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Liébana R, Viver T, Ramos-Barbero MD, Bustos-Caparros E, Urdiain M, López C, Amoozegar MA, Antón J, Rossello-Mora R. Extremely halophilic brine community manipulation shows higher robustness of microbiomes inhabiting human-driven solar saltern than naturally driven lake. mSystems 2024:e0053824. [PMID: 38934645 DOI: 10.1128/msystems.00538-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Hypersaline ecosystems display taxonomically similar assemblages with low diversities and highly dense accompanying viromes. The ecological implications of viral infection on natural microbial populations remain poorly understood, especially at finer scales of diversity. Here, we sought to investigate the influence of changes in environmental physicochemical conditions and viral predation pressure by autochthonous and allochthonous viruses on host dynamics. For this purpose, we transplanted two microbiomes coming from distant hypersaline systems (solar salterns of Es Trenc in Spain and the thalassohaline lake of Aran-Bidgol lake in Iran), by exchanging the cellular fractions with the sterile-filtered accompanying brines with and without the free extracellular virus fraction. The midterm exposure (1 month) of the microbiomes to the new conditions showed that at the supraspecific taxonomic range, the assemblies from the solar saltern brine more strongly resisted the environmental changes and viral predation than that of the lake. The metagenome-assembled genomes (MAGs) analysis revealed an intraspecific transition at the ecotype level, mainly driven by changes in viral predation pressure, by both autochthonous and allochthonous viruses. IMPORTANCE Viruses greatly influence succession and diversification of their hosts, yet the effects of viral infection on the ecological dynamics of natural microbial populations remain poorly understood, especially at finer scales of diversity. By manipulating the viral predation pressure by autochthonous and allochthonous viruses, we uncovered potential phage-host interaction, and their important role in structuring the prokaryote community at an ecotype level.
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Affiliation(s)
- Raquel Liébana
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - María Dolores Ramos-Barbero
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Esteban Bustos-Caparros
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain
| | - Cristina López
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain
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2
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Zhang J, Tang A, Jin T, Sun D, Guo F, Lei H, Lin L, Shu W, Yu P, Li X, Li B. A panoramic view of the virosphere in three wastewater treatment plants by integrating viral-like particle-concentrated and traditional non-concentrated metagenomic approaches. IMETA 2024; 3:e188. [PMID: 38898980 PMCID: PMC11183165 DOI: 10.1002/imt2.188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 06/21/2024]
Abstract
Wastewater biotreatment systems harbor a rich diversity of microorganisms, and the effectiveness of biotreatment systems largely depends on the activity of these microorganisms. Specifically, viruses play a crucial role in altering microbial behavior and metabolic processes throughout their infection phases, an aspect that has recently attracted considerable interest. Two metagenomic approaches, viral-like particle-concentrated (VPC, representing free viral-like particles) and non-concentrated (NC, representing the cellular fraction), were employed to assess their efficacy in revealing virome characteristics, including taxonomy, diversity, host interactions, lifestyle, dynamics, and functional genes across processing units of three wastewater treatment plants (WWTPs). Our findings indicate that each approach offers unique insights into the viral community and functional composition. Their combined use proved effective in elucidating WWTP viromes. We identified nearly 50,000 viral contigs, with Cressdnaviricota and Uroviricota being the predominant phyla in the VPC and NC fractions, respectively. Notably, two pathogenic viral families, Asfarviridae and Adenoviridae, were commonly found in these WWTPs. We also observed significant differences in the viromes of WWTPs processing different types of wastewater. Additionally, various phage-derived auxiliary metabolic genes (AMGs) were active at the RNA level, contributing to the metabolism of the microbial community, particularly in carbon, sulfur, and phosphorus cycling. Moreover, we identified 29 virus-carried antibiotic resistance genes (ARGs) with potential for host transfer, highlighting the role of viruses in spreading ARGs in the environment. Overall, this study provides a detailed and integrated view of the virosphere in three WWTPs through the application of VPC and NC metagenomic approaches. Our findings enhance the understanding of viral communities, offering valuable insights for optimizing the operation and regulation of wastewater treatment systems.
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Affiliation(s)
- Jiayu Zhang
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
- Research Center for Eco‐Environmental EngineeringDongguan University of TechnologyDongguanChina
| | - Aixi Tang
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
| | - Tao Jin
- Guangdong Magigene Biotechnology Co., Ltd.ShenzhenChina
| | - Deshou Sun
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
- Shenzhen Tongchen Biotechnology Co., LimitedShenzhenChina
| | - Fangliang Guo
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
| | - Huaxin Lei
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
| | - Lin Lin
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
| | - Wensheng Shu
- Guangdong Magigene Biotechnology Co., Ltd.ShenzhenChina
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life SciencesSouth China Normal UniversityGuangzhouChina
| | - Pingfeng Yu
- College of Environmental and Resource SciencesZhejiang UniversityHangzhouChina
| | - Xiaoyan Li
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
| | - Bing Li
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
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3
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Dutcher CA, Andreas MP, Giessen TW. A two-component quasi-icosahedral protein nanocompartment with variable shell composition and irregular tiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591138. [PMID: 38712103 PMCID: PMC11071501 DOI: 10.1101/2024.04.25.591138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Protein shells or capsids are a widespread form of compartmentalization in nature. Viruses use protein capsids to protect and transport their genomes while many cellular organisms use protein shells for varied metabolic purposes. These protein-based compartments often exhibit icosahedral symmetry and consist of a small number of structural components with defined roles. Encapsulins are a prevalent protein-based compartmentalization strategy in prokaryotes. All encapsulins studied thus far consist of a single shell protein that adopts the viral HK97-fold. Here, we report the characterization of a Family 2B two-component encapsulin from Streptomyces lydicus. We show the differential assembly behavior of the two shell components and demonstrate their ability to co-assemble into mixed shells with variable shell composition. We determined the structures of both shell proteins using cryo-electron microscopy. Using 3D-classification and crosslinking studies, we highlight the irregular tiling of mixed shells. Our work expands the known assembly modes of HK97-fold proteins and lays the foundation for future functional and engineering studies on two-component encapsulins.
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Affiliation(s)
- Cassandra A. Dutcher
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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4
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Reva ON, La Cono V, Crisafi F, Smedile F, Mudaliyar M, Ghosal D, Giuliano L, Krupovic M, Yakimov MM. Interplay of intracellular and trans-cellular DNA methylation in natural archaeal consortia. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13258. [PMID: 38589217 PMCID: PMC11001535 DOI: 10.1111/1758-2229.13258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/15/2024] [Indexed: 04/10/2024]
Abstract
DNA methylation serves a variety of functions across all life domains. In this study, we investigated archaeal methylomics within a tripartite xylanolytic halophilic consortium. This consortium includes Haloferax lucertense SVX82, Halorhabdus sp. SVX81, and an ectosymbiotic Candidatus Nanohalococcus occultus SVXNc, a nano-sized archaeon from the DPANN superphylum. We utilized PacBio SMRT and Illumina cDNA sequencing to analyse samples from consortia of different compositions for methylomics and transcriptomics. Endogenous cTAG methylation, typical of Haloferax, was accompanied in this strain by methylation at four other motifs, including GDGcHC methylation, which is specific to the ectosymbiont. Our analysis of the distribution of methylated and unmethylated motifs suggests that autochthonous cTAG methylation may influence gene regulation. The frequency of GRAGAaG methylation increased in highly expressed genes, while CcTTG and GTCGaGG methylation could be linked to restriction-modification (RM) activity. Generally, the RM activity might have been reduced during the evolution of this archaeon to balance the protection of cells from intruders, the reduction of DNA damage due to self-restriction in stressful environments, and the benefits of DNA exchange under extreme conditions. Our methylomics, transcriptomics and complementary electron cryotomography (cryo-ET) data suggest that the nanohaloarchaeon exports its methyltransferase to methylate the Haloferax genome, unveiling a new aspect of the interaction between the symbiont and its host.
