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Roux S, Páez-Espino D, Chen IMA, Palaniappan K, Ratner A, Chu K, Reddy TBK, Nayfach S, Schulz F, Call L, Neches RY, Woyke T, Ivanova NN, Eloe-Fadrosh EA, Kyrpides NC. IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses. Nucleic Acids Res 2021; 49:D764-D775. [PMID: 33137183 PMCID: PMC7778971 DOI: 10.1093/nar/gkaa946] [Citation(s) in RCA: 201] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/02/2020] [Accepted: 10/09/2020] [Indexed: 12/28/2022] Open
Abstract
Viruses are integral components of all ecosystems and microbiomes on Earth. Through pervasive infections of their cellular hosts, viruses can reshape microbial community structure and drive global nutrient cycling. Over the past decade, viral sequences identified from genomes and metagenomes have provided an unprecedented view of viral genome diversity in nature. Since 2016, the IMG/VR database has provided access to the largest collection of viral sequences obtained from (meta)genomes. Here, we present the third version of IMG/VR, composed of 18 373 cultivated and 2 314 329 uncultivated viral genomes (UViGs), nearly tripling the total number of sequences compared to the previous version. These clustered into 935 362 viral Operational Taxonomic Units (vOTUs), including 188 930 with two or more members. UViGs in IMG/VR are now reported as single viral contigs, integrated proviruses or genome bins, and are annotated with a new standardized pipeline including genome quality estimation using CheckV, taxonomic classification reflecting the latest ICTV update, and expanded host taxonomy prediction. The new IMG/VR interface enables users to efficiently browse, search, and select UViGs based on genome features and/or sequence similarity. IMG/VR v3 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.
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Affiliation(s)
- Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David Páez-Espino
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - I-Min A Chen
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Krishna Palaniappan
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anna Ratner
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ken Chu
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - T B K Reddy
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stephen Nayfach
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lee Call
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Russell Y Neches
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Natalia N Ivanova
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emiley A Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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52
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Vik D, Gazitúa MC, Sun CL, Zayed AA, Aldunate M, Mulholland MR, Ulloa O, Sullivan MB. Genome-resolved viral ecology in a marine oxygen minimum zone. Environ Microbiol 2020; 23:2858-2874. [PMID: 33185964 DOI: 10.1111/1462-2920.15313] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 11/09/2020] [Indexed: 11/28/2022]
Abstract
Oxygen minimum zones (OMZs) are critical to marine nitrogen cycling and global climate change. While OMZ microbial communities are relatively well-studied, little is known about their viruses. Here, we assess the viral community ecology of 22 deeply sequenced viral metagenomes along a gradient of oxygenated to anoxic waters (<0.02 μmol/l O2 ) in the Eastern Tropical South Pacific (ETSP) OMZ. We identified 46 127 viral populations (≥5 kb), which augments the known viruses from ETSP by 10-fold. Viral communities clustered into six groups that correspond to oceanographic features. Oxygen concentration was the predominant environmental feature driving viral community structure. Alpha and beta diversity of viral communities in the anoxic zone were lower than in surface waters, which parallels the low microbial diversity seen in other studies. ETSP viruses were largely endemic, with the majority of shared viruses (87%) also present in other OMZ samples. We detected 543 putative viral-encoded auxiliary metabolic genes (AMGs), of which some have a distribution that reflects physico-chemical characteristics across depth. Together these findings provide an ecological baseline for viral community structure, drivers and population variability in OMZs that will help future studies assess the role of viruses in these climate-critical environments.
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Affiliation(s)
- Dean Vik
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Maria Consuelo Gazitúa
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.,Viromica Consulting, Santiago, Chile
| | - Christine L Sun
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Montserrat Aldunate
- Department of Oceanography, Universidad de Concepción, Concepción, Chile.,Millennium Institute of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Margaret R Mulholland
- Department of Ocean, Earth and Atmospheric Sciences, Old Dominion University, Norfolk, VA, USA
| | - Osvaldo Ulloa
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.,Millennium Institute of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
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53
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Coutinho FH, Cabello-Yeves PJ, Gonzalez-Serrano R, Rosselli R, López-Pérez M, Zemskaya TI, Zakharenko AS, Ivanov VG, Rodriguez-Valera F. New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal. MICROBIOME 2020; 8:163. [PMID: 33213521 PMCID: PMC7678222 DOI: 10.1186/s40168-020-00936-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/12/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Lake Baikal is the largest body of liquid freshwater on Earth. Previous studies have described the microbial composition of this habitat, but the viral communities from this ecosystem have not been characterized in detail. RESULTS Here, we describe the viral diversity of this habitat across depth and seasonal gradients. We discovered 19,475 bona fide viral sequences, which are derived from viruses predicted to infect abundant and ecologically important taxa that reside in Lake Baikal, such as Nitrospirota, Methylophilaceae, and Crenarchaeota. Diversity analysis revealed significant changes in viral community composition between epipelagic and bathypelagic zones. Analysis of the gene content of individual viral populations allowed us to describe one of the first bacteriophages that infect Nitrospirota, and their extensive repertoire of auxiliary metabolic genes that might enhance carbon fixation through the reductive TCA cycle. We also described bacteriophages of methylotrophic bacteria with the potential to enhance methanol oxidation and the S-adenosyl-L-methionine cycle. CONCLUSIONS These findings unraveled new ways by which viruses influence the carbon cycle in freshwater ecosystems, namely, by using auxiliary metabolic genes that act upon metabolisms of dark carbon fixation and methylotrophy. Therefore, our results shed light on the processes through which viruses can impact biogeochemical cycles of major ecological relevance. Video Abstract.
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Affiliation(s)
- F H Coutinho
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain.
| | - P J Cabello-Yeves
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain
| | - R Gonzalez-Serrano
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain
| | - R Rosselli
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
- Utrecht University, Utrecht, The Netherlands
| | - M López-Pérez
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain
| | - T I Zemskaya
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - A S Zakharenko
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - V G Ivanov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - F Rodriguez-Valera
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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54
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Zhang Z, Qin F, Chen F, Chu X, Luo H, Zhang R, Du S, Tian Z, Zhao Y. Culturing novel and abundant pelagiphages in the ocean. Environ Microbiol 2020; 23:1145-1161. [PMID: 33047445 DOI: 10.1111/1462-2920.15272] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/27/2020] [Accepted: 10/03/2020] [Indexed: 11/26/2022]
Abstract
Viruses play a key role in biogeochemical cycling and host mortality, metabolism, physiology and evolution in the ocean. Viruses that infect the globally abundant SAR11 bacteria (pelagiphages) were reported to be an important component of the marine viral communities. Our current knowledge of pelagiphages is based on a few studies and therefore is limited. In this study, 10 new pelagiphages were isolated and genomically characterized. These pelagiphages represent the first cultivated representatives of four viral lineages only found in metagenomic sequencing datasets previously. Many abundant environmental viral sequences, i.e., single-virus vSAG 37-F6 and several Global Ocean Viromes (GOV) viral populations, are now further confirmed with these pelagiphages. Viromic read mapping reveals that these new pelagiphages are globally distributed in the ocean and can be detected throughout the water column. Remarkably, isolation of these pelagiphages contributed up to 12% of all viromic reads annotated in the analysed viromes. Altogether, this study has greatly broadened our understanding of pelagiphages regarding their morphology, genetic diversity, infection strategies, and distribution pattern. The availability of these newly isolated pelagiphages and their genome sequences will allow us to further explore their infectivities and ecological strategies.
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Affiliation(s)
- Zefeng Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Fang Qin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Xiao Chu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, China
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, China
| | - Sen Du
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhen Tian
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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55
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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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56
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Brown JM, Labonté JM, Brown J, Record NR, Poulton NJ, Sieracki ME, Logares R, Stepanauskas R. Single Cell Genomics Reveals Viruses Consumed by Marine Protists. Front Microbiol 2020; 11:524828. [PMID: 33072003 PMCID: PMC7541821 DOI: 10.3389/fmicb.2020.524828] [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: 01/06/2020] [Accepted: 08/28/2020] [Indexed: 11/29/2022] Open
Abstract
The predominant model of the role of viruses in the marine trophic web is that of the “viral shunt,” where viral infection funnels a substantial fraction of the microbial primary and secondary production back to the pool of dissolved organic matter. Here, we analyzed the composition of non-eukaryotic DNA associated with individual cells of small, planktonic protists in the Gulf of Maine (GoM) and the Mediterranean Sea. We found viral DNA associated with a substantial fraction cells from the GoM (51%) and the Mediterranean Sea (35%). While Mediterranean SAGs contained a larger proportion of cells containing bacterial sequences (49%), a smaller fraction of cells contained bacterial sequences in the GoM (19%). In GoM cells, nearly identical bacteriophage and ssDNA virus sequences where found across diverse lineages of protists, suggesting many of these viruses are non-infective. The fraction of cells containing viral DNA varied among protistan lineages and reached 100% in Picozoa and Choanozoa. These two groups also contained significantly higher numbers of viral sequences than other identified taxa. We consider mechanisms that may explain the presence of viral DNA in protistan cells and conclude that protistan predation on free viral particles contributed to the observed patterns. These findings confirm prior experiments with protistan isolates and indicate that the viral shunt is complemented by a viral link in the marine microbial food web. This link may constitute a sink of viral particles in the ocean and has implications for the flow of carbon through the microbial food web.
