1
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Feltin C, Garneau JR, Morris CE, Bérard A, Torres-Barceló C. Novel phages of Pseudomonas syringae unveil numerous potential auxiliary metabolic genes. J Gen Virol 2024; 105:001990. [PMID: 38833289 PMCID: PMC11256456 DOI: 10.1099/jgv.0.001990] [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: 02/21/2024] [Accepted: 05/07/2024] [Indexed: 06/06/2024] Open
Abstract
Relatively few phages that infect plant pathogens have been isolated and investigated. The Pseudomonas syringae species complex is present in various environments, including plants. It can cause major crop diseases, such as bacterial canker on apricot trees. This study presents a collection of 25 unique phage genomes that infect P. syringae. These phages were isolated from apricot orchards with bacterial canker symptoms after enrichment with 21 strains of P. syringae. This collection comprises mostly virulent phages, with only three being temperate. They belong to 14 genera, 11 of which are newly discovered, and 18 new species, revealing great genetic diversity within this collection. Novel DNA packaging systems have been identified bioinformatically in one of the new phage species, but experimental confirmation is required to define the precise mechanism. Additionally, many phage genomes contain numerous potential auxiliary metabolic genes with diversified putative functions. At least three phages encode genes involved in bacterial tellurite resistance, a toxic metalloid. This suggests that viruses could play a role in bacterial stress tolerance. This research emphasizes the significance of continuing the search for new phages in the agricultural ecosystem to unravel novel ecological diversity and new gene functions. This work contributes to the foundation for future fundamental and applied research on phages infecting phytopathogenic bacteria.
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Affiliation(s)
- Chloé Feltin
- INRAE, Pathologie Végétale, F-84140, Montfavet, France
| | - Julian R. Garneau
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
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2
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Gios E, Mosley OE, Hoggard M, Handley KM. High niche specificity and host genetic diversity of groundwater viruses. THE ISME JOURNAL 2024; 18:wrae035. [PMID: 38452204 PMCID: PMC10980836 DOI: 10.1093/ismejo/wrae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/14/2024] [Accepted: 02/29/2024] [Indexed: 03/09/2024]
Abstract
Viruses are key members of microbial communities that exert control over host abundance and metabolism, thereby influencing ecosystem processes and biogeochemical cycles. Aquifers are known to host taxonomically diverse microbial life, yet little is known about viruses infecting groundwater microbial communities. Here, we analysed 16 metagenomes from a broad range of groundwater physicochemistries. We recovered 1571 viral genomes that clustered into 468 high-quality viral operational taxonomic units. At least 15% were observed to be transcriptionally active, although lysis was likely constrained by the resource-limited groundwater environment. Most were unclassified (95%), and the remaining 5% were Caudoviricetes. Comparisons with viruses inhabiting other aquifers revealed no shared species, indicating substantial unexplored viral diversity. In silico predictions linked 22.4% of the viruses to microbial host populations, including to ultra-small prokaryotes, such as Patescibacteria and Nanoarchaeota. Many predicted hosts were associated with the biogeochemical cycling of carbon, nitrogen, and sulfur. Metabolic predictions revealed the presence of 205 putative auxiliary metabolic genes, involved in diverse processes associated with the utilization of the host's intracellular resources for biosynthesis and transformation reactions, including those involved in nucleotide sugar, glycan, cofactor, and vitamin metabolism. Viruses, prokaryotes overall, and predicted prokaryotic hosts exhibited narrow spatial distributions, and relative abundance correlations with the same groundwater parameters (e.g. dissolved oxygen, nitrate, and iron), consistent with host control over viral distributions. Results provide insights into underexplored groundwater viruses, and indicate the large extent to which viruses may manipulate microbial communities and biogeochemistry in the terrestrial subsurface.
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Affiliation(s)
- Emilie Gios
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- NINA, Norwegian Institute for Nature Research, Trondheim 7034, Norway
| | - Olivia E Mosley
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- NatureMetrics Ltd, Surrey Research Park, Guildford GU2 7HJ, United Kingdom
| | - Michael Hoggard
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Kim M Handley
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
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3
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Duan C, Liu Y, Liu Y, Liu L, Cai M, Zhang R, Zeng Q, Koonin EV, Krupovic M, Li M. Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554615. [PMID: 37781628 PMCID: PMC10541130 DOI: 10.1101/2023.08.24.554615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Bathyarchaeia represent a class of archaea common and abundant in sedimentary ecosystems. The virome of Bathyarchaeia so far has not been characterized. Here we report 56 metagenome-assembled genomes of Bathyarchaeia viruses identified in metagenomes from different environments. Gene sharing network and phylogenomic analyses led to the proposal of four virus families, including viruses of the realms Duplodnaviria and Adnaviria, and archaea-specific spindle-shaped viruses. Genomic analyses uncovered diverse CRISPR elements in these viruses. Viruses of the proposed family 'Fuxiviridae' harbor an atypical type IV-B CRISPR-Cas system and a Cas4 protein that might interfere with host immunity. Viruses of the family 'Chiyouviridae' encode a Cas2-like endonuclease and two mini-CRISPR arrays, one with a repeat identical to that in the host CRISPR array, potentially allowing the virus to recruit the host CRISPR adaptation machinery to acquire spacers that could contribute to competition with other mobile genetic elements or to inhibition of host defenses. These findings present an outline of the Bathyarchaeia virome and offer a glimpse into their counter-defense mechanisms.
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Affiliation(s)
- Changhai Duan
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, 518060 Shenzhen, China
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
| | - Ying Liu
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 75015 Paris, France
| | - Lirui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
| | - Mingwei Cai
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
| | - Rui Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 75015 Paris, France
| | - Meng Li
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, 518060 Shenzhen, China
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
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4
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Luo L, Ma X, Guo R, Jiang T, Wang T, Shao H, He H, Wang H, Liang Y, McMinn A, Guo C, Wang M. Characterization and genomic analysis of a novel Synechococcus phage S-H9-2 belonging to Bristolvirus genus isolated from the Yellow Sea. Virus Res 2023; 328:199072. [PMID: 36781075 DOI: 10.1016/j.virusres.2023.199072] [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: 07/30/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023]
Abstract
Cyanophages are known to influence the population dynamics and community structure of cyanobacteria and thus play an important role in biogeochemical cycles in aquatic ecosystems. In this study, a novel Synechococcus phage S-H9-2 infecting Synechococcus sp. WH 8102 was isolated from the coastal water of the Yellow Sea. Synechococcus phage S-H9-2 contains a 187,320 bp genome of double-stranded DNA with a G + C content of 40.3%, 202 potential open reading frames (ORFs), and 15 tRNAs. Phylogenetic analysis and nucleotide-based intergenomic similarity suggest that Synechococcus phage S-H9-2 belongs to the Bristolvirus genus under the family Kyanoviridae. Homologs of the S-H9-2 open reading frame can be found in a variety of marine environments, as shown by the results of mapping the genome sequence of S-H9-2 to the Global Ocean Viromes 2.0 dataset. The presence of auxiliary metabolic genes (AMGs) related to photosynthesis, carbon metabolism, and phosphorus assimilation, as well as phylogenetic relationships based on complete genome sequences, reflect the mechanism of phage-host interaction and host-specific strategies for adaptation to environmental conditions. This study enriches the current genomic database of cyanophage and contributed to our understanding of the virus-host interactions and their adaption to the environment.
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Affiliation(s)
- Lin Luo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xiaohong Ma
- Department of Pediatrics, Qingdao Municipal Hospital, Qingdao266011, China
| | - Ruizhe Guo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Tong Jiang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Tiancong Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Hongbing Shao
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China
| | - Hui He
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China
| | - Hualong Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China
| | - Yantao Liang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China
| | - Andrew McMinn
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7001, SA
| | - Cui Guo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China.
| | - Min Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China; The Affiliated Hospital of Qingdao University, Qingdao 266000, China.
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5
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Cyanophages as an important factor in the early evolution of oxygenic photosynthesis. Sci Rep 2022; 12:20581. [PMID: 36446879 PMCID: PMC9709159 DOI: 10.1038/s41598-022-24795-1] [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: 08/19/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
Cyanophages are viruses that infect cyanobacteria. An interesting feature of many of them is the presence of psbA and psbD, genes that encode D1 and D2 proteins, respectively. The D1 and D2 are core proteins of the photosystem II (PSII) in cyanobacteria, algae and plants and influence the proper function of oxygenic photosynthesis (OP) in all oxyphototrophs on Earth. The frequent occurrence of psbA and psbD in cyanophages raises the question whether these genes coevolved with hosts during the early stages of cyanophage and cyanobacterial evolution, or whether they are direct descendants of genes adopted from the genomes of cyanobacterial hosts. The phylogeny of D1/D2 proteins encoded in the genomes of selected cyanophages and oxyphototrophs was reconstructed. In addition, common ancestral sequences of D1 and D2 proteins were predicted for cyanophages and oxyphototrophs. Based on this, the reconstruction of the 3D structures of D1 and D2 proteins was performed. In addition, the ratio of non-synonymous to synonymous (dN/dS) nucleotide substitutions in the coding sequences (CDSs) of psbA and psbD was determined. The results of the predicted spatial structures of the D1 and D2 proteins and purifying selection for the CDSs of psbA and psbD suggest that they belong to the ancient proteins, which may have formed the primordial PSII. It cannot be ruled out that they involved in water oxidation in cyanobacteria-like organisms at early stages of the evolution of life on Earth and coevolved with ancient cyanophages. The data are also discussed in the context of the origin of viruses.
