1
|
Unterer M, Khan Mirzaei M, Deng L. Targeted Single-Phage Isolation Reveals Phage-Dependent Heterogeneous Infection Dynamics. Microbiol Spectr 2023; 11:e0514922. [PMID: 37067443 PMCID: PMC10269501 DOI: 10.1128/spectrum.05149-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/21/2023] [Indexed: 04/18/2023] Open
Abstract
Due to rising antibiotic resistance, there is an urgent need for different treatment options for multidrug-resistant infections. One alternative under investigation is phage therapy, which uses phages to treat bacterial infections. Although phages are highly abundant in the environment, not all phages are suitable for phage therapy, and finding efficient phages that lack undesirable traits such as bacterial virulence factors is challenging. Here, we developed a targeted single-phage isolation method to detect and isolate phages of interest and to characterize their kinetics in a high-throughput manner. This assay has also revealed cell-to-cell variations at a single-cell level among cells infected with the same phage species, as well as among cells infected with different phage species. IMPORTANCE The spread of multidrug-resistant bacteria is a global human health threat, and without immediate action we are fast approaching a postantibiotic era. One possible alternative to antibiotics is the use of phages, that is, bacterial viruses. However, the isolation of phages that effectively kill their target bacteria has proven challenging. In addition, isolated phages must go through significant characterization before their efficacy is measured. The method developed in this work can isolate single phage particles on the basis of their similarity to previously characterized phages while excluding those with known undesirable traits, such as bacterial toxins, as well as characterizing their kinetics. Using this method, we revealed significant cell-to-cell variations in phage kinetics at a single-cell level among highly virulent phages. These results shed some light on unknown phage-bacterium interactions at the single-cell level.
Collapse
Affiliation(s)
- Magdalena Unterer
- Institute of Virology, Helmholtz Centre Munich, German Research Centre for Environmental Health, Neuherberg, Germany
- Chair for Prevention of Microbial Infectious Diseases, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mohammadali Khan Mirzaei
- Institute of Virology, Helmholtz Centre Munich, German Research Centre for Environmental Health, Neuherberg, Germany
- Chair for Prevention of Microbial Infectious Diseases, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Li Deng
- Institute of Virology, Helmholtz Centre Munich, German Research Centre for Environmental Health, Neuherberg, Germany
- Chair for Prevention of Microbial Infectious Diseases, School of Life Sciences, Technical University of Munich, Freising, Germany
| |
Collapse
|
2
|
Lloréns-Rico V, Simcock JA, Huys GR, Raes J. Single-cell approaches in human microbiome research. Cell 2022; 185:2725-2738. [DOI: 10.1016/j.cell.2022.06.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/20/2022] [Accepted: 06/20/2022] [Indexed: 10/17/2022]
|
3
|
Jang HB, Chittick L, Li YF, Zablocki O, Sanderson CM, Carrillo A, van den Engh G, Sullivan MB. Viral tag and grow: a scalable approach to capture and characterize infectious virus-host pairs. ISME COMMUNICATIONS 2022; 2:12. [PMID: 37938680 PMCID: PMC9723727 DOI: 10.1038/s43705-022-00093-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/06/2022] [Accepted: 01/13/2022] [Indexed: 04/27/2023]
Abstract
Viral metagenomics (viromics) has reshaped our understanding of DNA viral diversity, ecology, and evolution across Earth's ecosystems. However, viromics now needs approaches to link newly discovered viruses to their host cells and characterize them at scale. This study adapts one such method, sequencing-enabled viral tagging (VT), to establish "Viral Tag and Grow" (VT + Grow) to rapidly capture and characterize viruses that infect a cultivated target bacterium, Pseudoalteromonas. First, baseline cytometric and microscopy data improved understanding of how infection conditions and host physiology impact populations in VT flow cytograms. Next, we extensively evaluated "and grow" capability to assess where VT signals reflect adsorption alone or wholly successful infections that lead to lysis. Third, we applied VT + Grow to a clonal virus stock, which, coupled to traditional plaque assays, revealed significant variability in burst size-findings that hint at a viral "individuality" parallel to the microbial phenotypic heterogeneity literature. Finally, we established a live protocol for public comment and improvement via protocols.io to maximally empower the research community. Together these efforts provide a robust foundation for VT researchers, and establish VT + Grow as a promising scalable technology to capture and characterize viruses from mixed community source samples that infect cultivable bacteria.
Collapse
Affiliation(s)
- Ho Bin Jang
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Lauren Chittick
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Yueh-Fen Li
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Olivier Zablocki
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | | | - Alfonso Carrillo
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | | | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA.
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|
4
|
Phages in the infant gut: a framework for virome development during early life. ISME JOURNAL 2021; 16:323-330. [PMID: 34417565 PMCID: PMC8776839 DOI: 10.1038/s41396-021-01090-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 01/21/2023]
|
5
|
Abstract
Bacteria acquire novel DNA through horizontal gene transfer (HGT), a process that enables an organism to rapidly adapt to changing environmental conditions, provides a competitive edge and potentially alters its relationship with its host. Although the HGT process is routinely exploited in laboratories, there is a surprising disconnect between what we know from laboratory experiments and what we know from natural environments, such as the human gut microbiome. Owing to a suite of newly available computational algorithms and experimental approaches, we have a broader understanding of the genes that are being transferred and are starting to understand the ecology of HGT in natural microbial communities. This Review focuses on these new technologies, the questions they can address and their limitations. As these methods are applied more broadly, we are beginning to recognize the full extent of HGT possible within a microbiome and the punctuated dynamics of HGT, specifically in response to external stimuli. Furthermore, we are better characterizing the complex selective pressures on mobile genetic elements and the mechanisms by which they interact with the bacterial host genome.
Collapse
Affiliation(s)
- Ilana Lauren Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
6
|
Silveira CB, Luque A, Rohwer F. The landscape of lysogeny across microbial community density, diversity and energetics. Environ Microbiol 2021; 23:4098-4111. [PMID: 34121301 DOI: 10.1111/1462-2920.15640] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 12/11/2022]
Abstract
Lysogens are common at high bacterial densities, an observation that contrasts with the prevailing view of lysogeny as a low-density refugium strategy. Here, we review the mechanisms regulating lysogeny in complex communities and show that the additive effects of coinfections, diversity and host energic status yield a bimodal distribution of lysogeny as a function of microbial densities. At high cell densities (above 106 cells ml-1 or g-1 ) and low diversity, coinfections by two or more phages are frequent and excess energy availability stimulates inefficient metabolism. Both mechanisms favour phage integration and characterize the Piggyback-the-Winner dynamic. At low densities (below 105 cells ml-1 or g-1 ), starvation represses lytic genes and extends the time window for lysogenic commitment, resulting in a higher frequency of coinfections that cause integration. This pattern follows the predictions of the refugium hypothesis. At intermediary densities (between 105 and 106 cells ml-1 or g-1 ), encounter rates and efficient energy metabolism favour lysis. This may involve Kill-the-Winner lytic dynamics and induction. Based on these three regimes, we propose a framework wherein phage integration occurs more frequently at both ends of the host density gradient, with distinct underlying molecular mechanisms (coinfections and host metabolism) dominating at each extreme.
Collapse
Affiliation(s)
- Cynthia B Silveira
- Department of Biology, University of Miami, 1301 Memorial Drive, Coral Gables, FL, 33143, USA.,Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - Antoni Luque
- Viral Information Institute, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA.,Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA.,Computational Science Research Center, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Forest Rohwer
- Viral Information Institute, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA.,Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| |
Collapse
|
7
|
Interaction dynamics and virus-host range for estuarine actinophages captured by epicPCR. Nat Microbiol 2021; 6:630-642. [PMID: 33633401 DOI: 10.1038/s41564-021-00873-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 01/28/2021] [Indexed: 01/31/2023]
Abstract
Viruses impact microbial diversity, gene flow and function through virus-host interactions. Although metagenomics surveys are rapidly cataloguing viral diversity, methods are needed to capture specific virus-host interactions in situ. Here, we leveraged metagenomics and repurposed emulsion paired isolation-concatenation PCR (epicPCR) to investigate viral diversity and virus-host interactions in situ over time in an estuarine environment. The method fuses a phage marker, the ribonucleotide reductase gene, with the host 16S rRNA gene of infected bacterial cells within emulsion droplets providing single-cell resolution for dozens of samples. EpicPCR captured in situ virus-host interactions for viral clades with no closely related database representatives. Abundant freshwater Actinobacteria lineages, in particular Rhodoluna sp., were the most common hosts for these poorly characterized viruses, with interactions correlated with environmental factors. Multiple methods used to identify virus-host interactions, including epicPCR, identified different and largely non-overlapping interactions within the vast virus-host interaction space. Tracking virus-host interaction dynamics also revealed that multi-host viruses had significantly longer periods with observed virus-host interactions, whereas single-host viruses were observed interacting with hosts at lower minimum abundances, suggesting more efficient interactions. Capturing in situ interactions with epicPCR revealed environmental and ecological factors shaping virus-host interactions, highlighting epicPCR as a valuable technique in viral ecology.
Collapse
|
8
|
Goettsch W, Beerenwinkel N, Deng L, Dölken L, Dutilh BE, Erhard F, Kaderali L, von Kleist M, Marquet R, Matthijnssens J, McCallin S, McMahon D, Rattei T, Van Rij RP, Robertson DL, Schwemmle M, Stern-Ginossar N, Marz M. ITN-VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics. Viruses 2021; 13:v13050766. [PMID: 33925452 PMCID: PMC8145447 DOI: 10.3390/v13050766] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/15/2021] [Accepted: 04/22/2021] [Indexed: 11/16/2022] Open
Abstract
Many recent studies highlight the fundamental importance of viruses. Besides their important role as human and animal pathogens, their beneficial, commensal or harmful functions are poorly understood. By developing and applying tailored bioinformatical tools in important virological models, the Marie Skłodowska-Curie Initiative International Training Network VIROINF will provide a better understanding of viruses and the interaction with their hosts. This will open the door to validate methods of improving viral growth, morphogenesis and development, as well as to control strategies against unwanted microorganisms. The key feature of VIROINF is its interdisciplinary nature, which brings together virologists and bioinformaticians to achieve common goals.
