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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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Hannat S, La Scola B, Andreani J, Aherfi S. Asfarviruses and Closely Related Giant Viruses. Viruses 2023; 15:v15041015. [PMID: 37112995 PMCID: PMC10146109 DOI: 10.3390/v15041015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/14/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Acanthamoeba polyphaga mimivirus, so called because of its "mimicking microbe", was discovered in 2003 and was the founding member of the first family of giant viruses isolated from amoeba. These giant viruses, present in various environments, have opened up a previously unexplored field of virology. Since 2003, many other giant viruses have been isolated, founding new families and taxonomical groups. These include a new giant virus which was isolated in 2015, the result of the first co-culture on Vermamoeba vermiformis. This new giant virus was named "Faustovirus". Its closest known relative at that time was African Swine Fever Virus. Pacmanvirus and Kaumoebavirus were subsequently discovered, exhibiting phylogenetic clustering with the two previous viruses and forming a new group with a putative common ancestor. In this study, we aimed to summarise the main features of the members of this group of giant viruses, including Abalone Asfarvirus, African Swine Fever Virus, Faustovirus, Pacmanvirus, and Kaumoebavirus.
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Affiliation(s)
- Sihem Hannat
- Institut Hospitalo-Universitaire Méditerranée Infection, 13005 Marseille, France
- MEPHI, Institut de Recherche pour le Développement (IRD), Aix-Marseille Université, 13005 Marseille, France
| | - Bernard La Scola
- Institut Hospitalo-Universitaire Méditerranée Infection, 13005 Marseille, France
- MEPHI, Institut de Recherche pour le Développement (IRD), Aix-Marseille Université, 13005 Marseille, France
- Assistance Publique des Hôpitaux de Marseille (AP-HM), 13005 Marseille, France
| | - Julien Andreani
- CHU Grenoble Alpes, 27 Boulevard de la Chantourne, 38700 La Tronche, France
| | - Sarah Aherfi
- Institut Hospitalo-Universitaire Méditerranée Infection, 13005 Marseille, France
- MEPHI, Institut de Recherche pour le Développement (IRD), Aix-Marseille Université, 13005 Marseille, France
- Assistance Publique des Hôpitaux de Marseille (AP-HM), 13005 Marseille, France
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Genomics discovery of giant fungal viruses from subsurface oceanic crustal fluids. ISME COMMUNICATIONS 2023; 3:10. [PMID: 36732595 PMCID: PMC9894930 DOI: 10.1038/s43705-022-00210-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 12/12/2022] [Accepted: 12/22/2022] [Indexed: 02/04/2023]
Abstract
The oceanic igneous crust is a vast reservoir for microbial life, dominated by diverse and active bacteria, archaea, and fungi. Archaeal and bacterial viruses were previously detected in oceanic crustal fluids at the Juan de Fuca Ridge (JdFR). Here we report the discovery of two eukaryotic Nucleocytoviricota genomes from the same crustal fluids by sorting and sequencing single virions. Both genomes have a tRNATyr gene with an intron (20 bps) at the canonical position between nucleotide 37 and 38, a common feature in eukaryotic and archaeal tRNA genes with short introns (<100 bps), and fungal genes acquired through horizontal gene transfer (HGT) events. The dominance of Ascomycota fungi as the main eukaryotes in crustal fluids and the evidence for HGT point to these fungi as the putative hosts, making these the first putative fungi-Nucleocytoviricota specific association. Our study suggests active host-viral dynamics for the only eukaryotic group found in the subsurface oceanic crust and raises important questions about the impact of viral infection on the productivity and biogeochemical cycling in this ecosystem.