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Affiliation(s)
- Oleg N. Reva
- Department of Biochemistry, Genetics and Microbiology, Centre for Bioinformatics and Computational BiologyUniversity of PretoriaPretoriaSouth Africa
| | - Violetta La Cono
- Extreme Microbiology, Biotechnology and Astrobiology GroupInstitute of Polar Sciences, ISP‐CNRMessinaItaly
| | - Francesca Crisafi
- Extreme Microbiology, Biotechnology and Astrobiology GroupInstitute of Polar Sciences, ISP‐CNRMessinaItaly
| | - Francesco Smedile
- Extreme Microbiology, Biotechnology and Astrobiology GroupInstitute of Polar Sciences, ISP‐CNRMessinaItaly
| | - Manasi Mudaliyar
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneMelbourneVictoriaAustralia
- ARC Centre for Cryo‐electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVictoriaAustralia
| | - Debnath Ghosal
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneMelbourneVictoriaAustralia
- ARC Centre for Cryo‐electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVictoriaAustralia
| | | | - Mart Krupovic
- Istitut Pasteur, Archaeal Virology UnitUniversité Paris CitéParisFrance
| | - Michail M. Yakimov
- Extreme Microbiology, Biotechnology and Astrobiology GroupInstitute of Polar Sciences, ISP‐CNRMessinaItaly
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5
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Dicks LMT, Vermeulen W. Bacteriophage-Host Interactions and the Therapeutic Potential of Bacteriophages. Viruses 2024; 16:478. [PMID: 38543843 PMCID: PMC10975011 DOI: 10.3390/v16030478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 05/23/2024] Open
Abstract
Healthcare faces a major problem with the increased emergence of antimicrobial resistance due to over-prescribing antibiotics. Bacteriophages may provide a solution to the treatment of bacterial infections given their specificity. Enzymes such as endolysins, exolysins, endopeptidases, endosialidases, and depolymerases produced by phages interact with bacterial surfaces, cell wall components, and exopolysaccharides, and may even destroy biofilms. Enzymatic cleavage of the host cell envelope components exposes specific receptors required for phage adhesion. Gram-positive bacteria are susceptible to phage infiltration through their peptidoglycan, cell wall teichoic acid (WTA), lipoteichoic acids (LTAs), and flagella. In Gram-negative bacteria, lipopolysaccharides (LPSs), pili, and capsules serve as targets. Defense mechanisms used by bacteria differ and include physical barriers (e.g., capsules) or endogenous mechanisms such as clustered regularly interspaced palindromic repeat (CRISPR)-associated protein (Cas) systems. Phage proteins stimulate immune responses against specific pathogens and improve antibiotic susceptibility. This review discusses the attachment of phages to bacterial cells, the penetration of bacterial cells, the use of phages in the treatment of bacterial infections, and the limitations of phage therapy. The therapeutic potential of phage-derived proteins and the impact that genomically engineered phages may have in the treatment of infections are summarized.
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Affiliation(s)
- Leon M. T. Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa;
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6
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Sensevdi ER, Sourrouille ZA, Quax TE. Host range and cell recognition of archaeal viruses. Curr Opin Microbiol 2024; 77:102423. [PMID: 38232492 DOI: 10.1016/j.mib.2023.102423] [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: 10/06/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/19/2024]
Abstract
Archaea are members of a separate domain of life that have unique properties, such as the composition of their cell walls and the structure of their lipid bilayers. Consequently, archaeal viruses face different challenges to infect host cells in comparison with viruses of bacteria and eukaryotes. Despite their significant impact on shaping microbial communities, our understanding of infection processes of archaeal viruses remains limited. Several receptors used by archaeal viruses to infect cells have recently been identified. The interactions between viruses and receptors are one of the determinants of the host range of viruses. Here, we review the current literature on host ranges of archaeal viruses and factors that might impact the width of these host ranges.
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Affiliation(s)
- Emine Rabia Sensevdi
- Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, 9747 Groningen AG, the Netherlands
| | - Zaloa Aguirre Sourrouille
- Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, 9747 Groningen AG, the Netherlands
| | - Tessa Ef Quax
- Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, 9747 Groningen AG, the Netherlands.
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7
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Wang Y, Xu N, Chen B, Zhang Z, Lei C, Zhang Q, Gu Y, Wang T, Wang M, Penuelas J, Qian H. Metagenomic analysis of antibiotic-resistance genes and viruses released from glaciers into downstream habitats. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168310. [PMID: 37944612 DOI: 10.1016/j.scitotenv.2023.168310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023]
Abstract
Glaciers serve as effective reservoirs of antibiotic resistance genes (ARGs) and viruses for millions of years. Climate change and anthropogenic activity have accelerated the melting of glaciers, but the patterns of release of ARGs and viruses from melting glaciers into downstream habitats remain unknown. We analyzed 171 metagenomic samples from glaciers and their downstream habitats and found that the abundance and diversity of ARGs were higher in glaciers (polar and plateau glaciers) than downstream habitats (Arctic Ocean, Qinghai Lake, and Yangtze River Basin), with the diversity of viruses having the opposite pattern. Proteobacteria and Actinobacteria were the main potential hosts of ARGs and viruses, and the richness of ARGs carried by the hosts was positively correlated with viral abundance, suggesting that the transmission of viruses in the hosts could disseminate ARGs. Source tracking indicated that >18 % of the ARGs and >25 % of the viruses detected in downstream habitats originated from glaciers, demonstrating that glaciers could be one of the potential sources of ARGs and viruses in downstream habitats. Increased solar radiation and emission of carbon dioxide mainly influenced the release of the ARGs and viruses from glaciers into downstream habitats. This study provides a systematic insight demonstrating the release of ARGs and viruses from the melting glaciers, potentially increasing ecological pressure.
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Affiliation(s)
- Yan Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Chaotang Lei
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Yanpeng Gu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, PR China
| | - Meixia Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, PR China
| | - Josep Penuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Barcelona 08193, Catalonia, Spain; CREAF, Campus Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona 08193, Catalonia, Spain
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China.
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8
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Koonin EV, Kuhn JH, Dolja VV, Krupovic M. Megataxonomy and global ecology of the virosphere. THE ISME JOURNAL 2024; 18:wrad042. [PMID: 38365236 PMCID: PMC10848233 DOI: 10.1093/ismejo/wrad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 02/18/2024]
Abstract
Nearly all organisms are hosts to multiple viruses that collectively appear to be the most abundant biological entities in the biosphere. With recent advances in metagenomics and metatranscriptomics, the known diversity of viruses substantially expanded. Comparative analysis of these viruses using advanced computational methods culminated in the reconstruction of the evolution of major groups of viruses and enabled the construction of a virus megataxonomy, which has been formally adopted by the International Committee on Taxonomy of Viruses. This comprehensive taxonomy consists of six virus realms, which are aspired to be monophyletic and assembled based on the conservation of hallmark proteins involved in capsid structure formation or genome replication. The viruses in different major taxa substantially differ in host range and accordingly in ecological niches. In this review article, we outline the latest developments in virus megataxonomy and the recent discoveries that will likely lead to reassessment of some major taxa, in particular, split of three of the current six realms into two or more independent realms. We then discuss the correspondence between virus taxonomy and the distribution of viruses among hosts and ecological niches, as well as the abundance of viruses versus cells in different habitats. The distribution of viruses across environments appears to be primarily determined by the host ranges, i.e. the virome is shaped by the composition of the biome in a given habitat, which itself is affected by abiotic factors.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, United States
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, United States
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, 75015 Paris, France
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9
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Kuiper BP, Schöntag AMC, Oksanen HM, Daum B, Quax TEF. Archaeal virus entry and egress. MICROLIFE 2024; 5:uqad048. [PMID: 38234448 PMCID: PMC10791045 DOI: 10.1093/femsml/uqad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/08/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Archaeal viruses display a high degree of structural and genomic diversity. Few details are known about the mechanisms by which these viruses enter and exit their host cells. Research on archaeal viruses has lately made significant progress due to advances in genetic tools and imaging techniques, such as cryo-electron tomography (cryo-ET). In recent years, a steady output of newly identified archaeal viral receptors and egress mechanisms has offered the first insight into how archaeal viruses interact with the archaeal cell envelope. As more details about archaeal viral entry and egress are unravelled, patterns are starting to emerge. This helps to better understand the interactions between viruses and the archaeal cell envelope and how these compare to infection strategies of viruses in other domains of life. Here, we provide an overview of recent developments in the field of archaeal viral entry and egress, shedding light onto the most elusive part of the virosphere.
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Affiliation(s)
- Bastiaan P Kuiper
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Anna M C Schöntag
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Bertram Daum
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Tessa E F Quax
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
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10
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Duan C, Liu Y, Liu Y, Liu L, Cai M, Zhang R, Zeng Q, Koonin EV, Krupovic M, Li M. Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components. ISME COMMUNICATIONS 2024; 4:ycad011. [PMID: 38328448 PMCID: PMC10848311 DOI: 10.1093/ismeco/ycad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 02/09/2024]
Abstract
Bathyarchaeia represent a class of archaea common and abundant in sedimentary ecosystems. Here we report 56 metagenome-assembled genomes of Bathyarchaeia viruses identified in metagenomes from different environments. Gene sharing network and phylogenomic analyses led to the proposal of four virus families, including viruses of the realms Duplodnaviria and Adnaviria, and archaea-specific spindle-shaped viruses. Genomic analyses uncovered diverse CRISPR elements in these viruses. Viruses of the proposed family "Fuxiviridae" harbor an atypical Type IV-B CRISPR-Cas system and a Cas4 protein that might interfere with host immunity. Viruses of the family "Chiyouviridae" encode a Cas2-like endonuclease and two mini-CRISPR arrays, one with a repeat identical to that in the host CRISPR array, potentially allowing the virus to recruit the host CRISPR adaptation machinery to acquire spacers that could contribute to competition with other mobile genetic elements or to inhibit host defenses. These findings present an outline of the Bathyarchaeia virome and offer a glimpse into their counter-defense mechanisms.