Collapse
Affiliation(s)
- Winfried Goettsch
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, 07743 Jena, Germany;
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland;
| | - Li Deng
- Institute of Virology, Helmholtz Centre Munich and Technical University Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany;
| | - Lars Dölken
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, 97078 Würzburg, Germany; (L.D.); (F.E.)
| | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Hugo R. Kruytgebouw, Padualaan 8, 3584 CH Utrecht, The Netherlands;
| | - Florian Erhard
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, 97078 Würzburg, Germany; (L.D.); (F.E.)
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Max von Kleist
- MF1 Bioinformatics, Robert Koch-Institute, 13353 Berlin, Germany;
| | - Roland Marquet
- CNRS, Architecture et Réactivité de l’ARN, Université de Strasbourg, UPR 9002 Strasbourg, France;
| | - Jelle Matthijnssens
- Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Herestraat 49 Box 1040, 3000 Leuven, Belgium;
| | - Shawna McCallin
- Department of Neuro-Urology, Balgrist University Hospital, University of Zürich, Forchstrasse 340, 8008 Zürich, Switzerland;
| | - Dino McMahon
- Institute of Biology, Freie Universität Berlin, Schwendenerstr. 1, 14195 Berlin, Germany;
| | - Thomas Rattei
- Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria;
| | - Ronald P. Van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands;
| | - David L. Robertson
- MRC, University of Glasgow Centre for Virus Research (CVR), 464 Bearsden Road, Glasgow G61 1QH, UK;
| | - Martin Schwemmle
- Institute of Virology, Medical Center—University of Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany;
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel;
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, 07743 Jena, Germany;
- FLI Leibniz Institute for Age Research, 07745 Jena, Germany
- Correspondence: ; Tel.: +49-3641-9-46480
| |
Collapse
|
9
|
Moon K, Cho JC. Metaviromics coupled with phage-host identification to open the viral 'black box'. J Microbiol 2021; 59:311-323. [PMID: 33624268 DOI: 10.1007/s12275-021-1016-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 12/22/2022]
Abstract
Viruses are found in almost all biomes on Earth, with bacteriophages (phages) accounting for the majority of viral particles in most ecosystems. Phages have been isolated from natural environments using the plaque assay and liquid medium-based dilution culturing. However, phage cultivation is restricted by the current limitations in the number of culturable bacterial strains. Unlike prokaryotes, which possess universally conserved 16S rRNA genes, phages lack universal marker genes for viral taxonomy, thus restricting cultureindependent analyses of viral diversity. To circumvent these limitations, shotgun viral metagenome sequencing (i.e., metaviromics) has been developed to enable the extensive sequencing of a variety of viral particles present in the environment and is now widely used. Using metaviromics, numerous studies on viral communities have been conducted in oceans, lakes, rivers, and soils, resulting in many novel phage sequences. Furthermore, auxiliary metabolic genes such as ammonic monooxygenase C and β-lactamase have been discovered in viral contigs assembled from viral metagenomes. Current attempts to identify putative bacterial hosts of viral metagenome sequences based on sequence homology have been limited due to viral sequence variations. Therefore, culture-independent approaches have been developed to predict bacterial hosts using single-cell genomics and fluorescentlabeling. This review focuses on recent viral metagenome studies conducted in natural environments, especially in aquatic ecosystems, and their contributions to phage ecology. Here, we concluded that although metaviromics is a key tool for the study of viral ecology, this approach must be supplemented with phage-host identification, which in turn requires the cultivation of phage-bacteria systems.
Collapse
Affiliation(s)
- Kira Moon
- Biological Resources Utilization Division, Honam National Institute of Biological Resources, Mokpo, 58762, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea.
| |
Collapse
|
10
|
Low HZ, Böhnlein C, Sprotte S, Wagner N, Fiedler G, Kabisch J, Franz CMAP. Fast and Easy Phage-Tagging and Live/Dead Analysis for the Rapid Monitoring of Bacteriophage Infection. Front Microbiol 2021; 11:602444. [PMID: 33391221 PMCID: PMC7775415 DOI: 10.3389/fmicb.2020.602444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/25/2020] [Indexed: 11/23/2022] Open
Abstract
Use of bacteriophages, which are viruses that kill bacteria, for biocontrol of pathogens and antimicrobial resistant bacteria has become increasingly important in recent years. As traditional culture-based methods are laborious and time-consuming, practicable use of bacteriophages will hinge on development of rapid and high throughput methods to analyze, characterize and screen large bacteriophage libraries. We thus established a novel method to fluorescently tag bacteriophages for virus screening and interaction studies, without the need for complicated and laborious purification procedures or genetic engineering of viruses to express fluorescent proteins. Bacteriophage PMBT14 was tagged using DNA dye Syto 13. Simply by using a membrane filter, tagged bacteriophages can be separated from non-sequestered excess dye rapidly, effortlessly, and cheaply. The procedure takes less than 30 min and makes use of simple laboratory consumables that are already commonly used for bacteriophage preparations. As proof of concept, we present here flow cytometric methods to analyze bacteriophage binding, infection and killing that are very accessible for high throughput analysis. We show that the resulting fluorescently tagged bacteriophage can be used to specifically stain its host bacterium Pseudomonas fluorescens DSM 50090. Individual fluorescent bacteriophages, their binding to and initial infection of bacteria could also be observed using confocal microscopy. The infection process was halted by the metabolic inhibitor sodium azide, suggesting a requirement of host metabolic processes for penetration by PMBT14. Flow cytometric live/dead assays was used as a complementary method to determine bacteriophage infection of its host. We made preliminary efforts to adapt the tagging method to two other bacteriophages and discuss potential pitfalls and solutions in the use of tagged phages. Fluorescent phage tagging has previously been demonstrated to facilitate analysis of bacteriophage–host interactions. The method adopted in this study makes it fast, easy as well as cost effective.
Collapse
Affiliation(s)
- Hui Zhi Low
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Christina Böhnlein
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Sabrina Sprotte
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Natalia Wagner
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Gregor Fiedler
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jan Kabisch
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| |
Collapse
|
11
|
de Jonge PA, von Meijenfeldt FB, Costa AR, Nobrega FL, Brouns SJ, Dutilh BE. Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts. iScience 2020; 23:101439. [PMID: 32823052 PMCID: PMC7452251 DOI: 10.1016/j.isci.2020.101439] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/23/2020] [Accepted: 08/03/2020] [Indexed: 01/08/2023] Open
Abstract
An important viromics challenge is associating bacteriophages to hosts. To address this, we developed adsorption sequencing (AdsorpSeq), a readily implementable method to measure phages that are preferentially adsorbed to specific host cell envelopes. AdsorpSeq thus captures the key initial infection cycle step. Phages are added to cell envelopes, adsorbed phages are isolated through gel electrophoresis, after which adsorbed phage DNA is sequenced and compared with the full virome. Here, we show that AdsorpSeq allows for separation of phages based on receptor-adsorbing capabilities. Next, we applied AdsorpSeq to identify phages in a wastewater virome that adsorb to cell envelopes of nine bacteria, including important pathogens. We detected 26 adsorbed phages including common and rare members of the virome, a minority being related to previously characterized phages. We conclude that AdsorpSeq is an effective new tool for rapid characterization of environmental phage adsorption, with a proof-of-principle application to Gram-negative host cell envelopes.
Collapse
Affiliation(s)
- Patrick A. de Jonge
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, 3584 CH Utrecht, the Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands
| | | | - Ana Rita Costa
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands
| | - Franklin L. Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands
| | - Stan J.J. Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands
| | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, 3584 CH Utrecht, the Netherlands
| |
Collapse
|
12
|
Quantification of Lysogeny Caused by Phage Coinfections in Microbial Communities from Biophysical Principles. mSystems 2020; 5:5/5/e00353-20. [PMID: 32934113 PMCID: PMC7498681 DOI: 10.1128/msystems.00353-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The association of temperate phages and bacterial hosts during lysogeny manipulates microbial dynamics from the oceans to the human gut. Lysogeny is well studied in laboratory models, but its environmental drivers remain unclear. Here, we quantified the probability of lysogenization caused by phage coinfections, a well-known trigger of lysogeny, in marine and gut microbial environments. Coinfections were quantified by developing a biophysical model that incorporated the traits of viral and bacterial communities. Lysogenization via coinfection was more frequent in highly productive environments like the gut, due to higher microbial densities and higher phage adsorption rates. At low cell densities, lysogenization occurred in bacteria with long duplication times. These results bridge the molecular understanding of lysogeny with the ecology of complex microbial communities. Temperate phages can associate with their bacterial host to form a lysogen, often modifying the phenotype of the host. Lysogens are dominant in the microbially dense environment of the mammalian gut. This observation contrasts with the long-standing hypothesis of lysogeny being favored at low microbial densities, such as in oligotrophic marine environments. Here, we hypothesized that phage coinfections—a well-understood molecular mechanism of lysogenization—increase at high microbial abundances. To test this hypothesis, we developed a biophysical model of coinfection for marine and gut microbiomes. The model stochastically sampled ranges of phage and bacterial concentrations, adsorption rates, lysogenic commitment times, and community diversity from each environment. In 90% of the sampled marine communities, less than 10% of the bacteria were predicted to be lysogenized via coinfection. In contrast, 25% of the sampled gut communities displayed more than 25% of lysogenization. The probability of lysogenization in the gut was a consequence of the higher densities and higher adsorption rates. These results suggest that, on average, coinfections can form two trillion lysogens in the human gut every day. In marine microbiomes, which were characterized by lower densities and phage adsorption rates, lysogeny via coinfection was still possible for communities with long lysogenic commitment times. Our study indicates that different physical factors causing coinfections can reconcile the traditional view of lysogeny at poor host growth (long commitment times) and the recent Piggyback-the-Winner framework proposing that lysogeny is favored in rich environments (high densities and adsorption rates). IMPORTANCE The association of temperate phages and bacterial hosts during lysogeny manipulates microbial dynamics from the oceans to the human gut. Lysogeny is well studied in laboratory models, but its environmental drivers remain unclear. Here, we quantified the probability of lysogenization caused by phage coinfections, a well-known trigger of lysogeny, in marine and gut microbial environments. Coinfections were quantified by developing a biophysical model that incorporated the traits of viral and bacterial communities. Lysogenization via coinfection was more frequent in highly productive environments like the gut, due to higher microbial densities and higher phage adsorption rates. At low cell densities, lysogenization occurred in bacteria with long duplication times. These results bridge the molecular understanding of lysogeny with the ecology of complex microbial communities.
