insight into the evolution and the potential metabolic functions of the hadal sediment virome.
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Affiliation(s)
- Hui Zhou
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Chen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
| | - Mengjie Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawang Chen
- Ocean College, Zhejiang University, Zhoushan 316021, China
- Correspondence: (J.C.); (J.F.); (X.L.)
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
- Correspondence: (J.C.); (J.F.); (X.L.)
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (J.C.); (J.F.); (X.L.)
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14
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Varona JF, Landete P, Lopez-Martin JA, Estrada V, Paredes R, Guisado-Vasco P, de Orueta LF, Torralba M, Fortún J, Vates R, Barberán J, Clotet B, Ancochea J, Carnevali D, Cabello N, Porras L, Gijón P, Monereo A, Abad D, Zúñiga S, Sola I, Rodon J, Izquierdo-Useros N, Fudio S, Pontes MJ, de Rivas B, Girón de Velasco P, Sopesén B, Nieto A, Gómez J, Avilés P, Lubomirov R, White KM, Rosales R, Yildiz S, Reuschl AK, Thorne LG, Jolly C, Towers GJ, Zuliani-Alvarez L, Bouhaddou M, Obernier K, Enjuanes L, Fernández-Sousa JM, Krogan NJ, Jimeno JM, García-Sastre A. Plitidepsin has a positive therapeutic index in adult patients with COVID-19 requiring hospitalization. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.05.25.21257505. [PMID: 34075384 PMCID: PMC8168388 DOI: 10.1101/2021.05.25.21257505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Plitidepsin is a marine-derived cyclic-peptide that inhibits SARS-CoV-2 replication at low nanomolar concentrations by the targeting of host protein eEF1A (eukaryotic translation-elongation-factor-1A). We evaluated a model of intervention with plitidepsin in hospitalized COVID-19 adult patients where three doses were assessed (1.5, 2 and 2.5 mg/day for 3 days, as a 90-minute intravenous infusion) in 45 patients (15 per dose-cohort). Treatment was well tolerated, with only two Grade 3 treatment-related adverse events observed (hypersensitivity and diarrhea). The discharge rates by Days 8 and 15 were 56.8% and 81.8%, respectively, with data sustaining dose-effect. A mean 4.2 log10 viral load reduction was attained by Day 15. Improvement in inflammation markers was also noted in a seemingly dose-dependent manner. These results suggest that plitidepsin impacts the outcome of patients with COVID-19. ONE-SENTENCE SUMMARY Plitidepsin, an inhibitor of SARS-Cov-2 in vitro , is safe and positively influences the outcome of patients hospitalized with COVID-19.
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Oliveira TMD, Burlamaqui TCT, Sá ALAD, Breaux B, Luna FDO, Attademo FLN, Klautau AGCDM, Oliveira JM, Sena L, Criscitiello MF, Schneider MPC. TLR4 and TLR8 variability in Amazonian and West Indian manatee species from Brazil. Genet Mol Biol 2021; 44:e20190252. [PMID: 33847701 PMCID: PMC8042642 DOI: 10.1590/1678-4685-gmb-2019-0252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/29/2021] [Indexed: 11/22/2022] Open
Abstract
Amazonian (Trichechus inunguis) and West Indian (Trichechus manatus) manatees are aquatic mammals vulnerable to extinction found in the Amazon basin and the coastal western Atlantic. Toll-like receptors (TLR) play a key role in recognizing pathogen-associated molecular patterns using leucine-rich repeats (LRRs). We described the diversity of TLR4 and TLR8 genes in these two species of manatee. Amazonian manatee showed seven SNPs in TLR4 and the eight in TLR8, while West Indian manatee shared four and six of those SNPs, respectively. In our analysis, TLR4 showed one non-conservative amino acid replacement substitution in LRR7 and LRR8, on the other hand, TLR8 was less variable and showed only conserved amino acid substitutions. Selection analysis showed that only one TLR4 site was subjected to positive selection and none in TLR8. TLR4 in manatees did not show any evidence of convergent evolution compared to species of the cetacean lineage. Differences in TLR4 and TLR8 polymorphism may be related to distinct selection by pathogens, population reduction of West Indian manatees, or an expected consequence of population expansion in Amazonian manatees. Future studies combining pathogen association and TLR polymorphism may clarify possible roles of these genes and be used for conservation purposes of manatee species.
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Affiliation(s)
| | | | - André Luiz Alves de Sá
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Belém, PA, Brazil.,Universidade Federal Rural da Amazônia, Instituto Socioambiental e dos Recursos Hídricos, Laboratório de Genética Aplicada, Belém, PA, Brazil
| | - Breanna Breaux
- Texas A&M University, College of Veterinary Medicine and Biomedical Sciences, Department of Veterinary Pathobiology, Comparative Immunogenetics Laboratory, College Station, TX, USA
| | - Fábia de Oliveira Luna
- Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos (CMA), Santos, SP, Brazil
| | - Fernanda Löffler Niemeyer Attademo
- Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos (CMA), Itamaracá, PE, Brazil.,Centro de Estudos e Monitoramento Ambiental (CEMAM), Areia Branca, RN, Brazil
| | - Alex Garcia Cavalleiro de Macedo Klautau
- Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Centro Nacional de Pesquisa e Conservação da Biodiversidade Marinha do Norte (CEPNOR), Belém, PA, Brazil
| | - Jairo Moura Oliveira
- Universidade da Amazônia, Parque Zoológico da UNAMA (ZOOUNAMA), Santarém, PA, Brazil
| | - Leonardo Sena
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Belém, PA, Brazil
| | - Michael F Criscitiello
- Texas A&M University, College of Veterinary Medicine and Biomedical Sciences, Department of Veterinary Pathobiology, Comparative Immunogenetics Laboratory, College Station, TX, USA.,Texas A&M University, Texas A&M Health Science Center, College of Medicine, Department of Microbial Pathogenesis and Immunology, College Station, TX, USA
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16
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Sadeghi M, Tomaru Y, Ahola T. RNA Viruses in Aquatic Unicellular Eukaryotes. Viruses 2021; 13:v13030362. [PMID: 33668994 PMCID: PMC7996518 DOI: 10.3390/v13030362] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/05/2021] [Accepted: 02/22/2021] [Indexed: 12/24/2022] Open
Abstract
Increasing sequence information indicates that RNA viruses constitute a major fraction of marine virus assemblages. However, only 12 RNA virus species have been described, infecting known host species of marine single-celled eukaryotes. Eight of these use diatoms as hosts, while four are resident in dinoflagellate, raphidophyte, thraustochytrid, or prasinophyte species. Most of these belong to the order Picornavirales, while two are divergent and fall into the families Alvernaviridae and Reoviridae. However, a very recent study has suggested that there is extraordinary diversity in aquatic RNA viromes, describing thousands of viruses, many of which likely use protist hosts. Thus, RNA viruses are expected to play a major ecological role for marine unicellular eukaryotic hosts. In this review, we describe in detail what has to date been discovered concerning viruses with RNA genomes that infect aquatic unicellular eukaryotes.
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Affiliation(s)
- Mohammadreza Sadeghi
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland
- Correspondence: (M.S.); (T.A.)
| | - Yuji Tomaru
- Environment and Fisheries Applied Techniques Research Department, Fisheries Technology Institute, Fisheries Research and Education Agency, Hatsukaichi, Hiroshima 739-0452, Japan;
| | - Tero Ahola
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland
- Correspondence: (M.S.); (T.A.)
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17
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Vishnyakov AE, Karagodina NP, Lim-Fong G, Ivanov PA, Schwaha TF, Letarov AV, Ostrovsky AN. First evidence of virus-like particles in the bacterial symbionts of Bryozoa. Sci Rep 2021; 11:4. [PMID: 33420126 PMCID: PMC7794531 DOI: 10.1038/s41598-020-78616-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/12/2020] [Indexed: 01/29/2023] Open
Abstract
Bacteriophage communities associated with humans and vertebrate animals have been extensively studied, but the data on phages living in invertebrates remain scarce. In fact, they have never been reported for most animal phyla. Our ultrastructural study showed for the first time a variety of virus-like particles (VLPs) and supposed virus-related structures inside symbiotic bacteria in two marine species from the phylum Bryozoa, the cheilostomes Bugula neritina and Paralicornia sinuosa. We also documented the effect of VLPs on bacterial hosts: we explain different bacterial 'ultrastructural types' detected in bryozoan tissues as stages in the gradual destruction of prokaryotic cells caused by viral multiplication during the lytic cycle. We speculate that viruses destroying bacteria regulate symbiont numbers in the bryozoan hosts, a phenomenon known in some insects. We develop two hypotheses explaining exo- and endogenous circulation of the viruses during the life-cycle of B. neritina. Finally, we compare unusual 'sea-urchin'-like structures found in the collapsed bacteria in P. sinuosa with so-called metamorphosis associated contractile structures (MACs) formed in the cells of the marine bacterium Pseudoalteromonas luteoviolacea which are known to trigger larval metamorphosis in a polychaete worm.
