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Lund MC, Larsen BB, Rowsey DM, Otto HW, Gryseels S, Kraberger S, Custer JM, Steger L, Yule KM, Harris RE, Worobey M, Van Doorslaer K, Upham NS, Varsani A. Using archived and biocollection samples towards deciphering the DNA virus diversity associated with rodent species in the families cricetidae and heteromyidae. Virology 2023; 585:42-60. [PMID: 37276766 DOI: 10.1016/j.virol.2023.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/07/2023]
Abstract
Rodentia is the most speciose order of mammals, and they are known to harbor a wide range of viruses. Although there has been significant research on zoonotic viruses in rodents, research on the diversity of other viruses has been limited, especially for rodents in the families Cricetidae and Heteromyidae. In fecal and liver samples of nine species of rodents, we identify 346 distinct circular DNA viral genomes. Of these, a large portion are circular, single-stranded DNA viruses in the families Anelloviridae (n = 3), Circoviridae (n = 5), Genomoviridae (n = 7), Microviridae (n = 297), Naryaviridae (n = 4), Vilyaviridae (n = 15) and in the phylum Cressdnaviricota (n = 13) that cannot be assigned established families. We also identified two large bacteriophages of 36 and 50 kb that are part of the class Caudoviricetes. Some of these viruses are clearly those that infect rodents, however, most of these likely infect various organisms associated with rodents, their environment or their diet.
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Affiliation(s)
- Michael C Lund
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Brendan B Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98102, USA
| | - Dakota M Rowsey
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Hans W Otto
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Sophie Gryseels
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000, Leuven, Belgium; Department of Biology, University of Antwerp, 2000, Antwerp, Belgium; OD Taxonomy and Phylogeny, Royal Belgian Museum of Natural Sciences, 1000, Brussels, Belgium
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Laura Steger
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Kelsey M Yule
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Robin E Harris
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, The BIO5 Institute, Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, UA Cancer Center, University of Arizona Tucson, AZ, 85724, USA
| | - Nathan S Upham
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, 7701, South Africa.
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Prado T, Brandão ML, Fumian TM, Freitas L, Chame M, Leomil L, Magalhães MGP, Degrave WMS, Leite JPG, Miagostovich MP. Virome analysis in lakes of the South Shetland Islands, Antarctica - 2020. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158537. [PMID: 36075413 DOI: 10.1016/j.scitotenv.2022.158537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/05/2022] [Accepted: 09/01/2022] [Indexed: 05/25/2023]
Abstract
Polar freshwater ecosystems are characterized by a distinct microbiota. However, little is known about viral diversity and abundance, especially regarding the ecology of RNA viruses. We used shotgun metagenomic analysis on samples from Antarctic ecosystems, and report here the characterization of the virome fraction, from different lakes located in the South Shetland Islands (Penguin, Ardley, Deception and King George Island) in the Peninsula Antarctica, in the summer season 2020. DNA viruses (99.4 %) prevailed over RNA viruses (0.6 %) in the lake samples. Six viral orders were identified in the metagenomic libraries: Caudovirales (dsDNA), which was prevalent in most lakes; Picornavirales (ssRNA+); Sobelivirales (ssRNA+); Tolivirales (ssRNA+); Petitvirales (ssDNA) and Baphyvirales (ssDNA), including eight viral families (Herelleviridae, Siphoviridae, Myoviridae, Microviridae, Marnaviridae, Bacilladnaviridae, Barnaviridae and Tombusviridae) and several other, mainly non-classified ssRNA(+) viruses in the lakes of Ardley Island. Bacteriophages (dsDNA) (Herelleviridae family) infecting the phylum Firmicutes and Siphoviridae were predominant in most lakes evaluated. Functional analysis demonstrated a prevalence of unknown proteins (68 %) in the virome. Our prospective study provides virome analysis data from different lakes in the South Shetland Islands, Antarctica, opening exploratory lines for future research related to the biodiversity and viral ecology in this extreme ecosystem.