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6
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Heyerhoff B, Engelen B, Bunse C. Auxiliary Metabolic Gene Functions in Pelagic and Benthic Viruses of the Baltic Sea. Front Microbiol 2022; 13:863620. [PMID: 35875520 PMCID: PMC9301287 DOI: 10.3389/fmicb.2022.863620] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
Marine microbial communities are facing various ecosystem fluctuations (e.g., temperature, organic matter concentration, salinity, or redox regimes) and thus have to be highly adaptive. This might be supported by the acquisition of auxiliary metabolic genes (AMGs) originating from virus infections. Marine bacteriophages frequently contain AMGs, which allow them to augment their host’s metabolism or enhance virus fitness. These genes encode proteins for the same metabolic functions as their highly similar host homologs. In the present study, we analyzed the diversity, distribution, and composition of marine viruses, focusing on AMGs to identify their putative ecologic role. We analyzed viruses and assemblies of 212 publicly available metagenomes obtained from sediment and water samples across the Baltic Sea. In general, the virus composition in both compartments differed compositionally. While the predominant viral lifestyle was found to be lytic, lysogeny was more prevalent in sediments than in the pelagic samples. The highest proportion of AMGs was identified in the genomes of Myoviridae. Overall, the most abundantly occurring AMGs are encoded for functions that protect viruses from degradation by their hosts, such as methylases. Additionally, some detected AMGs are known to be involved in photosynthesis, 7-cyano-7-deazaguanine synthesis, and cobalamin biosynthesis among other functions. Several AMGs that were identified in this study were previously detected in a large-scale analysis including metagenomes from various origins, i.e., different marine sites, wastewater, and the human gut. This supports the theory of globally conserved core AMGs that are spread over virus genomes, regardless of host or environment.
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7
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Abstract
Microbial communities have essential roles in ocean ecology and planetary health. Microbes participate in nutrient cycles, remove huge quantities of carbon dioxide from the air and support ocean food webs. The taxonomic and functional diversity of the global ocean microbiome has been revealed by technological advances in sampling, DNA sequencing and bioinformatics. A better understanding of the ocean microbiome could underpin strategies to address environmental and societal challenges, including achievement of multiple Sustainable Development Goals way beyond SDG 14 'life below water'. We propose a set of priorities for understanding and protecting the ocean microbiome, which include delineating interactions between microbiota, sustainably applying resources from oceanic microorganisms and creating policy- and funder-friendly ocean education resources, and discuss how to achieve these ambitious goals.
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8
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Shen A, Millard A. Phage Genome Annotation: Where to Begin and End. PHAGE (NEW ROCHELLE, N.Y.) 2021; 2:183-193. [PMID: 36159890 PMCID: PMC9041514 DOI: 10.1089/phage.2021.0015] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
With the renewed interest in phage research, coupled with the rising accessibility to affordable sequencing, ever increasing numbers of phage genomes are being sequenced. Therefore, there is an increased need to assemble and annotate phage genomes. There is a plethora of tools and platforms that allow phage genomes to be assembled and annotated. The choice of tools can often be bewildering for those new to phage genome assembly. Here we provide an overview of the assembly and annotation process from obtaining raw reads to genome submission, with worked examples, providing those new to genome assembly and annotation with a guided pathway to genome submission. We focus on the use of open access tools that can be incorporated into workflows to allow easy repetition of steps, highlighting multiple tools that can be used and common pitfalls that may occur.
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Affiliation(s)
- Anastasiya Shen
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, United Kingdom.,Address correspondence to: Andrew Millard, BSc, PhD, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
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9
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Jacobson TB, Callaghan MM, Amador-Noguez D. Hostile Takeover: How Viruses Reprogram Prokaryotic Metabolism. Annu Rev Microbiol 2021; 75:515-539. [PMID: 34348026 DOI: 10.1146/annurev-micro-060621-043448] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To reproduce, prokaryotic viruses must hijack the cellular machinery of their hosts and redirect it toward the production of viral particles. While takeover of the host replication and protein synthesis apparatus has long been considered an essential feature of infection, recent studies indicate that extensive reprogramming of host primary metabolism is a widespread phenomenon among prokaryotic viruses that is required to fulfill the biosynthetic needs of virion production. In this review we provide an overview of the most significant recent findings regarding virus-induced reprogramming of prokaryotic metabolism and suggest how quantitative systems biology approaches may be used to provide a holistic understanding of metabolic remodeling during lytic viral infection. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Tyler B Jacobson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Melanie M Callaghan
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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10
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Wang M, Gao C, Jiang T, You S, Jiang Y, Guo C, He H, Liu Y, Zhang X, Shao H, Liu H, Liang Y, Wang M, McMinn A. Genomic analysis of Synechococcus phage S-B43 and its adaption to the coastal environment. Virus Res 2020; 289:198155. [PMID: 32941942 DOI: 10.1016/j.virusres.2020.198155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 11/17/2022]
Abstract
Synechococcus dominate picocyanobacterial communities in coastal environments. However, only a few Synechococcus phages have been described from the coastal seas of the Northwest Pacific Ocean. Here a new Synechococcus phage, S-B43 was isolated from the Bohai Sea, a semi-closed coastal sea of the Northwest Pacific Ocean. S-B43 is a member of Myoviridae, containing 275 predicted open reading frames. Fourteen auxiliary metabolic genes (AMG) were identified from the genome of S-B43, including five photosynthetic associated genes and several AMGs related to its adaption to the high turbidity and eutrophic coastal environment with a low ratio of phosphorus to nitrogen (HNLP). The occurrences of 31 AMGs among 34 cyanophage genomes indicates that AMGs zwf, gnd, speD, petF and those coding for FECH and thioredoxin were more common in coastal areas than in the open ocean and AMGs pebS and ho1 were more prevalent in the open ocean. The occurrence of cyanophage AMGs in different environments might be a reflection of the environmental adaption of their hosts. This study contributes to our understanding of the interactions between cyanobacteria and cyanophages and their environmental adaption to the coastal environment.
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Affiliation(s)
- Meiwen Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Chen Gao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Tong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Siyuan You
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Cui Guo
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Hui He
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yundan Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xinran Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Hongbing Shao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Hongbin Liu
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yantao Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Andrew McMinn
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia
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11
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Fuchsman CA, Carlson MCG, Garcia Prieto D, Hays MD, Rocap G. Cyanophage host-derived genes reflect contrasting selective pressures with depth in the oxic and anoxic water column of the Eastern Tropical North Pacific. Environ Microbiol 2020; 23:2782-2800. [PMID: 32869473 DOI: 10.1111/1462-2920.15219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 08/14/2020] [Accepted: 08/27/2020] [Indexed: 01/19/2023]
Abstract
Cyanophages encode host-derived genes that may increase their fitness. We examined the relative abundance of 18 host-derived cyanophages genes in metagenomes and viromes along depth profiles from the Eastern Tropical North Pacific Oxygen Deficient Zone (ETNP ODZ) where Prochlorococcus dominates a secondary chlorophyll maximum within the ODZ. Cyanophages at the oxic primary chlorophyll maximum encoded genes related to light and phosphate stress (psbA, psbD and pstS in T4-like and psbA in T7-like), but the proportion of cyanophage with these genes decreased with depth. The proportion of cyanophage with purine biosynthesis genes increased with depth in T4-like, but not T7-like cyanophages. No additional host-derived genes were found in deep T7-like cyanophages, suggesting that T4-like and T7-like cyanophages have different host-derived gene acquisition strategies, possibly linked to their different genome packaging mechanisms. In contrast to the ETNP, in the oxic North Atlantic T4-like cyanophages encoded psbA and pstS throughout the euphotic zone. Differences in pstS between the ETNP and the North Atlantic stations were consistent with differences in phosphate concentrations in those regimes. We suggest that the low proportion of cyanophage with psbA within the ODZ reflects the stably stratified low-light conditions occupied by their hosts, a Prochlorococcus ecotype endemic to ODZs.
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Affiliation(s)
- Clara A Fuchsman
- School of Oceanography, University of Washington, Seattle, WA, USA.,Horn Point Laboratory, University of Maryland Center of Environmental Science, Cambridge, MD, 21613, USA
| | - Michael C G Carlson
- School of Oceanography, University of Washington, Seattle, WA, USA.,Technion-Israel Institute of Technology, Haifa, Israel
| | - David Garcia Prieto
- School of Oceanography, University of Washington, Seattle, WA, USA.,Horn Point Laboratory, University of Maryland Center of Environmental Science, Cambridge, MD, 21613, USA
| | - Matthew D Hays
- Horn Point Laboratory, University of Maryland Center of Environmental Science, Cambridge, MD, 21613, USA
| | - Gabrielle Rocap
- School of Oceanography, University of Washington, Seattle, WA, USA
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12
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Jiang T, Guo C, Wang M, Wang M, Zhang X, Liu Y, Liang Y, Jiang Y, He H, Shao H, McMinn A. Genome Analysis of Two Novel Synechococcus Phages That Lack Common Auxiliary Metabolic Genes: Possible Reasons and Ecological Insights by Comparative Analysis of Cyanomyoviruses. Viruses 2020; 12:v12080800. [PMID: 32722486 PMCID: PMC7472177 DOI: 10.3390/v12080800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 02/01/2023] Open
Abstract
The abundant and widespread unicellular cyanobacteria Synechococcus plays an important role in contributing to global phytoplankton primary production. In the present study, two novel cyanomyoviruses, S-N03 and S-H34 that infected Synechococcus MW02, were isolated from the coastal waters of the Yellow Sea. S-N03 contained a 167,069-bp genome comprising double-stranded DNA with a G + C content of 50.1%, 247 potential open reading frames and 1 tRNA; S-H34 contained a 167,040-bp genome with a G + C content of 50.1%, 246 potential open reading frames and 5 tRNAs. These two cyanophages contain fewer auxiliary metabolic genes (AMGs) than other previously isolated cyanophages. S-H34 in particular, is currently the only known cyanomyovirus that does not contain any AMGs related to photosynthesis. The absence of such common AMGs in S-N03 and S-H34, their distinct evolutionary history and ecological features imply that the energy for phage production might be obtained from other sources rather than being strictly dependent on the maintenance of photochemical ATP under high light. Phylogenetic analysis showed that the two isolated cyanophages clustered together and had a close relationship with two other cyanophages of low AMG content. Comparative genomic analysis, habitats and hosts across 81 representative cyanomyovirus showed that cyanomyovirus with less AMGs content all belonged to Synechococcus phages isolated from eutrophic waters. The relatively small genome size and high G + C content may also relate to the lower AMG content, as suggested by the significant correlation between the number of AMGs and G + C%. Therefore, the lower content of AMG in S-N03 and S-H34 might be a result of viral evolution that was likely shaped by habitat, host, and their genomic context. The genomic content of AMGs in cyanophages may have adaptive significance and provide clues to their evolution.
