401
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Brüssow H. Environmental microbiology: Too much food for thought? - An argument for reductionism. Environ Microbiol 2018; 20:1929-1935. [PMID: 29626370 DOI: 10.1111/1462-2920.14125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 03/31/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Harald Brüssow
- Editor of Microbial Biotechnology, KU Leuven, Laboratory of Gene Technology, Leuven, Belgium
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402
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Pratama AA, Chaib De Mares M, van Elsas JD. Evolutionary History of Bacteriophages in the Genus Paraburkholderia. Front Microbiol 2018; 9:835. [PMID: 29867788 PMCID: PMC5968390 DOI: 10.3389/fmicb.2018.00835] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/12/2018] [Indexed: 12/17/2022] Open
Abstract
The genus Paraburkholderia encompasses mostly environmental isolates with diverse predicted lifestyles. Genome analyses have shown that bacteriophages form a considerable portion of some Paraburkholderia genomes. Here, we analyzed the evolutionary history of prophages across all Paraburkholderia spp. Specifically, we investigated to what extent the presence of prophages and their distribution affect the diversity/diversification of Paraburkholderia spp., as well as to what extent phages coevolved with their respective hosts. Particular attention was given to the presence of CRISPR-Cas arrays as a reflection of past interactions with phages. We thus analyzed 36 genomes of Paraburkholderia spp., including those of 11 new strains, next to those of three Burkholderia species. Most genomes were found to contain at least one full prophage sequence. The highest number was found in Paraburkholderia sp. strain MF2-27; the nine prophages found amount to up to 4% of its genome. Among all prophages, potential moron genes (e.g., DNA adenine methylase) were found that might be advantageous for host cell fitness. Co-phylogenetic analyses indicated the existence of complex evolutionary scenarios between the different Paraburkholderia hosts and their prophages, including short-term co-speciation, duplication, host-switching and phage loss events. Analysis of the CRISPR-Cas systems showed a record of diverse, potentially recent, phage infections. We conclude that, overall, different phages have interacted in diverse ways with their Paraburkholderia hosts over evolutionary time.
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Affiliation(s)
- Akbar Adjie Pratama
- Department of Microbial Ecology, Microbial Ecology—Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | | | - Jan Dirk van Elsas
- Department of Microbial Ecology, Microbial Ecology—Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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403
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Abstract
Viruses infect all kingdoms of marine life from bacteria to whales. Viruses in the world's oceans play important roles in the mortality of phytoplankton, and as drivers of evolution and biogeochemical cycling. They shape host population abundance and distribution and can lead to the termination of algal blooms. As discoveries about this huge reservoir of genetic and biological diversity grow, our understanding of the major influences viruses exert in the global marine environment continues to expand. This chapter discusses the key discoveries that have been made to date about marine viruses and the current direction of this field of research.
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Affiliation(s)
- Karen D Weynberg
- School of Chemistry & Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia.
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404
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Laffy PW, Wood‐Charlson EM, Turaev D, Jutz S, Pascelli C, Botté ES, Bell SC, Peirce TE, Weynberg KD, van Oppen MJH, Rattei T, Webster NS. Reef invertebrate viromics: diversity, host specificity and functional capacity. Environ Microbiol 2018; 20:2125-2141. [DOI: 10.1111/1462-2920.14110] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/16/2018] [Accepted: 03/16/2018] [Indexed: 01/14/2023]
Affiliation(s)
- Patrick W. Laffy
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
| | | | - Dmitrij Turaev
- Department of Microbiology and Ecosystem Science, Division of Computational Systems BiologyUniversity of ViennaVienna Austria
| | - Sabrina Jutz
- Department of Microbiology and Ecosystem Science, Division of Computational Systems BiologyUniversity of ViennaVienna Austria
| | - Cecilia Pascelli
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
- College of Science and EngineeringJames Cook UniversityTownsville QLD Australia
- AIMS@JCU, Australian Institute of Marine Science and James Cook UniversityTownsville QLD Australia
| | | | - Sara C. Bell
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
| | - Tyler E. Peirce
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
| | - Karen D. Weynberg
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
| | - Madeleine J. H. van Oppen
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
- School of BiosciencesUniversity of Melbourne, ParkvilleMelbourneVIC 3010 Australia
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems BiologyUniversity of ViennaVienna Austria
| | - Nicole S. Webster
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
- Austalian Centre for Ecogenomics, University of QueenslandBrisbaneQLD 4072 Australia
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405
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Mahmoudabadi G, Phillips R. A comprehensive and quantitative exploration of thousands of viral genomes. eLife 2018; 7:31955. [PMID: 29624169 PMCID: PMC5908442 DOI: 10.7554/elife.31955] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 03/30/2018] [Indexed: 01/27/2023] Open
Abstract
The complete assembly of viral genomes from metagenomic datasets (short genomic sequences gathered from environmental samples) has proven to be challenging, so there are significant blind spots when we view viral genomes through the lens of metagenomics. One approach to overcoming this problem is to leverage the thousands of complete viral genomes that are publicly available. Here we describe our efforts to assemble a comprehensive resource that provides a quantitative snapshot of viral genomic trends – such as gene density, noncoding percentage, and abundances of functional gene categories – across thousands of viral genomes. We have also developed a coarse-grained method for visualizing viral genome organization for hundreds of genomes at once, and have explored the extent of the overlap between bacterial and bacteriophage gene pools. Existing viral classification systems were developed prior to the sequencing era, so we present our analysis in a way that allows us to assess the utility of the different classification systems for capturing genomic trends.
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Affiliation(s)
- Gita Mahmoudabadi
- Department of Bioengineering, California Institute of Technology, Pasadena, United States
| | - Rob Phillips
- Department of Bioengineering, California Institute of Technology, Pasadena, United States.,Department of Applied Physics, California Institute of Technology, Pasadena, United States
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406
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Hannigan GD, Duhaime MB, Koutra D, Schloss PD. Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome. PLoS Comput Biol 2018; 14:e1006099. [PMID: 29668682 PMCID: PMC5927471 DOI: 10.1371/journal.pcbi.1006099] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 04/30/2018] [Accepted: 03/21/2018] [Indexed: 01/17/2023] Open
Abstract
Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks. The human microbiome, the collection of microbial communities that colonize the human body, is a crucial component to health and disease. Two major components of the human microbiome are the bacterial and viral communities. These communities have primarily been studied separately using metrics of community composition and diversity. These approaches have failed to capture the complex dynamics of interacting bacteria and phage communities, which frequently share genetic information and work together to maintain ecosystem homestatsis (e.g. kill-the-winner dynamics). Removal of bacteria or phage can disrupt or even collapse those ecosystems. Relationship-based network approaches allow us to capture this interaction information. Using this network-based approach with three independent human cohorts, we were able to present an initial understanding of how phage-bacteria networks differ throughout the human body, so as to provide a baseline for future studies of how and why microbiome networks differ in disease states.
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Affiliation(s)
- Geoffrey D. Hannigan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Melissa B. Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Danai Koutra
- Department of Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Patrick D. Schloss
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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407
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Nishimura Y, Yoshida T, Kuronishi M, Uehara H, Ogata H, Goto S. ViPTree: the viral proteomic tree server. Bioinformatics 2018; 33:2379-2380. [PMID: 28379287 DOI: 10.1093/bioinformatics/btx157] [Citation(s) in RCA: 348] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/21/2017] [Indexed: 11/12/2022] Open
Abstract
Summary ViPTree is a web server provided through GenomeNet to generate viral proteomic trees for classification of viruses based on genome-wide similarities. Users can upload viral genomes sequenced either by genomics or metagenomics. ViPTree generates proteomic trees for the uploaded genomes together with flexibly selected reference viral genomes. ViPTree also serves as a platform to visually investigate genomic alignments and automatically annotated gene functions for the uploaded viral genomes, thus providing virus researchers the first choice for classifying and understanding newly sequenced viral genomes. Availability and Implementation ViPTree is freely available at: http://www.genome.jp/viptree . Contact goto@kuicr.kyoto-u.ac.jp. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yosuke Nishimura
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.,Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan
| | - Megumi Kuronishi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hideya Uehara
- SGI Japan, Ltd., Yebisu Garden Place Tower 31F, 4-20-3 Ebisu, Shibuya-ku, Tokyo 150-6031, Japan
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Susumu Goto
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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408
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de la Cruz Peña MJ, Martinez-Hernandez F, Garcia-Heredia I, Lluesma Gomez M, Fornas Ò, Martinez-Garcia M. Deciphering the Human Virome with Single-Virus Genomics and Metagenomics. Viruses 2018; 10:v10030113. [PMID: 29509721 PMCID: PMC5869506 DOI: 10.3390/v10030113] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/28/2018] [Accepted: 03/01/2018] [Indexed: 12/20/2022] Open
Abstract
Single-cell genomics has unveiled the metabolic potential of dominant microbes inhabiting different environments, including the human body. The lack of genomic information for predominant microbes of the human body, such as bacteriophages, hinders our ability to answer fundamental questions about our viral communities. Here, we applied single-virus genomics (SVGs) to natural human salivary samples in combination with viral metagenomics to gain some insights into the viral community structure of the oral cavity. Saliva samples were processed for viral metagenomics (n = 15) and SVGs (n = 3). A total of 1328 uncultured single viruses were sorted by fluorescence-activated virus sorting followed by whole genome amplification. Sequencing of 24 viral single amplified genomes (vSAGs) showed that half of the vSAGs contained viral hallmark genes. Among those bona fide viruses, the uncultured single virus 92-C13 putatively infecting oral Streptococcus-like species was within the top ≈10 most abundant viruses in the oral virome. Viral gene network and viral metagenomics analyses of 439 oral viruses from cultures, metagenomics, and SVGs revealed that salivary viruses were tentatively structured into ≈200 major viral clusters, corresponding to approximately genus-level groupings. Data showed that none of the publicly available viral isolates, excepting an Actinomyces phage, were significantly abundant in the oral viromes. In addition, none of the obtained viral contigs and vSAGs from this study were present in all viromes. Overall, the data demonstrates that most viral isolates are not naturally abundant in saliva, and furthermore, the predominant viruses in the oral cavity are yet uncharacterized. Results suggest a variable, complex, and interpersonal viral profile. Finally, we demonstrated the power of SVGs in combination with viral metagenomics to unveil the genetic information of the uncultured viruses of the human virome.
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Affiliation(s)
| | | | - Inmaculada Garcia-Heredia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, 03690 Alicante, Spain.
| | - Mónica Lluesma Gomez
- Department of Physiology, Genetics, and Microbiology, University of Alicante, 03690 Alicante, Spain.
| | - Òscar Fornas
- Flow Cytometry Unit: Pompeu Fabra University (UPF) and Centre for Genomic Regulation (CRG), The Barcelona Institute for Sciences and Technology (BIST), 08003 Barcelona, Spain.
