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Wallace BA, Varona NS, Hesketh-Best PJ, Stiffler AK, Silveira CB. Globally distributed bacteriophage genomes reveal mechanisms of tripartite phage-bacteria-coral interactions. THE ISME JOURNAL 2024; 18:wrae132. [PMID: 39030686 PMCID: PMC11309003 DOI: 10.1093/ismejo/wrae132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/23/2024] [Accepted: 07/18/2024] [Indexed: 07/21/2024]
Abstract
Reef-building corals depend on an intricate community of microorganisms for functioning and resilience. The infection of coral-associated bacteria by bacteriophages can modify bacterial ecological interactions, yet very little is known about phage functions in the holobiont. This gap stems from methodological limitations that have prevented the recovery of high-quality viral genomes and bacterial host assignment from coral samples. Here, we introduce a size fractionation approach that increased bacterial and viral recovery in coral metagenomes by 9-fold and 2-fold, respectively, and enabled the assembly and binning of bacterial and viral genomes at relatively low sequencing coverage. We combined these viral genomes with those derived from 677 publicly available metagenomes, viromes, and bacterial isolates from stony corals to build a global coral virus database of over 20,000 viral genomic sequences spanning four viral realms. The tailed bacteriophage families Kyanoviridae and Autographiviridae were the most abundant, replacing groups formerly referred to as Myoviridae and Podoviridae, respectively. Prophage and CRISPR spacer linkages between these viruses and 626 bacterial metagenome-assembled genomes and bacterial isolates showed that most viruses infected Alphaproteobacteria, the most abundant class, and less abundant taxa like Halanaerobiia and Bacteroidia. A host-phage-gene network identified keystone viruses with the genomic capacity to modulate bacterial metabolic pathways and direct molecular interactions with eukaryotic cells. This study reveals the genomic basis of nested symbioses between bacteriophage, bacteria, and the coral host and its endosymbiotic algae.
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Affiliation(s)
- Bailey A Wallace
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
| | - Natascha S Varona
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
| | - Poppy J Hesketh-Best
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
- Department Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108, United States
| | - Alexandra K Stiffler
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
| | - Cynthia B Silveira
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL 33149, United States
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2
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Veglia AJ, Bistolas KSI, Voolstra CR, Hume BCC, Ruscheweyh HJ, Planes S, Allemand D, Boissin E, Wincker P, Poulain J, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Zoccola D, Correa AMS, Vega Thurber RL. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes. Commun Biol 2023; 6:566. [PMID: 37264063 DOI: 10.1038/s42003-023-04917-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 04/24/2023] [Indexed: 06/03/2023] Open
Abstract
Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.
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Affiliation(s)
- Alex J Veglia
- BioSciences Department, Rice University, Houston, TX, USA
| | | | | | | | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Paola Furla
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur mer, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Department of Medical Genetics, CHU of Nice, Nice, France
| | - Fabien Lombard
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, F-06230, Villefranche-sur-Mer, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road H91 TK33, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | - Didier Zoccola
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
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Mohamed AR, Ochsenkühn MA, Kazlak AM, Moustafa A, Amin SA. The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions. FEMS Microbiol Rev 2023; 47:fuad005. [PMID: 36882224 PMCID: PMC10045912 DOI: 10.1093/femsre/fuad005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.