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Affiliation(s)
- Tatiana Prado
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil.
| | - Martha Lima Brandão
- FioAntar Project/ VPPIS - Fiocruz, Av Brasil 4365, Manguinhos, Rio de Janeiro, RJ 21040-360, Brazil
| | - Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil
| | - Lucas Freitas
- Laboratory of Respiratory Virus and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro CEP 21040-360, Brazil
| | - Marcia Chame
- Institutional Platform for Biodiversity and Wildlife Health, Av Brasil 4365, Manguinhos, Rio de Janeiro, RJ 21040-360, Brazil
| | - Luciana Leomil
- SENAI Innovation Institute for Biosynthetics and Fibers, Technology Center for Chemical and Textile Industry, 4° Andar: Biotecnologia, Rua Fernando de Souza Barros, 120, Parque Tecnológico da UFRJ, Cidade Universitária, Rio de Janeiro CEP 21941-857, Brazil
| | - Maithê Gaspar Pontes Magalhães
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ 21040-360, Brazil
| | - Wim Maurits Sylvain Degrave
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ 21040-360, Brazil
| | - José Paulo Gagliardi Leite
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil
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Butina TV, Petrushin IS, Khanaev IV, Bukin YS. Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera. Microorganisms 2022; 10:microorganisms10020480. [PMID: 35208935 PMCID: PMC8876492 DOI: 10.3390/microorganisms10020480] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/10/2022] Open
Abstract
Sponges (type Porifera) are multicellular organisms that give shelter to a variety of microorganisms: fungi, algae, archaea, bacteria, and viruses. The studies concerning the composition of viral communities in sponges have appeared rather recently, and the diversity and role of viruses in sponge holobionts remain largely undisclosed. In this study, we assessed the diversity of DNA viruses in the associated community of the Baikal endemic sponge, Baikalospongia bacillifera, using a metagenomic approach, and compared the virome data from samples of sponges and Baikal water (control sample). Significant differences in terms of taxonomy, putative host range of identified scaffolds, and functional annotation of predicted viral proteins were revealed in viromes of sponge B. bacillifera and the Baikal water. This is the evidence in favor of specificity of viral communities in sponges. The diversity shift of viral communities in a diseased specimen, in comparison with a visually healthy sponge, probably reflects the changes in the composition of microbial communities in affected sponges. We identified many viral genes encoding the proteins with metabolic functions; therefore, viruses in Baikal sponges regulate the number and diversity of their associated community, and also take a part in the vital activity of the holobiont, and this is especially significant in the case of damage (or disease) of these organisms in unfavorable conditions. When comparing the Baikal viromes with similar datasets of marine sponge (Ianthella basta), in addition to significant differences in the taxonomic and functional composition of viral communities, we revealed common scaffolds/virotypes in the cross-assembly of reads, which may indicate the presence of some closely related sponge-specific viruses in marine and freshwater sponges.
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Val-Calvo J, Miguel-Arribas A, Abia D, Wu LJ, Meijer WJJ. pLS20 is the archetype of a new family of conjugative plasmids harboured by Bacillus species. NAR Genom Bioinform 2021; 3:lqab096. [PMID: 34729475 PMCID: PMC8557374 DOI: 10.1093/nargab/lqab096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/03/2021] [Accepted: 10/04/2021] [Indexed: 12/12/2022] Open
Abstract
Conjugation plays important roles in genome plasticity, adaptation and evolution but is also the major horizontal gene-transfer route responsible for spreading toxin, virulence and antibiotic resistance genes. A better understanding of the conjugation process is required for developing drugs and strategies to impede the conjugation-mediated spread of these genes. So far, only a limited number of conjugative elements have been studied. For most of them, it is not known whether they represent a group of conjugative elements, nor about their distribution patterns. Here we show that pLS20 from the Gram-positive bacterium Bacillus subtilis is the prototype conjugative plasmid of a family of at least 35 members that can be divided into four clades, and which are harboured by different Bacillus species found in different global locations and environmental niches. Analyses of their phylogenetic relationship and their conjugation operons have expanded our understanding of a family of conjugative plasmids of Gram-positive origin.