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Affiliation(s)
- Tong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
| | - Cui Guo
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- Correspondence:
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
| | - Meiwen Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
| | - Xinran Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
| | - Yundan Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
| | - Yantao Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
| | - Yong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
| | - Hui He
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
| | - Hongbing Shao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
| | - Andrew McMinn
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia
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Rihtman B, Bowman‐Grahl S, Millard A, Corrigan RM, Clokie MRJ, Scanlan DJ. Cyanophage MazG is a pyrophosphohydrolase but unable to hydrolyse magic spot nucleotides. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:448-455. [PMID: 30809954 PMCID: PMC6850273 DOI: 10.1111/1758-2229.12741] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/26/2019] [Accepted: 02/26/2019] [Indexed: 05/28/2023]
Abstract
Bacteriophage possess a variety of auxiliary metabolic genes of bacterial origin. These proteins enable them to maximize infection efficiency, subverting bacterial metabolic processes for the purpose of viral genome replication and synthesis of the next generation of virion progeny. Here, we examined the enzymatic activity of a cyanophage MazG protein - a putative pyrophosphohydrolase previously implicated in regulation of the stringent response via reducing levels of the central alarmone molecule (p)ppGpp. We demonstrate, however, that the purified viral MazG shows no binding or hydrolysis activity against (p)ppGpp. Instead, dGTP and dCTP appear to be the preferred substrates of this protein, consistent with a role preferentially hydrolysing deoxyribonucleotides from the high GC content host Synechococcus genome. This showcases a new example of the fine-tuned nature of viral metabolic processes.
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Affiliation(s)
| | | | - Andrew Millard
- Department of Infection, Immunity and InflammationUniversity of LeicesterLeicesterUK
| | - Rebecca M. Corrigan
- Department of Molecular Biology & BiotechnologyUniversity of SheffieldSheffieldUK
| | - Martha R. J. Clokie
- Department of Infection, Immunity and InflammationUniversity of LeicesterLeicesterUK
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Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes. Nat Commun 2019; 10:1169. [PMID: 30862830 PMCID: PMC6414667 DOI: 10.1038/s41467-019-09106-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/21/2019] [Indexed: 12/11/2022] Open
Abstract
Viruses provide top-down control on microbial communities, yet their direct study in natural environments was hindered by culture limitations. The advance of bioinformatics enables cultivation-independent study of viruses. Many studies assemble new viral genomes and study viral diversity using marker genes from free viruses. Here we use cellular metatranscriptomics to study active community-wide viral infections. Recruitment to viral contigs allows tracking infection dynamics over time and space. Our assemblies represent viral populations, but appear biased towards low diversity viral taxa. Tracking relatives of published T4-like cyanophages and pelagiphages reveals high genomic continuity. We determine potential hosts by matching dynamics of infection with abundance of particular microbial taxa. Finally, we quantify the relative contribution of cyanobacteria and viruses to photosystem-II psbA (reaction center) expression in our study sites. We show sometimes >50% of all cyanobacterial+viral psbA expression is of viral origin, highlighting the contribution of viruses to photosynthesis and oxygen production. Here, Sieradzki et al. use metatranscriptomics to study active community-wide viral infections at three coastal California sites throughout a year, identify potential viral hosts, and show that viruses can contribute a substantial amount to photosystem-II psbA expression.
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15
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Chénard C, Kolundžija S, Lauro FM. Complete genome sequence of the cyanophage S-PRM1 isolated from Singapore coastal waters. Mar Genomics 2019. [DOI: 10.1016/j.margen.2018.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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16
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Fang X, Jiang Y, Li K, Zeng Q. F-CphI represents a new homing endonuclease family using the Endo VII catalytic motif. Mob DNA 2018; 9:27. [PMID: 30100927 PMCID: PMC6083498 DOI: 10.1186/s13100-018-0132-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/31/2018] [Indexed: 11/16/2022] Open
Abstract
Background There are six known families of homing endonucleases, LAGLIDADG, GIY-YIG, HNH, His-Cys box, PD-(D/E)-XK, and EDxHD, which are characterized by their conserved residues. Previously, we discovered a novel homing endonuclease F-CphI encoded by ORF177 of cyanophage S-PM2. F-CphI does not resemble any characterized homing endonucleases. Instead, the C-terminus of F-CphI aligns well with the N-terminal catalytic domain of a Holliday junction DNA resolvase, phage T4 endonuclease VII (Endo VII). Results A PSI-BLAST search resulted in a total of 313 Endo VII motif–containing sequences in sequenced genomes. Multiple sequence alignment showed that the catalytically important residues of T4 Endo VII were all well conserved in these proteins. Our site-directed mutagenesis studies further confirmed that the catalytically important residues of T4 Endo VII were also essential for F-CphI activity, and thus F-CphI might use a similar protein fold as Endo VII for DNA cleavage. A phylogenetic tree of the Endo VII motif–containing sequences showed that putative resolvases grouped into one clade while putative homing endonucleases and restriction endonucleases grouped into another clade. Conclusions Based on the unique conserved residues, we proposed that F-CphI represents a new homing endonuclease family, which was named the DHHRN family. Our phylogenetic analysis could be used to predict the functions of many previously unknown proteins. Electronic supplementary material The online version of this article (10.1186/s13100-018-0132-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoting Fang
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - YongLiang Jiang
- 2School of Life Sciences, University of Science and Technology of China, Hefei, 230027 Anhui China
| | - Kim Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.,HKUST Shenzhen Research Institute, Shenzhen, China
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17
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Puxty RJ, Evans DJ, Millard AD, Scanlan DJ. Energy limitation of cyanophage development: implications for marine carbon cycling. ISME JOURNAL 2018; 12:1273-1286. [PMID: 29379179 PMCID: PMC5931967 DOI: 10.1038/s41396-017-0043-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/25/2017] [Accepted: 12/09/2017] [Indexed: 11/16/2022]
Abstract
Marine cyanobacteria are responsible for ~25% of the fixed carbon that enters the ocean biosphere. It is thought that abundant co-occurring viruses play an important role in regulating population dynamics of cyanobacteria and thus the cycling of carbon in the oceans. Despite this, little is known about how viral infections ‘play-out’ in the environment, particularly whether infections are resource or energy limited. Photoautotrophic organisms represent an ideal model to test this since available energy is modulated by the incoming light intensity through photophosphorylation. Therefore, we exploited phototrophy of the environmentally relevant marine cyanobacterium Synechococcus and monitored growth of a cyanobacterial virus (cyanophage). We found that light intensity has a marked effect on cyanophage infection dynamics, but that this is not manifest by a change in DNA synthesis. Instead, cyanophage development appears energy limited for the synthesis of proteins required during late infection. We posit that acquisition of auxiliary metabolic genes (AMGs) involved in light-dependent photosynthetic reactions acts to overcome this limitation. We show that cyanophages actively modulate expression of these AMGs in response to light intensity and provide evidence that such regulation may be facilitated by a novel mechanism involving light-dependent splicing of a group I intron in a photosynthetic AMG. Altogether, our data offers a mechanistic link between diurnal changes in irradiance and observed community level responses in metabolism, i.e., through an irradiance-dependent, viral-induced release of dissolved organic matter (DOM).
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Affiliation(s)
- Richard J Puxty
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, UK
| | - David J Evans
- School of Biology and BSRC, Biomolecular Sciences Building, North Haugh, St Andrews, KY16 9AJ, UK
| | - Andrew D Millard
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, LE1 9HNL, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, UK.
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18
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Hurwitz BL, Ponsero A, Thornton J, U'Ren JM. Phage hunters: Computational strategies for finding phages in large-scale 'omics datasets. Virus Res 2017; 244:110-115. [PMID: 29100906 DOI: 10.1016/j.virusres.2017.10.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 10/27/2017] [Accepted: 10/30/2017] [Indexed: 01/26/2023]
Abstract
A plethora of tools exist for identifying phage sequences in bacterial genomes, single cell amplified genomes, and host-associated and environmental metagenomes. Yet because the genetics of phages and their hosts are closely intertwined, distinguishing viral from bacterial signal remains an ongoing challenge. Further the size, quantity and fragmentary nature of modern 'omics datasets ushers in a new set of computational challenges. Here, we detail the promises and pitfalls of using currently available gene-centric or k-mer based tools for identifying prophage sequences in genomes and prophage and viral contigs in metagenomes. Each of these methods offers a unique piece of the puzzle to elucidating the intriguing signatures of phage-host coevolution.
