1
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Koonin EV, Kuhn JH, Dolja VV, Krupovic M. Megataxonomy and global ecology of the virosphere. THE ISME JOURNAL 2024; 18:wrad042. [PMID: 38365236 PMCID: PMC10848233 DOI: 10.1093/ismejo/wrad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 02/18/2024]
Abstract
Nearly all organisms are hosts to multiple viruses that collectively appear to be the most abundant biological entities in the biosphere. With recent advances in metagenomics and metatranscriptomics, the known diversity of viruses substantially expanded. Comparative analysis of these viruses using advanced computational methods culminated in the reconstruction of the evolution of major groups of viruses and enabled the construction of a virus megataxonomy, which has been formally adopted by the International Committee on Taxonomy of Viruses. This comprehensive taxonomy consists of six virus realms, which are aspired to be monophyletic and assembled based on the conservation of hallmark proteins involved in capsid structure formation or genome replication. The viruses in different major taxa substantially differ in host range and accordingly in ecological niches. In this review article, we outline the latest developments in virus megataxonomy and the recent discoveries that will likely lead to reassessment of some major taxa, in particular, split of three of the current six realms into two or more independent realms. We then discuss the correspondence between virus taxonomy and the distribution of viruses among hosts and ecological niches, as well as the abundance of viruses versus cells in different habitats. The distribution of viruses across environments appears to be primarily determined by the host ranges, i.e. the virome is shaped by the composition of the biome in a given habitat, which itself is affected by abiotic factors.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, United States
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, United States
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, 75015 Paris, France
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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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Liu Y, Jiao N, Xu Zhong K, Zang L, Zhang R, Xiao X, Shi Y, Zhang Z, Tao Y, Bai L, Gao B, Yang Y, Huang X, Ji M, Liu J, Liu P, Yao T. Diversity and function of mountain and polar supraglacial DNA viruses. Sci Bull (Beijing) 2023; 68:2418-2433. [PMID: 37739838 DOI: 10.1016/j.scib.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/29/2023] [Accepted: 06/30/2023] [Indexed: 09/24/2023]
Abstract
Mountain and polar glaciers cover 10% of the Earth's surface and are typically extreme environments that challenge life of all forms. Viruses are abundant and active in supraglacial ecosystems and play a crucial role in controlling the supraglacial microbial communities. However, our understanding of virus ecology on glacier surfaces and their potential impacts on downstream ecosystems remains limited. Here, we present the supraglacial virus genome (SgVG) catalog, a 15-fold expanded genomic inventory of 10,840 DNA-virus species from 38 mountain and polar glaciers, spanning habitats such as snow, ice, meltwater, and cryoconite. Supraglacial DNA-viruses were highly specific compared to viruses in other ecosystems yet exhibited low public health risks. Supraglacial viral communities were primarily constrained by habitat, with cryoconite displaying the highest viral activity levels. We observed a prevalence of lytic viruses in all habitats, especially in cryoconite, but a high level of lysogenic viruses in snow and ice. Additionally, we found that supraglacial viruses could be linked to ∼83% of obtained prokaryotic phyla/classes and possessed the genetic potential to promote metabolism and increase cold adaptation, cell mobility, and phenolic carbon use of hosts in hostile environmental conditions using diverse auxiliary metabolic genes. Our results provide the first systematic characterization of the diversity, function, and public health risks evaluation of mountain and polar supraglacial DNA viruses. This understanding of glacial viruses is crucial for function assessments and ecological modeling of glacier ecosystems, especially for the Tibetan Plateau's Mountain glaciers, which support ∼20% of the human populations on Earth.
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Affiliation(s)
- Yongqin Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China.
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Kevin Xu Zhong
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Lin Zang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen 518000, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yi Shi
- University of Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Ye Tao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Liping Bai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, China
| | - Bianli Gao
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Xingyu Huang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Mukan Ji
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Junzhi Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Pengfei Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China.
| | - Tandong Yao
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
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4
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Ettinger CL, Saunders M, Selbmann L, Delgado-Baquerizo M, Donati C, Albanese D, Roux S, Tringe S, Pennacchio C, Del Rio TG, Stajich JE, Coleine C. Highly diverse and unknown viruses may enhance Antarctic endoliths' adaptability. MICROBIOME 2023; 11:103. [PMID: 37158954 PMCID: PMC10165816 DOI: 10.1186/s40168-023-01554-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, and further still, viruses in these communities have been largely unexplored despite important roles related to host metabolism and nutrient cycling. To begin to address this, we present a large-scale viral catalog from Antarctic rock microbial communities. RESULTS We performed metagenomic analyses on rocks from across Antarctica representing a broad range of environmental and spatial conditions, and which resulted in a predicted viral catalog comprising > 75,000 viral operational taxonomic units (vOTUS). We found largely undescribed, highly diverse and spatially structured virus communities which had predicted auxiliary metabolic genes (AMGs) with functions indicating that they may be potentially influencing bacterial adaptation and biogeochemistry. CONCLUSION This catalog lays the foundation for expanding knowledge of virosphere diversity, function, spatial ecology, and dynamics in extreme environments. This work serves as a step towards exploring adaptability of microbial communities in the face of a changing climate. Video Abstract.
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Affiliation(s)
- Cassandra L Ettinger
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.
| | - Morgan Saunders
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA, USA
- The University of Arizona, Tucson, AZ, USA
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad Y Funcionamiento Ecosistémico, Instituto de Recursos Naturales Y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, Seville, E-41012, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Seville, 41013, Spain
| | - Claudio Donati
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele All'Adige, 38098, Italy
| | - Davide Albanese
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele All'Adige, 38098, Italy
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Susannah Tringe
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Christa Pennacchio
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Tijana G Del Rio
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Claudia Coleine
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.
- Laboratorio de Biodiversidad Y Funcionamiento Ecosistémico, Instituto de Recursos Naturales Y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, Seville, E-41012, Spain.
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5
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Bassi C, Guerriero P, Pierantoni M, Callegari E, Sabbioni S. Novel Virus Identification through Metagenomics: A Systematic Review. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122048. [PMID: 36556413 PMCID: PMC9784588 DOI: 10.3390/life12122048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.
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Affiliation(s)
- Cristian Bassi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Paola Guerriero
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Marina Pierantoni
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Elisa Callegari
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Silvia Sabbioni
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Correspondence: ; Tel.: +39-053-245-5319
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6
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Liao M, Xie Y, Shi M, Cui J. Over two decades of research on the marine RNA virosphere. IMETA 2022; 1:e59. [PMID: 38867898 PMCID: PMC10989941 DOI: 10.1002/imt2.59] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/30/2022] [Accepted: 09/14/2022] [Indexed: 06/14/2024]
Abstract
RNA viruses (realm: Riboviria), including RNA phages and eukaryote-infecting RNA viruses, are essential components of marine ecosystems. A large number of marine RNA viruses have been discovered in the last two decades because of the rapid development of next-generation sequencing (NGS) technology. Indeed, the combination of NGS and state-of-the-art meta-omics methods (viromics, the study of all viruses in a specific environment) has led to a fundamental understanding of the taxonomy and genetic diversity of RNA viruses in the sea, suggesting the complex ecological roles played by RNA viruses in this complex ecosystem. Furthermore, comparisons of viromes in the context of highly variable marine niches reveal the biogeographic patterns and ecological impact of marine RNA viruses, whose role in global ecology is becoming increasingly clearer. In this review, we summarize the characteristics of the global marine RNA virosphere and outline the taxonomic hierarchy of RNA viruses with a specific focus on their ancient evolutionary history. We also review the development of methodology and the major progress resulting from its applications in RNA viromics. The aim of this review is not only to provide an in-depth understanding of multifaceted aspects of marine RNA viruses, but to offer future perspectives on developing a better methodology for discovery, and exploring the evolutionary origin and major ecological significance of marine RNA virosphere.
