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Abstract
Viruses are extremely diverse and modulate important biological and ecological processes globally. However, much of viral diversity remains uncultured and yet to be discovered. Several powerful culture-independent tools, in particular metagenomics, have substantially advanced virus discovery. Among those tools is single-virus genomics, which yields sequenced reference genomes from individual sorted virus particles without the need for cultivation. This new method complements virus culturing and metagenomic approaches and its advantages include targeted investigation of specific virus groups and investigation of genomic microdiversity within viral populations. In this Review, we provide a brief history of single-virus genomics, outline how this emergent method has facilitated advances in virus ecology and discuss its current limitations and future potential. Finally, we address how this method may synergistically intersect with other single-virus and single-cell approaches.
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252
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de Jonge PA, von Meijenfeldt FB, Costa AR, Nobrega FL, Brouns SJ, Dutilh BE. Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts. iScience 2020; 23:101439. [PMID: 32823052 PMCID: PMC7452251 DOI: 10.1016/j.isci.2020.101439] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/23/2020] [Accepted: 08/03/2020] [Indexed: 01/08/2023] Open
Abstract
An important viromics challenge is associating bacteriophages to hosts. To address this, we developed adsorption sequencing (AdsorpSeq), a readily implementable method to measure phages that are preferentially adsorbed to specific host cell envelopes. AdsorpSeq thus captures the key initial infection cycle step. Phages are added to cell envelopes, adsorbed phages are isolated through gel electrophoresis, after which adsorbed phage DNA is sequenced and compared with the full virome. Here, we show that AdsorpSeq allows for separation of phages based on receptor-adsorbing capabilities. Next, we applied AdsorpSeq to identify phages in a wastewater virome that adsorb to cell envelopes of nine bacteria, including important pathogens. We detected 26 adsorbed phages including common and rare members of the virome, a minority being related to previously characterized phages. We conclude that AdsorpSeq is an effective new tool for rapid characterization of environmental phage adsorption, with a proof-of-principle application to Gram-negative host cell envelopes.
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Affiliation(s)
- Patrick A. de Jonge
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, 3584 CH Utrecht, the Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands
| | | | - Ana Rita Costa
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands
| | - Franklin L. Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands
| | - Stan J.J. Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands
| | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, 3584 CH Utrecht, the Netherlands
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253
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Predetermined clockwork microbial worlds: Current understanding of aquatic microbial diel response from model systems to complex environments. ADVANCES IN APPLIED MICROBIOLOGY 2020; 113:163-191. [PMID: 32948266 DOI: 10.1016/bs.aambs.2020.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In the photic zone of aquatic ecosystems, microorganisms with different metabolisms and their viruses form complex interactions and food webs. Within these interactions, phototrophic microorganisms such as eukaryotic microalgae and cyanobacteria interact directly with sunlight, and thereby generate circadian rhythms. Diel cycling originally generated in microbial phototrophs is directly transmitted toward heterotrophic microorganisms utilizing the photosynthetic products as they are excreted or exuded. Such diel cycling seems to be indirectly propagated toward heterotrophs as a result of complex biotic interactions. For example, cell death of phototrophic microorganisms induced by viral lysis and protistan grazing provides additional resources of dissolved organic matter to the microbial community, and so generates diel cycling in other heterotrophs with different nutrient dependencies. Likewise, differences in the diel transmitting pathway via complex interactions among heterotrophs, and between heterotrophs and their viruses, may also generate higher variation and time lag diel rhythms in different heterotrophic taxa. Thus, sunlight and photosynthesis not only contribute energy and carbon supply, but also directly or indirectly control diel cycling of the microbial community through complex interactions in the photic zone of aquatic ecosystems.
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254
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Bellas CM, Schroeder DC, Edwards A, Barker G, Anesio AM. Flexible genes establish widespread bacteriophage pan-genomes in cryoconite hole ecosystems. Nat Commun 2020; 11:4403. [PMID: 32879312 PMCID: PMC7468147 DOI: 10.1038/s41467-020-18236-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/10/2020] [Indexed: 12/20/2022] Open
Abstract
Bacteriophage genomes rapidly evolve via mutation and horizontal gene transfer to counter evolving bacterial host defenses; such arms race dynamics should lead to divergence between phages from similar, geographically isolated ecosystems. However, near-identical phage genomes can reoccur over large geographical distances and several years apart, conversely suggesting many are stably maintained. Here, we show that phages with near-identical core genomes in distant, discrete aquatic ecosystems maintain diversity by possession of numerous flexible gene modules, where homologous genes present in the pan-genome interchange to create new phage variants. By repeatedly reconstructing the core and flexible regions of phage genomes from different metagenomes, we show a pool of homologous gene variants co-exist for each module in each location, however, the dominant variant shuffles independently in each module. These results suggest that in a natural community, recombination is the largest contributor to phage diversity, allowing a variety of host recognition receptors and genes to counter bacterial defenses to co-exist for each phage. Bacteriophages and their hosts are involved in a constant evolutionary arms race that should lead to divergence between phage genes over time. Here, the authors recruit metagenomic reads to virus reference genomes and genome fragments in samples from cryoconite holes and show that phages with near-identical core genomes maintain diversity by possession of numerous flexible gene modules, where homologous genes present in the pan-genome interchange to create new phage variants.
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Affiliation(s)
- Christopher M Bellas
- Department of Ecology, Lake and Glacier Ecology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - Declan C Schroeder
- Department of Veterinary Population Medicine, University of Minnesota, 1333 Gortner Avenue, St. Paul, MN, 55108, USA.,School of Biological Sciences, University of Reading, Reading, UK
| | - Arwyn Edwards
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EE, UK
| | - Gary Barker
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Alexandre M Anesio
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
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255
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Chen LX, Méheust R, Crits-Christoph A, McMahon KD, Nelson TC, Slater GF, Warren LA, Banfield JF. Large freshwater phages with the potential to augment aerobic methane oxidation. Nat Microbiol 2020; 5:1504-1515. [PMID: 32839536 PMCID: PMC7674155 DOI: 10.1038/s41564-020-0779-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/21/2020] [Indexed: 12/31/2022]
Abstract
There is growing evidence that phages with unusually large genomes are common across various microbiomes, but little is known about their genetic inventories or potential ecosystem impacts. In the present study, we reconstructed large phage genomes from freshwater lakes known to contain bacteria that oxidize methane. Of manually curated genomes, 22 (18 are complete), ranging from 159 kilobase (kb) to 527 kb in length, were found to encode the pmoC gene, an enzymatically critical subunit of the particulate methane monooxygenase, the predominant methane oxidation catalyst in nature. The phage-associated PmoC sequences show high similarity to (>90%), and affiliate phylogenetically with, those of coexisting bacterial methanotrophs, including members of Methyloparacoccus, Methylocystis and Methylobacter spp. In addition, pmoC-phage abundance patterns correlate with those of the coexisting bacterial methanotrophs, supporting host-phage relationships. Future work is needed to determine whether phage-associated PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contributing to growth on methane. Transcriptomics data from Lake Rotsee (Switzerland) showed that some phage-associated pmoC genes were highly expressed in situ and, of interest, that the most rapidly growing methanotroph was infected by three pmoC-phages. Thus, augmentation of bacterial methane oxidation by pmoC-phages during infection could modulate the efflux of this potent greenhouse gas into the environment.
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Affiliation(s)
- Lin-Xing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Raphaël Méheust
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | | | - Katherine D McMahon
- Departments of Civil and Environmental Engineering, and Bacteriology, University of Wisconsin, Madison, WI, USA
| | | | - Gregory F Slater
- School of Geography and Earth Science, McMaster University, Hamilton, Ontario, Canada
| | - Lesley A Warren
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Ontario, Canada.,School of Geography and Earth Science, McMaster University, Hamilton, Ontario, Canada
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA. .,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA. .,Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA. .,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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256
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Overholt WA, Hölzer M, Geesink P, Diezel C, Marz M, Küsel K. Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome‐assembled genomes from a complex aquifer system. Environ Microbiol 2020; 22:4000-4013. [DOI: 10.1111/1462-2920.15186] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 07/31/2020] [Accepted: 08/02/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Will A. Overholt
- Institute of Biodiversity, Aquatic Geomicrobiology Friedrich Schiller University Jena Germany
| | - Martin Hölzer
- RNA Bioinformatics and High‐Throughput Analysis Friedrich Schiller University Jena Germany
- European Virus Bioinformatics Center Friedrich Schiller University Jena Germany
| | - Patricia Geesink
- Institute of Biodiversity, Aquatic Geomicrobiology Friedrich Schiller University Jena Germany
| | - Celia Diezel
- RNA Bioinformatics and High‐Throughput Analysis Friedrich Schiller University Jena Germany
| | - Manja Marz
- RNA Bioinformatics and High‐Throughput Analysis Friedrich Schiller University Jena Germany
- European Virus Bioinformatics Center Friedrich Schiller University Jena Germany
- FLI Leibniz Institute for Age Research Jena Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Aquatic Geomicrobiology Friedrich Schiller University Jena Germany
- German Center for Integrative Biodiversity Research Halle‐Jena‐Leipzig Leipzig Germany
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257
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Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline. ISME JOURNAL 2020; 14:3079-3092. [PMID: 32801311 PMCID: PMC7785012 DOI: 10.1038/s41396-020-00739-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 07/18/2020] [Accepted: 08/05/2020] [Indexed: 02/02/2023]
Abstract
Little is known about viruses in oxygen-deficient water columns (ODWCs). In surface ocean waters, viruses are known to act as gene vectors among susceptible hosts. Some of these genes may have metabolic functions and are thus termed auxiliary metabolic genes (AMGs). AMGs introduced to new hosts by viruses can enhance viral replication and/or potentially affect biogeochemical cycles by modulating key microbial pathways. Here we identify 748 viral populations that cluster into 94 genera along a vertical geochemical gradient in the Cariaco Basin, a permanently stratified and euxinic ocean basin. The viral communities in this ODWC appear to be relatively novel as 80 of these viral genera contained no reference viral sequences, likely due to the isolation and unique features of this system. We identify viral elements that encode AMGs implicated in distinctive processes, such as sulfur cycling, acetate fermentation, signal transduction, [Fe–S] formation, and N-glycosylation. These AMG-encoding viruses include two putative Mu-like viruses, and viral-like regions that may constitute degraded prophages that have been modified by transposable elements. Our results provide an insight into the ecological and biogeochemical impact of viruses oxygen-depleted and euxinic habitats.