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Affiliation(s)
- Amin R Mohamed
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Michael A Ochsenkühn
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Ahmed M Kazlak
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Ahmed Moustafa
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
- Department of Biology, American University in Cairo, New Cairo 11835, Egypt
| | - Shady A Amin
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
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4
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Benites LF, Stephens TG, Bhattacharya D. Multiple waves of viral invasions in Symbiodiniaceae algal genomes. Virus Evol 2022; 8:veac101. [PMID: 36381231 PMCID: PMC9651163 DOI: 10.1093/ve/veac101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 08/29/2022] [Accepted: 10/25/2022] [Indexed: 08/13/2023] Open
Abstract
Dinoflagellates from the family Symbiodiniaceae are phototrophic marine protists that engage in symbiosis with diverse hosts. Their large and distinct genomes are characterized by pervasive gene duplication and large-scale retroposition events. However, little is known about the role and scale of horizontal gene transfer (HGT) in the evolution of this algal family. In other dinoflagellates, high levels of HGTs have been observed, linked to major genomic transitions, such as the appearance of a viral-acquired nucleoprotein that originated via HGT from a large DNA algal virus. Previous work showed that Symbiodiniaceae from different hosts are actively infected by viral groups, such as giant DNA viruses and ssRNA viruses, that may play an important role in coral health. Latent viral infections may also occur, whereby viruses could persist in the cytoplasm or integrate into the host genome as a provirus. This hypothesis received experimental support; however, the cellular localization of putative latent viruses and their taxonomic affiliation are still unknown. In addition, despite the finding of viral sequences in some genomes of Symbiodiniaceae, viral origin, taxonomic breadth, and metabolic potential have not been explored. To address these questions, we searched for putative viral-derived proteins in thirteen Symbiodiniaceae genomes. We found fifty-nine candidate viral-derived HGTs that gave rise to twelve phylogenies across ten genomes. We also describe the taxonomic affiliation of these virus-related sequences, their structure, and their genomic context. These results lead us to propose a model to explain the origin and fate of Symbiodiniaceae viral acquisitions.
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Affiliation(s)
- L Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
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5
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Langenfeld K, Chin K, Roy A, Wigginton K, Duhaime MB. Comparison of ultrafiltration and iron chloride flocculation in the preparation of aquatic viromes from contrasting sample types. PeerJ 2021; 9:e11111. [PMID: 33996275 PMCID: PMC8106395 DOI: 10.7717/peerj.11111] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/23/2021] [Indexed: 12/24/2022] Open
Abstract
Viral metagenomes (viromes) are a valuable untargeted tool for studying viral diversity and the central roles viruses play in host disease, ecology, and evolution. Establishing effective methods to concentrate and purify viral genomes prior to sequencing is essential for high quality viromes. Using virus spike-and-recovery experiments, we stepwise compared two common approaches for virus concentration, ultrafiltration and iron chloride flocculation, across diverse matrices: wastewater influent, wastewater secondary effluent, river water, and seawater. Viral DNA was purified by removing cellular DNA via chloroform cell lysis, filtration, and enzymatic degradation of extra-viral DNA. We found that viral genomes were concentrated 1-2 orders of magnitude more with ultrafiltration than iron chloride flocculation for all matrices and resulted in higher quality DNA suitable for amplification-free and long-read sequencing. Given its widespread use and utility as an inexpensive field method for virome sampling, we nonetheless sought to optimize iron flocculation. We found viruses were best concentrated in seawater with five-fold higher iron concentrations than the standard used, inhibition of DNase activity reduced purification effectiveness, and five-fold more iron was needed to flocculate viruses from freshwater than seawater—critical knowledge for those seeking to apply this broadly used method to freshwater virome samples. Overall, our results demonstrated that ultrafiltration and purification performed better than iron chloride flocculation and purification in the tested matrices. Given that the method performance depended on the solids content and salinity of the samples, we suggest spike-and-recovery experiments be applied when concentrating and purifying sample types that diverge from those tested here.
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Affiliation(s)
- Kathryn Langenfeld
- Department of Civil and Environmental Engineering, University of Michigan - Ann Arbor, Ann Arbor, MI, United States of America
| | - Kaitlyn Chin
- Department of Civil and Environmental Engineering, University of Michigan - Ann Arbor, Ann Arbor, MI, United States of America
| | - Ariel Roy
- Department of Civil and Environmental Engineering, University of Michigan - Ann Arbor, Ann Arbor, MI, United States of America
| | - Krista Wigginton
- Department of Civil and Environmental Engineering, University of Michigan - Ann Arbor, Ann Arbor, MI, United States of America
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan - Ann Arbor, Ann Arbor, MI, United States of America
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6