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Affiliation(s)
- Jorge Val-Calvo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049, Madrid, Spain
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049, Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049, Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Wilfried J J Meijer
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049, Madrid, Spain
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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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Abstract
The Arctic is warming at an accelerating pace, and the rise in temperature has increasing impacts on the Arctic biome. Lakes are integrators of their surroundings and thus excellent sentinels of environmental change. Despite their importance in the regulation of key microbial processes, viruses remain largely uncharacterized in Arctic lacustrine environments. We sampled a highly stratified meromictic lake near the northern limit of the Canadian High Arctic, a region in rapid transition due to climate change. We found that the different layers of the lake harbored viral communities that were strikingly dissimilar and highly divergent from known viruses. Viruses were more abundant in the deepest part of the lake containing ancient Arctic Ocean seawater that was trapped during glacial retreat and were genomically unlike any viruses previously described. This research demonstrates the complexity and novelty of viral communities in an environment that is vulnerable to ongoing perturbation. High-latitude, perennially stratified (meromictic) lakes are likely to be especially vulnerable to climate warming because of the importance of ice in maintaining their water column structure and associated distribution of microbial communities. This study aimed to characterize viral abundance, diversity, and distribution in a meromictic lake of marine origin on the far northern coast of Ellesmere Island, in the Canadian High Arctic. We collected triplicate samples for double-stranded DNA (dsDNA) viromics from five depths that encompassed the major features of the lake, as determined by limnological profiling of the water column. Viral abundance and virus-to-prokaryote ratios were highest at greater depths, while bacterial and cyanobacterial counts were greatest in the surface waters. The viral communities from each zone of the lake defined by salinity, temperature, and dissolved oxygen concentrations were markedly distinct, suggesting that there was little exchange of viral types among lake strata. Ten viral assembled genomes were obtained from our libraries, and these also segregated with depth. This well-defined structure of viral communities was consistent with that of potential hosts. Viruses from the monimolimnion, a deep layer of ancient Arctic Ocean seawater, were more diverse and relatively abundant, with few similarities to available viral sequences. The Lake A viral communities also differed from published records from the Arctic Ocean and meromictic Ace Lake in Antarctica. This first characterization of viral diversity from this sentinel environment underscores the microbial richness and complexity of an ecosystem type that is increasingly exposed to major perturbations in the fast-changing Arctic. IMPORTANCE The Arctic is warming at an accelerating pace, and the rise in temperature has increasing impacts on the Arctic biome. Lakes are integrators of their surroundings and thus excellent sentinels of environmental change. Despite their importance in the regulation of key microbial processes, viruses remain largely uncharacterized in Arctic lacustrine environments. We sampled a highly stratified meromictic lake near the northern limit of the Canadian High Arctic, a region in rapid transition due to climate change. We found that the different layers of the lake harbored viral communities that were strikingly dissimilar and highly divergent from known viruses. Viruses were more abundant in the deepest part of the lake containing ancient Arctic Ocean seawater that was trapped during glacial retreat and were genomically unlike any viruses previously described. This research demonstrates the complexity and novelty of viral communities in an environment that is vulnerable to ongoing perturbation.
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Zolfo M, Pinto F, Asnicar F, Manghi P, Tett A, Bushman FD, Segata N. Detecting contamination in viromes using ViromeQC. Nat Biotechnol 2020; 37:1408-1412. [PMID: 31748692 DOI: 10.1038/s41587-019-0334-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Adrian Tett
- Department CIBIO, University of Trento, Trento, Italy
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
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Abstract
Virus-virus interactions in plants can modify host symptoms. As a result, disease management strategies may be unsuccessful if they are based solely on visual assessment and diagnostic assays for known individual viruses. Papaya ringspot virus is an important limiting factor for papaya production and likely has interactions with other viruses that are not yet known. Using high-throughput sequencing, we recovered known and novel RNA and DNA viruses from papaya orchards in Chiapas, Mexico, and categorized them by host and, in the case of papaya, symptom type: asymptomatic papaya, papaya with ringspot virus symptoms, papaya with nonringspot symptoms, weeds, and insects. Using network analysis, we demonstrated virus associations within and among host types and described the ecological community patterns. Recovery of viruses from weeds and asymptomatic papaya suggests the need for additional management attention. These analyses contribute to the understanding of the community structure of viruses in the agroecological landscape. The study of complex ecological interactions, such as those among host, pathogen, and vector communities, can help to explain host ranges and the emergence of novel pathogens. We evaluated the viromes of papaya orchards, including weed and insect viromes, to identify common viruses in intensive production of papaya in the Pacific Coastal Plain and the Central Depression of Chiapas, Mexico. Samples of papaya cultivar Maradol, susceptible to papaya ringspot virus (PRSV), were categorized by symptoms by local farmers (papaya ringspot symptoms, non-PRSV symptoms, or asymptomatic). These analyses revealed the presence of 61 viruses, where only 4 species were shared among both regions, 16 showed homology to known viruses, and 36 were homologous with genera including Potyvirus, Comovirus, and Tombusvirus (RNA viruses) and Begomovirus and Mastrevirus (DNA viruses). We analyzed the network of associations between viruses and host-location combinations, revealing ecological properties of the network, such as an asymmetric nested pattern, and compared the observed network to null models of network association. Understanding the network structure informs management strategies, for example, revealing the potential role of PRSV in asymptomatic papaya and that weeds may be an important pathogen reservoir. We identify three key management implications: (i) each region may need a customized management strategy; (ii) visual assessment of papaya may be insufficient for PRSV, requiring diagnostic assays; and (iii) weed control within orchards may reduce the risk of virus spread to papaya. Network analysis advances understanding of host-pathogen interactions in the agroecological landscape. IMPORTANCE Virus-virus interactions in plants can modify host symptoms. As a result, disease management strategies may be unsuccessful if they are based solely on visual assessment and diagnostic assays for known individual viruses. Papaya ringspot virus is an important limiting factor for papaya production and likely has interactions with other viruses that are not yet known. Using high-throughput sequencing, we recovered known and novel RNA and DNA viruses from papaya orchards in Chiapas, Mexico, and categorized them by host and, in the case of papaya, symptom type: asymptomatic papaya, papaya with ringspot virus symptoms, papaya with nonringspot symptoms, weeds, and insects. Using network analysis, we demonstrated virus associations within and among host types and described the ecological community patterns. Recovery of viruses from weeds and asymptomatic papaya suggests the need for additional management attention. These analyses contribute to the understanding of the community structure of viruses in the agroecological landscape.