Collapse
|
13
|
Guerin E, Hill C. Shining Light on Human Gut Bacteriophages. Front Cell Infect Microbiol 2020; 10:481. [PMID: 33014897 PMCID: PMC7511551 DOI: 10.3389/fcimb.2020.00481] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/04/2020] [Indexed: 12/15/2022] Open
Abstract
The human gut is a complex environment that contains a multitude of microorganisms that are collectively termed the microbiome. Multiple factors have a role to play in driving the composition of human gut bacterial communities either toward homeostasis or the instability that is associated with many disease states. One of the most important forces are likely to be bacteriophages, bacteria-infecting viruses that constitute by far the largest portion of the human gut virome. Despite this, bacteriophages (phages) are the one of the least studied residents of the gut. This is largely due to the challenges associated with studying these difficult to culture entities. Modern high throughput sequencing technologies have played an important role in improving our understanding of the human gut phageome but much of the generated sequencing data remains uncharacterised. Overcoming this requires database-independent bioinformatic pipelines and even those phages that are successfully characterized only provide limited insight into their associated biological properties, and thus most viral sequences have been characterized as “viral dark matter.” Fundamental to understanding the role of phages in shaping the human gut microbiome, and in turn perhaps influencing human health, is how they interact with their bacterial hosts. An essential aspect is the isolation of novel phage-bacteria host pairs by direct isolation through various screening methods, which can transform in silico phages into a biological reality. However, this is also beset with multiple challenges including culturing difficulties and the use of traditional methods, such as plaquing, which may bias which phage-host pairs that can be successfully isolated. Phage-bacteria interactions may be influenced by many aspects of complex human gut biology which can be difficult to reproduce under laboratory conditions. Here we discuss some of the main findings associated with the human gut phageome to date including composition, our understanding of phage-host interactions, particularly the observed persistence of virulent phages and their hosts, as well as factors that may influence these highly intricate relationships. We also discuss current methodologies and bottlenecks hindering progression in this field and identify potential steps that may be useful in overcoming these hurdles.
Collapse
Affiliation(s)
- Emma Guerin
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| |
Collapse
|
14
|
Göller PC, Haro-Moreno JM, Rodriguez-Valera F, Loessner MJ, Gómez-Sanz E. Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil. MICROBIOME 2020; 8:17. [PMID: 32046783 PMCID: PMC7014677 DOI: 10.1186/s40168-020-0795-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 01/20/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND Bacteriophages (phages) are the most numerous biological entities on Earth and play a crucial role in shaping microbial communities. Investigating the bacteriophage community from soil will shed light not only on the yet largely unknown phage diversity, but may also result in novel insights towards their functioning in the global biogeochemical nutrient cycle and their significance in earthbound ecosystems. Unfortunately, information about soil viromes is rather scarce compared to aquatic environments, due to the heterogeneous soil matrix, which rises major technical difficulties in the extraction process. Resolving these technical challenges and establishing a standardized extraction protocol is, therefore, a fundamental prerequisite for replicable results and comparative virome studies. RESULTS We here report the optimization of protocols for the extraction of phage DNA from agricultural soil preceding metagenomic analysis such that the protocol can equally be harnessed for phage isolation. As an optimization strategy, soil samples were spiked with Listeria phage A511 (Myovirus), Staphylococcus phage 2638AΔLCR (Siphovirus) and Escherichia phage T7 (Podovirus) (each 106 PFU/g soil). The efficacy of phage (i) elution, (ii) filtration, (iii) concentration and (iv) DNA extraction methods was tested. Successful extraction routes were selected based on spiked phage recovery and low bacterial 16S rRNA gene contaminants. Natural agricultural soil viromes were then extracted with the optimized methods and shotgun sequenced. Our approach yielded sufficient amounts of inhibitor-free viral DNA for shotgun sequencing devoid of amplification prior library preparation, and low 16S rRNA gene contamination levels (≤ 0.2‰). Compared to previously published protocols, the number of bacterial read contamination was decreased by 65%. In addition, 379 novel putative complete soil phage genomes (≤ 235 kb) were obtained from over 13,000 manually identified viral contigs, promising the discovery of a large, previously inaccessible viral diversity. CONCLUSION We have shown a considerably enhanced extraction of the soil phage community by protocol optimization that has proven robust in both culture-dependent as well as through viromic analyses. Our huge data set of manually curated soil viral contigs substantially increases the amount of currently available soil virome data, and provides insights into the yet largely undescribed soil viral sequence space.
Collapse
Affiliation(s)
- Pauline C Göller
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland
| | - Jose M Haro-Moreno
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland
| | - Elena Gómez-Sanz
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland.
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain.
| |
Collapse
|
15
|
Ghanem N, Stanley CE, Harms H, Chatzinotas A, Wick LY. Mycelial Effects on Phage Retention during Transport in a Microfluidic Platform. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:11755-11763. [PMID: 31532190 DOI: 10.1021/acs.est.9b03502] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phages (i.e., viruses that infect bacteria) have been considered as good tracers for the hydrological transport of colloids and (pathogenic) viruses. However, little is known about interactions of phages with (fungal) mycelia as the prevalent soil microbial biomass. Forming extensive and dense networks, mycelia provide significant surfaces for phage-hyphal interactions. Here, for the first time, we quantified the mycelial retention of phages in a microfluidic platform that allowed for defined fluid exchange around hyphae. Two common lytic tracer phages (Escherichia coli phage T4 and marine phage PSA-HS2) and two mycelia of differing surface properties (Coprinopsis cinerea and Pythium ultimum) were employed. Phage-hyphal interaction energies were approximated by the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) approach of colloidal interaction. Our data show initial hyphal retention of phages of up to ≈4 × 107 plaque-forming unit (PFU) mm-2 (≈2550 PFU mm-2 s-1) with a retention efficiency depending on the hyphal and, to a lesser extent, the phage surface properties. Experimental data were supported by XDLVO calculations, which revealed the highest attractive forces for the interaction between hydrophobic T4 phages and hydrophobic C. cinerea surfaces. Our data suggest that mycelia may be relevant for the retention of phages in the subsurface and need to be considered in subsurface phage tracer studies. Mycelia-phage interactions may further be exploited for the development of novel strategies to reduce or hinder the transport of undesirable (bio) colloidal entities in environmental filter systems.
Collapse
Affiliation(s)
- Nawras Ghanem
- Department of Environmental Microbiology , Helmholtz Centre for Environmental Research - UFZ , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Claire E Stanley
- Agroecology and Environment Research Division , Agroscope , Reckenholzstrasse 191 , 8046 Zurich , Switzerland
| | - Hauke Harms
- Department of Environmental Microbiology , Helmholtz Centre for Environmental Research - UFZ , Permoserstraße 15 , 04318 Leipzig , Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , Deutscher Platz 5e , 04103 Leipzig , Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology , Helmholtz Centre for Environmental Research - UFZ , Permoserstraße 15 , 04318 Leipzig , Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , Deutscher Platz 5e , 04103 Leipzig , Germany
| | - Lukas Y Wick
- Department of Environmental Microbiology , Helmholtz Centre for Environmental Research - UFZ , Permoserstraße 15 , 04318 Leipzig , Germany
| |
Collapse
|
16
|
Castillo YM, Mangot J, Benites LF, Logares R, Kuronishi M, Ogata H, Jaillon O, Massana R, Sebastián M, Vaqué D. Assessing the viral content of uncultured picoeukaryotes in the global‐ocean by single cell genomics. Mol Ecol 2019; 28:4272-4289. [DOI: 10.1111/mec.15210] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 07/23/2019] [Accepted: 08/01/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Yaiza M. Castillo
- Department of Marine Biology and Oceanography Institute of Marine Sciences (ICM) CSIC Barcelona Spain
| | - Jean‐François Mangot
- Department of Marine Biology and Oceanography Institute of Marine Sciences (ICM) CSIC Barcelona Spain
| | - Luiz Felipe Benites
- Integrative Biology of Marine Organisms (BIOM) CNRS Oceanological Observatory of Banyuls Sorbonne University Banyuls‐sur‐Mer France
| | - Ramiro Logares
- Department of Marine Biology and Oceanography Institute of Marine Sciences (ICM) CSIC Barcelona Spain
| | - Megumi Kuronishi
- Bioinformatic Center Institute for Chemical Research Kyoto University Uji Japan
| | - Hiroyuki Ogata
- Bioinformatic Center Institute for Chemical Research Kyoto University Uji Japan
| | - Olivier Jaillon
- Génomique Métabolique Genoscope Institut de biologie François Jacob CEA CNRS Université d'Evry Université Paris‐Saclay Evry France
| | - Ramon Massana
- Department of Marine Biology and Oceanography Institute of Marine Sciences (ICM) CSIC Barcelona Spain
| | - Marta Sebastián
- Department of Marine Biology and Oceanography Institute of Marine Sciences (ICM) CSIC Barcelona Spain
- Institute of Oceanography and Global Change (IOCAG) University of Las Palmas de Gran Canaria Telde Spain
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography Institute of Marine Sciences (ICM) CSIC Barcelona Spain
| |
Collapse
|
17
|
Defining the human gut host–phage network through single-cell viral tagging. Nat Microbiol 2019; 4:2192-2203. [DOI: 10.1038/s41564-019-0526-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 06/25/2019] [Indexed: 12/18/2022]
|
18
|
Gałan W, Bąk M, Jakubowska M. Host Taxon Predictor - A Tool for Predicting Taxon of the Host of a Newly Discovered Virus. Sci Rep 2019; 9:3436. [PMID: 30837511 PMCID: PMC6400966 DOI: 10.1038/s41598-019-39847-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 01/30/2019] [Indexed: 12/04/2022] Open
Abstract
Recent advances in metagenomics provided a valuable alternative to culture-based approaches for better sampling viral diversity. However, some of newly identified viruses lack sequence similarity to any of previously sequenced ones, and cannot be easily assigned to their hosts. Here we present a bioinformatic approach to this problem. We developed classifiers capable of distinguishing eukaryotic viruses from the phages achieving almost 95% prediction accuracy. The classifiers are wrapped in Host Taxon Predictor (HTP) software written in Python which is freely available at https://github.com/wojciech-galan/viruses_classifier. HTP’s performance was later demonstrated on a collection of newly identified viral genomes and genome fragments. In summary, HTP is a culture- and alignment-free approach for distinction between phages and eukaryotic viruses. We have also shown that it is possible to further extend our method to go up the evolutionary tree and predict whether a virus can infect narrower taxa.