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Pascelli C, Laffy PW, Botté E, Kupresanin M, Rattei T, Lurgi M, Ravasi T, Webster NS. Viral ecogenomics across the Porifera. MICROBIOME 2020; 8:144. [PMID: 33008461 PMCID: PMC7532657 DOI: 10.1186/s40168-020-00919-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/08/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Viruses directly affect the most important biological processes in the ocean via their regulation of prokaryotic and eukaryotic populations. Marine sponges form stable symbiotic partnerships with a wide diversity of microorganisms and this high symbiont complexity makes them an ideal model for studying viral ecology. Here, we used morphological and molecular approaches to illuminate the diversity and function of viruses inhabiting nine sponge species from the Great Barrier Reef and seven from the Red Sea. RESULTS Viromic sequencing revealed host-specific and site-specific patterns in the viral assemblages, with all sponge species dominated by the bacteriophage order Caudovirales but also containing variable representation from the nucleocytoplasmic large DNA virus families Mimiviridae, Marseilleviridae, Phycodnaviridae, Ascoviridae, Iridoviridae, Asfarviridae and Poxviridae. Whilst core viral functions related to replication, infection and structure were largely consistent across the sponge viromes, functional profiles varied significantly between species and sites largely due to differential representation of putative auxiliary metabolic genes (AMGs) and accessory genes, including those associated with herbicide resistance, heavy metal resistance and nylon degradation. Furthermore, putative AMGs varied with the composition and abundance of the sponge-associated microbiome. For instance, genes associated with antimicrobial activity were enriched in low microbial abundance sponges, genes associated with nitrogen metabolism were enriched in high microbial abundance sponges and genes related to cellulose biosynthesis were enriched in species that host photosynthetic symbionts. CONCLUSIONS Our results highlight the diverse functional roles that viruses can play in marine sponges and are consistent with our current understanding of sponge ecology. Differential representation of putative viral AMGs and accessory genes across sponge species illustrate the diverse suite of beneficial roles viruses can play in the functional ecology of these complex reef holobionts. Video Abstract.
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Affiliation(s)
- Cecília Pascelli
- AIMS@JCU, Townsville, Queensland, Australia
- Australian Institute of Marine Science, PMB No.3, Townsville MC, Townsville, Queensland, 4810, Australia
- James Cook University, Townsville, Australia
| | - Patrick W Laffy
- AIMS@JCU, Townsville, Queensland, Australia
- Australian Institute of Marine Science, PMB No.3, Townsville MC, Townsville, Queensland, 4810, Australia
| | - Emmanuelle Botté
- Australian Institute of Marine Science, PMB No.3, Townsville MC, Townsville, Queensland, 4810, Australia
| | - Marija Kupresanin
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Miguel Lurgi
- Biosciences Department, University of Swansea, Swansea, Wales
| | - Timothy Ravasi
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Nicole S Webster
- AIMS@JCU, Townsville, Queensland, Australia.
- Australian Institute of Marine Science, PMB No.3, Townsville MC, Townsville, Queensland, 4810, Australia.
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, Australia.
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7
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Viral metagenomic analysis of the cheese surface: A comparative study of rapid procedures for extracting viral particles. Food Microbiol 2020; 85:103278. [DOI: 10.1016/j.fm.2019.103278] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 07/18/2019] [Accepted: 07/23/2019] [Indexed: 01/12/2023]
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8
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Zolfo M, Pinto F, Asnicar F, Manghi P, Tett A, Bushman FD, Segata N. Detecting contamination in viromes using ViromeQC. Nat Biotechnol 2020; 37:1408-1412. [PMID: 31748692 DOI: 10.1038/s41587-019-0334-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Adrian Tett
- Department CIBIO, University of Trento, Trento, Italy
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
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9
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O'Brien PA, Webster NS, Miller DJ, Bourne DG. Host-Microbe Coevolution: Applying Evidence from Model Systems to Complex Marine Invertebrate Holobionts. mBio 2019; 10:e02241-18. [PMID: 30723123 PMCID: PMC6428750 DOI: 10.1128/mbio.02241-18] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Marine invertebrates often host diverse microbial communities, making it difficult to identify important symbionts and to understand how these communities are structured. This complexity has also made it challenging to assign microbial functions and to unravel the myriad of interactions among the microbiota. Here we propose to address these issues by applying evidence from model systems of host-microbe coevolution to complex marine invertebrate microbiomes. Coevolution is the reciprocal adaptation of one lineage in response to another and can occur through the interaction of a host and its beneficial symbiont. A classic indicator of coevolution is codivergence of host and microbe, and evidence of this is found in both corals and sponges. Metabolic collaboration between host and microbe is often linked to codivergence and appears likely in complex holobionts, where microbial symbionts can interact with host cells through production and degradation of metabolic compounds. Neutral models are also useful to distinguish selected microbes against a background population consisting predominately of random associates. Enhanced understanding of the interactions between marine invertebrates and their microbial communities is urgently required as coral reefs face unprecedented local and global pressures and as active restoration approaches, including manipulation of the microbiome, are proposed to improve the health and tolerance of reef species. On the basis of a detailed review of the literature, we propose three research criteria for examining coevolution in marine invertebrates: (i) identifying stochastic and deterministic components of the microbiome, (ii) assessing codivergence of host and microbe, and (iii) confirming the intimate association based on shared metabolic function.