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Schulz F, Abergel C, Woyke T. Giant virus biology and diversity in the era of genome-resolved metagenomics. Nat Rev Microbiol 2022; 20:721-736. [PMID: 35902763 DOI: 10.1038/s41579-022-00754-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/09/2022]
Abstract
The discovery of giant viruses, with capsids as large as some bacteria, megabase-range genomes and a variety of traits typically found only in cellular organisms, was one of the most remarkable breakthroughs in biology. Until recently, most of our knowledge of giant viruses came from ~100 species-level isolates for which genome sequences were available. However, these isolates were primarily derived from laboratory-based co-cultivation with few cultured protists and algae and, thus, did not reflect the true diversity of giant viruses. Although virus co-cultures enabled valuable insights into giant virus biology, many questions regarding their origin, evolution and ecological importance remain unanswered. With advances in sequencing technologies and bioinformatics, our understanding of giant viruses has drastically expanded. In this Review, we summarize our understanding of giant virus diversity and biology based on viral isolates as laboratory cultivation has enabled extensive insights into viral morphology and infection strategies. We then explore how cultivation-independent approaches have heightened our understanding of the coding potential and diversity of the Nucleocytoviricota. We discuss how metagenomics has revolutionized our perspective of giant viruses by revealing their distribution across our planet's biomes, where they impact the biology and ecology of a wide range of eukaryotic hosts and ultimately affect global nutrient cycles.
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Affiliation(s)
- Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Chantal Abergel
- Aix Marseille University, CNRS, IGS UMR7256, IMM FR3479, IM2B, IO, Marseille, France
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,University of California Merced, Merced, CA, USA.
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Kothari A, Roux S, Zhang H, Prieto A, Soneja D, Chandonia JM, Spencer S, Wu X, Altenburg S, Fields MW, Deutschbauer AM, Arkin AP, Alm EJ, Chakraborty R, Mukhopadhyay A. Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance. mSystems 2021; 6:e0053721. [PMID: 34184913 PMCID: PMC8269241 DOI: 10.1128/msystems.00537-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 05/26/2021] [Indexed: 01/21/2023] Open
Abstract
Viruses are ubiquitous microbiome components, shaping ecosystems via strain-specific predation, horizontal gene transfer and redistribution of nutrients through host lysis. Viral impacts are important in groundwater ecosystems, where microbes drive many nutrient fluxes and metabolic processes; however, little is known about the diversity of viruses in these environments. We analyzed four groundwater plasmidomes (the entire plasmid content of an environment) and identified 200 viral sequences, which clustered into 41 genus-level viral clusters (approximately equivalent to viral genera) including 9 known and 32 putative new genera. We used publicly available bacterial whole-genome sequences (WGS) and WGS from 261 bacterial isolates from this groundwater environment to identify potential viral hosts. We linked 76 of the 200 viral sequences to a range of bacterial phyla, the majority associated with Proteobacteria, followed by Firmicutes, Bacteroidetes, and Actinobacteria. The publicly available WGS enabled mapping bacterial hosts to several viral sequences. The WGS of groundwater isolates increased the depth of host prediction by allowing host identification at the strain level. The latter included 4 viruses that were almost entirely (>99% query coverage, >99% identity) identified as integrated in the genomes of Pseudomonas, Acidovorax, and Castellaniella strains, resulting in high-confidence host assignments. Lastly, 21 of these viruses carried putative auxiliary metabolite genes for metal and antibiotic resistance, which might drive their infection cycles and/or provide selective advantage to infected hosts. Exploring the groundwater virome provides a necessary foundation for integration of viruses into ecosystem models where they are key players in microbial adaption to environmental stress. IMPORTANCE To our knowledge, this is the first study to identify the bacteriophage distribution in a groundwater ecosystem shedding light on their prevalence and distribution across metal-contaminated and background sites. Our study is uniquely based on selective sequencing of solely the extrachromosomal elements of a microbiome followed by analysis for viral signatures, thus establishing a more focused approach for phage identifications. Using this method, we detected several novel phage genera along with those previously established. Our approach of using the whole-genome sequences of hundreds of bacterial isolates from the same site enabled us to make host assignments with high confidence, several at strain levels. Certain phage genes suggest that they provide an environment-specific selective advantage to their bacterial hosts. Our study lays the foundation for future research on directed phage isolations using specific bacterial host strains to further characterize groundwater phages, their life cycles, and their effects on groundwater microbiome and biogeochemistry.