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, 03690 Alicante, Spain.
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409
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Eichorst SA, Trojan D, Roux S, Herbold C, Rattei T, Woebken D. Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments. Environ Microbiol 2018; 20:1041-1063. [PMID: 29327410 PMCID: PMC5900883 DOI: 10.1111/1462-2920.14043] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 12/16/2017] [Accepted: 01/08/2018] [Indexed: 12/11/2022]
Abstract
Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed a large-scale comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8 and 23 (n = 24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. Our analysis revealed that bacteriophage integration events along with transposable and mobile elements influenced the structure and plasticity of these genomes. Low- and high-affinity respiratory oxygen reductases were detected in multiple genomes, suggesting the capacity for growing across different oxygen gradients. Among many genomes, the capacity to use a diverse collection of carbohydrates, as well as inorganic and organic nitrogen sources (such as via extracellular peptidases), was detected - both advantageous traits in environments with fluctuating nutrient environments. We also identified multiple soil acidobacteria with the potential to scavenge atmospheric concentrations of H2 , now encompassing mesophilic soil strains within the subdivision 1 and 3, in addition to a previously identified thermophilic strain in subdivision 4. This large-scale acidobacteria genome analysis reveal traits that provide genomic, physiological and metabolic versatility, presumably allowing flexibility and versatility in the challenging and fluctuating soil environment.
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Affiliation(s)
- Stephanie A. Eichorst
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
| | - Daniela Trojan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
| | - Simon Roux
- Department of EnergyJoint Genome InstituteWalnut CreekCAUSA
| | - Craig Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
| | - Thomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
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410
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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.
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411
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Berliner AJ, Mochizuki T, Stedman KM. Astrovirology: Viruses at Large in the Universe. ASTROBIOLOGY 2018; 18:207-223. [PMID: 29319335 DOI: 10.1089/ast.2017.1649] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Viruses are the most abundant biological entities on modern Earth. They are highly diverse both in structure and genomic sequence, play critical roles in evolution, strongly influence terran biogeochemistry, and are believed to have played important roles in the origin and evolution of life. However, there is yet very little focus on viruses in astrobiology. Viruses arguably have coexisted with cellular life-forms since the earliest stages of life, may have been directly involved therein, and have profoundly influenced cellular evolution. Viruses are the only entities on modern Earth to use either RNA or DNA in both single- and double-stranded forms for their genetic material and thus may provide a model for the putative RNA-protein world. With this review, we hope to inspire integration of virus research into astrobiology and also point out pressing unanswered questions in astrovirology, particularly regarding the detection of virus biosignatures and whether viruses could be spread extraterrestrially. We present basic virology principles, an inclusive definition of viruses, review current virology research pertinent to astrobiology, and propose ideas for future astrovirology research foci. Key Words: Astrobiology-Virology-Biosignatures-Origin of life-Roadmap. Astrobiology 18, 207-223.
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Affiliation(s)
| | | | - Kenneth M Stedman
- 3 Center for Life in Extreme Environments and Biology Department, Portland State University , Oregon, USA
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412
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Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan. ISME JOURNAL 2018; 12:1287-1295. [PMID: 29382948 PMCID: PMC5932082 DOI: 10.1038/s41396-018-0052-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/10/2017] [Accepted: 12/20/2017] [Indexed: 12/31/2022]
Abstract
Viruses infecting microorganisms are ubiquitous and abundant in the ocean. However, it is unclear when and where the numerous viral particles we observe in the sea are produced and whether they are active. To address these questions, we performed time-series analyses of viral metagenomes and microbial metatranscriptomes collected over a period of 24 h at a Japanese coastal site. Through mapping the metatranscriptomic reads on three sets of viral genomes ((i) 878 contigs of Osaka Bay viromes (OBV), (ii) 1766 environmental viral genomes from marine viromes, and (iii) 2429 reference viral genomes), we revealed that all the local OBV contigs were transcribed in the host fraction. This indicates that the majority of viral populations detected in viromes are active, and suggests that virions are rapidly diluted as a result of diffusion, currents, and mixing. Our data further revealed a peak of cyanophage gene expression in the afternoon/dusk followed by an increase of genomes from their virions at night and less-coherent infectious patterns for viruses putatively infecting various groups of heterotrophs. This suggests that cyanophages drive the diel release of cyanobacteria-derived organic matter into the environment and viruses of heterotrophic bacteria might have adapted to the population-specific life cycles of hosts.
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413
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Danovaro R, Corinaldesi C, Dell'Anno A, Rastelli E. Potential impact of global climate change on benthic deep-sea microbes. FEMS Microbiol Lett 2018; 364:4553516. [PMID: 29045616 DOI: 10.1093/femsle/fnx214] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/12/2017] [Indexed: 11/12/2022] Open
Abstract
Benthic deep-sea environments are the largest ecosystem on Earth, covering ∼65% of the Earth surface. Microbes inhabiting this huge biome at all water depths represent the most abundant biological components and a relevant portion of the biomass of the biosphere, and play a crucial role in global biogeochemical cycles. Increasing evidence suggests that global climate changes are affecting also deep-sea ecosystems, both directly (causing shifts in bottom-water temperature, oxygen concentration and pH) and indirectly (through changes in surface oceans' productivity and in the consequent export of organic matter to the seafloor). However, the responses of the benthic deep-sea biota to such shifts remain largely unknown. This applies particularly to deep-sea microbes, which include bacteria, archaea, microeukaryotes and their viruses. Understanding the potential impacts of global change on the benthic deep-sea microbial assemblages and the consequences on the functioning of the ocean interior is a priority to better forecast the potential consequences at global scale. Here we explore the potential changes in the benthic deep-sea microbiology expected in the coming decades using case studies on specific systems used as test models.
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Affiliation(s)
- Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy.,Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Cinzia Corinaldesi
- Department of Sciences and Engineering of Materials, Environment and Urbanistics, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Eugenio Rastelli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy.,Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
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414
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Abstract
While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry. Marine microbial eukaryotes and zooplankton display enormous diversity and largely unexplored physiologies. Here, the authors use metatranscriptomics to analyze four organismal size fractions from open-ocean stations, providing the largest reference collection of eukaryotic transcripts from any single biome.
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415
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Sheyn U, Rosenwasser S, Lehahn Y, Barak-Gavish N, Rotkopf R, Bidle KD, Koren I, Schatz D, Vardi A. Expression profiling of host and virus during a coccolithophore bloom provides insights into the role of viral infection in promoting carbon export. ISME JOURNAL 2018; 12:704-713. [PMID: 29335637 DOI: 10.1038/s41396-017-0004-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 09/19/2017] [Accepted: 10/08/2017] [Indexed: 11/09/2022]
Abstract
The cosmopolitan coccolithophore Emiliania huxleyi is a unicellular eukaryotic alga that forms vast blooms in the oceans impacting large biogeochemical cycles. These blooms are often terminated due to infection by the large dsDNA virus, E. huxleyi virus (EhV). It was recently established that EhV-induced modulation of E. huxleyi metabolism is a key factor for optimal viral infection cycle. Despite the huge ecological importance of this host-virus interaction, the ability to assess its spatial and temporal dynamics and its possible impact on nutrient fluxes is limited by current approaches that focus on quantification of viral abundance and biodiversity. Here, we applied a host and virus gene expression analysis as a sensitive tool to quantify the dynamics of this interaction during a natural E. huxleyi bloom in the North Atlantic. We used viral gene expression profiling as an index for the level of active infection and showed that the latter correlated with water column depth. Intriguingly, this suggests a possible sinking mechanism for removing infected cells as aggregates from the E. huxleyi population in the surface layer into deeper waters. Viral infection was also highly correlated with induction of host metabolic genes involved in host life cycle, sphingolipid, and antioxidant metabolism, providing evidence for modulation of host metabolism under natural conditions. The ability to track and quantify defined phases of infection by monitoring co-expression of viral and host genes, coupled with advance omics approaches, will enable a deeper understanding of the impact that viruses have on the environment.
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Affiliation(s)
- Uri Sheyn
- Departments of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shilo Rosenwasser
- Departments of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.,The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University, Rehovot, 7610001, Israel
| | - Yoav Lehahn
- Departments of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Noa Barak-Gavish
- Departments of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ron Rotkopf
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Kay D Bidle
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Ilan Koren
- Departments of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Daniella Schatz
- Departments of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Assaf Vardi
- Departments of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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416
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Tithi SS, Aylward FO, Jensen RV, Zhang L. FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data. PeerJ 2018; 6:e4227. [PMID: 29340239 PMCID: PMC5768174 DOI: 10.7717/peerj.4227] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 12/12/2017] [Indexed: 11/20/2022] Open
Abstract
With the increase in the availability of metagenomic data generated by next generation sequencing, there is an urgent need for fast and accurate tools for identifying viruses in host-associated and environmental samples. In this paper, we developed a stand-alone pipeline called FastViromeExplorer for the detection and abundance quantification of viruses and phages in large metagenomic datasets by performing rapid searches of virus and phage sequence databases. Both simulated and real data from human microbiome and ocean environmental samples are used to validate FastViromeExplorer as a reliable tool to quickly and accurately identify viruses and their abundances in large datasets.
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Affiliation(s)
- Saima Sultana Tithi
- Department of Computer Science, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Roderick V Jensen
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Liqing Zhang
- Department of Computer Science, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
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417
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Pratama AA, van Elsas JD. The 'Neglected' Soil Virome - Potential Role and Impact. Trends Microbiol 2018; 26:649-662. [PMID: 29306554 DOI: 10.1016/j.tim.2017.12.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/10/2017] [Accepted: 12/11/2017] [Indexed: 12/29/2022]
Abstract
Bacteriophages are among the most abundant and diverse biological units in the biosphere. They have contributed to our understanding of the central dogma of biology and have been instrumental in the evolutionary success of bacterial pathogens. In contrast to our current understanding of marine viral communities, the soil virome and its function in terrestrial ecosystems has remained relatively understudied. Here, we examine, in a comparative fashion, the knowledge gathered from studies performed in soil versus marine settings. We address the information with respect to the abundance, diversity, ecological significance, and effects of, in particular, bacteriophages on their host's evolutionary trajectories. We also identify the main challenges that soil virology faces and the studies that are required to accompany the current developments in marine settings.
