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Watkins SC, Sible E, Putonti C. Pseudomonas PB1-Like Phages: Whole Genomes from Metagenomes Offer Insight into an Abundant Group of Bacteriophages. Viruses 2018; 10:v10060331. [PMID: 29914169 PMCID: PMC6024596 DOI: 10.3390/v10060331] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/11/2018] [Accepted: 06/11/2018] [Indexed: 02/07/2023] Open
Abstract
Despite the abundance, ubiquity and impact of environmental viruses, their inherent genomic plasticity and extreme diversity pose significant challenges for the examination of bacteriophages on Earth. Viral metagenomic studies have offered insight into broader aspects of phage ecology and repeatedly uncover genes to which we are currently unable to assign function. A combined effort of phage isolation and metagenomic survey of Chicago’s nearshore waters of Lake Michigan revealed the presence of Pbunaviruses, relatives of the Pseudomonas phage PB1. This prompted our expansive investigation of PB1-like phages. Genomic signatures of PB1-like phages and Pbunaviruses were identified, permitting the unambiguous distinction between the presence/absence of these phages in soils, freshwater and wastewater samples, as well as publicly available viral metagenomic datasets. This bioinformatic analysis led to the de novo assembly of nine novel PB1-like phage genomes from a metagenomic survey of samples collected from Lake Michigan. While this study finds that Pbunaviruses are abundant in various environments of Northern Illinois, genomic variation also exists to a considerable extent within individual communities.
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Affiliation(s)
- Siobhan C Watkins
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA.
| | - Emily Sible
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA.
| | - Catherine Putonti
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA.
- Department of Computer Science, Loyola University Chicago, Chicago, IL 60660, USA.
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA.
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102
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Breitbart M, Bonnain C, Malki K, Sawaya NA. Phage puppet masters of the marine microbial realm. Nat Microbiol 2018; 3:754-766. [PMID: 29867096 DOI: 10.1038/s41564-018-0166-y] [Citation(s) in RCA: 322] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 04/20/2018] [Indexed: 11/09/2022]
Abstract
Viruses numerically dominate our oceans; however, we have only just begun to document the diversity, host range and infection dynamics of marine viruses, as well as the subsequent effects of infection on both host cell metabolism and oceanic biogeochemistry. Bacteriophages (that is, phages: viruses that infect bacteria) are highly abundant and are known to play critical roles in bacterial mortality, biogeochemical cycling and horizontal gene transfer. This Review Article summarizes current knowledge of marine viral ecology and highlights the importance of phage particles to the dissolved organic matter pool, as well as the complex interactions between phages and their bacterial hosts. We emphasize the newly recognized roles of phages as puppet masters of their bacterial hosts, where phages are capable of altering the metabolism of infected bacteria through the expression of auxiliary metabolic genes and the redirection of host gene expression patterns. Finally, we propose the 'royal family model' as a hypothesis to describe successional patterns of bacteria and phages over time in marine systems, where despite high richness and significant seasonal differences, only a small number of phages appear to continually dominate a given marine ecosystem. Although further testing is required, this model provides a framework for assessing the specificity and ecological consequences of phage-host dynamics.
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Affiliation(s)
- Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA.
| | - Chelsea Bonnain
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Kema Malki
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Natalie A Sawaya
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
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103
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Fernández-Ruiz I, Coutinho FH, Rodriguez-Valera F. Thousands of Novel Endolysins Discovered in Uncultured Phage Genomes. Front Microbiol 2018; 9:1033. [PMID: 29867909 PMCID: PMC5968864 DOI: 10.3389/fmicb.2018.01033] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/01/2018] [Indexed: 12/05/2022] Open
Abstract
Bacteriophages express endolysins toward the end of their replication cycle to degrade the microbial cell wall from within, allowing viral progeny to be released. Endolysins can also degrade the prokaryotic cell wall from the outside, thus have potential to be used for biotechnological and medical purposes. Multiple endolysins have been identified within the genomes of isolated phages, but their diversity in uncultured phages has been overlooked. We used a bioinformatics pipeline to identify novel endolysins from nearly 200,000 uncultured viruses. We report the discovery of 2,628 putative endolysins, many of which displayed novel domain architectures. In addition, several of the identified proteins are predicted to be active against genera that include pathogenic bacteria. These discoveries enhance the diversity of known endolysins and are a stepping stone for developing medical and biotechnological applications that rely on bacteriophages, the most diverse biological entities on Earth.
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Affiliation(s)
- Iris Fernández-Ruiz
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche, San Juan de Alicante, Spain
| | - Felipe H Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche, San Juan de Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche, San Juan de Alicante, Spain
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104
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The Geographic Structure of Viruses in the Cuatro Ciénegas Basin, a Unique Oasis in Northern Mexico, Reveals a Highly Diverse Population on a Small Geographic Scale. Appl Environ Microbiol 2018; 84:AEM.00465-18. [PMID: 29625974 DOI: 10.1128/aem.00465-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/21/2018] [Indexed: 12/28/2022] Open
Abstract
The Cuatro Ciénegas Basin (CCB) is located in the Chihuahuan desert in the Mexican state of Coahuila; it has been characterized as a site with high biological diversity despite its extreme oligotrophic conditions. It has the greatest number of endemic species in North America, containing abundant living microbialites (including stromatolites and microbial mats) and diverse microbial communities. With the hypothesis that this high biodiversity and the geographic structure should be reflected in the virome, the viral communities in 11 different locations of three drainage systems, Churince, La Becerra, and Pozas Rojas, and in the intestinal contents of 3 different fish species, were analyzed for both eukaryotic and prokaryotic RNA and DNA viruses using next-generation sequencing methods. Double-stranded DNA (dsDNA) virus families were the most abundant (72.5% of reads), followed by single-stranded DNA (ssDNA) viruses (2.9%) and ssRNA and dsRNA virus families (0.5%). Thirteen families had dsDNA genomes, five had ssDNA, three had dsRNA, and 16 had ssRNA. A highly diverse viral community was found, with an ample range of hosts and a strong geographical structure, with very even distributions and signals of endemicity in the phylogenetic trees from several different virus families. The majority of viruses found were bacteriophages but eukaryotic viruses were also frequent, and the large diversity of viruses related to algae were a surprise, since algae are not evident in the previously analyzed aquatic systems of this ecosystem. Animal viruses were also frequently found, showing the large diversity of aquatic animals in this oasis, where plants, protozoa, and archaea are rare.IMPORTANCE In this study, we tested whether the high biodiversity and geographic structure of CCB is reflected in its virome. CCB is an extraordinarily biodiverse oasis in the Chihuahuan desert, where a previous virome study suggested that viruses had followed the marine ancestry of the marine bacteria and, as a result of their long isolation, became endemic to the site. In this study, which includes a larger sequencing coverage and water samples from other sites within the valley, we confirmed the high virus biodiversity and uniqueness as well as the strong biogeographical diversification of the CCB. In addition, we also analyzed fish intestinal contents, finding that each fish species eats different prey and, as a result, presents different viral compositions even if they coexist in the same pond. These facts highlight the high and novel virus diversity of CCB and its "lost world" status.
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105
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Hou W, Wang S, Briggs BR, Li G, Xie W, Dong H. High Diversity of Myocyanophage in Various Aquatic Environments Revealed by High-Throughput Sequencing of Major Capsid Protein Gene With a New Set of Primers. Front Microbiol 2018; 9:887. [PMID: 29774020 PMCID: PMC5943533 DOI: 10.3389/fmicb.2018.00887] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 04/18/2018] [Indexed: 12/02/2022] Open
Abstract
Myocyanophages, a group of viruses infecting cyanobacteria, are abundant and play important roles in elemental cycling. Here we investigated the particle-associated viral communities retained on 0.2 μm filters and in sediment samples (representing ancient cyanophage communities) from four ocean and three lake locations, using high-throughput sequencing and a newly designed primer pair targeting a gene fragment (∼145-bp in length) encoding the cyanophage gp23 major capsid protein (MCP). Diverse viral communities were detected in all samples. The fragments of 142-, 145-, and 148-bp in length were most abundant in the amplicons, and most sequences (>92%) belonged to cyanophages. Additionally, different sequencing depths resulted in different diversity estimates of the viral community. Operational taxonomic units obtained from deep sequencing of the MCP gene covered the majority of those obtained from shallow sequencing, suggesting that deep sequencing exhibited a more complete picture of cyanophage community than shallow sequencing. Our results also revealed a wide geographic distribution of marine myocyanophages, i.e., higher dissimilarities of the myocyanophage communities corresponded with the larger distances between the sampling sites. Collectively, this study suggests that the newly designed primer pair can be effectively used to study the community and diversity of myocyanophage from different environments, and the high-throughput sequencing represents a good method to understand viral diversity.
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Affiliation(s)
- Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
| | - Shang Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Brandon R Briggs
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, United States
| | - Gaoyuan Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
| | - Wei Xie
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China.,Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, United States
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106
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Chopyk J, Allard S, Nasko DJ, Bui A, Mongodin EF, Sapkota AR. Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations. Front Microbiol 2018; 9:792. [PMID: 29740420 PMCID: PMC5928236 DOI: 10.3389/fmicb.2018.00792] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/09/2018] [Indexed: 12/26/2022] Open
Abstract
Agricultural ponds have a great potential as a means of capture and storage of water for irrigation. However, pond topography (small size, shallow depth) leaves them susceptible to environmental, agricultural, and anthropogenic exposures that may influence microbial dynamics. Therefore, the aim of this project was to characterize the bacterial and viral communities of pond water in the Mid-Atlantic United States with a focus on the late season (October-December), where decreasing temperature and nutrient levels can affect the composition of microbial communities. Ten liters of freshwater from an agricultural pond were sampled monthly, and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, and the bacterial communities were characterized using 16S rRNA gene sequencing. The remaining filtrate was chemically concentrated for viruses, DNA-extracted, and shotgun sequenced. Bacterial community profiling showed significant fluctuations over the sampling period, corresponding to changes in the condition of the pond freshwater (e.g., pH, nutrient load). In addition, there were significant differences in the alpha-diversity and core bacterial operational taxonomic units (OTUs) between water fractions filtered through different pore sizes. The viral fraction was dominated by tailed bacteriophage of the order Caudovirales, largely those of the Siphoviridae family. Moreover, while present, genes involved in virulence/antimicrobial resistance were not enriched within the viral fraction during the study period. Instead, the viral functional profile was dominated by phage associated proteins, as well as those related to nucleotide production. Overall, these data suggest that agricultural pond water harbors a diverse core of bacterial and bacteriophage species whose abundance and composition are influenced by environmental variables characteristic of pond topology and the late season.