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Affiliation(s)
- Ankita Kothari
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hanqiao Zhang
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Anatori Prieto
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Drishti Soneja
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sarah Spencer
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Xiaoqin Wu
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sara Altenburg
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - Matthew W. Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Microbiology & Immunology, Montana State University, Bozeman, Montana, USA
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Energy Biosciences Institute, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Eric J. Alm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Broad Institute of MIT Cambridge, Cambridge, Massachusetts, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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6
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de Souza GAP, Queiroz VF, Coelho LFL, Abrahão JS. Alohomora! What the entry mechanisms tell us about the evolution and diversification of giant viruses and their hosts. Curr Opin Virol 2021; 47:79-85. [PMID: 33647556 DOI: 10.1016/j.coviro.2021.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/18/2022]
Abstract
The virosphere is fascinatingly vast and diverse, but as mandatory intracellular parasites, viral particles must reach the intracellular space to guarantee their species' permanence on the planet. While most known viruses that infect animals explore the endocytic pathway to enter the host cell, a diverse group of ancient viruses that make up the phylum Nucleocytoviricota appear to have evolved to explore new access' routes to the cell's cytoplasm. Giant viruses of amoeba take advantage of the phagocytosis process that these organisms exploit a lot, while phycodnavirus must actively break through a algal cellulose cell wall. The mechanisms of entry into the cell and the viruses themselves are diverse, varying in the steps of adhesion, entry, and uncoating. These are clues left by evolution about how these organisms shaped and were shaped by convoluting with eukaryotes.
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Affiliation(s)
- Gabriel Augusto Pires de Souza
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brasil
| | - Victória Fulgêncio Queiroz
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brasil
| | - Luiz Felipe Leomil Coelho
- Laboratório de Vacinas, Departamento de Microbiologia e Imunologia, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva, 700, Alfenas, 37130-001, Brasil
| | - Jônatas Santos Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brasil.
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7
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Schulz F, Andreani J, Francis R, Boudjemaa H, Bou Khalil JY, Lee J, La Scola B, Woyke T. Advantages and Limits of Metagenomic Assembly and Binning of a Giant Virus. mSystems 2020; 5:e00048-20. [PMID: 32576649 PMCID: PMC7311315 DOI: 10.1128/msystems.00048-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/26/2020] [Indexed: 12/31/2022] Open
Abstract
Giant viruses have large genomes, often within the size range of cellular organisms. This distinguishes them from most other viruses and demands additional effort for the successful recovery of their genomes from environmental sequence data. Here, we tested the performance of genome-resolved metagenomics on a recently isolated giant virus, Fadolivirus, by spiking it into an environmental sample from which two other giant viruses were isolated. At high spike-in levels, metagenome assembly and binning led to the successful genomic recovery of Fadolivirus from the sample. A complementary survey of the major capsid protein indicated the presence of other giant viruses in the sample matrix but did not detect the two isolated from this sample. Our results indicate that genome-resolved metagenomics is a valid approach for the recovery of near-complete giant virus genomes given that sufficient clonal particles are present. However, our data also underline that a vast majority of giant viruses remain currently undetected, even in an era of terabase-scale metagenomics.IMPORTANCE The discovery of large and giant nucleocytoplasmic large DNA viruses (NCLDV) with genomes in the megabase range and equipped with a wide variety of features typically associated with cellular organisms was one of the most unexpected, intriguing, and spectacular breakthroughs in virology. Recent studies suggest that these viruses are highly abundant in the oceans, freshwater, and soil, impact the biology and ecology of their eukaryotic hosts, and ultimately affect global nutrient cycles. Genome-resolved metagenomics is becoming an increasingly popular tool to assess the diversity and coding potential of giant viruses, but this approach is currently lacking validation.
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Affiliation(s)
| | - Julien Andreani
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Rania Francis
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Hadjer Boudjemaa
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
- Department of Biology, Hassiba Ben Bouali University Chlef, Chlef, Algeria
| | | | - Janey Lee
- DOE Joint Genome Institute, Berkeley, California, USA
| | - Bernard La Scola
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, California, USA
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Schulz F, Roux S, Paez-Espino D, Jungbluth S, Walsh DA, Denef VJ, McMahon KD, Konstantinidis KT, Eloe-Fadrosh EA, Kyrpides NC, Woyke T. Giant virus diversity and host interactions through global metagenomics. Nature 2020; 578:432-436. [PMID: 31968354 PMCID: PMC7162819 DOI: 10.1038/s41586-020-1957-x] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 01/09/2020] [Indexed: 12/11/2022]
Abstract
Our current knowledge about nucleocytoplasmic large DNA viruses (NCLDVs) is largely derived from viral isolates that are co-cultivated with protists and algae. Here we reconstructed 2,074 NCLDV genomes from sampling sites across the globe by building on the rapidly increasing amount of publicly available metagenome data. This led to an 11-fold increase in phylogenetic diversity and a parallel 10-fold expansion in functional diversity. Analysis of 58,023 major capsid proteins from large and giant viruses using metagenomic data revealed the global distribution patterns and cosmopolitan nature of these viruses. The discovered viral genomes encoded a wide range of proteins with putative roles in photosynthesis and diverse substrate transport processes, indicating that host reprogramming is probably a common strategy in the NCLDVs. Furthermore, inferences of horizontal gene transfer connected viral lineages to diverse eukaryotic hosts. We anticipate that the global diversity of NCLDVs that we describe here will establish giant viruses-which are associated with most major eukaryotic lineages-as important players in ecosystems across Earth's biomes.
