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Liang JL, Feng SW, Jia P, Lu JL, Yi X, Gao SM, Wu ZH, Liao B, Shu WS, Li JT. Unraveling the habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses across China. MICROBIOME 2024; 12:136. [PMID: 39039586 PMCID: PMC11265010 DOI: 10.1186/s40168-024-01851-8] [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: 09/20/2023] [Accepted: 05/30/2024] [Indexed: 07/24/2024]
Abstract
BACKGROUND Soil giant viruses are increasingly believed to have profound effects on ecological functioning by infecting diverse eukaryotes. However, their biogeography and ecology remain poorly understood. RESULTS In this study, we analyzed 333 soil metagenomes from 5 habitat types (farmland, forest, grassland, Gobi desert, and mine wasteland) across China and identified 533 distinct giant virus phylotypes affiliated with nine families, thereby greatly expanding the diversity of soil giant viruses. Among the nine families, Pithoviridae were the most diverse. The majority of phylotypes exhibited a heterogeneous distribution among habitat types, with a remarkably high proportion of unique phylotypes in mine wasteland. The abundances of phylotypes were negatively correlated with their environmental ranges. A total of 76 phylotypes recovered in this study were detectable in a published global topsoil metagenome dataset. Among climatic, geographical, edaphic, and biotic characteristics, soil eukaryotes were identified as the most important driver of beta-diversity of giant viral communities across habitat types. Moreover, co-occurrence network analysis revealed some pairings between giant viral phylotypes and eukaryotes (protozoa, fungi, and algae). Analysis of 44 medium- to high-quality giant virus genomes recovered from our metagenomes uncovered not only their highly shared functions but also their novel auxiliary metabolic genes related to carbon, sulfur, and phosphorus cycling. CONCLUSIONS These findings extend our knowledge of diversity, habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses. Video Abstract.
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Affiliation(s)
- Jie-Liang Liang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Shi-Wei Feng
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Pu Jia
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Jing-Li Lu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Xinzhu Yi
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Shao-Ming Gao
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zhuo-Hui Wu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Bin Liao
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Sheng Shu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Jin-Tian Li
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China.
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Blanco-Melo D, Campbell MA, Zhu H, Dennis TPW, Modha S, Lytras S, Hughes J, Gatseva A, Gifford RJ. A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record. Genome Biol 2024; 25:120. [PMID: 38741126 PMCID: PMC11089739 DOI: 10.1186/s13059-024-03258-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Genomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (EVEs)-virus-derived sequences that can dramatically impact host biology and serve as a virus fossil record. In this study, we introduce a database-integrated genome screening (DIGS) approach to investigate the dark genome in silico, focusing on EVEs found within vertebrate genomes. RESULTS Using DIGS on 874 vertebrate genomes, we uncover approximately 1.1 million EVE sequences, with over 99% originating from endogenous retroviruses or transposable elements that contain EVE DNA. We show that the remaining 6038 sequences represent over a thousand distinct horizontal gene transfer events across 10 virus families, including some that have not previously been reported as EVEs. We explore the genomic and phylogenetic characteristics of non-retroviral EVEs and determine their rates of acquisition during vertebrate evolution. Our study uncovers novel virus diversity, broadens knowledge of virus distribution among vertebrate hosts, and provides new insights into the ecology and evolution of vertebrate viruses. CONCLUSIONS We comprehensively catalog and analyze EVEs within 874 vertebrate genomes, shedding light on the distribution, diversity, and long-term evolution of viruses and reveal their extensive impact on vertebrate genome evolution. Our results demonstrate the power of linking a relational database management system to a similarity search-based screening pipeline for in silico exploration of the dark genome.
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Affiliation(s)
- Daniel Blanco-Melo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | | | - Henan Zhu
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Tristan P W Dennis
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Sejal Modha
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Spyros Lytras
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Anna Gatseva
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Robert J Gifford
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK.
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
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Balestreri C, Schroeder DC, Sampedro F, Marqués G, Palowski A, Urriola PE, van de Ligt JLG, Yancy HF, Shurson GC. Unexpected thermal stability of two enveloped megaviruses, Emiliania huxleyi virus and African swine fever virus, as measured by viability PCR. Virol J 2024; 21:1. [PMID: 38172919 PMCID: PMC10765680 DOI: 10.1186/s12985-023-02272-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The particle structure of Emiliania huxleyi virus (EhV), an algal infecting member of nucleocytoplasmic large DNA viruses (NCLDVs), contains an outer lipid membrane envelope similar to that found in animal viruses such as African swine fever virus (ASFV). Despite both being enveloped NCLDVs, EhV and ASFV are known for their stability outside their host environment. METHOD Here we report for the first time, the application of a viability qPCR (V-qPCR) method to describe the unprecedented and similar virion thermal stability of both EhV and ASFV. This result contradicts the cell culture-based assay method that suggests that virus "infectivity" is lost in a matter of seconds (for EhV) and minutes (for ASFV) at temperature greater than 50 °C. Confocal microscopy and analytical flow cytometry methods was used to validate the V-qPCR data for EhV. RESULTS We observed that both EhV and ASFV particles has unprecedented thermal tolerances. These two NCLDVs are exceptions to the rule that having an enveloped virion anatomy is a predicted weakness, as is often observed in enveloped RNA viruses (i.e., the viruses causing Porcine Reproductive and Respiratory Syndrome (PRRS), COVID-19, Ebola, or seasonal influenza). Using the V-qPCR method, we confirm that no PRRSV particles were detectable after 20 min of exposure to temperatures up to 100 °C. We also show that the EhV particles that remain after 50 °C 20 min exposure was in fact still infectious only after the three blind passages in bioassay experiments. CONCLUSIONS This study raises the possibility that ASFV is not always eliminated or contained after applying time and temperature inactivation treatments in current decontamination or biosecurity protocols. This observation has practical implications for industries involved in animal health and food security. Finally, we propose that EhV could be used as a surrogate for ASFV under certain circumstances.