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258
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Zheng X, Liu W, Dai X, Zhu Y, Wang J, Zhu Y, Zheng H, Huang Y, Dong Z, Du W, Zhao F, Huang L. Extraordinary diversity of viruses in deep-sea sediments as revealed by metagenomics without prior virion separation. Environ Microbiol 2020; 23:728-743. [PMID: 32627268 DOI: 10.1111/1462-2920.15154] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/03/2020] [Indexed: 12/18/2022]
Abstract
Our current knowledge of the virosphere in deep-sea sediments remains rudimentary. Here we investigated viral diversity at both gene and genomic levels in deep-sea sediments of Southwest Indian Ocean. Analysis of 19 676 106 non-redundant genes from the metagenomic DNA sequences revealed a large number of unclassified viral groups in these samples. A total of 1106 high-confidence viral contigs were obtained after two runs of assemblies, and 217 of these contigs with sizes up to ~120 kb were shown to represent complete viral genomes. These contigs are clustered with no known viral genomes, and over 2/3 of the ORFs on the viral contigs encode no known functions. Furthermore, most of the complete viral contigs show limited similarity to known viral genomes in genome organization. Most of the classified viral contigs are derived from dsDNA viruses belonging to the order Caudovirales, including primarily members of the families Myoviridae, Podoviridae and Siphoviridae. Most of these viruses infect Proteobacteria and, less frequently, Planctomycetes, Firmicutes, Chloroflexi, etc. Auxiliary metabolic genes (AMGs), present in abundance on the viral contigs, appear to function in modulating the host ability to sense environmental gradients and community changes, and to uptake and metabolize nutrients.
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Affiliation(s)
- Xiaowei Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Dai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yaxin Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfeng Wang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongqiang Zhu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhiyang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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259
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Tsiola A, Michoud G, Fodelianakis S, Karakassis I, Kotoulas G, Pavlidou A, Pavloudi C, Pitta P, Simboura N, Daffonchio D, Tsapakis M. Viral Metagenomic Content Reflects Seawater Ecological Quality in the Coastal Zone. Viruses 2020; 12:v12080806. [PMID: 32722579 PMCID: PMC7472104 DOI: 10.3390/v12080806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 01/21/2023] Open
Abstract
Viruses interfere with their host’s metabolism through the expression of auxiliary metabolic genes (AMGs) that, until now, are mostly studied under large physicochemical gradients. Here, we focus on coastal marine ecosystems and we sequence the viral metagenome (virome) of samples with discrete levels of human-driven disturbances. We aim to describe the relevance of viromics with respect to ecological quality status, defined by the classic seawater trophic index (TRIX). Neither viral (family level) nor bacterial (family level, based on 16S rRNA sequencing) community structure correlated with TRIX. AMGs involved in the Calvin and tricarboxylic acid cycles were found at stations with poor ecological quality, supporting viral lysis by modifying the host’s energy supply. AMGs involved in “non-traditional” energy-production pathways (3HP, sulfur oxidation) were found irrespective of ecological quality, highlighting the importance of recognizing the prevalent metabolic paths and their intermediate byproducts. Various AMGs explained the variability between stations with poor vs. good ecological quality. Our study confirms the pivotal role of the virome content in ecosystem functioning, acting as a “pool” of available functions that may be transferred to the hosts. Further, it suggests that AMGs could be used as an ultra-sensitive metric of energy-production pathways with relevance in the vulnerable coastal zone and its ecological quality.
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Affiliation(s)
- Anastasia Tsiola
- Institute of Oceanography, Hellenic Centre for Marine Research, 71003 Heraklion Crete, Greece; (P.P.); (M.T.)
- Department of Biology, University of Crete, 70013 Heraklion Crete, Greece;
- Institute of Marine Biology, Biotechnology & Aquaculture, 71003 Heraklion Crete, Greece; (G.K.); (C.P.)
- Correspondence: ; Tel.: +30-2810-337713; Fax: +30-2810-337822
| | - Grégoire Michoud
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division (BESE), Thuwal 23955-6900, Saudi Arabia; (G.M.); (S.F.); (D.D.)
| | - Stilianos Fodelianakis
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division (BESE), Thuwal 23955-6900, Saudi Arabia; (G.M.); (S.F.); (D.D.)
| | - Ioannis Karakassis
- Department of Biology, University of Crete, 70013 Heraklion Crete, Greece;
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology & Aquaculture, 71003 Heraklion Crete, Greece; (G.K.); (C.P.)
| | - Alexandra Pavlidou
- Institute of Oceanography, Hellenic Centre for Marine Research, 19013 Anavyssos Attiki, Greece; (A.P.); (N.S.)
| | - Christina Pavloudi
- Institute of Marine Biology, Biotechnology & Aquaculture, 71003 Heraklion Crete, Greece; (G.K.); (C.P.)
| | - Paraskevi Pitta
- Institute of Oceanography, Hellenic Centre for Marine Research, 71003 Heraklion Crete, Greece; (P.P.); (M.T.)
| | - Nomiki Simboura
- Institute of Oceanography, Hellenic Centre for Marine Research, 19013 Anavyssos Attiki, Greece; (A.P.); (N.S.)
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division (BESE), Thuwal 23955-6900, Saudi Arabia; (G.M.); (S.F.); (D.D.)
| | - Manolis Tsapakis
- Institute of Oceanography, Hellenic Centre for Marine Research, 71003 Heraklion Crete, Greece; (P.P.); (M.T.)
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260
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Jarett JK, Džunková M, Schulz F, Roux S, Paez-Espino D, Eloe-Fadrosh E, Jungbluth SP, Ivanova N, Spear JR, Carr SA, Trivedi CB, Corsetti FA, Johnson HA, Becraft E, Kyrpides N, Stepanauskas R, Woyke T. Insights into the dynamics between viruses and their hosts in a hot spring microbial mat. ISME JOURNAL 2020; 14:2527-2541. [PMID: 32661357 PMCID: PMC7490370 DOI: 10.1038/s41396-020-0705-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 06/03/2020] [Accepted: 06/11/2020] [Indexed: 12/28/2022]
Abstract
Our current knowledge of host-virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host-virus interactions in a natural biofilm. Using single-cell genomics and metagenomics applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus-host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. Analysis of single-cell amplification kinetics revealed a lack of active viral replication on the single-cell level. These findings were further supported by mapping metagenomic reads from different mat layers to the obtained host-virus pairs, which indicated a low copy number of viral genomes compared to their hosts. Lastly, the metagenomic data revealed high layer specificity of viruses, suggesting limited diffusion to other mat layers. Taken together, these observations indicate that in low mobility environments with high microbial abundance, lysogeny is the predominant viral lifestyle, in line with the previously proposed "Piggyback-the-Winner" theory.
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Affiliation(s)
- Jessica K Jarett
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,AnimalBiome, Oakland, CA, USA
| | - Mária Džunková
- Department of Energy Joint Genome Institute, Berkeley, CA, USA. .,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Simon Roux
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Paez-Espino
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Emiley Eloe-Fadrosh
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sean P Jungbluth
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John R Spear
- Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
| | | | | | | | - Hope A Johnson
- California State University Fullerton, Fullerton, CA, USA
| | - Eric Becraft
- University of North Alabama, Florence, AL, USA.,Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkeley, CA, USA. .,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,University of California, Merced, CA, USA.
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261
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Ledormand P, Desmasures N, Dalmasso M. Phage community involvement in fermented beverages: an open door to technological advances? Crit Rev Food Sci Nutr 2020; 61:2911-2920. [PMID: 32649837 DOI: 10.1080/10408398.2020.1790497] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacteriophages (phages) are considered the most abundant biological entities on Earth. An increasing interest in understanding phage communities, also called viromes or phageomes, has arisen over the past decade especially thanks to the development and the accessibility of Next Generation Sequencing techniques. Despite the increasing amount of available metagenomic data on microbial communities in various habitats, viromes remain poorly described in the scientific literature particularly when it comes to fermented food and beverages such as wine and cider. In this review, a particular attention is paid to the current knowledge on phage communities, with a special focus on fermented food viromes and the methodological tools available to undertake their study. There is a striking lack of available data on the fermented foods and beverages viromes. As far as we know, and although a number of phages have been isolated from wine, no general study has to date been carried out to assess the diversity of viromes in fermented beverages and their possible interactions with microbiota throughout the fermentation process. With the aim of establishing connections between the currently used technologies to carry out the analysis of viromes, possible applications of current knowledge to fermented beverages are examined.
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262
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Wu S, Zhou L, Zhou Y, Wang H, Xiao J, Yan S, Wang Y. Diverse and unique viruses discovered in the surface water of the East China Sea. BMC Genomics 2020; 21:441. [PMID: 32590932 PMCID: PMC7318539 DOI: 10.1186/s12864-020-06861-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 06/22/2020] [Indexed: 11/23/2022] Open
Abstract
Background Viruses are the most abundant biological entities on earth and play import roles in marine biogeochemical cycles. Here, viral communities in the surface water of the East China Sea (ECS) were collected from three representative regions of Yangshan Harbor (YSH), Gouqi Island (GQI), and the Yangtze River Estuary (YRE) and explored primarily through epifluorescence microscopy (EM), transmission electron microscopy (TEM), and metagenomics analysis. Results The virus-like particles (VLPs) in the surface water of the ECS were measured to be 106 to 107 VLPs/ml. Most of the isolated viral particles possessed a head-and-tail structure, but VLPs with unique morphotypes that had never before been observed in the realm of viruses were also found. The sequences related to known viruses in GenBank accounted for 21.1–22.8% of the viromic datasets from YSH, GQI, and YRE. In total, 1029 viral species were identified in the surface waters of the ECS. Among them, tailed phages turn out to make up the majority of viral communities, however a small number of Phycodnaviridae or Mimiviridae related sequences were also detected. The diversity of viruses did not appear to be a big difference among these three aquatic environments but their relative abundance was geographically variable. For example, the Pelagibacter phage HTVC010P accounted for 50.4% of the identified viral species in GQI, but only 9.1% in YSH and 11.7% in YRE. Sequences, almost identical to those of uncultured marine thaumarchaeal dsDNA viruses and magroviruses that infect Marine Group II Euryarchaeota, were confidently detected in the ECS viromes. The predominant classes of virome ORFs with functional annotations that were found were those involved in viral biogenesis. Virus-host connections, inferred from CRISPR spacer-protospacer mapping, implied newly discovered infection relationships in response to arms race between them. Conclusions Together, both identified viruses and unknown viral assemblages observed in this study were indicative of the complex viral community composition found in the ECS. This finding fills a major gap in the dark world of oceanic viruses of China and additionally contributes to the better understanding of global marine viral diversity, composition, and distribution.
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Affiliation(s)
- Shuang Wu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Liang Zhou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yifan Zhou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Hongming Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jinzhou Xiao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Shuling Yan
- Institute of Biochemistry and Molecular Cell Biology, University of Göttingen, Göttingen, Germany
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China. .,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China.