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Affiliation(s)
- Meng‐en Liao
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega‐ScienceChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yunyi Xie
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega‐ScienceChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Mang Shi
- School of MedicineSun Yat‐sen UniversityShenzhen Campus of Sun Yat‐sen UniversityShenzhenChina
| | - Jie Cui
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega‐ScienceChinese Academy of SciencesShanghaiChina
- Laboatory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and Technology (Qingdao)QingdaoChina
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7
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Potapov S, Krasnopeev A, Tikhonova I, Podlesnaya G, Gorshkova A, Belykh O. The Viral Fraction Metatranscriptomes of Lake Baikal. Microorganisms 2022; 10:1937. [PMID: 36296212 PMCID: PMC9611531 DOI: 10.3390/microorganisms10101937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/24/2022] Open
Abstract
This article characterises viral fraction metatranscriptomes (smaller than 0.2 µm) from the pelagic zone of oligotrophic Lake Baikal (Russia). The study revealed the dominance of transcripts of DNA viruses: bacteriophages and algal viruses. We identified transcripts similar to Pithovirus sibericum, a nucleocytoplasmic large DNA virus (NCLDV) isolated from the permafrost region of Eastern Siberia. Among the families detected were RNA viruses assigned to Retroviridae, Metaviridae, Potyviridae, Astroviridae, and Closteroviridae. Using the PHROG, SEED subsystems databases, and the VOGDB, we indicated that the bulk of transcripts belong to the functional replication of viruses. In a comparative unweighted pair group method with arithmetic mean (UPGMA) analysis, the transcripts from Lake Baikal formed a separate cluster included in the clade with transcripts from other freshwater lakes, as well as marine and oceanic waters, while there was no separation based on the trophic state of the water bodies, the size of the plankton fraction, or salinity.
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Affiliation(s)
- Sergey Potapov
- Limnological Institute SB RAS, 3, Ulan-Batorskaya, 664033 Irkutsk, Russia
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8
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Chitcharoen S, Sivapornnukul P, Payungporn S. Revolutionized virome research using systems microbiology approaches. Exp Biol Med (Maywood) 2022; 247:1135-1147. [PMID: 35723062 PMCID: PMC9335507 DOI: 10.1177/15353702221102895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Currently, both pathogenic and commensal viruses are continuously being discovered and acknowledged as ubiquitous components of microbial communities. The advancements of systems microbiological approaches have changed the face of virome research. Here, we focus on viral metagenomic approach to study virus community and their interactions with other microbial members as well as their hosts. This review also summarizes challenges, limitations, and benefits of the current virome approaches. Potentially, the studies of virome can be further applied in various biological and clinical fields.
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Affiliation(s)
- Suwalak Chitcharoen
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand,Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pavaret Sivapornnukul
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Sunchai Payungporn.
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9
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Dominguez-Huerta G, Zayed AA, Wainaina JM, Guo J, Tian F, Pratama AA, Bolduc B, Mohssen M, Zablocki O, Pelletier E, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Bowler C, Eveillard D, Guidi L, Karsenti E, Kuhn JH, Ogata H, Wincker P, Culley A, Chaffron S, Sullivan MB. Diversity and ecological footprint of Global Ocean RNA viruses. Science 2022; 376:1202-1208. [PMID: 35679415 DOI: 10.1126/science.abn6358] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global marine RNA virus diversity, ecology, and ecosystem roles. In this study, we uncover patterns and predictors of marine RNA virus community- and "species"-level diversity and contextualize their ecological impacts from pole to pole. Our analyses revealed four ecological zones, latitudinal and depth diversity patterns, and environmental correlates for RNA viruses. Our findings only partially parallel those of cosampled plankton and show unexpectedly high polar ecological interactions. The influence of RNA viruses on ecosystems appears to be large, as predicted hosts are ecologically important. Moreover, the occurrence of auxiliary metabolic genes indicates that RNA viruses cause reprogramming of diverse host metabolisms, including photosynthesis and carbon cycling, and that RNA virus abundances predict ocean carbon export.
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Affiliation(s)
- Guillermo Dominguez-Huerta
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - James M Wainaina
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - Jiarong Guo
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - Funing Tian
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - Akbar Adjie Pratama
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - Mohamed Mohssen
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA.,The Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The 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
| | - Erwan Delage
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France.,Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, 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
| | - 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
| | - 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
| | | | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure, Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Damien Eveillard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France.,Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000 Nantes, France
| | - Lionel Guidi
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, F-06230 Villefranche-sur-mer, France
| | - Eric Karsenti
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure, Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France.,Directors' Research European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - 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
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan
| | - 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
| | - Alexander Culley
- Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Samuel Chaffron
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France.,Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000 Nantes, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA.,The Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, USA.,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210, USA
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10
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Zayed AA, Wainaina JM, Dominguez-Huerta G, Pelletier E, Guo J, Mohssen M, Tian F, Pratama AA, Bolduc B, Zablocki O, Cronin D, Solden L, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Ruscheweyh HJ, Salazar G, Shatoff E, Coordinators TO, Bundschuh R, Fredrick K, Kubatko LS, Chaffron S, Culley AI, Sunagawa S, Kuhn JH, Wincker P, Sullivan MB. Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome. Science 2022; 376:156-162. [PMID: 35389782 PMCID: PMC10990476 DOI: 10.1126/science.abm5847] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of the new phyla "Taraviricota," a missing link in early RNA virus evolution, and "Arctiviricota" are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.
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Affiliation(s)
- Ahmed A. Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - James M. Wainaina
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Guillermo Dominguez-Huerta
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Jiarong Guo
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Mohamed Mohssen
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
| | - Funing Tian
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Akbar Adjie Pratama
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Dylan Cronin
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Lindsey Solden
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Erwan Delage
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Nantes Université, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Corinne da Silva
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Elan Shatoff
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | | | - Ralf Bundschuh
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
- Division of Hematology, Department of Internal Medicine, Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Laura S. Kubatko
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
- Department of Statistics, Ohio State University, Columbus, OH 43210, USA
| | - Samuel Chaffron
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Nantes Université, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Alexander I. Culley
- Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA
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11
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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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12
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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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13
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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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14
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Alarcón-Schumacher T, Guajardo-Leiva S, Martinez-Garcia M, Díez B. Ecogenomics and Adaptation Strategies of Southern Ocean Viral Communities. mSystems 2021; 6:e0039621. [PMID: 34374561 PMCID: PMC8407431 DOI: 10.1128/msystems.00396-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/21/2021] [Indexed: 11/20/2022] Open
Abstract
The Southern Ocean (SO) represents up to one-fifth of the total carbon drawdown worldwide. Intense selective pressures (low temperature, high UV radiation, and strong seasonality) and physical isolation characterize the SO, serving as a "natural" laboratory for the study of ecogenomics and unique adaptations of endemic viral populations. Here, we report 2,416 novel viral genomes from the SO, obtained from newly sequenced viral metagenomes in combination with mining of publicly available data sets, which represents a 25% increase in the SO viral genomes reported to date. They comprised 567 viral clusters (defined as approximately genus-level groups), with 186 genera endemic to the SO, demonstrating that the SO viral community is predominantly constituted by a large pool of genetically divergent viral species from widespread viral families. The predicted proteome from SO viruses revealed that several protein clusters related to cold-shock-event responses and quorum-sensing mechanisms involved in the lysogenic-lytic cycle shift decision were under positive selection, which is ultimately important for fine adaptation of viral populations in response to the strong selective pressures of the SO. Finally, changes in the hydrophobicity patterns and amino acid frequencies suggested marked temperature-driven genetic selection of the SO viral proteome. Our data provide valuable insights into how viruses adapt and remain successful in this extreme polar marine environment. IMPORTANCE Viruses are the most abundant biologic entities in marine systems and strongly influence the microbial community composition and diversity. However, little is known about viral communities' adaptation and diversification in the ocean. In this work, we take advantage of the geographical isolation and the intense selective pressures of the SO, to which viruses are exposed, to identify potential viral adaptations due to positive environmental selection and dispersal limitation. To that end, we recovered more than two thousand novel viral genomes, revealing a high degree of divergence in these SO endemic communities. Furthermore, we describe remarkable viral adaptations in amino acid frequencies and accessory proteins related to cold shock response and quorum sensing that allow them to thrive at lower temperatures. Consequently, our work greatly expands the understanding of the diversification of the viral communities of the SO and their particular adaptations to low temperatures.