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Affiliation(s)
- Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Jessica M Labonté
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, United States
| | - Joseph Brown
- Department of Human Genetics, University of Utah, Salt Lake City, UT, United States
| | - Nicholas R Record
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Nicole J Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Michael E Sieracki
- Division of Ocean Sciences, National Science Foundation, Alexandria, VA, United States
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
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57
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Enteric Viral Co-Infections: Pathogenesis and Perspective. Viruses 2020; 12:v12080904. [PMID: 32824880 PMCID: PMC7472086 DOI: 10.3390/v12080904] [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: 07/13/2020] [Revised: 08/10/2020] [Accepted: 08/14/2020] [Indexed: 02/06/2023] Open
Abstract
Enteric viral co-infections, infections involving more than one virus, have been reported for a diverse group of etiological agents, including rotavirus, norovirus, astrovirus, adenovirus, and enteroviruses. These pathogens are causative agents for acute gastroenteritis and diarrheal disease in immunocompetent and immunocompromised individuals of all ages globally. Despite virus–virus co-infection events in the intestine being increasingly detected, little is known about their impact on disease outcomes or human health. Here, we review what is currently known about the clinical prevalence of virus–virus co-infections and how co-infections may influence vaccine responses. While experimental investigations into enteric virus co-infections have been limited, we highlight in vivo and in vitro models with exciting potential to investigate viral co-infections. Many features of virus–virus co-infection mechanisms in the intestine remain unclear, and further research will be critical.
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58
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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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59
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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: 33] [Impact Index Per Article: 8.3] [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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60
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Khan Mirzaei M, Xue J, Costa R, Ru J, Schulz S, Taranu ZE, Deng L. Challenges of Studying the Human Virome - Relevant Emerging Technologies. Trends Microbiol 2020; 29:171-181. [PMID: 32622559 DOI: 10.1016/j.tim.2020.05.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 01/17/2023]
Abstract
In this review we provide an overview of current challenges and advances in bacteriophage research within the growing field of viromics. In particular, we discuss, from a human virome study perspective, the current and emerging technologies available, their limitations in terms of de novo discoveries, and possible solutions to overcome present experimental and computational biases associated with low abundance of viral DNA or RNA. We summarize recent breakthroughs in metagenomics assembling tools and single-cell analysis, which have the potential to increase our understanding of phage biology, diversity, and interactions with both the microbial community and the human body. We expect that these recent and future advances in the field of viromics will have a strong impact on how we develop phage-based therapeutic approaches.
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Affiliation(s)
- Mohammadali Khan Mirzaei
- Institute of Virology, Helmholtz Centre Munich and Technical University of Munich, Neuherberg, Bavaria 85764, Germany
| | - Jinling Xue
- Institute of Virology, Helmholtz Centre Munich and Technical University of Munich, Neuherberg, Bavaria 85764, Germany
| | - Rita Costa
- Institute of Virology, Helmholtz Centre Munich and Technical University of Munich, Neuherberg, Bavaria 85764, Germany
| | - Jinlong Ru
- Institute of Virology, Helmholtz Centre Munich and Technical University of Munich, Neuherberg, Bavaria 85764, Germany
| | - Sarah Schulz
- Institute of Virology, Helmholtz Centre Munich and Technical University of Munich, Neuherberg, Bavaria 85764, Germany
| | - Zofia E Taranu
- Aquatic Contaminants Research Division (ACRD), Environment and Climate Change Canada (ECCC), Montréal, QC H2Y 2E7, Canada
| | - Li Deng
- Institute of Virology, Helmholtz Centre Munich and Technical University of Munich, Neuherberg, Bavaria 85764, Germany.
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61
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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: 50] [Impact Index Per Article: 12.5] [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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Kieft K, Zhou Z, Anantharaman K. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. MICROBIOME 2020; 8:90. [PMID: 32522236 PMCID: PMC7288430 DOI: 10.1186/s40168-020-00867-0] [Citation(s) in RCA: 407] [Impact Index Per Article: 101.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/13/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Viruses are central to microbial community structure in all environments. The ability to generate large metagenomic assemblies of mixed microbial and viral sequences provides the opportunity to tease apart complex microbiome dynamics, but these analyses are currently limited by the tools available for analyses of viral genomes and assessing their metabolic impacts on microbiomes. DESIGN Here we present VIBRANT, the first method to utilize a hybrid machine learning and protein similarity approach that is not reliant on sequence features for automated recovery and annotation of viruses, determination of genome quality and completeness, and characterization of viral community function from metagenomic assemblies. VIBRANT uses neural networks of protein signatures and a newly developed v-score metric that circumvents traditional boundaries to maximize identification of lytic viral genomes and integrated proviruses, including highly diverse viruses. VIBRANT highlights viral auxiliary metabolic genes and metabolic pathways, thereby serving as a user-friendly platform for evaluating viral community function. VIBRANT was trained and validated on reference virus datasets as well as microbiome and virome data. RESULTS VIBRANT showed superior performance in recovering higher quality viruses and concurrently reduced the false identification of non-viral genome fragments in comparison to other virus identification programs, specifically VirSorter, VirFinder, and MARVEL. When applied to 120,834 metagenome-derived viral sequences representing several human and natural environments, VIBRANT recovered an average of 94% of the viruses, whereas VirFinder, VirSorter, and MARVEL achieved less powerful performance, averaging 48%, 87%, and 71%, respectively. Similarly, VIBRANT identified more total viral sequence and proteins when applied to real metagenomes. When compared to PHASTER, Prophage Hunter, and VirSorter for the ability to extract integrated provirus regions from host scaffolds, VIBRANT performed comparably and even identified proviruses that the other programs did not. To demonstrate applications of VIBRANT, we studied viromes associated with Crohn's disease to show that specific viral groups, namely Enterobacteriales-like viruses, as well as putative dysbiosis associated viral proteins are more abundant compared to healthy individuals, providing a possible viral link to maintenance of diseased states. CONCLUSIONS The ability to accurately recover viruses and explore viral impacts on microbial community metabolism will greatly advance our understanding of microbiomes, host-microbe interactions, and ecosystem dynamics. Video Abstract.
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Affiliation(s)
- Kristopher Kieft
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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63
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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: 67] [Impact Index Per Article: 16.8] [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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64
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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: 381] [Impact Index Per Article: 95.3] [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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65
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Diversity and Host Interactions Among Virulent and Temperate Baltic Sea Flavobacterium Phages. Viruses 2020; 12:v12020158. [PMID: 32019073 PMCID: PMC7077304 DOI: 10.3390/v12020158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 02/06/2023] Open
Abstract
Viruses in aquatic environments play a key role in microbial population dynamics and nutrient cycling. In particular, bacteria of the phylum Bacteriodetes are known to participate in recycling algal blooms. Studies of phage–host interactions involving this phylum are hence important to understand the processes shaping bacterial and viral communities in the ocean as well as nutrient cycling. In this study, we isolated and sequenced three strains of flavobacteria—LMO6, LMO9, LMO8—and 38 virulent phages infecting them. These phages represent 15 species, occupying three novel genera. Additionally, one temperate phage was induced from LMO6 and was found to be competent at infecting LMO9. Functions could be predicted for a limited number of phage genes, mainly representing roles in DNA replication and virus particle formation. No metabolic genes were detected. While the phages isolated on LMO8 could infect all three bacterial strains, the LMO6 and LMO9 phages could not infect LMO8. Of the phages isolated on LMO9, several showed a host-derived reduced efficiency of plating on LMO6, potentially due to differences in DNA methyltransferase genes. Overall, these phage–host systems contribute novel genetic information to our sequence databases and present valuable tools for the study of both virulent and temperate phages.
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66
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Hellweger FL. Combining Molecular Observations and Microbial Ecosystem Modeling: A Practical Guide. ANNUAL REVIEW OF MARINE SCIENCE 2020; 12:267-289. [PMID: 31226029 DOI: 10.1146/annurev-marine-010419-010829] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Advances in technologies for molecular observation are leading to novel types of data, including gene, transcript, protein, and metabolite levels, which are fundamentally different from the types traditionally compared with microbial ecosystem models, such as biomass (e.g., chlorophyll a) and nutrient concentrations. A grand challenge is to use these data to improve predictive models and use models to explain observed patterns. This article presents a framework that aligns observations and models along the dimension of abstraction or biological organization-from raw sequences to ecosystem patterns for observations, and from sequence simulators to ecological theory for models. It then reviews 16 studies that compared model results with molecular observations. Molecular data can and are being combined with microbial ecosystem models, but to keep up with and take advantage of the full scope of observations, models need to become more mechanistically detailed and complex, which is a technical and cultural challenge for the ecological modeling community.