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Affiliation(s)
- Bonnie L Hurwitz
- Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, AZ 85719, United States; BIO5 Research Institute, University of Arizona, Tucson, AZ 85719, United States.
| | - Alise Ponsero
- Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, AZ 85719, United States
| | - James Thornton
- Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, AZ 85719, United States
| | - Jana M U'Ren
- Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, AZ 85719, United States; BIO5 Research Institute, University of Arizona, Tucson, AZ 85719, United States
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19
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Cyanophage-encoded lipid desaturases: oceanic distribution, diversity and function. ISME JOURNAL 2017; 12:343-355. [PMID: 29028002 PMCID: PMC5776448 DOI: 10.1038/ismej.2017.159] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 08/17/2017] [Accepted: 08/22/2017] [Indexed: 11/08/2022]
Abstract
Cyanobacteria are among the most abundant photosynthetic organisms in the oceans; viruses infecting cyanobacteria (cyanophages) can alter cyanobacterial populations, and therefore affect the local food web and global biochemical cycles. These phages carry auxiliary metabolic genes (AMGs), which rewire various metabolic pathways in the infected host cell, resulting in increased phage fitness. Coping with stress resulting from photodamage appears to be a central necessity of cyanophages, yet the overall mechanism is poorly understood. Here we report a novel, widespread cyanophage AMG, encoding a fatty acid desaturase (FAD), found in two genotypes with distinct geographical distribution. FADs are capable of modulating the fluidity of the host’s membrane, a fundamental stress response in living cells. We show that both viral FAD (vFAD) families are Δ9 lipid desaturases, catalyzing the desaturation at carbon 9 in C16 fatty acid chains. In addition, we present a comprehensive fatty acid profiling for marine cyanobacteria, which suggests a unique desaturation pathway of medium- to long-chain fatty acids no longer than C16, in accordance with the vFAD activity. Our findings suggest that cyanophages are capable of fiddling with the infected host’s membranes, possibly leading to increased photoprotection and potentially enhancing viral-encoded photosynthetic proteins, resulting in a new viral metabolic network.
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20
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21
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Fridman S, Flores-Uribe J, Larom S, Alalouf O, Liran O, Yacoby I, Salama F, Bailleul B, Rappaport F, Ziv T, Sharon I, Cornejo-Castillo FM, Philosof A, Dupont CL, Sánchez P, Acinas SG, Rohwer FL, Lindell D, Béjà O. A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells. Nat Microbiol 2017; 2:1350-1357. [PMID: 28785078 DOI: 10.1038/s41564-017-0002-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 06/28/2017] [Indexed: 01/27/2023]
Abstract
Cyanobacteria are important contributors to primary production in the open oceans. Over the past decade, various photosynthesis-related genes have been found in viruses that infect cyanobacteria (cyanophages). Although photosystem II (PSII) genes are common in both cultured cyanophages and environmental samples 1-4 , viral photosystem I (vPSI) genes have so far only been detected in environmental samples 5,6 . Here, we have used a targeted strategy to isolate a cyanophage from the tropical Pacific Ocean that carries a PSI gene cassette with seven distinct PSI genes (psaJF, C, A, B, K, E, D) as well as two PSII genes (psbA, D). This cyanophage, P-TIM68, belongs to the T4-like myoviruses, has a prolate capsid, a long contractile tail and infects Prochlorococcus sp. strain MIT9515. Phage photosynthesis genes from both photosystems are expressed during infection, and the resultant proteins are incorporated into membranes of the infected host. Moreover, photosynthetic capacity in the cell is maintained throughout the infection cycle with enhancement of cyclic electron flow around PSI. Analysis of metagenomic data from the Tara Oceans expedition 7 shows that phages carrying PSI gene cassettes are abundant in the tropical Pacific Ocean, composing up to 28% of T4-like cyanomyophages. They are also present in the tropical Indian and Atlantic Oceans. P-TIM68 populations, specifically, compose on average 22% of the PSI-gene-cassette carrying phages. Our results suggest that cyanophages carrying PSI and PSII genes are likely to maintain and even manipulate photosynthesis during infection of their Prochlorococcus hosts in the tropical oceans.
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Affiliation(s)
- Svetlana Fridman
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - José Flores-Uribe
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Shirley Larom
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Onit Alalouf
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Oded Liran
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Iftach Yacoby
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Faris Salama
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Benjamin Bailleul
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS and Université Pierre et Marie Curie, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Fabrice Rappaport
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS and Université Pierre et Marie Curie, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Tamar Ziv
- Smoler Proteomics Center, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Itai Sharon
- Migal Galilee Research Institute, Kiryat Shmona, 11016, Israel.,Tel Hai College, Upper Galilee, 12210, Israel
| | - Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, 08003, Barcelona, Spain
| | - Alon Philosof
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Christopher L Dupont
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, 08003, Barcelona, Spain
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, 08003, Barcelona, Spain
| | - Forest L Rohwer
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Debbie Lindell
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel.
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel.
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22
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Ren J, Ahlgren NA, Lu YY, Fuhrman JA, Sun F. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. MICROBIOME 2017. [PMID: 28683828 DOI: 10.1186/s40168-017-0283-285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
BACKGROUND Identifying viral sequences in mixed metagenomes containing both viral and host contigs is a critical first step in analyzing the viral component of samples. Current tools for distinguishing prokaryotic virus and host contigs primarily use gene-based similarity approaches. Such approaches can significantly limit results especially for short contigs that have few predicted proteins or lack proteins with similarity to previously known viruses. METHODS We have developed VirFinder, the first k-mer frequency based, machine learning method for virus contig identification that entirely avoids gene-based similarity searches. VirFinder instead identifies viral sequences based on our empirical observation that viruses and hosts have discernibly different k-mer signatures. VirFinder's performance in correctly identifying viral sequences was tested by training its machine learning model on sequences from host and viral genomes sequenced before 1 January 2014 and evaluating on sequences obtained after 1 January 2014. RESULTS VirFinder had significantly better rates of identifying true viral contigs (true positive rates (TPRs)) than VirSorter, the current state-of-the-art gene-based virus classification tool, when evaluated with either contigs subsampled from complete genomes or assembled from a simulated human gut metagenome. For example, for contigs subsampled from complete genomes, VirFinder had 78-, 2.4-, and 1.8-fold higher TPRs than VirSorter for 1, 3, and 5 kb contigs, respectively, at the same false positive rates as VirSorter (0, 0.003, and 0.006, respectively), thus VirFinder works considerably better for small contigs than VirSorter. VirFinder furthermore identified several recently sequenced virus genomes (after 1 January 2014) that VirSorter did not and that have no nucleotide similarity to previously sequenced viruses, demonstrating VirFinder's potential advantage in identifying novel viral sequences. Application of VirFinder to a set of human gut metagenomes from healthy and liver cirrhosis patients reveals higher viral diversity in healthy individuals than cirrhosis patients. We also identified contig bins containing crAssphage-like contigs with higher abundance in healthy patients and a putative Veillonella genus prophage associated with cirrhosis patients. CONCLUSIONS This innovative k-mer based tool complements gene-based approaches and will significantly improve prokaryotic viral sequence identification, especially for metagenomic-based studies of viral ecology.
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Affiliation(s)
- Jie Ren
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Nathan A Ahlgren
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Pkwy, Los Angeles, CA, 90089, USA.
- Present address: Biology Department, Clark University, 950 Main St, Worcester, MA, 01610, USA.
| | - Yang Young Lu
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Pkwy, Los Angeles, CA, 90089, USA
| | - Fengzhu Sun
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA.
- Center for Computational Systems Biology, Fudan University, 200433, Shanghai, China.
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23
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Ren J, Ahlgren NA, Lu YY, Fuhrman JA, Sun F. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. MICROBIOME 2017; 5:69. [PMID: 28683828 PMCID: PMC5501583 DOI: 10.1186/s40168-017-0283-5] [Citation(s) in RCA: 325] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/05/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND Identifying viral sequences in mixed metagenomes containing both viral and host contigs is a critical first step in analyzing the viral component of samples. Current tools for distinguishing prokaryotic virus and host contigs primarily use gene-based similarity approaches. Such approaches can significantly limit results especially for short contigs that have few predicted proteins or lack proteins with similarity to previously known viruses. METHODS We have developed VirFinder, the first k-mer frequency based, machine learning method for virus contig identification that entirely avoids gene-based similarity searches. VirFinder instead identifies viral sequences based on our empirical observation that viruses and hosts have discernibly different k-mer signatures. VirFinder's performance in correctly identifying viral sequences was tested by training its machine learning model on sequences from host and viral genomes sequenced before 1 January 2014 and evaluating on sequences obtained after 1 January 2014. RESULTS VirFinder had significantly better rates of identifying true viral contigs (true positive rates (TPRs)) than VirSorter, the current state-of-the-art gene-based virus classification tool, when evaluated with either contigs subsampled from complete genomes or assembled from a simulated human gut metagenome. For example, for contigs subsampled from complete genomes, VirFinder had 78-, 2.4-, and 1.8-fold higher TPRs than VirSorter for 1, 3, and 5 kb contigs, respectively, at the same false positive rates as VirSorter (0, 0.003, and 0.006, respectively), thus VirFinder works considerably better for small contigs than VirSorter. VirFinder furthermore identified several recently sequenced virus genomes (after 1 January 2014) that VirSorter did not and that have no nucleotide similarity to previously sequenced viruses, demonstrating VirFinder's potential advantage in identifying novel viral sequences. Application of VirFinder to a set of human gut metagenomes from healthy and liver cirrhosis patients reveals higher viral diversity in healthy individuals than cirrhosis patients. We also identified contig bins containing crAssphage-like contigs with higher abundance in healthy patients and a putative Veillonella genus prophage associated with cirrhosis patients. CONCLUSIONS This innovative k-mer based tool complements gene-based approaches and will significantly improve prokaryotic viral sequence identification, especially for metagenomic-based studies of viral ecology.
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Affiliation(s)
- Jie Ren
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Nathan A Ahlgren
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Pkwy, Los Angeles, CA, 90089, USA.
- Present address: Biology Department, Clark University, 950 Main St, Worcester, MA, 01610, USA.
| | - Yang Young Lu
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Pkwy, Los Angeles, CA, 90089, USA
| | - Fengzhu Sun
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA.
- Center for Computational Systems Biology, Fudan University, 200433, Shanghai, China.