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Affiliation(s)
- Changhai Duan
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen 518060, China
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Ying Liu
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris 75015, France
| | - Lirui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Mingwei Cai
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Rui Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris 75015, France
| | - Meng Li
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen 518060, China
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
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11
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Zhou Y, Wang Y, Prangishvili D, Krupovic M. Exploring the Archaeal Virosphere by Metagenomics. Methods Mol Biol 2024; 2732:1-22. [PMID: 38060114 DOI: 10.1007/978-1-0716-3515-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
During the past decade, environmental research has demonstrated that archaea are abundant and widespread in nature and play important ecological roles at a global scale. Currently, however, the majority of archaeal lineages cannot be cultivated under laboratory conditions and are known exclusively or nearly exclusively through metagenomics. A similar trend extends to the archaeal virosphere, where isolated representatives are available for a handful of model archaeal virus-host systems. Viral metagenomics provides an alternative way to circumvent the limitations of culture-based virus discovery and offers insight into the diversity, distribution, and environmental impact of uncultured archaeal viruses. Presently, metagenomics approaches have been successfully applied to explore the viromes associated with various lineages of extremophilic and mesophilic archaea, including Asgard archaea (Asgardarchaeota), ANME-1 archaea (Methanophagales), thaumarchaea (Nitrososphaeria), altiarchaea (Altiarchaeota), and marine group II archaea (Poseidoniales). Here, we provide an overview of methods widely used in archaeal virus metagenomics, covering metavirome preparation, genome annotation, phylogenetic and phylogenomic analyses, and archaeal host assignment. We hope that this summary will contribute to further exploration and characterization of the enigmatic archaeal virome lurking in diverse environments.
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Affiliation(s)
- Yifan Zhou
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China
| | - David Prangishvili
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
- Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France.
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12
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Choe J, Kim SH, Han JM, Kim JH, Kwak MS, Jeong DW, Park MK. Prevalence of Indigenous Antibiotic-Resistant Salmonella Isolates and Their Application to Explore a Lytic Phage vB_SalS_KFSSM with an Intra-Broad Specificity. J Microbiol 2023; 61:1063-1073. [PMID: 38165607 DOI: 10.1007/s12275-023-00098-6] [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: 11/10/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 01/04/2024]
Abstract
The consumption of fresh produce has led to increase in antibiotic-resistant (AR) Salmonella outbreaks. In this study, indigenous Salmonella was isolated from a total of two hundred-two samples including fresh produce and agricultural environmental samples in Korea. After biochemical confirmation using the Indole, Methyl Red, Voges-Proskauer, Citrate tests, presumable Salmonella isolates were identified by 16S rRNA sequencing. Identified Salmonella isolates were evaluated for antibiotic susceptibility against twenty-two antibiotics. The specificity and the efficiency of plating (EOP) of vB_SalS_KFSSM were evaluated against fifty-three bacterial strains. Twenty-five suspected Salmonella were isolated and confirmed by the positive result for methyl red and citrate, of which ten were identified as Salmonella spp. through 16S rRNA gene sequencing. Eight Salmonella isolates (4.0%, n = 8/202) were resistant to at least one antibiotic, among which five were multi-drug resistant. As a lytic phage against Salmonella spp. CMGS-1, vB_SalS_KFSSM was isolated from cow manure. The phage was observed as a tailed phage belonging to the class Caudoviricetes. It exhibited an intra-broad specificity against four indigenous AR Salmonella isolates, two indigenous Salmonella isolates, and five other Salmonella serotypes with great efficiencies (EOP ≥ 0.75). Thus, this study suggested the potential of vB_SalS_KFSSM to combat indigenous AR Salmonella.
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Affiliation(s)
- Jaein Choe
- School of Food Science and Biotechnology, and Food and Bio-Industry Research Institute, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Su-Hyeon Kim
- School of Food Science and Biotechnology, and Food and Bio-Industry Research Institute, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Ji Min Han
- School of Food Science and Biotechnology, and Food and Bio-Industry Research Institute, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jong-Hoon Kim
- KookminBio Corporation, Seoul, 02826, Republic of Korea
| | - Mi-Sun Kwak
- KookminBio Corporation, Seoul, 02826, Republic of Korea
| | - Do-Won Jeong
- Department of Food and Nutrition, Dongduk Women's University, Seoul, 02748, Republic of Korea
| | - Mi-Kyung Park
- School of Food Science and Biotechnology, and Food and Bio-Industry Research Institute, Kyungpook National University, Daegu, 41566, Republic of Korea.
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13
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Zhou Y, Wang Y, Krupovic M. ICTV Virus Taxonomy Profile: Aoguangviridae 2023. J Gen Virol 2023; 104:001922. [PMID: 38010130 PMCID: PMC10768690 DOI: 10.1099/jgv.0.001922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
The family Aoguangviridae includes dsDNA viruses that have been associated with marine archaea. Currently, members of this virus family are known through metagenomics. Virions are predicted to consist of an icosahedral capsid and a helical tail, characteristic of members in the class Caudoviricetes. Aoguangviruses have some of the largest genomes among archaeal viruses and possess most of the components of the DNA replication machinery as well as auxiliary functions. The family Aoguangviridae includes the species Aobingvirus yangshanense. Many unclassified relatives of this virus group, referred to as 'magroviruses', have been discovered by metagenomics in globally distributed marine samples. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Aoguangviridae, which is available at ictv.global/report/aoguangviridae.
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Affiliation(s)
- Yifan Zhou
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris 75015, France
- Sorbonne Université, Collège Doctoral, Paris 75005, France
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, PR China
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris 75015, France
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14
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Medvedeva S, Borrel G, Krupovic M, Gribaldo S. A compendium of viruses from methanogenic archaea reveals their diversity and adaptations to the gut environment. Nat Microbiol 2023; 8:2170-2182. [PMID: 37749252 DOI: 10.1038/s41564-023-01485-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/30/2023] [Indexed: 09/27/2023]
Abstract
Methanogenic archaea are major producers of methane, a potent greenhouse gas and biofuel, and are widespread in diverse environments, including the animal gut. The ecophysiology of methanogens is likely impacted by viruses, which remain, however, largely uncharacterized. Here we carried out a global investigation of viruses associated with all current diversity of methanogens by assembling an extensive CRISPR database consisting of 156,000 spacers. We report 282 high-quality (pro)viral and 205 virus-like/plasmid sequences assigned to hosts belonging to ten main orders of methanogenic archaea. Viruses of methanogens can be classified into 87 families, underscoring a still largely undiscovered genetic diversity. Viruses infecting gut-associated archaea provide evidence of convergence in adaptation with viruses infecting gut-associated bacteria. These viruses contain a large repertoire of lysin proteins that cleave archaeal pseudomurein and are enriched in glycan-binding domains (Ig-like/Flg_new) and diversity-generating retroelements. The characterization of this vast repertoire of viruses paves the way towards a better understanding of their role in regulating methanogen communities globally, as well as the development of much-needed genetic tools.
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Affiliation(s)
- Sofia Medvedeva
- Institut Pasteur, Université Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Guillaume Borrel
- Institut Pasteur, Université Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Unit Archaeal Virology, Paris, France.
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France.
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15
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López-García P, Gutiérrez-Preciado A, Krupovic M, Ciobanu M, Deschamps P, Jardillier L, López-Pérez M, Rodríguez-Valera F, Moreira D. Metagenome-derived virus-microbe ratios across ecosystems. THE ISME JOURNAL 2023; 17:1552-1563. [PMID: 37169871 PMCID: PMC10504350 DOI: 10.1038/s41396-023-01431-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/20/2023] [Accepted: 05/03/2023] [Indexed: 05/13/2023]
Abstract
It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of fluorescently labelled virus-like particles. However, these exclude intracellular viruses and potentially include false positives (DNA-containing vesicles, gene-transfer agents, unspecifically stained inert particles). Here, we develop a metagenome-based VMR estimate (mVRM) that accounts for DNA viruses across all stages of their replication cycles (virion, intracellular lytic and lysogenic) by using normalised RPKM (reads per kilobase of gene sequence per million of mapped metagenome reads) counts of the major capsid protein (MCP) genes and cellular universal single-copy genes (USCGs) as proxies for virus and cell counts, respectively. After benchmarking this strategy using mock metagenomes with increasing VMR, we inferred mVMR across different biomes. To properly estimate mVMR in aquatic ecosystems, we generated metagenomes from co-occurring cellular and viral fractions (>50 kDa-200 µm size-range) in freshwater, seawater and solar saltern ponds (10 metagenomes, 2 control metaviromes). Viruses outnumbered cells in freshwater by ~13 fold and in plankton from marine and saline waters by ~2-4 fold. However, across an additional set of 121 diverse non-aquatic metagenomes including microbial mats, microbialites, soils, freshwater and marine sediments and metazoan-associated microbiomes, viruses, on average, outnumbered cells by barely two-fold. Although viruses likely are the most diverse biological entities on Earth, their global numbers might be closer to those of cells than previously estimated.