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Affiliation(s)
- Akbar Adjie Pratama
- Department of Microbial Ecology, Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
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418
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Amgarten D, Braga LPP, da Silva AM, Setubal JC. MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins. Front Genet 2018. [PMID: 30131825 DOI: 10.3389/fgene.2018.00304/full] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Here we present MARVEL, a tool for prediction of double-stranded DNA bacteriophage sequences in metagenomic bins. MARVEL uses a random forest machine learning approach. We trained the program on a dataset with 1,247 phage and 1,029 bacterial genomes, and tested it on a dataset with 335 bacterial and 177 phage genomes. We show that three simple genomic features extracted from contig sequences were sufficient to achieve a good performance in separating bacterial from phage sequences: gene density, strand shifts, and fraction of significant hits to a viral protein database. We compared the performance of MARVEL to that of VirSorter and VirFinder, two popular programs for predicting viral sequences. Our results show that all three programs have comparable specificity, but MARVEL achieves much better performance on the recall (sensitivity) measure. This means that MARVEL should be able to identify many more phage sequences in metagenomic bins than heretofore has been possible. In a simple test with real data, containing mostly bacterial sequences, MARVEL classified 58 out of 209 bins as phage genomes; other evidence suggests that 57 of these 58 bins are novel phage sequences. MARVEL is freely available at https://github.com/LaboratorioBioinformatica/MARVEL.
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Affiliation(s)
- Deyvid Amgarten
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Lucas P P Braga
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- INRA, UMR 1347, Agroécologie, Dijon, France
| | - Aline M da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - João C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Biocomplexity Institute of Virginia Tech, Blacksburg, VA, United States
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419
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Cabello-Yeves PJ, Zemskaya TI, Rosselli R, Coutinho FH, Zakharenko AS, Blinov VV, Rodriguez-Valera F. Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal. Appl Environ Microbiol 2018; 84:e02132-17. [PMID: 29079621 PMCID: PMC5734018 DOI: 10.1128/aem.02132-17] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 10/19/2017] [Indexed: 11/20/2022] Open
Abstract
We present a metagenomic study of Lake Baikal (East Siberia). Two samples obtained from the water column under the ice cover (5 and 20 m deep) in March 2016 have been deep sequenced and the reads assembled to generate metagenome-assembled genomes (MAGs) that are representative of the microbes living in this special environment. Compared with freshwater bodies studied around the world, Lake Baikal had an unusually high fraction of Verrucomicrobia Other groups, such as Actinobacteria and Proteobacteria, were in proportions similar to those found in other lakes. The genomes (and probably cells) tended to be small, presumably reflecting the extremely oligotrophic and cold prevalent conditions. Baikal microbes are novel lineages recruiting very little from other water bodies and are distantly related to other freshwater microbes. Despite their novelty, they showed the closest relationship to genomes discovered by similar approaches from other freshwater lakes and reservoirs. Some of them were particularly similar to MAGs from the Baltic Sea, which, although it is brackish, connected to the ocean, and much more eutrophic, has similar climatological conditions. Many of the microbes contained rhodopsin genes, indicating that, in spite of the decreased light penetration allowed by the thick ice/snow cover, photoheterotrophy could be widespread in the water column, either because enough light penetrates or because the microbes are already adapted to the summer ice-less conditions. We have found a freshwater SAR11 subtype I/II representative showing striking synteny with Pelagibacterubique strains, as well as a phage infecting the widespread freshwater bacterium PolynucleobacterIMPORTANCE Despite the increasing number of metagenomic studies on different freshwater bodies, there is still a missing component in oligotrophic cold lakes suffering from long seasonal frozen cycles. Here, we describe microbial genomes from metagenomic assemblies that appear in the upper water column of Lake Baikal, the largest and deepest freshwater body on Earth. This lake is frozen from January to May, which generates conditions that include an inverted temperature gradient (colder up), decrease in light penetration due to ice, and, especially, snow cover, and oligotrophic conditions more similar to the open-ocean and high-altitude lakes than to other freshwater or brackish systems. As could be expected, most reconstructed genomes are novel lineages distantly related to others in cold environments, like the Baltic Sea and other freshwater lakes. Among them, there was a broad set of streamlined microbes with small genomes/intergenic spacers, including a new nonmarine Pelagibacter-like (subtype I/II) genome.
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Affiliation(s)
- Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Tamara I Zemskaya
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Riccardo Rosselli
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Felipe H Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Alexandra S Zakharenko
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Vadim V Blinov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
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420
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Ogilvie LA, Nzakizwanayo J, Guppy FM, Dedi C, Diston D, Taylor H, Ebdon J, Jones BV. Resolution of habitat-associated ecogenomic signatures in bacteriophage genomes and application to microbial source tracking. ISME JOURNAL 2017; 12:942-958. [PMID: 29259289 PMCID: PMC5864186 DOI: 10.1038/s41396-017-0015-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/06/2017] [Accepted: 11/11/2017] [Indexed: 12/28/2022]
Abstract
Just as the expansion in genome sequencing has revealed and permitted the exploitation of phylogenetic signals embedded in bacterial genomes, the application of metagenomics has begun to provide similar insights at the ecosystem level for microbial communities. However, little is known regarding this aspect of bacteriophage associated with microbial ecosystems, and if phage encode discernible habitat-associated signals diagnostic of underlying microbiomes. Here we demonstrate that individual phage can encode clear habitat-related 'ecogenomic signatures', based on relative representation of phage-encoded gene homologues in metagenomic data sets. Furthermore, we show the ecogenomic signature encoded by the gut-associated ɸB124-14 can be used to segregate metagenomes according to environmental origin, and distinguish 'contaminated' environmental metagenomes (subject to simulated in silico human faecal pollution) from uncontaminated data sets. This indicates phage-encoded ecological signals likely possess sufficient discriminatory power for use in biotechnological applications, such as development of microbial source tracking tools for monitoring water quality.
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Affiliation(s)
- Lesley A Ogilvie
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK.
| | | | - Fergus M Guppy
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK
| | - Cinzia Dedi
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK
| | - David Diston
- Mikrobiologische & Biotechnologische Risiken Bundesamt für Gesundheit BAG, 3003, Bern, Switzerland
| | - Huw Taylor
- School of Environment and Technology, University of Brighton, Brighton, UK
| | - James Ebdon
- School of Environment and Technology, University of Brighton, Brighton, UK
| | - Brian V Jones
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK.
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421
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Pasulka AL, Thamatrakoln K, Kopf SH, Guan Y, Poulos B, Moradian A, Sweredoski MJ, Hess S, Sullivan MB, Bidle KD, Orphan VJ. Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods. Environ Microbiol 2017; 20:671-692. [DOI: 10.1111/1462-2920.13996] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/10/2017] [Accepted: 11/12/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Alexis L. Pasulka
- Division of Geological and Planetary Sciences; California Institute of Technology; CA USA
| | | | - Sebastian H. Kopf
- Department of Geological Sciences, University of Colorado Boulder; CO USA
| | - Yunbin Guan
- Division of Geological and Planetary Sciences; California Institute of Technology; CA USA
| | - Bonnie Poulos
- Department of Ecology and Evolutionary Biology, University of Arizona; AZ USA
| | - Annie Moradian
- Proteome Exploration Laboratory, California Institute of Technology; CA USA
| | | | - Sonja Hess
- Proteome Exploration Laboratory, California Institute of Technology; CA USA
| | | | - Kay D. Bidle
- Department of Marine and Coastal Studies; Rutgers University; NJ USA
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences; California Institute of Technology; CA USA
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422
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Shi W, Li J, Zhou H, Gao GF. Pathogen genomic surveillance elucidates the origins, transmission and evolution of emerging viral agents in China. SCIENCE CHINA. LIFE SCIENCES 2017; 60:1317-1330. [PMID: 29270793 PMCID: PMC7088571 DOI: 10.1007/s11427-017-9211-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/01/2017] [Indexed: 02/06/2023]
Abstract
In the past twenty years, numerous novel zoonotic viral agents with pandemic potential have emerged in China, such as the severe acute respiratory syndrome (SARS) coronavirus and, more recently, the avian-origin influenza A/H7N9 virus, which have caused outbreaks among humans with high morbidity and mortality. In addition, several emerging and re-emerging viral pathogens have also been imported into China from travelers, e.g. the Middle East respiratory syndrome (MERS) coronavirus and Zika virus (ZIKV). Herein, we review these emerging viral pathogens in China and focus on how surveillance by pathogen genomics has been employed to discover and annotate novel pathogenic agents, identify natural reservoirs, monitor the transmission events and delineate their evolution and adaption to the human host. We also highlight the application of genomic sequencing in the recent Ebola epidemics in Western Africa. In summary, genomic sequencing has become a standard research tool in the field of emerging infectious diseases which has been proven invaluable in containing these viral infections and reducing burden of disease in humans and animals. Genomic surveillance of pathogenic agents will serve as a key epidemiological and research tool in the modern era of precision infectious diseases and in the future studies of virosphere.
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Affiliation(s)
- Weifeng Shi
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong (Taishan Medical College), Taishan Medical College, Taian, 271000, China.
| | - Juan Li
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong (Taishan Medical College), Taishan Medical College, Taian, 271000, China
| | - Hong Zhou
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong (Taishan Medical College), Taishan Medical College, Taian, 271000, China
| | - George F Gao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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423
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Anderson CL, Sullivan MB, Fernando SC. Dietary energy drives the dynamic response of bovine rumen viral communities. MICROBIOME 2017; 5:155. [PMID: 29179741 PMCID: PMC5704599 DOI: 10.1186/s40168-017-0374-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 11/14/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND Rumen microbes play a greater role in host energy acquisition than that of gut-associated microbes in monogastric animals. Although genome-enabled advancements are providing access to the vast diversity of uncultivated microbes, our understanding of variables shaping rumen microbial communities is in its infancy. Viruses have been shown to impact microbial populations through a myriad of processes, including cell lysis and reprogramming of host metabolism. However, little is known about the processes shaping the distribution of rumen viruses or how viruses may modulate microbial-driven processes in the rumen. To this end, we investigated how rumen bacterial and viral community structure and function responded in five steers fed four randomized dietary treatments in a crossover design. RESULTS Total digestible nutrients (TDN), a measure of dietary energy, best explained the variation in bacterial and viral communities. Additional ecological drivers of viral communities included dietary zinc content and microbial functional diversity. Using partial least squares regression, we demonstrate significant associations between the abundances of 267 viral populations and variables driving the variation in rumen viral communities. While rumen viruses were dynamic, 14 near ubiquitous viral populations were identified, suggesting the presence of a core rumen virome largely comprised of novel viruses. Moreover, analysis of virally encoded auxiliary metabolic genes (AMGs) indicates rumen viruses have glycosidic hydrolases to potentially augment the breakdown of complex carbohydrates to increase energy production. Other AMGs identified have a role in redirecting carbon to the pentose phosphate pathway and one carbon pools by folate to boost viral replication. CONCLUSIONS We demonstrate that rumen bacteria and viruses have differing responses and ecological drivers to dietary perturbation. Our results show that rumen viruses have implications for understanding the structuring of the previously identified core rumen microbiota and impacting microbial metabolism through a vast array of AMGs. AMGs in the rumen appear to have consequences for microbial metabolism that are largely in congruence with the current paradigm established in marine systems. This study provides a foundation for future hypotheses regarding the dynamics of viral-mediated processes in the rumen.