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Affiliation(s)
- A. E. Vishnyakov
- grid.15447.330000 0001 2289 6897Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaja nab. 7/9, Saint Petersburg, Russian Federation 199034
| | - N. P. Karagodina
- grid.15447.330000 0001 2289 6897Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaja nab. 7/9, Saint Petersburg, Russian Federation 199034
| | - G. Lim-Fong
- grid.262455.20000 0001 2205 6070Department of Biology, Randolph-Macon College, 304 Caroline Street, Ashland, VA 23005 USA
| | - P. A. Ivanov
- grid.4886.20000 0001 2192 9124Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7 bld. 2, Moscow, Russian Federation 117312
| | - T. F. Schwaha
- grid.10420.370000 0001 2286 1424Department of Evolutionary Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - A. V. Letarov
- grid.4886.20000 0001 2192 9124Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7 bld. 2, Moscow, Russian Federation 117312 ,grid.14476.300000 0001 2342 9668Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, Moscow, Russian Federation 119234
| | - A. N. Ostrovsky
- grid.15447.330000 0001 2289 6897Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaja nab. 7/9, Saint Petersburg, Russian Federation 199034 ,grid.10420.370000 0001 2286 1424Department of Palaeontology, Faculty of Earth Sciences, Geography and Astronomy, Geozentrum, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
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18
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Hewson I, Aquino CA, DeRito CM. Virome Variation during Sea Star Wasting Disease Progression in Pisaster ochraceus (Asteroidea, Echinodermata). Viruses 2020; 12:E1332. [PMID: 33233680 PMCID: PMC7699681 DOI: 10.3390/v12111332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/08/2020] [Accepted: 11/19/2020] [Indexed: 12/27/2022] Open
Abstract
Sea star wasting disease (SSWD) is a condition that has affected asteroids for over 120 years, yet mechanistic understanding of this wasting etiology remains elusive. We investigated temporal virome variation in two Pisaster ochraceus specimens that wasted in the absence of external stimuli and two specimens that did not experience SSWD for the duration of our study, and compared viromes of wasting lesion margin tissues to both artificial scar margins and grossly normal tissues over time. Global assembly of all SSWD-affected tissue libraries resulted in 24 viral genome fragments represented in >1 library. Genome fragments mostly matched densoviruses and picornaviruses with fewer matching nodaviruses, and a sobemovirus. Picornavirus-like and densovirus-like genome fragments were most similar to viral genomes recovered in metagenomic study of other marine invertebrates. Read recruitment revealed only two picornavirus-like genome fragments that recruited from only SSWD-affected specimens, but neither was unique to wasting lesions. Wasting lesion margin reads recruited to a greater number of viral genotypes (i.e., richness) than did either scar tissue and grossly normal tissue reads. Taken together, these data suggest that no single viral genome fragment was associated with SSWD. Rather, wasting lesion margins may generally support viral proliferation.
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Affiliation(s)
- Ian Hewson
- Department of Microbiology, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14850, USA;
| | - Citlalli A. Aquino
- Department of Biology, Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA 94920, USA;
| | - Christopher M. DeRito
- Department of Microbiology, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14850, USA;
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19
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Girard C, Langlois V, Vigneron A, Vincent WF, Culley AI. Seasonal Regime Shift in the Viral Communities of a Permafrost Thaw Lake. Viruses 2020; 12:v12111204. [PMID: 33105728 PMCID: PMC7690404 DOI: 10.3390/v12111204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/20/2020] [Indexed: 12/18/2022] Open
Abstract
Permafrost thaw lakes including thermokarst lakes and ponds are ubiquitous features of Subarctic and Arctic landscapes and are hotspots of microbial activity. Input of terrestrial organic matter into the planktonic microbial loop of these lakes may greatly amplify global greenhouse gas emissions. This microbial loop, dominated in the summer by aerobic microorganisms including phototrophs, is radically different in the winter, when metabolic processes shift to the anaerobic degradation of organic matter. Little is known about the viruses that infect these microbes, despite evidence that viruses can control microbial populations and influence biogeochemical cycling in other systems. Here, we present the results of a metagenomics-based study of viruses in the larger than 0.22 µm fraction across two seasons (summer and winter) in a permafrost thaw lake in Subarctic Canada. We uncovered 351 viral populations (vOTUs) in the surface waters of this lake, with diversity significantly greater during the summer. We also identified and characterized several phage genomes and prophages, which were mostly present in the summer. Finally, we compared the viral community of this waterbody to other habitats and found unexpected similarities with distant bog lakes in North America.
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Affiliation(s)
- Catherine Girard
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC G1V 0A6, Canada; (C.G.); (V.L.)
- Centre d’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
| | - Valérie Langlois
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC G1V 0A6, Canada; (C.G.); (V.L.)
- Centre d’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
| | - Adrien Vigneron
- Centre d’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Warwick F. Vincent
- Centre d’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Alexander I. Culley
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC G1V 0A6, Canada; (C.G.); (V.L.)
- Centre d’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
- Correspondence:
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Charon J, Marcelino VR, Wetherbee R, Verbruggen H, Holmes EC. Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures. Viruses 2020; 12:v12101180. [PMID: 33086653 PMCID: PMC7594059 DOI: 10.3390/v12101180] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Our knowledge of the diversity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae within which few RNA viruses have been documented. By combining total RNA sequencing with sequence and structural-based homology detection, we identified 18 novel RNA viruses in cultured samples from two major groups of microbial algae: the chlorophytes and the chlorarachniophytes. Most of the RNA viruses identified in the green algae class Ulvophyceae were related to the Tombusviridae and Amalgaviridae viral families commonly associated with land plants. This suggests that the evolutionary history of these viruses extends to divergence events between algae and land plants. Seven Ostreobium sp-associated viruses exhibited sequence similarity to the mitoviruses most commonly found in fungi, compatible with horizontal virus transfer between algae and fungi. We also document, for the first time, RNA viruses associated with chlorarachniophytes, including the first negative-sense (bunya-like) RNA virus in microalgae, as well as a distant homolog of the plant virus Virgaviridae, potentially signifying viral inheritance from the secondary chloroplast endosymbiosis that marked the origin of the chlorarachniophytes. More broadly, these data suggest that the scarcity of RNA viruses in algae results from limited investigation rather than their absence.
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Affiliation(s)
- Justine Charon
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.); (V.R.M.)
| | - Vanessa Rossetto Marcelino
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.); (V.R.M.)
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Richard Wetherbee
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia; (R.W.); (H.V.)
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia; (R.W.); (H.V.)
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.); (V.R.M.)
- Correspondence: ; Tel.: +61-2-9351-5591
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Charon J, Marcelino VR, Wetherbee R, Verbruggen H, Holmes EC. Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures. Viruses 2020; 12:v12101180. [PMID: 33086653 DOI: 10.1101/2020.06.08.141184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 05/26/2023] Open
Abstract
Our knowledge of the diversity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae within which few RNA viruses have been documented. By combining total RNA sequencing with sequence and structural-based homology detection, we identified 18 novel RNA viruses in cultured samples from two major groups of microbial algae: the chlorophytes and the chlorarachniophytes. Most of the RNA viruses identified in the green algae class Ulvophyceae were related to the Tombusviridae and Amalgaviridae viral families commonly associated with land plants. This suggests that the evolutionary history of these viruses extends to divergence events between algae and land plants. Seven Ostreobium sp-associated viruses exhibited sequence similarity to the mitoviruses most commonly found in fungi, compatible with horizontal virus transfer between algae and fungi. We also document, for the first time, RNA viruses associated with chlorarachniophytes, including the first negative-sense (bunya-like) RNA virus in microalgae, as well as a distant homolog of the plant virus Virgaviridae, potentially signifying viral inheritance from the secondary chloroplast endosymbiosis that marked the origin of the chlorarachniophytes. More broadly, these data suggest that the scarcity of RNA viruses in algae results from limited investigation rather than their absence.