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Affiliation(s)
- Purificación López-García
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France.
| | - Ana Gutiérrez-Preciado
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Maria Ciobanu
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Philippe Deschamps
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Ludwig Jardillier
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Mario López-Pérez
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | | | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
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16
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Kirchberger PC, Ochman H. Microviruses: A World Beyond phiX174. Annu Rev Virol 2023; 10:99-118. [PMID: 37774127 DOI: 10.1146/annurev-virology-100120-011239] [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] [Indexed: 10/01/2023]
Abstract
Two decades of metagenomic analyses have revealed that in many environments, small (∼5 kb), single-stranded DNA phages of the family Microviridae dominate the virome. Although the emblematic microvirus phiX174 is ubiquitous in the laboratory, most other microviruses, particularly those of the gokushovirus and amoyvirus lineages, have proven to be much more elusive. This puzzling lack of representative isolates has hindered insights into microviral biology. Furthermore, the idiosyncratic size and nature of their genomes have resulted in considerable misjudgments of their actual abundance in nature. Fortunately, recent successes in microvirus isolation and improved metagenomic methodologies can now provide us with more accurate appraisals of their abundance, their hosts, and their interactions. The emerging picture is that phiX174 and its relatives are rather rare and atypical microviruses, and that a tremendous diversity of other microviruses is ready for exploration.
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Affiliation(s)
- Paul C Kirchberger
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA;
| | - Howard Ochman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
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17
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Camargo AP, Roux S, Schulz F, Babinski M, Xu Y, Hu B, Chain PSG, Nayfach S, Kyrpides NC. Identification of mobile genetic elements with geNomad. Nat Biotechnol 2023:10.1038/s41587-023-01953-y. [PMID: 37735266 DOI: 10.1038/s41587-023-01953-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/17/2023] [Indexed: 09/23/2023]
Abstract
Identifying and characterizing mobile genetic elements in sequencing data is essential for understanding their diversity, ecology, biotechnological applications and impact on public health. Here we introduce geNomad, a classification and annotation framework that combines information from gene content and a deep neural network to identify sequences of plasmids and viruses. geNomad uses a dataset of more than 200,000 marker protein profiles to provide functional gene annotation and taxonomic assignment of viral genomes. Using a conditional random field model, geNomad also detects proviruses integrated into host genomes with high precision. In benchmarks, geNomad achieved high classification performance for diverse plasmids and viruses (Matthews correlation coefficient of 77.8% and 95.3%, respectively), substantially outperforming other tools. Leveraging geNomad's speed and scalability, we processed over 2.7 trillion base pairs of sequencing data, leading to the discovery of millions of viruses and plasmids that are available through the IMG/VR and IMG/PR databases. geNomad is available at https://portal.nersc.gov/genomad .
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Affiliation(s)
- Antonio Pedro Camargo
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michal Babinski
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Yan Xu
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Bin Hu
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Stephen Nayfach
- 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.
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18
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Mercier C, Thies D, Zhong L, Raftery MJ, Erdmann S. Characterization of an archaeal virus-host system reveals massive genomic rearrangements in a laboratory strain. Front Microbiol 2023; 14:1274068. [PMID: 37789858 PMCID: PMC10544981 DOI: 10.3389/fmicb.2023.1274068] [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: 08/07/2023] [Accepted: 09/04/2023] [Indexed: 10/05/2023] Open
Abstract
Halophilic archaea (haloarchaea) are known to exhibit multiple chromosomes, with one main chromosome and one or several smaller secondary chromosomes or megaplasmids. Halorubrum lacusprofundi, a model organism for studying cold adaptation, exhibits one secondary chromosome and one megaplasmid that include a large arsenal of virus defense mechanisms. We isolated a virus (Halorubrum tailed virus DL1, HRTV-DL1) infecting Hrr. lacusprofundi, and present an in-depth characterization of the virus and its interactions with Hrr. lacusprofundi. While studying virus-host interactions between Hrr. lacusprofundi and HRTV-DL1, we uncover that the strain in use (ACAM34_UNSW) lost the entire megaplasmid and about 38% of the secondary chromosome. The loss included the majority of virus defense mechanisms, making the strain sensitive to HRTV-DL1 infection, while the type strain (ACAM34_DSMZ) appears to prevent virus replication. Comparing infection of the type strain ACAM34_DSMZ with infection of the laboratory derived strain ACAM34_UNSW allowed us to identify host responses to virus infection that were only activated in ACAM34_UNSW upon the loss of virus defense mechanisms. We identify one of two S-layer proteins as primary receptor for HRTV-DL1 and conclude that the presence of two different S-layer proteins in one strain provides a strong advantage in the arms race with viruses. Additionally, we identify archaeal homologs to eukaryotic proteins potentially being involved in the defense against virus infection.
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Affiliation(s)
- Coraline Mercier
- Max Planck Institute for Marine Microbiology, Archaeal Virology, Bremen, Germany
| | - Daniela Thies
- Max Planck Institute for Marine Microbiology, Archaeal Virology, Bremen, Germany
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, NSW, Australia
| | - Mark J. Raftery
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, NSW, Australia
| | - Susanne Erdmann
- Max Planck Institute for Marine Microbiology, Archaeal Virology, Bremen, Germany
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
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19
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Duan C, Liu Y, Liu Y, Liu L, Cai M, Zhang R, Zeng Q, Koonin EV, Krupovic M, Li M. Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554615. [PMID: 37781628 PMCID: PMC10541130 DOI: 10.1101/2023.08.24.554615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Bathyarchaeia represent a class of archaea common and abundant in sedimentary ecosystems. The virome of Bathyarchaeia so far has not been characterized. Here we report 56 metagenome-assembled genomes of Bathyarchaeia viruses identified in metagenomes from different environments. Gene sharing network and phylogenomic analyses led to the proposal of four virus families, including viruses of the realms Duplodnaviria and Adnaviria, and archaea-specific spindle-shaped viruses. Genomic analyses uncovered diverse CRISPR elements in these viruses. Viruses of the proposed family 'Fuxiviridae' harbor an atypical type IV-B CRISPR-Cas system and a Cas4 protein that might interfere with host immunity. Viruses of the family 'Chiyouviridae' encode a Cas2-like endonuclease and two mini-CRISPR arrays, one with a repeat identical to that in the host CRISPR array, potentially allowing the virus to recruit the host CRISPR adaptation machinery to acquire spacers that could contribute to competition with other mobile genetic elements or to inhibition of host defenses. These findings present an outline of the Bathyarchaeia virome and offer a glimpse into their counter-defense mechanisms.
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Affiliation(s)
- Changhai Duan
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, 518060 Shenzhen, China
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
| | - Ying Liu
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 75015 Paris, France
| | - Lirui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
| | - Mingwei Cai
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
| | - Rui Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 75015 Paris, France
| | - Meng Li
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, 518060 Shenzhen, China
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
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20
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Vik D, Bolduc B, Roux S, Sun CL, Pratama AA, Krupovic M, Sullivan MB. MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets. ISME COMMUNICATIONS 2023; 3:87. [PMID: 37620369 PMCID: PMC10449787 DOI: 10.1038/s43705-023-00295-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/04/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
Our knowledge of viral sequence space has exploded with advancing sequencing technologies and large-scale sampling and analytical efforts. Though archaea are important and abundant prokaryotes in many systems, our knowledge of archaeal viruses outside of extreme environments is limited. This largely stems from the lack of a robust, high-throughput, and systematic way to distinguish between bacterial and archaeal viruses in datasets of curated viruses. Here we upgrade our prior text-based tool (MArVD) via training and testing a random forest machine learning algorithm against a newly curated dataset of archaeal viruses. After optimization, MArVD2 presented a significant improvement over its predecessor in terms of scalability, usability, and flexibility, and will allow user-defined custom training datasets as archaeal virus discovery progresses. Benchmarking showed that a model trained with viral sequences from the hypersaline, marine, and hot spring environments correctly classified 85% of the archaeal viruses with a false detection rate below 2% using a random forest prediction threshold of 80% in a separate benchmarking dataset from the same habitats.
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Affiliation(s)
- Dean Vik
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA.
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christine L Sun
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Akbar Adjie Pratama
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, Paris, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA.
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA.
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21
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Krupovic M, Dolja VV, Koonin EV. The virome of the last eukaryotic common ancestor and eukaryogenesis. Nat Microbiol 2023; 8:1008-1017. [PMID: 37127702 PMCID: PMC11130978 DOI: 10.1038/s41564-023-01378-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/29/2023] [Indexed: 05/03/2023]
Abstract
All extant eukaryotes descend from the last eukaryotic common ancestor (LECA), which is thought to have featured complex cellular organization. To gain insight into LECA biology and eukaryogenesis-the origin of the eukaryotic cell, which remains poorly understood-we reconstructed the LECA virus repertoire. We compiled an inventory of eukaryotic hosts of all major virus taxa and reconstructed the LECA virome by inferring the origins of these groups of viruses. The origin of the LECA virome can be traced back to a small set of bacterial-not archaeal-viruses. This provenance of the LECA virome is probably due to the bacterial origin of eukaryotic membranes, which is most compatible with two endosymbiosis events in a syntrophic model of eukaryogenesis. In the first endosymbiosis, a bacterial host engulfed an Asgard archaeon, preventing archaeal viruses from entry owing to a lack of archaeal virus receptors on the external membranes.