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Vik DR, Roux S, Brum JR, Bolduc B, Emerson JB, Padilla CC, Stewart FJ, Sullivan MB. Putative archaeal viruses from the mesopelagic ocean. PeerJ 2017; 5:e3428. [PMID: 28630803 PMCID: PMC5474096 DOI: 10.7717/peerj.3428] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 05/16/2017] [Indexed: 01/21/2023] Open
Abstract
Oceanic viruses that infect bacteria, or phages, are known to modulate host diversity, metabolisms, and biogeochemical cycling, while the viruses that infect marine Archaea remain understudied despite the critical ecosystem roles played by their hosts. Here we introduce "MArVD", for Metagenomic Archaeal Virus Detector, an annotation tool designed to identify putative archaeal virus contigs in metagenomic datasets. MArVD is made publicly available through the online iVirus analytical platform. Benchmarking analysis of MArVD showed it to be >99% accurate and 100% sensitive in identifying the 127 known archaeal viruses among the 12,499 viruses in the VirSorter curated dataset. Application of MArVD to 10 viral metagenomes from two depth profiles in the Eastern Tropical North Pacific (ETNP) oxygen minimum zone revealed 43 new putative archaeal virus genomes and large genome fragments ranging in size from 10 to 31 kb. Network-based classifications, which were consistent with marker gene phylogenies where available, suggested that these putative archaeal virus contigs represented six novel candidate genera. Ecological analyses, via fragment recruitment and ordination, revealed that the diversity and relative abundances of these putative archaeal viruses were correlated with oxygen concentration and temperature along two OMZ-spanning depth profiles, presumably due to structuring of the host Archaea community. Peak viral diversity and abundances were found in surface waters, where Thermoplasmata 16S rRNA genes are prevalent, suggesting these archaea as hosts in the surface habitats. Together these findings provide a baseline for identifying archaeal viruses in sequence datasets, and an initial picture of the ecology of such viruses in non-extreme environments.
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Affiliation(s)
- Dean R. Vik
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Simon Roux
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Jennifer R. Brum
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Ben Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Joanne B. Emerson
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Cory C. Padilla
- Department of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Frank J. Stewart
- Department of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, United States of America
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25
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Gao EB, Huang Y, Ning D. Metabolic Genes within Cyanophage Genomes: Implications for Diversity and Evolution. Genes (Basel) 2016; 7:genes7100080. [PMID: 27690109 PMCID: PMC5083919 DOI: 10.3390/genes7100080] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/30/2016] [Accepted: 09/15/2016] [Indexed: 11/16/2022] Open
Abstract
Cyanophages, a group of viruses specifically infecting cyanobacteria, are genetically diverse and extensively abundant in water environments. As a result of selective pressure, cyanophages often acquire a range of metabolic genes from host genomes. The host-derived genes make a significant contribution to the ecological success of cyanophages. In this review, we summarize the host-derived metabolic genes, as well as their origin and roles in cyanophage evolution and important host metabolic pathways, such as the light-dependent reactions of photosynthesis, the pentose phosphate pathway, nutrient acquisition and nucleotide biosynthesis. We also discuss the suitability of the host-derived metabolic genes as potential diagnostic markers for the detection of genetic diversity of cyanophages in natural environments.
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Affiliation(s)
- E-Bin Gao
- School of The Environment and Safety Engineering, Jiangsu University, No. 301, Xuefu Road, Zhenjiang 212013, Jiangsu Province, China.
| | - Youhua Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 164, Xingangxi Road, Haizhu District, Guangzhou 5103401, Guangdong Province, China.
| | - Degang Ning
- ACS Key Laboratory of Algae Biology, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7, Donghu South Road, Wuchang District, Wuhan 430072, Hubei Province, China.
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26
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Bourrelle-Langlois M, Morrow G, Finet S, Tanguay RM. In Vitro Structural and Functional Characterization of the Small Heat Shock Proteins (sHSP) of the Cyanophage S-ShM2 and Its Host, Synechococcus sp. WH7803. PLoS One 2016; 11:e0162233. [PMID: 27643500 PMCID: PMC5028025 DOI: 10.1371/journal.pone.0162233] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/21/2016] [Indexed: 11/22/2022] Open
Abstract
We previously reported the in silico characterization of Synechococcus sp. phage 18 kDa small heat shock protein (HspSP-ShM2). This small heat shock protein (sHSP) contains a highly conserved core alpha crystalline domain of 92 amino acids and relatively short N- and C-terminal arms, the later containing the classical C-terminal anchoring module motif (L-X-I/L/V). Here we establish the oligomeric profile of HspSP-ShM2 and its structural dynamics under in vitro experimental conditions using size exclusion chromatography (SEC/FPLC), gradient native gels electrophoresis and dynamic light scattering (DLS). Under native conditions, HspSP-ShM2 displays the ability to form large oligomers and shows a polydisperse profile. At higher temperatures, it shows extensive structural dynamics and undergoes conformational changes through an increased of subunit rearrangement and formation of sub-oligomeric species. We also demonstrate its capacity to prevent the aggregation of citrate synthase, malate dehydrogenase and luciferase under heat shock conditions through the formation of stable and soluble hetero-oligomeric complexes (sHSP:substrate). In contrast, the host cyanobacteria Synechococcus sp. WH7803 15 kDa sHSP (HspS-WH7803) aggregates when in the same conditions as HspSP-ShM2. However, its solubility can be maintained in the presence of non-ionic detergent Triton™X-100 and forms an oligomeric structure estimated to be between dimer and tetramer but exhibits no apparent inducible structural dynamics neither chaperon-like activity in all the assays and molar ratios tested. SEC/FPLC and thermal aggregation prevention assays results indicate no formation of hetero-oligomeric complex or functional interactions between both sHSPs. Taken together these in vitro results portray the phage HspSP-ShM2 as a classical sHSP and suggest that it may be functional at the in vivo level while behaving differently than its host amphitropic sHSP.
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Affiliation(s)
- Maxime Bourrelle-Langlois
- Laboratoire de Biologie Cellulaire et Moléculaire, Institut de Biologie Intégrative et des Systémes (IBIS) and PROTEO, Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de Médecine, Québec, Canada
| | - Geneviève Morrow
- Laboratoire de Biologie Cellulaire et Moléculaire, Institut de Biologie Intégrative et des Systémes (IBIS) and PROTEO, Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de Médecine, Québec, Canada
| | - Stéphanie Finet
- IMPMC UMR7590, CNRS/Sorbonne-Universités, UPMC/IRD/MNHN Paris 6, Paris, France
| | - Robert M. Tanguay
- Laboratoire de Biologie Cellulaire et Moléculaire, Institut de Biologie Intégrative et des Systémes (IBIS) and PROTEO, Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de Médecine, Québec, Canada
- * E-mail:
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27
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Dann LM, Rosales S, McKerral J, Paterson JS, Smith RJ, Jeffries TC, Oliver RL, Mitchell JG. Marine and giant viruses as indicators of a marine microbial community in a riverine system. Microbiologyopen 2016; 5:1071-1084. [PMID: 27506856 PMCID: PMC5221468 DOI: 10.1002/mbo3.392] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/13/2016] [Accepted: 06/17/2016] [Indexed: 12/30/2022] Open
Abstract
Viral communities are important for ecosystem function as they are involved in critical biogeochemical cycles and controlling host abundance. This study investigates riverine viral communities around a small rural town that influences local water inputs. Myoviridae, Siphoviridae, Phycodnaviridae, Mimiviridae, Herpesviridae, and Podoviridae were the most abundant families. Viral species upstream and downstream of the town were similar, with Synechoccocus phage, salinus, Prochlorococcus phage, Mimivirus A, and Human herpes 6A virus most abundant, contributing to 4.9-38.2% of average abundance within the metagenomic profiles, with Synechococcus and Prochlorococcus present in metagenomes as the expected hosts for the phage. Overall, the majority of abundant viral species were or were most similar to those of marine origin. At over 60 km to the river mouth, the presence of marine communities provides some support for the Baas-Becking hypothesis "everything is everywhere, but, the environment selects." We conclude marine microbial species may occur more frequently in freshwater systems than previously assumed, and hence may play important roles in some freshwater ecosystems within tens to a hundred kilometers from the sea.
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Affiliation(s)
- Lisa M Dann
- School of Biological Sciences at Flinders University, Adelaide, South Australia, Australia
| | - Stephanie Rosales
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Jody McKerral
- School of Computer Science, Engineering and Mathematics, Flinders University, Adelaide, Australia
| | - James S Paterson
- School of Biological Sciences at Flinders University, Adelaide, South Australia, Australia
| | - Renee J Smith
- School of Biological Sciences at Flinders University, Adelaide, South Australia, Australia
| | - Thomas C Jeffries
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Rod L Oliver
- Land and Water Research Division at the Commonwealth Scientific and Industrial Research Organisation (CSIRO), Adelaide, South Australia, Australia
| | - James G Mitchell
- School of Biological Sciences at Flinders University, Adelaide, South Australia, Australia
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Perez Sepulveda B, Redgwell T, Rihtman B, Pitt F, Scanlan DJ, Millard A. Marine phage genomics: the tip of the iceberg. FEMS Microbiol Lett 2016; 363:fnw158. [PMID: 27338950 PMCID: PMC4928673 DOI: 10.1093/femsle/fnw158] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2016] [Indexed: 01/07/2023] Open
Abstract
Marine viruses are the most abundant biological entity in the oceans, the majority of which infect bacteria and are known as bacteriophages. Yet, the bulk of bacteriophages form part of the vast uncultured dark matter of the microbial biosphere. In spite of the paucity of cultured marine bacteriophages, it is known that marine bacteriophages have major impacts on microbial population structure and the biogeochemical cycling of key elements. Despite the ecological relevance of marine bacteriophages, there are relatively few isolates with complete genome sequences. This minireview focuses on knowledge gathered from these genomes put in the context of viral metagenomic data and highlights key advances in the field, particularly focusing on genome structure and auxiliary metabolic genes. Only a tiny fraction of marine phages have been discovered, yet are known to have important roles in the ocean.