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263
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Wang W, Ren J, Tang K, Dart E, Ignacio-Espinoza JC, Fuhrman JA, Braun J, Sun F, Ahlgren NA. A network-based integrated framework for predicting virus-prokaryote interactions. NAR Genom Bioinform 2020; 2:lqaa044. [PMID: 32626849 PMCID: PMC7324143 DOI: 10.1093/nargab/lqaa044] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 03/12/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
Metagenomic sequencing has greatly enhanced the discovery of viral genomic sequences; however, it remains challenging to identify the host(s) of these new viruses. We developed VirHostMatcher-Net, a flexible, network-based, Markov random field framework for predicting virus–prokaryote interactions using multiple, integrated features: CRISPR sequences and alignment-free similarity measures (\documentclass[12pt]{minimal}
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}{}$s_2^*$\end{document} and WIsH). Evaluation of this method on a benchmark set of 1462 known virus–prokaryote pairs yielded host prediction accuracy of 59% and 86% at the genus and phylum levels, representing 16–27% and 6–10% improvement, respectively, over previous single-feature prediction approaches. We applied our host prediction tool to crAssphage, a human gut phage, and two metagenomic virus datasets: marine viruses and viral contigs recovered from globally distributed, diverse habitats. Host predictions were frequently consistent with those of previous studies, but more importantly, this new tool made many more confident predictions than previous tools, up to nearly 3-fold more (n > 27 000), greatly expanding the diversity of known virus–host interactions.
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Affiliation(s)
- Weili Wang
- Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Jie Ren
- Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Kujin Tang
- Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Emily Dart
- Biology Department, Clark University, Worcester, MA 01610, USA
| | | | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Jonathan Braun
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Fengzhu Sun
- Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
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264
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Khot V, Strous M, Hawley AK. Computational approaches in viral ecology. Comput Struct Biotechnol J 2020; 18:1605-1612. [PMID: 32670501 PMCID: PMC7334295 DOI: 10.1016/j.csbj.2020.06.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 01/21/2023] Open
Abstract
Dynamic virus-host interactions play a critical role in regulating microbial community structure and function. Yet for decades prior to the genomics era, viruses were largely overlooked in microbial ecology research, as only low-throughput culture-based methods of discovering viruses were available. With the advent of metagenomics, culture-independent techniques have provided exciting opportunities to discover and study new viruses. Here, we review recently developed computational methods for identifying viral sequences, exploring viral diversity in environmental samples, and predicting hosts from metagenomic sequence data. Methods to analyze viruses in silico utilize unconventional approaches to tackle challenges unique to viruses, such as vast diversity, mosaic viral genomes, and the lack of universal marker genes. As the field of viral ecology expands exponentially, computational advances have become increasingly important to gain insight into the role viruses in diverse habitats.
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Affiliation(s)
- Varada Khot
- Department of Geoscience, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Alyse K. Hawley
- Department of Geoscience, University of Calgary, Calgary, AB T2N 1N4, Canada
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265
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Abstract
Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment. Bacteriophages are abundant members of all microbiomes studied to date, influencing microbial communities through interactions with their bacterial hosts. Despite their functional importance and ubiquity, phages have been underexplored in urban environments compared to their bacterial counterparts. We profiled the viral communities in New York City (NYC) wastewater using metagenomic data collected in November 2014 from 14 wastewater treatment plants. We show that phages accounted for the largest viral component of the sewage samples and that specific virus communities were associated with local environmental conditions within boroughs. The vast majority of the virus sequences had no homology matches in public databases, forming an average of 1,700 unique virus clusters (putative genera). These new clusters contribute to elucidating the overwhelming proportion of data that frequently goes unidentified in viral metagenomic studies. We assigned potential hosts to these phages, which appear to infect a wide range of bacterial genera, often outside their presumed host. We determined that infection networks form a modular-nested pattern, indicating that phages include a range of host specificities, from generalists to specialists, with most interactions organized into distinct groups. We identified genes in viral contigs involved in carbon and sulfur cycling, suggesting functional importance of viruses in circulating pathways and gene functions in the wastewater environment. In addition, we identified virophage genes as well as a nearly complete novel virophage genome. These findings provide an understanding of phage abundance and diversity in NYC wastewater, previously uncharacterized, and further examine geographic patterns of phage-host association in urban environments. IMPORTANCE Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment.
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266
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Zhong ZP, Rapp JZ, Wainaina JM, Solonenko NE, Maughan H, Carpenter SD, Cooper ZS, Jang HB, Bolduc B, Deming JW, Sullivan MB. Viral Ecogenomics of Arctic Cryopeg Brine and Sea Ice. mSystems 2020; 5:e00246-20. [PMID: 32546670 PMCID: PMC7300359 DOI: 10.1128/msystems.00246-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/24/2020] [Indexed: 01/09/2023] Open
Abstract
Arctic regions, which are changing rapidly as they warm 2 to 3 times faster than the global average, still retain microbial habitats that serve as natural laboratories for understanding mechanisms of microbial adaptation to extreme conditions. Seawater-derived brines within both sea ice (sea-ice brine) and ancient layers of permafrost (cryopeg brine) support diverse microbes adapted to subzero temperatures and high salinities, yet little is known about viruses in these extreme environments, which, if analogous to other systems, could play important evolutionary and ecosystem roles. Here, we characterized viral communities and their functions in samples of cryopeg brine, sea-ice brine, and melted sea ice. Viral abundance was high in cryopeg brine (1.2 × 108 ml-1) and much lower in sea-ice brine (1.3 × 105 to 2.1 × 105 ml-1), which roughly paralleled the differences in cell concentrations in these samples. Five low-input, quantitative viral metagenomes were sequenced to yield 476 viral populations (i.e., species level; ≥10 kb), only 12% of which could be assigned taxonomy by traditional database approaches, indicating a high degree of novelty. Additional analyses revealed that these viruses: (i) formed communities that differed between sample type and vertically with sea-ice depth; (ii) infected hosts that dominated these extreme ecosystems, including Marinobacter, Glaciecola, and Colwellia; and (iii) encoded fatty acid desaturase (FAD) genes that likely helped their hosts overcome cold and salt stress during infection, as well as mediated horizontal gene transfer of FAD genes between microbes. Together, these findings contribute to understanding viral abundances and communities and how viruses impact their microbial hosts in subzero brines and sea ice.IMPORTANCE This study explores viral community structure and function in remote and extreme Arctic environments, including subzero brines within marine layers of permafrost and sea ice, using a modern viral ecogenomics toolkit for the first time. In addition to providing foundational data sets for these climate-threatened habitats, we found evidence that the viruses had habitat specificity, infected dominant microbial hosts, encoded host-derived metabolic genes, and mediated horizontal gene transfer among hosts. These results advance our understanding of the virosphere and how viruses influence extreme ecosystems. More broadly, the evidence that virally mediated gene transfers may be limited by host range in these extreme habitats contributes to a mechanistic understanding of genetic exchange among microbes under stressful conditions in other systems.
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Affiliation(s)
- Zhi-Ping Zhong
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, Ohio, USA
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Josephine Z Rapp
- School of Oceanography, University of Washington, Seattle, Washington, USA
| | - James M Wainaina
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | | | | | - Shelly D Carpenter
- School of Oceanography, University of Washington, Seattle, Washington, USA
| | - Zachary S Cooper
- School of Oceanography, University of Washington, Seattle, Washington, USA
| | - Ho Bin Jang
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Jody W Deming
- School of Oceanography, University of Washington, Seattle, Washington, USA
| | - Matthew B Sullivan
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, Ohio, USA
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
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267
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Bárdy P, Füzik T, Hrebík D, Pantůček R, Thomas Beatty J, Plevka P. Structure and mechanism of DNA delivery of a gene transfer agent. Nat Commun 2020; 11:3034. [PMID: 32541663 PMCID: PMC7296036 DOI: 10.1038/s41467-020-16669-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/17/2020] [Indexed: 11/09/2022] Open
Abstract
Alphaproteobacteria, which are the most abundant microorganisms of temperate oceans, produce phage-like particles called gene transfer agents (GTAs) that mediate lateral gene exchange. However, the mechanism by which GTAs deliver DNA into cells is unknown. Here we present the structure of the GTA of Rhodobacter capsulatus (RcGTA) and describe the conformational changes required for its DNA ejection. The structure of RcGTA resembles that of a tailed phage, but it has an oblate head shortened in the direction of the tail axis, which limits its packaging capacity to less than 4,500 base pairs of linear double-stranded DNA. The tail channel of RcGTA contains a trimer of proteins that possess features of both tape measure proteins of long-tailed phages from the family Siphoviridae and tail needle proteins of short-tailed phages from the family Podoviridae. The opening of a constriction within the RcGTA baseplate enables the ejection of DNA into bacterial periplasm.
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Affiliation(s)
- Pavol Bárdy
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Tibor Füzik
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Dominik Hrebík
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Roman Pantůček
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - J Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada
| | - Pavel Plevka
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.
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268
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Alteromonas Myovirus V22 Represents a New Genus of Marine Bacteriophages Requiring a Tail Fiber Chaperone for Host Recognition. mSystems 2020; 5:5/3/e00217-20. [PMID: 32518192 PMCID: PMC7289586 DOI: 10.1128/msystems.00217-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Marine phages play a variety of critical roles in regulating the microbial composition of our oceans. Despite constituting the majority of genetic diversity within these environments, there are relatively few isolates with complete genome sequences or in-depth analyses of their host interaction mechanisms, such as characterization of their receptor binding proteins (RBPs). Here, we present the 92,760-bp genome of the Alteromonas-targeting phage V22. Genomic and morphological analyses identify V22 as a myovirus; however, due to a lack of sequence similarity to any other known myoviruses, we propose that V22 be classified as the type phage of a new Myoalterovirus genus within the Myoviridae family. V22 shows gene homology and synteny with two different subfamilies of phages infecting enterobacteria, specifically within the structural region of its genome. To improve our understanding of the V22 adsorption process, we identified putative RBPs (gp23, gp24, and gp26) and tested their ability to decorate the V22 propagation strain, Alteromonas mediterranea PT11, as recombinant green fluorescent protein (GFP)-tagged constructs. Only GFP-gp26 was capable of bacterial recognition and identified as the V22 RBP. Interestingly, production of functional GFP-gp26 required coexpression with the downstream protein gp27. GFP-gp26 could be expressed alone but was incapable of host recognition. By combining size-exclusion chromatography with fluorescence microscopy, we reveal how gp27 is not a component of the final RBP complex but instead is identified as a new type of phage-encoded intermolecular chaperone that is essential for maturation of the gp26 RBP.IMPORTANCE Host recognition by phage-encoded receptor binding proteins (RBPs) constitutes the first step in all phage infections and the most critical determinant of host specificity. By characterizing new types of RBPs and identifying their essential chaperones, we hope to expand the repertoire of known phage-host recognition machineries. Due to their genetic plasticity, studying RBPs and their associated chaperones can shed new light onto viral evolution affecting phage-host interactions, which is essential for fields such as phage therapy or biotechnology. In addition, since marine phages constitute one of the most important reservoirs of noncharacterized genetic diversity on the planet, their genomic and functional characterization may be of paramount importance for the discovery of novel genes with potential applications.