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Affiliation(s)
- Justine Charon
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Vanessa Rossetto Marcelino
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Richard Wetherbee
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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Abstract
Interest in coronaviruses because of the 2019 novel coronavirus (SARS-CoV-2) pandemic has generated concern about their occurrence and persistence in aquatic habitats. Coronaviruses are not quantitatively significant constituents of marine virioplankton. Members of the Nidovirales (to which human coronaviruses belong) infect marine mammals, teleosts and possibly invertebrates, and human coronaviruses may persist in marine plankton receiving wastewater effluent. However, virions likely experience significant particle and infectivity decay rates in surface seawater, similar to other enveloped RNA viruses.
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Affiliation(s)
- Gideon J. Mordecai
- Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY, United States
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Abstract
The Arctic is warming at an accelerating pace, and the rise in temperature has increasing impacts on the Arctic biome. Lakes are integrators of their surroundings and thus excellent sentinels of environmental change. Despite their importance in the regulation of key microbial processes, viruses remain largely uncharacterized in Arctic lacustrine environments. We sampled a highly stratified meromictic lake near the northern limit of the Canadian High Arctic, a region in rapid transition due to climate change. We found that the different layers of the lake harbored viral communities that were strikingly dissimilar and highly divergent from known viruses. Viruses were more abundant in the deepest part of the lake containing ancient Arctic Ocean seawater that was trapped during glacial retreat and were genomically unlike any viruses previously described. This research demonstrates the complexity and novelty of viral communities in an environment that is vulnerable to ongoing perturbation. High-latitude, perennially stratified (meromictic) lakes are likely to be especially vulnerable to climate warming because of the importance of ice in maintaining their water column structure and associated distribution of microbial communities. This study aimed to characterize viral abundance, diversity, and distribution in a meromictic lake of marine origin on the far northern coast of Ellesmere Island, in the Canadian High Arctic. We collected triplicate samples for double-stranded DNA (dsDNA) viromics from five depths that encompassed the major features of the lake, as determined by limnological profiling of the water column. Viral abundance and virus-to-prokaryote ratios were highest at greater depths, while bacterial and cyanobacterial counts were greatest in the surface waters. The viral communities from each zone of the lake defined by salinity, temperature, and dissolved oxygen concentrations were markedly distinct, suggesting that there was little exchange of viral types among lake strata. Ten viral assembled genomes were obtained from our libraries, and these also segregated with depth. This well-defined structure of viral communities was consistent with that of potential hosts. Viruses from the monimolimnion, a deep layer of ancient Arctic Ocean seawater, were more diverse and relatively abundant, with few similarities to available viral sequences. The Lake A viral communities also differed from published records from the Arctic Ocean and meromictic Ace Lake in Antarctica. This first characterization of viral diversity from this sentinel environment underscores the microbial richness and complexity of an ecosystem type that is increasingly exposed to major perturbations in the fast-changing Arctic. IMPORTANCE The Arctic is warming at an accelerating pace, and the rise in temperature has increasing impacts on the Arctic biome. Lakes are integrators of their surroundings and thus excellent sentinels of environmental change. Despite their importance in the regulation of key microbial processes, viruses remain largely uncharacterized in Arctic lacustrine environments. We sampled a highly stratified meromictic lake near the northern limit of the Canadian High Arctic, a region in rapid transition due to climate change. We found that the different layers of the lake harbored viral communities that were strikingly dissimilar and highly divergent from known viruses. Viruses were more abundant in the deepest part of the lake containing ancient Arctic Ocean seawater that was trapped during glacial retreat and were genomically unlike any viruses previously described. This research demonstrates the complexity and novelty of viral communities in an environment that is vulnerable to ongoing perturbation.
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Starr EP, Nuccio EE, Pett-Ridge J, Banfield JF, Firestone MK. Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil. Proc Natl Acad Sci U S A 2019; 116:25900-25908. [PMID: 31772013 PMCID: PMC6926006 DOI: 10.1073/pnas.1908291116] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health, and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in soil, 1 of the most complex microbial systems. Here, we assembled 48 individual metatranscriptomes from 4 habitats within a planted soil sampled over a 22-d time series: Rhizosphere alone, detritosphere alone, rhizosphere with added root detritus, and unamended soil (4 time points and 3 biological replicates). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker genes. Based on viral phylogeny, much of the diversity was Narnaviridae that may parasitize fungi or Leviviridae, which may infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral and host communities were structured based on the presence of root litter. Clear temporal dynamics by Leviviridae and their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant, and active in soil. When viral infection causes host cell death, it may mobilize cell carbon in a process that may represent an overlooked component of soil carbon cycling.
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Affiliation(s)
- Evan P Starr
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Erin E Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA 94720;
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720
- Chan Zuckerberg Biohub, San Francisco, CA 94158
- Innovative Genomics Institute, Berkeley, CA 94720
| | - Mary K Firestone
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720
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Xue X, Woldemariam NT, Caballero-Solares A, Umasuthan N, Fast MD, Taylor RG, Rise ML, Andreassen R. Dietary Immunostimulant CpG Modulates MicroRNA Biomarkers Associated with Immune Responses in Atlantic Salmon ( Salmo salar). Cells 2019; 8:E1592. [PMID: 31817907 PMCID: PMC6952924 DOI: 10.3390/cells8121592] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are key regulators in fish immune responses. However, no study has previously characterized the impact of polyriboinosinic polyribocytidylic acid (pIC) and formalin-killed typical Aeromonas salmonicida (ASAL) on miRNA expression in Atlantic salmon fed a commercial diet with and without immunostimulant CpG. To this end, first, we performed small RNA deep sequencing and qPCR analyses to identify and confirm pIC- and/or ASAL-responsive miRNAs in the head kidney of salmon fed a control diet. DESeq2 analyses identified 12 and 18 miRNAs differentially expressed in pIC and ASAL groups, respectively, compared to the controls. Fifteen of these miRNAs were studied by qPCR; nine remained significant by qPCR. Five miRNAs (miR-27d-1-2-5p, miR-29b-2-5p, miR-146a-5p, miR-146a-1-2-3p, miR-221-5p) were shown by qPCR to be significantly induced by both pIC and ASAL. Second, the effect of CpG-containing functional feed on miRNA expression was investigated by qPCR. In pre-injection samples, 6 of 15 miRNAs (e.g., miR-181a-5-3p, miR-462a-3p, miR-722-3p) had significantly lower expression in fish fed CpG diet than control diet. In contrast, several miRNAs (e.g., miR-146a-1-2-3p, miR-192a-5p, miR-194a-5p) in the PBS- and ASAL-injected groups had significantly higher expression in CpG-fed fish. Multivariate statistical analyses confirmed that the CpG diet had a greater impact on miRNA expression in ASAL-injected compared with pIC-injected fish. This study identified immune-relevant miRNA biomarkers that will be valuable in the development of diets to combat infectious diseases of salmon.
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Affiliation(s)
- Xi Xue
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada; (A.C.-S.); (N.U.)
| | - Nardos Tesfaye Woldemariam
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet–Oslo Metropolitan University, N-0130 Oslo, Norway; (N.T.W.); (R.A.)
| | - Albert Caballero-Solares
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada; (A.C.-S.); (N.U.)
| | - Navaneethaiyer Umasuthan
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada; (A.C.-S.); (N.U.)
| | - Mark D. Fast
- Hoplite Laboratory, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada;
| | - Richard G. Taylor
- Cargill Animal Nutrition, 10383 165th Avenue NW, Elk River, MN 55330, USA;
| | - Matthew L. Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada; (A.C.-S.); (N.U.)
| | - Rune Andreassen
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet–Oslo Metropolitan University, N-0130 Oslo, Norway; (N.T.W.); (R.A.)