Collapse
Affiliation(s)
- Wojciech Gałan
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, ul. Gronostajowa 7, 30-387, Kraków, Poland.
| | - Maciej Bąk
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Małgorzata Jakubowska
- AGH University of Science and Technology, Faculty of Materials Science and Ceramics, al. Mickiewicza 30, 30-059, Kraków, Poland
| |
Collapse
|
19
|
Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities. mSystems 2018; 3:mSystems00084-18. [PMID: 30175237 PMCID: PMC6113591 DOI: 10.1128/msystems.00084-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/24/2018] [Indexed: 11/25/2022] Open
Abstract
Inferring interactions from population time series is an active and ongoing area of research. It is relevant across many biological systems—particularly in virus-microbe communities, but also in gene regulatory networks, neural networks, and ecological communities broadly. Correlation-based inference—using correlations to predict interactions—is widespread. However, it is well-known that “correlation does not imply causation.” Despite this, many studies apply correlation-based inference methods to experimental time series without first assessing the potential scope for accurate inference. Here, we find that several correlation-based inference methods fail to recover interactions within in silico virus-microbe communities, raising questions on their relevance when applied in situ. Microbes are present in high abundances in the environment and in human-associated microbiomes, often exceeding 1 million per ml. Viruses of microbes are present in even higher abundances and are important in shaping microbial populations, communities, and ecosystems. Given the relative specificity of viral infection, it is essential to identify the functional linkages between viruses and their microbial hosts, particularly given dynamic changes in virus and host abundances. Multiple approaches have been proposed to infer infection networks from time series of in situ communities, among which correlation-based approaches have emerged as the de facto standard. In this work, we evaluate the accuracy of correlation-based inference methods using an in silico approach. In doing so, we compare predicted networks to actual networks to assess the self-consistency of correlation-based inference. At odds with assumptions underlying its widespread use, we find that correlation is a poor predictor of interactions in the context of viral infection and lysis of microbial hosts. The failure to predict interactions holds for methods that leverage product-moment, time-lagged, and relative-abundance-based correlations. In closing, we discuss alternative inference methods, particularly model-based methods, as a means to infer interactions in complex microbial communities with viruses. IMPORTANCE Inferring interactions from population time series is an active and ongoing area of research. It is relevant across many biological systems—particularly in virus-microbe communities, but also in gene regulatory networks, neural networks, and ecological communities broadly. Correlation-based inference—using correlations to predict interactions—is widespread. However, it is well-known that “correlation does not imply causation.” Despite this, many studies apply correlation-based inference methods to experimental time series without first assessing the potential scope for accurate inference. Here, we find that several correlation-based inference methods fail to recover interactions within in silico virus-microbe communities, raising questions on their relevance when applied in situ.
Collapse
|
20
|
Archaeal Viruses from High-Temperature Environments. Genes (Basel) 2018; 9:genes9030128. [PMID: 29495485 PMCID: PMC5867849 DOI: 10.3390/genes9030128] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/19/2018] [Accepted: 02/21/2018] [Indexed: 12/21/2022] Open
Abstract
Archaeal viruses are some of the most enigmatic viruses known, due to the small number that have been characterized to date. The number of known archaeal viruses lags behind known bacteriophages by over an order of magnitude. Despite this, the high levels of genetic and morphological diversity that archaeal viruses display has attracted researchers for over 45 years. Extreme natural environments, such as acidic hot springs, are almost exclusively populated by Archaea and their viruses, making these attractive environments for the discovery and characterization of new viruses. The archaeal viruses from these environments have provided insights into archaeal biology, gene function, and viral evolution. This review focuses on advances from over four decades of archaeal virology, with a particular focus on archaeal viruses from high temperature environments, the existing challenges in understanding archaeal virus gene function, and approaches being taken to overcome these limitations.
Collapse
|
21
|
A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extreme environments. ISME JOURNAL 2018; 12:1706-1714. [PMID: 29467398 DOI: 10.1038/s41396-018-0071-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 12/04/2017] [Accepted: 12/20/2017] [Indexed: 01/23/2023]
Abstract
The application of viral and cellular metagenomics to natural environments has expanded our understanding of the structure, functioning, and diversity of microbial and viral communities. The high diversity of many communities, e.g., soils, surface ocean waters, and animal-associated microbiomes, make it difficult to establish virus-host associations at the single cell (rather than population) level, assign cellular hosts, or determine the extent of viral host range from metagenomics studies alone. Here, we combine single-cell sequencing with environmental metagenomics to characterize the structure of virus-host associations in a Yellowstone National Park (YNP) hot spring microbial community. Leveraging the relatively low diversity of the YNP environment, we are able to overlay evidence at the single-cell level with contextualized viral and cellular community structure. Combining evidence from hexanucelotide analysis, single cell read mapping, network-based analytics, and CRISPR-based inference, we conservatively estimate that >60% of cells contain at least one virus type and a majority of these cells contain two or more virus types. Of the detected virus types, nearly 50% were found in more than 2 cellular clades, indicative of a broad host range. The new lens provided by the combination of metaviromics and single-cell genomics reveals a network of virus-host interactions in extreme environments, provides evidence that extensive virus-host associations are common, and further expands the unseen impact of viruses on cellular life.
Collapse
|
22
|
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.
Collapse
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.
| |
Collapse
|
23
|
Zhang M, Yang L, Ren J, Ahlgren NA, Fuhrman JA, Sun F. Prediction of virus-host infectious association by supervised learning methods. BMC Bioinformatics 2017; 18:60. [PMID: 28361670 PMCID: PMC5374558 DOI: 10.1186/s12859-017-1473-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background The study of virus-host infectious association is important for understanding the functions and dynamics of microbial communities. Both cellular and fractionated viral metagenomic data generate a large number of viral contigs with missing host information. Although relative simple methods based on the similarity between the word frequency vectors of viruses and bacterial hosts have been developed to study virus-host associations, the problem is significantly understudied. We hypothesize that machine learning methods based on word frequencies can be efficiently used to study virus-host infectious associations. Methods We investigate four different representations of word frequencies of viral sequences including the relative word frequency and three normalized word frequencies by subtracting the number of expected from the observed word counts. We also study five machine learning methods including logistic regression, support vector machine, random forest, Gaussian naive Bayes and Bernoulli naive Bayes for separating infectious from non-infectious viruses for nine bacterial host genera with at least 45 infecting viruses. Area under the receiver operating characteristic curve (AUC) is used to compare the performance of different machine learning method and feature combinations. We then evaluate the performance of the best method for the identification of the hosts of contigs in metagenomic studies. We also develop a maximum likelihood method to estimate the fraction of true infectious viruses for a given host in viral tagging experiments. Results Based on nine bacterial host genera with at least 45 infectious viruses, we show that random forest together with the relative word frequency vector performs the best in identifying viruses infecting particular hosts. For all the nine host genera, the AUC is over 0.85 and for five of them, the AUC is higher than 0.98 when the word size is 6 indicating the high accuracy of using machine learning approaches for identifying viruses infecting particular hosts. We also show that our method can predict the hosts of viral contigs of length at least 1kbps in metagenomic studies with high accuracy. The random forest together with word frequency vector outperforms current available methods based on Manhattan and \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$d_{2}^{*}$\end{document}d2∗ dissimilarity measures. Based on word frequencies, we estimate that about 95% of the identified T4-like viruses in viral tagging experiment infect Synechococcus, while only about 29% of the identified non-T4-like viruses and 30% of the contigs in the study potentially infect Synechococcus. Conclusions The random forest machine learning method together with the relative word frequencies as features of viruses can be used to predict viruses and viral contigs for specific bacterial hosts. The maximum likelihood approach can be used to estimate the fraction of true infectious associated viruses in viral tagging experiments. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1473-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Mengge Zhang
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA
| | - Lianping Yang
- College of Sciences, Northeastern University, Shenyang, China
| | - Jie Ren
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA
| | - Nathan A Ahlgren
- Department of Biological Sciences and Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, California, USA.,Biology Department, Clark University, Worcester, Massachusetts, USA
| | - Jed A Fuhrman
- Department of Biological Sciences and Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, California, USA
| | - Fengzhu Sun
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA. .,Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanhai, China.
| |
Collapse
|
24
|
Visualizing Adsorption of Cyanophage P-SSP7 onto Marine Prochlorococcus. Sci Rep 2017; 7:44176. [PMID: 28281671 PMCID: PMC5345008 DOI: 10.1038/srep44176] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/06/2017] [Indexed: 12/17/2022] Open
Abstract
Marine cyanobacteria perform roughly a quarter of global carbon fixation, and cyanophages that infect them liberate some of this carbon during infection and cell lysis. Studies of the cyanobacterium Prochlorococcus MED4 and its associated cyanophage P-SSP7 have revealed complex gene expression dynamics once infection has begun, but the initial cyanophage-host interactions remain poorly understood. Here, we used single particle cryo-electron tomography (cryo-ET) to investigate cyanophage-host interactions in this model system, based on 170 cyanophage-to-host adsorption events. Subtomogram classification and averaging revealed three main conformations characterized by different angles between the phage tail and the cell surface. Namely, phage tails were (i) parallel to, (ii) ~45 degrees to, or (iii) perpendicular to the cell surface. Furthermore, different conformations of phage tail fibers correlated with the aforementioned orientations of the tails. We also observed density beyond the tail tip in vertically-oriented phages that had penetrated the cell wall, capturing the final stage of adsorption. Together, our data provide a quantitative characterization of the orientation of phages as they adsorb onto cells, and suggest that cyanophages that abut their cellular targets are only transiently in the “perpendicular” orientation required for successful infection.