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Affiliation(s)
| | - Tamsin Redgwell
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Branko Rihtman
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Frances Pitt
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Andrew Millard
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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29
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Ou T, Gao XC, Li SH, Zhang QY. Genome analysis and gene nblA identification of Microcystis aeruginosa myovirus (MaMV-DC) reveal the evidence for horizontal gene transfer events between cyanomyovirus and host. J Gen Virol 2016; 96:3681-3697. [PMID: 26399243 DOI: 10.1099/jgv.0.000290] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genome sequence, genetic characterization and nblA gene function of Microcystis aeruginosa myovirus isolated from Lake Dianchi in China (MaMV-DC) have been analysed. The genome DNA is 169 223 bp long, with 170 predicted protein-coding genes (001L–170L) and a tRNA gene. About one-sixth of these genes have homologues in the host cyanobacteria M. aeruginosa. The genome carries a gene homologous to host nblA, which encodes a protein involved in the degradation of cyanobacterial phycobilisome. Its expression during MaMV-DC infection was confirmed by reverse transcriptase PCR and Western blot detection and abundant expression was companied by the significant decline of phycocyanin content and massive release of progeny MaMV-DC. In addition, expressing MaMV-DC nblA reduced the phycocyanin peak and the phycocyanin to chlorophyll ratio in model cyanobacteria. These results confirm that horizontal gene transfer events have occurred between cyanobacterial host and cyanomyovirus and suggest that MaMV-DC carrying host-derived genes (such as 005L, that codes for NblA) is responsible for more efficient expression of cyanophage genes and release of progeny cyanophage. This study provides novel insight into the horizontal gene transfer in cyanophage and the interactions between cyanophage and their host.
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Affiliation(s)
- Tong Ou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Xiao-Chan Gao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - San-Hua Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Qi-Ya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
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30
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Hurwitz BL, U’Ren JM. Viral metabolic reprogramming in marine ecosystems. Curr Opin Microbiol 2016; 31:161-168. [DOI: 10.1016/j.mib.2016.04.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 12/19/2022]
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31
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Rihtman B, Meaden S, Clokie MRJ, Koskella B, Millard AD. Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes. PeerJ 2016; 4:e2055. [PMID: 27280068 PMCID: PMC4893331 DOI: 10.7717/peerj.2055] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 04/29/2016] [Indexed: 11/20/2022] Open
Abstract
Bacteriophages are the most abundant biological entities on the planet, playing crucial roles in the shaping of bacterial populations. Phages have smaller genomes than their bacterial hosts, yet there are currently fewer fully sequenced phage than bacterial genomes. We assessed the suitability of Illumina technology for high-throughput sequencing and subsequent assembly of phage genomes. In silico datasets reveal that 30× coverage is sufficient to correctly assemble the complete genome of ~98.5% of known phages, with experimental data confirming that the majority of phage genomes can be assembled at 30× coverage. Furthermore, in silico data demonstrate it is possible to co-sequence multiple phages from different hosts, without introducing assembly errors.
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Affiliation(s)
- Branko Rihtman
- School of Life Sciences, University of Warwick , Coventry , United Kingdom
| | - Sean Meaden
- College of Life and Environmental Sciences, University of Exeter , United Kingdom
| | - Martha R J Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester
| | - Britt Koskella
- College of Life and Environmental Sciences, University of Exeter, United Kingdom; Department of Integrative Biology, University of California, Berkeley, California, United States
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Hatzopoulos T, Watkins SC, Putonti C. PhagePhisher: a pipeline for the discovery of covert viral sequences in complex genomic datasets. Microb Genom 2016; 2:e000053. [PMID: 28348848 PMCID: PMC5320576 DOI: 10.1099/mgen.0.000053] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/21/2016] [Indexed: 01/09/2023] Open
Abstract
Obtaining meaningful viral information from large sequencing datasets presents unique challenges distinct from prokaryotic and eukaryotic sequencing efforts. The difficulties surrounding this issue can be ascribed in part to the genomic plasticity of viruses themselves as well as the scarcity of existing information in genomic databases. The open-source software PhagePhisher (http://www.putonti-lab.com/phagephisher) has been designed as a simple pipeline to extract relevant information from complex and mixed datasets, and will improve the examination of bacteriophages, viruses, and virally related sequences, in a range of environments. Key aspects of the software include speed and ease of use; PhagePhisher can be used with limited operator knowledge of bioinformatics on a standard workstation. As a proof-of-concept, PhagePhisher was successfully implemented with bacteria–virus mixed samples of varying complexity. Furthermore, viral signals within microbial metagenomic datasets were easily and quickly identified by PhagePhisher, including those from prophages as well as lysogenic phages, an important and often neglected aspect of examining phage populations in the environment. PhagePhisher resolves viral-related sequences which may be obscured by or imbedded in bacterial genomes.
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33
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Komenda J, Sobotka R. Cyanobacterial high-light-inducible proteins — Protectors of chlorophyll–protein synthesis and assembly. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:288-95. [DOI: 10.1016/j.bbabio.2015.08.011] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/28/2015] [Accepted: 08/30/2015] [Indexed: 12/24/2022]
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34
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Lin X, Ding H, Zeng Q. Transcriptomic response during phage infection of a marine cyanobacterium under phosphorus-limited conditions. Environ Microbiol 2015; 18:450-60. [DOI: 10.1111/1462-2920.13104] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 10/20/2015] [Accepted: 10/23/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Xingqin Lin
- Division of Life Science; The Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Huiming Ding
- Department of Civil and Environmental Engineering; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | - Qinglu Zeng
- Division of Life Science; The Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
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35
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36
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Roitman S, Flores-Uribe J, Philosof A, Knowles B, Rohwer F, Ignacio-Espinoza JC, Sullivan MB, Cornejo-Castillo FM, Sánchez P, Acinas SG, Dupont CL, Béjà O. Closing the gaps on the viral photosystem-I psaDCAB gene organization. Environ Microbiol 2015; 17:5100-8. [PMID: 26310718 PMCID: PMC5019241 DOI: 10.1111/1462-2920.13036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 08/20/2015] [Indexed: 11/30/2022]
Abstract
Marine photosynthesis is largely driven by cyanobacteria, namely Synechococcus and Prochlorococcus. Genes encoding for photosystem (PS) I and II reaction centre proteins are found in cyanophages and are believed to increase their fitness. Two viral PSI gene arrangements are known, psaJF→C→A→B→K→E→D and psaD→C→A→B. The shared genes between these gene cassettes and their encoded proteins are distinguished by %G + C and protein sequence respectively. The data on the psaD→C→A→B gene organization were reported from only two partial gene cassettes coming from Global Ocean Sampling stations in the Pacific and Indian oceans. Now we have extended our search to 370 marine stations from six metagenomic projects. Genes corresponding to both PSI gene arrangements were detected in the Pacific, Indian and Atlantic oceans, confined to a strip along the equator (30°N and 30°S). In addition, we found that the predicted structure of the viral PsaA protein from the psaD→C→A→B organization contains a lumenal loop conserved in PsaA proteins from Synechococcus, but is completely absent in viral PsaA proteins from the psaJF→C→A→B→K→E→D gene organization and most Prochlorococcus strains. This may indicate a co-evolutionary scenario where cyanophages containing either of these gene organizations infect cyanobacterial ecotypes biogeographically restricted to the 30°N and 30°S equatorial strip.
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Affiliation(s)
- Sheila Roitman
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - José Flores-Uribe
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Alon Philosof
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Ben Knowles
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | - Pablo Sánchez
- Departament of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Silvia G Acinas
- Departament of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Chris L Dupont
- Microbial and Environmental Genomics Group, J Craig Venter Institute, San Diego, CA, USA
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
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37
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Puxty RJ, Millard AD, Evans DJ, Scanlan DJ. Shedding new light on viral photosynthesis. PHOTOSYNTHESIS RESEARCH 2015; 126:71-97. [PMID: 25381655 DOI: 10.1007/s11120-014-0057-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 10/29/2014] [Indexed: 06/04/2023]
Abstract
Viruses infecting the environmentally important marine cyanobacteria Prochlorococcus and Synechococcus encode 'auxiliary metabolic genes' (AMGs) involved in the light and dark reactions of photosynthesis. Here, we discuss progress on the inventory of such AMGs in the ever-increasing number of viral genome sequences as well as in metagenomic datasets. We contextualise these gene acquisitions with reference to a hypothesised fitness gain to the phage. We also report new evidence with regard to the sequence and predicted structural properties of viral petE genes encoding the soluble electron carrier plastocyanin. Viral copies of PetE exhibit extensive modifications to the N-terminal signal peptide and possess several novel residues in a region responsible for interaction with redox partners. We also highlight potential knowledge gaps in this field and discuss future opportunities to discover novel phage-host interactions involved in the photosynthetic process.
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Affiliation(s)
- Richard J Puxty
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Andrew D Millard
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - David J Evans
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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38
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Using signature genes as tools to assess environmental viral ecology and diversity. Appl Environ Microbiol 2015; 80:4470-80. [PMID: 24837394 DOI: 10.1128/aem.00878-14] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viruses (including bacteriophages) are the most abundant biological entities on the planet. As such, they are thought to have a major impact on all aspects of microbial community structure and function. Despite this critical role in ecosystem processes, the study of virus/phage diversity has lagged far behind parallel studies of the bacterial and eukaryotic kingdoms, largely due to the absence of any universal phylogenetic marker. Here we review the development and use of signature genes to investigate viral diversity, as a viable strategy for data sets of specific virus groups. Genes that have been used include those encoding structural proteins, such as portal protein, major capsid protein, and tail sheath protein, auxiliary metabolism genes, such as psbA, psbB,and phoH, and several polymerase genes. These marker genes have been used in combination with PCR-based fingerprinting and/or sequencing strategies to investigate spatial, temporal, and seasonal variations and diversity in a wide range of habitats.