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Affiliation(s)
- Tomás Alarcón-Schumacher
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sergio Guajardo-Leiva
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, Spain
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center for Climate and Resilience Research (CR) 2, Santiago, Chile
- Center for Genome Regulation (CGR), Santiago, Chile
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15
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Tomaru Y, Yamaguchi H, Miki T. Growth Rate-dependent Cell Death of Diatoms due to Viral Infection and Their Subsequent Coexistence in a Semi-continuous Culture System. Microbes Environ 2021; 36. [PMID: 33390375 PMCID: PMC7966941 DOI: 10.1264/jsme2.me20116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Viral infections are a major factor in diatom cell death. However, the effects of viruses on diatom dynamics remain unclear. Based on laboratory studies, it is hypothesized that virus-induced diatom mortality is dependent on the diatom growth rate. The present study aimed to elucidate the relationship between the diatom growth rate and virus-induced mortality using model systems of the marine planktonic diatom, Chaetoceros tenuissimus and its infectious viruses. We also examined the fate of diatom populations in a semi-continuous dilution culture system, in which host growth rates were controlled at 0.69, 2.08, and 3.47 day–1. Diatom populations gradually decreased following the viral inoculation of each culture system, and virus-induced mortality inversely correlated with the diatom growth rate. Furthermore, the viral burst size was slightly higher in lower growth rate cultures. These results suggested that the host physiological status related to the growth rate affected viral infection and proliferation. Diatom populations were not completely lysed or washed out in any of the dilution systems; they showed steady growth in the presence of infectious viruses. This may be partially explained by defective interference particles from viruses and cell debris. The present results indicate that diatoms in dilution environments maintain their populations, even under viral pressure. Moreover, diatom populations with a low growth rate may partially sustain higher growth populations through nutrient recycling following virus-induced cell death. The results of the present study provide insights into diatom dynamics in natural environments in the presence of infectious viruses.
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Affiliation(s)
- Yuji Tomaru
- Hatsukaichi Field Station, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, National Research and Development Agency
| | | | - Takeshi Miki
- Ecology and Environmental Engineering, Faculty of Advanced Science and Technology, Ryukoku University
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16
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Role of Phylogenetic Structure in the Dynamics of Coastal Viral Assemblages. Appl Environ Microbiol 2021; 87:AEM.02704-20. [PMID: 33741635 DOI: 10.1128/aem.02704-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/16/2021] [Indexed: 11/20/2022] Open
Abstract
Marine microbes, including viruses, are an essential part of the marine ecosystem, forming the base of the food web and driving biogeochemical cycles. Within this system, the composition of viral assemblages changes markedly with time, and some of these changes are repeatable through time; however, the extent to which these dynamics are reflected within versus among evolutionarily related groups of viruses is largely unexplored. To examine these dynamics, changes in the composition of two groups of ecologically important viruses and communities of their potential hosts were sampled every 2 weeks for 13 months at a coastal site in British Columbia, Canada. We sequenced two marker genes for viruses-the gene encoding the major capsid protein of T4-like phages and their relatives (gp23) and the RNA-dependent RNA polymerase (RdRp) gene of marnavirus-like RNA viruses-as well as marker genes for their bacterial and eukaryotic host communities, the genes encoding 16S rRNA and 18S rRNA. There were strong lagged correlations between viral diversity and community similarity of putative hosts, implying that the viruses influenced the composition of the host communities. The results showed that for both viral assemblages, the dominant clusters of phylogenetically related viruses shifted over time, and this was correlated with environmental changes. Viral clusters contained many ephemeral taxa and few persistent taxa, but within a viral assemblage, the ephemeral and persistent taxa were closely related, implying ecological dynamics within these clusters. Furthermore, these dynamics occurred in both the RNA and DNA viral assemblages surveyed, implying that this structure is common in natural viral assemblages.IMPORTANCE Viruses are major agents of microbial mortality in marine systems, yet little is known about changes in the composition of viral assemblages in relation to those of the microbial communities that they infect. Here, we sampled coastal seawater every 2 weeks for 1 year and used high-throughput sequencing of marker genes to follow changes in the composition of two groups of ecologically important viruses, as well as the communities of bacteria and protists that serve as their respective hosts. Different subsets of genetically related viruses dominated at different times. These results demonstrate that although the genetic composition of viral assemblages is highly dynamic temporally, for the most part the shuffling of genotypes occurs within a few clusters of phylogenetically related viruses. Thus, it appears that even in temperate coastal waters with large seasonal changes, the highly dynamic shuffling of viral genotypes occurs largely within a few subsets of related individuals.
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17
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Sadeghi M, Tomaru Y, Ahola T. RNA Viruses in Aquatic Unicellular Eukaryotes. Viruses 2021; 13:v13030362. [PMID: 33668994 PMCID: PMC7996518 DOI: 10.3390/v13030362] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/05/2021] [Accepted: 02/22/2021] [Indexed: 12/24/2022] Open
Abstract
Increasing sequence information indicates that RNA viruses constitute a major fraction of marine virus assemblages. However, only 12 RNA virus species have been described, infecting known host species of marine single-celled eukaryotes. Eight of these use diatoms as hosts, while four are resident in dinoflagellate, raphidophyte, thraustochytrid, or prasinophyte species. Most of these belong to the order Picornavirales, while two are divergent and fall into the families Alvernaviridae and Reoviridae. However, a very recent study has suggested that there is extraordinary diversity in aquatic RNA viromes, describing thousands of viruses, many of which likely use protist hosts. Thus, RNA viruses are expected to play a major ecological role for marine unicellular eukaryotic hosts. In this review, we describe in detail what has to date been discovered concerning viruses with RNA genomes that infect aquatic unicellular eukaryotes.
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Affiliation(s)
- Mohammadreza Sadeghi
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland
- Correspondence: (M.S.); (T.A.)
| | - Yuji Tomaru
- Environment and Fisheries Applied Techniques Research Department, Fisheries Technology Institute, Fisheries Research and Education Agency, Hatsukaichi, Hiroshima 739-0452, Japan;
| | - Tero Ahola
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland
- Correspondence: (M.S.); (T.A.)
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18
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Moon K, Cho JC. Metaviromics coupled with phage-host identification to open the viral 'black box'. J Microbiol 2021; 59:311-323. [PMID: 33624268 DOI: 10.1007/s12275-021-1016-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 12/22/2022]
Abstract
Viruses are found in almost all biomes on Earth, with bacteriophages (phages) accounting for the majority of viral particles in most ecosystems. Phages have been isolated from natural environments using the plaque assay and liquid medium-based dilution culturing. However, phage cultivation is restricted by the current limitations in the number of culturable bacterial strains. Unlike prokaryotes, which possess universally conserved 16S rRNA genes, phages lack universal marker genes for viral taxonomy, thus restricting cultureindependent analyses of viral diversity. To circumvent these limitations, shotgun viral metagenome sequencing (i.e., metaviromics) has been developed to enable the extensive sequencing of a variety of viral particles present in the environment and is now widely used. Using metaviromics, numerous studies on viral communities have been conducted in oceans, lakes, rivers, and soils, resulting in many novel phage sequences. Furthermore, auxiliary metabolic genes such as ammonic monooxygenase C and β-lactamase have been discovered in viral contigs assembled from viral metagenomes. Current attempts to identify putative bacterial hosts of viral metagenome sequences based on sequence homology have been limited due to viral sequence variations. Therefore, culture-independent approaches have been developed to predict bacterial hosts using single-cell genomics and fluorescentlabeling. This review focuses on recent viral metagenome studies conducted in natural environments, especially in aquatic ecosystems, and their contributions to phage ecology. Here, we concluded that although metaviromics is a key tool for the study of viral ecology, this approach must be supplemented with phage-host identification, which in turn requires the cultivation of phage-bacteria systems.
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Affiliation(s)
- Kira Moon
- Biological Resources Utilization Division, Honam National Institute of Biological Resources, Mokpo, 58762, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea.
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Pelusi A, De Luca P, Manfellotto F, Thamatrakoln K, Bidle KD, Montresor M. Virus-induced spore formation as a defense mechanism in marine diatoms. THE NEW PHYTOLOGIST 2021; 229:2251-2259. [PMID: 32978816 PMCID: PMC7894508 DOI: 10.1111/nph.16951] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/09/2020] [Indexed: 05/03/2023]
Abstract
Algal viruses are important contributors to carbon cycling, recycling nutrients and organic material through host lysis. Although viral infection has been described as a primary mechanism of phytoplankton mortality, little is known about host defense responses. We show that viral infection of the bloom-forming, planktonic diatom Chaetoceros socialis induces the mass formation of resting spores, a heavily silicified life cycle stage associated with carbon export due to rapid sinking. Although viral RNA was detected within spores, mature virions were not observed. 'Infected' spores were capable of germinating, but did not propagate or transmit infectious viruses. These results demonstrate that diatom spore formation is an effective defense strategy against viral-mediated mortality. They provide a possible mechanistic link between viral infection, bloom termination, and mass carbon export events and highlight an unappreciated role of viruses in regulating diatom life cycle transitions and ecological success.
