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Mietzsch M, Kailasan S, Bennett A, Chipman P, Fane B, Huiskonen JT, Clarke IN, McKenna R. The Structure of Spiroplasma Virus 4: Exploring the Capsid Diversity of the Microviridae. Viruses 2024; 16:1103. [PMID: 39066266 PMCID: PMC11281519 DOI: 10.3390/v16071103] [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: 06/11/2024] [Revised: 07/02/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
Spiroplasma virus 4 (SpV4) is a bacteriophage of the Microviridae, which packages circular ssDNA within non-enveloped T = 1 icosahedral capsids. It infects spiroplasmas, which are known pathogens of honeybees. Here, the structure of the SpV4 virion is determined using cryo-electron microscopy to a resolution of 2.5 Å. A striking feature of the SpV4 capsid is the mushroom-like protrusions at the 3-fold axes, which is common among all members of the subfamily Gokushovirinae. While the function of the protrusion is currently unknown, this feature varies widely in this subfamily and is therefore possibly an adaptation for host recognition. Furthermore, on the interior of the SpV4 capsid, the location of DNA-binding protein VP8 was identified and shown to have low structural conservation to the capsids of other viruses in the family. The structural characterization of SpV4 will aid future studies analyzing the virus-host interaction, to understand disease mechanisms at a molecular level. Furthermore, the structural comparisons in this study, including a low-resolution structure of the chlamydia phage 2, provide an overview of the structural repertoire of the viruses in this family that infect various bacterial hosts, which in turn infect a wide range of animals and plants.
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Affiliation(s)
- Mario Mietzsch
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA (A.B.)
| | - Shweta Kailasan
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA (A.B.)
| | - Antonette Bennett
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA (A.B.)
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA (A.B.)
| | - Bentley Fane
- The BIO5 Institute, Keating Building, University of Arizona, Tucson, AZ 85721, USA
| | - Juha T. Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Ian N. Clarke
- Molecular Microbiology Group, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA (A.B.)
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2
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Xie K, Lin B, Sun X, Zhu P, Liu C, Liu G, Cao X, Pan J, Qiu S, Yuan X, Liang M, Jiang J, Yuan L. Identification and classification of the genomes of novel microviruses in poultry slaughterhouse. Front Microbiol 2024; 15:1393153. [PMID: 38756731 PMCID: PMC11096546 DOI: 10.3389/fmicb.2024.1393153] [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: 02/28/2024] [Accepted: 04/11/2024] [Indexed: 05/18/2024] Open
Abstract
Microviridae is a family of phages with circular ssDNA genomes and they are widely found in various environments and organisms. In this study, virome techniques were employed to explore potential members of Microviridae in a poultry slaughterhouse, leading to the identification of 98 novel and complete microvirus genomes. Using a similarity clustering network classification approach, these viruses were found to belong to at least 6 new subfamilies within Microviridae and 3 higher-level taxonomic units. Genome size, GC content and genome structure of these new taxa showed evident regularities, validating the rationality of our classification method. Our method can divide microviruses into about 45 additional detailed clusters, which may serve as a new standard for classifying Microviridae members. Furthermore, by addressing the scarcity of host information for microviruses, the current study significantly broadened their host range and discovered over 20 possible new hosts, including important pathogenic bacteria such as Helicobacter pylori and Vibrio cholerae, as well as different taxa demonstrated different host specificities. The findings of this study effectively expand the diversity of the Microviridae family, providing new insights for their classification and identification. Additionally, it offers a novel perspective for monitoring and controlling pathogenic microorganisms in poultry slaughterhouse environments.
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Affiliation(s)
- Keming Xie
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Benfu Lin
- Huadu District Animal Health Supervision Institution, Guangzhou, Guangdong, China
| | - Xinyu Sun
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Peng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Chang Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Guangfeng Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Xudong Cao
- Department of Chemical and Biological Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Jingqi Pan
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Suiping Qiu
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Xiaoqi Yuan
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Mengshi Liang
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Jingzhe Jiang
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Lihong Yuan
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
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3
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Yu M, Zhang M, Zeng R, Cheng R, Zhang R, Hou Y, Kuang F, Feng X, Dong X, Li Y, Shao Z, Jin M. Diversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments. Nat Commun 2024; 15:3228. [PMID: 38622147 PMCID: PMC11018836 DOI: 10.1038/s41467-024-47600-1] [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: 10/18/2023] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Seamounts are globally distributed across the oceans and form one of the major oceanic biomes. Here, we utilized combined analyses of bulk metagenome and virome to study viral communities in seamount sediments in the western Pacific Ocean. Phylogenetic analyses and the protein-sharing network demonstrate extensive diversity and previously unknown viral clades. Inference of virus-host linkages uncovers extensive interactions between viruses and dominant prokaryote lineages, and suggests that viruses play significant roles in carbon, sulfur, and nitrogen cycling by compensating or augmenting host metabolisms. Moreover, temperate viruses are predicted to be prevalent in seamount sediments, which tend to carry auxiliary metabolic genes for host survivability. Intriguingly, the geographical features of seamounts likely compromise the connectivity of viral communities and thus contribute to the high divergence of viral genetic spaces and populations across seamounts. Altogether, these findings provides knowledge essential for understanding the biogeography and ecological roles of viruses in globally widespread seamounts.
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Affiliation(s)
- Meishun Yu
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Menghui Zhang
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Runying Zeng
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Ruolin Cheng
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Yanping Hou
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Fangfang Kuang
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Xuejin Feng
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Xiyang Dong
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Yinfang Li
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China.
| | - Min Jin
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China.
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4
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Iqbal S, Begum F. Identification and characterization of integrated prophages and CRISPR-Cas system in Bacillus subtilis RS10 genome. Braz J Microbiol 2024; 55:537-542. [PMID: 38216797 PMCID: PMC10920515 DOI: 10.1007/s42770-024-01249-6] [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: 07/05/2023] [Accepted: 01/04/2024] [Indexed: 01/14/2024] Open
Abstract
Bacteriophages have been extensively investigated due to their prominent role in the virulence and resistance of pathogenic bacteria. However, little attention has been given to the non-pathogenic Bacillus phages, and their role in the ecological bacteria genome is overlooked. In the present study, we characterized two Bacillus phages with a linear DNA genome of 33.6 kb with 44.83% GC contents and 129.3 kb with 34.70% GC contents. A total of 46 and 175 putative coding DNA sequences (CDS) were identified in prophage 1 (P1) and prophage 2 (P2), respectively, with no tRNA genes. Comparative genome sequence analysis revealed that P1 shares eight CDS with phage Jimmer 2 (NC-041976), and phage Osiris (NC-028969), and six with phage phi CT9441A (NC-029022). On the other hand, P2 showed high similarity with Bacill_SPbeta_NC_001884 and Bacillus phage phi 105. Further, genome analysis indicates several horizontal gene transfer events in both phages during the evolution process. In addition, we detected two CRISPR-Cas systems for the first time in B. subtilis. The identified CRISPR system consists of 24 and 25 direct repeats and integrase coding genes, while the cas gene which encodes Cas protein involved in the cleavage of a target sequence is missing. These findings will expand the current knowledge of soil phages as well as help to develop a new perspective for investigating more ecological phages to understand their role in bacterial communities and diversity.
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Affiliation(s)
- Sajid Iqbal
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan.
- Oujiang Laboratory (Zhejiang Laboratory for Regenerative Medicine, Vision and Brain Health), Wenzhou, 325000, China.
| | - Farida Begum
- Department of Biochemistry, Abdul Wali Khan University Mardan (AWKUM), Mardan, Pakistan
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5
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Cortés-Martín A, Denise R, Guerin E, Stockdale SR, Draper LA, Ross RP, Shkoporov AN, Hill C. Isolation and characterization of a novel lytic Parabacteroides distasonis bacteriophage φPDS1 from the human gut. Gut Microbes 2024; 16:2298254. [PMID: 38178369 PMCID: PMC10773633 DOI: 10.1080/19490976.2023.2298254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024] Open
Abstract
The human gut microbiome plays a significant role in health and disease. The viral component (virome) is predominantly composed of bacteriophages (phages) and has received significantly less attention in comparison to the bacteriome. This knowledge gap is largely due to challenges associated with the isolation and characterization of novel gut phages, and bioinformatic hurdles such as the lack of a universal phage marker gene and the absence of sufficient numbers of homologs in viral databases. Here, we describe the isolation from human feces of a novel lytic phage with siphovirus morphology, φPDS1, infecting Parabacteroides distasonis APCS2/PD, and classified within a newly proposed Sagittacolavirus genus. In silico and biological characterization of this phage is presented in this study. Key to the isolation of φPDS1 was the antibiotic-driven selective enrichment of the bacterial host in a fecal fermenter. Despite producing plaques and lacking genes associated with lysogeny, φPDS1 demonstrates the ability to coexist in liquid culture for multiple days without affecting the abundance of its host. Multiple studies have shown that changes in Parabacteroides distasonis abundance can be linked to various disease states, rendering this novel phage-host pair and their interactions of particular interest.
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Affiliation(s)
- Adrián Cortés-Martín
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Rémi Denise
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Emma Guerin
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Stephen R. Stockdale
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Lorraine A. Draper
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Andrey N. Shkoporov
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
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6
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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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7
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Behera BK, Patra B, Chakraborty HJ, Rout AK, Dixit S, Rai A, Das BK, Mohapatra T. Bacteriophages diversity in India's major river Ganga: a repository to regulate pathogenic bacteria in the aquatic environment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:34101-34114. [PMID: 36508095 DOI: 10.1007/s11356-022-24637-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 12/03/2022] [Indexed: 06/18/2023]
Abstract
Bacteriophages are key viruses that can kill thousands of harmful microbes generally present at polluted sites. Such bacteriophages are abundantly present in the river Ganga, where millions of people in India and abroad drink its water and take baths every day for spiritual reasons. Besides bacteriophages, several pathogenic and zoonotic microbes are present in the river Ganga. It is interesting to study the diversity and abundance of bacteria and their respective phages present in polluted or non-polluted sites. Thus, the metagenomics study was carried out at the most polluted sites of river Ganga near Kanpur and non-polluted sites at Farakka, which harbors several harmful bacteria and their phages. The results revealed a significantly higher percentage of Microviridae phage family, ssDNA viruses, and Mimiviridae virus family near Kanpur than Farakka. In addition, compared to Kanpur, Farakka has a more significant percentage of Myoviridae, an unidentified phage family, and Retroviridae viral families. Despite heavy drainage of untreated and contaminated effluents from the leather industry, pesticide industry, paper mills, metropolitan cities, and other sources, the vast number of said phages kills several harmful pathogenic microbes in polluted sites to maintain the Ganga water's healing power or natural sterility. In a polluted aquatic environment, the varieties of bacteriophages were identified in the Ganga and their interaction with the microbial host. The taxonomic diversity of several bacteriophages found in pathogenic host systems was investigated to get exceptional knowledge of these small viruses in the aquatic environment.