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Affiliation(s)
- Cecilia Balestreri
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Declan C Schroeder
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, 55108, USA.
| | - Fernando Sampedro
- Environmental Health Sciences Division, University of Minnesota, St. Paul, MN, 55455, USA
| | - Guillermo Marqués
- Department of Neuroscience, University Imaging Centers, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Amanda Palowski
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Pedro E Urriola
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Animal Science, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Haile F Yancy
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD, 20708, USA
| | - Gerald C Shurson
- Department of Animal Science, University of Minnesota, St. Paul, MN, 55108, USA.
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Zhao H, Zhang R, Wu J, Meng L, Okazaki Y, Hikida H, Ogata H. A 1.5-Mb continuous endogenous viral region in the arbuscular mycorrhizal fungus Rhizophagus irregularis. Virus Evol 2023; 9:vead064. [PMID: 37953976 PMCID: PMC10640383 DOI: 10.1093/ve/vead064] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/21/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023] Open
Abstract
Most fungal viruses are RNA viruses, and no double-stranded DNA virus that infects fungi is known to date. A recent study detected DNA polymerase genes that originated from large dsDNA viruses in the genomes of basal fungi, suggestive of the existence of dsDNA viruses capable of infecting fungi. In this study, we searched for viral infection signatures in chromosome-level genome assemblies of the arbuscular mycorrhizal fungus Rhizophagus irregularis. We identified a continuous 1.5-Mb putative viral region on a chromosome in R. irregularis strain 4401. Phylogenetic analyses revealed that the viral region is related to viruses in the family Asfarviridae of the phylum Nucleocytoviricota. This viral region was absent in the genomes of four other R. irregularis strains and had fewer signals of fungal transposable elements than the other genomic regions, suggesting a recent and single insertion of a large dsDNA viral genome in the genome of this fungal strain. We also incidentally identified viral-like sequences in the genome assembly of the sea slug Elysia marginata that are evolutionally close to the 1.5-Mb putative viral region. In conclusion, our findings provide strong evidence of the recent infection of the fungus by a dsDNA virus.
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Affiliation(s)
- Hongda Zhao
- Chemical Life Science, Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Ruixuan Zhang
- Chemical Life Science, Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Junyi Wu
- Chemical Life Science, Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Lingjie Meng
- Chemical Life Science, Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Yusuke Okazaki
- Chemical Life Science, Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Hiroyuki Hikida
- Chemical Life Science, Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Hiroyuki Ogata
- Chemical Life Science, Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan
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Barreat JGN, Katzourakis A. Paleovirology of the DNA viruses of eukaryotes. Trends Microbiol 2021; 30:281-292. [PMID: 34483047 DOI: 10.1016/j.tim.2021.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 12/17/2022]
Abstract
Paleovirology is the study of ancient viruses and how they have coevolved with their hosts. An increasingly detailed understanding of the diversity, origins, and evolution of the DNA viruses of eukaryotes has been obtained through the lens of paleovirology in recent years. Members of multiple viral families have been found integrated in the genomes of eukaryotes, providing a rich fossil record to study. These elements have extended our knowledge of exogenous viral diversity, host ranges, and the timing of viral evolution, and are revealing the existence of entire new families of eukaryotic integrating dsDNA viruses and transposons. Future work in paleovirology will continue to provide insights into antiviral immunity, viral diversity, and potential applications, and reveal other secrets of the viral world.
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Affiliation(s)
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford, OX1 3SY, UK.
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Rolland C, Andreani J, Sahmi-Bounsiar D, Krupovic M, La Scola B, Levasseur A. Clandestinovirus: A Giant Virus With Chromatin Proteins and a Potential to Manipulate the Cell Cycle of Its Host Vermamoeba vermiformis. Front Microbiol 2021; 12:715608. [PMID: 34447361 PMCID: PMC8383183 DOI: 10.3389/fmicb.2021.715608] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/14/2021] [Indexed: 11/13/2022] Open
Abstract
For several decades, the vast world of DNA viruses has been expanding constantly. Various discoveries in this field have broadened our knowledge and revealed that DNA viruses encode many functional features, which were once thought to be exclusive to cellular life. Here, we report the isolation of a giant virus named "clandestinovirus," grown on the amoebal host Vermamoeba vermiformis. This virus was discovered in a mixed co-culture associated with another giant virus, Faustovirus ST1. Clandestinovirus possesses a linear dsDNA genome of 581,987 base pairs containing 617 genes. Phylogenetically, clandestinovirus is most closely related to Acanthamoeba castellanii medusavirus and was considered a member of the proposed Medusaviridae family. However, clandestinovirus genome is 65% larger than that of medusavirus, emphasizing the considerable genome size variation within this virus family. Functional annotation of the clandestinovirus genes suggests that the virus encodes four core histones. Furthermore, clandestinovirus appears to orchestrate the cell cycle and mitochondrial activities of the infected host by virtue of encoding a panel of protein kinases and phosphatases, and a suite of functionally diverse mitochondrial protein homologs, respectively. Collectively, these observations illuminate a strategy employed by clandestinovirus to optimize the intracellular environment for efficient virus propagation.
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Affiliation(s)
- Clara Rolland
- Aix-Marseille Université (AMU), UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Julien Andreani
- Aix-Marseille Université (AMU), UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, France
| | - Dehia Sahmi-Bounsiar
- Aix-Marseille Université (AMU), UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Bernard La Scola
- Aix-Marseille Université (AMU), UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Anthony Levasseur
- Aix-Marseille Université (AMU), UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Institut Universitaire de France, Paris, France
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