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269
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Gao SM, Schippers A, Chen N, Yuan Y, Zhang MM, Li Q, Liao B, Shu WS, Huang LN. Depth-related variability in viral communities in highly stratified sulfidic mine tailings. MICROBIOME 2020; 8:89. [PMID: 32517753 PMCID: PMC7285708 DOI: 10.1186/s40168-020-00848-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 04/27/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Recent studies have significantly expanded our knowledge of viral diversity and functions in the environment. Exploring the ecological relationships between viruses, hosts, and the environment is a crucial first step towards a deeper understanding of the complex and dynamic interplays among them. RESULTS Here, we obtained extensive 16S rRNA gene amplicon, metagenomics sequencing, and geochemical datasets from different depths of two highly stratified sulfidic mine tailings cores with steep geochemical gradients especially pH, and explored how variations in viral community composition and functions were coupled to the co-existing prokaryotic assemblages and the varying environmental conditions. Our data showed that many viruses in the mine tailings represented novel genera, based on gene-sharing networks. Siphoviridae, Podoviridae, and Myoviridae dominated the classified viruses in the surface tailings and deeper layers. Both viral richness and normalized coverage increased with depth in the tailings cores and were significantly correlated with geochemical properties, for example, pH. Viral richness was also coupled to prokaryotic richness (Pearson's r = 0.65, P = 0.032). The enrichment of prophages in the surface mine tailings suggested a preference of lysogenic viral lifestyle in more acidic conditions. Community-wide comparative analyses clearly showed that viruses in the surface tailings encoded genes mostly with unknown functions while viruses in the deeper layers contained genes mainly annotated as conventional functions related to metabolism and structure. Notably, significantly abundant assimilatory sulfate reduction genes were identified from the deeper tailings layers and they were widespread in viruses predicted to infect diverse bacterial phyla. CONCLUSIONS Overall, our results revealed a depth-related distribution of viral populations in the extreme and heterogeneous tailings system. The viruses may interact with diverse hosts and dynamic environmental conditions and likely play a role in the functioning of microbial community and modulate sulfur cycles in situ. Video Abstract.
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Affiliation(s)
- Shao-Ming Gao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 People’s Republic of China
| | - Axel Schippers
- Resource Geochemistry, Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg 2, 30655 Hannover, Germany
| | - Nan Chen
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 People’s Republic of China
| | - Yang Yuan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 People’s Republic of China
| | - Miao-Miao Zhang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 People’s Republic of China
| | - Qi Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 People’s Republic of China
| | - Bin Liao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 People’s Republic of China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, 510631 People’s Republic of China
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 People’s Republic of China
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270
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Elworth RAL, Wang Q, Kota PK, Barberan CJ, Coleman B, Balaji A, Gupta G, Baraniuk RG, Shrivastava A, Treangen T. To Petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics. Nucleic Acids Res 2020; 48:5217-5234. [PMID: 32338745 PMCID: PMC7261164 DOI: 10.1093/nar/gkaa265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/20/2020] [Accepted: 04/04/2020] [Indexed: 02/01/2023] Open
Abstract
As computational biologists continue to be inundated by ever increasing amounts of metagenomic data, the need for data analysis approaches that keep up with the pace of sequence archives has remained a challenge. In recent years, the accelerated pace of genomic data availability has been accompanied by the application of a wide array of highly efficient approaches from other fields to the field of metagenomics. For instance, sketching algorithms such as MinHash have seen a rapid and widespread adoption. These techniques handle increasingly large datasets with minimal sacrifices in quality for tasks such as sequence similarity calculations. Here, we briefly review the fundamentals of the most impactful probabilistic and signal processing algorithms. We also highlight more recent advances to augment previous reviews in these areas that have taken a broader approach. We then explore the application of these techniques to metagenomics, discuss their pros and cons, and speculate on their future directions.
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Affiliation(s)
| | - Qi Wang
- Systems, Synthetic, and Physical Biology (SSPB) Graduate Program, Houston, TX 77005, USA
| | - Pavan K Kota
- Department of Bioengineering, Houston, TX 77005, USA
| | - C J Barberan
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Benjamin Coleman
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Advait Balaji
- Department of Computer Science, Houston, TX 77005, USA
| | - Gaurav Gupta
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Richard G Baraniuk
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Anshumali Shrivastava
- Department of Computer Science, Houston, TX 77005, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Todd J Treangen
- Department of Computer Science, Houston, TX 77005, USA
- Systems, Synthetic, and Physical Biology (SSPB) Graduate Program, Houston, TX 77005, USA
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271
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Kumata R, Ito J, Takahashi K, Suzuki T, Sato K. A tissue level atlas of the healthy human virome. BMC Biol 2020; 18:55. [PMID: 32493363 PMCID: PMC7269688 DOI: 10.1186/s12915-020-00785-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/22/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Human-resident microbes can influence both health and disease. Investigating the microbiome using next-generation sequencing technology has revealed examples of mutualism and conflict between microbes and humans. Comparing to bacteria, the viral component of the microbiome (i.e., the "virome") is understudied. Somatic tissues of healthy individuals are usually inaccessible for the virome sampling; therefore, there is limited understanding of the presence and distribution of viruses in tissues in healthy individuals and how virus infection associates with human gene expression and perturbs immunological homeostasis. RESULTS To characterize the human virome in a tissue-specific manner, here we performed meta-transcriptomic analysis using the RNA-sequencing dataset from the Genotype-Tissue Expression (GTEx) Project. We analyzed the 8991 RNA-sequencing data obtained from 51 somatic tissues from 547 individuals and successfully detected 39 viral species in at least one tissue. We then investigated associations between virus infection and human gene expression and human disease onset. We detected some expected relationships; for instance, hepatitis C virus infection in the liver was strongly associated with interferon-stimulated gene upregulation and pathological findings of chronic hepatitis. The presence of herpes simplex virus type 1 in one subject's brain strongly associated with immune gene expression. While torque teno virus was detected in a broad range of human tissues, it was not associated with interferon responses. Being notable in light of its association with lymphoproliferative disorders, Epstein-Barr virus infection in the spleen and blood was associated with an increase in plasma cells in healthy subjects. Human herpesvirus 7 was often detected in the stomach; intriguingly, it associated with the proportion of human leukocytes in the stomach as well as digestive gene expression. Moreover, virus infections in the local tissues associated with systemic immune responses in circulating blood. CONCLUSIONS To our knowledge, this study is the first comprehensive investigation of the human virome in a variety of tissues in healthy individuals through meta-transcriptomic analysis. Further investigation of the associations described here, and application of this analytical pipeline to additional datasets, will be useful to reveal the impact of viral infections on human health.
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Affiliation(s)
- Ryuichi Kumata
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 1088639, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 1088639, Japan
| | - Kenta Takahashi
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 1628640, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 1628640, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 1088639, Japan. .,CREST, Japan Science and Technology Agency, Saitama, 3220012, Japan.
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272
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Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Roux S, Sánchez P, Uehara H, Zayed AA, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J, Acinas SG, Babin M, Bork P, Bowler C, de Vargas C, Guidi L, Hingamp P, Iudicone D, Karp-Boss L, Karsenti E, Ogata H, Pesant S, Speich S, Sullivan MB, Wincker P, Sunagawa S. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. Cell 2020; 179:1068-1083.e21. [PMID: 31730850 PMCID: PMC6912165 DOI: 10.1016/j.cell.2019.10.014] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 07/26/2019] [Accepted: 10/11/2019] [Indexed: 12/02/2022]
Abstract
Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. Video Abstract
A catalog of 47 million genes was generated from 370 globally distributed metagenomes Meta-omics data integration disentangled the mechanisms of changes in transcript pools Transcript pool changes of metabolic marker genes show distinct mechanistic patterns Community turnover as a response to ocean warming may be strongest in polar regions
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Affiliation(s)
- Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid 28223, Spain; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Miguelangel Cuenca
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Christopher M Field
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Corinne Cruaud
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Stefan Engelen
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Ann C Gregory
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Karine Labadie
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Claudie Marec
- Département de biologie, Université Laval, QC G1V 0A6, Canada; Laboratoire d'Oceanographie Physique et Spatiale, UMR 6523, CNRS-IFREMER-IRD-UBO, Plouzané, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Simon Roux
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Hideya Uehara
- Institute for Chemical Research, Kyoto Univerisity, Gokasho, Uji 611-0011, Japan; Hewlett-Packard Japan, 2-2-1, Ojima, Koto-ku, Tokyo 136-8711, Japan
| | - Ahmed A Zayed
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Margaux Carmichael
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Céline Dimier
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, Villefranche-sur-mer 06230, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Joannie Ferland
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Takuvik Joint International Laboratory, CNRS-Université Laval, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Marc Picheral
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, Villefranche-sur-mer 06230, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow 117997, Russia
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Marcel Babin
- Takuvik Joint International Laboratory, CNRS-Université Laval, QC G1V 0A6, Canada
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany; Max Delbrück Centre for Molecular Medicine, Berlin 13125, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Lionel Guidi
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France; Department of Oceanography, University of Hawaii, Honolulu, HI 96822, USA
| | - Pascal Hingamp
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | | | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
| | - Eric Karsenti
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France; Directors' Research European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto Univerisity, Gokasho, Uji 611-0011, Japan
| | - Stephane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | | | - Matthew B Sullivan
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, the Ohio State University, Columbus, OH 43214, USA; Center for RNA Biology, the Ohio State University, Columbus, OH 43214, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland.
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274
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Ibarbalz FM, Henry N, Brandão MC, Martini S, Busseni G, Byrne H, Coelho LP, Endo H, Gasol JM, Gregory AC, Mahé F, Rigonato J, Royo-Llonch M, Salazar G, Sanz-Sáez I, Scalco E, Soviadan D, Zayed AA, Zingone A, Labadie K, Ferland J, Marec C, Kandels S, Picheral M, Dimier C, Poulain J, Pisarev S, Carmichael M, Pesant S, Babin M, Boss E, Iudicone D, Jaillon O, Acinas SG, Ogata H, Pelletier E, Stemmann L, Sullivan MB, Sunagawa S, Bopp L, de Vargas C, Karp-Boss L, Wincker P, Lombard F, Bowler C, Zinger L. Global Trends in Marine Plankton Diversity across Kingdoms of Life. Cell 2020; 179:1084-1097.e21. [PMID: 31730851 PMCID: PMC6912166 DOI: 10.1016/j.cell.2019.10.008] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/22/2019] [Accepted: 10/07/2019] [Indexed: 12/31/2022]
Abstract
The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation. Video Abstract
Most epipelagic planktonic groups exhibit a poleward decline of diversity No latitudinal diversity gradient was observed below the photic zone Temperature emerges as the best predictor of epipelagic plankton diversity Global warming may increase plankton diversity, particularly at high latitudes
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Affiliation(s)
- Federico M Ibarbalz
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Nicolas Henry
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Manoela C Brandão
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Séverine Martini
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Greta Busseni
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Hannah Byrne
- Department of Earth and Planetary Sciences, Harvard University, 20 Oxford St., Cambridge, MA 02138, USA
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Hisashi Endo
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain; Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
| | - Ann C Gregory
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Frédéric Mahé
- CIRAD, UMR BGPI, 34398, Montpellier, France; BGPI, Université Montpellier, CIRAD, IRD, Montpellier SupAgro, Montpellier, France
| | - Janaina Rigonato
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Isabel Sanz-Sáez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Eleonora Scalco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Dodji Soviadan
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Énergie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Joannie Ferland
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Claudie Marec
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany; Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Marc Picheral
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Céline Dimier
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology of the Russian Academy of Sciences, 36 Nakhimovsky Prosp., 117997 Moscow, Russia
| | - Margaux Carmichael
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France
| | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | | | - Marcel Babin
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Olivier Jaillon
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Eric Pelletier
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Lars Stemmann
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA; Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Laurent Bopp
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; LMD/IPSL, ENS, PSL Research University, École Polytechnique, Sorbonne Université, CNRS, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Patrick Wincker
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France.
| | - Lucie Zinger
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France.