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Affiliation(s)
- Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India.
| | - Biswanath Patra
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
| | - Hirak Jyoti Chakraborty
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
| | - Ajaya Kumar Rout
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
| | - Sangita Dixit
- Center for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to Be University), Bhubaneswar, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Basanta Kumar Das
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
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8
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Phage Therapy for Crops: Concepts, Experimental and Bioinformatics Approaches to Direct Its Application. Int J Mol Sci 2022; 24:ijms24010325. [PMID: 36613768 PMCID: PMC9820149 DOI: 10.3390/ijms24010325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/28/2022] Open
Abstract
Phage therapy consists of applying bacteriophages, whose natural function is to kill specific bacteria. Bacteriophages are safe, evolve together with their host, and are environmentally friendly. At present, the indiscriminate use of antibiotics and salt minerals (Zn2+ or Cu2+) has caused the emergence of resistant strains that infect crops, causing difficulties and loss of food production. Phage therapy is an alternative that has shown positive results and can improve the treatments available for agriculture. However, the success of phage therapy depends on finding effective bacteriophages. This review focused on describing the potential, up to now, of applying phage therapy as an alternative treatment against bacterial diseases, with sustainable improvement in food production. We described the current isolation techniques, characterization, detection, and selection of lytic phages, highlighting the importance of complementary studies using genome analysis of the phage and its host. Finally, among these studies, we concentrated on the most relevant bacteriophages used for biocontrol of Pseudomonas spp., Xanthomonas spp., Pectobacterium spp., Ralstonia spp., Burkholderia spp., Dickeya spp., Clavibacter michiganensis, and Agrobacterium tumefaciens as agents that cause damage to crops, and affect food production around the world.
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Olo Ndela E, Roux S, Henke C, Sczyrba A, Sime Ngando T, Varsani A, Enault F. Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages. Virus Evol 2022; 9:veac123. [PMID: 36694818 PMCID: PMC9865509 DOI: 10.1093/ve/veac123] [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: 07/15/2022] [Revised: 10/19/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022] Open
Abstract
Small circular single-stranded DNA viruses of the Microviridae family are both prevalent and diverse in all ecosystems. They usually harbor a genome between 4.3 and 6.3 kb, with a microvirus recently isolated from a marine Alphaproteobacteria being the smallest known genome of a DNA phage (4.248 kb). A subfamily, Amoyvirinae, has been proposed to classify this virus and other related small Alphaproteobacteria-infecting phages. Here, we report the discovery, in meta-omics data sets from various aquatic ecosystems, of sixteen complete microvirus genomes significantly smaller (2.991-3.692 kb) than known ones. Phylogenetic analysis reveals that these sixteen genomes represent two related, yet distinct and diverse, novel groups of microviruses-amoyviruses being their closest known relatives. We propose that these small microviruses are members of two tentatively named subfamilies Reekeekeevirinae and Roodoodoovirinae. As known microvirus genomes encode many overlapping and overprinted genes that are not identified by gene prediction software, we developed a new methodology to identify all genes based on protein conservation, amino acid composition, and selection pressure estimations. Surprisingly, only four to five genes could be identified per genome, with the number of overprinted genes lower than that in phiX174. These small genomes thus tend to have both a lower number of genes and a shorter length for each gene, leaving no place for variable gene regions that could harbor overprinted genes. Even more surprisingly, these two Microviridae groups had specific and different gene content, and major differences in their conserved protein sequences, highlighting that these two related groups of small genome microviruses use very different strategies to fulfill their lifecycle with such a small number of genes. The discovery of these genomes and the detailed prediction and annotation of their genome content expand our understanding of ssDNA phages in nature and are further evidence that these viruses have explored a wide range of possibilities during their long evolution.
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Affiliation(s)
| | | | - Christian Henke
- Computational Metagenomics, Bielefeld University, Universitätsstraße 27, Bielefeld 30501, Germany,Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Alexander Sczyrba
- Computational Metagenomics, Bielefeld University, Universitätsstraße 27, Bielefeld 30501, Germany,Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Télesphore Sime Ngando
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, Clermont-Ferrand F-63000, France
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10
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Prado T, Brandão ML, Fumian TM, Freitas L, Chame M, Leomil L, Magalhães MGP, Degrave WMS, Leite JPG, Miagostovich MP. Virome analysis in lakes of the South Shetland Islands, Antarctica - 2020. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158537. [PMID: 36075413 DOI: 10.1016/j.scitotenv.2022.158537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/05/2022] [Accepted: 09/01/2022] [Indexed: 05/25/2023]
Abstract
Polar freshwater ecosystems are characterized by a distinct microbiota. However, little is known about viral diversity and abundance, especially regarding the ecology of RNA viruses. We used shotgun metagenomic analysis on samples from Antarctic ecosystems, and report here the characterization of the virome fraction, from different lakes located in the South Shetland Islands (Penguin, Ardley, Deception and King George Island) in the Peninsula Antarctica, in the summer season 2020. DNA viruses (99.4 %) prevailed over RNA viruses (0.6 %) in the lake samples. Six viral orders were identified in the metagenomic libraries: Caudovirales (dsDNA), which was prevalent in most lakes; Picornavirales (ssRNA+); Sobelivirales (ssRNA+); Tolivirales (ssRNA+); Petitvirales (ssDNA) and Baphyvirales (ssDNA), including eight viral families (Herelleviridae, Siphoviridae, Myoviridae, Microviridae, Marnaviridae, Bacilladnaviridae, Barnaviridae and Tombusviridae) and several other, mainly non-classified ssRNA(+) viruses in the lakes of Ardley Island. Bacteriophages (dsDNA) (Herelleviridae family) infecting the phylum Firmicutes and Siphoviridae were predominant in most lakes evaluated. Functional analysis demonstrated a prevalence of unknown proteins (68 %) in the virome. Our prospective study provides virome analysis data from different lakes in the South Shetland Islands, Antarctica, opening exploratory lines for future research related to the biodiversity and viral ecology in this extreme ecosystem.
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Affiliation(s)
- Tatiana Prado
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil.
| | - Martha Lima Brandão
- FioAntar Project/ VPPIS - Fiocruz, Av Brasil 4365, Manguinhos, Rio de Janeiro, RJ 21040-360, Brazil
| | - Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil
| | - Lucas Freitas
- Laboratory of Respiratory Virus and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro CEP 21040-360, Brazil
| | - Marcia Chame
- Institutional Platform for Biodiversity and Wildlife Health, Av Brasil 4365, Manguinhos, Rio de Janeiro, RJ 21040-360, Brazil
| | - Luciana Leomil
- SENAI Innovation Institute for Biosynthetics and Fibers, Technology Center for Chemical and Textile Industry, 4° Andar: Biotecnologia, Rua Fernando de Souza Barros, 120, Parque Tecnológico da UFRJ, Cidade Universitária, Rio de Janeiro CEP 21941-857, Brazil
| | - Maithê Gaspar Pontes Magalhães
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ 21040-360, Brazil
| | - Wim Maurits Sylvain Degrave
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ 21040-360, Brazil
| | - José Paulo Gagliardi Leite
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil
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11
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Bora SS, Naorem RS, Hazarika DJ, Dasgupta A, Churaman A, Gogoi M, Barooah M. Agricultural Land Use Influences Bacteriophage Community Diversity, Richness, and Heterogeneity. Curr Microbiol 2022; 80:10. [PMID: 36445553 DOI: 10.1007/s00284-022-03129-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
The last two decades have witnessed a large-scale conversion of crop cultivation areas into small and mid-sized tea plantations in Assam, India. Agricultural land-use pattern positively or negatively influences native hydrology and above- and belowground biodiversity. Very little is known about the effect of agricultural land-use patterns on the soil virus (especially, bacteriophage) community structure and function. This metagenomic-based study evaluated the rhizosphere viral community structure of three interlinked cultivation areas, viz., mixed cropping area (coded as CP1), tea-seed orchard (CP2), and monocropping tea cultivation (CP3). The bacteriophages belonged to four major classes with the dominance of Malgrandaviricetes (CP1: 79.37%; CP2: 64.62%; CP3: 4.85%) followed by Caudoviricetes (CP1: 20.49%; CP2: 35.22%; CP3: 90.29%), Faserviricetes (CP1: 0.03%; CP2: 0.08%; CP3: 3.88%), and Tectiliviricetes (CP1: 0.12%; CP2: 0.07%; CP3: 0.97%). Microviruses dominated the phage population in both CP1 and CP2, representing 79.35% and 64.59% of total bacteriophage abundance. Both CP1 and CP2 had higher bacteriophage richness (species richness, R in CP1: 65; R in CP2: 66) and lower evenness (Pielou's evenness index, J in CP1: 0.531; J in CP2: 0.579) compared to the CP3 (R: 30; J: 0.902). Principal component analysis of edaphic soil factors and bacteriophage community structure showed a reverse-proportional correlation between the levels of Al saturation, and exchangeable Al3+ ions with that of soil pH, and bacteriophage abundance. Our study indicates that monocropping tea cultivation soil bears less viral richness, abundance, and heterogeneity.
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Affiliation(s)
- Sudipta Sankar Bora
- DBT-North East Centre for Agricultural Biotechnology (DBT-NECAB), Assam Agricultural University, Jorhat, Assam, India
| | - Romen Singh Naorem
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Dibya Jyoti Hazarika
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Abhisek Dasgupta
- DBT-North East Centre for Agricultural Biotechnology (DBT-NECAB), Assam Agricultural University, Jorhat, Assam, India
| | - Amrita Churaman
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Manuranjan Gogoi
- Department of Tea Husbandry and Technology, Assam Agricultural University, Jorhat, Assam, India
| | - Madhumita Barooah
- DBT-North East Centre for Agricultural Biotechnology (DBT-NECAB), Assam Agricultural University, Jorhat, Assam, India. .,Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India.