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Wang Q, Liu Y, Liu Q, Liu X, Yang F, Wang M, Shao H, Jiang Y. Isolation and Complete Genome of the Marine Pseudoalteromonas Phage C7 from Coastal Seawater of Yellow Sea, China. Curr Microbiol 2019; 77:279-285. [DOI: 10.1007/s00284-019-01815-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/14/2019] [Indexed: 12/11/2022]
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de Farias ST, Jheeta S, Prosdocimi F. Viruses as a survival strategy in the armory of life. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2019; 41:45. [PMID: 31612293 DOI: 10.1007/s40656-019-0287-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/08/2019] [Indexed: 06/10/2023]
Abstract
Viruses have generally been thought of as infectious agents. New data on mimivirus, however, suggests a reinterpretation of this thought. Earth's biosphere seems to contain many more viruses than previously thought and they are relevant in the maintenance of ecosystems and biodiversity. Viruses are not considered to be alive because they are not free-living entities and do not have cellular units. Current hypotheses indicate that some viruses may have been the result of genomic reduction of cellular life forms. However, new studies relating to the origins of biological systems suggest that viruses could also have originated during the transition from First to the Last Universal Common Ancestor (from FUCA to LUCA). Within this setting, life has been established as chemical informational system and could be interpreted as a macrocode of multiple layers. The first entity to acquire these features was the First Universal Common Ancestor (FUCA) that evolved to an intermediate ancestral that could be named T-LUCA (Transitional-LUCA) and be equated to Woese's concept of progenotes. T-LUCA may have remained as undifferentiated subsystems with viruses-like structures. The net result is that both cellular life forms and viruses shared protein synthesis apparatuses. In short, virus is a strategy of life reached by two paths: T-LUCAs like entities and the reduction of cellular life forms.
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Affiliation(s)
- Sávio Torres de Farias
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil.
- Departamento de Filosofia, Programa de Pós-Graduação em Filosofia, Universidade Federal de Santa Catarina, Florianopólis, Santa Catarina, Brazil.
| | - Sohan Jheeta
- Network of Researchers on the Chemical Evolution of Life, Leeds, UK
| | - Francisco Prosdocimi
- Laboratório de Biologia Teórica e de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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Tschá MK, Suzukawa AA, Gräf T, Piancini LDS, da Silva AM, Faoro H, Riediger IN, Medeiros LC, Wowk PF, Zanluca C, Duarte Dos Santos CN. Identification of a novel alphavirus related to the encephalitis complexes circulating in southern Brazil. Emerg Microbes Infect 2019; 8:920-933. [PMID: 31237479 PMCID: PMC6598490 DOI: 10.1080/22221751.2019.1632152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In early 2017, an outbreak caused by an unknown and supposedly viral agent in the Marilena region of southern Brazil was investigated. Since the etiological agent causing the outbreak was not identified from human samples, mosquitoes from this region were collected. Three out of 121 mosquito pools collected from the region tested positive for alphavirus in molecular tests. Next generation sequencing results revealed the presence of a novel alphavirus, tentatively named here as Caainguá virus (CAAV). DNA barcoding analyses indicated that different species of Culex are hosts for CAAV. This new virus was basal to the New World encephalitic alphaviruses in a comprehensive and robust phylogenetic approach using complete genomes. Viral particles were observed in the cytosol and inside of intracellular compartments of cells in mosquito-derived cell cultures. Despite being noninfectious in vertebrate derived cell cultures, primary culturing of CAAV in human mononuclear cells suggests monocytes and lymphocytes as CAAV targets. However, the epidemiological link of CAAV on the human outbreak should be further explored.
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Affiliation(s)
- Marcel Kruchelski Tschá
- a Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz PR , Curitiba , Brazil
| | - Andreia Akemi Suzukawa
- a Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz PR , Curitiba , Brazil
| | - Tiago Gräf
- b Departamento de Genética , Instituto de Biologia, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
| | | | - Allan Martins da Silva
- c Laboratório Central, Secretaria da Saúde do Estado do Paraná , São José dos Pinhais , Brazil
| | - Helisson Faoro
- d Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas/Fiocruz PR , Curitiba , Brazil
| | | | - Lia Carolina Medeiros
- e Laboratório de Biologia Celular, Instituto Carlos Chagas/Fiocruz PR , Curitiba , Brazil
| | - Pryscilla Fanini Wowk
- a Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz PR , Curitiba , Brazil
| | - Camila Zanluca
- a Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz PR , Curitiba , Brazil
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Zhang Z, Mu Y, Shan L, Sun D, Guo W, Yu Z, Tian R, Xu S, Yang G. Divergent Evolution of TRC Genes in Mammalian Niche Adaptation. Front Immunol 2019; 10:871. [PMID: 31068942 PMCID: PMC6491686 DOI: 10.3389/fimmu.2019.00871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/04/2019] [Indexed: 12/01/2022] Open
Abstract
Mammals inhabit a wide variety of ecological niches, which in turn can be affected by various ecological factors, especially in relation to immunity. The canonical TRC repertoire (TRAC, TRBC, TRGC, and TRDC) codes C regions of T cell receptor chains that form the primary antigen receptors involved in the activation of cellular immunity. At present, little is known about the correlation between the evolution of mammalian TRC genes and ecological factors. In this study, four types canonical of TRC genes were identified from 37 mammalian species. Phylogenetic comparative methods (phyANOVA and PGLS) and selective pressure analyses among different groups of ecological factors (habitat, diet, and sociality) were carried out. The results showed that habitat was the major ecological factor shaping mammalian TRC repertoires. Specifically, trade-off between TRGC numbers and positive selection of TRAC and the balanced evolutionary rates between TRAC and TRDC genes were speculated as two main mechanisms in adaption to habitat and sociality. Overall, our study suggested divergent mechanisms for the evolution of TRCs, prompting mammalian immunity adaptions within diverse niches.
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Affiliation(s)
- Zepeng Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yuan Mu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lei Shan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Di Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Weijian Guo
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhenpeng Yu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ran Tian
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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Abstract
Very little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new viruses discovered in this study are representative of the most abundant family of marine RNA viruses, the Marnaviridae, and expand our view of the diversity of this important group. Overall, our data and analyses provide a foundation for interpreting marine RNA virus diversity and evolution. RNA viruses, particularly genetically diverse members of the Picornavirales, are widespread and abundant in the ocean. Gene surveys suggest that there are spatial and temporal patterns in the composition of RNA virus assemblages, but data on their diversity and genetic variability in different oceanographic settings are limited. Here, we show that specific RNA virus genomes have widespread geographic distributions and that the dominant genotypes are under purifying selection. Genomes from three previously unknown picorna-like viruses (BC-1, -2, and -3) assembled from a coastal site in British Columbia, Canada, as well as marine RNA viruses JP-A, JP-B, and Heterosigma akashiwo RNA virus exhibited different biogeographical patterns. Thus, biotic factors such as host specificity and viral life cycle, and not just abiotic processes such as dispersal, affect marine RNA virus distribution. Sequence differences relative to reference genomes imply that virus quasispecies are under purifying selection, with synonymous single-nucleotide variations dominating in genomes from geographically distinct regions resulting in conservation of amino acid sequences. Conversely, sequences from coastal South Africa that mapped to marine RNA virus JP-A exhibited more nonsynonymous mutations, probably representing amino acid changes that accumulated over a longer separation. This biogeographical analysis of marine RNA viruses demonstrates that purifying selection is occurring across oceanographic provinces. These data add to the spectrum of known marine RNA virus genomes, show the importance of dispersal and purifying selection for these viruses, and indicate that closely related RNA viruses are pathogens of eukaryotic microbes across oceans. IMPORTANCE Very little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new viruses discovered in this study are representative of the most abundant family of marine RNA viruses, the Marnaviridae, and expand our view of the diversity of this important group. Overall, our data and analyses provide a foundation for interpreting marine RNA virus diversity and evolution.