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Affiliation(s)
- Ferdi L Hellweger
- Specialty Area of Water Quality Engineering (Wasserreinhaltung), Institute of Environmental Science and Engineering, Technical University of Berlin, 10623 Berlin, Germany;
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67
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Zimmerman AE, Howard-Varona C, Needham DM, John SG, Worden AZ, Sullivan MB, Waldbauer JR, Coleman ML. Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. Nat Rev Microbiol 2019; 18:21-34. [PMID: 31690825 DOI: 10.1038/s41579-019-0270-x] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2019] [Indexed: 12/23/2022]
Abstract
Ecosystems are controlled by 'bottom-up' (resources) and 'top-down' (predation) forces. Viral infection is now recognized as a ubiquitous top-down control of microbial growth across ecosystems but, at the same time, cell death by viral predation influences, and is influenced by, resource availability. In this Review, we discuss recent advances in understanding the biogeochemical impact of viruses, focusing on how metabolic reprogramming of host cells during lytic viral infection alters the flow of energy and nutrients in aquatic ecosystems. Our synthesis revealed several emerging themes. First, viral infection transforms host metabolism, in part through virus-encoded metabolic genes; the functions performed by these genes appear to alleviate energetic and biosynthetic bottlenecks to viral production. Second, viral infection depends on the physiological state of the host cell and on environmental conditions, which are challenging to replicate in the laboratory. Last, metabolic reprogramming of infected cells and viral lysis alter nutrient cycling and carbon export in the oceans, although the net impacts remain uncertain. This Review highlights the need for understanding viral infection dynamics in realistic physiological and environmental contexts to better predict their biogeochemical consequences.
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Affiliation(s)
- Amy E Zimmerman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | | | - David M Needham
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Seth G John
- Department of Earth Science, University of Southern California, Los Angeles, CA, USA
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, USA.,Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA
| | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA.
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68
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Potential Interactions between Clade SUP05 Sulfur-Oxidizing Bacteria and Phages in Hydrothermal Vent Sponges. Appl Environ Microbiol 2019; 85:AEM.00992-19. [PMID: 31492669 DOI: 10.1128/aem.00992-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/03/2019] [Indexed: 01/27/2023] Open
Abstract
In deep-sea hydrothermal vent environments, sulfur-oxidizing bacteria belonging to the clade SUP05 are crucial symbionts of invertebrate animals. Marine viruses, as the most abundant biological entities in the ocean, play essential roles in regulating the sulfur metabolism of the SUP05 bacteria. To date, vent sponge-associated SUP05 and their phages have not been well documented. The current study analyzed microbiomes of Haplosclerida sponges from hydrothermal vents in the Okinawa Trough and recovered the dominant SUP05 genome, designated VS-SUP05. Phylogenetic analysis showed that VS-SUP05 was closely related to endosymbiotic SUP05 strains from mussels living in deep-sea hydrothermal vent fields. Homology and metabolic pathway comparisons against free-living and symbiotic SUP05 strains revealed that the VS-SUP05 genome shared many features with the deep-sea mussel symbionts. Supporting a potentially symbiotic lifestyle, the VS-SUP05 genome contained genes involved in the synthesis of essential amino acids and cofactors that are desired by the host. Analysis of sponge-associated viral sequences revealed putative VS-SUP05 phages, all of which were double-stranded viruses belonging to the families Myoviridae, Siphoviridae, Podoviridae, and Microviridae Among the phage sequences, one contig contained metabolic genes (iscR, iscS, and iscU) involved in iron-sulfur cluster formation. Interestingly, genome sequence comparison revealed horizontal transfer of the iscS gene among phages, VS-SUP05, and other symbiotic SUP05 strains, indicating an interaction between marine phages and SUP05 symbionts. Overall, our findings confirm the presence of SUP05 bacteria and their phages in sponges from deep-sea vents and imply a beneficial interaction that allows adaptation of the host sponge to the hydrothermal vent environment.IMPORTANCE Chemosynthetic SUP05 bacteria dominate the microbial communities of deep-sea hydrothermal vents around the world, SUP05 bacteria utilize reduced chemical compounds in vent fluids and commonly form symbioses with invertebrate organisms. This symbiotic relationship could be key to adapting to such unique and extreme environments. Viruses are the most abundant biological entities on the planet and have been identified in hydrothermal vent environments. However, their interactions with the symbiotic microbes of the SUP05 clade, along with their role in the symbiotic system, remain unclear. Here, using metagenomic sequence-based analyses, we determined that bacteriophages may support metabolism in SUP05 bacteria and play a role in the sponge-associated symbiosis system in hydrothermal vent environments.
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69
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Cheng M, Cao L, Ning K. Microbiome Big-Data Mining and Applications Using Single-Cell Technologies and Metagenomics Approaches Toward Precision Medicine. Front Genet 2019; 10:972. [PMID: 31649735 PMCID: PMC6794611 DOI: 10.3389/fgene.2019.00972] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/12/2019] [Indexed: 12/20/2022] Open
Abstract
With the development of high-throughput sequencing technologies as well as various bioinformatics analytic tools, microbiome is not a “microbial dark matter” anymore. In this review, we first summarized the current analytical strategies used for big-data mining such as single-cell sequencing and metagenomics. We then provided insights into the integration of these strategies, showing significant advantages in fully describing microbiome from multiple aspects. Moreover, we discussed the correlation between gut microbiome with host organs and diseases, confirming the importance of big-data mining in clinical practices. We finally proposed new ideas about the trend of big-data mining in microbiome using multi-omics approaches and single-cell sequencing. The integration of multi-omics approaches and single-cell sequencing can provide full understanding of microbiome at both macroscopic level and microscopic level, thus contributing to precision medicine.
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Affiliation(s)
- Mingyue Cheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Le Cao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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70
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Castillo YM, Mangot J, Benites LF, Logares R, Kuronishi M, Ogata H, Jaillon O, Massana R, Sebastián M, Vaqué D. Assessing the viral content of uncultured picoeukaryotes in the global‐ocean by single cell genomics. Mol Ecol 2019; 28:4272-4289. [DOI: 10.1111/mec.15210] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 07/23/2019] [Accepted: 08/01/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Yaiza M. Castillo
- Department of Marine Biology and Oceanography Institute of Marine Sciences (ICM) CSIC Barcelona Spain
| | - Jean‐François Mangot
- Department of Marine Biology and Oceanography Institute of Marine Sciences (ICM) CSIC Barcelona Spain
| | - Luiz Felipe Benites
- Integrative Biology of Marine Organisms (BIOM) CNRS Oceanological Observatory of Banyuls Sorbonne University Banyuls‐sur‐Mer France
| | - Ramiro Logares
- Department of Marine Biology and Oceanography Institute of Marine Sciences (ICM) CSIC Barcelona Spain
| | - Megumi Kuronishi
- Bioinformatic Center Institute for Chemical Research Kyoto University Uji Japan
| | - Hiroyuki Ogata
- Bioinformatic Center Institute for Chemical Research Kyoto University Uji Japan
| | - Olivier Jaillon
- Génomique Métabolique Genoscope Institut de biologie François Jacob CEA CNRS Université d'Evry Université Paris‐Saclay Evry France
| | - Ramon Massana
- Department of Marine Biology and Oceanography Institute of Marine Sciences (ICM) CSIC Barcelona Spain
| | - Marta Sebastián
- Department of Marine Biology and Oceanography Institute of Marine Sciences (ICM) CSIC Barcelona Spain
- Institute of Oceanography and Global Change (IOCAG) University of Las Palmas de Gran Canaria Telde Spain
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography Institute of Marine Sciences (ICM) CSIC Barcelona Spain
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71
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Rates of Molecular Evolution in a Marine Synechococcus Phage Lineage. Viruses 2019; 11:v11080720. [PMID: 31390807 PMCID: PMC6722890 DOI: 10.3390/v11080720] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/27/2019] [Accepted: 07/31/2019] [Indexed: 12/30/2022] Open
Abstract
Cyanophages are characterized by vast genomic diversity and the formation of stable ecotypes over time. The evolution of phage diversity includes vertical processes, such as mutation, and horizontal processes, such as recombination and gene transfer. Here, we study the contribution of vertical and horizontal processes to short-term evolution of marine cyanophages. Analyzing time series data of Synechococcus-infecting Myoviridae ecotypes spanning up to 17 years, we found a high contribution of recombination relative to mutation (r/m) in all ecotypes. Additionally, we found a molecular clock of substitution and recombination in one ecotype, RIM8. The estimated RIM8 evolutionary rates are 2.2 genome-wide substitutions per year (1.275 × 10−5 substitutions/site/year) and 29 genome-wide nucleotide alterations due to recombination per year. We found 26 variable protein families, of which only two families have a predicted functional annotation, suggesting that they are auxiliary metabolic genes with bacterial homologs. A comparison of our rate estimates to other phage evolutionary rate estimates in the literature reveals a negative correlation of phage substitution rates with their genome size. A comparison to evolutionary rates in bacterial organisms further shows that phages have high rates of mutation and recombination compared to their bacterial hosts. We conclude that the increased recombination rate in phages likely contributes to their vast genomic diversity.