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12
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Yang S, Mao Q, Wang Y, He J, Yang J, Chen X, Xiao Y, He Y, Zhao M, Lu J, Yang Z, Dai Z, Liu Q, Yao Y, Lu X, Li H, Zhou R, Zeng J, Li W, Zhou C, Wang X, Shen Q, Xu H, Deng X, Delwart E, Shan T, Zhang W. Expanding known viral diversity in plants: virome of 161 species alongside an ancient canal. ENVIRONMENTAL MICROBIOME 2022; 17:58. [PMID: 36437477 PMCID: PMC9703751 DOI: 10.1186/s40793-022-00453-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Since viral metagenomic approach was applied to discover plant viruses for the first time in 2006, many plant viruses had been identified from cultivated and non-cultivated plants. These previous researches exposed that the viral communities (virome) of plants have still largely uncharacterized. Here, we investigated the virome in 161 species belonging to 38 plant orders found in a riverside ecosystem. RESULTS We identified 245 distinct plant-associated virus genomes (88 DNA and 157 RNA viruses) belonging to 27 known viral families, orders, or unclassified virus groups. Some viral genomes were sufficiently divergent to comprise new species, genera, families, or even orders. Some groups of viruses were detected that currently are only known to infect organisms other than plants. It indicates a wider host range for members of these clades than previously recognized theoretically. We cannot rule out that some viruses could be from plant contaminating organisms, although some methods were taken to get rid of them as much as possible. The same viral species could be found in different plants and co-infections were common. CONCLUSIONS Our data describe a complex viral community within a single plant ecosystem and expand our understanding of plant-associated viral diversity and their possible host ranges.
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Affiliation(s)
- Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
- International Genome Center, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Qingqing Mao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yan Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jingxian He
- Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Jie Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xu Chen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yuqing Xiao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yumin He
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Min Zhao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Juan Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Zijun Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Ziyuan Dai
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Qi Liu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yuxin Yao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xiang Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Hong Li
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Rui Zhou
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jian Zeng
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Wang Li
- Department of Laboratory Medicine, Jiangsu Taizhou People's Hospital, Taizhou, 225300, Jiangsu, China
| | - Chenglin Zhou
- Department of Laboratory Medicine, Jiangsu Taizhou People's Hospital, Taizhou, 225300, Jiangsu, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Hui Xu
- The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA, 94118, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94118, USA
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
- International Genome Center, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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13
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Van Cauwenberghe J, Santamaría RI, Bustos P, González V. Novel lineages of single-stranded DNA phages that coevolved with the symbiotic bacteria Rhizobium. Front Microbiol 2022; 13:990394. [PMID: 36177468 PMCID: PMC9512667 DOI: 10.3389/fmicb.2022.990394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/19/2022] [Indexed: 11/27/2022] Open
Abstract
This study describes novel single-stranded DNA phages isolated from common bean agriculture soils by infection of the nitrogen-fixing symbiotic bacteria Rhizobium etli and R. phaseoli. A total of 29 phages analyzed have 4.3-6 kb genomes in size and GC 59-60%. They belong to different clades unrelated to other Microviridae subfamilies. Three-dimensional models of the major capsid protein (MCP) showed a conserved β-barrel structural "jelly-roll" fold. A variable-length loop in the MCPs distinguished three Rhizobium microvirus groups. Microviridae subfamilies were consistent with viral clusters determined by the protein-sharing network. All viral clusters, except for Bullavirinae, included mostly microviruses identified in metagenomes from distinct ecosystems. Two Rhizobium microvirus clusters, chaparroviruses, and chicoviruses, were included within large viral unknown clusters with microvirus genomes identified in diverse metagenomes. A third Rhizobium microvirus cluster belonged to the subfamily Amoyvirinae. Phylogenetic analysis of the MCP confirms the divergence of the Rhizobium microviruses into separate clades. The phylogeny of the bacterial hosts matches the microvirus MCP phylogeny, suggesting a coevolutionary history between the phages and their bacterial host. This study provided essential biological information on cultivated microvirus for understanding the evolution and ecological diversification of the Microviridae family in diverse microbial ecosystems.
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Affiliation(s)
- Jannick Van Cauwenberghe
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Cuernavaca, Mexico
- Department of Integrative Biology, University of California, Berkeley, CA, United States
| | - Rosa I. Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Cuernavaca, Mexico
| | - Patricia Bustos
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Cuernavaca, Mexico
| | - Víctor González
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Cuernavaca, Mexico
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14
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Wang J, Xiao J, Zhu Z, Wang S, Zhang L, Fan Z, Deng Y, Hu Z, Peng F, Shen S, Deng F. Diverse viromes in polar regions: A retrospective study of metagenomic data from Antarctic animal feces and Arctic frozen soil in 2012-2014. Virol Sin 2022; 37:883-893. [PMID: 36028202 PMCID: PMC9797369 DOI: 10.1016/j.virs.2022.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/17/2022] [Indexed: 01/01/2023] Open
Abstract
Antarctica and the Arctic are the coldest places, containing a high diversity of microorganisms, including viruses, which are important components of polar ecosystems. However, owing to the difficulties in obtaining access to animal and environmental samples, the current knowledge of viromes in polar regions is still limited. To better understand polar viromes, this study performed a retrospective analysis using metagenomic sequencing data of animal feces from Antarctica and frozen soil from the Arctic collected during 2012-2014. The results reveal diverse communities of DNA and RNA viruses from at least 23 families from Antarctic animal feces and 16 families from Arctic soils. Although the viral communities from Antarctica and the Arctic show a large diversity, they have genetic similarities with known viruses from different ecosystems and organisms with similar viral proteins. Phylogenetic analysis of Microviridae, Parvoviridae, and Larvidaviridae was further performed, and complete genomic sequences of two novel circular replication-associated protein (rep)-encoding single-stranded (CRESS) DNA viruses closely related to Circoviridae were identified. These results reveal the high diversity, complexity, and novelty of viral communities from polar regions, and suggested the genetic similarity and functional correlations of viromes between the Antarctica and Arctic. Variations in viral families in Arctic soils, Arctic freshwater, and Antarctic soils are discussed. These findings improve our understanding of polar viromes and suggest the importance of performing follow-up in-depth investigations of animal and environmental samples from Antarctica and the Arctic, which would reveal the substantial role of these viruses in the global viral community.
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Affiliation(s)
- Jun Wang
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jian Xiao
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zheng Zhu
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Siyuan Wang
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China,Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Lei Zhang
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zhaojun Fan
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yali Deng
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zhihong Hu
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, 430072, China,Corresponding authors.
| | - Shu Shen
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China,Corresponding authors.
| | - Fei Deng
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China,Corresponding authors.
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15
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Cui Y, Zhang L, Wang X, Yi Y, Shan Y, Liu B, Zhou Y, Lü X. Roles of intestinal Parabacteroides in human health and diseases. FEMS Microbiol Lett 2022; 369:6659190. [PMID: 35945336 DOI: 10.1093/femsle/fnac072] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 06/09/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
The stability of gut microbiota is essential for the host health. Parabacteroides spp., core members of the human gut microbiota, have average abundance of 1.27% in the human of 12 populations. Parabacteroides has been recently reported to have a close relationship with host health (E.g., metabolic syndrome, inflammatory bowel disease and obesity). Parabacteroides have the physiological characteristics of carbohydrate metabolism and secreting SCFAs. However, antimicrobial resistance of Parabacteroides to antibiotic (such as clindamycin, moxifloxacin and cefoxitin) should not be ignored. In this review, we primarily focused on Parabacteroides distasoniss, Parabacteroides goldsteinii, Parabacteroides johnsonii and Parabacteroides merdae and discussed their relationships with host disease, diet and the prevention or induction of diseases. P. distasonis and P. goldsteinii may be viewed as the potential next generation probiotics (NGP) candidate due to their protective effects on inflammation and obesity in mice. We also discussed the potential therapeutic application of Parabacteroides spp. in maintaining host-intestine homeostasis.
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Affiliation(s)
- Yanlong Cui
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Leshan Zhang
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Xin Wang
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yanglei Yi
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yuanyuan Shan
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Bianfang Liu
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yuan Zhou
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Xin Lü
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
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16
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Zucker F, Bischoff V, Olo Ndela E, Heyerhoff B, Poehlein A, Freese HM, Roux S, Simon M, Enault F, Moraru C. New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria. Virus Evol 2022; 8:veac070. [PMID: 36533142 PMCID: PMC9753089 DOI: 10.1093/ve/veac070] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/24/2022] [Accepted: 07/28/2022] [Indexed: 10/01/2023] Open
Abstract
The Microviridae family represents one of the major clades of single-stranded DNA (ssDNA) phages. Their cultivated members are lytic and infect Proteobacteria, Bacteroidetes, and Chlamydiae. Prophages have been predicted in the genomes from Bacteroidales, Hyphomicrobiales, and Enterobacteriaceae and cluster within the 'Alpavirinae', 'Amoyvirinae', and Gokushovirinae. We have isolated 'Ascunsovirus oldenburgi' ICBM5, a novel phage distantly related to known Microviridae. It infects Sulfitobacter dubius SH24-1b and uses both a lytic and a carrier-state life strategy. Using ICBM5 proteins as a query, we uncovered in publicly available resources sixty-five new Microviridae prophages and episomes in bacterial genomes and retrieved forty-seven environmental viral genomes (EVGs) from various viromes. Genome clustering based on protein content and phylogenetic analysis showed that ICBM5, together with Rhizobium phages, new prophages, episomes, and EVGs cluster within two new phylogenetic clades, here tentatively assigned the rank of subfamily and named 'Tainavirinae' and 'Occultatumvirinae'. They both infect Rhodobacterales. Occultatumviruses also infect Hyphomicrobiales, including nitrogen-fixing endosymbionts from cosmopolitan legumes. A biogeographical assessment showed that tainaviruses and occultatumviruses are spread worldwide, in terrestrial and marine environments. The new phage isolated here sheds light onto new and diverse branches of the Microviridae tree, suggesting that much of the ssDNA phage diversity remains in the dark.