Collapse
|
25
|
The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses. mSystems 2017; 2:mSystems00125-16. [PMID: 28217745 PMCID: PMC5309335 DOI: 10.1128/msystems.00125-16] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 12/27/2016] [Indexed: 11/20/2022] Open
Abstract
Inferred virus-host relationships, community structures of ubiquitous ecologically relevant groups, and identification of transcriptionally active populations have been achieved with our Baltic Sea study. Further, these data, highlighting the transcriptional activity of viruses, represent one of the more powerful uses of omics concerning ecosystem health. The use of omics-related data to assess ecosystem health holds great promise for rapid and relatively inexpensive determination of perturbations and risk, explicitly with regard to viral assemblages, as no single marker gene is suitable for widespread taxonomic coverage. Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Torneträsk in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as impacted aspects of Baltic Sea viral communities. Taxonomic signatures representative of phages within the widely distributed order Caudovirales were identified with enrichments in lesser-known families such as Podoviridae and Siphoviridae. The distribution of phage reported to infect diverse and ubiquitous heterotrophic bacteria (SAR11 clades) and cyanobacteria (Synechococcus sp.) displayed population-level shifts in diversity. Samples from higher-salinity conditions (>14 practical salinity units [PSU]) had increased abundances of viruses for picoeukaryotes, i.e., Ostreococcus. These data, combined with host diversity estimates, suggest viral modulation of diversity on the whole-community scale, as well as in specific prokaryotic and eukaryotic lineages. RNA libraries revealed single-stranded DNA (ssDNA) and RNA viral populations throughout the Baltic Sea, with ssDNA phage highly represented in Lake Torneträsk. Further, our data suggest relatively high transcriptional activity of fish viruses within diverse families known to have broad host ranges, such as Nodoviridae (RNA), Iridoviridae (DNA), and predicted zoonotic viruses that can cause ecological and economic damage as well as impact human health. IMPORTANCE Inferred virus-host relationships, community structures of ubiquitous ecologically relevant groups, and identification of transcriptionally active populations have been achieved with our Baltic Sea study. Further, these data, highlighting the transcriptional activity of viruses, represent one of the more powerful uses of omics concerning ecosystem health. The use of omics-related data to assess ecosystem health holds great promise for rapid and relatively inexpensive determination of perturbations and risk, explicitly with regard to viral assemblages, as no single marker gene is suitable for widespread taxonomic coverage.
Collapse
|
26
|
Lim SW, Lance ST, Stedman KM, Abate AR. PCR-activated cell sorting as a general, cultivation-free method for high-throughput identification and enrichment of virus hosts. J Virol Methods 2016; 242:14-21. [PMID: 28042018 DOI: 10.1016/j.jviromet.2016.12.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 11/24/2016] [Accepted: 12/05/2016] [Indexed: 01/27/2023]
Abstract
Characterizing virus-host relationships is critical for understanding the impact of a virus on an ecosystem, but is challenging with existing techniques, particularly for uncultivable species. We present a general, cultivation-free approach for identifying phage-associated bacterial cells. Using PCR-activated cell sorting, we interrogate millions of individual bacteria for the presence of specific phage nucleic acids. If the nucleic acids are present, the bacteria are recovered via sorting and their genomes analyzed. This allows targeted recovery of all possible host species in a diverse population associated with a specific phage, and can be easily targeted to identify the hosts of different phages by modifying the PCR primers used for detection. Moreover, this technique allows quantification of free phage particles, as benchmarked against the "gold standard" of virus enumeration, the plaque assay.
Collapse
Affiliation(s)
- Shaun W Lim
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Shea T Lance
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Kenneth M Stedman
- Biology Department and Center for Life in Extreme Environments, Biology Department, Portland State University, Portland, OR, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA.
| |
Collapse
|
27
|
Jover LF, Romberg J, Weitz JS. Inferring phage-bacteria infection networks from time-series data. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160654. [PMID: 28018655 PMCID: PMC5180153 DOI: 10.1098/rsos.160654] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 10/03/2016] [Indexed: 05/09/2023]
Abstract
In communities with bacterial viruses (phage) and bacteria, the phage-bacteria infection network establishes which virus types infect which host types. The structure of the infection network is a key element in understanding community dynamics. Yet, this infection network is often difficult to ascertain. Introduced over 60 years ago, the plaque assay remains the gold standard for establishing who infects whom in a community. This culture-based approach does not scale to environmental samples with increased levels of phage and bacterial diversity, much of which is currently unculturable. Here, we propose an alternative method of inferring phage-bacteria infection networks. This method uses time-series data of fluctuating population densities to estimate the complete interaction network without having to test each phage-bacteria pair individually. We use in silico experiments to analyse the factors affecting the quality of network reconstruction and find robust regimes where accurate reconstructions are possible. In addition, we present a multi-experiment approach where time series from different experiments are combined to improve estimates of the infection network. This approach also mitigates against the possibility of evolutionary changes to relevant phenotypes during the time course of measurement.
Collapse
Affiliation(s)
| | - Justin Romberg
- School of Electrical and Computer Engineering, Atlanta, GA, USA
| | - Joshua S. Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Author for correspondence: Joshua S. Weitz e-mail:
| |
Collapse
|
28
|
Kirzner S, Barak E, Lindell D. Variability in progeny production and virulence of cyanophages determined at the single-cell level. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:605-613. [PMID: 27084786 DOI: 10.1111/1758-2229.12409] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Little information regarding viral progeny production (burst size) and host mortality (viral virulence) is currently available for environmentally relevant phages. This is partially due to the difficulty in accurately measuring these infection properties with existing methods. Here, we set up a simple system for determining viral virulence and burst size at the single-cell level following flow cytometric separation of infected cells. We applied this assay to two distinct cyanomyoviruses, Syn9 and S-TIM5, during infection of two marine Synechococcus strains each. We found that virulence ranged from 44%-82%, differing for the same phage on different hosts. Average burst sizes ranged from 21-43 infective viruses/cell, and differed with host for Syn9, whereas the burst size of S-TIM5 was similar for both hosts. In addition, virulence and burst sizes were different for the two phages when infecting their common host. Furthermore, wide-ranging cell-to-cell variability was found for single-cell burst sizes in each of the four interactions, ranging from 2 to over 100 infective viruses/cell. This variability, discerned at both the population and single-cell levels under controlled laboratory conditions, is likely to be much more complex in natural environments.
Collapse
Affiliation(s)
- Shay Kirzner
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Efrat Barak
- Life Sciences and Engineering Infrastructure Unit, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Debbie Lindell
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| |
Collapse
|
29
|
Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction. ISME JOURNAL 2016; 11:543-554. [PMID: 27648812 PMCID: PMC5183456 DOI: 10.1038/ismej.2016.116] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 06/24/2016] [Accepted: 07/08/2016] [Indexed: 01/01/2023]
Abstract
Bacteriophages are recognized DNA vectors and transduction is considered as a common mechanism of lateral gene transfer (LGT) during microbial evolution. Anecdotal events of phage-mediated gene transfer were studied extensively, however, a coherent evolutionary viewpoint of LGT by transduction, its extent and characteristics, is still lacking. Here we report a large-scale evolutionary reconstruction of transduction events in 3982 genomes. We inferred 17 158 recent transduction events linking donors, phages and recipients into a phylogenomic transduction network view. We find that LGT by transduction is mostly restricted to closely related donors and recipients. Furthermore, a substantial number of the transduction events (9%) are best described as gene duplications that are mediated by mobile DNA vectors. We propose to distinguish this type of paralogy by the term autology. A comparison of donor and recipient genomes revealed that genome similarity is a superior predictor of species connectivity in the network in comparison to common habitat. This indicates that genetic similarity, rather than ecological opportunity, is a driver of successful transduction during microbial evolution. A striking difference in the connectivity pattern of donors and recipients shows that while lysogenic interactions are highly species-specific, the host range for lytic phage infections can be much wider, serving to connect dense clusters of closely related species. Our results thus demonstrate that DNA transfer via transduction occurs within the context of phage–host specificity, but that this tight constraint can be breached, on rare occasions, to produce long-range LGTs of profound evolutionary consequences.
Collapse
|
30
|
Holmfeldt K, Solonenko N, Howard-Varona C, Moreno M, Malmstrom RR, Blow MJ, Sullivan MB. Large-scale maps of variable infection efficiencies in aquatic Bacteroidetes phage-host model systems. Environ Microbiol 2016; 18:3949-3961. [PMID: 27235779 DOI: 10.1111/1462-2920.13392] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 05/21/2015] [Indexed: 01/21/2023]
Abstract
Microbes drive ecosystem functioning and their viruses modulate these impacts through mortality, gene transfer and metabolic reprogramming. Despite the importance of virus-host interactions and likely variable infection efficiencies of individual phages across hosts, such variability is seldom quantified. Here, we quantify infection efficiencies of 38 phages against 19 host strains in aquatic Cellulophaga (Bacteroidetes) phage-host model systems. Binary data revealed that some phages infected only one strain while others infected 17, whereas quantitative data revealed that efficiency of infection could vary 10 orders of magnitude, even among phages within one population. This provides a baseline for understanding and modeling intrapopulation host range variation. Genera specific host ranges were also informative. For example, the Cellulophaga Microviridae, showed a markedly broader intra-species host range than previously observed in Escherichia coli systems. Further, one phage genus, Cba41, was examined to investigate nonheritable changes in plating efficiency and burst size that depended on which host strain it most recently infected. While consistent with host modification of phage DNA, no differences in nucleotide sequence or DNA modifications were detected, leaving the observation repeatable, but the mechanism unresolved. Overall, this study highlights the importance of quantitatively considering replication variations in studies of phage-host interactions.
Collapse
Affiliation(s)
- Karin Holmfeldt
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA.,Department of Biology and Environmental Sciences, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Natalie Solonenko
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | | | - Mario Moreno
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | | | | | - Matthew B Sullivan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| |
Collapse
|
31
|
Hanson CA, Marston MF, Martiny JBH. Biogeographic Variation in Host Range Phenotypes and Taxonomic Composition of Marine Cyanophage Isolates. Front Microbiol 2016; 7:983. [PMID: 27446023 PMCID: PMC4919323 DOI: 10.3389/fmicb.2016.00983] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/07/2016] [Indexed: 11/13/2022] Open
Abstract
Despite the important role of phages in marine systems, little is understood about how their diversity is distributed in space. Biogeographic patterns of marine phages may be difficult to detect due to their vast genetic diversity, which may not be accurately represented by conserved marker genes. To investigate the spatial biogeographic structure of marine phages, we isolated over 400 cyanophages on Synechococcus host strain WH7803 at three coastal locations in the United States (Rhode Island, Washington, and southern California). Approximately 90% of the cyanophage isolates were myoviruses, while the other 10% were podoviruses. The diversity of isolates was further characterized in two ways: (i) taxonomically, using conserved marker genes and (ii) phenotypically, by testing isolates for their ability to infect a suite of hosts, or their "host range." Because host range is a highly variable trait even among closely related isolates, we hypothesized that host range phenotypes of cyanophage isolates would vary more strongly among locations than would taxonomic composition. Instead, we found evidence for strong biogeographic variation both in taxonomic composition and host range phenotypes, with little taxonomic overlap among the three coastal regions. For both taxonomic composition and host range phenotypes, cyanophage communities from California and Rhode Island were the most dissimilar, while Washington communities exhibited similarity to each of the other two locations. These results suggest that selection imposed by spatial variation in host dynamics influence the biogeographic distribution of cyanophages.