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72
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Kupczok A, Neve H, Huang KD, Hoeppner MP, Heller KJ, Franz CMAP, Dagan T. Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades. Mol Biol Evol 2019; 35:1147-1159. [PMID: 29688542 PMCID: PMC5913663 DOI: 10.1093/molbev/msy027] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The evolution of asexual organisms is driven not only by the inheritance of genetic modification but also by the acquisition of foreign DNA. The contribution of vertical and horizontal processes to genome evolution depends on their rates per year and is quantified by the ratio of recombination to mutation. These rates have been estimated for bacteria; however, no estimates have been reported for phages. Here, we delineate the contribution of mutation and recombination to dsDNA phage genome evolution. We analyzed 34 isolates of the 936 group of Siphoviridae phages using a Lactococcus lactis strain from a single dairy over 29 years. We estimate a constant substitution rate of 1.9 × 10−4 substitutions per site per year due to mutation that is within the range of estimates for eukaryotic RNA and DNA viruses. The reconstruction of recombination events reveals a constant rate of five recombination events per year and 4.5 × 10−3 nucleotide alterations due to recombination per site per year. Thus, the recombination rate exceeds the substitution rate, resulting in a relative effect of recombination to mutation (r/m) of ∼24 that is homogenous over time. Especially in the early transcriptional region, we detect frequent gene loss and regain due to recombination with phages of the 936 group, demonstrating the role of the 936 group pangenome as a reservoir of genetic variation. The observed substitution rate homogeneity conforms to the neutral theory of evolution; hence, the neutral theory can be applied to phage genome evolution and also to genetic variation brought about by recombination.
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Affiliation(s)
- Anne Kupczok
- Genomic Microbiology Group, Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Kiel, Germany
| | - Kun D Huang
- Genomic Microbiology Group, Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Marc P Hoeppner
- Institute of Clinical Molecular Biology (IKMB), Kiel University, Kiel, Germany
| | - Knut J Heller
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Kiel, Germany
| | - Tal Dagan
- Genomic Microbiology Group, Institute of General Microbiology, Kiel University, Kiel, Germany
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73
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Roux S, Brum JR. A viral reckoning: viruses emerge as essential manipulators of global ecosystems. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:3-8. [PMID: 30298570 DOI: 10.1111/1758-2229.12700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 09/30/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Simon Roux
- US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, 94598, USA
| | - Jennifer R Brum
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, 70808, USA
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74
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Woyke T, Schulz F. Entities inside one another - a matryoshka doll in biology? ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:26-28. [PMID: 30588764 PMCID: PMC7379638 DOI: 10.1111/1758-2229.12716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Tanja Woyke
- U.S. Department of Energy Joint Genome InstituteWalnut Creek, CA94598USA
| | - Frederik Schulz
- U.S. Department of Energy Joint Genome InstituteWalnut Creek, CA94598USA
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75
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Warwick-Dugdale J, Buchholz HH, Allen MJ, Temperton B. Host-hijacking and planktonic piracy: how phages command the microbial high seas. Virol J 2019; 16:15. [PMID: 30709355 PMCID: PMC6359870 DOI: 10.1186/s12985-019-1120-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 01/17/2019] [Indexed: 12/22/2022] Open
Abstract
Microbial communities living in the oceans are major drivers of global biogeochemical cycles. With nutrients limited across vast swathes of the ocean, marine microbes eke out a living under constant assault from predatory viruses. Viral concentrations exceed those of their bacterial prey by an order of magnitude in surface water, making these obligate parasites the most abundant biological entities in the ocean. Like the pirates of the 17th and 18th centuries that hounded ships plying major trade and exploration routes, viruses have evolved mechanisms to hijack microbial cells and repurpose their cargo and indeed the vessels themselves to maximise viral propagation. Phenotypic reconfiguration of the host is often achieved through Auxiliary Metabolic Genes - genes originally derived from host genomes but maintained and adapted in viral genomes to redirect energy and substrates towards viral synthesis. In this review, we critically evaluate the literature describing the mechanisms used by bacteriophages to reconfigure host metabolism and to plunder intracellular resources to optimise viral production. We also highlight the mechanisms used when, in challenging environments, a 'batten down the hatches' strategy supersedes that of 'plunder and pillage'. Here, the infecting virus increases host fitness through phenotypic augmentation in order to ride out the metaphorical storm, with a concomitant impact on host substrate uptake and metabolism, and ultimately, their interactions with their wider microbial community. Thus, the traditional view of the virus-host relationship as predator and prey does not fully characterise the variety or significance of the interactions observed. Recent advances in viral metagenomics have provided a tantalising glimpse of novel mechanisms of viral metabolic reprogramming in global oceans. Incorporation of these new findings into global biogeochemical models requires experimental evidence from model systems and major improvements in our ability to accurately predict protein function from sequence data.
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Affiliation(s)
- Joanna Warwick-Dugdale
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH UK
- University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD UK
| | - Holger H. Buchholz
- University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD UK
| | - Michael J. Allen
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH UK
- University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD UK
| | - Ben Temperton
- University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD UK
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76
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Abstract
Bacteriophages, discovered about a century ago, have been pivotal as models for understanding the fundamental principles of molecular biology. While interest in phage biology declined after the phage "golden era," key recent developments, including advances in phage genomics, microscopy, and the discovery of the CRISPR-Cas anti-phage defense system, have sparked a renaissance in phage research in the past decade. This review highlights recently discovered unexpected complexities in phage biology, describes a new arsenal of phage genes that help them overcome bacterial defenses, and discusses advances toward documentation of the phage biodiversity on a global scale.
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Affiliation(s)
- Gal Ofir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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77
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Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA. Minimum Information about an Uncultivated Virus Genome (MIUViG). Nat Biotechnol 2019; 37:29-37. [PMID: 30556814 PMCID: PMC6871006 DOI: 10.1038/nbt.4306] [Citation(s) in RCA: 326] [Impact Index Per Article: 65.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 11/01/2018] [Indexed: 12/22/2022]
Abstract
We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.
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Affiliation(s)
- Simon Roux
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | | | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland USA
| | - Andrew M Kropinski
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario Canada
| | - Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Paris, France
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland USA
| | - Rob Lavigne
- KU Leuven, Laboratory of Gene Technology, Heverlee, Belgium
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland USA
| | - Arvind Varsani
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona USA
- Department of Integrative Biomedical Sciences, Structural Biology Research Unit, University of Cape Town, Observatory, Cape Town, South Africa
| | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Seth R Bordenstein
- Departments of Biological Sciences and Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee USA
| | - Peer Bork
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, Florida USA
| | - Guy R Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Rebecca A Daly
- Soil and Crop Sciences Department, Colorado State University, Fort Collins, Colorado USA
| | - Christelle Desnues
- Aix-Marseille Université, CNRS, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Melissa B Duhaime
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan USA
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, Davis, California USA
| | - François Enault
- LMGE,UMR 6023 CNRS, Université Clermont Auvergne, Aubiére, France
| | - Jed A Fuhrman
- University of Southern California, Los Angeles, Los Angeles, California USA
| | - Pascal Hingamp
- Aix Marseille Université,
- , Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland Australia
| | - Bonnie L Hurwitz
- Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, Arizona USA
- BIO5 Research Institute, University of Arizona, Tucson, Arizona USA
| | - Natalia N Ivanova
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Jessica M Labonté
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, Texas USA
| | - Kyung-Bum Lee
- DDBJ Center, National Institute of Genetics, Mishima, Shizuoka Japan
| | - Rex R Malmstrom
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Ilene Karsch Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland USA
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Uji, Japan
| | - David Páez-Espino
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Marie-Agnès Petit
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Catherine Putonti
- Department of Biology, Loyola University Chicago, Chicago, Illinois USA
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois USA
- Department of Computer Science, Loyola University Chicago, Chicago, Illinois USA
| | - Thomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry Meets Microbiology,” University of Vienna, Vienna, Austria
| | - Alejandro Reyes
- Department of Biological Sciences, Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia
| | - Francisco Rodriguez-Valera
- Departamento de Producción Vegetal y Microbiología, Evolutionary Genomics Group, Universidad Miguel Hernández, Alicante, Spain
| | - Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, Florida USA
| | - Lynn Schriml
- University of Maryland School of Medicine, Baltimore, Maryland USA
| | - Frederik Schulz
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Grieg F Steward
- Department of Oceanography, Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, Hawai'i USA
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, Ohio USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio USA
| | | | - Curtis A Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia Canada
- Institute of Oceans and Fisheries, University of British Columbia, Vancouver, British Columbia Canada
| | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, UK
| | - Susannah G Tringe
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | | | - Nicole S Webster
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland Australia
- Australian Institute of Marine Science, Townsville, Queensland Australia
| | - Katrine L Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California USA
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee USA
| | - K Eric Wommack
- University of Delaware, Delaware Biotechnology Institute, Newark, Delaware USA
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Kelly C Wrighton
- Soil and Crop Sciences Department, Colorado State University, Fort Collins, Colorado USA
| | - Pelin Yilmaz
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Kyoto, Japan
| | - Mark J Young
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland USA
| | - Lisa Zeigler Allen
- J Craig Venter Institute, La Jolla, California USA
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA.,
| | - Nikos C Kyrpides
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
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78
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Keen EC, Dantas G. Close Encounters of Three Kinds: Bacteriophages, Commensal Bacteria, and Host Immunity. Trends Microbiol 2018; 26:943-954. [PMID: 29909042 PMCID: PMC6436384 DOI: 10.1016/j.tim.2018.05.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/08/2018] [Accepted: 05/17/2018] [Indexed: 12/22/2022]
Abstract
Recent years have witnessed an explosion of interest in the human microbiota. Although commensal bacteria have dominated research efforts to date, mounting evidence suggests that endogenous viral populations (the 'virome') play key roles in basic human physiology. The most numerous constituents of the human virome are not eukaryotic viruses but rather bacteriophages, viruses that infect bacteria. Here, we review phages' interactions with their immediate (prokaryotic) and extended (eukaryotic) hosts and with each other, with a particular emphasis on the temperate phages and prophages which dominate the human virome. We also discuss key outstanding questions in this emerging field and emphasize the urgent need for functional studies in animal models to complement previous in vitro work and current computational approaches.