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Affiliation(s)
- Christopher L. Anderson
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA
- Department of Animal Science, University of Nebraska-Lincoln, C220K Animal Science Complex, Lincoln, NE 68583-0908 USA
| | - Matthew B. Sullivan
- Departments of Microbiology, and Civil, Environmental and Geodetic Engineering, The Ohio State University, Riffe Building 266, 496 W 12th Ave, Columbus, OH 43210 USA
| | - Samodha C. Fernando
- Department of Animal Science, University of Nebraska-Lincoln, C220K Animal Science Complex, Lincoln, NE 68583-0908 USA
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424
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Virus-host protein-protein interactions of mycobacteriophage Giles. Sci Rep 2017; 7:16514. [PMID: 29184079 PMCID: PMC5705681 DOI: 10.1038/s41598-017-16303-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/31/2017] [Indexed: 01/21/2023] Open
Abstract
Mycobacteriophage are viruses that infect mycobacteria. More than 1,400 mycobacteriophage genomes have been sequenced, coding for over one hundred thousand proteins of unknown functions. Here we investigate mycobacteriophage Giles-host protein-protein interactions (PPIs) using yeast two-hybrid screening (Y2H). A total of 25 reproducible PPIs were found for a selected set of 10 Giles proteins, including a putative virion assembly protein (gp17), the phage integrase (gp29), the endolysin (gp31), the phage repressor (gp47), and six proteins of unknown function (gp34, gp35, gp54, gp56, gp64, and gp65). We note that overexpression of the proteins is toxic to M. smegmatis, although whether this toxicity and the associated changes in cellular morphology are related to the putative interactions revealed in the Y2H screen is unclear.
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425
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Abstract
Bacteriophages are numerically the most abundant DNA-containing entities in the oligotrophic ocean, yet how specific phage populations vary over time and space remains to be fully explored. Here, we conducted a metagenomic time-series survey of double-stranded DNA phages throughout the water column in the North Pacific Subtropical Gyre, encompassing 1.5 years from depths of 25 to 1,000 m. Viral gene sequences were identified in assembled metagenomic samples, yielding an estimated 172,385 different viral gene families. Viral marker gene distributions suggested that lysogeny was more prevalent at mesopelagic depths than in surface waters, consistent with prior prophage induction studies using mitomycin C. A total of 129 ALOHA viral genomes and genome fragments from 20 to 108 kbp were selected for further study, which represented the most abundant phages in the water column. Phage genotypes displayed discrete population structures. Most phages persisted throughout the time-series and displayed a strong depth structure that mirrored the stratified depth distributions of co-occurring bacterial taxa in the water column. Mesopelagic phages were distinct from surface water phages with respect to diversity, gene content, putative life histories, and temporal persistence, reflecting depth-dependent differences in host genomic architectures and phage reproductive strategies. The spatiotemporal distributions of the most abundant open-ocean bacteriophages that we report here provide new insight into viral temporal persistence, life history, and virus-host-environment interactions throughout the open-ocean water column. The North Pacific Subtropical Gyre represents one of the largest biomes on the planet, where microbial communities are central mediators of ecosystem dynamics and global biogeochemical cycles. Critical members of these communities are the viruses of marine bacteria, which can alter microbial metabolism and significantly influence their survival and productivity. To better understand these viral assemblages, we conducted genomic analyses of planktonic viruses over a seasonal cycle to ocean depths of 1,000 m. We identified 172,385 different viral gene families and 129 unique virus genotypes in this open-ocean setting. The spatiotemporal distributions of the most abundant open-ocean viruses that we report here provide new insights into viral temporal variability, life history, and virus-host-environment interactions throughout the water column.
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426
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Krupovic M, Cvirkaite-Krupovic V, Iranzo J, Prangishvili D, Koonin EV. Viruses of archaea: Structural, functional, environmental and evolutionary genomics. Virus Res 2017; 244:181-193. [PMID: 29175107 DOI: 10.1016/j.virusres.2017.11.025] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 11/20/2017] [Accepted: 11/20/2017] [Indexed: 11/18/2022]
Abstract
Viruses of archaea represent one of the most enigmatic parts of the virosphere. Most of the characterized archaeal viruses infect extremophilic hosts and display remarkable diversity of virion morphotypes, many of which have never been observed among viruses of bacteria or eukaryotes. The uniqueness of the virion morphologies is matched by the distinctiveness of the genomes of these viruses, with ∼75% of genes encoding unique proteins, refractory to functional annotation based on sequence analyses. In this review, we summarize the state-of-the-art knowledge on various aspects of archaeal virus genomics. First, we outline how structural and functional genomics efforts provided valuable insights into the functions of viral proteins and revealed intricate details of the archaeal virus-host interactions. We then highlight recent metagenomics studies, which provided a glimpse at the diversity of uncultivated viruses associated with the ubiquitous archaea in the oceans, including Thaumarchaeota, Marine Group II Euryarchaeota, and others. These findings, combined with the recent discovery that archaeal viruses mediate a rapid turnover of thaumarchaea in the deep sea ecosystems, illuminate the prominent role of these viruses in the biosphere. Finally, we discuss the origins and evolution of archaeal viruses and emphasize the evolutionary relationships between viruses and non-viral mobile genetic elements. Further exploration of the archaeal virus diversity as well as functional studies on diverse virus-host systems are bound to uncover novel, unexpected facets of the archaeal virome.
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Affiliation(s)
- Mart Krupovic
- Department of Microbiology, Institut Pasteur, 25 rue du Dr. Roux, Paris 75015, Paris, France.
| | | | - Jaime Iranzo
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - David Prangishvili
- Department of Microbiology, Institut Pasteur, 25 rue du Dr. Roux, Paris 75015, Paris, France
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
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427
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Abstract
One of the most prominent features of archaea is the extraordinary diversity of their DNA viruses. Many archaeal viruses differ substantially in morphology from bacterial and eukaryotic viruses and represent unique virus families. The distinct nature of archaeal viruses also extends to the gene composition and architectures of their genomes and the properties of the proteins that they encode. Environmental research has revealed prominent roles of archaeal viruses in influencing microbial communities in ocean ecosystems, and recent metagenomic studies have uncovered new groups of archaeal viruses that infect extremophiles and mesophiles in diverse habitats. In this Review, we summarize recent advances in our understanding of the genomic and morphological diversity of archaeal viruses and the molecular biology of their life cycles and virus-host interactions, including interactions with archaeal CRISPR-Cas systems. We also examine the potential origins and evolution of archaeal viruses and discuss their place in the global virosphere.
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428
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Culley A. New insight into the RNA aquatic virosphere via viromics. Virus Res 2017; 244:84-89. [PMID: 29138044 DOI: 10.1016/j.virusres.2017.11.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 01/09/2023]
Abstract
RNA viruses that infect microbes are now recognized as an active, persistent and important component of the aquatic microbial community. While some information about the diversity and dynamics of the RNA virioplankton has been derived from culture-based and single gene approaches, research based on viromic and metatransciptomic methods has generated unprecedented insight into this relatively understudied class of microbes. Here, the relevant literature is summarized and discussed, including viromic studies of extracellular aquatic RNA viral assemblages, and transcriptomic studies of active and associated RNA viruses from aquatic environments followed by commentary on the present challenges and future directions of this field of research.
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Affiliation(s)
- Alexander Culley
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Québec, G1V 0A6, Canada; Centre d'études nordiques (CEN), Université Laval, Québec, Québec, G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada; Takuvik, Unité Mixte Interntionale (UMI 3376) Université Laval (Canada) & Centre National de la Recherche Scientifique (France), Québec QC GIV 0A6, Canada.
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429
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Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic Bacteroidetes. ISME JOURNAL 2017; 12:424-437. [PMID: 29099492 PMCID: PMC5776456 DOI: 10.1038/ismej.2017.175] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/16/2017] [Accepted: 08/23/2017] [Indexed: 12/12/2022]
Abstract
Hypersaline environments close to saturation harbor the highest density of virus-like particles reported for aquatic systems as well as low microbial diversity. Thus, they offer unique settings for studying virus–host interactions in nature. However, no viruses have been isolated so far infecting the two most abundant inhabitants of these systems (that is, the euryarchaeon Haloquadratum walsbyi and the bacteroidetes Salinibacter ruber). Here, using three different co-occurring strains, we have isolated eight viruses infecting the ubiquitous S. ruber that constitute three new different genera (named as ‘Holosalinivirus’, ‘Kryptosalinivirus’ and ‘Kairosalinivirus’) according to their genomic traits, different host range, virus–host interaction capabilities and abundances in natural systems worldwide. Furthermore, to get a more complete and comprehensive view of S. ruber virus assemblages in nature, a microcosm experiment was set with a mixture of S. ruber strains challenged with a brine virus concentrate, and changes of viral populations were monitored by viral metagenomics. Only viruses closely related to kairosalinivirus (strictly lytic and wide host range) were enriched, despite their low initial abundance in the natural sample. Metagenomic analyses of the mesocosms allowed the complete recovery of kairosalinivirus genomes using an ad hoc assembly strategy as common viral metagenomic assembly tools failed despite their abundance, which underlines the limitations of current approaches. The increase of this type of viruses was accompanied by an increase in the diversity of the group, as shown by contig recruitment. These results are consistent with a scenario in which host range, not only virus and host abundances, is a key factor in determining virus fate in nature.