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Affiliation(s)
- Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Paez-Espino
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sean Jungbluth
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David A Walsh
- Groupe de recherche interuniversitaire en limnologie, Department of Biology, Concordia University, Montréal, Québec, Canada
| | - Vincent J Denef
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Emiley A Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Barnby E, Reynolds M, O'Neal P. Genomic Science-From 2001 to Present Day: What School Nurses Need to Know. NASN Sch Nurse 2019; 34:235-239. [PMID: 30382772 DOI: 10.1177/1942602x18810790] [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] [Indexed: 06/08/2023]
Abstract
Genetic science has made remarkable advances in the 21st century. As genetic and genomic sciences continue to expand, school nurses will become thoroughly immersed in data, information, and technology. As new diseases, treatments, and therapies are discovered, school nurses will need to implement and assess best practices for the complex and medically fragile student population. This article will discuss the top 10 recent discoveries in genomic science and how school nurses can use this information in clinical practice.
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Affiliation(s)
- Elizabeth Barnby
- Clinical Associate Professor, University of Alabama in Huntsville, Huntsville, AL
| | - Mark Reynolds
- Clinical Assistant Professor; RN-BSN/MSN, Program Coordinator, University of Alabama in Huntsville, Huntsville, AL
| | - Pamela O'Neal
- Associate Professor, University of Alabama in Huntsville, Huntsville, AL
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10
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Abstract
Genes encoding cytochrome P450 (CYP; P450) enzymes occur widely in the Archaea, Bacteria, and Eukarya, where they play important roles in metabolism of endogenous regulatory molecules and exogenous chemicals. We now report that genes for multiple and unique P450s occur commonly in giant viruses in the Mimiviridae, Pandoraviridae, and other families in the proposed order Megavirales. P450 genes were also identified in a herpesvirus (Ranid herpesvirus 3) and a phage (Mycobacterium phage Adler). The Adler phage P450 was classified as CYP102L1, and the crystal structure of the open form was solved at 2.5 Å. Genes encoding known redox partners for P450s (cytochrome P450 reductase, ferredoxin and ferredoxin reductase, and flavodoxin and flavodoxin reductase) were not found in any viral genome so far described, implying that host redox partners may drive viral P450 activities. Giant virus P450 proteins share no more than 25% identity with the P450 gene products we identified in Acanthamoeba castellanii, an amoeba host for many giant viruses. Thus, the origin of the unique P450 genes in giant viruses remains unknown. If giant virus P450 genes were acquired from a host, we suggest it could have been from an as yet unknown and possibly ancient host. These studies expand the horizon in the evolution and diversity of the enormously important P450 superfamily. Determining the origin and function of P450s in giant viruses may help to discern the origin of the giant viruses themselves.