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Affiliation(s)
- Angela Pelusi
- Department of Integrative Marine EcologyStazione Zoologica Anton DohrnVilla ComunaleNaples80121Italy
| | - Pasquale De Luca
- Research Infrastructures for Marine Biological ResourcesStazione Zoologica Anton DohrnVilla ComunaleNaples80121Italy
| | - Francesco Manfellotto
- Department of Integrative Marine EcologyStazione Zoologica Anton DohrnVilla ComunaleNaples80121Italy
| | | | - Kay D. Bidle
- Department of Marine and Coastal SciencesRutgers UniversityNew BrunswickNJ08901‐8520USA
| | - Marina Montresor
- Department of Integrative Marine EcologyStazione Zoologica Anton DohrnVilla ComunaleNaples80121Italy
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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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Edwards KF, Steward GF, Schvarcz CR. Making sense of virus size and the tradeoffs shaping viral fitness. Ecol Lett 2020; 24:363-373. [PMID: 33146939 DOI: 10.1111/ele.13630] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/26/2020] [Accepted: 09/27/2020] [Indexed: 12/18/2022]
Abstract
Viruses span an impressive size range, with genome length varying a thousandfold and virion volume nearly a millionfold. For cellular organisms the scaling of traits with size is a pervasive influence on ecological processes, but whether size plays a central role in viral ecology is unknown. Here, we focus on viruses of aquatic unicellular organisms, which exhibit the greatest known range of virus size. We outline hypotheses within a quantitative framework, and analyse data where available, to consider how size affects the primary components of viral fitness. We argue that larger viruses have fewer offspring per infection and slower contact rates with host cells, but a larger genome tends to increase infection efficiency, broaden host range, and potentially increase attachment success and decrease decay rate. These countervailing selective pressures may explain why a breadth of sizes exist and even coexist when infecting the same host populations. Oligotrophic ecosystems may be enriched in "giant" viruses, because environments with resource-limited phagotrophs at low concentrations may select for broader host range, better control of host metabolism, lower decay rate and a physical size that mimics bacterial prey. Finally, we describe where further research is needed to understand the ecology and evolution of viral size diversity.
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Affiliation(s)
- Kyle F Edwards
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Grieg F Steward
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
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22
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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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McCall C, Wu H, Miyani B, Xagoraraki I. Identification of multiple potential viral diseases in a large urban center using wastewater surveillance. WATER RESEARCH 2020; 184:116160. [PMID: 32738707 PMCID: PMC7342010 DOI: 10.1016/j.watres.2020.116160] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/27/2020] [Accepted: 07/05/2020] [Indexed: 05/08/2023]
Abstract
Viruses are linked to a multitude of human illnesses and can disseminate widely in urbanized environments causing global adverse impacts on communities and healthcare infrastructures. Wastewater-based epidemiology was employed using metagenomics and quantitative polymerase chain reaction (qPCR) assays to identify enteric and non-enteric viruses collected from a large urban area for potential public health monitoring and outbreak analysis. Untreated wastewater samples were collected from November 2017 to February 2018 (n = 54) to evaluate the diversity of human viral pathogens in collected samples. Viruses were classified into virus types based on primary transmission routes and reviewed against viral associated diseases reported in the catchment area. Metagenomics detected the presence of viral pathogens that cause clinically significant diseases reported within the study area during the sampling year. Detected viruses belong to the Adenoviridae, Astroviridae, Caliciviridae, Coronaviridae, Flaviviridae, Hepeviridae, Herpesviridae, Matonaviridae, Papillomaviridae, Parvoviridae, Picornaviridae, Poxviridae, Retroviridae, and Togaviridae families. Furthermore, concentrations of adenovirus, norovirus GII, sapovirus, hepatitis A virus, human herpesvirus 6, and human herpesvirus 8 were measured in wastewater samples and compared to metagenomic findings to confirm detected viral genus. Hepatitis A virus obtained the greatest average viral load (1.86 × 107 genome copies/L) in wastewater samples compared to other viruses quantified using qPCR with a 100% detection rate in metagenomic samples. Average concentration of sapovirus (1.36 × 106 genome copies/L) was significantly greater than norovirus GII (2.94 × 104 genome copies/L) indicating a higher burden within the study area. Findings obtained from this study aid in evaluating the utility of wastewater-based epidemiology for identification and routine monitoring of various viruses in large communities. This methodology has the potential to improve public health responses to large scale outbreaks and viral pandemics.
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Affiliation(s)
- Camille McCall
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA
| | - Huiyun Wu
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA
| | - Brijen Miyani
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA.
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25
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Hewson I, Johnson MR, Tibbetts IR. An Unconventional Flavivirus and Other RNA Viruses in the Sea Cucumber (Holothuroidea; Echinodermata) Virome. Viruses 2020; 12:v12091057. [PMID: 32972018 PMCID: PMC7551563 DOI: 10.3390/v12091057] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/11/2022] Open
Abstract
Sea cucumbers (Holothuroidea; Echinodermata) are ecologically significant constituents of benthic marine habitats. We surveilled RNA viruses inhabiting eight species (representing four families) of holothurian collected from four geographically distinct locations by viral metagenomics, including a single specimen of Apostichopus californicus affected by a hitherto undocumented wasting disease. The RNA virome comprised genome fragments of both single-stranded positive sense and double stranded RNA viruses, including those assigned to the Picornavirales, Ghabrivirales, and Amarillovirales. We discovered an unconventional flavivirus genome fragment which was most similar to a shark virus. Ghabivirales-like genome fragments were most similar to fungal totiviruses in both genome architecture and homology and had likely infected mycobiome constituents. Picornavirales, which are commonly retrieved in host-associated viral metagenomes, were similar to invertebrate transcriptome-derived picorna-like viruses. The greatest number of viral genome fragments was recovered from the wasting A. californicus library compared to the asymptomatic A. californicus library. However, reads from the asymptomatic library recruited to nearly all recovered wasting genome fragments, suggesting that they were present but not well represented in the grossly normal specimen. These results expand the known host range of flaviviruses and suggest that fungi and their viruses may play a role in holothurian ecology.
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Affiliation(s)
- Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA;
- Correspondence: ; Tel.: +1-607-255-0151
| | | | - Ian R. Tibbetts
- School of Biological Sciences, University of Queensland, St Lucia, Brisbane, QLD 4072, Australia;
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Identification and Distribution of Novel Cressdnaviruses and Circular molecules in Four Penguin Species in South Georgia and the Antarctic Peninsula. Viruses 2020; 12:v12091029. [PMID: 32947826 PMCID: PMC7551938 DOI: 10.3390/v12091029] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/26/2022] Open
Abstract
There is growing interest in uncovering the viral diversity present in wild animal species. The remote Antarctic region is home to a wealth of uncovered microbial diversity, some of which is associated with its megafauna, including penguin species, the dominant avian biota. Penguins interface with a number of other biota in their roles as marine mesopredators and several species overlap in their ranges and habitats. To characterize the circular single-stranded viruses related to those in the phylum Cressdnaviricota from these environmental sentinel species, cloacal swabs (n = 95) were obtained from King Penguins in South Georgia, and congeneric Adélie Penguins, Chinstrap Penguins, and Gentoo Penguins across the South Shetland Islands and Antarctic Peninsula. Using a combination of high-throughput sequencing, abutting primers-based PCR recovery of circular genomic elements, cloning, and Sanger sequencing, we detected 97 novel sequences comprising 40 ssDNA viral genomes and 57 viral-like circular molecules from 45 individual penguins. We present their detection patterns, with Chinstrap Penguins harboring the highest number of new sequences. The novel Antarctic viruses identified appear to be host-specific, while one circular molecule was shared between sympatric Chinstrap and Gentoo Penguins. We also report viral genotype sharing between three adult-chick pairs, one in each Pygoscelid species. Sequence similarity network approaches coupled with Maximum likelihood phylogenies of the clusters indicate the 40 novel viral genomes do not fall within any known viral families and likely fall within the recently established phylum Cressdnaviricota based on their replication-associated protein sequences. Similarly, 83 capsid protein sequences encoded by the viruses or viral-like circular molecules identified in this study do not cluster with any of those encoded by classified viral groups. Further research is warranted to expand knowledge of the Antarctic virome and would help elucidate the importance of viral-like molecules in vertebrate host evolution.