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Sanchez SE, Cuevas DA, Rostron JE, Liang TY, Pivaroff CG, Haynes MR, Nulton J, Felts B, Bailey BA, Salamon P, Edwards RA, Burgin AB, Segall AM, Rohwer F. Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins. J Vis Exp 2015:e52854. [PMID: 26132888 PMCID: PMC4544906 DOI: 10.3791/52854] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Current investigations into phage-host interactions are dependent on extrapolating knowledge from (meta)genomes. Interestingly, 60 - 95% of all phage sequences share no homology to current annotated proteins. As a result, a large proportion of phage genes are annotated as hypothetical. This reality heavily affects the annotation of both structural and auxiliary metabolic genes. Here we present phenomic methods designed to capture the physiological response(s) of a selected host during expression of one of these unknown phage genes. Multi-phenotype Assay Plates (MAPs) are used to monitor the diversity of host substrate utilization and subsequent biomass formation, while metabolomics provides bi-product analysis by monitoring metabolite abundance and diversity. Both tools are used simultaneously to provide a phenotypic profile associated with expression of a single putative phage open reading frame (ORF). Representative results for both methods are compared, highlighting the phenotypic profile differences of a host carrying either putative structural or metabolic phage genes. In addition, the visualization techniques and high throughput computational pipelines that facilitated experimental analysis are presented.
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Affiliation(s)
| | - Daniel A Cuevas
- Computational Science Research Center, San Diego State University
| | | | - Tiffany Y Liang
- Bioinformatics and Medical Informatics Research Center, San Diego State University
| | | | | | - Jim Nulton
- Department of Mathematics and Statistics, San Diego State University
| | - Ben Felts
- Department of Mathematics and Statistics, San Diego State University
| | - Barbara A Bailey
- Department of Mathematics and Statistics, San Diego State University
| | - Peter Salamon
- Department of Mathematics and Statistics, San Diego State University
| | - Robert A Edwards
- Department of Biology, San Diego State University; Department of Computer Science, San Diego State University; Mathematics and Computer Science Division, Argonne National Laboratory
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Chénard C, Chan AM, Vincent WF, Suttle CA. Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages. ISME JOURNAL 2015; 9:2046-58. [PMID: 25822482 DOI: 10.1038/ismej.2015.24] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 01/02/2015] [Accepted: 01/06/2015] [Indexed: 11/09/2022]
Abstract
Cyanobacteria are often the dominant phototrophs in polar freshwater communities; yet, the phages that infect them remain unknown. Here, we present a genomic and morphological characterization of cyanophage S-EIV1 that was isolated from freshwaters on Ellesmere Island (Nunavut, High Arctic Canada), and which infects the polar Synechococcus sp., strain PCCC-A2c. S-EIV1 represents a newly discovered evolutionary lineage of bacteriophages whose representatives are widespread in aquatic systems. Among the 130 predicted open reading frames (ORFs) there is no recognizable similarity to genes that encode structural proteins other than the large terminase subunit and a distant viral morphogenesis protein, indicating that the genes encoding the structural proteins of S-EIV1 are distinct from other viruses. As well, only 19 predicted coding sequences on the 79 178 bp circularly permuted genome have homology with genes encoding proteins of known function. Although S-EIV1 is divergent from other sequenced phage isolates, it shares synteny with phage genes captured on a fosmid from the deep-chlorophyll maximum in the Mediterranean Sea, as well as with an incision element in the genome of Anabaena variabilis (ATCC 29413). Sequence recruitment of metagenomic data indicates that S-EIV1-like viruses are cosmopolitan and abundant in a wide range of aquatic systems, suggesting they have an important ecological role.
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Affiliation(s)
- C Chénard
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - A M Chan
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - W F Vincent
- Département de Biologie and Centre d'études nordiques (CEN), Laval University, Quebec City, Quebec, Canada
| | - C A Suttle
- 1] Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada [2] Departments of Botany, and Microbiology & Immunology, University of British Columbia, Vancouver, British Columbia, Canada [3] Canadian Institute for Advanced Research, Toronto, Ontario, Canada
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Roux S, Enault F, Ravet V, Pereira O, Sullivan MB. Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages. Front Microbiol 2015; 6:199. [PMID: 25852662 PMCID: PMC4360716 DOI: 10.3389/fmicb.2015.00199] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/24/2015] [Indexed: 11/13/2022] Open
Abstract
Viral metagenomics (viromics) is a tremendous tool to reveal viral taxonomic and functional diversity across ecosystems ranging from the human gut to the world's oceans. As with microbes however, there appear vast swaths of “dark matter” yet to be documented for viruses, even among relatively well-studied viral types. Here, we use viromics to explore the “Far-T4 phages” sequence space, a neighbor clade from the well-studied T4-like phages that was first detected through PCR study in seawater and subsequently identified in freshwater lakes through 454-sequenced viromes. To advance the description of these viruses beyond this single marker gene, we explore Far-T4 genome fragments assembled from two deeply-sequenced freshwater viromes. Single gene phylogenetic trees confirm that the Far-T4 phages are divergent from the T4-like phages, genome fragments reveal largely collinear genome organizations, and both data led to the delineation of five Far-T4 clades. Three-dimensional models of major capsid proteins are consistent with a T4-like structure, and highlight a highly conserved core flanked by variable insertions. Finally, we contextualize these now better characterized Far-T4 phages by re-analyzing 196 previously published viromes. These suggest that Far-T4 are common in freshwater and seawater as only four of 82 aquatic viromes lacked Far-T4-like sequences. Variability in representation across the five newly identified clades suggests clade-specific niche differentiation may be occurring across the different biomes, though the underlying mechanism remains unidentified. While complete genome assembly from complex communities and the lack of host linkage information still bottleneck virus discovery through viromes, these findings exemplify the power of metagenomics approaches to assess the diversity, evolutionary history, and genomic characteristics of novel uncultivated phages.
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Affiliation(s)
- Simon Roux
- Ecology and Evolutionary Biology, University of Arizona Tucson, AZ, USA
| | - François Enault
- Laboratoire "Microorganismes: Génome et Environnement," Clermont Université, Université Blaise Pascal Clermont-Ferrand, France ; Centre National de la Recherche Scientifique, UMR 6023, Laboratoire Microorganismes: Génome et Environnement Aubière, France
| | - Viviane Ravet
- Laboratoire "Microorganismes: Génome et Environnement," Clermont Université, Université Blaise Pascal Clermont-Ferrand, France ; Centre National de la Recherche Scientifique, UMR 6023, Laboratoire Microorganismes: Génome et Environnement Aubière, France
| | - Olivier Pereira
- Laboratoire "Microorganismes: Génome et Environnement," Clermont Université, Université Blaise Pascal Clermont-Ferrand, France ; Centre National de la Recherche Scientifique, UMR 6023, Laboratoire Microorganismes: Génome et Environnement Aubière, France
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An inexpensive, accurate, and precise wet-mount method for enumerating aquatic viruses. Appl Environ Microbiol 2015; 81:2995-3000. [PMID: 25710369 DOI: 10.1128/aem.03642-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/12/2015] [Indexed: 11/20/2022] Open
Abstract
Viruses affect biogeochemical cycling, microbial mortality, gene flow, and metabolic functions in diverse environments through infection and lysis of microorganisms. Fundamental to quantitatively investigating these roles is the determination of viral abundance in both field and laboratory samples. One current, widely used method to accomplish this with aquatic samples is the "filter mount" method, in which samples are filtered onto costly 0.02-μm-pore-size ceramic filters for enumeration of viruses by epifluorescence microscopy. Here we describe a cost-effective (ca. 500-fold-lower materials cost) alternative virus enumeration method in which fluorescently stained samples are wet mounted directly onto slides, after optional chemical flocculation of viruses in samples with viral concentrations of <5×10(7) viruses ml(-1). The concentration of viruses in the sample is then determined from the ratio of viruses to a known concentration of added microsphere beads via epifluorescence microscopy. Virus concentrations obtained by using this wet-mount method, with and without chemical flocculation, were significantly correlated with, and had precision equivalent to, those obtained by the filter mount method across concentrations ranging from 2.17×10(6) to 1.37×10(8) viruses ml(-1) when tested by using cultivated viral isolates and natural samples from marine and freshwater environments. In summary, the wet-mount method is significantly less expensive than the filter mount method and is appropriate for rapid, precise, and accurate enumeration of aquatic viruses over a wide range of viral concentrations (≥1×10(6) viruses ml(-1)) encountered in field and laboratory samples.
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Chan YW, Millard AD, Wheatley PJ, Holmes AB, Mohr R, Whitworth AL, Mann NH, Larkum AWD, Hess WR, Scanlan DJ, Clokie MRJ. Genomic and proteomic characterization of two novel siphovirus infecting the sedentary facultative epibiont cyanobacterium Acaryochloris marina. Environ Microbiol 2015; 17:4239-52. [PMID: 25472545 DOI: 10.1111/1462-2920.12735] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 11/26/2014] [Accepted: 11/27/2003] [Indexed: 11/28/2022]
Abstract
Acaryochloris marina is a symbiotic species of cyanobacteria that is capable of utilizing far-red light. We report the characterization of the phages A-HIS1 and A-HIS2, capable of infecting Acaryochloris. Morphological characterization of these phages places them in the family Siphoviridae. However, molecular characterization reveals that they do not show genetic similarity with any known siphoviruses. While the phages do show synteny between each other, the nucleotide identity between the phages is low at 45-67%, suggesting they diverged from each other some time ago. The greatest number of genes shared with another phage (a myovirus infecting marine Synechococcus) was four. Unlike most other cyanophages and in common with the Siphoviridae infecting Synechococcus, no photosynthesis-related genes were found in the genome. CRISPR (clustered regularly interspaced short palindromic repeats) spacers from the host Acaryochloris had partial matches to sequences found within the phages, which is the first time CRISPRs have been reported in a cyanobacterial/cyanophage system. The phages also encode a homologue of the proteobacterial RNase T. The potential function of RNase T in the mark-up or digestion of crRNA hints at a novel mechanism for evading the host CRISPR system.