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Aoki K, Hagiwara R, Akashi M, Sasaki K, Murata K, Ogata H, Takemura M. Fifteen Marseilleviruses Newly Isolated From Three Water Samples in Japan Reveal Local Diversity of Marseilleviridae. Front Microbiol 2019; 10:1152. [PMID: 31178850 PMCID: PMC6543897 DOI: 10.3389/fmicb.2019.01152] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/06/2019] [Indexed: 11/13/2022] Open
Abstract
The family Marseilleviridae, defined as a group of icosahedral double-stranded DNA viruses with particle size of approximately 250 nm and genome size of 350-380 kbp, belongs to the nucleo-cytoplasmic family of large DNA viruses. The family Marseilleviridae is currently classified into lineages A-E. In this study, we isolated 12 or 15 new members of the family Marseilleviridae from three sampling locations in Japan. Molecular phylogenetic analysis of the MCP genes showed that the new viruses could be further classified into three groups, hokutoviruses, kashiwazakiviruses, and kyotoviruses. Hokutoviruses were closely related to lineage B, kyotoviruses were related to lineage A, and kashiwazakiviruses were also classified into lineage B but a new putative subgroup of lineage B, revealing the diversity of this lineage. Interestingly, more than two viruses with slightly different MCP genes were isolated from a single water sample from a single location, i.e., two hokutoviruses and one kashiwazakivirus were isolated from a small reservoir, five kashiwazakiviruses from the mouth of a river, and five kyotoviruses from fresh water of a river, suggesting that several milliliters of water samples contain several types of giant viruses. Amoeba cells infected with hokutoviruses or kashiwazakiviruses exhibited a "bunch" formation consisting of normal and infected cells similarly to a tupanvirus, whereas cells infected with kyotoviruses or tokyovirus did not. These results suggest the previously unrecognized local diversity of the family Marseilleviridae in aquatic environments.
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Affiliation(s)
- Keita Aoki
- Laboratory of Biology, Graduate School of Mathematics and Science Education, Tokyo University of Science, Tokyo, Japan
| | - Reika Hagiwara
- Laboratory of Biology, Department of Liberal Arts, Faculty of Science, Tokyo University of Science, Tokyo, Japan
| | - Motohiro Akashi
- Laboratory of Biology, Department of Liberal Arts, Faculty of Science, Tokyo University of Science, Tokyo, Japan
| | - Kenta Sasaki
- Laboratory of Biology, Department of Liberal Arts, Faculty of Science, Tokyo University of Science, Tokyo, Japan
| | | | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Japan
| | - Masaharu Takemura
- Laboratory of Biology, Graduate School of Mathematics and Science Education, Tokyo University of Science, Tokyo, Japan.,Laboratory of Biology, Department of Liberal Arts, Faculty of Science, Tokyo University of Science, Tokyo, Japan
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12
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Brandes N, Linial M. Giant Viruses-Big Surprises. Viruses 2019; 11:v11050404. [PMID: 31052218 PMCID: PMC6563228 DOI: 10.3390/v11050404] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/17/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
Viruses are the most prevalent infectious agents, populating almost every ecosystem on earth. Most viruses carry only a handful of genes supporting their replication and the production of capsids. It came as a great surprise in 2003 when the first giant virus was discovered and found to have a >1 Mbp genome encoding almost a thousand proteins. Following this first discovery, dozens of giant virus strains across several viral families have been reported. Here, we provide an updated quantitative and qualitative view on giant viruses and elaborate on their shared and variable features. We review the complexity of giant viral proteomes, which include functions traditionally associated only with cellular organisms. These unprecedented functions include components of the translation machinery, DNA maintenance, and metabolic enzymes. We discuss the possible underlying evolutionary processes and mechanisms that might have shaped the diversity of giant viruses and their genomes, highlighting their remarkable capacity to hijack genes and genomic sequences from their hosts and environments. This leads us to examine prominent theories regarding the origin of giant viruses. Finally, we present the emerging ecological view of giant viruses, found across widespread habitats and ecological systems, with respect to the environment and human health.
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Affiliation(s)
- Nadav Brandes
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michal Linial
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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13
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Rolland C, Andreani J, Louazani AC, Aherfi S, Francis R, Rodrigues R, Silva LS, Sahmi D, Mougari S, Chelkha N, Bekliz M, Silva L, Assis F, Dornas F, Khalil JYB, Pagnier I, Desnues C, Levasseur A, Colson P, Abrahão J, La Scola B. Discovery and Further Studies on Giant Viruses at the IHU Mediterranee Infection That Modified the Perception of the Virosphere. Viruses 2019; 11:E312. [PMID: 30935049 PMCID: PMC6520786 DOI: 10.3390/v11040312] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 12/17/2022] Open
Abstract
The history of giant viruses began in 2003 with the identification of Acanthamoeba polyphaga mimivirus. Since then, giant viruses of amoeba enlightened an unknown part of the viral world, and every discovery and characterization of a new giant virus modifies our perception of the virosphere. This notably includes their exceptional virion sizes from 200 nm to 2 µm and their genomic complexity with length, number of genes, and functions such as translational components never seen before. Even more surprising, Mimivirus possesses a unique mobilome composed of virophages, transpovirons, and a defense system against virophages named Mimivirus virophage resistance element (MIMIVIRE). From the discovery and isolation of new giant viruses to their possible roles in humans, this review shows the active contribution of the University Hospital Institute (IHU) Mediterranee Infection to the growing knowledge of the giant viruses' field.