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Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome. Nat Microbiol 2020; 5:1262-1270. [PMID: 32690954 PMCID: PMC7508674 DOI: 10.1038/s41564-020-0755-4] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 06/16/2020] [Indexed: 12/26/2022]
Abstract
RNA viruses in aquatic environments remain poorly studied. Here, we analysed the RNA virome from approximately 10 l water from Yangshan Deep-Water Harbour near the Yangtze River estuary in China and identified more than 4,500 distinct RNA viruses, doubling the previously known set of viruses. Phylogenomic analysis identified several major lineages, roughly, at the taxonomic ranks of class, order and family. The 719-member-strong Yangshan virus assemblage is the sister clade to the expansive class Alsuviricetes and consists of viruses with simple genomes that typically encode only RNA-dependent RNA polymerase (RdRP), capping enzyme and capsid protein. Several clades within the Yangshan assemblage independently evolved domain permutation in the RdRP. Another previously unknown clade shares ancestry with Potyviridae, the largest known plant virus family. The ‘Aquatic picorna-like viruses/Marnaviridae’ clade was greatly expanded, with more than 800 added viruses. Several RdRP-linked protein domains not previously detected in any RNA viruses were identified, such as the small ubiquitin-like modifier (SUMO) domain, phospholipase A2 and PrsW-family protease domain. Multiple viruses utilize alternative genetic codes implying protist (especially ciliate) hosts. The results reveal a vast RNA virome that includes many previously unknown groups. However, phylogenetic analysis of the RdRPs supports the previously established five-branch structure of the RNA virus evolutionary tree, with no additional phyla. Metagenomic analysis of a single RNA virome from the Yangshan Deep-Water Harbour in China enabled the recovery of more than 4,500 distinct RNA viruses, doubling the known set of RNA viruses to date, and provided insights into their biology.
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Assessing Viral Abundance and Community Composition in Four Contrasting Regions of the Southern Ocean. Life (Basel) 2020; 10:life10070107. [PMID: 32635627 PMCID: PMC7400478 DOI: 10.3390/life10070107] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 12/20/2022] Open
Abstract
We explored how changes of viral abundance and community composition among four contrasting regions in the Southern Ocean relied on physicochemical and microbiological traits. During January-February 2015, we visited areas north and south of the South Orkney Islands (NSO and SSO) characterized by low temperature and salinity and high inorganic nutrient concentration, north of South Georgia Island (NSG) and west of Anvers Island (WA), which have relatively higher temperatures and lower inorganic nutrient concentrations. Surface viral abundance (VA) was highest in NSG (21.50 ± 10.70 × 106 viruses mL-1) and lowest in SSO (2.96 ± 1.48 × 106 viruses mL-1). VA was positively correlated with temperature, prokaryote abundance and prokaryotic heterotrophic production, chlorophyll a, diatoms, haptophytes, fluorescent organic matter, and isoprene concentration, and was negatively correlated with inorganic nutrients (NO3-, SiO42-, PO43-), and dimethyl sulfide (DMS) concentrations. Viral communities determined by randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) were grouped according to the sampling location, being more similar within them than among regions. The first two axes of a canonical correspondence analysis, including physicochemical (temperature, salinity, inorganic nutrients-NO3-, SiO42-, and dimethyl sulfoniopropionate -DMSP- and isoprene concentrations) and microbiological (chlorophyll a, haptophytes and diatom, and prokaryote abundance and prokaryotic heterotrophic production) factors accounted for 62.9% of the variance. The first axis, temperature-related, accounted for 33.8%; the second one, salinity-related, accounted for 29.1%. Thus, different environmental situations likely select different hosts for viruses, leading to distinct viral communities.
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Novel Protocol for Estimating Viruses Specifically Infecting the Marine Planktonic Diatoms. DIVERSITY 2020. [DOI: 10.3390/d12060225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Since their discovery, at least 15 diatom viruses have been isolated and characterised using a culture method with two cycles of extinction dilution. However, the method is time consuming and laborious, and it isolates only the most dominant virus in a water sample. Recent studies have suggested inter-species host specificity of diatom viruses. Here, we describe a new protocol to estimate previously unrecognised host-virus relationships. Host cell cultures after inoculation of natural sediment pore water samples were obtained before complete lysis. The proliferated viral genomes in the host cells were amplified using degenerate primer pairs targeting protein replication regions of single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA) viruses, and then sequenced. Diverse ssRNA virus types within known diatom virus group were detected from inoculated Chaetoceros tenuissimus and C. setoensis cells. A previously unknown ssDNA virus type was detected in inoculated C. tenuissimus cells, but not in C. setoensis cells. Despite the possible protocol biases, for example non-specific adsorptions of virions onto the host cells, the present method helps to estimate the viruses infectious to a single host species. Further improvements to this protocol targeting the proliferated viral genomes might reveal unexpected diatom–virus ecological relationships.
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Vlok M, Lang AS, Suttle CA. Application of a sequence-based taxonomic classification method to uncultured and unclassified marine single-stranded RNA viruses in the order Picornavirales. Virus Evol 2019; 5:vez056. [PMID: 31908848 PMCID: PMC6938265 DOI: 10.1093/ve/vez056] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Metagenomics has altered our understanding of microbial diversity and ecology. This includes its applications to viruses in marine environments that have demonstrated their enormous diversity. Within these are RNA viruses, many of which share genetic features with members of the order Picornavirales; yet, very few of these have been taxonomically classified. The only recognized family of marine RNA viruses is the Marnaviridae, which was founded based on discovery and characterization of the species Heterosigma akashiwo RNA virus. Two additional genera of marine RNA viruses, Labyrnavirus (one species) and Bacillarnavirus (three species), were subsequently defined within the order Picornavirales but not assigned to a family. We have defined a sequence-based framework for taxonomic classification of twenty marine RNA viruses into the family Marnaviridae. Using RNA-dependent RNA polymerase (RdRp) phylogeny and distance-based analyses, we assigned the genera Labyrnavirus and Bacillarnavirus to the family Marnaviridae and created four additional genera in the family: Locarnavirus (four species), Kusarnavirus (one species), Salisharnavirus (four species) and Sogarnavirus (six species). We used pairwise capsid protein comparisons to delineate species within families, with 75 per cent identity as the species demarcation threshold. The family displays high sequence diversities and Jukes-Cantor distances for both the RdRp and capsid genes, suggesting that the classified viruses are not representative of all of the virus diversity within the family and that there are many more extant taxa. Our proposed taxonomic framework provides a sound classification system for this group of viruses that will have broadly applicable principles for other viral groups. It is based on sequence data alone and provides a robust taxonomic framework to include viruses discovered via metagenomic studies, thereby greatly expanding the realm of viruses subject to taxonomic classification.
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Affiliation(s)
- Marli Vlok
- Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.,Institute for the Oceans and Fisheries, University of British Columbia, 2202 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada
| | - Curtis A Suttle
- Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.,Institute for the Oceans and Fisheries, University of British Columbia, 2202 Main Mall, Vancouver, BC V6T 1Z4, Canada.,Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, 2207 Main Mall, Vancouver, BC V6T 1Z4, Canada.,Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z4, Canada
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Van Etten JL, Agarkova IV, Dunigan DD. Chloroviruses. Viruses 2019; 12:E20. [PMID: 31878033 PMCID: PMC7019647 DOI: 10.3390/v12010020] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 12/20/2022] Open
Abstract
Chloroviruses are large dsDNA, plaque-forming viruses that infect certain chlorella-like green algae; the algae are normally mutualistic endosymbionts of protists and metazoans and are often referred to as zoochlorellae. The viruses are ubiquitous in inland aqueous environments throughout the world and occasionally single types reach titers of thousands of plaque-forming units per ml of native water. The viruses are icosahedral in shape with a spike structure located at one of the vertices. They contain an internal membrane that is required for infectivity. The viral genomes are 290 to 370 kb in size, which encode up to 16 tRNAs and 330 to ~415 proteins, including many not previously seen in viruses. Examples include genes encoding DNA restriction and modification enzymes, hyaluronan and chitin biosynthetic enzymes, polyamine biosynthetic enzymes, ion channel and transport proteins, and enzymes involved in the glycan synthesis of the virus major capsid glycoproteins. The proteins encoded by many of these viruses are often the smallest or among the smallest proteins of their class. Consequently, some of the viral proteins are the subject of intensive biochemical and structural investigation.
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Affiliation(s)
- James L. Van Etten
- Department of Plant Pathology, Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA; (I.V.A.); (D.D.D.)