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Affiliation(s)
- Eric C Keen
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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79
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Parvathi A, Jasna V, Aparna S, Pradeep Ram AS, Aswathy VK, Balachandran KK, Muraleedharan KR, Mathew D, Sime-Ngando T. High Incidence of Lysogeny in the Oxygen Minimum Zones of the Arabian Sea (Southwest Coast of India). Viruses 2018; 10:v10110588. [PMID: 30373217 PMCID: PMC6267222 DOI: 10.3390/v10110588] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/19/2018] [Accepted: 09/20/2018] [Indexed: 12/24/2022] Open
Abstract
Though microbial processes in the oxygen minimum zones (OMZs) of the Arabian Sea (AS) are well documented, prokaryote-virus interactions are less known. The present study was carried out to determine the potential physico-chemical factors influencing viral abundances and their life strategies (lytic and lysogenic) along the vertical gradient in the OMZ of the AS (southwest coast of India). Water samples were collected during the southwest monsoon (SWM) season in two consecutive years (2015 and 2016) from different depths, namely, the surface layer, secondary chlorophyll a maxima (~30–40 m), oxycline (~70–80 m), and hypoxic/suboxic layers (~200–350 m). The high viral abundances observed in oxygenated surface waters (mean ± SD = 6.1 ± 3.4 × 106 viral-like particles (VLPs) mL−1), drastically decreased with depth in the oxycline region (1.2 ± 0.5 × 106 VLPs mL−1) and hypoxic/suboxic waters (0.3 ± 0.3 × 106 VLPs mL−1). Virus to prokaryote ratio fluctuated in the mixed layer (~10) and declined significantly (p < 0.001) to 1 in the hypoxic layer. Viral production (VP) and frequency of virus infected cells (FIC) were maximum in the surface and minimum in the oxycline layer, whereas the viral lysis was undetectable in the suboxic/hypoxic layer. The detection of a high percentage of lysogeny in suboxic (48%) and oxycline zones (9–24%), accompanied by undetectable rates of lytic viral infection support the hypothesis that lysogeny may represent the major survival strategy for viruses in unproductive or harsh nutrient/host conditions in deoxygenated waters.
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Affiliation(s)
- Ammini Parvathi
- CSIR-National Institute of Oceanography, Regional Centre (CSIR), Kochi 682 018, India.
| | - Vijayan Jasna
- CSIR-National Institute of Oceanography, Regional Centre (CSIR), Kochi 682 018, India.
| | - Sreekumar Aparna
- CSIR-National Institute of Oceanography, Regional Centre (CSIR), Kochi 682 018, India.
| | - Angia Sriram Pradeep Ram
- Laboratoire Microorganismes, Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, 1 Impasse Amélie Murat, 63178 Aubière CEDEX, France.
| | | | | | | | - Dayana Mathew
- CSIR-National Institute of Oceanography, Regional Centre (CSIR), Kochi 682 018, India.
| | - Telesphore Sime-Ngando
- Laboratoire Microorganismes, Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, 1 Impasse Amélie Murat, 63178 Aubière CEDEX, France.
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80
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Ahlgren NA, Fuchsman CA, Rocap G, Fuhrman JA. Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes. ISME JOURNAL 2018; 13:618-631. [PMID: 30315316 DOI: 10.1038/s41396-018-0289-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 06/15/2018] [Accepted: 09/19/2018] [Indexed: 12/22/2022]
Abstract
Much of the diversity of prokaryotic viruses has yet to be described. In particular, there are no viral isolates that infect abundant, globally significant marine archaea including the phylum Thaumarchaeota. This phylum oxidizes ammonia, fixes inorganic carbon, and thus contributes to globally significant nitrogen and carbon cycles in the oceans. Metagenomics provides an alternative to culture-dependent means for identifying and characterizing viral diversity. Some viruses carry auxiliary metabolic genes (AMGs) that are acquired via horizontal gene transfer from their host(s), allowing inference of what host a virus infects. Here we present the discovery of 15 new genomically and ecologically distinct Thaumarchaeota virus populations, identified as contigs that encode viral capsid and thaumarchaeal ammonia monooxygenase genes (amoC). These viruses exhibit depth and latitude partitioning and are distributed globally in various marine habitats including pelagic waters, estuarine habitats, and hydrothermal plume water and sediments. We found evidence of viral amoC expression and that viral amoC AMGs sometimes comprise up to half of total amoC DNA copies in cellular fraction metagenomes, highlighting the potential impact of these viruses on N cycling in the oceans. Phylogenetics suggest they are potentially tailed viruses and share a common ancestor with related marine Euryarchaeota viruses. This work significantly expands our view of viruses of globally important marine Thaumarchaeota.
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Affiliation(s)
- Nathan A Ahlgren
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA. .,Clark University, Worcester, MA, USA.
| | - Clara A Fuchsman
- School of Oceanography, University of Washington, Seattle, WA, USA.,Horn Point Laboratory, University of Maryland, Cambridge, MD, USA
| | - Gabrielle Rocap
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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81
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Martinez-Hernandez F, Fornas Ò, Lluesma Gomez M, Garcia-Heredia I, Maestre-Carballa L, López-Pérez M, Haro-Moreno JM, Rodriguez-Valera F, Martinez-Garcia M. Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean. ISME JOURNAL 2018; 13:232-236. [PMID: 30228380 DOI: 10.1038/s41396-018-0278-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/31/2018] [Accepted: 08/26/2018] [Indexed: 11/09/2022]
Abstract
The identification of relevant virus-host pairs that globally account for a large pool of carbon and nutrients in the ocean is paramount to build accurate ecological models. A previous work using single-virus genomics led to the discovery of the uncultured single-virus vSAG 37-F6, originally sorted from the Mediterranean Sea (Blanes Bay Microbial Observatory), that represents one of the most abundant dsDNA viral population in the marine surface virosphere. Here, from same sampling site, we report that a Pelagibacter single-cell contained a viral member of vSAG 37-F6 population, by means of PCR screening of sorted, genome-amplified single cells with vSAG 37-F6-specific primers and whole-genome sequencing. Furthermore, viruses from this population were also found in three other Pelagibacter single cells from the South Pacific and Atlantic oceans. These new uncultured pelagiphages were genetically different from the previously characterized pelagiphage isolates. Data showed that the uncultured vSAG 37-F6 population represents the Pelagibacter phages that inhabit the sunlit ocean better, and contains a vast unrecognized microdiversity.
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Affiliation(s)
| | - Òscar Fornas
- Flow Cytometry Unit: Pompeu Fabra University (UPF) and Centre for Genomic Regulation (CRG), The Barcelona Institute for Sciences and Technology (BIST), Barcelona, Spain
| | - Monica Lluesma Gomez
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | | | - Lucia Maestre-Carballa
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan, Alicante, 03550, Spain
| | - Jose M Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan, Alicante, 03550, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan, Alicante, 03550, Spain
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain.