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Moniruzzaman M, Gann ER, Wilhelm SW. Infection by a Giant Virus (AaV) Induces Widespread Physiological Reprogramming in Aureococcus anophagefferens CCMP1984 - A Harmful Bloom Algae. Front Microbiol 2018; 9:752. [PMID: 29725322 PMCID: PMC5917014 DOI: 10.3389/fmicb.2018.00752] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/03/2018] [Indexed: 01/05/2023] Open
Abstract
While viruses with distinct phylogenetic origins and different nucleic acid types can infect and lyse eukaryotic phytoplankton, “giant” dsDNA viruses have been found to be associated with important ecological processes, including the collapse of algal blooms. However, the molecular aspects of giant virus–host interactions remain largely unknown. Aureococcus anophagefferens virus (AaV), a giant virus in the Mimiviridae clade, is known to play a critical role in regulating the fate of brown tide blooms caused by the pelagophyte Aureococcus anophagefferens. To understand the physiological response of A. anophagefferens CCMP1984 upon AaV infection, we studied the transcriptomic landscape of this host–virus pair over an entire infection cycle using a RNA-sequencing approach. A massive transcriptional response of the host was evident as early as 5 min post-infection, with modulation of specific processes likely related to both host defense mechanism(s) and viral takeover of the cell. Infected Aureococcus showed a relative suppression of host-cell transcripts associated with photosynthesis, cytoskeleton formation, fatty acid, and carbohydrate biosynthesis. In contrast, host cell processes related to protein synthesis, polyamine biosynthesis, cellular respiration, transcription, and RNA processing were overrepresented compared to the healthy cultures at different stages of the infection cycle. A large number of redox active host-selenoproteins were overexpressed, which suggested that viral replication and assembly progresses in a highly oxidative environment. The majority (99.2%) of annotated AaV genes were expressed at some point during the infection cycle and demonstrated a clear temporal–expression pattern and an increasing relative expression for the majority of the genes through the time course. We detected a putative early promoter motif for AaV, which was highly similar to the early promoter elements of two other Mimiviridae members, indicating some degree of evolutionary conservation of gene regulation within this clade. This large-scale transcriptome study provides insights into the Aureococcus cells infected by a giant virus and establishes a foundation to test hypotheses regarding metabolic and regulatory processes critical for AaV and other Mimiviridae members.
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Affiliation(s)
- Mohammad Moniruzzaman
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA, United States
| | - Eric R Gann
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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Abstract
Viruses are integral to ecological and evolutionary processes, but we have a poor understanding of what drives variation in key traits across diverse viruses. For lytic viruses, burst size, latent period, and genome size are primary characteristics controlling host-virus dynamics. Here we synthesize data on these traits for 75 strains of phytoplankton viruses, which play an important role in global biogeochemistry. We find that primary traits of the host (genome size, growth rate) explain 40%-50% of variation in burst size and latent period. Specifically, burst size and latent period both exhibit saturating relationships versus the host∶virus genome size ratio, with both traits increasing at low genome size ratios while showing no relationship at high size ratios. In addition, latent period declines as host growth rate increases. We analyze a model of latent period evolution to explore mechanisms that could cause these patterns. The model predicts that burst size may often be set by the host genomic resources available for viral construction, while latent period evolves to permit this maximal burst size, modulated by host metabolic rate. These results suggest that general mechanisms may underlie the evolution of diverse viruses. Future extensions of this work could help explain viral regulation of host populations, viral influence on community structure and diversity, and viral roles in biogeochemical cycles.
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Hewson I, Bistolas KSI, Button JB, Jackson EW. Occurrence and seasonal dynamics of RNA viral genotypes in three contrasting temperate lakes. PLoS One 2018; 13:e0194419. [PMID: 29543885 PMCID: PMC5854377 DOI: 10.1371/journal.pone.0194419] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/04/2018] [Indexed: 11/18/2022] Open
Abstract
Decades of research have demonstrated the crucial importance of viruses in freshwater ecosystems. However, few studies have focused on the seasonal dynamics and potential hosts of RNA viruses. We surveyed microbial-sized (i.e. 5-0.2 μm) mixed community plankton transcriptomes for RNA viral genomes and investigated their distribution between microbial and macrobial plankton over a seasonal cycle across three temperate lakes by quantitative reverse transcriptase PCR (qRT-PCR). A total of 30 contigs bearing similarity to RNA viral genomes were recovered from a global assembly of 30 plankton RNA libraries. Of these, only 13 were found in >2 libraries and recruited >100 reads (of 9.13 x 107 total reads), representing several picornaviruses, two tobamoviruses and a reovirus. We quantified the abundance of four picornaviruses and the reovirus monthly from August 2014 to May 2015. Patterns of viral abundance in the >5 μm size fraction and representation in microbial-sized community RNA libraries over time suggest that one picornavirus genotype (TS24835) and the reovirus (TS148892) may infect small (<5 μm) eukaryotic microorganisms, while two other picornaviruses (TS24641 and TS4340) may infect larger (>5 μm) eukaryotic microorganisms or metazoa. Our data also suggest that picornavirus TS152062 may originate from an allochthonous host. All five viral genotypes were present in at least one size fraction across all 3 lakes during the year, suggesting that RNA viruses may easily disperse between adjacent aquatic habitats. Our data therefore demonstrate that RNA viruses are widespread in temperate lacustrine ecosystems, and may provide evidence of viral infection in larger eukaryotes (including metazoa) inhabiting the lakes.
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Affiliation(s)
- Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
| | - Kalia S. I. Bistolas
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
| | - Jason B. Button
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
| | - Elliot W. Jackson
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
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Discovery of microRNAs associated with the antiviral immune response of Atlantic cod macrophages. Mol Immunol 2017; 93:152-161. [PMID: 29190475 DOI: 10.1016/j.molimm.2017.11.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/13/2017] [Accepted: 11/17/2017] [Indexed: 02/08/2023]
Abstract
MicroRNAs (miRNAs) are known to play important immunoregulatory roles in teleosts, although miRNAs involved in the antiviral immune response of Atlantic cod (Gadus morhua) were previously uncharacterised. Using deep sequencing and qPCR, the present study was conducted to identify miRNAs responsive to the viral mimic, polyriboinosinic polyribocytidylic acid (pIC) in Atlantic cod macrophages. Macrophage samples isolated from Atlantic cod (n=3) and treated with pIC or phosphate buffered saline (PBS control) for 24 and 72h were used for miRNA profiling. Following deep sequencing, DESeq2 analyses identified four (miR-731-3p, miR-125b-3-3p, miR-150-3p and miR-462-3p) and two (miR-2188-3p and miR-462-3p) significantly differentially expressed miRNAs at 24 and 72h post-stimulation (HPS), respectively. Sequencing-identified miRNAs were subjected to qPCR validation using a larger number of biological replicates (n=6) exposed to pIC or PBS over time (i.e. 12, 24, 48 and 72 HPS). As in sequencing, miR-731-3p, miR-462-3p and miR-2188-3p showed significant up-regulation by pIC. The sequencing results were not qPCR-validated for miR-125b-3-3p and miR-150-3p as up- and down-regulated miRNAs at 24 HPS, respectively; however, qPCR results showed significant up-regulation in response to pIC stimulation at later time points (i.e. 48 and/or 72 HPS). We also used qPCR to assess the expression of other miRNAs that were previously shown as immune responsive in other vertebrates. qPCR results at 48 and/or 72 HPS revealed that miR-128-3-5p, miR-214-1-5p and miR-451-3p were induced by pIC, whereas miR-30b-3p and miR-199-1-3p expression were repressed in response to pIC. The present study identified ten pIC-stimulated miRNAs, suggesting them as important in antiviral immune responses of Atlantic cod macrophages. Some pIC-responsive miRNAs identified in this study were predicted to target putative immune-related genes of Atlantic cod (e.g. miR-30b-3p targeting herc4), although the regulatory functions of these miRNAs need to be validated by future studies.
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Culley A. New insight into the RNA aquatic virosphere via viromics. Virus Res 2017; 244:84-89. [PMID: 29138044 DOI: 10.1016/j.virusres.2017.11.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 01/09/2023]
Abstract
RNA viruses that infect microbes are now recognized as an active, persistent and important component of the aquatic microbial community. While some information about the diversity and dynamics of the RNA virioplankton has been derived from culture-based and single gene approaches, research based on viromic and metatransciptomic methods has generated unprecedented insight into this relatively understudied class of microbes. Here, the relevant literature is summarized and discussed, including viromic studies of extracellular aquatic RNA viral assemblages, and transcriptomic studies of active and associated RNA viruses from aquatic environments followed by commentary on the present challenges and future directions of this field of research.
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Affiliation(s)
- Alexander Culley
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Québec, G1V 0A6, Canada; Centre d'études nordiques (CEN), Université Laval, Québec, Québec, G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada; Takuvik, Unité Mixte Interntionale (UMI 3376) Université Laval (Canada) & Centre National de la Recherche Scientifique (France), Québec QC GIV 0A6, Canada.