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Affiliation(s)
- Falk Zucker
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Vera Bischoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Eric Olo Ndela
- Laboratoire Microorganismes: Genome Environment (LMGE), Université Clermont Auvergne, CNRS, 1 Imp. Amélie Murat, Aubière 63170, Frankreich
| | - Benedikt Heyerhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August-University Göttingen, Institute of Microbiology and Genetics, Grisebachstr. 8, Göttingen D-37077, Germany
| | - Heike M Freese
- Leibniz-Institut DSMZ, Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7 B, Braunschweig D-38124, Germany
| | - Simon Roux
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA 94720, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Francois Enault
- Laboratoire Microorganismes: Genome Environment (LMGE), Université Clermont Auvergne, CNRS, 1 Imp. Amélie Murat, Aubière 63170, Frankreich
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
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17
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Chen KH, Nelson J. A scoping review of bryophyte microbiota: diverse microbial communities in small plant packages. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4496-4513. [PMID: 35536989 DOI: 10.1093/jxb/erac191] [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: 12/31/2021] [Accepted: 05/05/2022] [Indexed: 06/14/2023]
Abstract
Plant health depends not only on the condition of the plant itself but also on its diverse community of microbes, or microbiota. Just like the better-studied angiosperms, bryophytes (mosses, liverworts, and hornworts) harbor diverse communities of bacteria, archaea, fungi, and other microbial eukaryotes. Bryophytes are increasingly recognized as important model systems for understanding plant evolution, development, physiology, and symbiotic interactions. Much of the work on bryophyte microbiota in the past focused on specific symbiont types for each bryophyte group, but more recent studies are taking a broader view acknowledging the coexistence of diverse microbial communities in bryophytes. Therefore, this review integrates studies of bryophyte microbes from both perspectives to provide a holistic view of the existing research for each bryophyte group and on key themes. The systematic search also reveals the taxonomic and geographic biases in this field, including a severe under-representation of the tropics, very few studies on viruses or eukaryotic microbes beyond fungi, and a focus on mycorrhizal fungi studies in liverworts. Such gaps may have led to errors in conclusions about evolutionary patterns in symbiosis. This analysis points to a wealth of future research directions that promise to reveal how the distinct life cycles and physiology of bryophytes interact with their microbiota.
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Affiliation(s)
- Ko-Hsuan Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jessica Nelson
- Maastricht Science Programme, Maastricht University, Maastricht, The Netherlands
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18
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Abstract
Microviruses encompass an astonishing array of small, single-stranded DNA phages that, due to the surge in metagenomic surveys, are now known to be prevalent in most environments. Current taxonomy concedes the considerable diversity within this lineage to a single family (the Microviridae), which has rendered it difficult to adequately and accurately assess the amount of variation that actually exists within this group. We amassed and curated the largest collection of microviral genomes to date and, through a combination of protein-sharing networks and phylogenetic analysis, discovered at least three meaningful taxonomic levels between the current ranks of family and genus. When considering more than 13,000 microviral genomes from recognized lineages and as-yet-unclassified microviruses in metagenomic samples, microviral diversity is better understood by elevating microviruses to the level of an order that consists of three suborders and at least 19 putative families, each with their respective subfamilies. These revisions enable fine-scale assessment of microviral dynamics: for example, in the human gut, there are considerable differences in the abundances of microviral families both between urban and rural populations and in individuals over time. In addition, our analysis of genome contents and gene exchange shows that microviral families carry no recognizable accessory metabolic genes and rarely, if ever, engage in horizontal gene transfer across microviral families or with their bacterial hosts. These insights bring microviral taxonomy in line with current developments in the taxonomy of other phages and increase the understanding of microvirus biology.
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19
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Complete genome analysis of the newly isolated Vibrio phage vB_VpP_WS1 of the family Microviridae. Arch Virol 2022; 167:1311-1316. [PMID: 35362803 DOI: 10.1007/s00705-022-05413-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 02/01/2022] [Indexed: 11/02/2022]
Abstract
Here, we describe the characterization and genome annotation of the newly isolated lytic Vibrio parahaemolyticus phage vB_VpP_WS1, isolated from sewage samples collected in Qingdao, China. Transmission electron microscopy revealed that vB_VpP_WS1 is about 22 nm in size and that the virions are isometric, likely icosahedral, particles similar to those of members of the Microviridae. The digestion patterns of phage nucleic acids and whole-genome sequencing analysis together revealed that phage vB_VpP_WS1 has a single-stranded DNA genome of 5564 nt. Eight open reading frames were identified, only four of which could be annotated. The proteins of vB_VpP_WS1 displayed low sequence similarity to their homologs encoded by other microviruses. Phylogenetic analysis based on the major capsid protein suggested that vB_VpP_WS1 is a tentative new member of the family Microviridae.
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20
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Genomes of Bacteriophages Belonging to the Orders Caudovirales and Petitvirales Identified in Fecal Samples from Pacific Flying Fox ( Pteropus tonganus) from the Kingdom of Tonga. Microbiol Resour Announc 2022; 11:e0003822. [PMID: 35175112 PMCID: PMC8852320 DOI: 10.1128/mra.00038-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Twenty-nine circular genomes of bacteriophages in the orders Caudovirales and Petitvirales were identified from fecal samples from Pacific flying foxes that were collected from their roosting sites on the Pacific Island of Tonga in 2014 and 2015. The vast majority are microviruses (n = 25), with 2 siphoviruses, 1 myovirus, and 1 podovirus.
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21
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Ezeji JC, Sarikonda DK, Hopperton A, Erkkila HL, Cohen DE, Martinez SP, Cominelli F, Kuwahara T, Dichosa AEK, Good CE, Jacobs MR, Khoretonenko M, Veloo A, Rodriguez-Palacios A. Parabacteroides distasonis: intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health. Gut Microbes 2022; 13:1922241. [PMID: 34196581 PMCID: PMC8253142 DOI: 10.1080/19490976.2021.1922241] [Citation(s) in RCA: 131] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Parabacteroides distasonis is the type strain for the genus Parabacteroides, a group of gram-negative anaerobic bacteria that commonly colonize the gastrointestinal tract of numerous species. First isolated in the 1930s from a clinical specimen as Bacteroides distasonis, the strain was re-classified to form the new genus Parabacteroides in 2006. Currently, the genus consists of 15 species, 10 of which are listed as 'validly named' (P. acidifaciens, P. chartae, P. chinchillae, P. chongii, P. distasonis, P. faecis, P. goldsteinii, P. gordonii, P. johnsonii, and P. merdae) and 5 'not validly named' (P. bouchesdurhonensis, P. massiliensis, P. pacaensis, P. provencensis, and P. timonensis) by the List of Prokaryotic names with Standing in Nomenclature. The Parabacteroides genus has been associated with reports of both beneficial and pathogenic effects in human health. Herein, we review the literature on the history, ecology, diseases, antimicrobial resistance, and genetics of this bacterium, illustrating the effects of P. distasonis on human and animal health.
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Affiliation(s)
- Jessica C. Ezeji
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Daven K. Sarikonda
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Austin Hopperton
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio, USA
| | - Hailey L. Erkkila
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Daniel E. Cohen
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | | | - Fabio Cominelli
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA,Germ-Free and Gut Microbiome Core, Case Western Reserve University, Cleveland, OH, United States
| | - Tomomi Kuwahara
- Department of Microbiology, Faculty of Medicine, Kagawa University, Miki, Kagawa, Japan
| | - Armand E. K. Dichosa
- B-10 Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Caryn E. Good
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Michael R. Jacobs
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | | | - Alida Veloo
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alexander Rodriguez-Palacios
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Germ-Free and Gut Microbiome Core, Case Western Reserve University, Cleveland, OH, United States,University Hospitals Research and Education Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA,CONTACT Alexander Rodriguez-Palacios Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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22
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Diverse single-stranded DNA viruses identified in New Zealand (Aotearoa) South Island robin (Petroica australis) fecal samples. Virology 2021; 565:38-51. [PMID: 34715607 DOI: 10.1016/j.virol.2021.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/16/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022]
Abstract
The South Island robin (Petroica australis) is a small passerine bird endemic to New Zealand (Aotearoa). Although its population has declined recently and it is considered 'at risk,' little research has been done to identify viruses in this species. This study aimed to survey the diversity of single-stranded DNA viruses associated with South Island robins in a small, isolated population on Nukuwaiata Island. In total, 108 DNA viruses were identified from pooled fecal samples collected from 38 individual robins sampled. These viruses belong to the Circoviridae (n = 10), Genomoviridae (n = 12), and Microviridae (n = 73) families. A number of genomes that belong to the phylum Cressdnaviricota but are otherwise unclassified (n = 13) were also identified. These results greatly expand the known viral diversity associated with South Island robins, and we identify a novel group of viruses most closely related genomoviruses.
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23
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Legionella pneumophila CRISPR-Cas Suggests Recurrent Encounters with One or More Phages in the Family Microviridae. Appl Environ Microbiol 2021; 87:e0046721. [PMID: 34132590 DOI: 10.1128/aem.00467-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Legionella pneumophila is a ubiquitous freshwater pathogen and the causative agent of Legionnaires' disease. L. pneumophila growth within protists provides a refuge from desiccation, disinfection, and other remediation strategies. One outstanding question has been whether this protection extends to phages. L. pneumophila isolates are remarkably devoid of prophages and to date no Legionella phages have been identified. Nevertheless, many L. pneumophila isolates maintain active CRISPR-Cas defenses. So far, the only known target of these systems is an episomal element that we previously named Legionella mobile element 1 (LME-1). The continued expansion of publicly available genomic data promises to further our understanding of the role of these systems. We now describe over 150 CRISPR-Cas systems across 600 isolates to establish the clearest picture yet of L. pneumophila's adaptive defenses. By searching for targets of 1,500 unique CRISPR-Cas spacers, LME-1 remains the only identified CRISPR-Cas targeted integrative element. We identified 3 additional LME-1 variants-all targeted by previously and newly identified CRISPR-Cas spacers-but no other similar elements. Notably, we also identified several spacers with significant sequence similarity to microviruses, specifically those within the subfamily Gokushovirinae. These spacers are found across several different CRISPR-Cas arrays isolated from geographically diverse isolates, indicating recurrent encounters with these phages. Our analysis of the extended Legionella CRISPR-Cas spacer catalog leads to two main conclusions: current data argue against CRISPR-Cas targeted integrative elements beyond LME-1, and the heretofore unknown L. pneumophila phages are most likely lytic gokushoviruses. IMPORTANCE Legionnaires' disease is an often-fatal pneumonia caused by Legionella pneumophila, which normally grows inside amoebae and other freshwater protists. L. pneumophila trades diminished access to nutrients for the protection and isolation provided by the host. One outstanding question is whether L. pneumophila is susceptible to phages, given the protection provided by its intracellular lifestyle. In this work, we use Legionella CRISPR spacer sequences as a record of phage infection to predict that the "missing" L. pneumophila phages belong to the microvirus subfamily Gokushovirinae. Gokushoviruses are known to infect another intracellular pathogen, Chlamydia. How do gokushoviruses access L. pneumophila (and Chlamydia) inside their "cozy niches"? Does exposure to phages happen during a transient extracellular period (during cell-to-cell spread) or is it indicative of a more complicated environmental lifestyle? One thing is clear, 100 years after their discovery, phages continue to hold important secrets about the bacteria upon which they prey.