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82
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Xu Y, Zhang R, Wang N, Cai L, Tong Y, Sun Q, Chen F, Jiao N. Novel phage-host interactions and evolution as revealed by a cyanomyovirus isolated from an estuarine environment. Environ Microbiol 2018; 20:2974-2989. [DOI: 10.1111/1462-2920.14326] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 06/09/2018] [Accepted: 06/13/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Yongle Xu
- Institute of Marine Science and Technology; Shandong University; Qingdao China
- School of Life Science; Shandong University; Qingdao China
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
| | - Rui Zhang
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
- State Key Laboratory of Marine Environmental Sciences, College of Ocean & Earth Sciences; Xiamen University; Xiamen China
| | - Nannan Wang
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
- State Key Laboratory of Marine Environmental Sciences, College of Ocean & Earth Sciences; Xiamen University; Xiamen China
| | - Lanlan Cai
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
- State Key Laboratory of Marine Environmental Sciences, College of Ocean & Earth Sciences; Xiamen University; Xiamen China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity; Beijing Institute of Microbiology and Epidemiology; Beijing China
| | - Qiang Sun
- State Key Laboratory of Pathogen and Biosecurity; Beijing Institute of Microbiology and Epidemiology; Beijing China
| | - Feng Chen
- Institute of Marine Science and Technology; Shandong University; Qingdao China
- Institute of Marine and Environmental Technology; University of Maryland Center for Environmental Science; Baltimore MD USA
| | - Nianzhi Jiao
- Institute of Marine Science and Technology; Shandong University; Qingdao China
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
- State Key Laboratory of Marine Environmental Sciences, College of Ocean & Earth Sciences; Xiamen University; Xiamen China
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83
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Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities. mSystems 2018; 3:mSystems00084-18. [PMID: 30175237 PMCID: PMC6113591 DOI: 10.1128/msystems.00084-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/24/2018] [Indexed: 11/25/2022] Open
Abstract
Inferring interactions from population time series is an active and ongoing area of research. It is relevant across many biological systems—particularly in virus-microbe communities, but also in gene regulatory networks, neural networks, and ecological communities broadly. Correlation-based inference—using correlations to predict interactions—is widespread. However, it is well-known that “correlation does not imply causation.” Despite this, many studies apply correlation-based inference methods to experimental time series without first assessing the potential scope for accurate inference. Here, we find that several correlation-based inference methods fail to recover interactions within in silico virus-microbe communities, raising questions on their relevance when applied in situ. Microbes are present in high abundances in the environment and in human-associated microbiomes, often exceeding 1 million per ml. Viruses of microbes are present in even higher abundances and are important in shaping microbial populations, communities, and ecosystems. Given the relative specificity of viral infection, it is essential to identify the functional linkages between viruses and their microbial hosts, particularly given dynamic changes in virus and host abundances. Multiple approaches have been proposed to infer infection networks from time series of in situ communities, among which correlation-based approaches have emerged as the de facto standard. In this work, we evaluate the accuracy of correlation-based inference methods using an in silico approach. In doing so, we compare predicted networks to actual networks to assess the self-consistency of correlation-based inference. At odds with assumptions underlying its widespread use, we find that correlation is a poor predictor of interactions in the context of viral infection and lysis of microbial hosts. The failure to predict interactions holds for methods that leverage product-moment, time-lagged, and relative-abundance-based correlations. In closing, we discuss alternative inference methods, particularly model-based methods, as a means to infer interactions in complex microbial communities with viruses. IMPORTANCE Inferring interactions from population time series is an active and ongoing area of research. It is relevant across many biological systems—particularly in virus-microbe communities, but also in gene regulatory networks, neural networks, and ecological communities broadly. Correlation-based inference—using correlations to predict interactions—is widespread. However, it is well-known that “correlation does not imply causation.” Despite this, many studies apply correlation-based inference methods to experimental time series without first assessing the potential scope for accurate inference. Here, we find that several correlation-based inference methods fail to recover interactions within in silico virus-microbe communities, raising questions on their relevance when applied in situ.
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84
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Breitbart M, Bonnain C, Malki K, Sawaya NA. Phage puppet masters of the marine microbial realm. Nat Microbiol 2018; 3:754-766. [PMID: 29867096 DOI: 10.1038/s41564-018-0166-y] [Citation(s) in RCA: 322] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 04/20/2018] [Indexed: 11/09/2022]
Abstract
Viruses numerically dominate our oceans; however, we have only just begun to document the diversity, host range and infection dynamics of marine viruses, as well as the subsequent effects of infection on both host cell metabolism and oceanic biogeochemistry. Bacteriophages (that is, phages: viruses that infect bacteria) are highly abundant and are known to play critical roles in bacterial mortality, biogeochemical cycling and horizontal gene transfer. This Review Article summarizes current knowledge of marine viral ecology and highlights the importance of phage particles to the dissolved organic matter pool, as well as the complex interactions between phages and their bacterial hosts. We emphasize the newly recognized roles of phages as puppet masters of their bacterial hosts, where phages are capable of altering the metabolism of infected bacteria through the expression of auxiliary metabolic genes and the redirection of host gene expression patterns. Finally, we propose the 'royal family model' as a hypothesis to describe successional patterns of bacteria and phages over time in marine systems, where despite high richness and significant seasonal differences, only a small number of phages appear to continually dominate a given marine ecosystem. Although further testing is required, this model provides a framework for assessing the specificity and ecological consequences of phage-host dynamics.
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Affiliation(s)
- Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA.
| | - Chelsea Bonnain
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Kema Malki
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Natalie A Sawaya
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
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85
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Munson-McGee JH, Peng S, Dewerff S, Stepanauskas R, Whitaker RJ, Weitz JS, Young MJ. A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extreme environments. THE ISME JOURNAL 2018; 12:1706-1714. [PMID: 29467398 PMCID: PMC6018696 DOI: 10.1038/s41396-018-0071-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 12/04/2017] [Accepted: 12/20/2017] [Indexed: 01/23/2023]
Abstract
The application of viral and cellular metagenomics to natural environments has expanded our understanding of the structure, functioning, and diversity of microbial and viral communities. The high diversity of many communities, e.g., soils, surface ocean waters, and animal-associated microbiomes, make it difficult to establish virus-host associations at the single cell (rather than population) level, assign cellular hosts, or determine the extent of viral host range from metagenomics studies alone. Here, we combine single-cell sequencing with environmental metagenomics to characterize the structure of virus-host associations in a Yellowstone National Park (YNP) hot spring microbial community. Leveraging the relatively low diversity of the YNP environment, we are able to overlay evidence at the single-cell level with contextualized viral and cellular community structure. Combining evidence from hexanucelotide analysis, single cell read mapping, network-based analytics, and CRISPR-based inference, we conservatively estimate that >60% of cells contain at least one virus type and a majority of these cells contain two or more virus types. Of the detected virus types, nearly 50% were found in more than 2 cellular clades, indicative of a broad host range. The new lens provided by the combination of metaviromics and single-cell genomics reveals a network of virus-host interactions in extreme environments, provides evidence that extensive virus-host associations are common, and further expands the unseen impact of viruses on cellular life.
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Affiliation(s)
- Jacob H Munson-McGee
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - Shengyun Peng
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Samantha Dewerff
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | - Rachel J Whitaker
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Mark J Young
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA.
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, USA.
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86
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Xu Y, Zhao F. Single-cell metagenomics: challenges and applications. Protein Cell 2018; 9:501-510. [PMID: 29696589 PMCID: PMC5960468 DOI: 10.1007/s13238-018-0544-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 04/18/2018] [Indexed: 02/01/2023] Open
Abstract
With the development of high throughput sequencing and single-cell genomics technologies, many uncultured bacterial communities have been dissected by combining these two techniques. Especially, by simultaneously leveraging of single-cell genomics and metagenomics, researchers can greatly improve the efficiency and accuracy of obtaining whole genome information from complex microbial communities, which not only allow us to identify microbes but also link function to species, identify subspecies variations, study host-virus interactions and etc. Here, we review recent developments and the challenges need to be addressed in single-cell metagenomics, including potential contamination, uneven sequence coverage, sequence chimera, genome assembly and annotation. With the development of sequencing and computational methods, single-cell metagenomics will undoubtedly broaden its application in various microbiome studies.
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Affiliation(s)
- Yuan Xu
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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87
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Archaeal Viruses from High-Temperature Environments. Genes (Basel) 2018; 9:genes9030128. [PMID: 29495485 PMCID: PMC5867849 DOI: 10.3390/genes9030128] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/19/2018] [Accepted: 02/21/2018] [Indexed: 12/21/2022] Open
Abstract
Archaeal viruses are some of the most enigmatic viruses known, due to the small number that have been characterized to date. The number of known archaeal viruses lags behind known bacteriophages by over an order of magnitude. Despite this, the high levels of genetic and morphological diversity that archaeal viruses display has attracted researchers for over 45 years. Extreme natural environments, such as acidic hot springs, are almost exclusively populated by Archaea and their viruses, making these attractive environments for the discovery and characterization of new viruses. The archaeal viruses from these environments have provided insights into archaeal biology, gene function, and viral evolution. This review focuses on advances from over four decades of archaeal virology, with a particular focus on archaeal viruses from high temperature environments, the existing challenges in understanding archaeal virus gene function, and approaches being taken to overcome these limitations.