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Affiliation(s)
- Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France.
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA.
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22
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Gebhard LJ, Duggin IG, Erdmann S. Improving the genetic system for Halorubrum lacusprofundi to allow in-frame deletions. Front Microbiol 2023; 14:1095621. [PMID: 37065119 PMCID: PMC10102395 DOI: 10.3389/fmicb.2023.1095621] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Halorubrum lacusprofundi is a cold-adapted halophilic archaeon isolated from Deep Lake, Antarctica. Hrr. lacusprofundi is commonly used to study adaptation to cold environments and thereby a potential source for biotechnological products. Additionally, in contrast to other haloarchaeal model organisms, Hrr. lacusprofundi is also susceptible to a range of different viruses and virus-like elements, making it a great model to study virus-host interactions in a cold-adapted organism. A genetic system has previously been reported for Hrr. lacusprofundi; however, it does not allow in-frame deletions and multiple gene knockouts. Here, we report the successful generation of uracil auxotrophic (pyrE2) mutants of two strains of Hrr. lacusprofundi. Subsequently, we attempted to generate knockout mutants using the auxotrophic marker for selection. However, surprisingly, only the combination of the auxotrophic marker and antibiotic selection allowed the timely and clean in-frame deletion of a target gene. Finally, we show that vectors established for the model organism Haloferax volcanii are deployable for genetic manipulation of Hrr. lacusprofundi, allowing the use of the portfolio of genetic tools available for H. volcanii in Hrr. lacusprofundi.
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Affiliation(s)
- L. Johanna Gebhard
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Iain G. Duggin
- The Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Susanne Erdmann
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen, Germany
- *Correspondence: Susanne Erdmann,
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23
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Feng X, Li Y, Tian C, Yang W, Liu X, Zhang C, Zeng Z. Isolation of archaeal viruses with lipid membrane from Tengchong acidic hot springs. Front Microbiol 2023; 14:1134935. [PMID: 37065132 PMCID: PMC10101205 DOI: 10.3389/fmicb.2023.1134935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
Archaeal viruses are one of the most mysterious parts of the virosphere because of their diverse morphologies and unique genome contents. The crenarchaeal viruses are commonly found in high temperature and acidic hot springs, and the number of identified crenarchaeal viruses is being rapidly increased in recent two decades. Over fifty viruses infecting the members of the order Sulfolobales have been identified, most of which are from hot springs distributed in the United States, Russia, Iceland, Japan, and Italy. To further expand the reservoir of viruses infecting strains of Sulfolobaceae, we investigated virus diversity through cultivation-dependent approaches in hot springs in Tengchong, Yunnan, China. Eight different virus-like particles were detected in enrichment cultures, among which five new archaeal viruses were isolated and characterized. We showed that these viruses can infect acidophilic hyperthermophiles belonging to three different genera of the family Sulfolobaceae, namely, Saccharolobus, Sulfolobus, and Metallosphaera. We also compared the lipid compositions of the viral and cellular membranes and found that the lipid composition of some viral envelopes was very different from that of the host membrane. Collectively, our results showed that the Tengchong hot springs harbor highly diverse viruses, providing excellent models for archaeal virus-host studies.
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Affiliation(s)
- Xi Feng
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yanan Li
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Chang Tian
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Wei Yang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Xinyu Liu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Changyi Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- *Correspondence: Zhirui Zeng, ; Changyi Zhang,
| | - Zhirui Zeng
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- *Correspondence: Zhirui Zeng, ; Changyi Zhang,
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Abstract
Viruses are highly abundant and the main predator of microorganisms. Microorganisms of each domain of life are infected by dedicated viruses. Viruses infecting archaea are genomically and structurally highly diverse. Archaea are undersampled for viruses in comparison with bacteria and eukaryotes. Consequently, the infection mechanisms of archaeal viruses are largely unknown, and most available knowledge stems from viruses infecting a select group of archaea, such as crenarchaea. We employed Haloferax tailed virus 1 (HFTV1) and its host, Haloferax gibbonsii LR2-5, to study viral infection in euryarchaea. We found that HFTV1, which has a siphovirus morphology, is virulent, and interestingly, viral particles adsorb to their host several orders of magnitude faster than most studied haloarchaeal viruses. As the binding site for infection, HFTV1 uses the cell wall component surface (S)-layer protein. Electron microscopy of infected cells revealed that viral particles often made direct contact with their heads to the cell surface, whereby the virion tails were perpendicular to the surface. This seemingly unfavorable orientation for genome delivery might represent a first reversible contact between virus and cell and could enhance viral adsorption rates. In a next irreversible step, the virion tail is orientated toward the cell surface for genome delivery. With these findings, we uncover parallels between entry mechanisms of archaeal viruses and those of bacterial jumbo phages and bacterial gene transfer agents. IMPORTANCE Archaeal viruses are the most enigmatic members of the virosphere. These viruses infect ubiquitous archaea and display an unusually high structural and genetic diversity. Unraveling their mechanisms of infection will shed light on the question if entry and egress mechanisms are highly conserved between viruses infecting a single domain of life or if these mechanisms are dependent on the morphology of the virus and the growth conditions of the host. We studied the entry mechanism of the tailed archaeal virus HFTV1. This showed that despite "typical" siphovirus morphology, the infection mechanism is different from standard laboratory models of tailed phages. We observed that particles bound first with their head to the host cell envelope, and, as such, we discovered parallels between archaeal viruses and nonmodel bacteriophages. This work contributes to a better understanding of entry mechanisms of archaeal viruses and a more complete view of microbial viruses in general.
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Zhou Y, Zhou L, Yan S, Chen L, Krupovic M, Wang Y. Diverse viruses of marine archaea discovered using metagenomics. Environ Microbiol 2023; 25:367-382. [PMID: 36385454 DOI: 10.1111/1462-2920.16287] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2022] [Indexed: 11/19/2022]
Abstract
During the past decade, metagenomics became a method of choice for the discovery of novel viruses. However, host assignment for uncultured viruses remains challenging, especially for archaeal viruses, which are grossly undersampled compared to viruses of bacteria and eukaryotes. Here, we assessed the utility of CRISPR spacer targeting, tRNA gene matching and homology searches for viral signature proteins, such as major capsid proteins, for the assignment of archaeal hosts and validated these approaches on metaviromes from Yangshan Harbor (YSH). We report 35 new genomes of viruses which could be confidently assigned to hosts representing diverse lineages of marine archaea. We show that the archaeal YSH virome is highly diverse, with some viruses enriching the previously described virus groups, such as magroviruses of Marine Group II Archaea (Poseidoniales), and others representing novel groups of marine archaeal viruses. Metagenomic recruitment of Tara Oceans datasets on the YSH viral genomes demonstrated the presence of YSH Poseidoniales and Nitrososphaeria viruses in the global oceans, but also revealed the endemic YSH-specific viral lineages. Furthermore, our results highlight the relationship between the soil and marine thaumarchaeal viruses. We propose three new families within the class Caudoviricetes for the classification of the five complete viral genomes predicted to replicate in marine Poseidoniales and Nitrososphaeria, two ecologically important and widespread archaeal groups. This study illustrates the utility of viral metagenomics in exploring the archaeal virome and provides new insights into the diversity, distribution and evolution of marine archaeal viruses.
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Affiliation(s)
- Yifan Zhou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Liang Zhou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Shuling Yan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Entwicklungsgenetik und Zellbiologie der Tiere, Philipps-Universität Marburg, Marburg, Germany
| | - Lanming Chen
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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26
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Laso-Pérez R, Wu F, Crémière A, Speth DR, Magyar JS, Zhao K, Krupovic M, Orphan VJ. Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome. Nat Microbiol 2023; 8:231-245. [PMID: 36658397 PMCID: PMC9894754 DOI: 10.1038/s41564-022-01297-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/29/2022] [Indexed: 01/21/2023]
Abstract
'Candidatus Methanophagales' (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus-host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, 'Candidatus Methanospirareceae', closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems.
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Affiliation(s)
- Rafael Laso-Pérez
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany.
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
| | - Fabai Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China.
- Ocean College, Zhejiang University, Zhoushan, China.
- Donghai Laboratory, Zhoushan, China.
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
| | - Antoine Crémière
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Daan R Speth
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
| | - John S Magyar
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Kehan Zhao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France.