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Affiliation(s)
- Jessica Chopyk
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, United States
| | - Sarah Allard
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, United States
| | - Daniel J. Nasko
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, United States
| | - Anthony Bui
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, United States
| | - Emmanuel F. Mongodin
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Amy R. Sapkota
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, United States
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107
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Yutin N, Bäckström D, Ettema TJG, Krupovic M, Koonin EV. Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis. Virol J 2018; 15:67. [PMID: 29636073 PMCID: PMC5894146 DOI: 10.1186/s12985-018-0974-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/28/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Analysis of metagenomic sequences has become the principal approach for the study of the diversity of viruses. Many recent, extensive metagenomic studies on several classes of viruses have dramatically expanded the visible part of the virosphere, showing that previously undetected viruses, or those that have been considered rare, actually are important components of the global virome. RESULTS We investigated the provenance of viruses related to tail-less bacteriophages of the family Tectiviridae by searching genomic and metagenomics sequence databases for distant homologs of the tectivirus-like Double Jelly-Roll major capsid proteins (DJR MCP). These searches resulted in the identification of numerous genomes of virus-like elements that are similar in size to tectiviruses (10-15 kilobases) and have diverse gene compositions. By comparison of the gene repertoires, the DJR MCP-encoding genomes were classified into 6 distinct groups that can be predicted to differ in reproduction strategies and host ranges. Only the DJR MCP gene that is present by design is shared by all these genomes, and most also encode a predicted DNA-packaging ATPase; the rest of the genes are present only in subgroups of this unexpectedly diverse collection of DJR MCP-encoding genomes. Only a minority encode a DNA polymerase which is a hallmark of the family Tectiviridae and the putative family "Autolykiviridae". Notably, one of the identified putative DJR MCP viruses encodes a homolog of Cas1 endonuclease, the integrase involved in CRISPR-Cas adaptation and integration of transposon-like elements called casposons. This is the first detected occurrence of Cas1 in a virus. Many of the identified elements are individual contigs flanked by inverted or direct repeats and appear to represent complete, extrachromosomal viral genomes, whereas others are flanked by bacterial genes and thus can be considered as proviruses. These contigs come from metagenomes of widely different environments, some dominated by archaea and others by bacteria, suggesting that collectively, the DJR MCP-encoding elements have a broad host range among prokaryotes. CONCLUSIONS The findings reported here greatly expand the known host range of (putative) viruses of bacteria and archaea that encode a DJR MCP. They also demonstrate the extreme diversity of genome architectures in these viruses that encode no universal proteins other than the capsid protein that was used as the marker for their identification. From a supposedly minor group of bacterial and archaeal viruses, these viruses are emerging as a substantial component of the prokaryotic virome.
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Affiliation(s)
- Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD, 20894, USA
| | - Disa Bäckström
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Box 596, -75123, Uppsala, SE, Sweden
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Box 596, -75123, Uppsala, SE, Sweden
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Institut Pasteur, Paris, France
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD, 20894, USA.
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108
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Nishimura Y, Yoshida T, Kuronishi M, Uehara H, Ogata H, Goto S. ViPTree: the viral proteomic tree server. Bioinformatics 2018; 33:2379-2380. [PMID: 28379287 DOI: 10.1093/bioinformatics/btx157] [Citation(s) in RCA: 381] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/21/2017] [Indexed: 11/12/2022] Open
Abstract
Summary ViPTree is a web server provided through GenomeNet to generate viral proteomic trees for classification of viruses based on genome-wide similarities. Users can upload viral genomes sequenced either by genomics or metagenomics. ViPTree generates proteomic trees for the uploaded genomes together with flexibly selected reference viral genomes. ViPTree also serves as a platform to visually investigate genomic alignments and automatically annotated gene functions for the uploaded viral genomes, thus providing virus researchers the first choice for classifying and understanding newly sequenced viral genomes. Availability and Implementation ViPTree is freely available at: http://www.genome.jp/viptree . Contact goto@kuicr.kyoto-u.ac.jp. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yosuke Nishimura
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.,Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan
| | - Megumi Kuronishi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hideya Uehara
- SGI Japan, Ltd., Yebisu Garden Place Tower 31F, 4-20-3 Ebisu, Shibuya-ku, Tokyo 150-6031, Japan
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Susumu Goto
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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109
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Abstract
Myalgic encephalomyelitis (ME)/chronic fatigue syndrome (CFS) (ME/CFS) is a disabling and debilitating disease of unknown aetiology. It is a heterogeneous disease characterized by various inflammatory, immune, viral, neurological and endocrine symptoms. Several microbiome studies have described alterations in the bacterial component of the microbiome (dysbiosis) consistent with a possible role in disease development. However, in focusing on the bacterial components of the microbiome, these studies have neglected the viral constituent known as the virome. Viruses, particularly those infecting bacteria (bacteriophages), have the potential to alter the function and structure of the microbiome via gene transfer and host lysis. Viral-induced microbiome changes can directly and indirectly influence host health and disease. The contribution of viruses towards disease pathogenesis is therefore an important area for research in ME/CFS. Recent advancements in sequencing technology and bioinformatics now allow more comprehensive and inclusive investigations of human microbiomes. However, as the number of microbiome studies increases, the need for greater consistency in study design and analysis also increases. Comparisons between different ME/CFS microbiome studies are difficult because of differences in patient selection and diagnosis criteria, sample processing, genome sequencing and downstream bioinformatics analysis. It is therefore important that microbiome studies adopt robust, reproducible and consistent study design to enable more reliable and valid comparisons and conclusions to be made between studies. This article provides a comprehensive review of the current evidence supporting microbiome alterations in ME/CFS patients. Additionally, the pitfalls and challenges associated with microbiome studies are discussed.
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110
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Yu DT, Han LL, Zhang LM, He JZ. Diversity and Distribution Characteristics of Viruses in Soils of a Marine-Terrestrial Ecotone in East China. MICROBIAL ECOLOGY 2018; 75:375-386. [PMID: 28825127 DOI: 10.1007/s00248-017-1049-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/20/2017] [Indexed: 06/07/2023]
Abstract
A substantial gap remains in our understanding of the abundance, diversity, and ecology of viruses in soil although some advances have been achieved in recent years. In this study, four soil samples according to the salinity gradient from shore to inland in East China have been characterized. Results showed that spherical virus particles represented the largest viral component in all of the four samples. The viromes had remarkably different taxonomic compositions, and most of the sequences were derived from single-stranded DNA viruses, especially from families Microviridae and Circoviridae. Compared with viromes from other aquatic and sediment samples, the community compositions of our four soil viromes resembled each other, meanwhile coastal sample virome closely congregated with sediment and hypersaline viromes, and high salinity paddy soil sample virome was similar with surface sediment virome. Phylogenetic analysis of functional genes showed that four viromes have high diversity of the subfamily Gokushovirinae in family Microviridae and most of Circoviridae replicase protein sequences grouped within the CRESS-DNA viruses. This work provided an initial outline of the viral communities in marine-terrestrial ecotone and will improve our understanding of the ecological functions of soil viruses.
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Affiliation(s)
- Dan-Ting Yu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, 3010, Australia.
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111
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Kauffman KM, Hussain FA, Yang J, Arevalo P, Brown JM, Chang WK, VanInsberghe D, Elsherbini J, Sharma RS, Cutler MB, Kelly L, Polz MF. A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria. Nature 2018; 554:118-122. [DOI: 10.1038/nature25474] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 12/28/2017] [Indexed: 02/06/2023]
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112
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Corallivory and the microbial debacle in two branching scleractinians. ISME JOURNAL 2018; 12:1109-1126. [PMID: 29339825 DOI: 10.1038/s41396-017-0033-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 11/21/2017] [Accepted: 12/01/2017] [Indexed: 02/01/2023]
Abstract
The grazing activity by specific marine organisms represents a growing threat to the survival of many scleractinian species. For example, the recent proliferation of the corallivorous gastropod Drupella now constitutes a critical case in all South-East Asian waters. If the damaging effects caused by this marine snail on coral polyps are relatively well known, the indirect incidence of predation on coral microbial associates is still obscure and might also potentially impair coral health. In this study, we compared the main ecological traits of coral-associated bacterial and viral communities living in the mucus layer of Acropora formosa and Acropora millepora, of healthy and predated individuals (i.e., colonized by Drupella rugosa), in the Bay of Van Phong (Vietnam). Our results show a substantial impact of the gastropod on a variety of microbiological markers. Colonized corals harbored much more abundant and active epibiotic bacteria whose community composition shifted toward more pathogenic taxa (belonging to the Vibrionales, Clostridiales, Campylobacterales, and Alteromonadales orders), together with their specific phages. Viral epibionts were also greatly influenced by Drupella corallivory with spectacular modifications in their concentrations, life strategies, genotype richness, and diversity. Novel and abundant circular Rep-encoding ssDNA viruses (CRESS-DNA viruses) were detected and characterized in grazed corals and we propose that their occurrence may serve as indicator of the coral health status. Finally, our results reveal that corallivory can cause severe dysbiosis by altering virus-bacteria interactions in the mucus layer, and ultimately favoring the development of local opportunistic infections.
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113
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Complete genome sequence of a phage hyperparasite of Candidatus Xenohaliotis californiensis (Rickettsiales) - a pathogen of Haliotis spp (Gasteropoda). Arch Virol 2018; 163:1101-1104. [PMID: 29327235 DOI: 10.1007/s00705-018-3703-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/21/2017] [Indexed: 01/08/2023]
Abstract
Bacteriophages are recognized as major mortality agents of microbes, among them intracellular marine rickettsiales-like bacteria. Recently, a phage hyperparasite of Candidatus Xenohaliotis californiensis (CXc) has been described. This bacterium is considered the causal agent of Withering Syndrome (WS) which is a chronic and potentially lethal disease of abalone species from California, USA and the peninsula of Baja California, Mexico. This hyperparasite which infects CXc could be used as a biocontrol agent for WS. Therefore, it is necessary to obtain genomic information to characterize this phage. In this study, the first complete genome sequence of a novel phage, Xenohaliotis phage (pCXc) was determined. The complete genome of pCXc from red abalone (Haliotis rufescens) is 35,728 bp, while the complete genome of pCXc from yellow abalone (Haliotis corrugata) is 35,736 bp. Both phage genomes consist of double-stranded DNA with a G + C content of 38.9%. In both genomes 33 open reading frames (ORFs) were predicted. Only 10 ORFs encode proteins that have identifiable functional homologues. These 10 ORFs were classified by function, including structural, DNA replication, DNA packaging, nucleotide transport and metabolism, life cycle regulation, recombination and repair, and additional functions. A PCR method for the specific detection of pCXc was developed. This information will help to understand a new group of phages that infect intracellular marine rickettsiales-like bacteria in mollusks.