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88
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Peering into the Genetic Makeup of Natural Microbial Populations Using Metagenomics. POPULATION GENOMICS: MICROORGANISMS 2018. [DOI: 10.1007/13836_2018_14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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89
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Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients. Nat Commun 2017; 8:1507. [PMID: 29142241 PMCID: PMC5688066 DOI: 10.1038/s41467-017-01376-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 09/11/2017] [Indexed: 12/22/2022] Open
Abstract
Microbial communities drive biogeochemical cycles through networks of metabolite exchange that are structured along energetic gradients. As energy yields become limiting, these networks favor co-metabolic interactions to maximize energy disequilibria. Here we apply single-cell genomics, metagenomics, and metatranscriptomics to study bacterial populations of the abundant "microbial dark matter" phylum Marinimicrobia along defined energy gradients. We show that evolutionary diversification of major Marinimicrobia clades appears to be closely related to energy yields, with increased co-metabolic interactions in more deeply branching clades. Several of these clades appear to participate in the biogeochemical cycling of sulfur and nitrogen, filling previously unassigned niches in the ocean. Notably, two Marinimicrobia clades, occupying different energetic niches, express nitrous oxide reductase, potentially acting as a global sink for the greenhouse gas nitrous oxide.
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90
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Analysis of single-cell genome sequences of bacteria and archaea. Emerg Top Life Sci 2017; 1:249-255. [PMID: 33525806 PMCID: PMC7289031 DOI: 10.1042/etls20160028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/29/2017] [Accepted: 08/31/2017] [Indexed: 11/17/2022]
Abstract
Single-cell genome sequencing of individual archaeal and bacterial cells is a vital approach to decipher the genetic makeup of uncultured microorganisms. With this review, we describe single-cell genome analysis with a focus on the unique properties of single-cell sequence data and with emphasis on quality assessment and assurance.
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91
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Hawley AK, Torres-Beltrán M, Zaikova E, Walsh DA, Mueller A, Scofield M, Kheirandish S, Payne C, Pakhomova L, Bhatia M, Shevchuk O, Gies EA, Fairley D, Malfatti SA, Norbeck AD, Brewer HM, Pasa-Tolic L, del Rio TG, Suttle CA, Tringe S, Hallam SJ. A compendium of multi-omic sequence information from the Saanich Inlet water column. Sci Data 2017; 4:170160. [PMID: 29087368 PMCID: PMC5663217 DOI: 10.1038/sdata.2017.160] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 08/02/2017] [Indexed: 01/08/2023] Open
Abstract
Marine oxygen minimum zones (OMZs) are widespread regions of the ocean that are currently expanding due to global warming. While inhospitable to most metazoans, OMZs are hotspots for microbial mediated biogeochemical cycling of carbon, nitrogen and sulphur, contributing disproportionately to marine nitrogen loss and climate active trace gas production. Our current understanding of microbial community responses to OMZ expansion is limited by a lack of time-resolved data sets linking multi-omic sequence information (DNA, RNA, protein) to geochemical parameters and process rates. Here, we present six years of time-resolved multi-omic observations in Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia, Canada that undergoes recurring changes in water column oxygenation status. This compendium provides a unique multi-omic framework for studying microbial community responses to ocean deoxygenation along defined geochemical gradients in OMZ waters.
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Affiliation(s)
- Alyse K. Hawley
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Mónica Torres-Beltrán
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Elena Zaikova
- Department of Biology, Georgetown University,
Washington, District Of Columbia 20057,
USA
| | - David A. Walsh
- Department of Biology, Concordia University,
Montreal, Quebec, Canada H4B 1R6
| | - Andreas Mueller
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Melanie Scofield
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Sam Kheirandish
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Chris Payne
- Earth, Ocean and Atmospheric Sciences, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Larysa Pakhomova
- Earth, Ocean and Atmospheric Sciences, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Maya Bhatia
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Olena Shevchuk
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Esther A. Gies
- Department of Civil Engineering, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Diane Fairley
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | | | - Angela D. Norbeck
- Biological and Computational Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington
99352, USA
| | - Heather M. Brewer
- Biological and Computational Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington
99352, USA
| | - Ljiljana Pasa-Tolic
- Biological and Computational Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington
99352, USA
| | | | - Curtis A. Suttle
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
- Earth, Ocean and Atmospheric Sciences, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
- Department of Botany, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Susannah Tringe
- Department of Energy Joint Genome Institute,
Walnut Creek, California 94598, USA
| | - Steven J. Hallam
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
- Peter Wall Institute for Advanced Studies, University of
British Columbia, Canada V6T 1Z2
- Genome Science and Technology Program, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z3
- Graduate Program in Bioinformatics, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z3
- ECOSCOPE Training Program, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z3
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92
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The trajectory of microbial single-cell sequencing. Nat Methods 2017; 14:1045-1054. [DOI: 10.1038/nmeth.4469] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 08/04/2017] [Indexed: 12/21/2022]
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93
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López-Pérez M, Haro-Moreno JM, Gonzalez-Serrano R, Parras-Moltó M, Rodriguez-Valera F. Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters. PLoS Genet 2017; 13:e1007018. [PMID: 28945750 PMCID: PMC5628999 DOI: 10.1371/journal.pgen.1007018] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/05/2017] [Accepted: 09/13/2017] [Indexed: 11/18/2022] Open
Abstract
Marine viruses play a critical role not only in the global geochemical cycles but also in the biology and evolution of their hosts. Despite their importance, viral diversity remains underexplored mostly due to sampling and cultivation challenges. Direct sequencing approaches such as viromics has provided new insights into the marine viral world. As a complementary approach, we analysed 24 microbial metagenomes (>0.2 μm size range) obtained from six sites in the Mediterranean Sea that vary by depth, season and filter used to retrieve the fraction. Filter-size comparison showed a significant number of viral sequences that were retained on the larger-pore filters and were different from those found in the viral fraction from the same sample, indicating that some important viral information is missing using only assembly from viromes. Besides, we were able to describe 1,323 viral genomic fragments that were more than 10Kb in length, of which 36 represented complete viral genomes including some of them retrieved from a cross-assembly from different metagenomes. Host prediction based on sequence methods revealed new phage groups belonging to marine prokaryotes like SAR11, Cyanobacteria or SAR116. We also identified the first complete virophage from deep seawater and a new endemic clade of the recently discovered Marine group II Euryarchaeota virus. Furthermore, analysis of viral distribution using metagenomes and viromes indicated that most of the new phages were found exclusively in the Mediterranean Sea and some of them, mostly the ones recovered from deep metagenomes, do not recruit in any database probably indicating higher variability and endemicity in Mediterranean bathypelagic waters. Together these data provide the first detailed picture of genomic diversity, spatial and depth variations of viral communities within the Mediterranean Sea using metagenome assembly.
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Affiliation(s)
- Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Campus de San Juan, San Juan de Alicante, Spain
| | - Jose M. Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Campus de San Juan, San Juan de Alicante, Spain
| | - Rafael Gonzalez-Serrano
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Campus de San Juan, San Juan de Alicante, Spain
| | - Marcos Parras-Moltó
- Centro de Biología Molecular 'Severo Ochoa' (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Cantoblanco, Madrid, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Campus de San Juan, San Juan de Alicante, Spain
- * E-mail:
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94
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Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles. Nat Commun 2017; 8:84. [PMID: 28729688 PMCID: PMC5519541 DOI: 10.1038/s41467-017-00128-z] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/02/2017] [Indexed: 01/13/2023] Open
Abstract
Microbial single-cell genomics can be used to provide insights into the metabolic potential, interactions, and evolution of uncultured microorganisms. Here we present WGA-X, a method based on multiple displacement amplification of DNA that utilizes a thermostable mutant of the phi29 polymerase. WGA-X enhances genome recovery from individual microbial cells and viral particles while maintaining ease of use and scalability. The greatest improvements are observed when amplifying high G+C content templates, such as those belonging to the predominant bacteria in agricultural soils. By integrating WGA-X with calibrated index-cell sorting and high-throughput genomic sequencing, we are able to analyze genomic sequences and cell sizes of hundreds of individual, uncultured bacteria, archaea, protists, and viral particles, obtained directly from marine and soil samples, in a single experiment. This approach may find diverse applications in microbiology and in biomedical and forensic studies of humans and other multicellular organisms. Single-cell genomics can be used to study uncultured microorganisms. Here, Stepanauskas et al. present a method combining improved multiple displacement amplification and FACS, to obtain genomic sequences and cell size information from uncultivated microbial cells and viral particles in environmental samples.