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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Simmonds P, Adriaenssens EM, Zerbini FM, Abrescia NGA, Aiewsakun P, Alfenas-Zerbini P, Bao Y, Barylski J, Drosten C, Duffy S, Duprex WP, Dutilh BE, Elena SF, García ML, Junglen S, Katzourakis A, Koonin EV, Krupovic M, Kuhn JH, Lambert AJ, Lefkowitz EJ, Łobocka M, Lood C, Mahony J, Meier-Kolthoff JP, Mushegian AR, Oksanen HM, Poranen MM, Reyes-Muñoz A, Robertson DL, Roux S, Rubino L, Sabanadzovic S, Siddell S, Skern T, Smith DB, Sullivan MB, Suzuki N, Turner D, Van Doorslaer K, Vandamme AM, Varsani A, Vasilakis N. Four principles to establish a universal virus taxonomy. PLoS Biol 2023; 21:e3001922. [PMID: 36780432 PMCID: PMC9925010 DOI: 10.1371/journal.pbio.3001922] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.
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Affiliation(s)
- Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - F. Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Nicola G. A. Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences—BRTA, Derio, Spain
- Basque Foundation for Science, IKERBASQUE, Bilbao, Spain
| | - Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jakub Barylski
- Department of Molecular Virology, Adam Mickiewicz University, Poznan, Poland
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt University, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - W. Paul Duprex
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Bas E. Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University, Jena, Germany
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Valencia, Spain
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Maria Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET, UNLP, La Plata, Argentina
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt University, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Aris Katzourakis
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
| | - Amy J. Lambert
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Elliot J. Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Cédric Lood
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics and Databases, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, Virginia, United States of America
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Minna M. Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Alejandro Reyes-Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, UOS Bari, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Stuart Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Tim Skern
- Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Donald B. Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Matthew B. Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, Ohio, United States of America
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Dann Turner
- School of Applied Sciences, College of Health, Science and Society, University of the West of England, Bristol, United Kingdom
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and University of Arizona Cancer Center, Tucson, Arizona, United States of America
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, United States of America
| | - Nikos Vasilakis
- Department of Pathology, Center of Vector-Borne and Zoonotic Diseases, Institute for Human Infection and Immunity and World Reference Center for Emerging Viruses and Arboviruses, The University of Texas Medical Branch, Galveston, Texas, United States of America
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Turner D, Shkoporov AN, Lood C, Millard AD, Dutilh BE, Alfenas-Zerbini P, van Zyl LJ, Aziz RK, Oksanen HM, Poranen MM, Kropinski AM, Barylski J, Brister JR, Chanisvili N, Edwards RA, Enault F, Gillis A, Knezevic P, Krupovic M, Kurtböke I, Kushkina A, Lavigne R, Lehman S, Lobocka M, Moraru C, Moreno Switt A, Morozova V, Nakavuma J, Reyes Muñoz A, Rūmnieks J, Sarkar BL, Sullivan MB, Uchiyama J, Wittmann J, Yigang T, Adriaenssens EM. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee. Arch Virol 2023; 168:74. [PMID: 36683075 PMCID: PMC9868039 DOI: 10.1007/s00705-022-05694-2] [Citation(s) in RCA: 107] [Impact Index Per Article: 107.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021-March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.
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Affiliation(s)
- Dann Turner
- School of Applied Sciences, College of Health, Science and Society, University of the West of England, Bristol, BS16 1QY UK
| | - Andrey N. Shkoporov
- Department of Medicine and APC Microbiome Ireland, School of Microbiology, University College Cork, Cork, Ireland
| | - Cédric Lood
- Department of Biosystems, Faculty of Bioscience Engineering, KU, Leuven, Belgium
| | - Andrew D. Millard
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, UK
| | - Bas E. Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, 07743 Jena, Germany
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH The Netherlands
| | | | - Leonardo J. van Zyl
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, 7535 Bellville, Cape Town, South Africa
| | - Ramy K. Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, 11562 Cairo, Egypt
- Egypt/ and Children’s Cancer Hospital, 57357, 11617 Cairo, Egypt
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Minna M. Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Andrew M. Kropinski
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1 Canada
| | - Jakub Barylski
- Department of Molecular Virology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - Nina Chanisvili
- The Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi, Georgia
| | - Rob A. Edwards
- Flinders Accelerator for Microbiome Exploration, Adelaide, Australia
| | - François Enault
- Université Clermont Auvergne, CNRS, LMGE, Clermont-Ferrand, France
| | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Université Catholique de Louvain, Croix du Sud 2, L7.05.12, 1348 Louvain-la-Neuve, Belgium
| | - Petar Knezevic
- PK Lab, Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, Novi Sad, Serbia
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, Paris, 75015 France
| | - Ipek Kurtböke
- School of Science, Technology and Engineering, University of the Sunshine Coast, 4558 Maroochydore, BC, QLD Australia
| | - Alla Kushkina
- Department of Bacteriophage molecular genetics, D.K.Zabolotny Institute of microbiology and virology, NAS of Ukraine, 154 Acad. Zabolotnoho str, 03143 Kyiv, Ukraine
- Department of Bacterial molecular genetics, Faculty of biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Rob Lavigne
- Department of Biosystems, Faculty of Bioscience Engineering, KU, Leuven, Belgium
| | - Susan Lehman
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Malgorzata Lobocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Andrea Moreno Switt
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Vera Morozova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Jesca Nakavuma
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, 111711 Bogotá, Colombia
| | - Jānis Rūmnieks
- Latvian Biomedical Research and Study Center, 1067 Riga, Latvia
| | - BL Sarkar
- ICMR-National Institute of Cholera and Enteric Diseases (NICED), Kolkata, India
| | - Matthew B. Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210 USA
| | - Jumpei Uchiyama
- Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama, 7008530 Japan
| | - Johannes Wittmann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7B, 38124 Braunschweig, Germany
| | - Tong Yigang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Evelien M. Adriaenssens
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ UK
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Xu B, Fan L, Wang W, Zhu Y, Zhang C. Diversity, distribution, and functional potentials of magroviruses from marine and brackish waters. Front Microbiol 2023; 14:1151034. [PMID: 37152742 PMCID: PMC10160649 DOI: 10.3389/fmicb.2023.1151034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/05/2023] [Indexed: 05/09/2023] Open
Abstract
Marine group II (MGII) archaea (Ca. Poseidoniales) are among the most abundant microbes in global oceanic surface waters and play an important role in driving marine biogeochemical cycles. Magroviruses - the viruses of MGII archaea have been recently found to occur ubiquitously in surface ocean. However, their diversity, distribution, and potential ecological functions in coastal zones especially brackish waters are unknown. Here we obtained 234 non-redundant magroviral genomes from brackish surface waters by using homology searches for viral signature proteins highlighting the uncovered vast diversity of this novel viral group. Phylogenetic analysis based on these brackish magroviruses along with previously reported marine ones identified six taxonomic groups with close evolutionary connection to both haloviruses and the viruses of Marine Group I archaea. Magroviruses were present abundantly both in brackish and open ocean samples with some showing habitat specification and others having broad spectrums of distribution between different habitats. Genome annotation suggests they may be involved in regulating multiple metabolic pathways of MGII archaea. Our results uncover the previously overlooked diversity and ecological potentials of a major archaeal virial group in global ocean and brackish waters and shed light on the cryptic evolutionary history of archaeal viruses.
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Affiliation(s)
- Bu Xu
- School of Environment, Harbin Institute of Technology, Harbin, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Lu Fan
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- *Correspondence: Lu Fan,
| | - Wenxiu Wang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yuanqing Zhu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai, China
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CryoEM structure and assembly mechanism of a bacterial virus genome gatekeeper. Nat Commun 2022; 13:7283. [PMID: 36435855 PMCID: PMC9701221 DOI: 10.1038/s41467-022-34999-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/15/2022] [Indexed: 11/28/2022] Open
Abstract
Numerous viruses package their dsDNA genome into preformed capsids through a portal gatekeeper that is subsequently closed. We report the structure of the DNA gatekeeper complex of bacteriophage SPP1 (gp612gp1512gp166) in the post-DNA packaging state at 2.7 Å resolution obtained by single particle cryo-electron microscopy. Comparison of the native SPP1 complex with assembly-naïve structures of individual components uncovered the complex program of conformational changes leading to its assembly. After DNA packaging, gp15 binds via its C-terminus to the gp6 oligomer positioning gp15 subunits for oligomerization. Gp15 refolds its inner loops creating an intersubunit β-barrel that establishes different types of contacts with six gp16 subunits. Gp16 binding and oligomerization is accompanied by folding of helices that close the portal channel to keep the viral genome inside the capsid. This mechanism of assembly has broad functional and evolutionary implications for viruses of the prokaryotic tailed viruses-herpesviruses lineage.