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24
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Chevallereau A, Pons BJ, van Houte S, Westra ER. Interactions between bacterial and phage communities in natural environments. Nat Rev Microbiol 2021; 20:49-62. [PMID: 34373631 DOI: 10.1038/s41579-021-00602-y] [Citation(s) in RCA: 176] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/28/2021] [Indexed: 12/20/2022]
Abstract
We commonly acknowledge that bacterial viruses (phages) shape the composition and evolution of bacterial communities in nature and therefore have important roles in ecosystem functioning. This view stems from studies in the 1990s to the first decade of the twenty-first century that revealed high viral abundance, high viral diversity and virus-induced microbial death in aquatic ecosystems as well as an association between collapses in bacterial density and peaks in phage abundance. The recent surge in metagenomic analyses has provided deeper insight into the abundance, genomic diversity and spatio-temporal dynamics of phages in a wide variety of ecosystems, ranging from deep oceans to soil and the mammalian digestive tract. However, the causes and consequences of variations in phage community compositions remain poorly understood. In this Review, we explore current knowledge of the composition and evolution of phage communities, as well as their roles in controlling the population and evolutionary dynamics of bacterial communities. We discuss the need for greater ecological realism in laboratory studies to capture the complexity of microbial communities that thrive in natural environments.
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Affiliation(s)
- Anne Chevallereau
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK. .,Department of Infection, Immunity and Inflammation, Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France.
| | - Benoît J Pons
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK
| | - Stineke van Houte
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK
| | - Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK.
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25
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Turner D, Kropinski AM, Adriaenssens EM. A Roadmap for Genome-Based Phage Taxonomy. Viruses 2021; 13:v13030506. [PMID: 33803862 PMCID: PMC8003253 DOI: 10.3390/v13030506] [Citation(s) in RCA: 256] [Impact Index Per Article: 85.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022] Open
Abstract
Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago. Genome sequencing has put pressure on the classification system and recent years have seen significant changes to phage taxonomy. Here, we reflect on the state of phage taxonomy and provide a roadmap for the future, including the abolition of the order Caudovirales and the families Myoviridae, Podoviridae, and Siphoviridae. Furthermore, we specify guidelines for the demarcation of species, genus, subfamily and family-level ranks of tailed phage taxonomy.
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Affiliation(s)
- Dann Turner
- Department of Applied Sciences, University of the West of England, Bristol BS16 1QY, UK;
| | - Andrew M. Kropinski
- Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
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26
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Genome Sequences of Microviruses Identified in Gila Monster Feces. Microbiol Resour Announc 2021; 10:10/11/e00163-21. [PMID: 33737363 PMCID: PMC7975881 DOI: 10.1128/mra.00163-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The complete genome sequences of 33 microviruses were determined from fecal samples collected from 14 Arizona-dwelling Gila monsters using high-throughput sequencing. These microviruses with genomes 4,383 to 6,782 nucleotides (nt) long were broadly distributed across the 14 samples. The complete genome sequences of 33 microviruses were determined from fecal samples collected from 14 Arizona-dwelling Gila monsters using high-throughput sequencing. These microviruses with genomes 4,383 to 6,782 nucleotides (nt) long were broadly distributed across the 14 samples.
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27
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Li M, Lin H, Wang L, Wang J. Complete genome sequence of the extreme-pH-resistant Salmonella bacteriophage αα of the family Microviridae. Arch Virol 2020; 166:325-329. [PMID: 33221988 DOI: 10.1007/s00705-020-04880-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 09/29/2020] [Indexed: 12/01/2022]
Abstract
A novel Salmonella bacteriophage (phage), named αα, was the first reported member of the family Microviridae to exhibit tolerance to both extreme acidic and alkaline conditions (pH 2-12 for 1 h). Phage αα has a circular single-stranded DNA genome of 5,387 nt with a G+C content of 44.66%. A total of 11 putative gene products and no tRNA genes are encoded in the phage αα genome. Whole-genome sequence comparisons revealed that phage αα shares 95% identity with coliphage phiX174 and had a close evolutionary relationship to the phages NC1 and NC7. Phylogenetic analysis of the structural proteins of phage αα and 18 other phiX174-like phages showed that a phylogenetic tree based on protein B sequences had a topology similar to that obtained using whole genome sequences. In addition, variable sites in proteins F and G distributed on the surface of the mature capsid and the conserved protein J were probably involved in maintaining the structural integrity of the phage under extreme pH conditions. Our findings could open up new perspectives for identifying more extreme-pH-resistant phages and their structural proteins and understanding the mechanism of phage adaptation and evolution under extreme environmental stress.
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Affiliation(s)
- Mengzhe Li
- Food Safety Laboratory, Department of Food Science and Engineering, Ocean University of China, Qingdao, 266003, People's Republic of China
| | - Hong Lin
- Food Safety Laboratory, Department of Food Science and Engineering, Ocean University of China, Qingdao, 266003, People's Republic of China
| | - Luokai Wang
- Food Safety Laboratory, Department of Food Science and Engineering, Ocean University of China, Qingdao, 266003, People's Republic of China
| | - Jingxue Wang
- Food Safety Laboratory, Department of Food Science and Engineering, Ocean University of China, Qingdao, 266003, People's Republic of China.
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28
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Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. Arch Virol 2020; 165:1253-1260. [PMID: 32162068 DOI: 10.1007/s00705-020-04577-8] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.
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29
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Kirchberger PC, Ochman H. Resurrection of a global, metagenomically defined gokushovirus. eLife 2020; 9:e51599. [PMID: 32101162 PMCID: PMC7062461 DOI: 10.7554/elife.51599] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/25/2020] [Indexed: 12/16/2022] Open
Abstract
Gokushoviruses are single-stranded, circular DNA bacteriophages found in metagenomic datasets from diverse ecosystems worldwide, including human gut microbiomes. Despite their ubiquity and abundance, little is known about their biology or host range: Isolates are exceedingly rare, known only from three obligate intracellular bacterial genera. By synthesizing circularized phage genomes from prophages embedded in diverse enteric bacteria, we produced gokushoviruses in an experimentally tractable model system, allowing us to investigate their features and biology. We demonstrate that virions can reliably infect and lysogenize hosts by hijacking a conserved chromosome-dimer resolution system. Sequence motifs required for lysogeny are detectable in other metagenomically defined gokushoviruses; however, we show that even partial motifs enable phages to persist cytoplasmically without leading to collapse of their host culture. This ability to employ multiple, disparate survival strategies is likely key to the long-term persistence and global distribution of Gokushovirinae.
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Affiliation(s)
- Paul C Kirchberger
- Department of Integrative Biology University of TexasAustinUnited States
| | - Howard Ochman
- Department of Integrative Biology University of TexasAustinUnited States
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30
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Circular Single-Stranded DNA Virus ( Microviridae: Gokushovirinae: Jodiemicrovirus) Associated with the Pathobiome of the Flat-Back Mud Crab, Eurypanopeus depressus. Microbiol Resour Announc 2019; 8:8/47/e01026-19. [PMID: 31753941 PMCID: PMC6872883 DOI: 10.1128/mra.01026-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A single-stranded DNA (ssDNA) virus is presented from a metagenomic data set derived from Alphaproteobacteria-infected hepatopancreatic tissues of the crab Eurypanopeus depressus. The circular virus genome (4,768 bp) encodes 14 hypothetical proteins, some similar to other bacteriophages (Microviridae). Based on its relatedness to other Microviridae, this virus represents a member of a novel genus. A single-stranded DNA (ssDNA) virus is presented from a metagenomic data set derived from Alphaproteobacteria-infected hepatopancreatic tissues of the crab Eurypanopeus depressus. The circular virus genome (4,768 bp) encodes 14 hypothetical proteins, some similar to other bacteriophages (Microviridae). Based on its relatedness to other Microviridae, this virus represents a member of a novel genus.
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31
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Wang H, Ling Y, Shan T, Yang S, Xu H, Deng X, Delwart E, Zhang W. Gut virome of mammals and birds reveals high genetic diversity of the family Microviridae. Virus Evol 2019; 5:vez013. [PMID: 31191981 PMCID: PMC6555873 DOI: 10.1093/ve/vez013] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Nineteen families of phages infecting bacteria or archaea are currently recognized by the International Committee on Taxonomy of Viruses (ICTV). Of these, only two have single-stranded DNA genomes, namely Inoviridae and Microviridae. The distribution, genetic characteristics, and ecological roles of Microviridae remain largely under explored. Here, using viral metagenomics, we investigate the intestinal virome from human and twenty-four species of animals, as well as freshwater samples, containing abundant sequence reads showing similarity to the Microviridae. Eight hundred and sixty complete or near complete Microviridae-related genomes were generated, showing high levels of co-infections and sequence divergence. Sequence comparison and phylogenetic analysis showed that the Microviridae subfamily Gokushovirinae was highly prevalent and that some strains may qualify as new subfamilies. This study significantly augments our knowledge of the genetic diversity, genome evolution, and distribution in animal species of members of the family Microviridae.