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Xie ZX, Chen F, Zhang SF, Wang MH, Zhang H, Kong LF, Dai MH, Hong HS, Lin L, Wang DZ. Metaproteomics of marine viral concentrates reveals key viral populations and abundant periplasmic proteins in the oligotrophic deep chlorophyll maximum of the South China Sea. Environ Microbiol 2017; 20:477-491. [PMID: 28925544 DOI: 10.1111/1462-2920.13937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 09/15/2017] [Accepted: 09/16/2017] [Indexed: 12/14/2022]
Abstract
Viral concentrates (VCs), containing bioinformative DNA and proteins, have been used to study viral diversity, viral metagenomics and virus-host interactions in natural ecosystems. Besides viruses, VCs also contain many noncellular biological components including diverse functional proteins. Here, we used a shotgun proteomic approach to characterize the proteins of VCs collected from the oligotrophic deep chlorophyll maximum (DCM) of the South China Sea. Proteins of viruses infecting picophytoplankton, that is, cyanobacteria and prasinophytes, and heterotrophic bacterioplankton, such as SAR11 and SAR116, dominated the viral proteome. Almost no proteins from RNA viruses or known gene transfer agents were detected, suggesting that they were not abundant at the sampling site. Remarkably, nonviral proteins made up about two thirds of VC proteins, including overwhelmingly abundant periplasmic transporters for nutrient acquisition and proteins for diverse cellular processes, that is, translation, energy metabolism and one carbon metabolism. Interestingly, three 56 kDa selenium-binding proteins putatively involved in peroxide reduction from gammaproteobacteria were abundant in the VCs, suggesting active removal of peroxide compounds at DCM. Our study demonstrated that metaproteomics provides a valuable avenue to explore the diversity and structure of the viral community and also the pivotal biological functions affiliated with microbes in the natural environment.
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Affiliation(s)
- Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Shu-Feng Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Ming-Hua Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Hao Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Ling-Fen Kong
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Min-Han Dai
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Hua-Sheng Hong
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
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Moniruzzaman M, Wurch LL, Alexander H, Dyhrman ST, Gobler CJ, Wilhelm SW. Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics. Nat Commun 2017; 8:16054. [PMID: 28656958 PMCID: PMC5493757 DOI: 10.1038/ncomms16054] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/16/2017] [Indexed: 01/12/2023] Open
Abstract
Establishing virus–host relationships has historically relied on culture-dependent approaches. Here we report on the use of marine metatranscriptomics to probe virus–host relationships. Statistical co-occurrence analyses of dsDNA, ssRNA and dsRNA viral markers of polyadenylation-selected RNA sequences from microbial communities dominated by Aureococcus anophagefferens (Quantuck Bay, NY), and diatoms (Narragansett Bay, RI) show active infections by diverse giant viruses (NCLDVs) associated with algal and nonalgal hosts. Ongoing infections of A. anophagefferens by a known Mimiviridae (AaV) occur during bloom peak and decline. Bloom decline is also accompanied by increased activity of viruses other than AaV, including (+) ssRNA viruses. In Narragansett Bay, increased temporal resolution reveals active NCLDVs with both ‘boom-and-bust’ and ‘steady-state infection’-like ecologies that include known as well as novel virus–host interactions. Our approach offers a method for screening active viral infections and develops links between viruses and their potential hosts in situ. Our observations further demonstrate that previously unknown virus–host relationships in marine systems are abundant. Viruses are partners in ecosystem ecology, yet their study has been primarily limited to laboratory models virus-host or derived from metagenomics. Here, Moniruzzaman et al. use metatranscriptomics to resolve interactions between giant viruses and single-celled eukaryotic hosts.
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Affiliation(s)
- Mohammad Moniruzzaman
- Department of Microbiology, The University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Louie L Wurch
- Department of Biology, James Madison University, Harrisonburg, Virginia 22807, USA
| | - Harriet Alexander
- Department of Earth and Environmental Science and Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York 10964, USA
| | - Sonya T Dyhrman
- Department of Earth and Environmental Science and Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York 10964, USA
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794, USA
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Tennessee 37996, USA
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Caballero-Solares A, Hall JR, Xue X, Eslamloo K, Taylor RG, Parrish CC, Rise ML. The dietary replacement of marine ingredients by terrestrial animal and plant alternatives modulates the antiviral immune response of Atlantic salmon (Salmo salar). FISH & SHELLFISH IMMUNOLOGY 2017; 64:24-38. [PMID: 28242361 DOI: 10.1016/j.fsi.2017.02.040] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/23/2017] [Indexed: 05/09/2023]
Abstract
The effects of replacing marine ingredients by terrestrial ingredients on the health of Atlantic salmon (Salmo salar) are poorly understood. During a 14-week trial, Atlantic salmon fed a fish meal-fish oil based diet (MAR) showed similar growth performance to others fed a plant protein/vegetable oil based diet (VEG), whereas poorer performance was observed in those fed an animal by-product meal/vegetable oil based diet (ABP). At the end of the trial, salmon were injected with either phosphate-buffered saline (PBS) or the viral mimic polyriboinosinic polyribocytidylic acid (pIC) and sampled for head kidney RNA after 24 h. The levels of 27 immune-related transcripts, and of 5 others involved in eicosanoid synthesis (including paralogues in both cases) were measured in the head kidney of the salmon using qPCR. All of the assayed immune-related genes and cox2 were pIC-induced, while the other eicosanoid synthesis-related genes were pIC-repressed. Linear regression was used to establish correlations between different immune transcripts, elucidating the cascade of responses to pIC and specialization among paralogues. Regarding the effect of diet on the antiviral immune response, pIC-treated fish fed diets ABP and VEG showed higher transcript levels of tlr3, irf1b, stat1a, isg15b, and gig1 compared to those fed diet MAR. We infer that the observed dietary immunomodulation could be due to the lower proportion of arachidonic acid (ARA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) in diets ABP and VEG. Furthermore, our results suggest a major role of dietary ARA in Atlantic salmon immunity, as low ARA proportion in diet VEG coincided with the highest pIC-induction of some immune transcripts (tlr7, stat1c, mxb, and gig1) and the lowest levels of transcripts encoding eicosanoid-synthesizing enzymes (5loxa, 5loxb, and pgds). In contrast, the high ARA/EPA ratio of diet ABP appeared to favor increased expression of transcripts involved in the synthesis of pro-inflammatory eicosanoids (5loxa and 5loxb) and chemotaxis (ccl19b). In conclusion, our findings show that nutritionally balanced plant-based diets may enhance the immune response of Atlantic salmon. Future studies should explore the possible advantages of plant-based diets in Atlantic salmon exposed to a viral infection.
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Affiliation(s)
- Albert Caballero-Solares
- Department of Ocean Sciences, Memorial University of Newfoundland, 1 Marine Lab Road, St. John's, NL A1C 5S7, Canada.
| | - Jennifer R Hall
- Aquatic Research Cluster, CREAIT Network, Memorial University of Newfoundland, 1 Marine Lab Road, St. John's, NL A1C 5S7, Canada.
| | - Xi Xue
- Department of Ocean Sciences, Memorial University of Newfoundland, 1 Marine Lab Road, St. John's, NL A1C 5S7, Canada.
| | - Khalil Eslamloo
- Department of Ocean Sciences, Memorial University of Newfoundland, 1 Marine Lab Road, St. John's, NL A1C 5S7, Canada.
| | | | - Christopher C Parrish
- Department of Ocean Sciences, Memorial University of Newfoundland, 1 Marine Lab Road, St. John's, NL A1C 5S7, Canada.
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, 1 Marine Lab Road, St. John's, NL A1C 5S7, Canada.