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430
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Moon K, Kang I, Kim S, Kim SJ, Cho JC. Genome characteristics and environmental distribution of the first phage that infects the LD28 clade, a freshwater methylotrophic bacterial group. Environ Microbiol 2017; 19:4714-4727. [PMID: 28925542 DOI: 10.1111/1462-2920.13936] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/09/2017] [Accepted: 09/11/2017] [Indexed: 11/29/2022]
Abstract
Bacteriophages infecting major groups of freshwater heterotrophic bacteria have been rarely isolated, hampering analyses of freshwater viromes. Here, we report the isolation and genomic characterization of P19250A, the first phage that infects the LD28 clade, an abundant freshwater methylotrophic bacterial group. P19250A was isolated from Lake Soyang, an oligotrophic reservoir, using an LD28 strain as a host. Morphological and genomic analyses revealed that P19250A is a lytic siphovirus with a ∼38.6-kb genome. To analyze the distribution of P19250A genome within its habitat, six seasonal viral metagenome (virome) samples were prepared from Lake Soyang. Through binning analysis of freshwater viromes, P19250A was shown to be the most highly assigned freshwater phage that infects heterotrophic bacteria (up to 8.21%) in five viromes. Furthermore, when freshwater virome data collected worldwide were analyzed, P19250A genome also showed high abundance, especially in Lough Neagh, UK, where P19250A genome was recorded as the most abundant bacteriophage. From metagenome analysis, the proportion of P19250A-assigned reads showed seasonal fluctuation following the abundance of the LD28 clade in Lake Soyang. These results showed that P19250A would be an essential resource for analyses of freshwater viromes, and also suggest that phages of other abundant freshwater bacteria need to be isolated for better understanding of freshwater viruses.
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Affiliation(s)
- Kira Moon
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Suhyun Kim
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Sang-Jong Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
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431
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Cyanophage-encoded lipid desaturases: oceanic distribution, diversity and function. ISME JOURNAL 2017; 12:343-355. [PMID: 29028002 PMCID: PMC5776448 DOI: 10.1038/ismej.2017.159] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 08/17/2017] [Accepted: 08/22/2017] [Indexed: 11/08/2022]
Abstract
Cyanobacteria are among the most abundant photosynthetic organisms in the oceans; viruses infecting cyanobacteria (cyanophages) can alter cyanobacterial populations, and therefore affect the local food web and global biochemical cycles. These phages carry auxiliary metabolic genes (AMGs), which rewire various metabolic pathways in the infected host cell, resulting in increased phage fitness. Coping with stress resulting from photodamage appears to be a central necessity of cyanophages, yet the overall mechanism is poorly understood. Here we report a novel, widespread cyanophage AMG, encoding a fatty acid desaturase (FAD), found in two genotypes with distinct geographical distribution. FADs are capable of modulating the fluidity of the host’s membrane, a fundamental stress response in living cells. We show that both viral FAD (vFAD) families are Δ9 lipid desaturases, catalyzing the desaturation at carbon 9 in C16 fatty acid chains. In addition, we present a comprehensive fatty acid profiling for marine cyanobacteria, which suggests a unique desaturation pathway of medium- to long-chain fatty acids no longer than C16, in accordance with the vFAD activity. Our findings suggest that cyanophages are capable of fiddling with the infected host’s membranes, possibly leading to increased photoprotection and potentially enhancing viral-encoded photosynthetic proteins, resulting in a new viral metabolic network.
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432
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Arkhipova K, Skvortsov T, Quinn JP, McGrath JW, Allen CC, Dutilh BE, McElarney Y, Kulakov LA. Temporal dynamics of uncultured viruses: a new dimension in viral diversity. ISME JOURNAL 2017; 12:199-211. [PMID: 29027998 DOI: 10.1038/ismej.2017.157] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/26/2017] [Accepted: 08/22/2017] [Indexed: 11/09/2022]
Abstract
Recent work has vastly expanded the known viral genomic sequence space, but the seasonal dynamics of viral populations at the genome level remain unexplored. Here we followed the viral community in a freshwater lake for 1 year using genome-resolved viral metagenomics, combined with detailed analyses of the viral community structure, associated bacterial populations and environmental variables. We reconstructed 8950 complete and partial viral genomes, the majority of which were not persistent in the lake throughout the year, but instead continuously succeeded each other. Temporal analysis of 732 viral genus-level clusters demonstrated that one-fifth were undetectable at specific periods of the year. Based on host predictions for a subset of reconstructed viral genomes, we for the first time reveal three distinct patterns of host-pathogen dynamics, where the viruses may peak before, during or after the peak in their host's abundance, providing new possibilities for modelling of their interactions. Time series metagenomics opens up a new dimension in viral profiling, which is essential to understand the full scale of viral diversity and evolution, and the ecological roles of these important factors in the global ecosystem.
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Affiliation(s)
- Ksenia Arkhipova
- School of Biological Sciences, The Queen's University of Belfast, Belfast, UK.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Timofey Skvortsov
- School of Biological Sciences, The Queen's University of Belfast, Belfast, UK.,Institute for Global Food Security, The Queen's University of Belfast, Belfast, UK
| | - John P Quinn
- School of Biological Sciences, The Queen's University of Belfast, Belfast, UK
| | - John W McGrath
- School of Biological Sciences, The Queen's University of Belfast, Belfast, UK.,Institute for Global Food Security, The Queen's University of Belfast, Belfast, UK
| | - Christopher Cr Allen
- School of Biological Sciences, The Queen's University of Belfast, Belfast, UK.,Institute for Global Food Security, The Queen's University of Belfast, Belfast, UK
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | | | - Leonid A Kulakov
- School of Biological Sciences, The Queen's University of Belfast, Belfast, UK
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433
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Abstract
Marine microbial communities exert a large influence on ocean ecosystem processes, and viruses in these communities play key roles in controlling microbial abundances, nutrient cycling, and productivity. We show here that dominant viruses in the open ocean persist for long time periods and that many appear tightly locked in coordinated diel oscillations with their bacterial hosts. The persistent structure of viral assemblages, as well as synchronized daily oscillations of viruses and hosts, are in part the result of the regular diurnal coupling of viral and host replication cycles. Collectively, our results suggest that viruses, as key components of marine ecosystems, are intrinsically synchronized with the daily rhythms of microbial community processes in the ocean’s photic zone. Viruses are fundamental components of marine microbial communities that significantly influence oceanic productivity, biogeochemistry, and ecosystem processes. Despite their importance, the temporal activities and dynamics of viral assemblages in natural settings remain largely unexplored. Here we report the transcriptional activities and variability of dominant dsDNA viruses in the open ocean’s euphotic zone over daily and seasonal timescales. While dsDNA viruses exhibited some fluctuation in abundance in both cellular and viral size fractions, the viral assemblage was remarkably stable, with the most abundant viral types persisting over many days. More extended time series indicated that long-term persistence (>1 y) was the rule for most dsDNA viruses observed, suggesting that both core viral genomes as well as viral community structure were conserved over interannual periods. Viral gene transcription in host cell assemblages revealed diel cycling among many different viral types. Most notably, an afternoon peak in cyanophage transcriptional activity coincided with a peak in Prochlorococcus DNA replication, indicating coordinated diurnal coupling of virus and host reproduction. In aggregate, our analyses suggested a tightly synchronized diel coupling of viral and cellular replication cycles in both photoautotrophic and heterotrophic bacterial hosts. A surprising consequence of these findings is that diel cycles in the ocean’s photic zone appear to be universal organizing principles that shape ecosystem dynamics, ecological interactions, and biogeochemical cycling of both cellular and acellular community components.
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434
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Aggarwala V, Liang G, Bushman FD. Viral communities of the human gut: metagenomic analysis of composition and dynamics. Mob DNA 2017; 8:12. [PMID: 29026445 PMCID: PMC5627405 DOI: 10.1186/s13100-017-0095-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/24/2017] [Indexed: 01/17/2023] Open
Abstract
Background The numerically most abundant biological entities on Earth are viruses. Vast populations prey on the cellular microbiota in all habitats, including the human gut. Main body Here we review approaches for studying the human virome, and some recent results on movement of viral sequences between bacterial cells and eukaryotic hosts. We first overview biochemical and bioinformatic methods, emphasizing that specific choices in the methods used can have strong effects on the results obtained. We then review studies characterizing the virome of the healthy human gut, which reveal that most of the viruses detected are typically uncharacterized phage - the viral dark matter - and that viruses that infect human cells are encountered only rarely. We then review movement of phage between bacterial cells during antibiotic treatment. Here a radical proposal for extensive movement of antibiotic genes on phage has been challenged by a careful reanalysis of the metagenomic annotation methods used. We then review two recent studies of movement of whole phage communities between human individuals during fecal microbial transplantation, which emphasize the possible role of lysogeny in dispersal. Short conclusion Methods for studying the human gut virome are improving, yielding interesting data on movement of phage genes between cells and mammalian host organisms. However, viral populations are vast, and studies of their composition and function are just beginning.
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Affiliation(s)
- Varun Aggarwala
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076 USA
| | - Guanxiang Liang
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076 USA.,Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104-4319 USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076 USA
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435
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López-Pérez M, Haro-Moreno JM, Gonzalez-Serrano R, Parras-Moltó M, Rodriguez-Valera F. Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters. PLoS Genet 2017; 13:e1007018. [PMID: 28945750 PMCID: PMC5628999 DOI: 10.1371/journal.pgen.1007018] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/05/2017] [Accepted: 09/13/2017] [Indexed: 11/18/2022] Open
Abstract
Marine viruses play a critical role not only in the global geochemical cycles but also in the biology and evolution of their hosts. Despite their importance, viral diversity remains underexplored mostly due to sampling and cultivation challenges. Direct sequencing approaches such as viromics has provided new insights into the marine viral world. As a complementary approach, we analysed 24 microbial metagenomes (>0.2 μm size range) obtained from six sites in the Mediterranean Sea that vary by depth, season and filter used to retrieve the fraction. Filter-size comparison showed a significant number of viral sequences that were retained on the larger-pore filters and were different from those found in the viral fraction from the same sample, indicating that some important viral information is missing using only assembly from viromes. Besides, we were able to describe 1,323 viral genomic fragments that were more than 10Kb in length, of which 36 represented complete viral genomes including some of them retrieved from a cross-assembly from different metagenomes. Host prediction based on sequence methods revealed new phage groups belonging to marine prokaryotes like SAR11, Cyanobacteria or SAR116. We also identified the first complete virophage from deep seawater and a new endemic clade of the recently discovered Marine group II Euryarchaeota virus. Furthermore, analysis of viral distribution using metagenomes and viromes indicated that most of the new phages were found exclusively in the Mediterranean Sea and some of them, mostly the ones recovered from deep metagenomes, do not recruit in any database probably indicating higher variability and endemicity in Mediterranean bathypelagic waters. Together these data provide the first detailed picture of genomic diversity, spatial and depth variations of viral communities within the Mediterranean Sea using metagenome assembly.