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114
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Dijkhuizen LW, Brouwer P, Bolhuis H, Reichart GJ, Koppers N, Huettel B, Bolger AM, Li FW, Cheng S, Liu X, Wong GKS, Pryer K, Weber A, Bräutigam A, Schluepmann H. Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N 2 but may denitrify. THE NEW PHYTOLOGIST 2018. [PMID: 26680538 DOI: 10.1111/nph] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Dinitrogen fixation by Nostoc azollae residing in specialized leaf pockets supports prolific growth of the floating fern Azolla filiculoides. To evaluate contributions by further microorganisms, the A. filiculoides microbiome and nitrogen metabolism in bacteria persistently associated with Azolla ferns were characterized. A metagenomic approach was taken complemented by detection of N2 O released and nitrogen isotope determinations of fern biomass. Ribosomal RNA genes in sequenced DNA of natural ferns, their enriched leaf pockets and water filtrate from the surrounding ditch established that bacteria of A. filiculoides differed entirely from surrounding water and revealed species of the order Rhizobiales. Analyses of seven cultivated Azolla species confirmed persistent association with Rhizobiales. Two distinct nearly full-length Rhizobiales genomes were identified in leaf-pocket-enriched samples from ditch grown A. filiculoides. Their annotation revealed genes for denitrification but not N2 -fixation. 15 N2 incorporation was active in ferns with N. azollae but not in ferns without. N2 O was not detectably released from surface-sterilized ferns with the Rhizobiales. N2 -fixing N. azollae, we conclude, dominated the microbiome of Azolla ferns. The persistent but less abundant heterotrophic Rhizobiales bacteria possibly contributed to lowering O2 levels in leaf pockets but did not release detectable amounts of the strong greenhouse gas N2 O.
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Affiliation(s)
- Laura W Dijkhuizen
- Molecular Plant Physiology Department, Utrecht University, Padualaan 8, Utrecht, 3584CH, the Netherlands
| | - Paul Brouwer
- Molecular Plant Physiology Department, Utrecht University, Padualaan 8, Utrecht, 3584CH, the Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Hoorn, 1797SZ, the Netherlands
| | - Gert-Jan Reichart
- Department of Earth Sciences, Utrecht University, Utrecht, 3508TA, the Netherlands
| | - Nils Koppers
- Department of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding ADIS/DNA Core Facility, Cologne, 50829, Germany
| | - Anthony M Bolger
- Institute of Botany and Molecular Genetics IBMG, IRWTH Aachen University, 52074, Aachen, Germany
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, NC, 27708, USA
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
| | - Shifeng Cheng
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
| | - Xin Liu
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
| | - Gane Ka-Shu Wong
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Kathleen Pryer
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Andreas Weber
- Department of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Andrea Bräutigam
- Department of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Henriette Schluepmann
- Molecular Plant Physiology Department, Utrecht University, Padualaan 8, Utrecht, 3584CH, the Netherlands
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Cabello-Yeves PJ, Zemskaya TI, Rosselli R, Coutinho FH, Zakharenko AS, Blinov VV, Rodriguez-Valera F. Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal. Appl Environ Microbiol 2018; 84:e02132-17. [PMID: 29079621 PMCID: PMC5734018 DOI: 10.1128/aem.02132-17] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 10/19/2017] [Indexed: 11/20/2022] Open
Abstract
We present a metagenomic study of Lake Baikal (East Siberia). Two samples obtained from the water column under the ice cover (5 and 20 m deep) in March 2016 have been deep sequenced and the reads assembled to generate metagenome-assembled genomes (MAGs) that are representative of the microbes living in this special environment. Compared with freshwater bodies studied around the world, Lake Baikal had an unusually high fraction of Verrucomicrobia Other groups, such as Actinobacteria and Proteobacteria, were in proportions similar to those found in other lakes. The genomes (and probably cells) tended to be small, presumably reflecting the extremely oligotrophic and cold prevalent conditions. Baikal microbes are novel lineages recruiting very little from other water bodies and are distantly related to other freshwater microbes. Despite their novelty, they showed the closest relationship to genomes discovered by similar approaches from other freshwater lakes and reservoirs. Some of them were particularly similar to MAGs from the Baltic Sea, which, although it is brackish, connected to the ocean, and much more eutrophic, has similar climatological conditions. Many of the microbes contained rhodopsin genes, indicating that, in spite of the decreased light penetration allowed by the thick ice/snow cover, photoheterotrophy could be widespread in the water column, either because enough light penetrates or because the microbes are already adapted to the summer ice-less conditions. We have found a freshwater SAR11 subtype I/II representative showing striking synteny with Pelagibacterubique strains, as well as a phage infecting the widespread freshwater bacterium PolynucleobacterIMPORTANCE Despite the increasing number of metagenomic studies on different freshwater bodies, there is still a missing component in oligotrophic cold lakes suffering from long seasonal frozen cycles. Here, we describe microbial genomes from metagenomic assemblies that appear in the upper water column of Lake Baikal, the largest and deepest freshwater body on Earth. This lake is frozen from January to May, which generates conditions that include an inverted temperature gradient (colder up), decrease in light penetration due to ice, and, especially, snow cover, and oligotrophic conditions more similar to the open-ocean and high-altitude lakes than to other freshwater or brackish systems. As could be expected, most reconstructed genomes are novel lineages distantly related to others in cold environments, like the Baltic Sea and other freshwater lakes. Among them, there was a broad set of streamlined microbes with small genomes/intergenic spacers, including a new nonmarine Pelagibacter-like (subtype I/II) genome.
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Affiliation(s)
- Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Tamara I Zemskaya
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Riccardo Rosselli
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Felipe H Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Alexandra S Zakharenko
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Vadim V Blinov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
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Dijkhuizen LW, Brouwer P, Bolhuis H, Reichart G, Koppers N, Huettel B, Bolger AM, Li F, Cheng S, Liu X, Wong GK, Pryer K, Weber A, Bräutigam A, Schluepmann H. Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N 2 but may denitrify. THE NEW PHYTOLOGIST 2018; 217:453-466. [PMID: 29084347 PMCID: PMC5901025 DOI: 10.1111/nph.14843] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 09/05/2017] [Indexed: 05/18/2023]
Abstract
Dinitrogen fixation by Nostoc azollae residing in specialized leaf pockets supports prolific growth of the floating fern Azolla filiculoides. To evaluate contributions by further microorganisms, the A. filiculoides microbiome and nitrogen metabolism in bacteria persistently associated with Azolla ferns were characterized. A metagenomic approach was taken complemented by detection of N2 O released and nitrogen isotope determinations of fern biomass. Ribosomal RNA genes in sequenced DNA of natural ferns, their enriched leaf pockets and water filtrate from the surrounding ditch established that bacteria of A. filiculoides differed entirely from surrounding water and revealed species of the order Rhizobiales. Analyses of seven cultivated Azolla species confirmed persistent association with Rhizobiales. Two distinct nearly full-length Rhizobiales genomes were identified in leaf-pocket-enriched samples from ditch grown A. filiculoides. Their annotation revealed genes for denitrification but not N2 -fixation. 15 N2 incorporation was active in ferns with N. azollae but not in ferns without. N2 O was not detectably released from surface-sterilized ferns with the Rhizobiales. N2 -fixing N. azollae, we conclude, dominated the microbiome of Azolla ferns. The persistent but less abundant heterotrophic Rhizobiales bacteria possibly contributed to lowering O2 levels in leaf pockets but did not release detectable amounts of the strong greenhouse gas N2 O.
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Affiliation(s)
- Laura W. Dijkhuizen
- Molecular Plant Physiology DepartmentUtrecht UniversityPadualaan 8Utrecht3584CHthe Netherlands
| | - Paul Brouwer
- Molecular Plant Physiology DepartmentUtrecht UniversityPadualaan 8Utrecht3584CHthe Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology and BiogeochemistryNetherlands Institute for Sea Research (NIOZ)Utrecht UniversityDen Hoorn1797SZthe Netherlands
| | - Gert‐Jan Reichart
- Department of Earth SciencesUtrecht UniversityUtrecht3508TAthe Netherlands
| | - Nils Koppers
- Department of Plant BiochemistryCluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorf40225Germany
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding ADIS/DNA Core FacilityCologne50829Germany
| | - Anthony M. Bolger
- Institute of Botany and Molecular Genetics IBMGIRWTH Aachen University52074AachenGermany
| | - Fay‐Wei Li
- Department of BiologyDuke UniversityDurhamNC27708USA
- Boyce Thompson Institute for Plant ResearchCornell UniversityIthacaNY14853USA
| | - Shifeng Cheng
- Beijing Genomics Institute‐ShenzhenShenzhen518083China
| | - Xin Liu
- Beijing Genomics Institute‐ShenzhenShenzhen518083China
| | - Gane Ka‐Shu Wong
- Beijing Genomics Institute‐ShenzhenShenzhen518083China
- Department of Biological SciencesUniversity of AlbertaEdmontonABT6G 2E9Canada
| | | | - Andreas Weber
- Department of Plant BiochemistryCluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorf40225Germany
| | - Andrea Bräutigam
- Department of Plant BiochemistryCluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorf40225Germany
| | - Henriette Schluepmann
- Molecular Plant Physiology DepartmentUtrecht UniversityPadualaan 8Utrecht3584CHthe Netherlands
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117
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Su J, Sun H, Liu J, Guo Z, Fan G, Gu G, Wang G. Complete genome sequence of a novel lytic bacteriophage isolated from Ralstonia solanacearum. Arch Virol 2017; 162:3919-3923. [PMID: 28929273 DOI: 10.1007/s00705-017-3555-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 07/31/2017] [Indexed: 10/18/2022]
Abstract
A lytic podophage RSPI1 was isolated from tobacco field soil collected in Fujian Province, South China using host bacterium Ralstonia solanacearum Tb15-14. Whole genome sequencing of this phage was performed using the high-throughput Ion Torrent PGM Sequencer. The complete genome of RSPI1 was 43,211 bp in length with a mean DNA G + C content of 61.5%. A total of 48 open reading frames were identified with lengths ranging from 132 bp to 5,061 bp, of which, 11, 12 and 25 were identified as functional, structural and unknown genes, respectively. A BLAST analysis revealed that this phage genome had a query cover of 78-79% and a highest identity of 84% with four podophages that infect Burkholderia pseudomallei. Two neighbor-joining phylogenetic trees were constructed using phage DNA polymerase I and tail fiber protein sequences and showed that this phage is closely related to Burkholderia phage Bp-AMP1, and also related to several phages that infect Ralstonia solanacearum. These findings indicate that RSPI1 is a novel phage that infects the notorious plant pathogen Ralstonia solanacearum.
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Affiliation(s)
- Jingfang Su
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Hongwei Sun
- Mudanjiang Tobacco Research Institute, Heilongjiang Branch of China National Tobacco Corporation, Mudangjiang, 157011, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Zhaokui Guo
- Mudanjiang Tobacco Research Institute, Heilongjiang Branch of China National Tobacco Corporation, Mudangjiang, 157011, China
| | - Guoquan Fan
- Virus-free Seedling, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Gang Gu
- Tobacco Agricultural Institute of Fujian Tobacco Monopoly Bureau, Fuzhou, 350003, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
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118
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Ren Q, Wang C, Jin M, Lan J, Ye T, Hui K, Tan J, Wang Z, Wyckoff GJ, Wang W, Han GZ. Co-option of bacteriophage lysozyme genes by bivalve genomes. Open Biol 2017; 7:rsob.160285. [PMID: 28100665 PMCID: PMC5303276 DOI: 10.1098/rsob.160285] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/14/2016] [Indexed: 01/08/2023] Open
Abstract
Eukaryotes have occasionally acquired genetic material through horizontal gene transfer (HGT). However, little is known about the evolutionary and functional significance of such acquisitions. Lysozymes are ubiquitous enzymes that degrade bacterial cell walls. Here, we provide evidence that two subclasses of bivalves (Heterodonta and Palaeoheterodonta) acquired a lysozyme gene via HGT, building on earlier findings. Phylogenetic analyses place the bivalve lysozyme genes within the clade of bacteriophage lysozyme genes, indicating that the bivalves acquired the phage-type lysozyme genes from bacteriophages, either directly or through intermediate hosts. These bivalve lysozyme genes underwent dramatic structural changes after their co-option, including intron gain and fusion with other genes. Moreover, evidence suggests that recurrent gene duplication occurred in the bivalve lysozyme genes. Finally, we show the co-opted lysozymes exhibit a capacity for antibacterial action, potentially augmenting the immune function of related bivalves. This represents an intriguing evolutionary strategy in the eukaryote–microbe arms race, in which the genetic materials of bacteriophages are co-opted by eukaryotes, and then used by eukaryotes to combat bacteria, using a shared weapon against a common enemy.