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95
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Doud DFR, Woyke T. Novel approaches in function-driven single-cell genomics. FEMS Microbiol Rev 2017; 41:538-548. [PMID: 28591840 PMCID: PMC5812545 DOI: 10.1093/femsre/fux009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/21/2017] [Indexed: 12/27/2022] Open
Abstract
Deeper sequencing and improved bioinformatics in conjunction with single-cell and metagenomic approaches continue to illuminate undercharacterized environmental microbial communities. This has propelled the 'who is there, and what might they be doing' paradigm to the uncultivated and has already radically changed the topology of the tree of life and provided key insights into the microbial contribution to biogeochemistry. While characterization of 'who' based on marker genes can describe a large fraction of the community, answering 'what are they doing' remains the elusive pinnacle for microbiology. Function-driven single-cell genomics provides a solution by using a function-based screen to subsample complex microbial communities in a targeted manner for the isolation and genome sequencing of single cells. This enables single-cell sequencing to be focused on cells with specific phenotypic or metabolic characteristics of interest. Recovered genomes are conclusively implicated for both encoding and exhibiting the feature of interest, improving downstream annotation and revealing activity levels within that environment. This emerging approach has already improved our understanding of microbial community functioning and facilitated the experimental analysis of uncharacterized gene product space. Here we provide a comprehensive review of strategies that have been applied for function-driven single-cell genomics and the future directions we envision.
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Affiliation(s)
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
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96
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Collingro A, Köstlbacher S, Mussmann M, Stepanauskas R, Hallam SJ, Horn M. Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae. ISME JOURNAL 2017. [PMID: 28644443 PMCID: PMC5604735 DOI: 10.1038/ismej.2017.95] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chlamydiae are obligate intracellular bacteria comprising important human pathogens and symbionts of protists. Molecular evidence indicates a tremendous diversity of chlamydiae particularly in marine environments, yet our current knowledge is based mainly on terrestrial representatives. Here we provide first insights into the biology of marine chlamydiae representing three divergent clades. Our analysis of single-cell amplified genomes revealed hallmarks of the chlamydial lifestyle, supporting the ancient origin of their characteristic developmental cycle and major virulence mechanisms. Surprisingly, these chlamydial genomes encode a complete flagellar apparatus, a previously unreported feature. We show that flagella are an ancient trait that was subject to differential gene loss among extant chlamydiae. Together with a chemotaxis system, these marine chlamydiae are likely motile, with flagella potentially playing a role during host cell infection. This study broadens our view on chlamydial biology and indicates a largely underestimated potential to adapt to different hosts and environments.
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Affiliation(s)
- Astrid Collingro
- Department of Microbial and Ecosystems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Stephan Köstlbacher
- Department of Microbial and Ecosystems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Marc Mussmann
- Department of Microbial and Ecosystems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | | | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.,Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada.,Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada.,Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, British Columbia, Canada.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthias Horn
- Department of Microbial and Ecosystems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
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97
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Genomic exploration of individual giant ocean viruses. ISME JOURNAL 2017; 11:1736-1745. [PMID: 28498373 DOI: 10.1038/ismej.2017.61] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 03/02/2017] [Accepted: 03/08/2017] [Indexed: 12/16/2022]
Abstract
Viruses are major pathogens in all biological systems. Virus propagation and downstream analysis remains a challenge, particularly in the ocean where the majority of their microbial hosts remain recalcitrant to current culturing techniques. We used a cultivation-independent approach to isolate and sequence individual viruses. The protocol uses high-speed fluorescence-activated virus sorting flow cytometry, multiple displacement amplification (MDA), and downstream genomic sequencing. We focused on 'giant viruses' that are readily distinguishable by flow cytometry. From a single-milliliter sample of seawater collected from off the dock at Boothbay Harbor, ME, USA, we sorted almost 700 single virus particles, and subsequently focused on a detailed genome analysis of 12. A wide diversity of viruses was identified that included Iridoviridae, extended Mimiviridae and even a taxonomically novel (unresolved) giant virus. We discovered a viral metacaspase homolog in one of our sorted virus particles and discussed its implications in rewiring host metabolism to enhance infection. In addition, we demonstrated that viral metacaspases are widespread in the ocean. We also discovered a virus that contains both a reverse transcriptase and a transposase; although highly speculative, we suggest such a genetic complement would potentially allow this virus to exploit a latency propagation mechanism. Application of single virus genomics provides a powerful opportunity to circumvent cultivation of viruses, moving directly to genomic investigation of naturally occurring viruses, with the assurance that the sequence data is virus-specific, non-chimeric and contains no cellular contamination.
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98
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Bolduc B, Jang HB, Doulcier G, You ZQ, Roux S, Sullivan MB. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. PeerJ 2017; 5:e3243. [PMID: 28480138 PMCID: PMC5419219 DOI: 10.7717/peerj.3243] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/28/2017] [Indexed: 12/15/2022] Open
Abstract
Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome 'sequence space' that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.
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Affiliation(s)
- Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH, United States
| | - Ho Bin Jang
- Department of Microbiology, Ohio State University, Columbus, OH, United States
| | - Guilhem Doulcier
- Institut de Biologie de l’ENS (IBENS), École normale supérieure, PSL Research University, Paris, France
- ESPCI, PSL Research University, Paris, France
| | - Zhi-Qiang You
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, United States
| | - Simon Roux
- Department of Microbiology, Ohio State University, Columbus, OH, United States
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, United States
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, United States
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99
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Díaz-Muñoz SL. Viral coinfection is shaped by host ecology and virus-virus interactions across diverse microbial taxa and environments. Virus Evol 2017; 3:vex011. [PMID: 28469939 PMCID: PMC5407056 DOI: 10.1093/ve/vex011] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Infection of more than one virus in a host, coinfection, is common across taxa and environments. Viral coinfection can enable genetic exchange, alter the dynamics of infections, and change the course of viral evolution. Yet, a systematic test of the factors explaining variation in viral coinfection across different taxa and environments awaits completion. Here I employ three microbial data sets of virus–host interactions covering cross-infectivity, culture coinfection, and single-cell coinfection (total: 6,564 microbial hosts, 13,103 viruses) to provide a broad, comprehensive picture of the ecological and biological factors shaping viral coinfection. I found evidence that ecology and virus–virus interactions are recurrent factors shaping coinfection patterns. Host ecology was a consistent and strong predictor of coinfection across all three data sets: cross-infectivity, culture coinfection, and single-cell coinfection. Host phylogeny or taxonomy was a less consistent predictor, being weak or absent in the cross-infectivity and single-cell coinfection models, yet it was the strongest predictor in the culture coinfection model. Virus–virus interactions strongly affected coinfection. In the largest test of superinfection exclusion to date, prophage sequences reduced culture coinfection by other prophages, with a weaker effect on extrachromosomal virus coinfection. At the single-cell level, prophage sequences eliminated coinfection. Virus–virus interactions also increased culture coinfection with ssDNA–dsDNA coinfections >2× more likely than ssDNA-only coinfections. The presence of CRISPR spacers was associated with a ∼50% reduction in single-cell coinfection in a marine bacteria, despite the absence of exact spacer matches in any active infection. Collectively, these results suggest the environment bacteria inhabit and the interactions among surrounding viruses are two factors consistently shaping viral coinfection patterns. These findings highlight the role of virus–virus interactions in coinfection with implications for phage therapy, microbiome dynamics, and viral infection treatments.
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Affiliation(s)
- Samuel L Díaz-Muñoz
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
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100
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Parmar KM, Gaikwad SL, Dhakephalkar PK, Kothari R, Singh RP. Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics. Front Microbiol 2017; 8:559. [PMID: 28439260 PMCID: PMC5383658 DOI: 10.3389/fmicb.2017.00559] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/16/2017] [Indexed: 01/09/2023] Open
Abstract
Innovations in next-generation sequencing technology have introduced new avenues in microbial studies through “omics” approaches. This technology has considerably augmented the knowledge of the microbial world without isolation prior to their identification. With an enormous volume of bacterial “omics” data, considerable attempts have been recently invested to improve an insight into virosphere. The interplay between bacteriophages and their host has created a significant influence on the biogeochemical cycles, microbial diversity, and bacterial population regulation. This review highlights various concepts such as genomics, transcriptomics, proteomics, and metabolomics to infer the phylogenetic affiliation and function of bacteriophages and their impact on diverse microbial communities. Omics technologies illuminate the role of bacteriophage in an environment, the influences of phage proteins on the bacterial host and provide information about the genes important for interaction with bacteria. These investigations will reveal some of bio-molecules and biomarkers of the novel phage which demand to be unveiled.
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Affiliation(s)
| | | | | | - Ramesh Kothari
- Department of Biosciences, Saurashtra UniversityRajkot, India
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