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Affiliation(s)
- Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Campus de San Juan, San Juan de Alicante, Spain
| | - Jose M. Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Campus de San Juan, San Juan de Alicante, Spain
| | - Rafael Gonzalez-Serrano
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Campus de San Juan, San Juan de Alicante, Spain
| | - Marcos Parras-Moltó
- Centro de Biología Molecular 'Severo Ochoa' (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Cantoblanco, Madrid, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Campus de San Juan, San Juan de Alicante, Spain
- * E-mail:
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436
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O’Hara NB, Reed HJ, Afshinnekoo E, Harvin D, Caplan N, Rosen G, Frye B, Woloszynek S, Ounit R, Levy S, Butler E, Mason CE. Metagenomic characterization of ambulances across the USA. MICROBIOME 2017; 5:125. [PMID: 28938903 PMCID: PMC5610413 DOI: 10.1186/s40168-017-0339-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/07/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Microbial communities in our built environments have great influence on human health and disease. A variety of built environments have been characterized using a metagenomics-based approach, including some healthcare settings. However, there has been no study to date that has used this approach in pre-hospital settings, such as ambulances, an important first point-of-contact between patients and hospitals. RESULTS We sequenced 398 samples from 137 ambulances across the USA using shotgun sequencing. We analyzed these data to explore the microbial ecology of ambulances including characterizing microbial community composition, nosocomial pathogens, patterns of diversity, presence of functional pathways and antimicrobial resistance, and potential spatial and environmental factors that may contribute to community composition. We found that the top 10 most abundant species are either common built environment microbes, microbes associated with the human microbiome (e.g., skin), or are species associated with nosocomial infections. We also found widespread evidence of antimicrobial resistance markers (hits ~ 90% samples). We identified six factors that may influence the microbial ecology of ambulances including ambulance surfaces, geographical-related factors (including region, longitude, and latitude), and weather-related factors (including temperature and precipitation). CONCLUSIONS While the vast majority of microbial species classified were beneficial, we also found widespread evidence of species associated with nosocomial infections and antimicrobial resistance markers. This study indicates that metagenomics may be useful to characterize the microbial ecology of pre-hospital ambulance settings and that more rigorous testing and cleaning of ambulances may be warranted.
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Affiliation(s)
- Niamh B. O’Hara
- Jacobs Technion-Cornell Institute, Cornell Tech, New York, NY USA
| | - Harry J. Reed
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY USA
- School of Medicine, New York Medical College, Valhalla, NY USA
| | - Donell Harvin
- SUNY Downstate Medical Center, State University of New York, Brooklyn, NY USA
| | - Nora Caplan
- SUNY Downstate Medical Center, State University of New York, Brooklyn, NY USA
| | - Gail Rosen
- Electrical and Computer Engineering, Drexel University, Philadelphia, PA USA
| | - Brook Frye
- School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA USA
| | - Stephen Woloszynek
- Electrical and Computer Engineering, Drexel University, Philadelphia, PA USA
| | - Rachid Ounit
- Department of Computer Science and Engineering, University of California, Riverside, CA USA
| | | | - Erin Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY USA
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437
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Rastelli E, Corinaldesi C, Dell'Anno A, Tangherlini M, Martorelli E, Ingrassia M, Chiocci FL, Lo Martire M, Danovaro R. High potential for temperate viruses to drive carbon cycling in chemoautotrophy-dominated shallow-water hydrothermal vents. Environ Microbiol 2017; 19:4432-4446. [DOI: 10.1111/1462-2920.13890] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/06/2017] [Accepted: 08/08/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Eugenio Rastelli
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
- Stazione Zoologica Anton Dohrn; Villa Comunale; Naples 80121 Italy
| | - Cinzia Corinaldesi
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Michael Tangherlini
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Eleonora Martorelli
- Institute of Environmental Geology and Geoengineering; Italian National Research Council; Rome Italy
| | - Michela Ingrassia
- Institute of Environmental Geology and Geoengineering; Italian National Research Council; Rome Italy
- Department of Earth Science; University of Rome Sapienza; Rome Italy
| | - Francesco L. Chiocci
- Institute of Environmental Geology and Geoengineering; Italian National Research Council; Rome Italy
- Department of Earth Science; University of Rome Sapienza; Rome Italy
| | - Marco Lo Martire
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Roberto Danovaro
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
- Stazione Zoologica Anton Dohrn; Villa Comunale; Naples 80121 Italy
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438
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Stough JMA, Tang X, Krausfeldt LE, Steffen MM, Gao G, Boyer GL, Wilhelm SW. Molecular prediction of lytic vs lysogenic states for Microcystis phage: Metatranscriptomic evidence of lysogeny during large bloom events. PLoS One 2017; 12:e0184146. [PMID: 28873456 PMCID: PMC5584929 DOI: 10.1371/journal.pone.0184146] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/18/2017] [Indexed: 11/18/2022] Open
Abstract
Microcystis aeruginosa is a freshwater bloom-forming cyanobacterium capable of producing the potent hepatotoxin, microcystin. Despite increased interest in this organism, little is known about the viruses that infect it and drive nutrient mobilization and transfer of genetic material between organisms. The genomic complement of sequenced phage suggests these viruses are capable of integrating into the host genome, though this activity has not been observed in the laboratory. While analyzing RNA-sequence data obtained from Microcystis blooms in Lake Tai (Taihu, China), we observed that a series of lysogeny-associated genes were highly expressed when genes involved in lytic infection were down-regulated. This pattern was consistent, though not always statistically significant, across multiple spatial and temporally distinct samples. For example, samples from Lake Tai (2014) showed a predominance of lytic virus activity from late July through October, while genes associated with lysogeny were strongly expressed in the early months (June–July) and toward the end of bloom season (October). Analyses of whole phage genome expression shows that transcription patterns are shared across sampling locations and that genes consistently clustered by co-expression into lytic and lysogenic groups. Expression of lytic-cycle associated genes was positively correlated to total dissolved nitrogen, ammonium concentration, and salinity. Lysogeny-associated gene expression was positively correlated with pH and total dissolved phosphorous. Our results suggest that lysogeny may be prevalent in Microcystis blooms and support the hypothesis that environmental conditions drive switching between temperate and lytic life cycles during bloom proliferation.
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Affiliation(s)
- Joshua M. A. Stough
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States of America
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing, PR China
| | - Lauren E. Krausfeldt
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States of America
| | - Morgan M. Steffen
- Department of Biology, James Madison University, Harrisonburg, VA, United States of America
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing, PR China
| | - Gregory L. Boyer
- College of Environmental Science and Forestry, The State University of New York, Syracuse, NY, United States of America
| | - Steven W. Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States of America
- * E-mail:
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439
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Lara E, Vaqué D, Sà EL, Boras JA, Gomes A, Borrull E, Díez-Vives C, Teira E, Pernice MC, Garcia FC, Forn I, Castillo YM, Peiró A, Salazar G, Morán XAG, Massana R, Catalá TS, Luna GM, Agustí S, Estrada M, Gasol JM, Duarte CM. Unveiling the role and life strategies of viruses from the surface to the dark ocean. SCIENCE ADVANCES 2017; 3:e1602565. [PMID: 28913418 PMCID: PMC5587022 DOI: 10.1126/sciadv.1602565] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 08/09/2017] [Indexed: 05/31/2023]
Abstract
Viruses are a key component of marine ecosystems, but the assessment of their global role in regulating microbial communities and the flux of carbon is precluded by a paucity of data, particularly in the deep ocean. We assessed patterns in viral abundance and production and the role of viral lysis as a driver of prokaryote mortality, from surface to bathypelagic layers, across the tropical and subtropical oceans. Viral abundance showed significant differences between oceans in the epipelagic and mesopelagic, but not in the bathypelagic, and decreased with depth, with an average power-law scaling exponent of -1.03 km-1 from an average of 7.76 × 106 viruses ml-1 in the epipelagic to 0.62 × 106 viruses ml-1 in the bathypelagic layer with an average integrated (0 to 4000 m) viral stock of about 0.004 to 0.044 g C m-2, half of which is found below 775 m. Lysogenic viral production was higher than lytic viral production in surface waters, whereas the opposite was found in the bathypelagic, where prokaryotic mortality due to viruses was estimated to be 60 times higher than grazing. Free viruses had turnover times of 0.1 days in the bathypelagic, revealing that viruses in the bathypelagic are highly dynamic. On the basis of the rates of lysed prokaryotic cells, we estimated that viruses release 145 Gt C year-1 in the global tropical and subtropical oceans. The active viral processes reported here demonstrate the importance of viruses in the production of dissolved organic carbon in the dark ocean, a major pathway in carbon cycling.
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Affiliation(s)
- Elena Lara
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
- Institute of Marine Sciences, National Research Council (CNR-ISMAR), Castello 2737/F Arsenale-Tesa 104, 30122 Venezia, Italy
| | - Dolors Vaqué
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Elisabet Laia Sà
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Julia A. Boras
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Ana Gomes
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Encarna Borrull
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Cristina Díez-Vives
- School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio-Innovation, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Eva Teira
- Departamento de Ecología y Biología Animal, Universidad de Vigo, University of Vigo, 36310 Vigo, Spain
| | - Massimo C. Pernice
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Francisca C. Garcia
- Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía, Avenida Príncipe de Asturias, 70, 33212 Gijón/Xixón, Spain
| | - Irene Forn
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Yaiza M. Castillo
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Aida Peiró
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Guillem Salazar
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Xosé Anxelu G. Morán
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ramon Massana
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Teresa S. Catalá
- Instituto de Investigaciones Marinas, CSIC, Eduardo Cabello, 6, 36208 Vigo, Spain
- Departamento de Ecología and Instituto del Agua, Universidad de Granada, Avenida del Hospicio, S/N, 18010 Granada, Spain
| | | | - Susana Agustí
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Marta Estrada
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Josep M. Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Carlos M. Duarte
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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440
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Pratama AA, van Elsas JD. A novel inducible prophage from the mycosphere inhabitant Paraburkholderia terrae BS437. Sci Rep 2017; 7:9156. [PMID: 28831124 PMCID: PMC5567305 DOI: 10.1038/s41598-017-09317-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 07/20/2017] [Indexed: 11/13/2022] Open
Abstract
Bacteriophages constitute key gene transfer agents in many bacteria. Specifically, they may confer gene mobility to Paraburkholderia spp. that dwells in soil and the mycosphere. In this study, we first screened mycosphere and bulk soils for phages able to produce plaques, however found these to be below detection. Then, prophage identification methods were applied to the genome sequences of the mycosphere-derived Paraburkholderia terrae strains BS001, BS007, BS110 and BS437, next to P. phytofirmans strains BS455, BIFAS53, J1U5 and PsJN. These analyses revealed all bacterial genomes to contain considerable amounts [up to 13.3%] of prophage-like sequences. One sequence predicted to encode a complete phage was found in the genome of P. terrae BS437. Using the inducing agent mitomycin C, we produced high-titered phage suspensions. These indeed encompassed the progeny of the identified prophage (denoted ɸ437), as evidenced using phage major capsid gene molecular detection. We obtained the full sequence of phage ɸ437, which, remarkably, had undergone a reshuffling of two large gene blocks. One predicted moron gene was found, and it is currently analyzed to understand the extent of its ecological significance for the host.