Collapse
Affiliation(s)
- China A Hanson
- School of Biological and Chemical Sciences, Queen Mary University of London, LondonUK; Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CAUSA
| | - Marcia F Marston
- Department of Biology and Marine Biology, Roger Williams University, Bristol, RI USA
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA USA
| |
Collapse
|
32
|
Perez Sepulveda B, Redgwell T, Rihtman B, Pitt F, Scanlan DJ, Millard A. Marine phage genomics: the tip of the iceberg. FEMS Microbiol Lett 2016; 363:fnw158. [PMID: 27338950 PMCID: PMC4928673 DOI: 10.1093/femsle/fnw158] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2016] [Indexed: 01/07/2023] Open
Abstract
Marine viruses are the most abundant biological entity in the oceans, the majority of which infect bacteria and are known as bacteriophages. Yet, the bulk of bacteriophages form part of the vast uncultured dark matter of the microbial biosphere. In spite of the paucity of cultured marine bacteriophages, it is known that marine bacteriophages have major impacts on microbial population structure and the biogeochemical cycling of key elements. Despite the ecological relevance of marine bacteriophages, there are relatively few isolates with complete genome sequences. This minireview focuses on knowledge gathered from these genomes put in the context of viral metagenomic data and highlights key advances in the field, particularly focusing on genome structure and auxiliary metabolic genes. Only a tiny fraction of marine phages have been discovered, yet are known to have important roles in the ocean.
Collapse
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
| |
Collapse
|
33
|
Trubl G, Solonenko N, Chittick L, Solonenko SA, Rich VI, Sullivan MB. Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient. PeerJ 2016; 4:e1999. [PMID: 27231649 PMCID: PMC4878379 DOI: 10.7717/peerj.1999] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 04/11/2016] [Indexed: 01/23/2023] Open
Abstract
Permafrost stores approximately 50% of global soil carbon (C) in a frozen form; it is thawing rapidly under climate change, and little is known about viral communities in these soils or their roles in C cycling. In permafrost soils, microorganisms contribute significantly to C cycling, and characterizing them has recently been shown to improve prediction of ecosystem function. In other ecosystems, viruses have broad ecosystem and community impacts ranging from host cell mortality and organic matter cycling to horizontal gene transfer and reprogramming of core microbial metabolisms. Here we developed an optimized protocol to extract viruses from three types of high organic-matter peatland soils across a permafrost thaw gradient (palsa, moss-dominated bog, and sedge-dominated fen). Three separate experiments were used to evaluate the impact of chemical buffers, physical dispersion, storage conditions, and concentration and purification methods on viral yields. The most successful protocol, amended potassium citrate buffer with bead-beating or vortexing and BSA, yielded on average as much as 2-fold more virus-like particles (VLPs) g−1 of soil than other methods tested. All method combinations yielded VLPs g−1 of soil on the 108 order of magnitude across all three soil types. The different storage and concentration methods did not yield significantly more VLPs g−1 of soil among the soil types. This research provides much-needed guidelines for resuspending viruses from soils, specifically carbon-rich soils, paving the way for incorporating viruses into soil ecology studies.
Collapse
Affiliation(s)
- Gareth Trubl
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, United States; Current affiliation: Department of Microbiology, Ohio State University, Columbus, OH, United States
| | - Natalie Solonenko
- Current affiliation: Department of Microbiology, Ohio State University, Columbus, OH, United States; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Lauren Chittick
- Current affiliation: Department of Microbiology, Ohio State University, Columbus, OH, United States; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Sergei A Solonenko
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States; Current affiliation: Department of Ecology, Evolution and Organismal Biology, Ohio State University, Columbus, OH, United States
| | - Virginia I Rich
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, United States; Current affiliation: Department of Microbiology, Ohio State University, Columbus, OH, United States
| | - Matthew B Sullivan
- Current affiliation: Department of Microbiology, Ohio State University, Columbus, OH, United States; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States; Current affiliation: Department of Ecology, Evolution and Organismal Biology, Ohio State University, Columbus, OH, United States; Current affiliation: Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, United States
| |
Collapse
|
34
|
Calusinska M, Marynowska M, Goux X, Lentzen E, Delfosse P. Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity. Environ Microbiol 2016; 18:1162-75. [PMID: 26568175 PMCID: PMC7163765 DOI: 10.1111/1462-2920.13127] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 08/17/2015] [Accepted: 11/06/2015] [Indexed: 01/08/2023]
Abstract
Although viruses are not the key players of the anaerobic digestion process, they may affect the dynamics of bacterial and archaeal populations involved in biogas production. Until now viruses have received very little attention in this specific habitat; therefore, as a first step towards their characterization, we optimized a virus filtration protocol from anaerobic sludge. Afterwards, to assess dsDNA and RNA viral diversity in sludge samples from nine different reactors fed either with waste water, agricultural residues or solid municipal waste plus agro‐food residues, we performed metagenomic analyses. As a result we showed that, while the dsDNA viromes (21 assigned families in total) were dominated by dsDNA phages of the order Caudovirales, RNA viruses (14 assigned families in total) were less diverse and were for the main part plant‐infecting viruses. Interestingly, less than 2% of annotated contigs were assigned as putative human and animal pathogens. Our study greatly extends the existing view of viral genetic diversity in methanogenic reactors and shows that these viral assemblages are distinct not only among the reactor types but also from nearly 30 other environments already studied, including the human gut, fermented food, deep sea sediments and other aquatic habitats.
Collapse
Affiliation(s)
- Magdalena Calusinska
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation (ERIN), 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - Martyna Marynowska
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation (ERIN), 41 rue du Brill, L-4422, Belvaux, Luxembourg.,Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, ul. Kladki 24, 80-822, Gdansk, Poland
| | - Xavier Goux
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation (ERIN), 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - Esther Lentzen
- Luxembourg Institute of Science and Technology, Materials Research and Technology (MRT), 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - Philippe Delfosse
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation (ERIN), 41 rue du Brill, L-4422, Belvaux, Luxembourg
| |
Collapse
|
35
|
Edwards RA, McNair K, Faust K, Raes J, Dutilh BE. Computational approaches to predict bacteriophage-host relationships. FEMS Microbiol Rev 2015; 40:258-72. [PMID: 26657537 PMCID: PMC5831537 DOI: 10.1093/femsre/fuv048] [Citation(s) in RCA: 273] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2015] [Indexed: 01/21/2023] Open
Abstract
Metagenomics has changed the face of virus discovery by enabling the accurate identification of viral genome sequences without requiring isolation of the viruses. As a result, metagenomic virus discovery leaves the first and most fundamental question about any novel virus unanswered: What host does the virus infect? The diversity of the global virosphere and the volumes of data obtained in metagenomic sequencing projects demand computational tools for virus–host prediction. We focus on bacteriophages (phages, viruses that infect bacteria), the most abundant and diverse group of viruses found in environmental metagenomes. By analyzing 820 phages with annotated hosts, we review and assess the predictive power of in silico phage–host signals. Sequence homology approaches are the most effective at identifying known phage–host pairs. Compositional and abundance-based methods contain significant signal for phage–host classification, providing opportunities for analyzing the unknowns in viral metagenomes. Together, these computational approaches further our knowledge of the interactions between phages and their hosts. Importantly, we find that all reviewed signals significantly link phages to their hosts, illustrating how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage–host relationships, with potential relevance for medical and industrial applications. New viruses infecting bacteria are increasingly being discovered in many environments through sequence-based explorations. To understand their role in microbial ecosystems, computational tools are indispensable to prioritize and guide experimental efforts. This review assesses and discusses a range of bioinformatic approaches to predict bacteriophage–host relationships when all that is known is their genome sequence.
Collapse
Affiliation(s)
- Robert A Edwards
- Department of Computer Science, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, CEP 21941-902, Brazil Division of Mathematics and Computer Science, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439, USA
| | - Katelyn McNair
- Department of Computer Science, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA
| | - Karoline Faust
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium Laboratory of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium Laboratory of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Bas E Dutilh
- Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, CEP 21941-902, Brazil Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands
| |
Collapse
|
36
|
Liu J, Yan R, Zhong Q, Ngo S, Bangayan NJ, Nguyen L, Lui T, Liu M, Erfe MC, Craft N, Tomida S, Li H. The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin. THE ISME JOURNAL 2015; 9:2078-93. [PMID: 25848871 PMCID: PMC4542041 DOI: 10.1038/ismej.2015.47] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 02/12/2015] [Accepted: 02/26/2015] [Indexed: 02/08/2023]
Abstract
The viral population, including bacteriophages, is an important component of the human microbiota, yet is poorly understood. We aim to determine whether bacteriophages modulate the composition of the bacterial populations, thus potentially playing a role in health or disease. We investigated the diversity and host interactions of the bacteriophages of Propionibacterium acnes, a major human skin commensal implicated in acne pathogenesis. By sequencing 48 P. acnes phages isolated from acne patients and healthy individuals and by analyzing the P. acnes phage populations in healthy skin metagenomes, we revealed that P. acnes phage populations in the skin microbial community are often dominated by one strain. We also found phage strains shared among both related and unrelated individuals, suggesting that a pool of common phages exists in the human population and that transmission of phages may occur between individuals. To better understand the bacterium-phage interactions in the skin microbiota, we determined the outcomes of 74 genetically defined Propionibacterium strains challenged by 15 sequenced phages. Depending on the Propionibacterium lineage, phage infection can result in lysis, pseudolysogeny, or resistance. In type II P. acnes strains, we found that encoding matching clustered regularly interspaced short palindromic repeat spacers is insufficient to confer phage resistance. Overall, our findings suggest that the prey-predator relationship between bacteria and phages may have a role in modulating the composition of the microbiota. Our study also suggests that the microbiome structure of an individual may be an important factor in the design of phage-based therapy.