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Affiliation(s)
- Clara Rolland
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Julien Andreani
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Amina Cherif Louazani
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Sarah Aherfi
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- IHU IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Rania Francis
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Rodrigo Rodrigues
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- Laboratório de Vírus, Instituto de Ciêncas Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil.
| | - Ludmila Santos Silva
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Dehia Sahmi
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Said Mougari
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Nisrine Chelkha
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Meriem Bekliz
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Lorena Silva
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- Laboratório de Vírus, Instituto de Ciêncas Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil.
| | - Felipe Assis
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Fábio Dornas
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | | | - Isabelle Pagnier
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- IHU IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Christelle Desnues
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Anthony Levasseur
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- IHU IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Philippe Colson
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- IHU IHU-Méditerranée Infection, 13005 Marseille, France.
| | - Jônatas Abrahão
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- Laboratório de Vírus, Instituto de Ciêncas Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil.
| | - Bernard La Scola
- MEPHI, APHM, IRD 198, Aix Marseille Univ, Department of Medicine, IHU-Méditerranée Infection, 13005 Marseille, France.
- IHU IHU-Méditerranée Infection, 13005 Marseille, France.
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14
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Chatterjee A, Sicheritz-Pontén T, Yadav R, Kondabagil K. Genomic and metagenomic signatures of giant viruses are ubiquitous in water samples from sewage, inland lake, waste water treatment plant, and municipal water supply in Mumbai, India. Sci Rep 2019; 9:3690. [PMID: 30842490 PMCID: PMC6403294 DOI: 10.1038/s41598-019-40171-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 02/04/2019] [Indexed: 11/09/2022] Open
Abstract
We report the detection of genomic signatures of giant viruses (GVs) in the metagenomes of three environment samples from Mumbai, India, namely, a pre-filter of a household water purifier, a sludge sample from wastewater treatment plant (WWTP), and a drying bed sample of the same WWTP. The de novo assembled contigs of each sample yielded 700 to 2000 maximum unique matches with the GV genomic database. In all three samples, the maximum number of reads aligned to Pandoraviridae, followed by Phycodnaviridae, Mimiviridae, Iridoviridae, and other Megaviruses. We also isolated GVs from every environmental sample (n = 20) we tested using co-culture of the sample with Acanthomoeba castellanii. From this, four randomly selected GVs were subjected to the genomic characterization that showed remarkable cladistic homology with the three GV families viz., Mimivirirdae (Mimivirus Bombay [MVB]), Megaviruses (Powai lake megavirus [PLMV] and Bandra megavius [BAV]), and Marseilleviridae (Kurlavirus [KV]). All 4 isolates exhibited remarkable genomic identity with respective GV families. Functionally, the genomes were indistinguishable from other previously reported GVs, encoding nearly all COGs across extant family members. Further, the uncanny genomic homogeneity exhibited by individual GV families across distant geographies indicate their yet to be ascertained ecological significance.