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Affiliation(s)
- Qian Ren
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, People's Republic of China
| | - Chunyang Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, People's Republic of China.,State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China
| | - Min Jin
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, SOA, Xiamen 361005, People's Republic of China
| | - Jiangfeng Lan
- College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Ting Ye
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
| | - Kaimin Hui
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, People's Republic of China
| | - Jingmin Tan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, People's Republic of China
| | - Zheng Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, People's Republic of China
| | - Gerald J Wyckoff
- Divison of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
| | - Wen Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, People's Republic of China
| | - Guan-Zhu Han
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, People's Republic of China
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119
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Abstract
Bacteriophages are numerically the most abundant DNA-containing entities in the oligotrophic ocean, yet how specific phage populations vary over time and space remains to be fully explored. Here, we conducted a metagenomic time-series survey of double-stranded DNA phages throughout the water column in the North Pacific Subtropical Gyre, encompassing 1.5 years from depths of 25 to 1,000 m. Viral gene sequences were identified in assembled metagenomic samples, yielding an estimated 172,385 different viral gene families. Viral marker gene distributions suggested that lysogeny was more prevalent at mesopelagic depths than in surface waters, consistent with prior prophage induction studies using mitomycin C. A total of 129 ALOHA viral genomes and genome fragments from 20 to 108 kbp were selected for further study, which represented the most abundant phages in the water column. Phage genotypes displayed discrete population structures. Most phages persisted throughout the time-series and displayed a strong depth structure that mirrored the stratified depth distributions of co-occurring bacterial taxa in the water column. Mesopelagic phages were distinct from surface water phages with respect to diversity, gene content, putative life histories, and temporal persistence, reflecting depth-dependent differences in host genomic architectures and phage reproductive strategies. The spatiotemporal distributions of the most abundant open-ocean bacteriophages that we report here provide new insight into viral temporal persistence, life history, and virus-host-environment interactions throughout the open-ocean water column. The North Pacific Subtropical Gyre represents one of the largest biomes on the planet, where microbial communities are central mediators of ecosystem dynamics and global biogeochemical cycles. Critical members of these communities are the viruses of marine bacteria, which can alter microbial metabolism and significantly influence their survival and productivity. To better understand these viral assemblages, we conducted genomic analyses of planktonic viruses over a seasonal cycle to ocean depths of 1,000 m. We identified 172,385 different viral gene families and 129 unique virus genotypes in this open-ocean setting. The spatiotemporal distributions of the most abundant open-ocean viruses that we report here provide new insights into viral temporal variability, life history, and virus-host-environment interactions throughout the water column.
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120
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Bistolas KSI, Besemer RM, Rudstam LG, Hewson I. Distribution and Inferred Evolutionary Characteristics of a Chimeric ssDNA Virus Associated with Intertidal Marine Isopods. Viruses 2017; 9:v9120361. [PMID: 29186875 PMCID: PMC5744136 DOI: 10.3390/v9120361] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/22/2017] [Accepted: 11/23/2017] [Indexed: 12/30/2022] Open
Abstract
Aquatic invertebrates are common reservoirs of a rapidly expanding group of circular Rep-encoding ssDNA (CRESS-DNA) viruses. This study identified and explored the phylogenetic relationship between novel CRESS-DNA viral genotypes associated with Pacific intertidal isopods Idotea wosnesenskii, Idotea resecata, and Gnorimosphaeroma oregonensis. One genotype associated with I. wosnesenskii, IWaV278, shared sequence similarity and genomic features with Tombusviridae (ssRNA) and Circoviridae (ssDNA) genomes and was putatively assigned to the Cruciviridae clade comprising chimeric viruses. The complete genome of IWaV278 (3478 nt) was computationally completed, validated via Sanger sequencing, and exhibited sequence conservation and codon usage patterns analogous to other members of the Cruciviridae. Viral surveillance (qPCR) indicated that this virus was temporally transient (present in 2015, but not 2017), specific to I. wosnesenskii at a single collection site (Washington, DC, USA), more prevalent among male specimens, and frequently detected within exoskeletal structures. 18S rRNA sequences identified two alveolate protists associated with IWaV278-positive tissues and mechanical epibiont removal of ciliated exoskeletal structures eliminated viral detection, suggesting that the putative host of IWaV278 may be an epibiont of I. wosnesenskii. This investigation provides additional phylogenetic evidence to resolve Cruciviridae evolution and offers insight into the biogeography, specificity, and potential host of a crucivirus genotype.
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Affiliation(s)
| | - Ryan M Besemer
- New Visions Life Sciences, Boards of Cooperative Educational Services of New York State, Ithaca, NY 14850, USA.
- University of North Carolina at Wilmington, Wilmington, NC 28403, USA.
| | - Lars G Rudstam
- Department of Natural Resources and the Cornell Biological Field Station, Cornell University, Bridgeport, NY 14850, USA.
| | - Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY 14850, USA.
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121
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Leigh BA, Djurhuus A, Breitbart M, Dishaw LJ. The gut virome of the protochordate model organism, Ciona intestinalis subtype A. Virus Res 2017; 244:137-146. [PMID: 29155033 DOI: 10.1016/j.virusres.2017.11.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 11/14/2017] [Accepted: 11/14/2017] [Indexed: 02/06/2023]
Abstract
The identification of host-specific bacterial and viral communities associated with diverse animals has led to the concept of the metaorganism, which defines the animal and all of its associated microbes as a single unit. Here we sequence the viruses found in the gut (i.e., the gut virome) of the marine invertebrate model system, Ciona intestinalis subtype A, in samples collected one year apart. We present evidence for a host-associated virome that is distinct from the surrounding seawater and contains some temporally-stable members. Comparison of gut tissues before and after starvation in virus-free water enabled the differentiation between the Ciona-specific virome and transient viral communities associated with dietary sources. The Ciona gut viromes were dominated by double-stranded DNA tailed phages (Order Caudovirales) and sequence assembly yielded a number of complete circular phage genomes, most of which were highly divergent from known genomes. Unique viral communities were found in distinct gut niches (stomach, midgut and hindgut), paralleling the compartmentalization of bacterial communities. Additionally, integrase and excisionase genes, including many that are similar to prophage sequences within the genomes of bacterial genera belonging to the Ciona core microbiome, were prevalent in the viromes, indicating the active induction of prophages within the gut ecosystem. Knowledge of the gut virome of this model organism lays the foundation for studying the interactions between viruses, bacteria, and host immunity.
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Affiliation(s)
- Brittany A Leigh
- University of South Florida, College of Marine Science, St. Petersburg, FL, USA; University of South Florida, Department of Pediatrics, Children's Research Institute, St. Petersburg, FL, USA
| | - Anni Djurhuus
- University of South Florida, College of Marine Science, St. Petersburg, FL, USA
| | - Mya Breitbart
- University of South Florida, College of Marine Science, St. Petersburg, FL, USA
| | - Larry J Dishaw
- University of South Florida, Department of Pediatrics, Children's Research Institute, St. Petersburg, FL, USA.
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122
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Abstract
Marine microbial communities exert a large influence on ocean ecosystem processes, and viruses in these communities play key roles in controlling microbial abundances, nutrient cycling, and productivity. We show here that dominant viruses in the open ocean persist for long time periods and that many appear tightly locked in coordinated diel oscillations with their bacterial hosts. The persistent structure of viral assemblages, as well as synchronized daily oscillations of viruses and hosts, are in part the result of the regular diurnal coupling of viral and host replication cycles. Collectively, our results suggest that viruses, as key components of marine ecosystems, are intrinsically synchronized with the daily rhythms of microbial community processes in the ocean’s photic zone. Viruses are fundamental components of marine microbial communities that significantly influence oceanic productivity, biogeochemistry, and ecosystem processes. Despite their importance, the temporal activities and dynamics of viral assemblages in natural settings remain largely unexplored. Here we report the transcriptional activities and variability of dominant dsDNA viruses in the open ocean’s euphotic zone over daily and seasonal timescales. While dsDNA viruses exhibited some fluctuation in abundance in both cellular and viral size fractions, the viral assemblage was remarkably stable, with the most abundant viral types persisting over many days. More extended time series indicated that long-term persistence (>1 y) was the rule for most dsDNA viruses observed, suggesting that both core viral genomes as well as viral community structure were conserved over interannual periods. Viral gene transcription in host cell assemblages revealed diel cycling among many different viral types. Most notably, an afternoon peak in cyanophage transcriptional activity coincided with a peak in Prochlorococcus DNA replication, indicating coordinated diurnal coupling of virus and host reproduction. In aggregate, our analyses suggested a tightly synchronized diel coupling of viral and cellular replication cycles in both photoautotrophic and heterotrophic bacterial hosts. A surprising consequence of these findings is that diel cycles in the ocean’s photic zone appear to be universal organizing principles that shape ecosystem dynamics, ecological interactions, and biogeochemical cycling of both cellular and acellular community components.