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Affiliation(s)
- Yi-Wah Chan
- Warwick Systems Biology Centre, Coventry, UK
| | | | | | - Antony B Holmes
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Remus Mohr
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Nicholas H Mann
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Anthony W D Larkum
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
| | - Wolfgang R Hess
- Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Martha R J Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, LE19HN, UK
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Hevroni G, Enav H, Rohwer F, Béjà O. Diversity of viral photosystem-I psaA genes. ISME JOURNAL 2014; 9:1892-8. [PMID: 25535938 PMCID: PMC4511924 DOI: 10.1038/ismej.2014.244] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 11/11/2014] [Accepted: 11/17/2014] [Indexed: 12/23/2022]
Abstract
Marine photosynthesis is one of the major contributors to the global carbon cycle and the world's oxygen supply. This process is largely driven by cyanobacteria, namely Synechococcus and Prochlorococcus. Genes encoding photosystem-II (PSII) reaction center proteins are found in many cyanophage genomes, and are expressed during the infection of their hosts. On the basis of metagenomics, cyanophage photosystem-I (PSI) gene cassettes were recently discovered with two gene arrangements psaJF→C→A→B→K→E→D and psaD→C→A→B. It was suggested that the horizontal transfer of PSII and PSI genes is increasing phage fitness. To better understand their diversity, we designed degenerate primers to cover a wide diversity of organisms, and using PCR we targeted the psaC→A arrangement, which is unique to cyanophages cassettes. We examined viral concentrates from four islands in the Pacific Ocean and found samples containing the psaC→A arrangement. Analyses of the amplified viral psaA gene revealed six subgroups varying in their level of similarity and %G+C content, suggesting that the diversity of cyanophage PSI genes is greater than originally thought.
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Affiliation(s)
- Gur Hevroni
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hagay Enav
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
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Clokie MR, Millard AD, Letarov AV, Heaphy S. Phages in nature. BACTERIOPHAGE 2014; 1:31-45. [PMID: 21687533 DOI: 10.4161/bact.1.1.14942] [Citation(s) in RCA: 633] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 01/17/2011] [Accepted: 01/18/2011] [Indexed: 12/28/2022]
Abstract
Bacteriophages or phages are the most abundant organisms in the biosphere and they are a ubiquitous feature of prokaryotic existence. A bacteriophage is a virus which infects a bacterium. Archaea are also infected by viruses, whether these should be referred to as 'phages' is debatable, but they are included as such in the scope this article. Phages have been of interest to scientists as tools to understand fundamental molecular biology, as vectors of horizontal gene transfer and drivers of bacterial evolution, as sources of diagnostic and genetic tools and as novel therapeutic agents. Unraveling the biology of phages and their relationship with their hosts is key to understanding microbial systems and their exploitation. In this article we describe the roles of phages in different host systems and show how modeling, microscopy, isolation, genomic and metagenomic based approaches have come together to provide unparalleled insights into these small but vital constituents of the microbial world.
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Affiliation(s)
- Martha Rj Clokie
- Department of Infection, Immunity and Inflammation; Medical Sciences Building; University of Leicester; Leicester, UK
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46
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Abbasifar R, Griffiths MW, Sabour PM, Ackermann HW, Vandersteegen K, Lavigne R, Noben JP, Alanis Villa A, Abbasifar A, Nash JHE, Kropinski AM. Supersize me: Cronobacter sakazakii phage GAP32. Virology 2014; 460-461:138-46. [PMID: 25010279 DOI: 10.1016/j.virol.2014.05.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 01/05/2014] [Accepted: 05/03/2014] [Indexed: 01/27/2023]
Abstract
Cronobacter sakazakii is a Gram-negative pathogen found in milk-based formulae that causes infant meningitis. Bacteriophages have been proposed to control bacterial pathogens; however, comprehensive knowledge about a phage is required to ensure its safety before clinical application. We have characterized C. sakazakii phage vB_CsaM_GAP32 (GAP32), which possesses the second largest sequenced phage genome (358,663bp). A total of 571 genes including 545 protein coding sequences and 26 tRNAs were identified, thus more genes than in the smallest bacterium, Mycoplasma genitalium G37. BLASTP and HHpred searches, together with proteomic analyses reveal that only 23.9% of the putative proteins have defined functions. Some of the unique features of this phage include: a chromosome condensation protein, two copies of the large subunit terminase, a predicted signal-arrest-release lysin; and an RpoD-like protein, which is possibly involved in the switch from immediate early to delayed early transcription. Its closest relatives are all extremely large myoviruses, namely coliphage PBECO4 and Klebsiella phage vB_KleM-RaK2, with whom it shares approximately 44% homologous proteins. Since the homologs are not evenly distributed, we propose that these three phages belong to a new subfamily.
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Affiliation(s)
- Reza Abbasifar
- Canadian Research Institute for Food Safety, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Mansel W Griffiths
- Canadian Research Institute for Food Safety, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Parviz M Sabour
- Agriculture and Agri-Food Canada, Guelph Food Research Centre, Guelph, ON, Canada N1G 5C9
| | - Hans-Wolfgang Ackermann
- Department of Microbiology-Infectiology and Immunology, Faculty of Medicine, Université Laval, Quebec, QC, Canada
| | | | - Rob Lavigne
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, School of Life Sciences, Hasselt University, Diepenbeek, Belgium
| | - Argentina Alanis Villa
- Canadian Research Institute for Food Safety, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Arash Abbasifar
- Canadian Research Institute for Food Safety, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - John H E Nash
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, ON, Canada N1G 3W4
| | - Andrew M Kropinski
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, ON, Canada N1G 3W4; Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada N1G 2W1.
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Profiles of photosynthetic pigment accumulation and expression of photosynthesis-related genes in the marine cyanobacteria Synechococcus sp.: Effects of LED wavelengths. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-013-0700-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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48
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Enav H, Mandel-Gutfreund Y, Béjà O. Comparative metagenomic analyses reveal viral-induced shifts of host metabolism towards nucleotide biosynthesis. MICROBIOME 2014; 2:9. [PMID: 24666644 PMCID: PMC4022391 DOI: 10.1186/2049-2618-2-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 02/13/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND Viral genomes often contain metabolic genes that were acquired from host genomes (auxiliary genes). It is assumed that these genes are fixed in viral genomes as a result of a selective force, favoring viruses that acquire specific metabolic functions. While many individual auxiliary genes were observed in viral genomes and metagenomes, there is great importance in investigating the abundance of auxiliary genes and metabolic functions in the marine environment towards a better understanding of their role in promoting viral reproduction. RESULTS In this study, we searched for enriched viral auxiliary genes and mapped them to metabolic pathways. To initially identify enriched auxiliary genes, we analyzed metagenomic microbial reads from the Global Ocean Survey (GOS) dataset that were characterized as viral, as well as marine virome and microbiome datasets from the Line Islands. Viral-enriched genes were mapped to a "global metabolism network" that comprises all KEGG metabolic pathways. Our analysis of the viral-enriched pathways revealed that purine and pyrimidine metabolism pathways are among the most enriched pathways. Moreover, many other viral-enriched metabolic pathways were found to be closely associated with the purine and pyrimidine metabolism pathways. Furthermore, we observed that sequential reactions are promoted in pathways having a high proportion of enriched genes. In addition, these enriched genes were found to be of modular nature, participating in several pathways. CONCLUSIONS Our naïve metagenomic analyses strongly support the well-established notion that viral auxiliary genes promote viral replication via both degradation of host DNA and RNA as well as a shift of the host metabolism towards nucleotide biosynthesis, clearly indicating that comparative metagenomics can be used to understand different environments and systems without prior knowledge of pathways involved.
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Affiliation(s)
- Hagay Enav
- Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
| | | | - Oded Béjà
- Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
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The evolutionary divergence of psbA gene in Synechococcus and their myoviruses in the East China Sea. PLoS One 2014; 9:e86644. [PMID: 24466184 PMCID: PMC3900582 DOI: 10.1371/journal.pone.0086644] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 12/11/2013] [Indexed: 11/19/2022] Open
Abstract
Marine Synechococcus is a principal component of the picophytoplankton and makes an important contribution to primary productivity in the ocean. Synechophages, infecting Synechococcus, are believed to have significant influences on the distribution and abundance of their hosts. Extensive previous ecological studies on cyanobacteria and viruses have been carried out in the East China Sea (ECS). Here we investigate the diversity and divergence of Synechococcus and their myoviruses (Synechomyoviruses) based on their shared photosynthesis psbA gene. Synechococcus is dominated by subclades 5.1A I, 5.1A II and 5.1A IV in the ECS, and clades I and II are the dominant groups in the Synechomyoviruses. As two phylogenetically independent clades, there is much higher diversity of the Synechomyoviruses than Synechococcus. Obvious partitioning characteristics of GC and GC3 (the GC content at the third codon position) contents are obtained among different picophytoplankton populations and their phages. The GC3 content causes the psbA gene in Synechococcus to have a higher GC content, while the opposite is true in the Synechomyoviruses. Analyzing more than one-time difference of the codon usage frequency of psbA sequences, the third position nucleotides of preferred codons for Synechococcus are all G and C, while most Synechomyoviral sequences (72.7%) have A and T at the third position of their preferred codons. This work shed light on the ecology and evolution of phage-host interactions in the environment.
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50
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Seasonal variations in PCR-DGGE fingerprinted viruses infecting phytoplankton in large and deep peri-alpine lakes. Ecol Res 2014. [DOI: 10.1007/s11284-013-1121-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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