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275
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Metaviral
SPAdes: assembly of viruses from metagenomic data. Bioinformatics 2020; 36:4126-4129. [DOI: 10.1093/bioinformatics/btaa490] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/21/2020] [Accepted: 05/08/2020] [Indexed: 11/14/2022] Open
Abstract
Abstract
Motivation
Although the set of currently known viruses has been steadily expanding, only a tiny fraction of the Earth’s virome has been sequenced so far. Shotgun metagenomic sequencing provides an opportunity to reveal novel viruses but faces the computational challenge of identifying viral genomes that are often difficult to detect in metagenomic assemblies.
Results
We describe a MetaviralSPAdes tool for identifying viral genomes in metagenomic assembly graphs that is based on analyzing variations in the coverage depth between viruses and bacterial chromosomes. We benchmarked MetaviralSPAdes on diverse metagenomic datasets, verified our predictions using a set of virus-specific Hidden Markov Models and demonstrated that it improves on the state-of-the-art viral identification pipelines.
Availability and implementation
Metaviral SPAdes includes ViralAssembly, ViralVerify and ViralComplete modules that are available as standalone packages: https://github.com/ablab/spades/tree/metaviral_publication, https://github.com/ablab/viralVerify/ and https://github.com/ablab/viralComplete/.
Contact
d.antipov@spbu.ru
Supplementary information
Supplementary data are available at Bioinformatics online.
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276
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Sunagawa S, Acinas SG, Bork P, Bowler C, Eveillard D, Gorsky G, Guidi L, Iudicone D, Karsenti E, Lombard F, Ogata H, Pesant S, Sullivan MB, Wincker P, de Vargas C. Tara Oceans: towards global ocean ecosystems biology. Nat Rev Microbiol 2020; 18:428-445. [PMID: 32398798 DOI: 10.1038/s41579-020-0364-5] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2020] [Indexed: 12/14/2022]
Abstract
A planetary-scale understanding of the ocean ecosystem, particularly in light of climate change, is crucial. Here, we review the work of Tara Oceans, an international, multidisciplinary project to assess the complexity of ocean life across comprehensive taxonomic and spatial scales. Using a modified sailing boat, the team sampled plankton at 210 globally distributed sites at depths down to 1,000 m. We describe publicly available resources of molecular, morphological and environmental data, and discuss how an ecosystems biology approach has expanded our understanding of plankton diversity and ecology in the ocean as a planetary, interconnected ecosystem. These efforts illustrate how global-scale concepts and data can help to integrate biological complexity into models and serve as a baseline for assessing ecosystem changes and the future habitability of our planet in the Anthropocene epoch.
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Affiliation(s)
- Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland.
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences-CSIC, Barcelona, Spain
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Chris Bowler
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | | | - Damien Eveillard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Université de Nantes, CNRS, UMR6004, LS2N, Nantes, France
| | - Gabriel Gorsky
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | - Lionel Guidi
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | | | - Eric Karsenti
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Directors' Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Stephane Pesant
- PANGAEA, University of Bremen, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Patrick Wincker
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie Francois Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France. .,Sorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, France.
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277
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Paez-Espino D, Roux S, Chen IMA, Palaniappan K, Ratner A, Chu K, Huntemann M, Reddy TBK, Pons JC, Llabrés M, Eloe-Fadrosh EA, Ivanova NN, Kyrpides NC. IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes. Nucleic Acids Res 2020; 47:D678-D686. [PMID: 30407573 PMCID: PMC6323928 DOI: 10.1093/nar/gky1127] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 10/31/2018] [Indexed: 01/06/2023] Open
Abstract
The Integrated Microbial Genome/Virus (IMG/VR) system v.2.0 (https://img.jgi.doe.gov/vr/) is the largest publicly available data management and analysis platform dedicated to viral genomics. Since the last report published in the 2016, NAR Database Issue, the data has tripled in size and currently contains genomes of 8389 cultivated reference viruses, 12 498 previously published curated prophages derived from cultivated microbial isolates, and 735 112 viral genomic fragments computationally predicted from assembled shotgun metagenomes. Nearly 60% of the viral genomes and genome fragments are clustered into 110 384 viral Operational Taxonomic Units (vOTUs) with two or more members. To improve data quality and predictions of host specificity, IMG/VR v.2.0 now separates prokaryotic and eukaryotic viruses, utilizes known prophage sequences to improve taxonomic assignments, and provides viral genome quality scores based on the estimated genome completeness. New features also include enhanced BLAST search capabilities for external queries. Finally, geographic map visualization to locate user-selected viral genomes or genome fragments has been implemented and download options have been extended. All of these features make IMG/VR v.2.0 a key resource for the study of viruses.
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Affiliation(s)
| | - Simon Roux
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - I-Min A Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | - Anna Ratner
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | - Ken Chu
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | - Marcel Huntemann
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - T B K Reddy
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Joan Carles Pons
- Department of Mathematics and Computer Science, University of the Balearic Islands, Spain
| | - Mercè Llabrés
- Department of Mathematics and Computer Science, University of the Balearic Islands, Spain
| | | | | | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
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278
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Edwards A, Cameron KA, Cook JM, Debbonaire AR, Furness E, Hay MC, Rassner SM. Microbial genomics amidst the Arctic crisis. Microb Genom 2020; 6:e000375. [PMID: 32392124 PMCID: PMC7371112 DOI: 10.1099/mgen.0.000375] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/16/2020] [Indexed: 12/16/2022] Open
Abstract
The Arctic is warming - fast. Microbes in the Arctic play pivotal roles in feedbacks that magnify the impacts of Arctic change. Understanding the genome evolution, diversity and dynamics of Arctic microbes can provide insights relevant for both fundamental microbiology and interdisciplinary Arctic science. Within this synthesis, we highlight four key areas where genomic insights to the microbial dimensions of Arctic change are urgently required: the changing Arctic Ocean, greenhouse gas release from the thawing permafrost, 'biological darkening' of glacial surfaces, and human activities within the Arctic. Furthermore, we identify four principal challenges that provide opportunities for timely innovation in Arctic microbial genomics. These range from insufficient genomic data to develop unifying concepts or model organisms for Arctic microbiology to challenges in gaining authentic insights to the structure and function of low-biomass microbiota and integration of data on the causes and consequences of microbial feedbacks across scales. We contend that our insights to date on the genomics of Arctic microbes are limited in these key areas, and we identify priorities and new ways of working to help ensure microbial genomics is in the vanguard of the scientific response to the Arctic crisis.
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Affiliation(s)
- Arwyn Edwards
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Karen A. Cameron
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Joseph M. Cook
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Aliyah R. Debbonaire
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Eleanor Furness
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Melanie C. Hay
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Sara M.E. Rassner
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
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279
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Tominaga K, Morimoto D, Nishimura Y, Ogata H, Yoshida T. In silico Prediction of Virus-Host Interactions for Marine Bacteroidetes With the Use of Metagenome-Assembled Genomes. Front Microbiol 2020; 11:738. [PMID: 32411107 PMCID: PMC7198788 DOI: 10.3389/fmicb.2020.00738] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 03/30/2020] [Indexed: 12/11/2022] Open
Abstract
Bacteroidetes is one of the most abundant heterotrophic bacterial taxa in the ocean and play crucial roles in recycling phytoplankton-derived organic matter. Viruses of Bacteroidetes are also expected to have an important role in the regulation of host communities. However, knowledge on marine Bacteroidetes viruses is biased toward cultured viruses from a few species, mainly fish pathogens or Bacteroidetes not abundant in marine environments. In this study, we investigated the recently reported 1,811 marine viral genomes to identify putative Bacteroidetes viruses using various in silico host prediction techniques. Notably, we used microbial metagenome-assembled genomes (MAGs) to augment the marine Bacteroidetes reference genomic data. The examined viral genomes and MAGs were derived from simultaneously collected samples. Using nucleotide sequence similarity-based host prediction methods, we detected 31 putative Bacteroidetes viral genomes. The MAG-based method substantially enhanced the predictions (26 viruses) when compared with the method that is solely based on the reference genomes from NCBI RefSeq (7 viruses). Previously unrecognized genus-level groups of Bacteroidetes viruses were detected only by the MAG-based method. We also developed a host prediction method based on the proportion of Bacteroidetes homologs in viral genomes, which detected 321 putative Bacteroidetes virus genomes including 81 that were newly recognized as Bacteroidetes virus genomes. The majority of putative Bacteroidetes viruses were detected based on the proportion of Bacteroidetes homologs in both RefSeq and MAGs; however, some were detected in only one of the two datasets. Putative Bacteroidetes virus lineages included not only relatives of known viruses but also those phylogenetically distant from the cultured viruses, such as marine Far-T4 like viruses known to be widespread in aquatic environments. Our MAG and protein homology-based host prediction approaches enhanced the existing knowledge on the diversity of Bacteroidetes viruses and their potential interaction with their hosts in marine environments.
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Affiliation(s)
- Kento Tominaga
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Daichi Morimoto
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yosuke Nishimura
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Hiroyuki Ogata
- Chemical Life Science, Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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280
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New virus isolates from Italian hydrothermal environments underscore the biogeographic pattern in archaeal virus communities. ISME JOURNAL 2020; 14:1821-1833. [PMID: 32322010 DOI: 10.1038/s41396-020-0653-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/28/2020] [Accepted: 03/31/2020] [Indexed: 12/22/2022]
Abstract
Viruses of hyperthermophilic archaea represent one of the least understood parts of the virosphere, showing little genomic and morphological similarity to viruses of bacteria or eukaryotes. Here, we investigated virus diversity in the active sulfurous fields of the Campi Flegrei volcano in Pozzuoli, Italy. Virus-like particles displaying eight different morphotypes, including lemon-shaped, droplet-shaped and bottle-shaped virions, were observed and five new archaeal viruses proposed to belong to families Rudiviridae, Globuloviridae and Tristromaviridae were isolated and characterized. Two of these viruses infect neutrophilic hyperthermophiles of the genus Pyrobaculum, whereas the remaining three have rod-shaped virions typical of the family Rudiviridae and infect acidophilic hyperthermophiles belonging to three different genera of the order Sulfolobales, namely, Saccharolobus, Acidianus, and Metallosphaera. Notably, Metallosphaera rod-shaped virus 1 is the first rudivirus isolated on Metallosphaera species. Phylogenomic analysis of the newly isolated and previously sequenced rudiviruses revealed a clear biogeographic pattern, with all Italian rudiviruses forming a monophyletic clade, suggesting geographical structuring of virus communities in extreme geothermal environments. Analysis of the CRISPR spacers suggests that isolated rudiviruses have experienced recent host switching across the genus boundary, potentially to escape the targeting by CRISPR-Cas immunity systems. Finally, we propose a revised classification of the Rudiviridae family, with the establishment of six new genera. Collectively, our results further show that high-temperature continental hydrothermal systems harbor a highly diverse virome and shed light on the evolution of archaeal viruses.