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123
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Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon. mSphere 2017; 2:mSphere00366-17. [PMID: 28989970 PMCID: PMC5628290 DOI: 10.1128/msphere.00366-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 08/18/2017] [Indexed: 11/20/2022] Open
Abstract
The Amazon River forms a vast plume in the Atlantic Ocean that can extend for more than 1,000 km. Microbial communities promote a globally relevant carbon sink system in the plume. Despite the importance of viruses for the global carbon cycle, the diversity and the possible roles of viruses in the Amazonia are poorly understood. The present work assesses, for the first time, the abundance and diversity of viruses simultaneously in the river and ocean in order to elucidate their possible roles. DNA sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes from the 12 river and ocean locations. Viral diversity was clearly distinguished by river and ocean. Bacteriophages were the most abundant and occurred throughout the continuum. Viruses that infect eukaryotes were more abundant in the river, whereas phages appeared to have strong control over the host prokaryotic populations in the plume. The Amazon River watershed and its associated plume comprise a vast continental and oceanic area. The microbial activities along this continuum contribute substantially to global carbon and nutrient cycling, and yet there is a dearth of information on the diversity, abundance, and possible roles of viruses in this globally important river. The aim of this study was to elucidate the diversity and structure of virus assemblages of the Amazon River-ocean continuum. Environmental viral DNA sequences were obtained for 12 locations along the river’s lower reach (n = 5) and plume (n = 7). Sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes. Despite the spatial connectivity mediated by the river, virome analyses and physical-chemical water parameters clearly distinguished river and plume ecosystems. Bacteriophages were ubiquitous in the continuum and were more abundant in the transition region. Eukaryotic viruses occurred mostly in the river, while the plume had more viruses of autotrophic organisms (Prochlorococcus, Synechococcus) and heterotrophic bacteria (Pelagibacter). The viral families Microviridae and Myoviridae were the most abundant and occurred throughout the continuum. The major functions of the genes in the continuum involved viral structures and life cycles, and viruses from plume locations and Tapajós River showed the highest levels of functional diversity. The distribution patterns of the viral assemblages were defined not only by the occurrence of possible hosts but also by water physical and chemical parameters, especially salinity. The findings presented here help to improve understanding of the possible roles of viruses in the organic matter cycle along the river-ocean continuum. IMPORTANCE The Amazon River forms a vast plume in the Atlantic Ocean that can extend for more than 1,000 km. Microbial communities promote a globally relevant carbon sink system in the plume. Despite the importance of viruses for the global carbon cycle, the diversity and the possible roles of viruses in the Amazon are poorly understood. The present work assesses, for the first time, the abundance and diversity of viruses simultaneously in the river and ocean in order to elucidate their possible roles. DNA sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes from the 12 river and ocean locations. Viral diversity was clearly distinguished by river and ocean. Bacteriophages were the most abundant and occurred throughout the continuum. Viruses that infect eukaryotes were more abundant in the river, whereas phages appeared to have strong control over the host prokaryotic populations in the plume.
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López-Pérez M, Haro-Moreno JM, Gonzalez-Serrano R, Parras-Moltó M, Rodriguez-Valera F. Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters. PLoS Genet 2017; 13:e1007018. [PMID: 28945750 PMCID: PMC5628999 DOI: 10.1371/journal.pgen.1007018] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/05/2017] [Accepted: 09/13/2017] [Indexed: 11/18/2022] Open
Abstract
Marine viruses play a critical role not only in the global geochemical cycles but also in the biology and evolution of their hosts. Despite their importance, viral diversity remains underexplored mostly due to sampling and cultivation challenges. Direct sequencing approaches such as viromics has provided new insights into the marine viral world. As a complementary approach, we analysed 24 microbial metagenomes (>0.2 μm size range) obtained from six sites in the Mediterranean Sea that vary by depth, season and filter used to retrieve the fraction. Filter-size comparison showed a significant number of viral sequences that were retained on the larger-pore filters and were different from those found in the viral fraction from the same sample, indicating that some important viral information is missing using only assembly from viromes. Besides, we were able to describe 1,323 viral genomic fragments that were more than 10Kb in length, of which 36 represented complete viral genomes including some of them retrieved from a cross-assembly from different metagenomes. Host prediction based on sequence methods revealed new phage groups belonging to marine prokaryotes like SAR11, Cyanobacteria or SAR116. We also identified the first complete virophage from deep seawater and a new endemic clade of the recently discovered Marine group II Euryarchaeota virus. Furthermore, analysis of viral distribution using metagenomes and viromes indicated that most of the new phages were found exclusively in the Mediterranean Sea and some of them, mostly the ones recovered from deep metagenomes, do not recruit in any database probably indicating higher variability and endemicity in Mediterranean bathypelagic waters. Together these data provide the first detailed picture of genomic diversity, spatial and depth variations of viral communities within the Mediterranean Sea using metagenome assembly.
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Affiliation(s)
- Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Campus de San Juan, San Juan de Alicante, Spain
| | - Jose M. Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Campus de San Juan, San Juan de Alicante, Spain
| | - Rafael Gonzalez-Serrano
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Campus de San Juan, San Juan de Alicante, Spain
| | - Marcos Parras-Moltó
- Centro de Biología Molecular 'Severo Ochoa' (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Cantoblanco, Madrid, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Campus de San Juan, San Juan de Alicante, Spain
- * E-mail:
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125
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Xie ZX, Chen F, Zhang SF, Wang MH, Zhang H, Kong LF, Dai MH, Hong HS, Lin L, Wang DZ. Metaproteomics of marine viral concentrates reveals key viral populations and abundant periplasmic proteins in the oligotrophic deep chlorophyll maximum of the South China Sea. Environ Microbiol 2017; 20:477-491. [PMID: 28925544 DOI: 10.1111/1462-2920.13937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 09/15/2017] [Accepted: 09/16/2017] [Indexed: 12/14/2022]
Abstract
Viral concentrates (VCs), containing bioinformative DNA and proteins, have been used to study viral diversity, viral metagenomics and virus-host interactions in natural ecosystems. Besides viruses, VCs also contain many noncellular biological components including diverse functional proteins. Here, we used a shotgun proteomic approach to characterize the proteins of VCs collected from the oligotrophic deep chlorophyll maximum (DCM) of the South China Sea. Proteins of viruses infecting picophytoplankton, that is, cyanobacteria and prasinophytes, and heterotrophic bacterioplankton, such as SAR11 and SAR116, dominated the viral proteome. Almost no proteins from RNA viruses or known gene transfer agents were detected, suggesting that they were not abundant at the sampling site. Remarkably, nonviral proteins made up about two thirds of VC proteins, including overwhelmingly abundant periplasmic transporters for nutrient acquisition and proteins for diverse cellular processes, that is, translation, energy metabolism and one carbon metabolism. Interestingly, three 56 kDa selenium-binding proteins putatively involved in peroxide reduction from gammaproteobacteria were abundant in the VCs, suggesting active removal of peroxide compounds at DCM. Our study demonstrated that metaproteomics provides a valuable avenue to explore the diversity and structure of the viral community and also the pivotal biological functions affiliated with microbes in the natural environment.
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Affiliation(s)
- Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Shu-Feng Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Ming-Hua Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Hao Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Ling-Fen Kong
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Min-Han Dai
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Hua-Sheng Hong
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
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Magill DJ, Krylov VN, Shaburova OV, McGrath JW, Allen CCR, Quinn JP, Kulakov LA. Pf16 and phiPMW: Expanding the realm of Pseudomonas putida bacteriophages. PLoS One 2017; 12:e0184307. [PMID: 28877269 PMCID: PMC5587285 DOI: 10.1371/journal.pone.0184307] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 08/21/2017] [Indexed: 12/22/2022] Open
Abstract
We present the analysis of two novel Pseudomonas putida phages, pf16 and phiPMW. Pf16 represents a peripherally related T4-like phage, and is the first of its kind infecting a Pseudomonad, with evidence suggesting cyanophage origins. Extensive divergence has resulted in pf16 occupying a newly defined clade designated as the pf16-related phages, lying at the interface of the Schizo T-Evens and Exo T-Evens. Recombination with an ancestor of the P. putida phage AF is likely responsible for the tropism of this phage. phiPMW represents a completely novel Pseudomonas phage with a genome containing substantial genetic novelty through its many hypothetical proteins. Evidence suggests that this phage has been extensively shaped through gene transfer events and vertical evolution. Phylogenetics shows that this phage has an evolutionary history involving FelixO1-related viruses but is in itself highly distinct from this group.
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Affiliation(s)
- Damian J. Magill
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, Northern Ireland
| | - Victor N. Krylov
- Department of Microbiology, Laboratory for Genetics of Bacteriophages, I.I. Mechnikov Research Institute for Vaccines and Sera, Moscow, Russia
| | - Olga V. Shaburova
- Department of Microbiology, Laboratory for Genetics of Bacteriophages, I.I. Mechnikov Research Institute for Vaccines and Sera, Moscow, Russia
| | - John W. McGrath
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, Northern Ireland
| | - Christopher C. R. Allen
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, Northern Ireland
| | - John P. Quinn
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, Northern Ireland
| | - Leonid A. Kulakov
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, Northern Ireland
- * E-mail:
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127
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Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data. Nat Protoc 2017; 12:1673-1682. [PMID: 28749930 DOI: 10.1038/nprot.2017.063] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The analysis of large microbiome data sets holds great promise for the delineation of the biological and metabolic functioning of living organisms and their role in the environment. In the midst of this genomic puzzle, viruses, especially those that infect microbial communities, represent a major reservoir of genetic diversity with great impact on biogeochemical cycles and organismal health. Overcoming the limitations associated with virus detection directly from microbiomes can provide key insights into how ecosystem dynamics are modulated. Here, we present a computational protocol for accurate detection and grouping of viral sequences from microbiome samples. Our approach relies on an expanded and curated set of viral protein families used as bait to identify viral sequences directly from metagenomic assemblies. This protocol describes how to use the viral protein families catalog (∼7 h) and recommended filters for the detection of viral contigs in metagenomic samples (∼6 h), and it describes the specific parameters for a nucleotide-sequence-identity-based method of organizing the viral sequences into quasi-species taxonomic-level groups (∼10 min).
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128
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Coutinho FH, Silveira CB, Gregoracci GB, Thompson CC, Edwards RA, Brussaard CPD, Dutilh BE, Thompson FL. Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans. Nat Commun 2017; 8:15955. [PMID: 28677677 PMCID: PMC5504273 DOI: 10.1038/ncomms15955] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 05/12/2017] [Indexed: 12/19/2022] Open
Abstract
Marine viruses are key drivers of host diversity, population dynamics and biogeochemical cycling and contribute to the daily flux of billions of tons of organic matter. Despite recent advancements in metagenomics, much of their biodiversity remains uncharacterized. Here we report a data set of 27,346 marine virome contigs that includes 44 complete genomes. These outnumber all currently known phage genomes in marine habitats and include members of previously uncharacterized lineages. We designed a new method for host prediction based on co-occurrence associations that reveals these viruses infect dominant members of the marine microbiome such as Prochlorococcus and Pelagibacter. A negative association between host abundance and the virus-to-host ratio supports the recently proposed Piggyback-the-Winner model of reduced phage lysis at higher host densities. An analysis of the abundance patterns of viruses throughout the oceans revealed how marine viral communities adapt to various seasonal, temperature and photic regimes according to targeted hosts and the diversity of auxiliary metabolic genes.