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Affiliation(s)
- Hao Wang
- Department of Microbiology, School of Medicine, Jiangsu University, 310 Xuefu Road, Zhenjiang, Jiangsu, China
| | - Yu Ling
- Department of Microbiology, School of Medicine, Jiangsu University, 310 Xuefu Road, Zhenjiang, Jiangsu, China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Shanghai, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, 310 Xuefu Road, Zhenjiang, Jiangsu, China
| | - Hui Xu
- The Affiliated Hospital of Jiangsu University, 438 Jiefang Road, Zhenjiang, Jiangsu, China
| | - Xutao Deng
- Vitalant Research Institute, 270 masonic avenue, San Francisco, CA, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 masonic avenue, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, 270 masonic avenue, San Francisco, San Francisco CA, USA
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, 310 Xuefu Road, Zhenjiang, Jiangsu, China
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32
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Diversity of Active Viral Infections within the Sphagnum Microbiome. Appl Environ Microbiol 2018; 84:AEM.01124-18. [PMID: 30217851 DOI: 10.1128/aem.01124-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 09/10/2018] [Indexed: 11/20/2022] Open
Abstract
Sphagnum-dominated peatlands play an important role in global carbon storage and represent significant sources of economic and ecological value. While recent efforts to describe microbial diversity and metabolic potential of the Sphagnum microbiome have demonstrated the importance of its microbial community, little is known about the viral constituents. We used metatranscriptomics to describe the diversity and activity of viruses infecting microbes within the Sphagnum peat bog. The vegetative portions of six Sphagnum plants were obtained from a peatland in northern Minnesota, and the total RNA was extracted and sequenced. Metatranscriptomes were assembled and contigs were screened for the presence of conserved virus marker genes. Using bacteriophage capsid protein gp23 as a marker for phage diversity, we identified 33 contigs representing undocumented phages that were active in the community at the time of sampling. Similarly, RNA-dependent RNA polymerase and the nucleocytoplasmic large DNA virus (NCLDV) major capsid protein were used as markers for single-stranded RNA (ssRNA) viruses and NCLDV, respectively. In total, 114 contigs were identified as originating from undescribed ssRNA viruses, 22 of which represent nearly complete genomes. An additional 64 contigs were identified as being from NCLDVs. Finally, 7 contigs were identified as putative virophage or polinton-like viruses. We developed co-occurrence networks with these markers in relation to the expression of potential-host housekeeping gene rpb1 to predict virus-host relationships, identifying 13 groups. Together, our approach offers new tools for the identification of virus diversity and interactions in understudied clades and suggests that viruses may play a considerable role in the ecology of the Sphagnum microbiome.IMPORTANCE Sphagnum-dominated peatlands play an important role in maintaining atmospheric carbon dioxide levels by modifying conditions in the surrounding soil to favor the growth of Sphagnum over that of other plant species. This lowers the rate of decomposition and facilitates the accumulation of fixed carbon in the form of partially decomposed biomass. The unique environment produced by Sphagnum enriches for the growth of a diverse microbial consortia that benefit from and support the moss's growth, while also maintaining the hostile soil conditions. While a growing body of research has begun to characterize the microbial groups that colonize Sphagnum, little is currently known about the ecological factors that constrain community structure and define ecosystem function. Top-down population control by viruses is almost completely undescribed. This study provides insight into the significant viral influence on the Sphagnum microbiome and identifies new potential model systems to study virus-host interactions in the peatland ecosystem.
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33
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Zhan Y, Chen F. The smallest ssDNA phage infecting a marine bacterium. Environ Microbiol 2018; 21:1916-1928. [PMID: 30160044 DOI: 10.1111/1462-2920.14394] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/22/2018] [Accepted: 08/24/2018] [Indexed: 11/28/2022]
Abstract
In the marine environment, only a few lytic single-stranded DNA (ssDNA) phages have been isolated and characterized, despite the fact that diverse ssDNA bacteriophages have been discovered via metagenomic studies. In this study, we isolated and characterized a new ssDNA phage, vB_RpoMi-Mini, which infects a marine bacterium Ruegeria pomeroyi DSS-3. With a genome size of 4248 bp and only four putative open reading frames (ORF), vB_RpoMi-Mini becomes the smallest ssDNA phage among the known ssDNA phage isolates and represents the DNA bacteriophage with the least number of ORFs. Genome-wide analysis reveals that bacteriophage Mini is distantly related to the known ssDNA phages and belongs to an unclassified ssDNA phage within the Microviridae family. The presence of peptidase in vB_RpoMi-Mini genome further implies that horizontal gene transfer could be an important driving force in the evolution of ssDNA phages. Bacteriophage Mini seems to have lost the spike protein commonly seen in ssDNA phages, suggesting that ssDNA phage can be more diverse than previously thought. Metagenomic analysis indicates that Mini-like phages are widely distributed in the environments. The discovery of vB_RpoMi-Mini expands our understanding of ssDNA phages in nature, and also indicates our dearth of knowledge regarding of ssDNA phages.
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Affiliation(s)
- Yuanchao Zhan
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Cambridge, MD, USA
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Cambridge, MD, USA
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34
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Creasy A, Rosario K, Leigh BA, Dishaw LJ, Breitbart M. Unprecedented Diversity of ssDNA Phages from the Family Microviridae Detected within the Gut of a Protochordate Model Organism ( Ciona robusta). Viruses 2018; 10:v10080404. [PMID: 30065169 PMCID: PMC6116155 DOI: 10.3390/v10080404] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 07/23/2018] [Accepted: 07/27/2018] [Indexed: 12/13/2022] Open
Abstract
Phages (viruses that infect bacteria) play important roles in the gut ecosystem through infection of bacterial hosts, yet the gut virome remains poorly characterized. Mammalian gut viromes are dominated by double-stranded DNA (dsDNA) phages belonging to the order Caudovirales and single-stranded DNA (ssDNA) phages belonging to the family Microviridae. Since the relative proportion of each of these phage groups appears to correlate with age and health status in humans, it is critical to understand both ssDNA and dsDNA phages in the gut. Building upon prior research describing dsDNA viruses in the gut of Ciona robusta, a marine invertebrate model system used to study gut microbial interactions, this study investigated ssDNA phages found in the Ciona gut. We identified 258 Microviridae genomes, which were dominated by novel members of the Gokushovirinae subfamily, but also represented several proposed phylogenetic groups (Alpavirinae, Aravirinae, Group D, Parabacteroides prophages, and Pequeñovirus) and a novel group. Comparative analyses between Ciona specimens with full and cleared guts, as well as the surrounding water, indicated that Ciona retains a distinct and highly diverse community of ssDNA phages. This study significantly expands the known diversity within the Microviridae family and demonstrates the promise of Ciona as a model system for investigating their role in animal health.
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Affiliation(s)
- Alexandria Creasy
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
- Department of Pediatrics, Children's Research Institute, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Karyna Rosario
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Brittany A Leigh
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
- Department of Pediatrics, Children's Research Institute, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Larry J Dishaw
- Department of Pediatrics, Children's Research Institute, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Mya Breitbart
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
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35
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Zheng Q, Chen Q, Xu Y, Suttle CA, Jiao N. A Virus Infecting Marine Photoheterotrophic Alphaproteobacteria ( Citromicrobium spp.) Defines a New Lineage of ssDNA Viruses. Front Microbiol 2018; 9:1418. [PMID: 29997609 PMCID: PMC6030365 DOI: 10.3389/fmicb.2018.01418] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/08/2018] [Indexed: 12/02/2022] Open
Abstract
In recent metagenomic studies, single-stranded DNA (ssDNA) viruses that infect bacteria have been shown to be diverse and prevalent in the ocean; however, there are few isolates of marine ssDNA phages. Here, we report on a cultivated ssDNA phage (vB_Cib_ssDNA_P1) that infects Citromicrobium bathyomarinum RCC1878 (family Sphingomonadaceae), and other members of the genus. This is the first ssDNA phage reported to infect marine alphaproteobacteria, and represents a newly recognized lineage of the Microviridae infecting members of Sphingomonadaceae, the Amoyvirinae. The ∼26 nm diameter polyhedral capsid contains a 4,360 bp genome with 6 open reading frames (ORFs) and a 59.3% G+C content. ORF1 encodes the capsid protein and ORF3 encodes the replication initiator protein. The replication cycle is ∼5 h, followed by a burst releasing about 180 infectious particles. The closest relative of vB_Cib_ssDNA_P1 is a prophage within the genome of Novosphingobium tardaugens strain NBRC16725. Phylogenetic analysis indicates that the vB_Cib_ssDNA_P1 phage and two related prophages, as well as an environmental sequence, form a novel group within the Microviridae. Our results indicate that this is a previously unknown lineage of ssDNA viruses which also supplies a new model system for studying interactions between ssDNA phages and marine bacteria.
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Affiliation(s)
- Qiang Zheng
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Qi Chen
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yongle Xu
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Institute of Marine Science and Technology, Shandong University, Jinan, China
| | - Curtis A. Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, Botany, The Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, BC, Canada
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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Yu DT, Han LL, Zhang LM, He JZ. Diversity and Distribution Characteristics of Viruses in Soils of a Marine-Terrestrial Ecotone in East China. MICROBIAL ECOLOGY 2018; 75:375-386. [PMID: 28825127 DOI: 10.1007/s00248-017-1049-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/20/2017] [Indexed: 06/07/2023]
Abstract
A substantial gap remains in our understanding of the abundance, diversity, and ecology of viruses in soil although some advances have been achieved in recent years. In this study, four soil samples according to the salinity gradient from shore to inland in East China have been characterized. Results showed that spherical virus particles represented the largest viral component in all of the four samples. The viromes had remarkably different taxonomic compositions, and most of the sequences were derived from single-stranded DNA viruses, especially from families Microviridae and Circoviridae. Compared with viromes from other aquatic and sediment samples, the community compositions of our four soil viromes resembled each other, meanwhile coastal sample virome closely congregated with sediment and hypersaline viromes, and high salinity paddy soil sample virome was similar with surface sediment virome. Phylogenetic analysis of functional genes showed that four viromes have high diversity of the subfamily Gokushovirinae in family Microviridae and most of Circoviridae replicase protein sequences grouped within the CRESS-DNA viruses. This work provided an initial outline of the viral communities in marine-terrestrial ecotone and will improve our understanding of the ecological functions of soil viruses.
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Affiliation(s)
- Dan-Ting Yu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, 3010, Australia.