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Sommers P, Fontenele RS, Kringen T, Kraberger S, Porazinska DL, Darcy JL, Schmidt SK, Varsani A. Single-Stranded DNA Viruses in Antarctic Cryoconite Holes. Viruses 2019; 11:E1022. [PMID: 31689942 PMCID: PMC6893807 DOI: 10.3390/v11111022] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 12/28/2022] Open
Abstract
Antarctic cryoconite holes, or small melt-holes in the surfaces of glaciers, create habitable oases for isolated microbial communities with tightly linked microbial population structures. Viruses may influence the dynamics of polar microbial communities, but the viromes of the Antarctic cryoconite holes have yet to be characterized. We characterize single-stranded DNA (ssDNA) viruses from three cryoconite holes in the Taylor Valley, Antarctica, using metagenomics. Half of the assembled metagenomes cluster with those in the viral family Microviridae (n = 7), and the rest with unclassified circular replication associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses (n = 7). An additional 18 virus-like circular molecules encoding either a Rep, a capsid protein gene, or other unidentified but viral-like open reading frames were identified. The samples from which the genomes were identified show a strong gradient in microbial diversity and abundances, and the number of viral genomes detected in each sample mirror that gradient. Additionally, one of the CRESS genomes assembled here shares ~90% genome-wide pairwise identity with a virus identified from a freshwater pond on the McMurdo Ice Shelf (Antarctica). Otherwise, the similarity of these viruses to those previously identified is relatively low. Together, these patterns are consistent with the presence of a unique regional virome present in fresh water host populations of the McMurdo Dry Valley region.
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Affiliation(s)
- Pacifica Sommers
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA.
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Tayele Kringen
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Dorota L Porazinska
- Entomology and Nematology Department, University of Florida, Gainesville, FL 32611, USA.
| | - John L Darcy
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Steven K Schmidt
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA.
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town 7701, South Africa.
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Metagenomic Analysis of Virus Diversity and Relative Abundance in a Eutrophic Freshwater Harbour. Viruses 2019; 11:v11090792. [PMID: 31466255 PMCID: PMC6784016 DOI: 10.3390/v11090792] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/13/2019] [Accepted: 08/25/2019] [Indexed: 11/17/2022] Open
Abstract
Aquatic viruses have been extensively studied over the past decade, yet fundamental aspects of freshwater virus communities remain poorly described. Our goal was to characterize virus communities captured in the >0.22 µm size-fraction seasonally and spatially in a freshwater harbour. Community DNA was extracted from water samples and sequenced on an Illumina HiSeq platform. Assembled contigs were annotated as belonging to the virus groups (i.e., order or family) Caudovirales, Mimiviridae, Phycodnaviridae, and virophages (Lavidaviridae), or to other groups of undefined viruses. Virophages were often the most abundant group, and discrete virophage taxa were remarkably stable across sites and dates despite fluctuations in Mimiviridae community composition. Diverse Mimiviridae contigs were detected in the samples and the two sites contained distinct Mimiviridae communities, suggesting that Mimiviridae are important algal viruses in this system. Caudovirales and Phycodnaviridae were present at low abundances in most samples. Of the 18 environmental parameters tested, only chlorophyll a explained the variation in the data at the order or family level of classification. Overall, our findings provide insight into freshwater virus community assemblages by expanding the documented diversity of freshwater virus communities, highlighting the potential ecological importance of virophages, and revealing distinct communities over small spatial scales.