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Guglielmini J, Gaia M, Da Cunha V, Criscuolo A, Krupovic M, Forterre P. Viral origin of eukaryotic type IIA DNA topoisomerases. Virus Evol 2022; 8:veac097. [PMID: 36533149 PMCID: PMC9752973 DOI: 10.1093/ve/veac097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/07/2022] [Indexed: 08/24/2023] Open
Abstract
Type II DNA topoisomerases of the family A (Topo IIAs) are present in all Bacteria (DNA gyrase) and eukaryotes. In eukaryotes, they play a major role in transcription, DNA replication, chromosome segregation, and modulation of chromosome architecture. The origin of eukaryotic Topo IIA remains mysterious since they are very divergent from their bacterial homologs and have no orthologs in Archaea. Interestingly, eukaryotic Topo IIAs have close homologs in viruses of the phylum Nucleocytoviricota, an expansive assemblage of large and giant viruses formerly known as the nucleocytoplasmic large DNA viruses. Topo IIAs are also encoded by some bacterioviruses of the class Caudoviricetes (tailed bacteriophages). To elucidate the origin of the eukaryotic Topo IIA, we performed in-depth phylogenetic analyses on a dataset combining viral and cellular Topo IIA homologs. Topo IIAs encoded by Bacteria and eukaryotes form two monophyletic groups nested within Topo IIA encoded by Caudoviricetes and Nucleocytoviricota, respectively. Importantly, Nucleocytoviricota remained well separated from eukaryotes after removing both Bacteria and Caudoviricetes from the data set, indicating that the separation of Nucleocytoviricota and eukaryotes is probably not due to long-branch attraction artifact. The topologies of our trees suggest that the eukaryotic Topo IIA was probably acquired from an ancestral member of the Nucleocytoviricota of the class Megaviricetes, before the emergence of the last eukaryotic common ancestor (LECA). This result further highlights a key role of these viruses in eukaryogenesis and suggests that early proto-eukaryotes used a Topo IIB instead of a Topo IIA for solving their DNA topological problems.
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Affiliation(s)
| | - Morgan Gaia
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, 91000 Evry, France
| | - Violette Da Cunha
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Alexis Criscuolo
- Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Archaeal Virology Unit, 75015 Paris, France
| | - Patrick Forterre
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Archaeal Virology Unit, 75015 Paris, France
- Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
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32
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Ngo VQH, Enault F, Midoux C, Mariadassou M, Chapleur O, Mazéas L, Loux V, Bouchez T, Krupovic M, Bize A. Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics. Environ Microbiol 2022; 24:4853-4868. [PMID: 35848130 PMCID: PMC9796341 DOI: 10.1111/1462-2920.16120] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/01/2022] [Accepted: 06/29/2022] [Indexed: 01/01/2023]
Abstract
Diversity of viruses infecting non-extremophilic archaea has been grossly understudied. This is particularly the case for viruses infecting methanogenic archaea, key players in the global carbon biogeochemical cycle. Only a dozen of methanogenic archaeal viruses have been isolated so far. In the present study, we implemented an original coupling between stable isotope probing and complementary shotgun metagenomic analyses to identify viruses of methanogens involved in the bioconversion of formate, which was used as the sole carbon source in batch anaerobic digestion microcosms. Under our experimental conditions, the microcosms were dominated by methanogens belonging to the order Methanobacteriales (Methanobacterium and Methanobrevibacter genera). Metagenomic analyses yielded several previously uncharacterized viral genomes, including a complete genome of a head-tailed virus (class Caudoviricetes, proposed family Speroviridae, Methanobacterium host) and several near-complete genomes of spindle-shaped viruses. The two groups of viruses are predicted to infect methanogens of the Methanobacterium and Methanosarcina genera and represent two new virus families. The metagenomics results are in good agreement with the electron microscopy observations, which revealed the dominance of head-tailed virus-like particles and the presence of spindle-shaped particles. The present study significantly expands the knowledge on the viral diversity of viruses of methanogens.
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Affiliation(s)
- Vuong Quoc Hoang Ngo
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - François Enault
- Université Clermont Auvergne, CNRS, LMGEClermont‐FerrandFrance
| | - Cédric Midoux
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance,Université Paris‐Saclay, INRAE, MaIAGEJouy‐en‐JosasFrance,Université Paris‐Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics FacilityJouy‐en‐JosasFrance
| | - Mahendra Mariadassou
- Université Paris‐Saclay, INRAE, MaIAGEJouy‐en‐JosasFrance,Université Paris‐Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics FacilityJouy‐en‐JosasFrance
| | - Olivier Chapleur
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - Laurent Mazéas
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - Valentin Loux
- Université Paris‐Saclay, INRAE, MaIAGEJouy‐en‐JosasFrance,Université Paris‐Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics FacilityJouy‐en‐JosasFrance
| | - Théodore Bouchez
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - Mart Krupovic
- Institut Pasteur, Université de Paris, CNRS UMR6047, Archaeal Virology UnitParisFrance
| | - Ariane Bize
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
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A Novel Freshwater Cyanophage Mae-Yong1326-1 Infecting Bloom-Forming Cyanobacterium Microcystis aeruginosa. Viruses 2022; 14:v14092051. [PMID: 36146857 PMCID: PMC9503304 DOI: 10.3390/v14092051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/02/2022] [Accepted: 09/13/2022] [Indexed: 11/25/2022] Open
Abstract
Microcystis aeruginosa is a major harmful cyanobacterium causing water bloom worldwide. Cyanophage has been proposed as a promising tool for cyanobacterial bloom. In this study, M. aeruginosa FACHB-1326 was used as an indicator host to isolate cyanophage from Lake Taihu. The isolated Microcystis cyanophage Mae-Yong1326-1 has an elliptical head of about 47 nm in diameter and a slender flexible tail of about 340 nm in length. Mae-Yong1326-1 could lyse cyanobacterial strains across three orders (Chroococcales, Nostocales, and Oscillatoriales) in the host range experiments. Mae-Yong1326-1 was stable in stability tests, maintaining high titers at 0–40 °C and at a wide pH range of 3–12. Mae-Yong 1326-1 has a burst size of 329 PFU/cell, which is much larger than the reported Microcystis cyanophages so far. The complete genome of Mae-Yong1326-1 is a double-stranded DNA of 48, 822 bp, with a G + C content of 71.80% and long direct terminal repeats (DTR) of 366 bp, containing 57 predicted ORFs. No Mae-Yong1326-1 ORF was found to be associated with virulence factor or antibiotic resistance. PASC scanning illustrated that the highest nucleotide sequence similarity between Mae-Yong1326-1 and all known phages in databases was only 17.75%, less than 70% (the threshold to define a genus), which indicates that Mae-Yong1326-1 belongs to an unknown new genus. In the proteomic tree based on genome-wide sequence similarities, Mae-Yong1326-1 distantly clusters with three unclassified Microcystis cyanophages (MinS1, Mwe-Yong1112-1, and Mwes-Yong2). These four Microcystis cyanophages form a monophyletic clade, which separates at a node from the other clade formed by two independent families (Zierdtviridae and Orlajensenviridae) of Caudoviricetes class. We propose to establish a new family to harbor the Microcystis cyanophages Mae-Yong1326-1, MinS1, Mwe-Yong1112-1, and Mwes-Yong2. This study enriched the understanding of freshwater cyanophages.
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Chen S, Tu D, Hong T, Luo Y, Shen L, Ren P, Lu P, Chen X. Genomic features of a new head-tail halovirus VOLN27B infecting a Halorubrum strain. Gene 2022; 841:146766. [PMID: 35908623 DOI: 10.1016/j.gene.2022.146766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/26/2022] [Accepted: 07/24/2022] [Indexed: 11/04/2022]
Abstract
Relatively few viruses infecting haloarchaea (haloviruses) have been reported. In this study, the genome sequence of VOLN27B, a recently described archaeal tailed virus (arTV) with a myovirus morphotype was described, along with the sequence of its host, Halorubrum spp. LN27. Halovirus VOLN27B contains a linear, dsDNA genome of 76,891 bp which is predicted to encode 109 proteins and four tRNAs (tRNAThr, tRNAArg, tRNAGly and tRNAAsn). The DNA G+C content of VOLN27B genome is 56.1 mol%, nearly 10% lower than that of its host strain. A 315 bp LTR (long terminal repeat) was detected in the genome. The genome of its host strain LN27 was 3,301,211 bp (chromosome and 1 plasmid) with a DNA G+C content of 68.3 mol% and 3,142 annotated protein coding genes. At least two hypothetical proviruses were detected in the genome. It lacked a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) locus. Sequence similarity and phylogenetic tree reconstructions placed it within the genus Halorubrum as a potential new species. VOLN27B exhibits a distinct difference in the frequency of codon usage against its host strain Halorubrum sp. LN27. The organization of VOLN27B genome shows remarkable synteny and amino acid sequence similarity to the genomes and predicted proteins of HF1-like haloviruses (genus Haloferacalesvirus) and a provirus in the genome of Halorubrum depositum Y78. VOLN27B and its host Halorubrum sp. LN27 comprise a new virus-host system from a hypersaline ecosystem and can be used to further understand the novel biology at extreme salt concentration.