Collapse
Affiliation(s)
- Jared Liu
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Riceley Yan
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Qiao Zhong
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Laboratory Medicine, Suzhou Municipal Hospital, Suzhou Hospital Affiliated to Nanjing Medical University, Suzhou, China
| | - Sam Ngo
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Nathanael J Bangayan
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Lin Nguyen
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Timothy Lui
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Minghsun Liu
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Marie C Erfe
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Los Angeles, CA, USA
| | - Noah Craft
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Los Angeles, CA, USA
| | - Shuta Tomida
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Huiying Li
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
| |
Collapse
|
37
|
Pope WH, Hatfull GF. Adding pieces to the puzzle: New insights into bacteriophage diversity from integrated research-education programs. BACTERIOPHAGE 2015; 5:e1084073. [PMID: 26904380 DOI: 10.1080/21597081.2015.1084073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/07/2015] [Accepted: 08/11/2015] [Indexed: 01/21/2023]
Abstract
Bacteriophages are the dark matter of the biological universe: the population is vast and replete with novel genes whose function is unknown. The genomic insights such as the mosaic architecture gleaned from perhaps 2,000 currently sequenced bacteriophage genomes is far from representative of the total number phage particles in the biosphere - about 10ˆ31. The recent comparative analysis of 627 mycobacteriophages isolated on Mycobacterium smegmatis mc2 155 is the most extensive examination yet in pursuit of this question.
Collapse
Affiliation(s)
- Welkin H Pope
- Department of Biological Sciences; University of Pittsburgh ; Pittsburgh, PA USA
| | - Graham F Hatfull
- Department of Biological Sciences; University of Pittsburgh ; Pittsburgh, PA USA
| |
Collapse
|
38
|
Halobacteriovorax, an underestimated predator on bacteria: potential impact relative to viruses on bacterial mortality. ISME JOURNAL 2015; 10:491-9. [PMID: 26251870 DOI: 10.1038/ismej.2015.129] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 06/16/2015] [Accepted: 06/24/2015] [Indexed: 12/11/2022]
Abstract
Predation on bacteria and accompanying mortality are important mechanisms in controlling bacterial populations and recycling of nutrients through the microbial loop. The agents most investigated and seen as responsible for bacterial mortality are viruses and protists. However, a body of evidence suggests that predatory bacteria such as the Halobacteriovorax (formerly Bacteriovorax), a Bdellovibrio-like organism, contribute substantially to bacterial death. Until now, conclusive evidence has been lacking. The goal of this study was to better understand the contributors to bacterial mortality by addressing the poorly understood role of Halobacteriovorax and how their role compares with that of viruses. The results revealed that when a concentrated suspension of Vibrio parahaemolyticus was added into microcosms of estuarine waters, the native Halobacteriovorax were the predators that responded first and most rapidly. Their numbers increased by four orders of magnitude, whereas V. parahaemolyticus prey numbers decreased by three orders of magnitude. In contrast, the extant virus population showed little increase and produced little change in the prey density. An independent experiment with stable isotope probing confirmed that Halobacteriovorax were the predators primarily responsible for the mortality of the V. parahaemolyticus. The results show that Halobacteriovorax have the potential to be significant contributors to bacterial mortality, and in such cases, predation by Halobacteriovorax may be an important mechanism of nutrient recycling. These conclusions add another dimension to bacterial mortality and the recycling of nutrients.
Collapse
|
39
|
Weitz JS, Stock CA, Wilhelm SW, Bourouiba L, Coleman ML, Buchan A, Follows MJ, Fuhrman JA, Jover LF, Lennon JT, Middelboe M, Sonderegger DL, Suttle CA, Taylor BP, Frede Thingstad T, Wilson WH, Eric Wommack K. A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes. THE ISME JOURNAL 2015; 9:1352-64. [PMID: 25635642 PMCID: PMC4438322 DOI: 10.1038/ismej.2014.220] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 11/08/2022]
Abstract
Viral lysis of microbial hosts releases organic matter that can then be assimilated by nontargeted microorganisms. Quantitative estimates of virus-mediated recycling of carbon in marine waters, first established in the late 1990s, were originally extrapolated from marine host and virus densities, host carbon content and inferred viral lysis rates. Yet, these estimates did not explicitly incorporate the cascade of complex feedbacks associated with virus-mediated lysis. To evaluate the role of viruses in shaping community structure and ecosystem functioning, we extend dynamic multitrophic ecosystem models to include a virus component, specifically parameterized for processes taking place in the ocean euphotic zone. Crucially, we are able to solve this model analytically, facilitating evaluation of model behavior under many alternative parameterizations. Analyses reveal that the addition of a virus component promotes the emergence of complex communities. In addition, biomass partitioning of the emergent multitrophic community is consistent with well-established empirical norms in the surface oceans. At steady state, ecosystem fluxes can be probed to characterize the effects that viruses have when compared with putative marine surface ecosystems without viruses. The model suggests that ecosystems with viruses will have (1) increased organic matter recycling, (2) reduced transfer to higher trophic levels and (3) increased net primary productivity. These model findings support hypotheses that viruses can have significant stimulatory effects across whole-ecosystem scales. We suggest that existing efforts to predict carbon and nutrient cycling without considering virus effects are likely to miss essential features of marine food webs that regulate global biogeochemical cycles.
Collapse
Affiliation(s)
- Joshua S Weitz
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Charles A Stock
- Geophysical Fluid Dynamics Laboratory, NOAA, Princeton, NJ, USA
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Lydia Bourouiba
- Department of Applied Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Luis F Jover
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Mathias Middelboe
- Marine Biological Section, University of Copenhagen, Copenhagen, Denmark
| | | | - Curtis A Suttle
- Department of Earth and Ocean Sciences, Department of Botany, and Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bradford P Taylor
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | | | | | - K Eric Wommack
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| |
Collapse
|
40
|
Abstract
Bacteriophages are the most abundant biological entities in the biosphere, and this dynamic and old population is, not surprisingly, highly diverse genetically. Relative to bacterial genomics, phage genomics has advanced slowly, and a higher-resolution picture of the phagosphere is only just emerging. This view reveals substantial diversity even among phages known to infect a common host strain, but the relationships are complex, with mosaic genomic architectures generated by illegitimate recombination over a long period of evolutionary history.
Collapse
|
41
|
Snyder JC, Bolduc B, Young MJ. 40 Years of archaeal virology: Expanding viral diversity. Virology 2015; 479-480:369-78. [PMID: 25866378 DOI: 10.1016/j.virol.2015.03.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/07/2015] [Accepted: 03/17/2015] [Indexed: 10/23/2022]
Abstract
The first archaeal virus was isolated over 40 years ago prior to the recognition of the three domain structure of life. In the ensuing years, our knowledge of Archaea and their viruses has increased, but they still remain the most mysterious of life's three domains. Currently, over 100 archaeal viruses have been discovered, but few have been described in biochemical or structural detail. However, those that have been characterized have revealed a new world of structural, biochemical and genetic diversity. Several model systems for studying archaeal virus-host interactions have been developed, revealing evolutionary linkages between viruses infecting the three domains of life, new viral lysis systems, and unusual features of host-virus interactions. It is likely that the study of archaeal viruses will continue to provide fertile ground for fundamental discoveries in virus diversity, structure and function.
Collapse
Affiliation(s)
- Jamie C Snyder
- Department of Biological Sciences, California State Polytechnic University - Pomona, Pomona, CA, USA
| | - Benjamin Bolduc
- Departments of Plant Sciences and Microbiology, Montana State University, Bozeman, MT, USA
| | - Mark J Young
- Departments of Plant Sciences and Microbiology, Montana State University, Bozeman, MT, USA.
| |
Collapse
|
42
|
Labonté JM, Swan BK, Poulos B, Luo H, Koren S, Hallam SJ, Sullivan MB, Woyke T, Wommack KE, Stepanauskas R. Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton. ISME JOURNAL 2015; 9:2386-99. [PMID: 25848873 PMCID: PMC4611503 DOI: 10.1038/ismej.2015.48] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/27/2015] [Accepted: 02/26/2015] [Indexed: 02/01/2023]
Abstract
Viral infections dynamically alter the composition and metabolic potential of marine microbial communities and the evolutionary trajectories of host populations with resulting feedback on biogeochemical cycles. It is quite possible that all microbial populations in the ocean are impacted by viral infections. Our knowledge of virus–host relationships, however, has been limited to a minute fraction of cultivated host groups. Here, we utilized single-cell sequencing to obtain genomic blueprints of viruses inside or attached to individual bacterial and archaeal cells captured in their native environment, circumventing the need for host and virus cultivation. A combination of comparative genomics, metagenomic fragment recruitment, sequence anomalies and irregularities in sequence coverage depth and genome recovery were utilized to detect viruses and to decipher modes of virus–host interactions. Members of all three tailed phage families were identified in 20 out of 58 phylogenetically and geographically diverse single amplified genomes (SAGs) of marine bacteria and archaea. At least four phage–host interactions had the characteristics of late lytic infections, all of which were found in metabolically active cells. One virus had genetic potential for lysogeny. Our findings include first known viruses of Thaumarchaeota, Marinimicrobia, Verrucomicrobia and Gammaproteobacteria clusters SAR86 and SAR92. Viruses were also found in SAGs of Alphaproteobacteria and Bacteroidetes. A high fragment recruitment of viral metagenomic reads confirmed that most of the SAG-associated viruses are abundant in the ocean. Our study demonstrates that single-cell genomics, in conjunction with sequence-based computational tools, enable in situ, cultivation-independent insights into host–virus interactions in complex microbial communities.