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Tikhe CV, Husseneder C. Metavirome Sequencing of the Termite Gut Reveals the Presence of an Unexplored Bacteriophage Community. Front Microbiol 2018; 8:2548. [PMID: 29354098 PMCID: PMC5759034 DOI: 10.3389/fmicb.2017.02548] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 12/08/2017] [Indexed: 12/25/2022] Open
Abstract
The Formosan subterranean termite; Coptotermes formosanus is nutritionally dependent on the complex and diverse community of bacteria and protozoa in their gut. Although, there have been many studies to decipher the taxonomic and functional diversity of bacterial communities in the guts of termites, their bacteriophages remain unstudied. We sequenced the metavirome of the guts of Formosan subterranean termite workers to study the diversity of bacteriophages and other associated viruses. Results showed that the termites harbor a virome in their gut comprised of varied and previously unknown bacteriophages. Between 87-90% of the predicted dsDNA virus genes by Metavir showed similarity to the tailed bacteriophages (Caudovirales). Many predicted genes from the virome matched to bacterial prophage regions. These data are suggestive of a virome dominated by temperate bacteriophages. We predicted the genomes of seven novel Caudovirales bacteriophages from the termite gut. Three of these predicted bacteriophage genomes were found in high proportions in all the three termite colonies tested. Two bacteriophages are predicted to infect endosymbiotic bacteria of the gut protozoa. The presence of these putative bacteriophages infecting endosymbionts of the gut protozoa, suggests a quadripartite relationship between the termites their symbiotic protozoa, endosymbiotic bacteria of the protozoa and their bacteriophages. Other than Caudovirales, ss-DNA virus related genes were also present in the termite gut. We predicted the genomes of 12 novel Microviridae phages from the termite gut and seven of those possibly represent a new proposed subfamily. Circovirus like genomes were also assembled from the termite gut at lower relative abundance. We predicted 10 novel circovirus genomes in this study. Whether these circoviruses infect the termites remains elusive at the moment. The functional and taxonomical annotations suggest that the termites may harbor a core virome comprised of the bacteriophages infecting endosymbionts of the gut protozoa.
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Affiliation(s)
- Chinmay V Tikhe
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Claudia Husseneder
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
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Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon. mSphere 2017; 2:mSphere00366-17. [PMID: 28989970 PMCID: PMC5628290 DOI: 10.1128/msphere.00366-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 08/18/2017] [Indexed: 11/20/2022] Open
Abstract
The Amazon River forms a vast plume in the Atlantic Ocean that can extend for more than 1,000 km. Microbial communities promote a globally relevant carbon sink system in the plume. Despite the importance of viruses for the global carbon cycle, the diversity and the possible roles of viruses in the Amazonia are poorly understood. The present work assesses, for the first time, the abundance and diversity of viruses simultaneously in the river and ocean in order to elucidate their possible roles. DNA sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes from the 12 river and ocean locations. Viral diversity was clearly distinguished by river and ocean. Bacteriophages were the most abundant and occurred throughout the continuum. Viruses that infect eukaryotes were more abundant in the river, whereas phages appeared to have strong control over the host prokaryotic populations in the plume. The Amazon River watershed and its associated plume comprise a vast continental and oceanic area. The microbial activities along this continuum contribute substantially to global carbon and nutrient cycling, and yet there is a dearth of information on the diversity, abundance, and possible roles of viruses in this globally important river. The aim of this study was to elucidate the diversity and structure of virus assemblages of the Amazon River-ocean continuum. Environmental viral DNA sequences were obtained for 12 locations along the river’s lower reach (n = 5) and plume (n = 7). Sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes. Despite the spatial connectivity mediated by the river, virome analyses and physical-chemical water parameters clearly distinguished river and plume ecosystems. Bacteriophages were ubiquitous in the continuum and were more abundant in the transition region. Eukaryotic viruses occurred mostly in the river, while the plume had more viruses of autotrophic organisms (Prochlorococcus, Synechococcus) and heterotrophic bacteria (Pelagibacter). The viral families Microviridae and Myoviridae were the most abundant and occurred throughout the continuum. The major functions of the genes in the continuum involved viral structures and life cycles, and viruses from plume locations and Tapajós River showed the highest levels of functional diversity. The distribution patterns of the viral assemblages were defined not only by the occurrence of possible hosts but also by water physical and chemical parameters, especially salinity. The findings presented here help to improve understanding of the possible roles of viruses in the organic matter cycle along the river-ocean continuum. IMPORTANCE The Amazon River forms a vast plume in the Atlantic Ocean that can extend for more than 1,000 km. Microbial communities promote a globally relevant carbon sink system in the plume. Despite the importance of viruses for the global carbon cycle, the diversity and the possible roles of viruses in the Amazon are poorly understood. The present work assesses, for the first time, the abundance and diversity of viruses simultaneously in the river and ocean in order to elucidate their possible roles. DNA sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes from the 12 river and ocean locations. Viral diversity was clearly distinguished by river and ocean. Bacteriophages were the most abundant and occurred throughout the continuum. Viruses that infect eukaryotes were more abundant in the river, whereas phages appeared to have strong control over the host prokaryotic populations in the plume.
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Viral metagenomics analysis of feces from coronary heart disease patients reveals the genetic diversity of the Microviridae. Virol Sin 2017; 32:130-138. [PMID: 28466442 DOI: 10.1007/s12250-016-3896-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 03/22/2017] [Indexed: 12/27/2022] Open
Abstract
Recent studies have declared that members of the ssDNA virus family Microviridae play an important role in multiple environments, as they have been found taking a dominant position in the human gut. The aim of this study was to analyze the overall composition of the gut virome in coronary heart disease (CHD) patients, and try to discover the potential link between the human gut virome and CHD. Viral metagenomics methods were performed to detect the viral sequences in fecal samples collected from CHD inpatients and healthy persons as controls. We present the analysis of the virome composition in these CHD patients and controls. Our data shows that the virome composition may be linked to daily living habits and the medical therapy of CHD. Virgaviridae and Microviridae were the two dominant types of viruses found in the enteric virome of CHD patients. Fourteen divergent viruses belonging to the family Microviridae were found, twelve of which were grouped into the subfamily Gokushovirinae, while the remaining two strains might represent two new subfamilies within Microviridae, according to the phylogenetic analysis. In addition, the genomic organization of these viruses has been characterized.
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40
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Genetic and functional diversity of ubiquitous DNA viruses in selected Chinese agricultural soils. Sci Rep 2017; 7:45142. [PMID: 28327667 PMCID: PMC5361096 DOI: 10.1038/srep45142] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/15/2017] [Indexed: 01/21/2023] Open
Abstract
Viral community structures in complex agricultural soils are largely unknown. Electron microscopy and viromic analyses were conducted on six typical Chinese agricultural soil samples. Tailed bacteriophages, spherical and filamentous viral particles were identified by the morphological analysis. Based on the metagenomic analysis, single-stranded DNA viruses represented the largest viral component in most of the soil habitats, while the double-stranded DNA viruses belonging to the Caudovirales order were predominanted in Jiangxi-maize soils. The majority of functional genes belonged to the subsystem “phages, prophages, transposable elements, and plasmids”. Non-metric multidimensional analysis of viral community showed that the environment medium type was the most important driving factor for the viral community structure. For the major viral groups detected in all samples (Microviridae and Caudovirales), the two groups gathered viruses from different sites and similar genetic composition, indicating that viral diversity was high on a local point but relatively limited on a global scale. This is a novel report of viral diversity in Chinese agricultural soils, and the abundance, taxonomic, and functional diversity of viruses that were observed in different types of soils will aid future soil virome studies and enhance our understanding of the ecological functions of soil viruses.
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Novel Single-Stranded DNA Virus Genomes Recovered from Chimpanzee Feces Sampled from the Mambilla Plateau in Nigeria. GENOME ANNOUNCEMENTS 2017; 5:5/9/e01715-16. [PMID: 28254982 PMCID: PMC5334589 DOI: 10.1128/genomea.01715-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Metagenomic approaches are rapidly expanding our knowledge of the diversity of viruses. In the fecal matter of Nigerian chimpanzees we recovered three gokushovirus genomes, one circular replication-associated protein encoding single-stranded DNA virus (CRESS), and a CRESS DNA molecule.
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Roux S, Solonenko NE, Dang VT, Poulos BT, Schwenck SM, Goldsmith DB, Coleman ML, Breitbart M, Sullivan MB. Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. PeerJ 2016; 4:e2777. [PMID: 28003936 PMCID: PMC5168678 DOI: 10.7717/peerj.2777] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/08/2016] [Indexed: 01/06/2023] Open
Abstract
Background Viruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenomes (viromes). This leaves the ecology of non-dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation). Methods Here we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation approach including an Adaptase step prior to Linker Amplification for quantitative amplification of both dsDNA and ssDNA templates. We then surveyed aquatic samples to provide first estimates of the abundance of ssDNA viruses. Results Mock community experiments confirmed the biased nature of existing library preparation methods for ssDNA templates (either largely enriched or selected against) and showed that the protocol using Adaptase plus Linker Amplification yielded viromes that were ±1.8-fold quantitative for ssDNA and dsDNA viruses. Application of this protocol to community virus DNA from three freshwater and three marine samples revealed that ssDNA viruses as a whole represent only a minor fraction (<5%) of DNA virus communities, though individual ssDNA genomes, both eukaryote-infecting Circular Rep-Encoding Single-Stranded DNA (CRESS-DNA) viruses and bacteriophages from the Microviridae family, can be among the most abundant viral genomes in a sample. Discussion Together these findings provide empirical data for a new virome library preparation protocol, and a first estimate of ssDNA virus abundance in aquatic systems.
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Affiliation(s)
- Simon Roux
- Department of Microbiology, The Ohio State University , Columbus , OH , United States
| | - Natalie E Solonenko
- Department of Microbiology, The Ohio State University , Columbus , OH , United States
| | - Vinh T Dang
- Department of Microbiology, Ha Long University , Uong Bi , Quang Ninh , Vietnam
| | - Bonnie T Poulos
- Department of Ecology and Evolutionary Biology, University of Arizona , Tucson , AZ , United States
| | - Sarah M Schwenck
- Department of Ecology and Evolutionary Biology, University of Arizona , Tucson , AZ , United States
| | - Dawn B Goldsmith
- College of Marine Science, University of South Florida , St. Petersburg , FL , United States
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago , Chicago , IL , United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida , St. Petersburg , FL , United States
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, United States; Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, United States
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Quaiser A, Krupovic M, Dufresne A, Francez AJ, Roux S. Diversity and comparative genomics of chimeric viruses in Sphagnum-dominated peatlands. Virus Evol 2016; 2:vew025. [PMID: 29492276 PMCID: PMC5822885 DOI: 10.1093/ve/vew025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A new group of viruses carrying naturally chimeric single-stranded (ss) DNA
genomes that encompass genes derived from eukaryotic ssRNA and ssDNA viruses has
been recently identified by metagenomic studies. The host range, genomic
diversity, and abundance of these chimeric viruses, referred to as cruciviruses,
remain largely unknown. In this article, we assembled and analyzed thirty-seven
new crucivirus genomes from twelve peat viromes, representing twenty-four
distinct genome organizations, and nearly tripling the number of available
genomes for this group. All genomes possess the two characteristic genes
encoding for the conserved capsid protein (CP) and a replication protein.