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Dávila-Ramos S, Castelán-Sánchez HG, Martínez-Ávila L, Sánchez-Carbente MDR, Peralta R, Hernández-Mendoza A, Dobson ADW, Gonzalez RA, Pastor N, Batista-García RA. A Review on Viral Metagenomics in Extreme Environments. Front Microbiol 2019; 10:2403. [PMID: 31749771 PMCID: PMC6842933 DOI: 10.3389/fmicb.2019.02403] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/04/2019] [Indexed: 12/22/2022] Open
Abstract
Viruses are the most abundant biological entities in the biosphere, and have the ability to infect Bacteria, Archaea, and Eukaryotes. The virome is estimated to be at least ten times more abundant than the microbiome with 107 viruses per milliliter and 109 viral particles per gram in marine waters and sediments or soils, respectively. Viruses represent a largely unexplored genetic diversity, having an important role in the genomic plasticity of their hosts. Moreover, they also play a significant role in the dynamics of microbial populations. In recent years, metagenomic approaches have gained increasing popularity in the study of environmental viromes, offering the possibility of extending our knowledge related to both virus diversity and their functional characterization. Extreme environments represent an interesting source of both microbiota and their virome due to their particular physicochemical conditions, such as very high or very low temperatures and >1 atm hydrostatic pressures, among others. Despite the fact that some progress has been made in our understanding of the ecology of the microbiota in these habitats, few metagenomic studies have described the viromes present in extreme ecosystems. Thus, limited advances have been made in our understanding of the virus community structure in extremophilic ecosystems, as well as in their biotechnological potential. In this review, we critically analyze recent progress in metagenomic based approaches to explore the viromes in extreme environments and we discuss the potential for new discoveries, as well as methodological challenges and perspectives.
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Affiliation(s)
- Sonia Dávila-Ramos
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Hugo G. Castelán-Sánchez
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Liliana Martínez-Ávila
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | | | - Raúl Peralta
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Armando Hernández-Mendoza
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Ramón A. Gonzalez
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
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Abstract
Although viruses comprise the most abundant genetic material in the biosphere, to date only several thousand virus species have been formally defined. Such a limited perspective on virus diversity has in part arisen because viruses were traditionally considered only as etiologic agents of overt disease in humans or economically important species and were often difficult to identify using cell culture. This view has dramatically changed with the rise of metagenomics, which is transforming virus discovery and revealing a remarkable diversity of viruses sampled from diverse cellular organisms. These newly discovered viruses help fill major gaps in the evolutionary history of viruses, revealing a near continuum of diversity among genera, families, and even orders of RNA viruses. Herein, we review some of the recent advances in our understanding of the RNA virosphere that have stemmed from metagenomics, note future directions, and highlight some of the remaining challenges to this rapidly developing field.
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Affiliation(s)
- Yong-Zhen Zhang
- Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 200433, China; .,Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Yan-Mei Chen
- Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 200433, China; .,Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Wen Wang
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Xin-Chen Qin
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Edward C Holmes
- Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 200433, China; .,Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
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34
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Gregory AC, Zayed AA, Conceição-Neto N, Temperton B, Bolduc B, Alberti A, Ardyna M, Arkhipova K, Carmichael M, Cruaud C, Dimier C, Domínguez-Huerta G, Ferland J, Kandels S, Liu Y, Marec C, Pesant S, Picheral M, Pisarev S, Poulain J, Tremblay JÉ, Vik D, Babin M, Bowler C, Culley AI, de Vargas C, Dutilh BE, Iudicone D, Karp-Boss L, Roux S, Sunagawa S, Wincker P, Sullivan MB. Marine DNA Viral Macro- and Microdiversity from Pole to Pole. Cell 2019; 177:1109-1123.e14. [PMID: 31031001 PMCID: PMC6525058 DOI: 10.1016/j.cell.2019.03.040] [Citation(s) in RCA: 384] [Impact Index Per Article: 76.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/05/2019] [Accepted: 03/20/2019] [Indexed: 01/04/2023]
Abstract
Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.
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Affiliation(s)
- Ann C Gregory
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Nádia Conceição-Neto
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium; Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, UK
| | - Ben Bolduc
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Mathieu Ardyna
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, 06230 Villefranche-sur-mer, France
| | - Ksenia Arkhipova
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands
| | - Margaux Carmichael
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M ECOMAP, 29680 Roscoff, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Corinne Cruaud
- CEA-Institut de Biologie François Jacob, Genoscope, Evry 91057, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Céline Dimier
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, 06230 Villefranche-sur-mer, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | | | - Joannie Ferland
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)-CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Directors' Research, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Yunxiao Liu
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Claudie Marec
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)-CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Stéphane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, 28359 Bremen, Germany; MARUM, Bremen University, 28359 Bremen, Germany
| | - Marc Picheral
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, 06230 Villefranche-sur-mer, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology of Russian Academy of Sciences, 36 Nakhimovsky prosp, 117997 Moscow, Russia
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Jean-Éric Tremblay
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)-CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Dean Vik
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Marcel Babin
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)-CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Alexander I Culley
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M ECOMAP, 29680 Roscoff, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Simon Roux
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, 8093 Zurich, Switzerland
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210, USA.
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35
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Alarcón-Schumacher T, Guajardo-Leiva S, Antón J, Díez B. Elucidating Viral Communities During a Phytoplankton Bloom on the West Antarctic Peninsula. Front Microbiol 2019; 10:1014. [PMID: 31139164 PMCID: PMC6527751 DOI: 10.3389/fmicb.2019.01014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 04/24/2019] [Indexed: 01/16/2023] Open
Abstract
In Antarctic coastal waters where nutrient limitations are low, viruses are expected to play a major role in the regulation of bloom events. Despite this, research in viral identification and dynamics is scarce, with limited information available for the Southern Ocean (SO). This study presents an integrative-omics approach, comparing variation in the viral and microbial active communities on two contrasting sample conditions from a diatom-dominated phytoplankton bloom occurring in Chile Bay in the West Antarctic Peninsula (WAP) in the summer of 2014. The known viral community, initially dominated by Myoviridae family (∼82% of the total assigned reads), changed to become dominated by Phycodnaviridae (∼90%), while viral activity was predominantly driven by dsDNA members of the Phycodnaviridae (∼50%) and diatom infecting ssRNA viruses (∼38%), becoming more significant as chlorophyll a increased. A genomic and phylogenetic characterization allowed the identification of a new viral lineage within the Myoviridae family. This new lineage of viruses infects Pseudoalteromonas and was dominant in the phage community. In addition, a new Phycodnavirus (PaV) was described, which is predicted to infect Phaeocystis antarctica, the main blooming haptophyte in the SO. This work was able to identify the changes in the main viral players during a bloom development and suggests that the changes observed in the virioplankton could be used as a model to understand the development and decay of blooms that occur throughout the WAP.
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Affiliation(s)
- Tomás Alarcón-Schumacher
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sergio Guajardo-Leiva
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Josefa Antón
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile.,Center for Climate and Resilience Research (CR2), University of Chile, Santiago, Chile
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36
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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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Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes. Nat Commun 2019; 10:1169. [PMID: 30862830 PMCID: PMC6414667 DOI: 10.1038/s41467-019-09106-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/21/2019] [Indexed: 12/11/2022] Open
Abstract
Viruses provide top-down control on microbial communities, yet their direct study in natural environments was hindered by culture limitations. The advance of bioinformatics enables cultivation-independent study of viruses. Many studies assemble new viral genomes and study viral diversity using marker genes from free viruses. Here we use cellular metatranscriptomics to study active community-wide viral infections. Recruitment to viral contigs allows tracking infection dynamics over time and space. Our assemblies represent viral populations, but appear biased towards low diversity viral taxa. Tracking relatives of published T4-like cyanophages and pelagiphages reveals high genomic continuity. We determine potential hosts by matching dynamics of infection with abundance of particular microbial taxa. Finally, we quantify the relative contribution of cyanobacteria and viruses to photosystem-II psbA (reaction center) expression in our study sites. We show sometimes >50% of all cyanobacterial+viral psbA expression is of viral origin, highlighting the contribution of viruses to photosynthesis and oxygen production. Here, Sieradzki et al. use metatranscriptomics to study active community-wide viral infections at three coastal California sites throughout a year, identify potential viral hosts, and show that viruses can contribute a substantial amount to photosystem-II psbA expression.
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38
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Yau S, Seth-Pasricha M. Viruses of Polar Aquatic Environments. Viruses 2019; 11:v11020189. [PMID: 30813316 PMCID: PMC6410135 DOI: 10.3390/v11020189] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/13/2019] [Accepted: 02/18/2019] [Indexed: 02/07/2023] Open
Abstract
The poles constitute 14% of the Earth’s biosphere: The aquatic Arctic surrounded by land in the north, and the frozen Antarctic continent surrounded by the Southern Ocean. In spite of an extremely cold climate in addition to varied topographies, the polar aquatic regions are teeming with microbial life. Even in sub-glacial regions, cellular life has adapted to these extreme environments where perhaps there are traces of early microbes on Earth. As grazing by macrofauna is limited in most of these polar regions, viruses are being recognized for their role as important agents of mortality, thereby influencing the biogeochemical cycling of nutrients that, in turn, impact community dynamics at seasonal and spatial scales. Here, we review the viral diversity in aquatic polar regions that has been discovered in the last decade, most of which has been revealed by advances in genomics-enabled technologies, and we reflect on the vast extent of the still-to-be explored polar microbial diversity and its “enigmatic virosphere”.