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Affiliation(s)
- Akbar Adjie Pratama
- Department of Microbial Ecology, Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, Groningen, 9747 AG, The Netherlands.
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, Groningen, 9747 AG, The Netherlands.
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441
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Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton. Proc Natl Acad Sci U S A 2017; 114:E7489-E7498. [PMID: 28827361 DOI: 10.1073/pnas.1708097114] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytoplankton community structure is shaped by both bottom-up factors, such as nutrient availability, and top-down processes, such as predation. Here we show that marine viruses can blur these distinctions, being able to amend how host cells acquire nutrients from their environment while also predating and lysing their algal hosts. Viral genomes often encode genes derived from their host. These genes may allow the virus to manipulate host metabolism to improve viral fitness. We identify in the genome of a phytoplankton virus, which infects the small green alga Ostreococcus tauri, a host-derived ammonium transporter. This gene is transcribed during infection and when expressed in yeast mutants the viral protein is located to the plasma membrane and rescues growth when cultured with ammonium as the sole nitrogen source. We also show that viral infection alters the nature of nitrogen compound uptake of host cells, by both increasing substrate affinity and allowing the host to access diverse nitrogen sources. This is important because the availability of nitrogen often limits phytoplankton growth. Collectively, these data show that a virus can acquire genes encoding nutrient transporters from a host genome and that expression of the viral gene can alter the nutrient uptake behavior of host cells. These results have implications for understanding how viruses manipulate the physiology and ecology of phytoplankton, influence marine nutrient cycles, and act as vectors for horizontal gene transfer.
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442
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Association of coral algal symbionts with a diverse viral community responsive to heat shock. BMC Microbiol 2017; 17:174. [PMID: 28818037 PMCID: PMC5561611 DOI: 10.1186/s12866-017-1084-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/09/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Stony corals provide the structural foundation of coral reef ecosystems and are termed holobionts given they engage in symbioses, in particular with photosynthetic dinoflagellates of the genus Symbiodinium. Besides Symbiodinium, corals also engage with bacteria affecting metabolism, immunity, and resilience of the coral holobiont, but the role of associated viruses is largely unknown. In this regard, the increase of studies using RNA sequencing (RNA-Seq) to assess gene expression provides an opportunity to elucidate viral signatures encompassed within the data via careful delineation of sequence reads and their source of origin. RESULTS Here, we re-analyzed an RNA-Seq dataset from a cultured coral symbiont (Symbiodinium microadriaticum, Clade A1) across four experimental treatments (control, cold shock, heat shock, dark shock) to characterize associated viral diversity, abundance, and gene expression. Our approach comprised the filtering and removal of host sequence reads, subsequent phylogenetic assignment of sequence reads of putative viral origin, and the assembly and analysis of differentially expressed viral genes. About 15.46% (123 million) of all sequence reads were non-host-related, of which <1% could be classified as archaea, bacteria, or virus. Of these, 18.78% were annotated as virus and comprised a diverse community consistent across experimental treatments. Further, non-host related sequence reads assembled into 56,064 contigs, including 4856 contigs of putative viral origin that featured 43 differentially expressed genes during heat shock. The differentially expressed genes included viral kinases, ubiquitin, and ankyrin repeat proteins (amongst others), which are suggested to help the virus proliferate and inhibit the algal host's antiviral response. CONCLUSION Our results suggest that a diverse viral community is associated with coral algal endosymbionts of the genus Symbiodinium, which prompts further research on their ecological role in coral health and resilience.
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443
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Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernández-Gómez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL, Pesant S, Karsenti E, Wincker P. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Sci Data 2017; 4:170093. [PMID: 28763055 PMCID: PMC5538240 DOI: 10.1038/sdata.2017.93] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/05/2017] [Indexed: 02/01/2023] Open
Abstract
A unique collection of oceanic samples was gathered by the Tara Oceans
expeditions (2009–2013), targeting plankton organisms ranging from viruses to
metazoans, and providing rich environmental context measurements. Thanks to recent advances in
the field of genomics, extensive sequencing has been performed for a deep genomic analysis of
this huge collection of samples. A strategy based on different approaches, such as
metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for
analysis of size-fractionated plankton communities. Here, we provide detailed procedures
applied for genomic data generation, from nucleic acids extraction to sequence production, and
we describe registries of genomics datasets available at the European Nucleotide Archive (ENA,
www.ebi.ac.uk/ena). The association of these metadata to the experimental
procedures applied for their generation will help the scientific community to access these data
and facilitate their analysis. This paper complements other efforts to provide a full
description of experiments and open science resources generated from the Tara
Oceans project, further extending their value for the study of the world’s planktonic
ecosystems.
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Affiliation(s)
- Adriana Alberti
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Julie Poulain
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Stefan Engelen
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Karine Labadie
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Sarah Romac
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Guillaume Albini
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Jean-Marc Aury
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Caroline Belser
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Alexis Bertrand
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Corinne Cruaud
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Corinne Da Silva
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Carole Dossat
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Frédérick Gavory
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Shahinaz Gas
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Julie Guy
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Maud Haquelle
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - E'krame Jacoby
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Olivier Jaillon
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
| | - Arnaud Lemainque
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Eric Pelletier
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
| | - Gaëlle Samson
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Mark Wessner
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | | | - Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Marta Royo-Llonch
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Francisco M Cornejo-Castillo
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Ramiro Logares
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Beatriz Fernández-Gómez
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain.,FONDAP Center for Genome Regulation, Moneda 1375, Santiago 8320000, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Libano Macul, Santiago 5524, Chile
| | - Chris Bowler
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, Paris F-75005, France
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Colomban De Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Nigel Grimsley
- CNRS UMR 7232, BIOM, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France.,Sorbonne Universités Paris 06, OOB UPMC, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France
| | - Elodie Desgranges
- CNRS UMR 7232, BIOM, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France.,Sorbonne Universités Paris 06, OOB UPMC, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France
| | - Stefanie Kandels-Lewis
- Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany.,Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany
| | - Hiroyuki Ogata
- for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine 04544, USA
| | - Michael E Sieracki
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine 04544, USA.,National Science Foundation, Arlington, Virginia 22230, USA
| | | | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, Ohio 43210, USA.,Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jennifer R Brum
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Bonnie L Hurwitz
- Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, Arizona 85719, USA
| | | | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Str. 8, Bremen 28359, Germany.,PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Leobener Str. 8, Bremen 28359, Germany
| | - Eric Karsenti
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, Paris F-75005, France.,Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany.,Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, 181 Chemin du Lazaret, Villefranche-sur-mer F-06230, France
| | - Patrick Wincker
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
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444
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Danovaro R, Rastelli E, Corinaldesi C, Tangherlini M, Dell'Anno A. Marine archaea and archaeal viruses under global change. F1000Res 2017; 6:1241. [PMID: 29034077 PMCID: PMC5532796 DOI: 10.12688/f1000research.11404.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/26/2017] [Indexed: 01/08/2023] Open
Abstract
Global change is altering oceanic temperature, salinity, pH, and oxygen concentration, directly and indirectly influencing marine microbial food web structure and function. As microbes represent >90% of the ocean’s biomass and are major drivers of biogeochemical cycles, understanding their responses to such changes is fundamental for predicting the consequences of global change on ecosystem functioning. Recent findings indicate that marine archaea and archaeal viruses are active and relevant components of marine microbial assemblages, far more abundant and diverse than was previously thought. Further research is urgently needed to better understand the impacts of global change on virus–archaea dynamics and how archaea and their viruses can interactively influence the ocean’s feedbacks on global change.
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Affiliation(s)
- Roberto Danovaro
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Eugenio Rastelli
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Cinzia Corinaldesi
- Department of Sciences and Engineering of Materials, Environment and Urbanistics, Polytechnic University of Marche, Ancona, Italy
| | - Michael Tangherlini
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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445
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Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data. Nat Protoc 2017; 12:1673-1682. [PMID: 28749930 DOI: 10.1038/nprot.2017.063] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The analysis of large microbiome data sets holds great promise for the delineation of the biological and metabolic functioning of living organisms and their role in the environment. In the midst of this genomic puzzle, viruses, especially those that infect microbial communities, represent a major reservoir of genetic diversity with great impact on biogeochemical cycles and organismal health. Overcoming the limitations associated with virus detection directly from microbiomes can provide key insights into how ecosystem dynamics are modulated. Here, we present a computational protocol for accurate detection and grouping of viral sequences from microbiome samples. Our approach relies on an expanded and curated set of viral protein families used as bait to identify viral sequences directly from metagenomic assemblies. This protocol describes how to use the viral protein families catalog (∼7 h) and recommended filters for the detection of viral contigs in metagenomic samples (∼6 h), and it describes the specific parameters for a nucleotide-sequence-identity-based method of organizing the viral sequences into quasi-species taxonomic-level groups (∼10 min).
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446
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On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires. mBio 2017; 8:mBio.00897-17. [PMID: 28698278 PMCID: PMC5513706 DOI: 10.1128/mbio.00897-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent) to a gene encoding a reverse transcriptase (RT) related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains. Nearly all such RTs are present within type III CRISPR-Cas loci, but their phylogeny does not parallel the CRISPR-Cas type classification, indicating that RT-Cas1 is an autonomous functional module that is disseminated by horizontal gene transfer and can function with diverse type III systems. To compare the sequence pools sampled by RT-Cas1-associated and RT-lacking CRISPR-Cas systems, we obtained samples of a commercially grown cyanobacterium—Arthrospira platensis. Sequencing of the CRISPR arrays uncovered a highly diverse population of spacers. Spacer diversity was particularly striking for the RT-Cas1-containing type III-B system, where no saturation was evident even with millions of sequences analyzed. In contrast, analysis of the RT-lacking type III-D system yielded a highly diverse pool but reached a point where fewer novel spacers were recovered as sequencing depth was increased. Matches could be identified for a small fraction of the non-RT-Cas1-associated spacers, and for only a single RT-Cas1-associated spacer. Thus, the principal source(s) of the spacers, particularly the hypervariable spacer repertoire of the RT-associated arrays, remains unknown. While the majority of CRISPR-Cas immune systems adapt to foreign genetic elements by capturing segments of invasive DNA, some systems carry reverse transcriptases (RTs) that enable adaptation to RNA molecules. From analysis of available bacterial sequence data, we find evidence that RT-based RNA adaptation machinery has been able to join with CRISPR-Cas immune systems in many, diverse bacterial species. To investigate whether the abilities to adapt to DNA and RNA molecules are utilized for defense against distinct classes of invaders in nature, we sequenced CRISPR arrays from samples of commercial-scale open-air cultures of Arthrospira platensis, a cyanobacterium that contains both RT-lacking and RT-containing CRISPR-Cas systems. We uncovered a diverse pool of naturally occurring immune memories, with the RT-lacking locus acquiring a number of segments matching known viral or bacterial genes, while the RT-containing locus has acquired spacers from a distinct sequence pool for which the source remains enigmatic.