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Affiliation(s)
- Felipe H. Coutinho
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21944970, Brazil
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen 6500 HB, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University (UU), Utrecht 3584 CH, The Netherlands
| | - Cynthia B. Silveira
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21944970, Brazil
- Biology Department, San Diego State University (SDSU), San Diego, California 92182, USA
| | - Gustavo B. Gregoracci
- Departamento de Ciências do Mar, Universidade Federal de São Paulo (UNIFESP), Baixada Santista 11070100, Brazil
| | - Cristiane C. Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21944970, Brazil
| | - Robert A. Edwards
- Biology Department, San Diego State University (SDSU), San Diego, California 92182, USA
| | - Corina P. D. Brussaard
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, PO Box 59, 1790 AB Den Burg Texel, The Netherlands
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Bas E. Dutilh
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21944970, Brazil
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen 6500 HB, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University (UU), Utrecht 3584 CH, The Netherlands
| | - Fabiano L. Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21944970, Brazil
- Universidade Federal do Rio de Janeiro (UFRJ)/COPPE/SAGE, Rio de Janeiro 21941950, Brazil
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Tang K, Lin D, Zheng Q, Liu K, Yang Y, Han Y, Jiao N. Genomic, proteomic and bioinformatic analysis of two temperate phages in Roseobacter clade bacteria isolated from the deep-sea water. BMC Genomics 2017; 18:485. [PMID: 28655355 PMCID: PMC5488378 DOI: 10.1186/s12864-017-3886-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 06/20/2017] [Indexed: 02/08/2023] Open
Abstract
Background Marine phages are spectacularly diverse in nature. Dozens of roseophages infecting members of Roseobacter clade bacteria were isolated and characterized, exhibiting a very high degree of genetic diversity. In the present study, the induction of two temperate bacteriophages, namely, vB_ThpS-P1 and vB_PeaS-P1, was performed in Roseobacter clade bacteria isolated from the deep-sea water, Thiobacimonas profunda JLT2016 and Pelagibaca abyssi JLT2014, respectively. Two novel phages in morphological, genomic and proteomic features were presented, and their phylogeny and evolutionary relationships were explored by bioinformatic analysis. Results Electron microscopy showed that the morphology of the two phages were similar to that of siphoviruses. Genome sequencing indicated that the two phages were similar in size, organization, and content, thereby suggesting that these shared a common ancestor. Despite the presence of Mu-like phage head genes, the phages are more closely related to Rhodobacter phage RC1 than Mu phages in terms of gene content and sequence similarity. Based on comparative genomic and phylogenetic analysis, we propose a Mu-like head phage group to allow for the inclusion of Mu-like phages and two newly phages. The sequences of the Mu-like head phage group were widespread, occurring in each investigated metagenomes. Furthermore, the horizontal exchange of genetic material within the Mu-like head phage group might have involved a gene that was associated with phage phenotypic characteristics. Conclusions This study is the first report on the complete genome sequences of temperate phages that infect deep-sea roseobacters, belonging to the Mu-like head phage group. The Mu-like head phage group might represent a small but ubiquitous fraction of marine viral diversity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3886-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kai Tang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China.
| | - Dan Lin
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Keshao Liu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Yujie Yang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Yu Han
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China.
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Martinez-Hernandez F, Fornas O, Lluesma Gomez M, Bolduc B, de la Cruz Peña MJ, Martínez JM, Anton J, Gasol JM, Rosselli R, Rodriguez-Valera F, Sullivan MB, Acinas SG, Martinez-Garcia M. Single-virus genomics reveals hidden cosmopolitan and abundant viruses. Nat Commun 2017; 8:15892. [PMID: 28643787 PMCID: PMC5490008 DOI: 10.1038/ncomms15892] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/10/2017] [Indexed: 12/22/2022] Open
Abstract
Microbes drive ecosystems under constraints imposed by viruses. However, a lack of virus genome information hinders our ability to answer fundamental, biological questions concerning microbial communities. Here we apply single-virus genomics (SVGs) to assess whether portions of marine viral communities are missed by current techniques. The majority of the here-identified 44 viral single-amplified genomes (vSAGs) are more abundant in global ocean virome data sets than published metagenome-assembled viral genomes or isolates. This indicates that vSAGs likely best represent the dsDNA viral populations dominating the oceans. Species-specific recruitment patterns and virome simulation data suggest that vSAGs are highly microdiverse and that microdiversity hinders the metagenomic assembly, which could explain why their genomes have not been identified before. Altogether, SVGs enable the discovery of some of the likely most abundant and ecologically relevant marine viral species, such as vSAG 37-F6, which were overlooked by other methodologies.
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Affiliation(s)
- Francisco Martinez-Hernandez
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante 03690, Spain
| | - Oscar Fornas
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Carrer del Doctor Aiguader, 88, PRBB Building, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Carrer del Doctor Aiguader, 88, PRBB Building, Barcelona 08003, Spain
| | - Monica Lluesma Gomez
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante 03690, Spain
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, 105 Biological Sciences Building, 484 West 12th Avenue Columbus, Ohio 43210, USA
| | - Maria Jose de la Cruz Peña
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante 03690, Spain
| | - Joaquín Martínez Martínez
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, PO Box 380, East Boothbay, Maine 04544, USA
| | - Josefa Anton
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante 03690, Spain
| | - Josep M. Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Passeig Marítim, 47, Barcelona 08003, Spain
| | - Riccardo Rosselli
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Campus San Juan, San Juan, Alicante 03550, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Campus San Juan, San Juan, Alicante 03550, Spain
| | - Matthew B. Sullivan
- Department of Microbiology, The Ohio State University, 105 Biological Sciences Building, 484 West 12th Avenue Columbus, Ohio 43210, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, The Ohio State University, 105 Biological Sciences Building, 484 West 12th Avenue Columbus, Ohio 43210, USA
| | - Silvia G. Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Passeig Marítim, 47, Barcelona 08003, Spain
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante 03690, Spain
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Hayes S, Mahony J, Nauta A, van Sinderen D. Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches. Viruses 2017; 9:v9060127. [PMID: 28538703 PMCID: PMC5490804 DOI: 10.3390/v9060127] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/18/2017] [Accepted: 05/19/2017] [Indexed: 12/15/2022] Open
Abstract
Bacteriophages are ubiquitous and numerous parasites of bacteria and play a critical evolutionary role in virtually every ecosystem, yet our understanding of the extent of the diversity and role of phages remains inadequate for many ecological niches, particularly in cases in which the host is unculturable. During the past 15 years, the emergence of the field of viral metagenomics has drastically enhanced our ability to analyse the so-called viral ‘dark matter’ of the biosphere. Here, we review the evolution of viral metagenomic methodologies, as well as providing an overview of some of the most significant applications and findings in this field of research.
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Affiliation(s)
- Stephen Hayes
- School of Microbiology, University College Cork, Cork T12 YT20, Ireland.
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork T12 YT20, Ireland.
- APC Microbiome Institute, University College Cork, Cork T12 YT20, Ireland.
| | - Arjen Nauta
- Friesland Campina, Amersfoort 3800 BN, The Netherlands.
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork T12 YT20, Ireland.
- APC Microbiome Institute, University College Cork, Cork T12 YT20, Ireland.
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Parmar KM, Gaikwad SL, Dhakephalkar PK, Kothari R, Singh RP. Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics. Front Microbiol 2017; 8:559. [PMID: 28439260 PMCID: PMC5383658 DOI: 10.3389/fmicb.2017.00559] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/16/2017] [Indexed: 01/09/2023] Open
Abstract
Innovations in next-generation sequencing technology have introduced new avenues in microbial studies through “omics” approaches. This technology has considerably augmented the knowledge of the microbial world without isolation prior to their identification. With an enormous volume of bacterial “omics” data, considerable attempts have been recently invested to improve an insight into virosphere. The interplay between bacteriophages and their host has created a significant influence on the biogeochemical cycles, microbial diversity, and bacterial population regulation. This review highlights various concepts such as genomics, transcriptomics, proteomics, and metabolomics to infer the phylogenetic affiliation and function of bacteriophages and their impact on diverse microbial communities. Omics technologies illuminate the role of bacteriophage in an environment, the influences of phage proteins on the bacterial host and provide information about the genes important for interaction with bacteria. These investigations will reveal some of bio-molecules and biomarkers of the novel phage which demand to be unveiled.
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Affiliation(s)
| | | | | | - Ramesh Kothari
- Department of Biosciences, Saurashtra UniversityRajkot, India
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133
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Modelling plankton ecosystems in the meta-omics era. Are we ready? Mar Genomics 2017; 32:1-17. [DOI: 10.1016/j.margen.2017.02.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 02/24/2017] [Accepted: 02/25/2017] [Indexed: 12/30/2022]
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134
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Genetic and functional diversity of ubiquitous DNA viruses in selected Chinese agricultural soils. Sci Rep 2017; 7:45142. [PMID: 28327667 PMCID: PMC5361096 DOI: 10.1038/srep45142] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/15/2017] [Indexed: 01/21/2023] Open
Abstract
Viral community structures in complex agricultural soils are largely unknown. Electron microscopy and viromic analyses were conducted on six typical Chinese agricultural soil samples. Tailed bacteriophages, spherical and filamentous viral particles were identified by the morphological analysis. Based on the metagenomic analysis, single-stranded DNA viruses represented the largest viral component in most of the soil habitats, while the double-stranded DNA viruses belonging to the Caudovirales order were predominanted in Jiangxi-maize soils. The majority of functional genes belonged to the subsystem “phages, prophages, transposable elements, and plasmids”. Non-metric multidimensional analysis of viral community showed that the environment medium type was the most important driving factor for the viral community structure. For the major viral groups detected in all samples (Microviridae and Caudovirales), the two groups gathered viruses from different sites and similar genetic composition, indicating that viral diversity was high on a local point but relatively limited on a global scale. This is a novel report of viral diversity in Chinese agricultural soils, and the abundance, taxonomic, and functional diversity of viruses that were observed in different types of soils will aid future soil virome studies and enhance our understanding of the ecological functions of soil viruses.
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135
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Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean. mSphere 2017; 2:mSphere00359-16. [PMID: 28261669 PMCID: PMC5332604 DOI: 10.1128/msphere.00359-16] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/02/2017] [Indexed: 11/27/2022] Open
Abstract
Viruses are diverse and play significant ecological roles in marine ecosystems. However, our knowledge of genome-level diversity in viruses is biased toward those isolated from few culturable hosts. Here, we determined 1,352 nonredundant complete viral genomes from marine environments. Lifting the uncertainty that clouds short incomplete sequences, whole-genome-wide analysis suggests that these environmental genomes represent hundreds of putative novel viral genera. Predicted hosts include dominant groups of marine bacteria and archaea with no isolated viruses to date. Some of the viral genomes encode many functionally related enzymes, suggesting a strong selection pressure on these marine viruses to control cellular metabolisms by accumulating genes. Metagenomics has revealed the existence of numerous uncharacterized viral lineages, which are referred to as viral “dark matter.” However, our knowledge regarding viral genomes is biased toward culturable viruses. In this study, we analyzed 1,600 (1,352 nonredundant) complete double-stranded DNA viral genomes (10 to 211 kb) assembled from 52 marine viromes. Together with 244 previously reported uncultured viral genomes, a genome-wide comparison delineated 617 genus-level operational taxonomic units (OTUs) for these environmental viral genomes (EVGs). Of these, 600 OTUs contained no representatives from known viruses, thus putatively corresponding to novel viral genera. Predicted hosts of the EVGs included major groups of marine prokaryotes, such as marine group II Euryarchaeota and SAR86, from which no viruses have been isolated to date, as well as Flavobacteriaceae and SAR116. Our analysis indicates that marine cyanophages are already well represented in genome databases and that one of the EVGs likely represents a new cyanophage lineage. Several EVGs encode many enzymes that appear to function for an efficient utilization of iron-sulfur clusters or to enhance host survival. This suggests that there is a selection pressure on these marine viruses to accumulate genes for specific viral propagation strategies. Finally, we revealed that EVGs contribute to a 4-fold increase in the recruitment of photic-zone viromes compared with the use of current reference viral genomes. IMPORTANCE Viruses are diverse and play significant ecological roles in marine ecosystems. However, our knowledge of genome-level diversity in viruses is biased toward those isolated from few culturable hosts. Here, we determined 1,352 nonredundant complete viral genomes from marine environments. Lifting the uncertainty that clouds short incomplete sequences, whole-genome-wide analysis suggests that these environmental genomes represent hundreds of putative novel viral genera. Predicted hosts include dominant groups of marine bacteria and archaea with no isolated viruses to date. Some of the viral genomes encode many functionally related enzymes, suggesting a strong selection pressure on these marine viruses to control cellular metabolisms by accumulating genes.