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Meng X, Wang M, You S, Wang D, Li Y, Liu Z, Gao Y, Liu L, Zhang Y, Yan Z, Liu C, Jiang Y, Shao H. Characterization and Complete Genome Sequence of a Novel Siphoviridae Bacteriophage BS5. Curr Microbiol 2017; 74:815-820. [DOI: 10.1007/s00284-017-1221-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 02/17/2017] [Indexed: 10/19/2022]
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40
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Ishengoma E, Agaba M. Evolution of toll-like receptors in the context of terrestrial ungulates and cetaceans diversification. BMC Evol Biol 2017; 17:54. [PMID: 28209121 PMCID: PMC5314619 DOI: 10.1186/s12862-017-0901-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 02/02/2017] [Indexed: 11/17/2022] Open
Abstract
Background Toll-like receptors (TLRs) are the frontline actors in the innate immune response to various pathogens and are expected to be targets of natural selection in species adapted to habitats with contrasting pathogen burdens. The recent publication of genome sequences of giraffe and okapi together afforded the opportunity to examine the evolution of selected TLRs in broad range of terrestrial ungulates and cetaceans during their complex habitat diversification. Through direct sequence comparisons and standard evolutionary approaches, the extent of nucleotide and protein sequence diversity in seven Toll-like receptors (TLR2, TLR3, TLR4, TLR5, TLR7, TLR9 and TLR10) between giraffe and closely related species was determined. In addition, comparison of the patterning of key TLR motifs and domains between giraffe and related species was performed. The quantification of selection pressure and divergence on TLRs among terrestrial ungulates and cetaceans was also performed. Results Sequence analysis shows that giraffe has 94–99% nucleotide identity with okapi and cattle for all TLRs analyzed. Variations in the number of Leucine-rich repeats were observed in some of TLRs between giraffe, okapi and cattle. Patterning of key TLR domains did not reveal any significant differences in the domain architecture among giraffe, okapi and cattle. Molecular evolutionary analysis for selection pressure identifies positive selection on key sites for all TLRs examined suggesting that pervasive evolutionary pressure has taken place during the evolution of terrestrial ungulates and cetaceans. Analysis of positively selected sites showed some site to be part of Leucine-rich motifs suggesting functional relevance in species-specific recognition of pathogen associated molecular patterns. Notably, clade analysis reveals significant selection divergence between terrestrial ungulates and cetaceans in viral sensing TLR3. Mapping of giraffe TLR3 key substitutions to the structure of the receptor indicates that at least one of giraffe altered sites coincides with TLR3 residue known to play a critical role in receptor signaling activity. Conclusion There is overall structural conservation in TLRs among giraffe, okapi and cattle indicating that the mechanism for innate immune response utilizing TLR pathways may not have changed very much during the evolution of these species. However, a broader phylogenetic analysis revealed signatures of adaptive evolution among terrestrial ungulates and cetaceans, including the observed selection divergence in TLR3. This suggests that long term ecological dynamics has led to species-specific innovation and functional variation in the mechanisms mediating innate immunity in terrestrial ungulates and cetaceans. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0901-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Edson Ishengoma
- School of Life Science and Biongineering, The Nelson Mandela African Institution of Sciences and Technology, P.O. Box 447, Arusha, Tanzania. .,Mkwawa University College of Education, University of Dar es Salaam, P.O. Box 2513, Iringa, Tanzania.
| | - Morris Agaba
- School of Life Science and Biongineering, The Nelson Mandela African Institution of Sciences and Technology, P.O. Box 447, Arusha, Tanzania.,Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, GPO00100, Kenya
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Higashi A, Fujitani Y, Nakayama N, Tani A, Ueki S. Selective growth promotion of bloom-forming raphidophyte Heterosigma akashiwo by a marine bacterial strain. HARMFUL ALGAE 2016; 60:150-156. [PMID: 28073558 DOI: 10.1016/j.hal.2016.11.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/28/2016] [Accepted: 11/14/2016] [Indexed: 06/06/2023]
Abstract
Algal bloom is typically caused by aberrant propagation of a single species, resulting in its predomination in the local population. While environmental factors including temperature and eutrophication are linked to bloom, the precise mechanism of its formation process is still obscure. Here, we isolated a bacterial strain that promotes growth of Heterosigma akashiwo, a Raphidophyceae that causes harmful algal blooms. Based on 16S rRNA gene sequence, the strain was identified as Altererythrobacter ishigakiensis, a member of the class Alphaproteobacteria. When added to culture, this strain facilitated growth of H. akashiwo and increased its cell culture yield significantly. Importantly, this strain did not affect the growth of other raphidophytes, Chattonella ovate and C. antiqua, indicating that it promotes growth of H. akashiwo in a species-specific manner. We also found that, in co-culture, H. akashiwo suppressed the growth of C. ovate. When A. ishigakiensis was added to the mixed culture, H. akashiwo growth was facilitated while C. ovate propagation was markedly suppressed, indicating that the presence of the bacterium enhances the dominance of H. akashiwo over C. ovate. This is the first example of selective growth promotion of H. akashiwo by a marine bacterium, and may exemplify importance of symbiotic bacterium on algal bloom forming process in general.
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Affiliation(s)
- Aiko Higashi
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Yoshiko Fujitani
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Natsuko Nakayama
- National Research and Development Agency, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
| | - Akio Tani
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Shoko Ueki
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan.
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Rousvoal S, Bouyer B, López-Cristoffanini C, Boyen C, Collén J. Mutant swarms of a totivirus-like entities are present in the red macroalga Chondrus crispus and have been partially transferred to the nuclear genome. JOURNAL OF PHYCOLOGY 2016; 52:493-504. [PMID: 27151076 DOI: 10.1111/jpy.12427] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/15/2016] [Indexed: 06/05/2023]
Abstract
Chondrus crispus Stackhouse (Gigartinales) is a red seaweed found on North Atlantic rocky shores. Electrophoresis of RNA extracts showed a prominent band with a size of around 6,000 bp. Sequencing of the band revealed several sequences with similarity to totiviruses, double-stranded RNA viruses that normally infect fungi. This virus-like entity was named C. crispus virus (CcV). It should probably be regarded as an extreme viral quasispecies or a mutant swarm since low identity (<65%) was found between sequences. Totiviruses typically code for two genes: one capsid gene (gag) and one RNA-dependent RNA polymerase gene (pol) with a pseudoknot structure between the genes. Both the genes and the intergenic structures were found in the CcV sequences. A nonidentical gag gene was also found in the nuclear genome of C. crispus, with associated expressed sequence tags (EST) and upstream regulatory features. The gene was presumably horizontally transferred from the virus to the alga. Similar dsRNA bands were seen in extracts from different life cycle stages of C. crispus and from all geographic locations tested. In addition, similar bands were also observed in RNA extractions from other red algae; however, the significance of this apparently widespread phenomenon is unknown. Neither phenotype caused by the infection nor any virus particles or capsid proteins were identified; thus, the presence of viral particles has not been validated. These findings increase the known host range of totiviruses to include marine red algae.
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Affiliation(s)
- Sylvie Rousvoal
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06, CS 90074, 29688, Roscoff Cedex, France
| | - Betty Bouyer
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06, CS 90074, 29688, Roscoff Cedex, France
| | - Camilo López-Cristoffanini
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06, CS 90074, 29688, Roscoff Cedex, France
| | - Catherine Boyen
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06, CS 90074, 29688, Roscoff Cedex, France
| | - Jonas Collén
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06, CS 90074, 29688, Roscoff Cedex, France
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Miranda JA, Culley AI, Schvarcz CR, Steward GF. RNA viruses as major contributors to Antarctic virioplankton. Environ Microbiol 2016; 18:3714-3727. [PMID: 26950773 DOI: 10.1111/1462-2920.13291] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 03/05/2016] [Indexed: 11/28/2022]
Abstract
Early work on marine algal viruses focused exclusively on those having DNA genomes, but recent studies suggest that RNA viruses, especially those with positive-sense, single-stranded RNA (+ssRNA) genomes, are abundant in tropical and temperate coastal seawater. To test whether this was also true of polar waters, we estimated the relative abundances of RNA and DNA viruses using a mass ratio approach and conducted shotgun metagenomics on purified viral samples collected from a coastal site near Palmer Station, Antarctica on six occasions throughout a summer phytoplankton bloom (November-March). Our data suggest that RNA viruses contributed up to 65% of the total virioplankton (8-65%), and that, as observed previously in warmer waters, the majority of RNA viruses in these Antarctic RNA virus metagenomes had +ssRNA genomes most closely related to viruses in the order Picornavirales. Assembly of the metagenomic reads resulted in five novel, nearly complete genomes, three of which had features similar to diatom-infecting viruses. Our data are consistent with the hypothesis that RNA viruses influence diatom bloom dynamics in Antarctic waters.