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Affiliation(s)
- Sheree Yau
- Integrative Marine Biology Laboratory (BIOM), CNRS, UMR7232, Sorbonne Université, 66650 Banyuls-sur-Mer, France.
| | - Mansha Seth-Pasricha
- Institute of Earth, Ocean, and Atmospheric Sciences, Rutgers University, New Brunswick, NJ 08901, USA.
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA.
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39
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Arsenieff L, Simon N, Rigaut-Jalabert F, Le Gall F, Chaffron S, Corre E, Com E, Bigeard E, Baudoux AC. First Viruses Infecting the Marine Diatom Guinardia delicatula. Front Microbiol 2019; 9:3235. [PMID: 30687251 PMCID: PMC6334475 DOI: 10.3389/fmicb.2018.03235] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/12/2018] [Indexed: 11/17/2022] Open
Abstract
The marine diatom Guinardia delicatula is a cosmopolitan species that dominates seasonal blooms in the English Channel and the North Sea. Several eukaryotic parasites are known to induce the mortality of this species. Here, we report the isolation and characterization of the first viruses that infect G. delicatula. Viruses were isolated from the Western English Channel (SOMLIT-Astan station) during the late summer bloom decline of G. delicatula. A combination of laboratory approaches revealed that these lytic viruses (GdelRNAV) are small tailless particles of 35–38 nm in diameter that replicate in the host cytoplasm where both unordered particles and crystalline arrays are formed. GdelRNAV display a linear single-stranded RNA genome of ~9 kb, including two open reading frames encoding for replication and structural polyproteins. Phylogenetic relationships based on the RNA-dependent-RNA-polymerase gene marker showed that GdelRNAV are new members of the Bacillarnavirus, a monophyletic genus belonging to the order Picornavirales. GdelRNAV are specific to several strains of G. delicatula. They were rapidly and largely produced (<12 h, 9.34 × 104 virions per host cell). Our analysis points out the host's variable viral susceptibilities during the early exponential growth phase. Interestingly, we consistently failed to isolate viruses during spring and early summer while G. delicatula developed important blooms. While our study suggests that viruses do contribute to the decline of G. delicatula's late summer bloom, they may not be the primary mortality agents during the remaining blooms at SOMLIT-Astan. Future studies should focus on the relative contribution of the viral and eukaryotic pathogens to the control of Guinardia's blooms to understand the fate of these prominent organisms in marine systems.
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Affiliation(s)
- Laure Arsenieff
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
| | - Nathalie Simon
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
| | - Fabienne Rigaut-Jalabert
- Sorbonne Université, CNRS Fédération de Recherche FR2424 - Station Biologique de Roscoff, Roscoff, France
| | - Florence Le Gall
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
| | - Samuel Chaffron
- Laboratoire des Sciences du Numérique de Nantes (LS2N), CNRS UMR 6004 - Université de Nantes, Nantes, France
| | - Erwan Corre
- Sorbonne Université, CNRS Fédération de Recherche FR2424 - Station Biologique de Roscoff, Roscoff, France
| | - Emmanuelle Com
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France.,Protim, Univ Rennes, Rennes, France
| | - Estelle Bigeard
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
| | - Anne-Claire Baudoux
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
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40
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Gong Z, Liang Y, Wang M, Jiang Y, Yang Q, Xia J, Zhou X, You S, Gao C, Wang J, He J, Shao H, McMinn A. Viral Diversity and Its Relationship With Environmental Factors at the Surface and Deep Sea of Prydz Bay, Antarctica. Front Microbiol 2018; 9:2981. [PMID: 30559737 PMCID: PMC6287040 DOI: 10.3389/fmicb.2018.02981] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 11/19/2018] [Indexed: 12/31/2022] Open
Abstract
A viral metagenomic analysis of five surface and two bottom water (878 meters below surface, mbs, and 3,357 mbs) samples from Prydz Bay, was conducted during February-March 2015. The results demonstrated that most of the DNA viruses were dsDNA viruses (79.73-94.06%, except at PBI1, 37.51%). Of these, Caudovirales (Siphoviridae, Myoviridae, and Podoviridae) phages were most abundant in surface seawater (67.67-71.99%), while nucleocytoplasmic large DNA viruses (NCLDVs) (Phycodnaviridae, Mimiviridae, and Pandoraviridae accounted for >30% of dsDNA viruses) were most abundant in the bottom water (3,357 mbs). Of the ssDNA viruses, Microviridae was the dominant family in PBI2, PBI3, PBOs, and PBI4b (57.09-87.55%), while Inoviridae (58.16%) was the dominant family in PBI1. Cellulophaga phages (phi38:1 and phi10:1) and Flavobacterium phage 11b, infecting the possible host strains affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes, were abundant in surface water dsDNA viromes. The long contig (PBI2_1_C) from the viral metagenomes were most similar to the genome architectures of Cellulophaga phage phi10:1 and Flavobacterium phage 11b from the Arctic Ocean. Comparative analysis showed that the surface viral community of Prydz Bay could be clearly separated from other marine and freshwater environments. The deep sea viral community was similar to the deep sea viral metagenome at A Long-term Oligotrophic Habitat Assessment Station (ALOHA, at 22°45'N, 158°00'W). The multivariable analysis indicated that nutrients probably played an important role in shaping the local viral community structure. This study revealed the preliminary characteristics of the viral community in Prydz Bay, from both the surface and the deep sea. It provided evidence of the relationships between the virome and the environment in Prydz Bay and provided the first data from the deep sea viral community of the Southern Ocean.
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Affiliation(s)
- Zheng Gong
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Qingwei Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jun Xia
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xinhao Zhou
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Siyuan You
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chen Gao
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jian Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jianfeng He
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Hongbing Shao
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
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Diversity of Active Viral Infections within the Sphagnum Microbiome. Appl Environ Microbiol 2018; 84:AEM.01124-18. [PMID: 30217851 DOI: 10.1128/aem.01124-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 09/10/2018] [Indexed: 11/20/2022] Open
Abstract
Sphagnum-dominated peatlands play an important role in global carbon storage and represent significant sources of economic and ecological value. While recent efforts to describe microbial diversity and metabolic potential of the Sphagnum microbiome have demonstrated the importance of its microbial community, little is known about the viral constituents. We used metatranscriptomics to describe the diversity and activity of viruses infecting microbes within the Sphagnum peat bog. The vegetative portions of six Sphagnum plants were obtained from a peatland in northern Minnesota, and the total RNA was extracted and sequenced. Metatranscriptomes were assembled and contigs were screened for the presence of conserved virus marker genes. Using bacteriophage capsid protein gp23 as a marker for phage diversity, we identified 33 contigs representing undocumented phages that were active in the community at the time of sampling. Similarly, RNA-dependent RNA polymerase and the nucleocytoplasmic large DNA virus (NCLDV) major capsid protein were used as markers for single-stranded RNA (ssRNA) viruses and NCLDV, respectively. In total, 114 contigs were identified as originating from undescribed ssRNA viruses, 22 of which represent nearly complete genomes. An additional 64 contigs were identified as being from NCLDVs. Finally, 7 contigs were identified as putative virophage or polinton-like viruses. We developed co-occurrence networks with these markers in relation to the expression of potential-host housekeeping gene rpb1 to predict virus-host relationships, identifying 13 groups. Together, our approach offers new tools for the identification of virus diversity and interactions in understudied clades and suggests that viruses may play a considerable role in the ecology of the Sphagnum microbiome.IMPORTANCE Sphagnum-dominated peatlands play an important role in maintaining atmospheric carbon dioxide levels by modifying conditions in the surrounding soil to favor the growth of Sphagnum over that of other plant species. This lowers the rate of decomposition and facilitates the accumulation of fixed carbon in the form of partially decomposed biomass. The unique environment produced by Sphagnum enriches for the growth of a diverse microbial consortia that benefit from and support the moss's growth, while also maintaining the hostile soil conditions. While a growing body of research has begun to characterize the microbial groups that colonize Sphagnum, little is currently known about the ecological factors that constrain community structure and define ecosystem function. Top-down population control by viruses is almost completely undescribed. This study provides insight into the significant viral influence on the Sphagnum microbiome and identifies new potential model systems to study virus-host interactions in the peatland ecosystem.