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136
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Nayfach S, Pollard KS. Toward Accurate and Quantitative Comparative Metagenomics. Cell 2016; 166:1103-1116. [PMID: 27565341 DOI: 10.1016/j.cell.2016.08.007] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 04/11/2016] [Accepted: 08/03/2016] [Indexed: 01/08/2023]
Abstract
Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized.
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Affiliation(s)
- Stephen Nayfach
- Integrative Program in Quantitative Biology, University of California, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA 94158, USA; Division of Biostatistics, Institute for Human Genetics, and Institute for Computational Health Sciences, University of California, San Francisco, CA 94158, USA.
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137
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Wang X, Liu J, Yu Z, Jin J, Liu X, Wang G. Novel groups and unique distribution of phage phoH genes in paddy waters in northeast China. Sci Rep 2016; 6:38428. [PMID: 27910929 PMCID: PMC5133604 DOI: 10.1038/srep38428] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/09/2016] [Indexed: 11/10/2022] Open
Abstract
Although bacteriophages are ubiquitous in various environments, their genetic diversity is primarily investigated in pelagic marine environments. Corresponding studies in terrestrial environments are few. In this study, we conducted the first survey of phage diversity in the paddy ecosystem by targeting a new viral biomarker gene, phoH. A total of 424 phoH sequences were obtained from four paddy waters generated from a pot experiment with different soils collected from open paddy fields in northeast China. The majority of phoH sequences in paddy waters were novel, with the highest identity of ≤70% with known phoH sequences. Four unique groups (Group α, Group β, Group γ and Group δ) and seven new subgroups (Group 2b, Group 3d, Group 3e, Group 6a, Group 6b, Group 6c and Group 6d) were formed exclusively with the clones from the paddy waters, suggesting novel phage phoH groups exist in the paddy ecosystem. Additionally, the distribution proportions of phoH clones in different groups varied among paddy water samples, suggesting the phage community in paddy fields is biogeographically distributed. Furthermore, non-metric multidimensional scaling analysis indicated that phage phoH assemblages in paddy waters were distinct from those in marine waters.
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Affiliation(s)
- Xinzhen Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Zhenhua Yu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Jian Jin
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Xiaobing Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
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138
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Yuan Y, Gao M. Characteristics and complete genome analysis of a novel jumbo phage infecting pathogenic Bacillus pumilus causing ginger rhizome rot disease. Arch Virol 2016; 161:3597-3600. [PMID: 27619796 DOI: 10.1007/s00705-016-3053-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/05/2016] [Indexed: 01/22/2023]
Abstract
Tailed phages with genomes larger than 200 kbp are classified as jumbo phage and exhibit extremely high diversity. In this study, a novel jumbo phage, vB_BpuM_BpSp, infecting pathogenic Bacillus pumilus, the cause of ginger rhizome rot disease, was isolated. Notable features of phage vB_BpuM_BpSp are the large phage capsid of 137 nm and baseplate-attached curly tail fibers. The genome of the phage is 255,569 bp in size with G+C content of 25.9 %, and it shows low similarity to known biological entities. The phage genome contains 318 predicted coding sequences. Among these predicted coding sequences, 26 genes responsible for nucleotide metabolism were found, and seven structural genes could be identified. The findings of this study provide new understanding of the genetic diversity of phages.
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Affiliation(s)
- Yihui Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Meiying Gao
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.
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139
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Paez-Espino D, Chen IMA, Palaniappan K, Ratner A, Chu K, Szeto E, Pillay M, Huang J, Markowitz VM, Nielsen T, Huntemann M, K Reddy TB, Pavlopoulos GA, Sullivan MB, Campbell BJ, Chen F, McMahon K, Hallam SJ, Denef V, Cavicchioli R, Caffrey SM, Streit WR, Webster J, Handley KM, Salekdeh GH, Tsesmetzis N, Setubal JC, Pope PB, Liu WT, Rivers AR, Ivanova NN, Kyrpides NC. IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Res 2016; 45:D457-D465. [PMID: 27799466 PMCID: PMC5210529 DOI: 10.1093/nar/gkw1030] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/15/2016] [Accepted: 10/27/2016] [Indexed: 12/19/2022] Open
Abstract
Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community.
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Affiliation(s)
- David Paez-Espino
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - I-Min A Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Anna Ratner
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Ken Chu
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Ernest Szeto
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Manoj Pillay
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jinghua Huang
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Victor M Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Torben Nielsen
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Marcel Huntemann
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - T B K Reddy
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | | | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Barbara J Campbell
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Katherine McMahon
- Department of Civil and Environmental Engineering, Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
| | - Steve J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.,Genome Science, Technology, and Program in Bioinformatics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.,Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, BC V6T 1Z2, Canada.,ECOSCOPE Training Program, University of British Columbia, Vancouver, BC V6T 0A1, Canada
| | - Vincent Denef
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Sean M Caffrey
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 4V8, Canada
| | - Wolfgang R Streit
- Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg 22609, Germany
| | - John Webster
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Kim M Handley
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Ghasem H Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj 31535-1897, Iran
| | - Nicolas Tsesmetzis
- Shell International Exploration and Production Inc., Houston, TX 77082, USA
| | - Joao C Setubal
- Department of Biochemistry, Institute of Chemistry, Universidade de Sao Paulo, SP 05508-000, Brazil
| | - Phillip B Pope
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås 1432, Norway
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Adam R Rivers
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Natalia N Ivanova
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
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140
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Grazziotin AL, Koonin EV, Kristensen DM. Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation. Nucleic Acids Res 2016; 45:D491-D498. [PMID: 27789703 PMCID: PMC5210652 DOI: 10.1093/nar/gkw975] [Citation(s) in RCA: 234] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/08/2016] [Accepted: 10/21/2016] [Indexed: 11/13/2022] Open
Abstract
Viruses are the most abundant and diverse biological entities on earth, and while most of this diversity remains completely unexplored, advances in genome sequencing have provided unprecedented glimpses into the virosphere. The Prokaryotic Virus Orthologous Groups (pVOGs, formerly called Phage Orthologous Groups, POGs) resource has aided in this task over the past decade by using automated methods to keep pace with the rapid increase in genomic data. The uses of pVOGs include functional annotation of viral proteins, identification of genes and viruses in uncharacterized DNA samples, phylogenetic analysis, large-scale comparative genomics projects, and more. The pVOGs database represents a comprehensive set of orthologous gene families shared across multiple complete genomes of viruses that infect bacterial or archaeal hosts (viruses of eukaryotes will be added at a future date). The pVOGs are constructed within the Clusters of Orthologous Groups (COGs) framework that is widely used for orthology identification in prokaryotes. Since the previous release of the POGs, the size has tripled to nearly 3000 genomes and 300 000 proteins, and the number of conserved orthologous groups doubled to 9518. User-friendly webpages are available, including multiple sequence alignments and HMM profiles for each VOG. These changes provide major improvements to the pVOGs database, at a time of rapid advances in virus genomics. The pVOGs database is hosted jointly at the University of Iowa at http://dmk-brain.ecn.uiowa.edu/pVOGs and the NCBI at ftp://ftp.ncbi.nlm.nih.gov/pub/kristensen/pVOGs/home.html.
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Affiliation(s)
- Ana Laura Grazziotin
- Department of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, IA 52242, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - David M Kristensen
- Department of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, IA 52242, USA .,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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141
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Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, Pesant S, Kandels-Lewis S, Dimier C, Picheral M, Searson S, Cruaud C, Alberti A, Duarte CM, Gasol JM, Vaqué D, Bork P, Acinas SG, Wincker P, Sullivan MB. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 2016; 537:689-693. [PMID: 27654921 DOI: 10.1038/nature19366] [Citation(s) in RCA: 466] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 08/12/2016] [Indexed: 12/26/2022]
Abstract
Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting 'global ocean virome' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.
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Affiliation(s)
- Simon Roux
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jennifer R Brum
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
- Department of Marine Biology, Federal University of Rio de Janeiro, Rio de Janeiro, CEP 21941-902, Brazil
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, A-1090 Vienna, Austria
- Austrian Polar Research Institute, A-1090 Vienna, Austria
| | - Bonnie T Poulos
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Natalie Solonenko
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Elena Lara
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC Barcelona E0800, Spain
- Institute of Marine Sciences (CNR-ISMAR), National Research Council, 30122 Venezia, Italy
| | - Julie Poulain
- CEA - Institut de Génomique, GENOSCOPE, 91057 Evry, France
| | - Stéphane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, 28359 Bremen, Germany
- MARUM, Bremen University, 28359 Bremen, Germany
| | - Stefanie Kandels-Lewis
- Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Directors' Research, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Céline Dimier
- CNRS, UMR 7144, EPEP, Station Biologique de Roscoff, 29680 Roscoff, France
- Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, 29680 Roscoff, France
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, Paris Sciences et Lettres Research University, CNRS UMR 8197, INSERM U1024, F-75005 Paris, France
| | - Marc Picheral
- CNRS, UMR 7093, Laboratoire d'océanographie de Villefranche, Observatoire Océanologique, 06230 Villefranche-sur-mer, France
- Sorbonne Universités, UPMC Université Paris 06, UMR 7093, Observatoire Océanologique, 06230 Villefranche-sur-mer, France
| | - Sarah Searson
- CNRS, UMR 7093, Laboratoire d'océanographie de Villefranche, Observatoire Océanologique, 06230 Villefranche-sur-mer, France
- Sorbonne Universités, UPMC Université Paris 06, UMR 7093, Observatoire Océanologique, 06230 Villefranche-sur-mer, France
| | - Corinne Cruaud
- CEA - Institut de Génomique, GENOSCOPE, 91057 Evry, France
| | | | - Carlos M Duarte
- Mediterranean Institute of Advanced Studies, CSIC-UiB, 21-07190 Esporles, Mallorca, Spain
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal 23955-6900, Saudi Arabia
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC Barcelona E0800, Spain
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC Barcelona E0800, Spain
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC Barcelona E0800, Spain
| | - Patrick Wincker
- CEA - Institut de Génomique, GENOSCOPE, 91057 Evry, France
- CNRS, UMR 8030, 91057 Evry, France
- Université d'Evry, UMR 8030, 91057 Evry, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio 43210, USA
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142
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Jurtz VI, Villarroel J, Lund O, Voldby Larsen M, Nielsen M. MetaPhinder-Identifying Bacteriophage Sequences in Metagenomic Data Sets. PLoS One 2016; 11:e0163111. [PMID: 27684958 PMCID: PMC5042410 DOI: 10.1371/journal.pone.0163111] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 09/04/2016] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages are the most abundant biological entity on the planet, but at the same time do not account for much of the genetic material isolated from most environments due to their small genome sizes. They also show great genetic diversity and mosaic genomes making it challenging to analyze and understand them. Here we present MetaPhinder, a method to identify assembled genomic fragments (i.e.contigs) of phage origin in metagenomic data sets. The method is based on a comparison to a database of whole genome bacteriophage sequences, integrating hits to multiple genomes to accomodate for the mosaic genome structure of many bacteriophages. The method is demonstrated to out-perform both BLAST methods based on single hits and methods based on k-mer comparisons. MetaPhinder is available as a web service at the Center for Genomic Epidemiology https://cge.cbs.dtu.dk/services/MetaPhinder/, while the source code can be downloaded from https://bitbucket.org/genomicepidemiology/metaphinder or https://github.com/vanessajurtz/MetaPhinder.