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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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Yang Q, Gao C, Jiang Y, Wang M, Zhou X, Shao H, Gong Z, McMinn A. Metagenomic Characterization of the Viral Community of the South Scotia Ridge. Viruses 2019; 11:E95. [PMID: 30678352 PMCID: PMC6410227 DOI: 10.3390/v11020095] [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: 10/24/2018] [Revised: 12/28/2018] [Accepted: 01/22/2019] [Indexed: 12/16/2022] Open
Abstract
Viruses are the most abundant biological entities in aquatic ecosystems and harbor an enormous amount of genetic diversity. Whereas their influence on marine ecosystems is widely acknowledged, current information about their diversity remains limited. We conducted a viral metagenomic analysis of water samples collected during the austral summer of 2016 from the South Scotia Ridge (SSR), near the Antarctic Peninsula. The taxonomic composition and diversity of the viral communities were investigated, and a functional assessment of the sequences was performed. Phylotypic analysis showed that most viruses belonged to the order Caudovirales, especially the family Podoviridae (41.92⁻48.7%), which is similar to the situation in the Pacific Ocean. Functional analysis revealed a relatively high frequency of phage-associated and metabolism genes. Phylogenetic analyses of phage TerL and Capsid_NCLDV (nucleocytoplasmic large DNA viruses) marker genes indicated that many sequences associated with Caudovirales and NCLDV were novel and distinct from known phage genomes. High Phaeocystis globosa virus virophage (Pgvv) signatures were found and complete and partial Pgvv-like were obtained, which influence host⁻virus interactions. Our study expands existing knowledge of viral communities and their diversities from the Antarctic region and provides basic data for further exploring polar microbiomes.
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Affiliation(s)
- Qingwei Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Chen Gao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Yong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Xinhao Zhou
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Hongbing Shao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Zheng Gong
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Andrew McMinn
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia.
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Genetic and functional diversity of double-stranded DNA viruses in a tropical monsoonal estuary, India. Sci Rep 2018; 8:16036. [PMID: 30375431 PMCID: PMC6207776 DOI: 10.1038/s41598-018-34332-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/04/2018] [Indexed: 11/08/2022] Open
Abstract
The present study illustrates the genetic diversity of four uncultured viral communities from the surface waters of Cochin Estuary (CE), India. Viral diversity inferred using Illumina HiSeq paired-end sequencing using a linker-amplified shotgun library (LASL) revealed different double-stranded DNA (dsDNA) viral communities. The water samples were collected from four stations PR1, PR2, PR3, and PR4, during the pre-monsoon (PRM) season. Analysis of virus families indicated that the Myoviridae was the most common viral community in the CE followed by Siphoviridae and Podoviridae. There were significant (p < 0.05) spatial variations in the relative abundance of dominant families in response to the salinity regimes. The relative abundance of Myoviridae and Podoviridae were high in the euryhaline region and Siphoviridae in the mesohaline region of the estuary. The predominant phage type in CE was phages that infected Synechococcus. The viral proteins were found to be involved in major functional activities such as ATP binding, DNA binding, and DNA replication. The study highlights the genetic diversity of dsDNA viral communities and their functional protein predictions from a highly productive estuarine system. Further, the metavirome data generated in this study will enhance the repertoire of publicly available dataset and advance our understanding of estuarine viral ecology.
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Microbial Diversity: The Gap between the Estimated and the Known. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10020046] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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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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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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Rastrojo A, Alcamí A. Aquatic viral metagenomics: Lights and shadows. Virus Res 2016; 239:87-96. [PMID: 27889617 DOI: 10.1016/j.virusres.2016.11.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/18/2016] [Indexed: 01/02/2023]
Abstract
Viruses are the most abundant biological entities on Earth, exceeding bacteria in most of the ecosystems. Specially in oceans, viruses are thought to be the major planktonic predators shaping microorganism communities and controlling ocean biological capacity. Plankton lysis by viruses plays an important role in ocean nutrient and energy cycles. Viral metagenomics has emerged as a powerful tool to uncover viral diversity in aquatic ecosystems through the use of Next Generation Sequencing. However, many of the commonly used viral sample preparation steps have several important biases that must be considered to avoid a misinterpretation of the results. In addition to biases caused by the purification of virus particles, viral DNA/RNA amplification and the preparation of genomic libraries could also introduce biases, and a detailed knowledge about such protocols is required. In this review, the main steps in the viral metagenomic workflow are described paying special attention to the potential biases introduced by each one.
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Affiliation(s)
- Alberto Rastrojo
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas y Universidad Autónoma de Madrid), Madrid, Spain
| | - Antonio Alcamí
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas y Universidad Autónoma de Madrid), Madrid, Spain.
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Elster J, Margesin R, Wagner D, Häggblom M. Editorial: Polar and Alpine Microbiology—Earth's cryobiosphere. FEMS Microbiol Ecol 2016; 93:fiw221. [DOI: 10.1093/femsec/fiw221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2016] [Indexed: 11/12/2022] Open
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