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Bukhari K, Mulley G, Gulyaeva AA, Zhao L, Shu G, Jiang J, Neuman BW. Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae, and from a sister group to the Coronavirinae, the proposed genus Alphaletovirus. Virology 2018; 524:160-171. [PMID: 30199753 PMCID: PMC7112036 DOI: 10.1016/j.virol.2018.08.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/11/2018] [Accepted: 08/11/2018] [Indexed: 01/12/2023]
Abstract
Transcriptomics has the potential to discover new RNA virus genomes by sequencing total intracellular RNA pools. In this study, we have searched publicly available transcriptomes for sequences similar to viruses of the Nidovirales order. We report two potential nidovirus genomes, a highly divergent 35.9 kb likely complete genome from the California sea hare Aplysia californica, which we assign to a nidovirus named Aplysia abyssovirus 1 (AAbV), and a coronavirus-like 22.3 kb partial genome from the ornamented pygmy frog Microhyla fissipes, which we assign to a nidovirus named Microhyla alphaletovirus 1 (MLeV). AAbV was shown to encode a functional main proteinase, and a translational readthrough signal. Phylogenetic analysis suggested that AAbV represents a new family, proposed here as Abyssoviridae. MLeV represents a sister group to the other known coronaviruses. The importance of MLeV and AAbV for understanding nidovirus evolution, and the origin of terrestrial nidoviruses are discussed.
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Affiliation(s)
| | | | - Anastasia A Gulyaeva
- Dept. Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Lanying Zhao
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Guocheng Shu
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Benjamin W Neuman
- Texas A&M University-Texarkana, 7101 University Ave, Texarkana, TX 75503, United States.
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Abstract
Viruses play an important role in the control of microbial communities, and it has been suggested that the influence of viruses in polar ecosystems, with low nutrients and under extreme environmental conditions, may be greater. Viral metagenomics allows the genetic characterization of complex viral communities without the need to isolate and grow viruses. Recent investigations in Antarctica and the Arctic are uncovering a great diversity of DNA viruses, including bacteriophages, circular single-stranded DNA viruses, algal-infecting phycodnaviruses, and virophages, adapted to these extreme environments. The limited sequence similarity between viruses in Antarctica and the Arctic suggests that viral communities in the two polar regions have evolved independently since the formation of the Antarctic continent, estimated to occur 25 million years ago. The community of RNA viruses in Antarctica is dominated by the order Picornavirales and their quasispecies composition suggests that higher genetic variability may correlate with viral adaptation to new environmental conditions.
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44
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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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45
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Yoshida M, Mochizuki T, Urayama SI, Yoshida-Takashima Y, Nishi S, Hirai M, Nomaki H, Takaki Y, Nunoura T, Takai K. Quantitative Viral Community DNA Analysis Reveals the Dominance of Single-Stranded DNA Viruses in Offshore Upper Bathyal Sediment from Tohoku, Japan. Front Microbiol 2018; 9:75. [PMID: 29467725 PMCID: PMC5807898 DOI: 10.3389/fmicb.2018.00075] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/12/2018] [Indexed: 11/25/2022] Open
Abstract
Previous studies on marine environmental virology have primarily focused on double-stranded DNA (dsDNA) viruses; however, it has recently been suggested that single-stranded DNA (ssDNA) viruses are more abundant in marine ecosystems. In this study, we performed a quantitative viral community DNA analysis to estimate the relative abundance and composition of both ssDNA and dsDNA viruses in offshore upper bathyal sediment from Tohoku, Japan (water depth = 500 m). The estimated dsDNA viral abundance ranged from 3 × 106 to 5 × 106 genome copies per cm3 sediment, showing values similar to the range of fluorescence-based direct virus counts. In contrast, the estimated ssDNA viral abundance ranged from 1 × 108 to 3 × 109 genome copies per cm3 sediment, thus providing an estimation that the ssDNA viral populations represent 96.3–99.8% of the benthic total DNA viral assemblages. In the ssDNA viral metagenome, most of the identified viral sequences were associated with ssDNA viral families such as Circoviridae and Microviridae. The principle components analysis of the ssDNA viral sequence components from the sedimentary ssDNA viral metagenomic libraries found that the different depth viral communities at the study site all exhibited similar profiles compared with deep-sea sediment ones at other reference sites. Our results suggested that deep-sea benthic ssDNA viruses have been significantly underestimated by conventional direct virus counts and that their contributions to deep-sea benthic microbial mortality and geochemical cycles should be further addressed by such a new quantitative approach.
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Affiliation(s)
- Mitsuhiro Yoshida
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Tomohiro Mochizuki
- Project Team for Analyses of Changes in East Japan Marine Ecosystems, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Syun-Ichi Urayama
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yukari Yoshida-Takashima
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Shinro Nishi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Miho Hirai
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Hidetaka Nomaki
- Project Team for Analyses of Changes in East Japan Marine Ecosystems, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan.,Department of Biogeochemistry, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
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46
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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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47
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Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer. Virus Res 2017; 244:36-52. [PMID: 29103997 PMCID: PMC5801114 DOI: 10.1016/j.virusres.2017.10.020] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 12/22/2022]
Abstract
Virus metagenomics is a young research filed but it has already transformed our understanding of virus diversity and evolution, and illuminated at a new level the connections between virus evolution and the evolution and ecology of the hosts. In this review article, we examine the new picture of the evolution of RNA viruses, the dominant component of the eukaryotic virome, that is emerging from metagenomic data analysis. The major expansion of many groups of RNA viruses through metagenomics allowed the construction of substantially improved phylogenetic trees for the conserved virus genes, primarily, the RNA-dependent RNA polymerases (RdRp). In particular, a new superfamily of widespread, small positive-strand RNA viruses was delineated that unites tombus-like and noda-like viruses. Comparison of the genome architectures of RNA viruses discovered by metagenomics and by traditional methods reveals an extent of gene module shuffling among diverse virus genomes that far exceeds the previous appreciation of this evolutionary phenomenon. Most dramatically, inclusion of the metagenomic data in phylogenetic analyses of the RdRp resulted in the identification of numerous, strongly supported groups that encompass RNA viruses from diverse hosts including different groups of protists, animals and plants. Notwithstanding potential caveats, in particular, incomplete and uneven sampling of eukaryotic taxa, these highly unexpected findings reveal horizontal virus transfer (HVT) between diverse hosts as the central aspect of RNA virus evolution. The vast and diverse virome of invertebrates, particularly nematodes and arthropods, appears to be the reservoir, from which the viromes of plants and vertebrates evolved via multiple HVT events.
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48
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Viruses associated with Antarctic wildlife: From serology based detection to identification of genomes using high throughput sequencing. Virus Res 2017; 243:91-105. [PMID: 29111456 PMCID: PMC7114543 DOI: 10.1016/j.virusres.2017.10.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/24/2017] [Accepted: 10/24/2017] [Indexed: 11/30/2022]
Abstract
Summary of identified viruses associated with Antarctic animals. Genomes of Antarctic animals viruses have only been determine in the last five years. Limited knowledge of animal virology relative to environmental virology in Antarctica.
The Antarctic, sub-Antarctic islands and surrounding sea-ice provide a unique environment for the existence of organisms. Nonetheless, birds and seals of a variety of species inhabit them, particularly during their breeding seasons. Early research on Antarctic wildlife health, using serology-based assays, showed exposure to viruses in the families Birnaviridae, Flaviviridae, Herpesviridae, Orthomyxoviridae and Paramyxoviridae circulating in seals (Phocidae), penguins (Spheniscidae), petrels (Procellariidae) and skuas (Stercorariidae). It is only during the last decade or so that polymerase chain reaction-based assays have been used to characterize viruses associated with Antarctic animals. Furthermore, it is only during the last five years that full/whole genomes of viruses (adenoviruses, anelloviruses, orthomyxoviruses, a papillomavirus, paramyoviruses, polyomaviruses and a togavirus) have been sequenced using Sanger sequencing or high throughput sequencing (HTS) approaches. This review summaries the knowledge of animal Antarctic virology and discusses potential future directions with the advent of HTS in virus discovery and ecology.
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49
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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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50
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Schroeder DC. Opening the door to new virus interactions in the aquatic world. JOURNAL OF PHYCOLOGY 2016; 52:491-492. [PMID: 27533348 DOI: 10.1111/jpy.12429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Declan C Schroeder
- The Marine Biological Association of the UK, Citadel Hill, Plymouth, PL1 2PB, UK
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