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Affiliation(s)
| | - Julia Villarroel
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Ole Lund
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Mette Voldby Larsen
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Morten Nielsen
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- * E-mail:
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143
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Wang X, Liu J, Yu Z, Jin J, Liu X, Wang G. Novel groups of cyanobacterial podovirus DNA polymerase (pol) genes exist in paddy waters in northeast China. FEMS Microbiol Ecol 2016; 92:fiw192. [DOI: 10.1093/femsec/fiw192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2016] [Indexed: 11/12/2022] Open
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144
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Ghai R, Mehrshad M, Mizuno CM, Rodriguez-Valera F. Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria. ISME JOURNAL 2016; 11:304-308. [PMID: 27505348 DOI: 10.1038/ismej.2016.110] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/09/2016] [Accepted: 07/04/2016] [Indexed: 01/20/2023]
Abstract
Low-GC Actinobacteria are among the most abundant and widespread microbes in freshwaters and have largely resisted all cultivation efforts. Consequently, their phages have remained totally unknown. In this work, we have used deep metagenomic sequencing to assemble eight complete genomes of the first tailed phages that infect freshwater Actinobacteria. Their genomes encode the actinobacterial-specific transcription factor whiB, frequently found in mycobacteriophages and also in phages infecting marine pelagic Actinobacteria. Its presence suggests a common and widespread strategy of modulation of host transcriptional machinery upon infection via this transcriptional switch. We present evidence that some whiB-carrying phages infect the acI lineage of Actinobacteria. At least one of them encodes the ADP-ribosylating component of the widespread bacterial AB toxins family (for example, clostridial toxin). We posit that the presence of this toxin reflects a 'trojan horse' strategy, providing protection at the population level to the abundant host microbes against eukaryotic predators.
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Affiliation(s)
- Rohit Ghai
- Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Center of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Maliheh Mehrshad
- Departamento de Producción Vegetal y Microbiología, Evolutionary Genomics Group, Universidad Miguel Hernandez, Alicante, Spain.,Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Carolina Megumi Mizuno
- Departamento de Producción Vegetal y Microbiología, Evolutionary Genomics Group, Universidad Miguel Hernandez, Alicante, Spain.,Unit of Molecular Biology of the Gene in Extremophiles, Department of Microbiology, Institut Pasteur, Paris, France
| | - Francisco Rodriguez-Valera
- Departamento de Producción Vegetal y Microbiología, Evolutionary Genomics Group, Universidad Miguel Hernandez, Alicante, Spain
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145
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A novel roseobacter phage possesses features of podoviruses, siphoviruses, prophages and gene transfer agents. Sci Rep 2016; 6:30372. [PMID: 27460944 PMCID: PMC4961962 DOI: 10.1038/srep30372] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/30/2016] [Indexed: 11/09/2022] Open
Abstract
Bacteria in the Roseobacter lineage have been studied extensively due to their significant biogeochemical roles in the marine ecosystem. However, our knowledge on bacteriophage which infects the Roseobacter clade is still very limited. Here, we report a new bacteriophage, phage DSS3Φ8, which infects marine roseobacter Ruegeria pomeroyi DSS-3. DSS3Φ8 is a lytic siphovirus. Genomic analysis showed that DSS3Φ8 is most closely related to a group of siphoviruses, CbK-like phages, which infect freshwater bacterium Caulobacter crescentus. DSS3Φ8 contains a smaller capsid and has a reduced genome size (146 kb) compared to the CbK-like phages (205-279 kb). DSS3Φ8 contains the DNA polymerase gene which is closely related to T7-like podoviruses. DSS3Φ8 also contains the integrase and repressor genes, indicating its potential to involve in lysogenic cycle. In addition, four GTA (gene transfer agent) genes were identified in the DSS3Φ8 genome. Genomic analysis suggests that DSS3Φ8 is a highly mosaic phage that inherits the genetic features from siphoviruses, podoviruses, prophages and GTAs. This is the first report of CbK-like phages infecting marine bacteria. We believe phage isolation is still a powerful tool that can lead to discovery of new phages and help interpret the overwhelming unknown sequences in the viral metagenomics.
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146
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Abstract
The deep sea is a massive, largely oligotrophic ecosystem, stretched over nearly 65% of the planet’s surface. Deep-sea planktonic communities are almost completely dependent upon organic carbon sinking from the productive surface, forming a vital component of global biogeochemical cycles. However, despite their importance, viruses from the deep ocean remain largely unknown. Here, we describe the first complete genomes of deep-sea viruses assembled from metagenomic fosmid libraries. “Candidatus Pelagibacter” (SAR11) phage HTVC010P and Puniceispirillum phage HMO-2011 are considered the most abundant cultured marine viruses known to date. Remarkably, some of the viruses described here recruited as many reads from deep waters as these viruses do in the photic zone, and, considering the gigantic scale of the bathypelagic habitat, these genomes provide information about what could be some of the most abundant viruses in the world at large. Their role in the viral shunt in the global ocean could be very significant. Despite the challenges encountered in inferring the identity of their hosts, we identified one virus predicted to infect members of the globally distributed SAR11 cluster. We also identified a number of putative proviruses from diverse taxa, including deltaproteobacteria, bacteroidetes, SAR11, and gammaproteobacteria. Moreover, our findings also indicate that lysogeny is the preferred mode of existence for deep-sea viruses inhabiting an energy-limited environment, in sharp contrast to the predominantly lytic lifestyle of their photic-zone counterparts. Some of the viruses show a widespread distribution, supporting the tenet “everything is everywhere” for the deep-ocean virome. The deep sea is among the largest known habitats and a critical cog in biogeochemical cycling but remains underexplored in its microbiology. Even more than is the case for its prokaryotic community, our knowledge of its viral component has remained limited by the paucity of information provided by studies dependent upon short sequence fragments. In this work, we attempt to fill this existing gap by using a combination of classical fosmid libraries with next-generation sequencing and assembly to recover long viral genomic fragments. We have sequenced ca. 6,000 fosmids from two metagenomics libraries made from prokaryotic biomass from the deep Mediterranean Sea and recovered twenty-eight complete viral genomes, all of them novel and quite distinct from all previously described viral genomes. They are preferentially found in deeper waters and are widely distributed all over the oceans. To our knowledge, this is the first report on complete and cosmopolitan viral genomes from the bathypelagic habitat.
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147
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López-Pérez M, Kimes NE, Haro-Moreno JM, Rodriguez-Valera F. Not All Particles Are Equal: The Selective Enrichment of Particle-Associated Bacteria from the Mediterranean Sea. Front Microbiol 2016; 7:996. [PMID: 27446036 PMCID: PMC4916215 DOI: 10.3389/fmicb.2016.00996] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/09/2016] [Indexed: 11/13/2022] Open
Abstract
We have used two metagenomic approaches, direct sequencing of natural samples and sequencing after enrichment, to characterize communities of prokaryotes associated to particles. In the first approximation, different size filters (0.22 and 5 μm) were used to identify prokaryotic microbes of free-living and particle-attached bacterial communities in the Mediterranean water column. A subtractive metagenomic approach was used to characterize the dominant microbial groups in the large size fraction that were not present in the free-living one. They belonged mainly to Actinobacteria, Planctomycetes, Flavobacteria and Proteobacteria. In addition, marine microbial communities enriched by incubation with different kinds of particulate material have been studied by metagenomic assembly. Different particle kinds (diatomaceous earth, sand, chitin and cellulose) were colonized by very different communities of bacteria belonging to Roseobacter, Vibrio, Bacteriovorax, and Lacinutrix that were distant relatives of genomes already described from marine habitats. Besides, using assembly from deep metagenomic sequencing from the particle-specific enrichments we were able to determine a total of 20 groups of contigs (eight of them with >50% completeness) and reconstruct de novo five new genomes of novel species within marine clades (>79% completeness and <1.8% contamination). We also describe for the first time the genome of a marine Rhizobiales phage that seems to infect a broad range of Alphaproteobacteria and live in habitats as diverse as soil, marine sediment and water column. The metagenomic recruitment of the communities found by direct sequencing of the large size filter and by enrichment had nearly no overlap. These results indicate that these reconstructed genomes are part of the rare biosphere which exists at nominal levels under natural conditions.
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148
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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: 37] [Impact Index Per Article: 4.6] [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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Shapiro JA. Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process. BIOLOGY 2016; 5:E27. [PMID: 27338490 PMCID: PMC4929541 DOI: 10.3390/biology5020027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/20/2016] [Accepted: 06/02/2016] [Indexed: 01/15/2023]
Abstract
The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess "Read-Write Genomes" they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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150
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Yuan Y, Gao M. Proteomic Analysis of a Novel Bacillus Jumbo Phage Revealing Glycoside Hydrolase As Structural Component. Front Microbiol 2016; 7:745. [PMID: 27242758 PMCID: PMC4870245 DOI: 10.3389/fmicb.2016.00745] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 05/03/2016] [Indexed: 12/31/2022] Open
Abstract
Tailed phages with genomes of larger than 200 kbp are classified as Jumbo phages and exhibited extremely high uncharted diversity. The genomic annotation of Jumbo phage is often disappointing because most of the predicted proteins, including structural proteins, failed to make good hits to the sequences in the databases. In this study, 23 proteins of a novel Bacillus Jumbo phage, vB_BpuM_BpSp, were identified as phage structural proteins by the structural proteome analysis, including 14 proteins of unknown function, 5 proteins with predicted function as structural proteins, a glycoside hydrolase, a Holliday junction resolvase, a RNA-polymerase β-subunit, and a host-coding portal protein, which might be hijacked from the host strain during phage virion assembly. The glycoside hydrolase (Gp255) was identified as phage virion component and was found to interact with the phage baseplate protein. Gp255 shows specific lytic activity against the phage host strain GR8 and has high temperature tolerance. In situ peptidoglycan-hydrolyzing activities analysis revealed that the expressed Gp255 and phage structural proteome exhibited glycoside hydrolysis activity against the tested GR8 cell extracts. This study identified the first functional individual structural glycoside hydrolase in phage virion. The presence of activated glycoside hydrolase in phage virions might facilitate the injection of the phage genome during infection by forming pores on the bacterial cell wall.
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Affiliation(s)
| | - Meiying Gao
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan, China
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