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447
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Duhaime MB, Solonenko N, Roux S, Verberkmoes NC, Wichels A, Sullivan MB. Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept. Front Microbiol 2017; 8:1241. [PMID: 28729861 PMCID: PMC5498523 DOI: 10.3389/fmicb.2017.01241] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/20/2017] [Indexed: 11/25/2022] Open
Abstract
Viruses influence the ecology and evolutionary trajectory of microbial communities. Yet our understanding of their roles in ecosystems is limited by the paucity of model systems available for hypothesis generation and testing. Further, virology is limited by the lack of a broadly accepted conceptual framework to classify viral diversity into evolutionary and ecologically cohesive units. Here, we introduce genomes, structural proteomes, and quantitative host range data for eight Pseudoalteromonas phages isolated from Helgoland (North Sea, Germany) and use these data to advance a genome-based viral operational taxonomic unit (OTU) definition. These viruses represent five new genera and inform 498 unaffiliated or unannotated protein clusters (PCs) from global virus metagenomes. In a comparison of previously sequenced Pseudoalteromonas phage isolates (n = 7) and predicted prophages (n = 31), the eight phages are unique. They share a genus with only one other isolate, Pseudoalteromonas podophage RIO-1 (East Sea, South Korea) and two Pseudoalteromonas prophages. Mass-spectrometry of purified viral particles identified 12–20 structural proteins per phage. When combined with 3-D structural predictions, these data led to the functional characterization of five previously unidentified major capsid proteins. Protein functional predictions revealed mechanisms for hijacking host metabolism and resources. Further, they uncovered a hybrid sipho-myovirus that encodes genes for Mu-like infection rarely described in ocean systems. Finally, we used these data to evaluate a recently introduced definition for virus populations that requires members of the same population to have >95% average nucleotide identity across at least 80% of their genes. Using physiological traits and genomics, we proposed a conceptual model for a viral OTU definition that captures evolutionarily cohesive and ecologically distinct units. In this trait-based framework, sensitive hosts are considered viral niches, while host ranges and infection efficiencies are tracked as viral traits. Quantitative host range assays revealed conserved traits within virus OTUs that break down between OTUs, suggesting the defined units capture niche and fitness differentiation. Together these analyses provide a foundation for model system-based hypothesis testing that will improve our understanding of marine copiotrophs, as well as phage–host interactions on the ocean particles and aggregates where Pseudoalteromonas thrive.
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Affiliation(s)
- Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann ArborMI, United States
| | - Natalie Solonenko
- Department of Microbiology, The Ohio State University, ColumbusOH, United States
| | - Simon Roux
- Department of Microbiology, The Ohio State University, ColumbusOH, United States
| | - Nathan C Verberkmoes
- Department of Biological Sciences, Border Biomedical Research Center, University of Texas at El Paso, El PasoTX, United States
| | - Antje Wichels
- Biologische Anstalt Helgoland, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine ResearchHelgoland, Germany
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, ColumbusOH, United States.,Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, ColumbusOH, United States
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448
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Coutinho FH, Silveira CB, Gregoracci GB, Thompson CC, Edwards RA, Brussaard CPD, Dutilh BE, Thompson FL. Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans. Nat Commun 2017; 8:15955. [PMID: 28677677 PMCID: PMC5504273 DOI: 10.1038/ncomms15955] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 05/12/2017] [Indexed: 12/19/2022] Open
Abstract
Marine viruses are key drivers of host diversity, population dynamics and biogeochemical cycling and contribute to the daily flux of billions of tons of organic matter. Despite recent advancements in metagenomics, much of their biodiversity remains uncharacterized. Here we report a data set of 27,346 marine virome contigs that includes 44 complete genomes. These outnumber all currently known phage genomes in marine habitats and include members of previously uncharacterized lineages. We designed a new method for host prediction based on co-occurrence associations that reveals these viruses infect dominant members of the marine microbiome such as Prochlorococcus and Pelagibacter. A negative association between host abundance and the virus-to-host ratio supports the recently proposed Piggyback-the-Winner model of reduced phage lysis at higher host densities. An analysis of the abundance patterns of viruses throughout the oceans revealed how marine viral communities adapt to various seasonal, temperature and photic regimes according to targeted hosts and the diversity of auxiliary metabolic genes.
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Affiliation(s)
- Felipe H. Coutinho
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21944970, Brazil
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen 6500 HB, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University (UU), Utrecht 3584 CH, The Netherlands
| | - Cynthia B. Silveira
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21944970, Brazil
- Biology Department, San Diego State University (SDSU), San Diego, California 92182, USA
| | - Gustavo B. Gregoracci
- Departamento de Ciências do Mar, Universidade Federal de São Paulo (UNIFESP), Baixada Santista 11070100, Brazil
| | - Cristiane C. Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21944970, Brazil
| | - Robert A. Edwards
- Biology Department, San Diego State University (SDSU), San Diego, California 92182, USA
| | - Corina P. D. Brussaard
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, PO Box 59, 1790 AB Den Burg Texel, The Netherlands
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Bas E. Dutilh
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21944970, Brazil
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen 6500 HB, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University (UU), Utrecht 3584 CH, The Netherlands
| | - Fabiano L. Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21944970, Brazil
- Universidade Federal do Rio de Janeiro (UFRJ)/COPPE/SAGE, Rio de Janeiro 21941950, Brazil
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449
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Moniruzzaman M, Wurch LL, Alexander H, Dyhrman ST, Gobler CJ, Wilhelm SW. Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics. Nat Commun 2017; 8:16054. [PMID: 28656958 PMCID: PMC5493757 DOI: 10.1038/ncomms16054] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/16/2017] [Indexed: 01/12/2023] Open
Abstract
Establishing virus–host relationships has historically relied on culture-dependent approaches. Here we report on the use of marine metatranscriptomics to probe virus–host relationships. Statistical co-occurrence analyses of dsDNA, ssRNA and dsRNA viral markers of polyadenylation-selected RNA sequences from microbial communities dominated by Aureococcus anophagefferens (Quantuck Bay, NY), and diatoms (Narragansett Bay, RI) show active infections by diverse giant viruses (NCLDVs) associated with algal and nonalgal hosts. Ongoing infections of A. anophagefferens by a known Mimiviridae (AaV) occur during bloom peak and decline. Bloom decline is also accompanied by increased activity of viruses other than AaV, including (+) ssRNA viruses. In Narragansett Bay, increased temporal resolution reveals active NCLDVs with both ‘boom-and-bust’ and ‘steady-state infection’-like ecologies that include known as well as novel virus–host interactions. Our approach offers a method for screening active viral infections and develops links between viruses and their potential hosts in situ. Our observations further demonstrate that previously unknown virus–host relationships in marine systems are abundant. Viruses are partners in ecosystem ecology, yet their study has been primarily limited to laboratory models virus-host or derived from metagenomics. Here, Moniruzzaman et al. use metatranscriptomics to resolve interactions between giant viruses and single-celled eukaryotic hosts.
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Affiliation(s)
- Mohammad Moniruzzaman
- Department of Microbiology, The University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Louie L Wurch
- Department of Biology, James Madison University, Harrisonburg, Virginia 22807, USA
| | - Harriet Alexander
- Department of Earth and Environmental Science and Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York 10964, USA
| | - Sonya T Dyhrman
- Department of Earth and Environmental Science and Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York 10964, USA
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794, USA
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Tennessee 37996, USA
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450
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Martinez-Hernandez F, Fornas O, Lluesma Gomez M, Bolduc B, de la Cruz Peña MJ, Martínez JM, Anton J, Gasol JM, Rosselli R, Rodriguez-Valera F, Sullivan MB, Acinas SG, Martinez-Garcia M. Single-virus genomics reveals hidden cosmopolitan and abundant viruses. Nat Commun 2017; 8:15892. [PMID: 28643787 PMCID: PMC5490008 DOI: 10.1038/ncomms15892] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/10/2017] [Indexed: 12/22/2022] Open
Abstract
Microbes drive ecosystems under constraints imposed by viruses. However, a lack of virus genome information hinders our ability to answer fundamental, biological questions concerning microbial communities. Here we apply single-virus genomics (SVGs) to assess whether portions of marine viral communities are missed by current techniques. The majority of the here-identified 44 viral single-amplified genomes (vSAGs) are more abundant in global ocean virome data sets than published metagenome-assembled viral genomes or isolates. This indicates that vSAGs likely best represent the dsDNA viral populations dominating the oceans. Species-specific recruitment patterns and virome simulation data suggest that vSAGs are highly microdiverse and that microdiversity hinders the metagenomic assembly, which could explain why their genomes have not been identified before. Altogether, SVGs enable the discovery of some of the likely most abundant and ecologically relevant marine viral species, such as vSAG 37-F6, which were overlooked by other methodologies.
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Affiliation(s)
- Francisco Martinez-Hernandez
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante 03690, Spain
| | - Oscar Fornas
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Carrer del Doctor Aiguader, 88, PRBB Building, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Carrer del Doctor Aiguader, 88, PRBB Building, Barcelona 08003, Spain
| | - Monica Lluesma Gomez
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante 03690, Spain
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, 105 Biological Sciences Building, 484 West 12th Avenue Columbus, Ohio 43210, USA
| | - Maria Jose de la Cruz Peña
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante 03690, Spain
| | - Joaquín Martínez Martínez
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, PO Box 380, East Boothbay, Maine 04544, USA
| | - Josefa Anton
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante 03690, Spain
| | - Josep M. Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Passeig Marítim, 47, Barcelona 08003, Spain
| | - Riccardo Rosselli
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Campus San Juan, San Juan, Alicante 03550, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Campus San Juan, San Juan, Alicante 03550, Spain
| | - Matthew B. Sullivan
- Department of Microbiology, The Ohio State University, 105 Biological Sciences Building, 484 West 12th Avenue Columbus, Ohio 43210, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, The Ohio State University, 105 Biological Sciences Building, 484 West 12th Avenue Columbus, Ohio 43210, USA
| | - Silvia G. Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Passeig Marítim, 47, Barcelona 08003, Spain
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante 03690, Spain
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