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281
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Coenen AR, Hu SK, Luo E, Muratore D, Weitz JS. A Primer for Microbiome Time-Series Analysis. Front Genet 2020; 11:310. [PMID: 32373155 PMCID: PMC7186479 DOI: 10.3389/fgene.2020.00310] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 03/16/2020] [Indexed: 12/22/2022] Open
Abstract
Time-series can provide critical insights into the structure and function of microbial communities. The analysis of temporal data warrants statistical considerations, distinct from comparative microbiome studies, to address ecological questions. This primer identifies unique challenges and approaches for analyzing microbiome time-series. In doing so, we focus on (1) identifying compositionally similar samples, (2) inferring putative interactions among populations, and (3) detecting periodic signals. We connect theory, code and data via a series of hands-on modules with a motivating biological question centered on marine microbial ecology. The topics of the modules include characterizing shifts in community structure and activity, identifying expression levels with a diel periodic signal, and identifying putative interactions within a complex community. Modules are presented as self-contained, open-access, interactive tutorials in R and Matlab. Throughout, we highlight statistical considerations for dealing with autocorrelated and compositional data, with an eye to improving the robustness of inferences from microbiome time-series. In doing so, we hope that this primer helps to broaden the use of time-series analytic methods within the microbial ecology research community.
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Affiliation(s)
- Ashley R. Coenen
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
| | - Sarah K. Hu
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, MA, United States
| | - Elaine Luo
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, United States
| | - Daniel Muratore
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Joshua S. Weitz
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
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282
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Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics. SOIL SYSTEMS 2020. [DOI: 10.3390/soilsystems4020023] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The study of soil viruses, though not new, has languished relative to the study of marine viruses. This is particularly due to challenges associated with separating virions from harboring soils. Generally, three approaches to analyzing soil viruses have been employed: (1) Isolation, to characterize virus genotypes and phenotypes, the primary method used prior to the start of the 21st century. (2) Metagenomics, which has revealed a vast diversity of viruses while also allowing insights into viral community ecology, although with limitations due to DNA from cellular organisms obscuring viral DNA. (3) Viromics (targeted metagenomics of virus-like-particles), which has provided a more focused development of ‘virus-sequence-to-ecology’ pipelines, a result of separation of presumptive virions from cellular organisms prior to DNA extraction. This separation permits greater sequencing emphasis on virus DNA and thereby more targeted molecular and ecological characterization of viruses. Employing viromics to characterize soil systems presents new challenges, however. Ones that only recently are being addressed. Here we provide a guide to implementing these three approaches to studying environmental viruses, highlighting benefits, difficulties, and potential contamination, all toward fostering greater focus on viruses in the study of soil ecology.
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283
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Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. Arch Virol 2020; 165:1253-1260. [PMID: 32162068 DOI: 10.1007/s00705-020-04577-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.
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284
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Bi L, Yu DT, Du S, Zhang LM, Zhang LY, Wu CF, Xiong C, Han LL, He JZ. Diversity and potential biogeochemical impacts of viruses in bulk and rhizosphere soils. Environ Microbiol 2020; 23:588-599. [PMID: 32249528 DOI: 10.1111/1462-2920.15010] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 12/31/2022]
Abstract
Viruses can affect microbial dynamics, metabolism and biogeochemical cycles in aquatic ecosystems. However, viral diversity and functions in agricultural soils are poorly known, especially in the rhizosphere. We used virome analysis of eight rhizosphere and bulk soils to study viral diversity and potential biogeochemical impacts in an agro-ecosystem. The order Caudovirales was the predominant viral type in agricultural soils, with Siphoviridae being the most abundant family. Phylogenetic analysis of the terminase large subunit of Caudovirales identified high viral diversity and three novel groups. Viral community composition differed significantly between bulk and rhizosphere soils. Soil pH was the main environmental driver of the viral community structure. Remarkably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes were detected in viromes, including glycoside hydrolases, carbohydrate esterases and carbohydrate-binding modules. These results demonstrate that virus-encoded putative auxiliary metabolic genes or metabolic genes that may change bacterial metabolism and indirectly contribute to biogeochemical cycling, especially carbon cycling, in agricultural soil.
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Affiliation(s)
- Li Bi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dan-Ting Yu
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China
| | - Shuai Du
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Yu Zhang
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Chuan-Fa Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Chao Xiong
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji-Zheng He
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
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285
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Genetically similar temperate phages form coalitions with their shared host that lead to niche-specific fitness effects. ISME JOURNAL 2020; 14:1688-1700. [PMID: 32242083 PMCID: PMC7305329 DOI: 10.1038/s41396-020-0637-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 03/08/2020] [Accepted: 03/16/2020] [Indexed: 01/07/2023]
Abstract
Temperate phages engage in long-term associations with their hosts that may lead to mutually beneficial interactions, of which the full extent is presently unknown. Here, we describe an environmentally relevant model system with a single host, a species of the Roseobacter clade of marine bacteria, and two genetically similar phages (ɸ-A and ɸ-D). Superinfection of a ɸ-D lysogenized strain (CB-D) with ɸ-A particles resulted in a lytic infection, prophage induction, and conversion of a subset of the host population, leading to isolation of a newly ɸ-A lysogenized strain (CB-A). Phenotypic differences, predicted to result from divergent lysogenic-lytic switch mechanisms, are evident between these lysogens, with CB-A displaying a higher incidence of spontaneous induction. Doubling times of CB-D and CB-A in liquid culture are 75 and 100 min, respectively. As cell cultures enter stationary phase, CB-A viable counts are half of CB-D. Consistent with prior evidence that cell lysis enhances biofilm formation, CB-A produces twice as much biofilm biomass as CB-D. As strains are susceptible to infection by the opposing phage type, co-culture competitions were performed to test fitness effects. When grown planktonically, CB-A outcompeted CB-D three to one. Yet, during biofilm growth, CB-D outcompeted CB-A three to one. These results suggest that genetically similar phages can have divergent influence on the competitiveness of their shared hosts in distinct environmental niches, possibly due to a complex form of phage-mediated allelopathy. These findings have implications for enhanced understanding of the eco-evolutionary dynamics of host-phage interactions that are pervasive in all ecosystems.
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286
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Martinez-Hernandez F, Luo E, Tominaga K, Ogata H, Yoshida T, DeLong EF, Martinez-Garcia M. Diel cycling of the cosmopolitan abundant Pelagibacter virus 37-F6: one of the most abundant viruses on earth. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:214-219. [PMID: 31997562 DOI: 10.1111/1758-2229.12825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/25/2020] [Indexed: 05/25/2023]
Abstract
The spatiotemporal dynamics for marine viral populations has only recently been explored. However, nothing is known about temporal activities of the uncultured Pelagibacter virus vSAG 37-F6, which was discovered by single-virus genomics as potentially the most abundant marine virus. Here, we investigate the diel cycling of 37-F6 virus and the putative SAR11 host using coastal and oceanic transcriptomic and viromic time-series data from Osaka Bay and North Pacific Subtropical Gyre. Virus 37-F6 and relatives displayed diel cycling of transcriptional activities synchronized with its putative host. In both virus and host, the lowest transcription rates were observed at 14:00-15:00, coinciding roughly with maximum solar irradiance, while higher transcriptional rates were detected during the night/early morning and afternoon. Diel abundance of free viruses of 37-F6 in seawater roughly mirrored the transcriptional activities of both virus and host. In Osaka Bay, among viral relatives (genus level), virus 37-F6 specifically showed the highest ratio of transcriptional activity to virome abundance, a proxy for viral transcriptional activity relative to free viral particle abundance. This high ratio suggests high infection rate efficiencies in vSAG 37-F6 virus compared to viral relatives. Thus, time-series data revealed temporal transcript activities in one of the most abundant viruses in Earth.
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Affiliation(s)
| | - Elaine Luo
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Manoa, Honolulu, HI, 96822, USA
| | - Kento Tominaga
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Uji, 611-0011, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Manoa, Honolulu, HI, 96822, USA
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
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287
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Bonilla-Rosso G, Steiner T, Wichmann F, Bexkens E, Engel P. Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota. Proc Natl Acad Sci U S A 2020; 117:7355-7362. [PMID: 32179689 PMCID: PMC7132132 DOI: 10.1073/pnas.2000228117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The honey bee gut microbiota influences bee health and has become an important model to study the ecology and evolution of microbiota-host interactions. Yet, little is known about the phage community associated with the bee gut, despite its potential to modulate bacterial diversity or to govern important symbiotic functions. Here we analyzed two metagenomes derived from virus-like particles, analyzed the prevalence of the identified phages across 73 bacterial metagenomes from individual bees, and tested the host range of isolated phages. Our results show that the honey bee gut virome is composed of at least 118 distinct clusters corresponding to both temperate and lytic phages and representing novel genera with a large repertoire of unknown gene functions. We find that the phage community is prevalent in honey bees across space and time and targets the core members of the bee gut microbiota. The large number and high genetic diversity of the viral clusters seems to mirror the high extent of strain-level diversity in the bee gut microbiota. We isolated eight lytic phages that target the core microbiota member Bifidobacterium asteroides, but that exhibited different host ranges at the strain level, resulting in a nested interaction network of coexisting phages and bacterial strains. Collectively, our results show that the honey bee gut virome consists of a complex and diverse phage community that likely plays an important role in regulating strain-level diversity in the bee gut and that holds promise as an experimental model to study bacteria-phage dynamics in natural microbial communities.