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Affiliation(s)
- Anirvan Chatterjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Thomas Sicheritz-Pontén
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Rajesh Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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15
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Koonin EV, Yutin N. Evolution of the Large Nucleocytoplasmic DNA Viruses of Eukaryotes and Convergent Origins of Viral Gigantism. Adv Virus Res 2019; 103:167-202. [PMID: 30635076 DOI: 10.1016/bs.aivir.2018.09.002] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Nucleocytoplasmic Large DNA Viruses (NCLDV) of eukaryotes (proposed order "Megavirales") comprise an expansive group of eukaryotic viruses that consists of the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae, Pithoviridae, and Mimiviridae, as well as Pandoraviruses, Molliviruses, and Faustoviruses that so far remain unaccounted by the official virus taxonomy. All these viruses have double-stranded DNA genomes that range in size from about 100 kilobases (kb) to more than 2.5 megabases. The viruses with genomes larger than 500kb are informally considered "giant," and the largest giant viruses surpass numerous bacteria and archaea in both particle and genome size. The discovery of giant viruses has been highly unexpected and has changed the perception of viral size and complexity, and even, arguably, the entire concept of a virus. Given that giant viruses encode multiple proteins that are universal among cellular life forms and are components of the translation system, the quintessential cellular molecular machinery, attempts have been made to incorporate these viruses in the evolutionary tree of cellular life. Moreover, evolutionary scenarios of the origin of giant viruses from a fourth, supposedly extinct domain of cellular life have been proposed. However, despite all the differences in the genome size and gene repertoire, the NCLDV can be confidently defined as monophyletic group, on the strength of the presence of about 40 genes that can be traced back to their last common ancestor. Using several most strongly conserved genes from this ancestral set, a well-resolved phylogenetic tree of the NCLDV was built and employed as the scaffold to reconstruct the history of gene gain and loss throughout the course of the evolution of this group of viruses. This reconstruction reveals extremely dynamic evolution that involved extensive gene gain and loss in many groups of viruses and indicates that giant viruses emerged independently in several clades of the NCLDV. Thus, these giants of the virus world evolved repeatedly from smaller and simpler viruses, rather than from a fourth domain of cellular life, and captured numerous genes, including those for translation system components, from eukaryotes, along with some bacterial genes. Even deeper evolutionary reconstructions reveal apparent links between the NCLDV and smaller viruses of eukaryotes, such as adenoviruses, and ultimately, derive all these viruses from tailless bacteriophages.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States.
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
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16
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Schulz F, Alteio L, Goudeau D, Ryan EM, Yu FB, Malmstrom RR, Blanchard J, Woyke T. Hidden diversity of soil giant viruses. Nat Commun 2018; 9:4881. [PMID: 30451857 PMCID: PMC6243002 DOI: 10.1038/s41467-018-07335-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/30/2018] [Indexed: 01/23/2023] Open
Abstract
Known giant virus diversity is currently skewed towards viruses isolated from aquatic environments and cultivated in the laboratory. Here, we employ cultivation-independent metagenomics and mini-metagenomics on soils from the Harvard Forest, leading to the discovery of 16 novel giant viruses, chiefly recovered by mini-metagenomics. The candidate viruses greatly expand phylogenetic diversity of known giant viruses and either represented novel lineages or are affiliated with klosneuviruses, Cafeteria roenbergensis virus or tupanviruses. One assembled genome with a size of 2.4 Mb represents the largest currently known viral genome in the Mimiviridae, and others encode up to 80% orphan genes. In addition, we find more than 240 major capsid proteins encoded on unbinned metagenome fragments, further indicating that giant viruses are underexplored in soil ecosystems. The fact that most of these novel viruses evaded detection in bulk metagenomes suggests that mini-metagenomics could be a valuable approach to unearth viral giants.
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Affiliation(s)
- Frederik Schulz
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.
| | - Lauren Alteio
- Department of Biology, University of Massachusetts, Amherst, MA, USA
| | - Danielle Goudeau
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Elizabeth M Ryan
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Feiqiao B Yu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rex R Malmstrom
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Jeffrey Blanchard
- Department of Biology, University of Massachusetts, Amherst, MA, USA.
| | - Tanja Woyke
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.
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17
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Andreani J, La Scola B. Metagenomic binning reconstruction coupled with automatic pipeline annotation and giant viruses: A potential source of mistake in annotations. Virus Res 2018; 255:36-38. [PMID: 29981362 DOI: 10.1016/j.virusres.2018.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/19/2018] [Accepted: 07/03/2018] [Indexed: 10/28/2022]
Abstract
Metagenomic binning reconstructions represent an emergent powerful tool to discover novel microbial genomes and explore the diversity in microbial communities. This method is sometimes coupled with automatic pipeline to perform automatic annotations. Nevertheless, we found a publish Alphaproteobacteria in public database that containing 20 contigs identified as a bacterium that were actually a novel giant viruses close to Aureococcus anophagefferens virus. This virus was completely misidentified by automatic pipeline and missed by control program and finally concern near to 20% of this 2,4 Mb.
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Affiliation(s)
- Julien Andreani
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France.
| | - Bernard La Scola
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France.
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