Additional ORFs were conserved only in nearly identical genomes with no
detectable similarity to known genes. Two cruciviruses possess putative introns
in their replication-associated genes. Sequence and phylogenetic analyses of the
replication proteins revealed intra-gene chimerism in at least eight chimeric
genomes. This highlights the large extent of horizontal gene transfer and
recombination events in the evolution of ssDNA viruses, as previously suggested.
Read mapping analysis revealed that members of the ‘Cruciviridae’ group are
particularly prevalent in peat viromes. Sequences matching the CP ranged from
0.6 up to 10.9 percent in the twelve peat viromes. In contrast, from sixty-nine
available viromes derived from other environments, only twenty-four contained
cruciviruses, which on average accounted for merely 0.2 percent of sequences.
Overall, this study provides new genome information and insights into the
diversity of chimeric viruses, a necessary first step in progressing toward an
accurate quantification and host range identification of these new viruses.
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Affiliation(s)
- Achim Quaiser
- Université de Rennes 1, CNRS UMR6553 EcoBio, Rennes, France.,Department of Microbiology, Institut Pasteur, Paris, France.,Department of Microbiology, Ohio State University, Columbus, OH, USA
| | - Mart Krupovic
- Université de Rennes 1, CNRS UMR6553 EcoBio, Rennes, France.,Department of Microbiology, Institut Pasteur, Paris, France.,Department of Microbiology, Ohio State University, Columbus, OH, USA
| | - Alexis Dufresne
- Université de Rennes 1, CNRS UMR6553 EcoBio, Rennes, France.,Department of Microbiology, Institut Pasteur, Paris, France.,Department of Microbiology, Ohio State University, Columbus, OH, USA
| | - André-Jean Francez
- Université de Rennes 1, CNRS UMR6553 EcoBio, Rennes, France.,Department of Microbiology, Institut Pasteur, Paris, France.,Department of Microbiology, Ohio State University, Columbus, OH, USA
| | - Simon Roux
- Université de Rennes 1, CNRS UMR6553 EcoBio, Rennes, France.,Department of Microbiology, Institut Pasteur, Paris, France.,Department of Microbiology, Ohio State University, Columbus, OH, USA
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Trubl G, Solonenko N, Chittick L, Solonenko SA, Rich VI, Sullivan MB. Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient. PeerJ 2016; 4:e1999. [PMID: 27231649 PMCID: PMC4878379 DOI: 10.7717/peerj.1999] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 04/11/2016] [Indexed: 01/23/2023] Open
Abstract
Permafrost stores approximately 50% of global soil carbon (C) in a frozen form; it is thawing rapidly under climate change, and little is known about viral communities in these soils or their roles in C cycling. In permafrost soils, microorganisms contribute significantly to C cycling, and characterizing them has recently been shown to improve prediction of ecosystem function. In other ecosystems, viruses have broad ecosystem and community impacts ranging from host cell mortality and organic matter cycling to horizontal gene transfer and reprogramming of core microbial metabolisms. Here we developed an optimized protocol to extract viruses from three types of high organic-matter peatland soils across a permafrost thaw gradient (palsa, moss-dominated bog, and sedge-dominated fen). Three separate experiments were used to evaluate the impact of chemical buffers, physical dispersion, storage conditions, and concentration and purification methods on viral yields. The most successful protocol, amended potassium citrate buffer with bead-beating or vortexing and BSA, yielded on average as much as 2-fold more virus-like particles (VLPs) g−1 of soil than other methods tested. All method combinations yielded VLPs g−1 of soil on the 108 order of magnitude across all three soil types. The different storage and concentration methods did not yield significantly more VLPs g−1 of soil among the soil types. This research provides much-needed guidelines for resuspending viruses from soils, specifically carbon-rich soils, paving the way for incorporating viruses into soil ecology studies.
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Affiliation(s)
- Gareth Trubl
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, United States; Current affiliation: Department of Microbiology, Ohio State University, Columbus, OH, United States
| | - Natalie Solonenko
- Current affiliation: Department of Microbiology, Ohio State University, Columbus, OH, United States; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Lauren Chittick
- Current affiliation: Department of Microbiology, Ohio State University, Columbus, OH, United States; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Sergei A Solonenko
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States; Current affiliation: Department of Ecology, Evolution and Organismal Biology, Ohio State University, Columbus, OH, United States
| | - Virginia I Rich
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, United States; Current affiliation: Department of Microbiology, Ohio State University, Columbus, OH, United States
| | - Matthew B Sullivan
- Current affiliation: Department of Microbiology, Ohio State University, Columbus, OH, United States; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States; Current affiliation: Department of Ecology, Evolution and Organismal Biology, Ohio State University, Columbus, OH, United States; Current affiliation: Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, United States
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Alves JMP, de Oliveira AL, Sandberg TOM, Moreno-Gallego JL, de Toledo MAF, de Moura EMM, Oliveira LS, Durham AM, Mehnert DU, Zanotto PMDA, Reyes A, Gruber A. GenSeed-HMM: A Tool for Progressive Assembly Using Profile HMMs as Seeds and its Application in Alpavirinae Viral Discovery from Metagenomic Data. Front Microbiol 2016; 7:269. [PMID: 26973638 PMCID: PMC4777721 DOI: 10.3389/fmicb.2016.00269] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/19/2016] [Indexed: 01/01/2023] Open
Abstract
This work reports the development of GenSeed-HMM, a program that implements seed-driven progressive assembly, an approach to reconstruct specific sequences from unassembled data, starting from short nucleotide or protein seed sequences or profile Hidden Markov Models (HMM). The program can use any one of a number of sequence assemblers. Assembly is performed in multiple steps and relatively few reads are used in each cycle, consequently the program demands low computational resources. As a proof-of-concept and to demonstrate the power of HMM-driven progressive assemblies, GenSeed-HMM was applied to metagenomic datasets in the search for diverse ssDNA bacteriophages from the recently described Alpavirinae subfamily. Profile HMMs were built using Alpavirinae-specific regions from multiple sequence alignments (MSA) using either the viral protein 1 (VP1; major capsid protein) or VP4 (genome replication initiation protein). These profile HMMs were used by GenSeed-HMM (running Newbler assembler) as seeds to reconstruct viral genomes from sequencing datasets of human fecal samples. All contigs obtained were annotated and taxonomically classified using similarity searches and phylogenetic analyses. The most specific profile HMM seed enabled the reconstruction of 45 partial or complete Alpavirinae genomic sequences. A comparison with conventional (global) assembly of the same original dataset, using Newbler in a standalone execution, revealed that GenSeed-HMM outperformed global genomic assembly in several metrics employed. This approach is capable of detecting organisms that have not been used in the construction of the profile HMM, which opens up the possibility of diagnosing novel viruses, without previous specific information, constituting a de novo diagnosis. Additional applications include, but are not limited to, the specific assembly of extrachromosomal elements such as plastid and mitochondrial genomes from metagenomic data. Profile HMM seeds can also be used to reconstruct specific protein coding genes for gene diversity studies, and to determine all possible gene variants present in a metagenomic sample. Such surveys could be useful to detect the emergence of drug-resistance variants in sensitive environments such as hospitals and animal production facilities, where antibiotics are regularly used. Finally, GenSeed-HMM can be used as an adjunct for gap closure on assembly finishing projects, by using multiple contig ends as anchored seeds.
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Affiliation(s)
- João M P Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - André L de Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Tatiana O M Sandberg
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | | | - Marcelo A F de Toledo
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Elisabeth M M de Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Liliane S Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São PauloSão Paulo, Brazil; Department of Computer Science, Institute of Mathematics and Statistics, University of São PauloSão Paulo, Brazil
| | - Alan M Durham
- Department of Computer Science, Institute of Mathematics and Statistics, University of São Paulo São Paulo, Brazil
| | - Dolores U Mehnert
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Paolo M de A Zanotto
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Alejandro Reyes
- Department of Biological Sciences, Universidad de los AndesBogotá, Colombia; Center for Genome Sciences and Systems Biology, Department of Pathology and Immunology, Washington University in Saint LouisMO, USA
| | - Arthur Gruber
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
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Ballaud F, Dufresne A, Francez AJ, Colombet J, Sime-Ngando T, Quaiser A. Dynamics of Viral Abundance and Diversity in a Sphagnum-Dominated Peatland: Temporal Fluctuations Prevail Over Habitat. Front Microbiol 2016; 6:1494. [PMID: 26779149 PMCID: PMC4701944 DOI: 10.3389/fmicb.2015.01494] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/11/2015] [Indexed: 11/23/2022] Open
Abstract
Viruses impact microbial activity and carbon cycling in various environments, but their diversity and ecological importance in Sphagnum-peatlands are unknown. Abundances of viral particles and prokaryotes were monitored bi-monthly at a fen and a bog at two different layers of the peat surface. Viral particle abundance ranged from 1.7 x 106 to 5.6 x 108 particles mL-1, and did not differ between fen and bog but showed seasonal fluctuations. These fluctuations were positively correlated with prokaryote abundance and dissolved organic carbon, and negatively correlated with water-table height and dissolved oxygen. Using shotgun metagenomics we observed a shift in viral diversity between winter/spring and summer/autumn, indicating a seasonal succession of viral communities, mainly driven by weather-related environmental changes. Based on the seasonal asynchrony between viral and microbial diversity, we hypothesize a seasonal shift in the active microbial communities associated with a shift from lysogenic to lytic lifestyles. Our results suggest that temporal variations of environmental conditions rather than current habitat differences control the dynamics of virus-host interactions in Sphagnum-dominated peatlands.
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Affiliation(s)
- Flore Ballaud
- UMR CNRS 6553 ECOBIO, Université de Rennes 1 Rennes, France
| | | | | | - Jonathan Colombet
- Université Clermont Auvergne, Université Blaise PascalClermont-Ferrand, France; CNRS, UMR 6023, Laboratoire Microorganismes: Génome et EnvironnementAubière, France
| | - Télesphore Sime-Ngando
- Université Clermont Auvergne, Université Blaise PascalClermont-Ferrand, France; CNRS, UMR 6023, Laboratoire Microorganismes: Génome et EnvironnementAubière, France
| | - Achim Quaiser
- UMR CNRS 6553 ECOBIO, Université de Rennes 1 Rennes, France
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