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Affiliation(s)
- Germán Bonilla-Rosso
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Théodora Steiner
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Fabienne Wichmann
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Evan Bexkens
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
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288
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Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems. mSystems 2020; 5:5/2/e00098-20. [PMID: 32184367 PMCID: PMC7380583 DOI: 10.1128/msystems.00098-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Interactions between viral communities and their microbial hosts have been the subject of many recent studies in a wide range of ecosystems. The degree of coordination between ecological assembly processes influencing viral and microbial communities, however, has been explored to a much lesser degree. By using a combined null modeling approach, this study investigated the ecological assembly processes influencing both viral and microbial community structure within hydraulically fractured shale environments. Among other results, significant relationships between the structuring processes affecting both the viral and microbial community were observed, indicating that ecological assembly might be coordinated between these communities despite differing selective pressures. Within this deep subsurface ecosystem, these results reveal a potentially important balance of ecological dynamics that must be maintained to enable long-term microbial community persistence. More broadly, this relationship begins to provide insight into the development of communities across trophic levels. The ecological drivers that concurrently act upon both a virus and its host and that drive community assembly are poorly understood despite known interactions between viral populations and their microbial hosts. Hydraulically fractured shale environments provide access to a closed ecosystem in the deep subsurface where constrained microbial and viral community assembly processes can be examined. Here, we used metagenomic analyses of time-resolved-produced fluid samples from two wells in the Appalachian Basin to track viral and host dynamics and to investigate community assembly processes. Hypersaline conditions within these ecosystems should drive microbial community structure to a similar configuration through time in response to common osmotic stress. However, viral predation appears to counterbalance this potentially strong homogeneous selection and pushes the microbial community toward undominated assembly. In comparison, while the viral community was also influenced by substantial undominated processes, it assembled, in part, due to homogeneous selection. When the overall assembly processes acting upon both these communities were directly compared with each other, a significant relationship was revealed, suggesting an association between microbial and viral community development despite differing selective pressures. These results reveal a potentially important balance of ecological dynamics that must be in maintained within this deep subsurface ecosystem in order for the microbial community to persist over extended time periods. More broadly, this relationship begins to provide knowledge underlying metacommunity development across trophic levels. IMPORTANCE Interactions between viral communities and their microbial hosts have been the subject of many recent studies in a wide range of ecosystems. The degree of coordination between ecological assembly processes influencing viral and microbial communities, however, has been explored to a much lesser degree. By using a combined null modeling approach, this study investigated the ecological assembly processes influencing both viral and microbial community structure within hydraulically fractured shale environments. Among other results, significant relationships between the structuring processes affecting both the viral and microbial community were observed, indicating that ecological assembly might be coordinated between these communities despite differing selective pressures. Within this deep subsurface ecosystem, these results reveal a potentially important balance of ecological dynamics that must be maintained to enable long-term microbial community persistence. More broadly, this relationship begins to provide insight into the development of communities across trophic levels.
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289
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Focardi A, Ostrowski M, Goossen K, Brown MV, Paulsen I. Investigating the Diversity of Marine Bacteriophage in Contrasting Water Masses Associated with the East Australian Current (EAC) System. Viruses 2020; 12:E317. [PMID: 32188136 PMCID: PMC7150976 DOI: 10.3390/v12030317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 12/13/2022] Open
Abstract
Virus- and bacteriophage-induced mortality can have a significant impact on marine productivity and alter the flux of nutrients in marine microbial food-webs. Viral mediated horizontal gene transfer can also influence host fitness and community composition. However, there are very few studies of marine viral diversity in the Southern Hemisphere, which hampers our ability to fully understand the complex interplay of biotic and abiotic factors that shape microbial communities. We carried out the first genetic study of bacteriophage communities within a dynamic western boundary current (WBC) system, the east Australian current (EAC). Virus DNA sequences were extracted from 63 assembled metagenomes and six metaviromes obtained from various depths at 24 different locations. More than 1700 bacteriophage genomic fragments (>9 kbps) were recovered from the assembled sequences. Bacteriophage diversity displayed distinct depth and regional patterns. There were clear differences in the bacteriophage populations associated with the EAC and Tasman Sea euphotic zones, at both the taxonomic and functional level. In contrast, bathypelagic phages were similar across the two oceanic regions. These data provide the first characterisation of viral diversity across a dynamic western boundary current, which is an emerging model for studying the response of microbial communities to climate change.
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Affiliation(s)
- Amaranta Focardi
- Department of Molecular Sciences, Macquarie University, 4 Wally’s Walk, Sydney, NSW 2109, Australia;
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology Sydney, 123 Broadway, Sydney, NSW 2007, Australia;
| | - Kirianne Goossen
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, TAS 7001, Australia (M.V.B.)
| | - Mark V. Brown
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, TAS 7001, Australia (M.V.B.)
- School of Environmental and Life Sciences, University of Newcastle, University Dr, Callaghan, NSW 2308, Australia
| | - Ian Paulsen
- Department of Molecular Sciences, Macquarie University, 4 Wally’s Walk, Sydney, NSW 2109, Australia;
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290
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Zhang Y, Qin W, Hou L, Zakem EJ, Wan X, Zhao Z, Liu L, Hunt KA, Jiao N, Kao SJ, Tang K, Xie X, Shen J, Li Y, Chen M, Dai X, Liu C, Deng W, Dai M, Ingalls AE, Stahl DA, Herndl GJ. Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean. Proc Natl Acad Sci U S A 2020; 117:4823-4830. [PMID: 32071230 PMCID: PMC7060736 DOI: 10.1073/pnas.1912367117] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Ammonia oxidation to nitrite and its subsequent oxidation to nitrate provides energy to the two populations of nitrifying chemoautotrophs in the energy-starved dark ocean, driving a coupling between reduced inorganic nitrogen (N) pools and production of new organic carbon (C) in the dark ocean. However, the relationship between the flux of new C production and the fluxes of N of the two steps of oxidation remains unclear. Here, we show that, despite orders-of-magnitude difference in cell abundances between ammonia oxidizers and nitrite oxidizers, the two populations sustain similar bulk N-oxidation rates throughout the deep waters with similarly high affinities for ammonia and nitrite under increasing substrate limitation, thus maintaining overall homeostasis in the oceanic nitrification pathway. Our observations confirm the theoretical predictions of a redox-informed ecosystem model. Using balances from this model, we suggest that consistently low ammonia and nitrite concentrations are maintained when the two populations have similarly high substrate affinities and their loss rates are proportional to their maximum growth rates. The stoichiometric relations between the fluxes of C and N indicate a threefold to fourfold higher C-fixation efficiency per mole of N oxidized by ammonia oxidizers compared to nitrite oxidizers due to nearly identical apparent energetic requirements for C fixation of the two populations. We estimate that the rate of chemoautotrophic C fixation amounts to ∼1 × 1013 to ∼2 × 1013 mol of C per year globally through the flux of ∼1 × 1014 to ∼2 × 1014 mol of N per year of the two steps of oxidation throughout the dark ocean.
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Affiliation(s)
- Yao Zhang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China;
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Wei Qin
- School of Oceanography, University of Washington, Seattle, WA 98195
| | - Lei Hou
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Emily J Zakem
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Xianhui Wan
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
| | - Zihao Zhao
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, A-1090 Vienna, Austria
| | - Li Liu
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Kristopher A Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Xiabing Xie
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
| | - Jiaming Shen
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Yufang Li
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Mingming Chen
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Xiaofeng Dai
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Chang Liu
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Wenchao Deng
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
| | - Minhan Dai
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101 Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, 361101 Xiamen, China
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA 98195
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195
| | - Gerhard J Herndl
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, A-1090 Vienna, Austria
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, 1790 AB Den Burg, The Netherlands
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291
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Abstract
Viruses are ubiquitous parasites of cellular life and the most abundant biological entities on Earth. It is widely accepted that viruses are polyphyletic, but a consensus scenario for their ultimate origin is still lacking. Traditionally, three scenarios for the origin of viruses have been considered: descent from primordial, precellular genetic elements, reductive evolution from cellular ancestors and escape of genes from cellular hosts, achieving partial replicative autonomy and becoming parasitic genetic elements. These classical scenarios give different timelines for the origin(s) of viruses and do not explain the provenance of the two key functional modules that are responsible, respectively, for viral genome replication and virion morphogenesis. Here, we outline a 'chimeric' scenario under which different types of primordial, selfish replicons gave rise to viruses by recruiting host proteins for virion formation. We also propose that new groups of viruses have repeatedly emerged at all stages of the evolution of life, often through the displacement of ancestral structural and genome replication genes.
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292
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Ren J, Song K, Deng C, Ahlgren NA, Fuhrman JA, Li Y, Xie X, Poplin R, Sun F. Identifying viruses from metagenomic data using deep learning. QUANTITATIVE BIOLOGY 2020; 8:64-77. [PMID: 34084563 PMCID: PMC8172088 DOI: 10.1007/s40484-019-0187-4] [Citation(s) in RCA: 225] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/08/2019] [Accepted: 10/14/2019] [Indexed: 01/08/2023]
Abstract
BACKGROUND The recent development of metagenomic sequencing makes it possible to massively sequence microbial genomes including viral genomes without the need for laboratory culture. Existing reference-based and gene homology-based methods are not efficient in identifying unknown viruses or short viral sequences from metagenomic data. METHODS Here we developed a reference-free and alignment-free machine learning method, DeepVirFinder, for identifying viral sequences in metagenomic data using deep learning. RESULTS Trained based on sequences from viral RefSeq discovered before May 2015, and evaluated on those discovered after that date, DeepVirFinder outperformed the state-of-the-art method VirFinder at all contig lengths, achieving AUROC 0.93, 0.95, 0.97, and 0.98 for 300, 500, 1000, and 3000 bp sequences respectively. Enlarging the training data with additional millions of purified viral sequences from metavirome samples further improved the accuracy for identifying virus groups that are under-represented. Applying DeepVirFinder to real human gut metagenomic samples, we identified 51,138 viral sequences belonging to 175 bins in patients with colorectal carcinoma (CRC). Ten bins were found associated with the cancer status, suggesting viruses may play important roles in CRC. CONCLUSIONS Powered by deep learning and high throughput sequencing metagenomic data, DeepVirFinder significantly improved the accuracy of viral identification and will assist the study of viruses in the era of metagenomics.
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Affiliation(s)
- Jie Ren
- Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Kai Song
- School of Mathematics and Statistics, Qingdao University, Qingdao 266071, China
| | - Chao Deng
- Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Jed A. Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Yi Li
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Xiaohui Xie
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | | | - Fengzhu Sun
- Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
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293
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Koonin EV, Yutin N. The crAss-like Phage Group: How Metagenomics Reshaped the Human Virome. Trends Microbiol 2020; 28:349-359. [PMID: 32298613 DOI: 10.1016/j.tim.2020.01.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 02/07/2023]
Abstract
Metagenomics is currently the primary means for identifying new viruses. One of the most impactful metagenomic discoveries is that of crAssphage, the most abundant human-associated virus that is found in about 50% of human gut viromes where it can comprise up to 90% of the virus sequences. Although initial genome analysis of crAssphage failed to detect related phages, or functionally annotate most of the genes, subsequent reanalysis with powerful computational methods and larger databases led to the identification of an expansive group of crAss-like phages. The functions of most crAssphage proteins were predicted, including unusual ones such as giant RNA polymerase polyproteins. The host range of the crAss-like phages consists of various members of the bacterial phylum Bacteroidetes as demonstrated by CRISPR spacer analysis and by analysis of genes acquired by phages from the hosts. New metagenomic studies vastly expanded the crAss-like phage group and demonstrated its global spread and ancient association with primates. The first members of the crAss-like group was recently isolated and shown to infect the bacterium Bacteroides intestinales. Characterization of this phage validated the predicted podovirus-like virion structure and the identity of the major capsid protein and other predicted virion proteins, including three RNA polymerase subunits.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA.
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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294
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Moore RM, Harrison AO, McAllister SM, Polson SW, Wommack KE. Iroki: automatic customization and visualization of phylogenetic trees. PeerJ 2020; 8:e8584. [PMID: 32149022 PMCID: PMC7049256 DOI: 10.7717/peerj.8584] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/17/2020] [Indexed: 12/26/2022] Open
Abstract
Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.