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Affiliation(s)
- Jaclyn A Miranda
- Department of Oceanography, Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, 1950 East-West Road, Honolulu, HI, 96822, USA
| | - Alexander I Culley
- Department of Oceanography, Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, 1950 East-West Road, Honolulu, HI, 96822, USA
| | - Christopher R Schvarcz
- Department of Oceanography, Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, 1950 East-West Road, Honolulu, HI, 96822, USA
| | - Grieg F Steward
- Department of Oceanography, Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, 1950 East-West Road, Honolulu, HI, 96822, USA
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44
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Ecosystem function decays by fungal outbreaks in Antarctic microbial mats. Sci Rep 2016; 6:22954. [PMID: 26972923 PMCID: PMC4789741 DOI: 10.1038/srep22954] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 02/17/2016] [Indexed: 11/12/2022] Open
Abstract
Antarctica harbours a remarkably diverse range of freshwater bodies and terrestrial ecosystems, where microbial mats are considered the most important systems in terms of biomass and metabolic capabilities. We describe the presence of lysis plaque-like macroscopic blighted patches within the predominant microbial mats on Livingston Island (Antarctic Peninsula). Those blighting circles are associated with decay in physiological traits as well as nitrogen depletion and changes in the spatial microstructure; these alterations were likely related to disruption of the biogeochemical gradients within the microbial ecosystem caused by an unusually high fungal abundance and consequent physical alterations. This phenomenon has been evidenced at a time of unprecedented rates of local warming in the Antarctic Peninsula area, and decay of these ecosystems is potentially stimulated by warmer temperatures.
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45
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Lachnit T, Thomas T, Steinberg P. Expanding our Understanding of the Seaweed Holobiont: RNA Viruses of the Red Alga Delisea pulchra. Front Microbiol 2016; 6:1489. [PMID: 26779145 PMCID: PMC4705237 DOI: 10.3389/fmicb.2015.01489] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/10/2015] [Indexed: 01/08/2023] Open
Abstract
Marine seaweeds are holobionts comprised of the macroalgal hosts and their associated microbiota. While the composition of the bacterial component of seaweed microbiomes is increasingly studied, almost nothing is known about the presence, diversity and composition of viruses in macroalgae in situ. In this study, we characterize for the first time the viruses associated with a red macroalga, Delisea pulchra. Using transmission electron microscopy we identified diverse morphotypes of virus-like particles in D. pulchra ranging from icosahedral to bacilliform to coiled pleomorphic as well as bacteriophages. Virome sequencing revealed the presence of a diverse group of dsRNA viruses affiliated to the genus Totivirus, known to infect plant pathogenic fungi. We further identified a ssRNA virus belonging to the order Picornavirales with a close phylogenetic relationship to a pathogenic virus infecting marine diatoms. The results of this study shed light on a so far neglected part of the seaweed holobiont, and suggest that some of the identified viruses may be possible pathogens for a host that is already known to be significantly impacted by bacterial infections.
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Affiliation(s)
- Tim Lachnit
- Centre for Marine Bio-Innovation, University of New South Wales, SydneyNSW, Australia
- Zoological Institute, Christian-Albrechts-University KielKiel, Germany
| | - Torsten Thomas
- Centre for Marine Bio-Innovation, University of New South Wales, SydneyNSW, Australia
- School for Biotechnology and Biomolecular Science, University of New South Wales, SydneyNSW, Australia
| | - Peter Steinberg
- Centre for Marine Bio-Innovation, University of New South Wales, SydneyNSW, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, SydneyNSW, Australia
- Sydney Institute of Marine Science, MosmanNSW, Australia
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46
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Abstract
Viral ecology is a rapidly progressing area of research, as molecular methods have improved significantly for targeted research on specific populations and whole communities. To interpret and synthesize global viral diversity and distribution, it is feasible to assess whether macroecology concepts can apply to marine viruses. We review how viral and host life history and physical properties can influence viral distribution in light of biogeography and metacommunity ecology paradigms. We highlight analytical approaches that can be applied to emerging global data sets and meta-analyses to identify individual taxa with global influence and drivers of emergent properties that influence microbial community structure by drawing on examples across the spectrum of viral taxa, from RNA to ssDNA and dsDNA viruses.
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Affiliation(s)
| | - Curtis A Suttle
- Department of Earth, Ocean, and Atmospheric Sciences.,Department of Botany, and.,Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada; .,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, Ontario M5G 1Z8, Canada
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47
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López-Bueno A, Rastrojo A, Peiró R, Arenas M, Alcamí A. Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake. Mol Ecol 2015. [DOI: 10.1111/mec.13321] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- A. López-Bueno
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
| | - A. Rastrojo
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
| | - R. Peiró
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
| | - M. Arenas
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
| | - A. Alcamí
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
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48
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Häder DP, Villafañe VE, Helbling EW. Productivity of aquatic primary producers under global climate change. Photochem Photobiol Sci 2015; 13:1370-92. [PMID: 25191675 DOI: 10.1039/c3pp50418b] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The productivity of aquatic primary producers depends on a number of biotic and abiotic factors, such as pH, CO2 concentration, temperature, nutrient availability, solar UV and PAR irradiances, mixing frequency as well as herbivore pressure and the presence of viruses, among others. The effects of these factors, within a climate change context, may be additive, synergistic or antagonistic. Since some of them, e.g. solar radiation and temperature, vary along a latitudinal gradient, this perspective about the effects of global climate change on primary producers will consider ecosystems individually, separated into polar (Arctic and Antarctic), temperate and tropical waters. As coastal waters are characterized by lower light penetration and higher DOM and nutrient concentrations, they are considered in a separate section. Freshwater systems are also governed by different conditions and therefore also treated in their own section. Overall, we show that although there are general common trends of changes in variables associated with global change (e.g. the impact of UVR on photosynthesis tends to decrease with increasing temperature and nutrient input), the responses of aquatic primary producers have great variability in the different ecosystems across latitudes. This is mainly due to direct or indirect effects associated with physico-chemical changes that occur within water bodies. Therefore we stress the need for regional predictions on the responses of primary producers to climate change as it is not warranted to extrapolate from one system to another.
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49
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Wang H, Yu Y, Liu T, Pan Y, Yan S, Wang Y. Diversity of putative archaeal RNA viruses in metagenomic datasets of a yellowstone acidic hot spring. SPRINGERPLUS 2015; 4:189. [PMID: 25918685 PMCID: PMC4405519 DOI: 10.1186/s40064-015-0973-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 04/09/2015] [Indexed: 12/02/2022]
Abstract
Two genomic fragments (5,662 and 1,269 nt in size, GenBank accession no. JQ756122 and JQ756123, respectively) of novel, positive-strand RNA viruses that infect archaea were first discovered in an acidic hot spring in Yellowstone National Park (Bolduc et al., 2012). To investigate the diversity of these newly identified putative archaeal RNA viruses, global metagenomic datasets were searched for sequences that were significantly similar to those of the viruses. A total of 3,757 associated reads were retrieved solely from the Yellowstone datasets and were used to assemble the genomes of the putative archaeal RNA viruses. Nine contigs with lengths ranging from 417 to 5,866 nt were obtained, 4 of which were longer than 2,200 nt; one contig was 204 nt longer than JQ756122, representing the longest genomic sequence of the putative archaeal RNA viruses. These contigs revealed more than 50% sequence similarity to JQ756122 or JQ756123 and may be partial or nearly complete genomes of novel genogroups or genotypes of the putative archaeal RNA viruses. Sequence and phylogenetic analyses indicated that the archaeal RNA viruses are genetically diverse, with at least 3 related viral lineages in the Yellowstone acidic hot spring environment.
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Affiliation(s)
- Hongming Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yongxin Yu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Taigang Liu
- College of Information Technology, Shanghai Ocean University, Shanghai, China
| | - Yingjie Pan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China ; Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation, Ministry of Agriculture, Shanghai, China ; Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China
| | - Shuling Yan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China ; Institute of Biochemistry and Molecular Cell Biology, University of Goettingen, Goettingen, Germany
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China ; Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation, Ministry of Agriculture, Shanghai, China ; Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China
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50
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Rising to the challenge: accelerated pace of discovery transforms marine virology. Nat Rev Microbiol 2015; 13:147-59. [PMID: 25639680 DOI: 10.1038/nrmicro3404] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Marine viruses have important roles in microbial mortality, gene transfer, metabolic reprogramming and biogeochemical cycling. In this Review, we discuss recent technological advances in marine virology including the use of near-quantitative, reproducible metagenomics for large-scale investigation of viral communities and the emergence of gene-based viral ecology. We also describe the reprogramming of microbially driven processes by viral metabolic genes, the identification of novel viruses using cultivation-dependent and cultivation-independent tools, and the potential for modelling studies to provide a framework for studying virus-host interactions. These transformative advances have set a rapid pace in exploring and predicting how marine viruses manipulate and respond to their environment.
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