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Affiliation(s)
- Shaoxing Chen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China.
| | - Demei Tu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Tao Hong
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Yuqing Luo
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Liang Shen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ping Ren
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Peng Lu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Xiangdong Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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35
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Abstract
Viruses are obligate intracellular parasites. Despite their dependence on host cells, viruses are evolutionarily autonomous, with their own genomes and evolutionary trajectories locked in arms races with the hosts. Here, we discuss a simple functional logic to explain virus macroevolution that appears to define the course of virus evolution. A small core of virus hallmark genes that are responsible for genome replication apparently descended from primordial replicators, whereas most virus genes, starting with those encoding capsid proteins, were subsequently acquired from hosts. The oldest of these acquisitions antedate the last universal cellular ancestor (LUCA). Host gene capture followed two major routes: convergent recruitment of genes with functions that directly benefit virus reproduction and exaptation when host proteins are repurposed for unique virus functions. These forms of host protein recruitment by viruses result in different levels of similarity between virus and host homologs, with the exapted ones often changing beyond easy recognition.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA.
| | - Valerian V Dolja
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA; Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, F-75015 Paris, France.
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36
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Medvedeva S, Sun J, Yutin N, Koonin EV, Nunoura T, Rinke C, Krupovic M. Three families of Asgard archaeal viruses identified in metagenome-assembled genomes. Nat Microbiol 2022; 7:962-973. [PMID: 35760839 PMCID: PMC11165672 DOI: 10.1038/s41564-022-01144-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 05/04/2022] [Indexed: 02/07/2023]
Abstract
Asgardarchaeota harbour many eukaryotic signature proteins and are widely considered to represent the closest archaeal relatives of eukaryotes. Whether similarities between Asgard archaea and eukaryotes extend to their viromes remains unknown. Here we present 20 metagenome-assembled genomes of Asgardarchaeota from deep-sea sediments of the basin off the Shimokita Peninsula, Japan. By combining a CRISPR spacer search of metagenomic sequences with phylogenomic analysis, we identify three family-level groups of viruses associated with Asgard archaea. The first group, verdandiviruses, includes tailed viruses of the class Caudoviricetes (realm Duplodnaviria); the second, skuldviruses, consists of viruses with predicted icosahedral capsids of the realm Varidnaviria; and the third group, wyrdviruses, is related to spindle-shaped viruses previously identified in other archaea. More than 90% of the proteins encoded by these viruses of Asgard archaea show no sequence similarity to proteins encoded by other known viruses. Nevertheless, all three proposed families consist of viruses typical of prokaryotes, providing no indication of specific evolutionary relationships between viruses infecting Asgard archaea and eukaryotes. Verdandiviruses and skuldviruses are likely to be lytic, whereas wyrdviruses potentially establish chronic infection and are released without host cell lysis. All three groups of viruses are predicted to play important roles in controlling Asgard archaea populations in deep-sea ecosystems.
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Affiliation(s)
- Sofia Medvedeva
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, Russia
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Evolutionary Biology of the Microbial Cell Unit, Paris, France
| | - Jiarui Sun
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France.
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37
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The Viral Susceptibility of the Haloferax Species. Viruses 2022; 14:v14061344. [PMID: 35746816 PMCID: PMC9229481 DOI: 10.3390/v14061344] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Abstract
Viruses can infect members of all three domains of life. However, little is known about viruses infecting archaea and the mechanisms that determine their host interactions are poorly understood. Investigations of molecular mechanisms of viral infection rely on genetically accessible virus–host model systems. Euryarchaea belonging to the genus Haloferax are interesting models, as a reliable genetic system and versatile microscopy methods are available. However, only one virus infecting the Haloferax species is currently available. In this study, we tested ~100 haloarchaeal virus isolates for their infectivity on 14 Haloferax strains. From this, we identified 10 virus isolates in total capable of infecting Haloferax strains, which represented myovirus or siphovirus morphotypes. Surprisingly, the only susceptible strain of all 14 tested was Haloferax gibbonsii LR2-5, which serves as an auspicious host for all of these 10 viruses. By applying comparative genomics, we shed light on factors determining the host range of haloarchaeal viruses on Haloferax. We anticipate our study to be a starting point in the study of haloarchaeal virus–host interactions.
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38
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Chen LX, Jaffe AL, Borges AL, Penev PI, Nelson TC, Warren LA, Banfield JF. Phage-encoded ribosomal protein S21 expression is linked to late-stage phage replication. ISME COMMUNICATIONS 2022; 2:31. [PMID: 37938675 PMCID: PMC9723584 DOI: 10.1038/s43705-022-00111-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/31/2022] [Accepted: 02/03/2022] [Indexed: 06/16/2023]
Abstract
The ribosomal protein S21 (bS21) gene has been detected in diverse viruses with a large range of genome sizes, yet its in situ expression and potential significance have not been investigated. Here, we report five closely related clades of bacteriophages (phages) represented by 47 genomes (8 curated to completion and up to 331 kbp in length) that encode a bS21 gene. The bS21 gene is on the reverse strand within a conserved region that encodes the large terminase, major capsid protein, prohead protease, portal vertex proteins, and some hypothetical proteins. Based on CRISPR spacer targeting, the predominance of bacterial taxonomic affiliations of phage genes with those from Bacteroidetes, and the high sequence similarity of the phage bS21 genes and those from Bacteroidetes classes of Flavobacteriia, Cytophagia and Saprospiria, these phages are predicted to infect diverse Bacteroidetes species that inhabit a range of depths in freshwater lakes. Thus, bS21 phages have the potential to impact microbial community composition and carbon turnover in lake ecosystems. The transcriptionally active bS21-encoding phages were likely in the late stage of replication when collected, as core structural genes and bS21 were highly expressed. Thus, our analyses suggest that the phage bS21, which is involved in translation initiation, substitutes into the Bacteroidetes ribosomes and selects preferentially for phage transcripts during the late-stage replication when large-scale phage protein production is required for assembly of phage particles.
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Affiliation(s)
- Lin-Xing Chen
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Adair L Borges
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Petar I Penev
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | | | - Lesley A Warren
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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Carascal MB, dela Cruz-Papa DM, Remenyi R, Cruz MCB, Destura RV. Phage Revolution Against Multidrug-Resistant Clinical Pathogens in Southeast Asia. Front Microbiol 2022; 13:820572. [PMID: 35154059 PMCID: PMC8830912 DOI: 10.3389/fmicb.2022.820572] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/04/2022] [Indexed: 12/16/2022] Open
Abstract
Southeast Asia (SEA) can be considered a hotspot of antimicrobial resistance (AMR) worldwide. As recent surveillance efforts in the region reported the emergence of multidrug-resistant (MDR) pathogens, the pursuit of therapeutic alternatives against AMR becomes a matter of utmost importance. Phage therapy, or the use of bacterial viruses called bacteriophages to kill bacterial pathogens, is among the standout therapeutic prospects. This narrative review highlights the current understanding of phages and strategies for a phage revolution in SEA. We define phage revolution as the radical use of phage therapy in infectious disease treatment against MDR infections, considering the scientific and regulatory standpoints of the region. We present a three-phase strategy to encourage a phage revolution in the SEA clinical setting, which involves: (1) enhancing phage discovery and characterization efforts, (2) creating and implementing laboratory protocols and clinical guidelines for the evaluation of phage activity, and (3) adapting regulatory standards for therapeutic phage formulations. We hope that this review will open avenues for scientific and policy-based discussions on phage therapy in SEA and eventually lead the way to its fullest potential in countering the threat of MDR pathogens in the region and worldwide.
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Affiliation(s)
- Mark B. Carascal
- Clinical and Translational Research Institute, The Medical City, Pasig, Philippines
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - Donna May dela Cruz-Papa
- Clinical and Translational Research Institute, The Medical City, Pasig, Philippines
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
- Research Center for Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Roland Remenyi
- Clinical and Translational Research Institute, The Medical City, Pasig, Philippines
| | - Mely Cherrylynne B. Cruz
- Clinical and Translational Research Institute, The Medical City, Pasig, Philippines
- The Graduate School, University of Santo Tomas, Manila, Philippines
| | - Raul V. Destura
- Clinical and Translational Research Institute, The Medical City, Pasig, Philippines
- National Institutes of Health, University of the Philippines Manila, Manila, Philippines
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40
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Halovirus HF2 Intergenic Repeat Sequences Carry Promoters. Viruses 2021; 13:v13122388. [PMID: 34960657 PMCID: PMC8707807 DOI: 10.3390/v13122388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 11/16/2022] Open
Abstract
Halovirus HF2 was the first member of the Haloferacalesvirus genus to have its genome fully sequenced, which revealed two classes of intergenic repeat (IR) sequences: class I repeats of 58 bp in length, and class II repeats of 29 bp in length. Both classes of repeat contain AT-rich motifs that were conjectured to represent promoters. In the present study, nine IRs were cloned upstream of the bgaH reporter gene, and all displayed promoter activity, providing experimental evidence for the previous conjecture. Comparative genomics showed that IR sequences and their relative genomic positions were strongly conserved among other members of the same virus genus. The transcription of HF2 was also examined by the reverse-transcriptase-PCR (RT-PCR) method, which demonstrated very long transcripts were produced that together covered most of the genome, and from both strands. The presence of long counter transcripts suggests a regulatory role or possibly unrecognized coding potential.
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