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Affiliation(s)
- Ryan M Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
| | - Amelia O Harrison
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States of America
| | - Sean M McAllister
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States of America
| | - Shawn W Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
| | - K Eric Wommack
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
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295
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Beaulaurier J, Luo E, Eppley JM, Uyl PD, Dai X, Burger A, Turner DJ, Pendelton M, Juul S, Harrington E, DeLong EF. Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities. Genome Res 2020; 30:437-446. [PMID: 32075851 PMCID: PMC7111524 DOI: 10.1101/gr.251686.119] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 02/13/2020] [Indexed: 12/20/2022]
Abstract
Viruses are the most abundant biological entities on Earth and play key roles in host ecology, evolution, and horizontal gene transfer. Despite recent progress in viral metagenomics, the inherent genetic complexity of virus populations still poses technical difficulties for recovering complete virus genomes from natural assemblages. To address these challenges, we developed an assembly-free, single-molecule nanopore sequencing approach, enabling direct recovery of complete virus genome sequences from environmental samples. Our method yielded thousands of full-length, high-quality draft virus genome sequences that were not recovered using standard short-read assembly approaches. Additionally, our analyses discriminated between populations whose genomes had identical direct terminal repeats versus those with circularly permuted repeats at their termini, thus providing new insight into native virus reproduction and genome packaging. Novel DNA sequences were discovered, whose repeat structures, gene contents, and concatemer lengths suggest they are phage-inducible chromosomal islands, which are packaged as concatemers in phage particles, with lengths that match the size ranges of co-occurring phage genomes. Our new virus sequencing strategy can provide previously unavailable information about the genome structures, population biology, and ecology of naturally occurring viruses and viral parasites.
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Affiliation(s)
- John Beaulaurier
- Oxford Nanopore Technologies Incorporated, San Francisco, California 94080, USA
| | - Elaine Luo
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - John M Eppley
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - Paul Den Uyl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - Xiaoguang Dai
- Oxford Nanopore Technologies Incorporated, New York, New York 10013, USA
| | - Andrew Burger
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - Daniel J Turner
- Oxford Nanopore Technologies Limited, Oxford, OX4 4DQ, United Kingdom
| | - Matthew Pendelton
- Oxford Nanopore Technologies Incorporated, New York, New York 10013, USA
| | - Sissel Juul
- Oxford Nanopore Technologies Incorporated, New York, New York 10013, USA
| | - Eoghan Harrington
- Oxford Nanopore Technologies Incorporated, New York, New York 10013, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii 96822, USA
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296
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Luo E, Eppley JM, Romano AE, Mende DR, DeLong EF. Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column. ISME JOURNAL 2020; 14:1304-1315. [PMID: 32060418 PMCID: PMC7174320 DOI: 10.1038/s41396-020-0604-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 12/17/2019] [Accepted: 01/30/2020] [Indexed: 12/11/2022]
Abstract
Microbial communities are critical to ecosystem dynamics and biogeochemical cycling in the open oceans. Viruses are essential elements of these communities, influencing the productivity, diversity, and evolution of cellular hosts. To further explore the natural history and ecology of open-ocean viruses, we surveyed the spatiotemporal dynamics of double-stranded DNA (dsDNA) viruses in both virioplankton and bacterioplankton size fractions in the North Pacific Subtropical Gyre, one of the largest biomes on the planet. Assembly and clustering of viral genomes revealed a peak in virioplankton diversity at the base of the euphotic zone, where virus populations and host species richness both reached their maxima. Simultaneous characterization of both extracellular and intracellular viruses suggested depth-specific reproductive strategies. In particular, analyses indicated elevated lytic interactions in the mixed layer, more temporally variable temperate phage interactions at the base of the euphotic zone, and increased lysogeny in the mesopelagic ocean. Furthermore, the depth variability of auxiliary metabolic genes suggested habitat-specific strategies for viral influence on light-energy, nitrogen, and phosphorus acquisition during host infection. Most virus populations were temporally persistent over several years in this environment at the 95% nucleic acid identity level. In total, our analyses revealed variable distributional patterns and diverse reproductive and metabolic strategies of virus populations in the open-ocean water column.
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Affiliation(s)
- Elaine Luo
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI, 96822, USA
| | - John M Eppley
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI, 96822, USA
| | - Anna E Romano
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI, 96822, USA
| | - Daniel R Mende
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI, 96822, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI, 96822, USA.
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297
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Silveira CB, Coutinho FH, Cavalcanti GS, Benler S, Doane MP, Dinsdale EA, Edwards RA, Francini-Filho RB, Thompson CC, Luque A, Rohwer FL, Thompson F. Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes. BMC Genomics 2020; 21:126. [PMID: 32024463 PMCID: PMC7003362 DOI: 10.1186/s12864-020-6523-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 01/21/2020] [Indexed: 12/14/2022] Open
Abstract
Background Bacteriophages encode genes that modify bacterial functions during infection. The acquisition of phage-encoded virulence genes is a major mechanism for the rise of bacterial pathogens. In coral reefs, high bacterial density and lysogeny has been proposed to exacerbate reef decline through the transfer of phage-encoded virulence genes. However, the functions and distribution of these genes in phage virions on the reef remain unknown. Results Here, over 28,000 assembled viral genomes from the free viral community in Atlantic and Pacific Ocean coral reefs were queried against a curated database of virulence genes. The diversity of virulence genes encoded in the viral genomes was tested for relationships with host taxonomy and bacterial density in the environment. These analyses showed that bacterial density predicted the profile of virulence genes encoded by phages. The Shannon diversity of virulence-encoding phages was negatively related with bacterial density, leading to dominance of fewer genes at high bacterial abundances. A statistical learning analysis showed that reefs with high microbial density were enriched in viruses encoding genes enabling bacterial recognition and invasion of metazoan epithelium. Over 60% of phages could not have their hosts identified due to limitations of host prediction tools; for those which hosts were identified, host taxonomy was not an indicator of the presence of virulence genes. Conclusions This study described bacterial virulence factors encoded in the genomes of bacteriophages at the community level. The results showed that the increase in microbial densities that occurs during coral reef degradation is associated with a change in the genomic repertoire of bacteriophages, specifically in the diversity and distribution of bacterial virulence genes. This suggests that phages are implicated in the rise of pathogens in disturbed marine ecosystems.
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Affiliation(s)
- Cynthia B Silveira
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA. .,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA. .,Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, FL, 33146, USA.
| | - Felipe H Coutinho
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Apartado 18, 03550, San Juan de Alicante, Spain
| | - Giselle S Cavalcanti
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Sean Benler
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Michael P Doane
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Sydney Institute of Marine Science, 19 Chowder Bay Rd, Mosman, NSW, 2088, Australia
| | - Elizabeth A Dinsdale
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Robert A Edwards
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Ronaldo B Francini-Filho
- Centro de Biologia Marinha, Universidade de São Paulo, Rodovia Manoel Hypólito do Rego, Km 131,50, São Sebastião, SP, 11600-000, Brazil
| | - Cristiane C Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, RJ, 21941- 599, Brazil
| | - Antoni Luque
- Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Computational Science Research Center, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Forest L Rohwer
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Fabiano Thompson
- SAGE/COPPE, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, RJ, 21941- 599, Brazil
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298
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Dion MB, Oechslin F, Moineau S. Phage diversity, genomics and phylogeny. Nat Rev Microbiol 2020; 18:125-138. [PMID: 32015529 DOI: 10.1038/s41579-019-0311-5] [Citation(s) in RCA: 375] [Impact Index Per Article: 93.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2019] [Indexed: 12/23/2022]
Abstract
Recent advances in viral metagenomics have enabled the rapid discovery of an unprecedented catalogue of phages in numerous environments, from the human gut to the deep ocean. Although these advances have expanded our understanding of phage genomic diversity, they also revealed that we have only scratched the surface in the discovery of novel viruses. Yet, despite the remarkable diversity of phages at the nucleotide sequence level, the structural proteins that form viral particles show strong similarities and conservation. Phages are uniquely interconnected from an evolutionary perspective and undergo multiple events of genetic exchange in response to the selective pressure of their hosts, which drives their diversity. In this Review, we explore phage diversity at the structural, genomic and community levels as well as the complex evolutionary relationships between phages, moulded by the mosaicity of their genomes.
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Affiliation(s)
- Moïra B Dion
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Frank Oechslin
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada. .,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada. .,Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Québec, Canada.
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299
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Al-Shayeb B, Sachdeva R, Chen LX, Ward F, Munk P, Devoto A, Castelle CJ, Olm MR, Bouma-Gregson K, Amano Y, He C, Méheust R, Brooks B, Thomas A, Lavy A, Matheus-Carnevali P, Sun C, Goltsman DSA, Borton MA, Sharrar A, Jaffe AL, Nelson TC, Kantor R, Keren R, Lane KR, Farag IF, Lei S, Finstad K, Amundson R, Anantharaman K, Zhou J, Probst AJ, Power ME, Tringe SG, Li WJ, Wrighton K, Harrison S, Morowitz M, Relman DA, Doudna JA, Lehours AC, Warren L, Cate JHD, Santini JM, Banfield JF. Clades of huge phages from across Earth's ecosystems. Nature 2020; 578:425-431. [PMID: 32051592 PMCID: PMC7162821 DOI: 10.1038/s41586-020-2007-4] [Citation(s) in RCA: 234] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 01/02/2020] [Indexed: 12/31/2022]
Abstract
Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.
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Affiliation(s)
- Basem Al-Shayeb
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Rohan Sachdeva
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Lin-Xing Chen
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Fred Ward
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Audra Devoto
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Cindy J Castelle
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Matthew R Olm
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Keith Bouma-Gregson
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | - Yuki Amano
- Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Tokai-mura, Japan
| | - Christine He
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Raphaël Méheust
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Brandon Brooks
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Alex Thomas
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Adi Lavy
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | | | - Christine Sun
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | | | - Mikayla A Borton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Allison Sharrar
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | - Alexander L Jaffe
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Tara C Nelson
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Rose Kantor
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Ray Keren
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Katherine R Lane
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Ibrahim F Farag
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Shufei Lei
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | - Kari Finstad
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA
| | - Ronald Amundson
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA
| | - Karthik Anantharaman
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | | | - Alexander J Probst
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Mary E Power
- Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | | | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Kelly Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Sue Harrison
- Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa
| | - Michael Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - David A Relman
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Anne-Catherine Lehours
- Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, CNRS, Clermont-Ferrand, France
| | - Lesley Warren
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Jamie H D Cate
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Joanne M Santini
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA.
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA.
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA.
- School of Earth Sciences, University of Melbourne, Melbourne, Victoria, Australia.
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300
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Zolfo M, Pinto F, Asnicar F, Manghi P, Tett A, Bushman FD, Segata N. Detecting contamination in viromes using ViromeQC. Nat Biotechnol 2020; 37:1408-1412. [PMID: 31748692 DOI: 10.1038/s41587-019-0334-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Adrian Tett
- Department CIBIO, University of Trento, Trento, Italy
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
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