Collapse
Affiliation(s)
| | - Brandon K Swan
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Bonnie Poulos
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Haiwei Luo
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Sergey Koren
- National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - K Eric Wommack
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA
| | | |
Collapse
|
43
|
Voorhies AA, Eisenlord SD, Marcus DN, Duhaime MB, Biddanda BA, Cavalcoli JD, Dick GJ. Ecological and genetic interactions between cyanobacteria and viruses in a low-oxygen mat community inferred through metagenomics and metatranscriptomics. Environ Microbiol 2015; 18:358-71. [DOI: 10.1111/1462-2920.12756] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 12/15/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Alexander A. Voorhies
- Department of Earth and Environmental Sciences; University of Michigan; Ann Arbor MI 48109 USA
| | - Sarah D. Eisenlord
- School of Natural Resources and Environment; University of Michigan; Ann Arbor MI 48109 USA
| | - Daniel N. Marcus
- Department of Earth and Environmental Sciences; University of Michigan; Ann Arbor MI 48109 USA
| | - Melissa B. Duhaime
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI 48109 USA
| | - Bopaiah A. Biddanda
- Annis Water Resources Institute; Grand Valley State University; Muskegon MI 49441 USA
| | - James D. Cavalcoli
- Department of Computational Medicine and Bioinformatics; University of Michigan; Ann Arbor MI 48109 USA
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences; University of Michigan; Ann Arbor MI 48109 USA
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI 48109 USA
| |
Collapse
|
44
|
Wommack KE, Nasko DJ, Chopyk J, Sakowski EG. Counts and sequences, observations that continue to change our understanding of viruses in nature. J Microbiol 2015; 53:181-92. [PMID: 25732739 DOI: 10.1007/s12275-015-5068-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 02/10/2015] [Indexed: 12/01/2022]
Abstract
The discovery of abundant viruses in the oceans and on land has ushered in a quarter century of groundbreaking advancements in our understanding of viruses within ecosystems. Two types of observations from environmental samples--direct counts of viral particles and viral metagenomic sequences--have been critical to these discoveries. Accurate direct counts have established ecosystem-scale trends in the impacts of viral infection on microbial host populations and have shown that viral communities within aquatic and soil environments respond to both short term and seasonal environmental change. Direct counts have been critical for estimating viral production rate, a measurement essential to quantifying the implications of viral infection for the biogeochemical cycling of nutrients within ecosystems. While direct counts have defined the magnitude of viral processes; shotgun sequences of environmental viral DNA--virome sequences--have enabled researchers to estimate the diversity and composition of natural viral communities. Virome-enabled studies have found the virioplankton to contain thousands of viral genotypes in communities where the most dominant viral population accounts for a small fraction of total abundance followed by a long tail of diverse populations. Detailed examination of long virome sequences has led to new understanding of genotype-to-phenotype connections within marine viruses and revealed that viruses carry metabolic genes that are important to maintaining cellular energy during viral replication. Increased access to long virome sequences will undoubtedly reveal more genetic secrets of viruses and enable us to build a genomics rulebook for predicting key biological and ecological features of unknown viruses.
Collapse
Affiliation(s)
- K Eri Wommack
- Delaware Biotechnology Institute, University of Delaware, Newark Delaware, USA,
| | | | | | | |
Collapse
|
45
|
Abstract
Recent advances in studying the dynamics of marine microbial communities have shown that the composition of these communities follows predictable patterns and involves complex network interactions, which shed light on the underlying processes regulating these globally important organisms. Such 'holistic' (or organism- and system-based) studies of these communities complement popular reductionist, often culture-based, approaches for understanding organism function one gene or protein at a time. In this Review, we summarize our current understanding of marine microbial community dynamics at various scales, from hours to decades. We also explain how the data illustrate community resilience and seasonality, and reveal interactions among microorganisms.
Collapse
|
46
|
Rising to the challenge: accelerated pace of discovery transforms marine virology. Nat Rev Microbiol 2015; 13:147-59. [PMID: 25639680 DOI: 10.1038/nrmicro3404] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Marine viruses have important roles in microbial mortality, gene transfer, metabolic reprogramming and biogeochemical cycling. In this Review, we discuss recent technological advances in marine virology including the use of near-quantitative, reproducible metagenomics for large-scale investigation of viral communities and the emergence of gene-based viral ecology. We also describe the reprogramming of microbially driven processes by viral metabolic genes, the identification of novel viruses using cultivation-dependent and cultivation-independent tools, and the potential for modelling studies to provide a framework for studying virus-host interactions. These transformative advances have set a rapid pace in exploring and predicting how marine viruses manipulate and respond to their environment.
Collapse
|
47
|
Dang VT, Sullivan MB. Emerging methods to study bacteriophage infection at the single-cell level. Front Microbiol 2014; 5:724. [PMID: 25566233 PMCID: PMC4274963 DOI: 10.3389/fmicb.2014.00724] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 12/02/2014] [Indexed: 11/26/2022] Open
Abstract
Bacteria and their viruses (phages) are abundant across diverse ecosystems and their interactions influence global biogeochemical cycles and incidence of disease. Problematically, both classical and metagenomic methods insufficiently assess the host specificity of phages and phage–host infection dynamics in nature. Here we review emerging methods to study phage–host interaction and infection dynamics with a focus on those that offer resolution at the single-cell level. These methods leverage ever-increasing sequence data to identify virus signals from single-cell amplified genome datasets or to produce primers/probes to target particular phage–bacteria pairs (digital PCR and phageFISH), even in complex communities. All three methods enable study of phage infection of uncultured bacteria from environmental samples, while the latter also discriminates between phage–host interaction outcomes (e.g., lytic, chronic, lysogenic) in model systems. Together these techniques enable quantitative, spatiotemporal studies of phage–bacteria interactions from environmental samples of any ecosystem, which will help elucidate and predict the ecological and evolutionary impacts of specific phage–host pairings in nature.
Collapse
Affiliation(s)
- Vinh T Dang
- Department of Ecology and Evolutionary Biology, University of Arizona Tucson, AZ, USA
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona Tucson, AZ, USA ; Department of Molecular and Cellular Biology, University of Arizona Tucson, AZ, USA
| |
Collapse
|
48
|
Payet JP, McMinds R, Burkepile DE, Vega Thurber RL. Unprecedented evidence for high viral abundance and lytic activity in coral reef waters of the South Pacific Ocean. Front Microbiol 2014; 5:493. [PMID: 25295032 PMCID: PMC4172022 DOI: 10.3389/fmicb.2014.00493] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 09/01/2014] [Indexed: 11/25/2022] Open
Abstract
Despite nutrient-depleted conditions, coral reef waters harbor abundant and diverse microbes; as major agents of microbial mortality, viruses are likely to influence microbial processes in these ecosystems. However, little is known about marine viruses in these rapidly changing ecosystems. Here we examined spatial and short-term temporal variability in marine viral abundance (VA) and viral lytic activity across various reef habitats surrounding Moorea Island (French Polynesia) in the South Pacific. Water samples were collected along four regional cross-reef transects and during a time-series in Opunohu Bay. Results revealed high VA (range: 5.6 × 10(6)-3.6 × 10(7) viruses ml(-1)) and lytic viral production (range: 1.5 × 10(9)-9.2 × 10(10) viruses l(-1) d(-1)). Flow cytometry revealed that viral assemblages were composed of three subsets that each displayed distinct spatiotemporal relationships with nutrient concentrations and autotrophic and heterotrophic microbial abundances. The results highlight dynamic shifts in viral community structure and imply that each of these three subsets is ecologically important and likely to infect distinct microbial hosts in reef waters. Based on viral-reduction approach, we estimate that lytic viruses were responsible for the removal of ca. 24-367% of bacterial standing stock d(-1) and the release of ca. 1.0-62 μg of organic carbon l(-1) d(-1) in reef waters. Overall, this work demonstrates the highly dynamic distribution of viruses and their critical roles in controlling microbial mortality and nutrient cycling in coral reef water ecosystems.
Collapse
Affiliation(s)
- Jérôme P. Payet
- Department of Microbiology, Oregon State UniversityCorvallis, OR, USA
- Institute for Pacific Coral ReefsMoorea, French Polynesia
| | - Ryan McMinds
- Department of Microbiology, Oregon State UniversityCorvallis, OR, USA
| | - Deron E. Burkepile
- Department of Biological Sciences, Florida International UniversityMiami, FL, USA
| | | |
Collapse
|
49
|
Jover LF, Effler TC, Buchan A, Wilhelm SW, Weitz JS. The elemental composition of virus particles: implications for marine biogeochemical cycles. Nat Rev Microbiol 2014; 12:519-28. [PMID: 24931044 DOI: 10.1038/nrmicro3289] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In marine environments, virus-mediated lysis of host cells leads to the release of cellular carbon and nutrients and is hypothesized to be a major driver of carbon recycling on a global scale. However, efforts to characterize the effects of viruses on nutrient cycles have overlooked the geochemical potential of the virus particles themselves, particularly with respect to their phosphorus content. In this Analysis article, we use a biophysical scaling model of intact virus particles that has been validated using sequence and structural information to quantify differences in the elemental stoichiometry of marine viruses compared with their microbial hosts. By extrapolating particle-scale estimates to the ecosystem scale, we propose that, under certain circumstances, marine virus populations could make an important contribution to the reservoir and cycling of oceanic phosphorus.
Collapse
Affiliation(s)
- Luis F Jover
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - T Chad Effler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Joshua S Weitz
- 1] School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA. [2] School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| |
Collapse
|
50
|
Deng L, Ignacio-Espinoza JC, Gregory AC, Poulos BT, Weitz JS, Hugenholtz P, Sullivan MB. Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature 2014; 513:242-5. [PMID: 25043051 DOI: 10.1038/nature13459] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 05/07/2014] [Indexed: 11/09/2022]
Abstract
Microbes and their viruses drive myriad processes across ecosystems ranging from oceans and soils to bioreactors and humans. Despite this importance, microbial diversity is only now being mapped at scales relevant to nature, while the viral diversity associated with any particular host remains little researched. Here we quantify host-associated viral diversity using viral-tagged metagenomics, which links viruses to specific host cells for high-throughput screening and sequencing. In a single experiment, we screened 10(7) Pacific Ocean viruses against a single strain of Synechococcus and found that naturally occurring cyanophage genome sequence space is statistically clustered into discrete populations. These population-based, host-linked viral ecological data suggest that, for this single host and seawater sample alone, there are at least 26 double-stranded DNA viral populations with estimated relative abundances ranging from 0.06 to 18.2%. These populations include previously cultivated cyanophage and new viral types missed by decades of isolate-based studies. Nucleotide identities of homologous genes mostly varied by less than 1% within populations, even in hypervariable genome regions, and by 42-71% between populations, which provides benchmarks for viral metagenomics and genome-based viral species definitions. Together these findings showcase a new approach to viral ecology that quantitatively links objectively defined environmental viral populations, and their genomes, to their hosts.
Collapse
Affiliation(s)
- Li Deng
- 1] Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85719, USA [2] Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Groundwater Ecology, Neuherberg 85764, Germany. [3]
| | - J Cesar Ignacio-Espinoza
- 1] Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85719, USA [2]
| | - Ann C Gregory
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85719, USA
| | - Bonnie T Poulos
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85719, USA
| | - Joshua S Weitz
- 1] School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA [2] School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences &Institute for Molecular Bioscience, The University of Queensland, St Lucia QLB 4072, Australia
| | - Matthew B Sullivan
- 1] Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85719, USA [2] Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85719, USA
| |
Collapse
|