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Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
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10
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Celis JS, Wibberg D, Ramírez-Portilla C, Rupp O, Sczyrba A, Winkler A, Kalinowski J, Wilke T. Binning enables efficient host genome reconstruction in cnidarian holobionts. Gigascience 2018; 7:5039706. [PMID: 29917104 PMCID: PMC6049006 DOI: 10.1093/gigascience/giy075] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/14/2018] [Indexed: 12/19/2022] Open
Abstract
Background Many cnidarians, including stony corals, engage in complex symbiotic associations, comprising the eukaryotic host, photosynthetic algae, and highly diverse microbial communities—together referred to as holobiont. This taxonomic complexity makes sequencing and assembling coral host genomes extremely challenging. Therefore, previous cnidarian genomic projects were based on symbiont-free tissue samples. However, this approach may not be applicable to the majority of cnidarian species for ecological reasons. We therefore evaluated the performance of an alternative method based on sequence binning for reconstructing the genome of the stony coral Porites rus from a hologenomic sample and compared it to traditional approaches. Results Our results demonstrate that binning performs well for hologenomic data, producing sufficient reads for assembling the draft genome of P. rus. An assembly evaluation based on operational criteria showed results that were comparable to symbiont-free approaches in terms of completeness and usefulness, despite a high degree of fragmentation in our assembly. In addition, we found that binning provides sufficient data for exploratory k-mer estimation of genomic features, such as genome size and heterozygosity. Conclusions Binning constitutes a powerful approach for disentangling taxonomically complex coral hologenomes. Considering the recent decline of coral reefs on the one hand and previous limitations to coral genome sequencing on the other hand, binning may facilitate rapid and reliable genome assembly. This study also provides an important milestone in advancing binning from the metagenomic to the hologenomic and from the prokaryotic to the eukaryotic level.
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Affiliation(s)
- Juan Sebastián Celis
- Animal Ecology and Systematics, Justus Liebig University Giessen. Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany.,Corporation Center of Excellence in Marine Sciences, Cra 54 No 106-18, Bogotá, Colombia
| | - Daniel Wibberg
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Catalina Ramírez-Portilla
- Animal Ecology and Systematics, Justus Liebig University Giessen. Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany.,Evolutionary Biology and Ecology, Université libre de Bruxelles, Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels, Belgium
| | - Oliver Rupp
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Alexander Sczyrba
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Anika Winkler
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Thomas Wilke
- Animal Ecology and Systematics, Justus Liebig University Giessen. Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany.,Corporation Center of Excellence in Marine Sciences, Cra 54 No 106-18, Bogotá, Colombia
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11
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Pascelli C, Laffy PW, Kupresanin M, Ravasi T, Webster NS. Morphological characterization of virus-like particles in coral reef sponges. PeerJ 2018; 6:e5625. [PMID: 30356950 PMCID: PMC6195793 DOI: 10.7717/peerj.5625] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/22/2018] [Indexed: 12/03/2022] Open
Abstract
Marine sponges host complex microbial consortia that vary in their abundance, diversity and stability amongst host species. While our understanding of sponge-microbe interactions has dramatically increased over the past decade, little is known about how sponges and their microbial symbionts interact with viruses, the most abundant entities in the ocean. In this study, we employed three transmission electron microscopy (TEM) preparation methods to provide the first comprehensive morphological assessment of sponge-associated viruses. The combined approaches revealed 50 different morphologies of viral-like particles (VLPs) represented across the different sponge species. VLPs were visualized within sponge cells, within the sponge extracellular mesohyl matrix, on the sponge ectoderm and within sponge-associated microbes. Non-enveloped, non-tailed icosahedral VLPs were the most commonly observed morphotypes, although tailed bacteriophage, brick-shaped, geminate and filamentous VLPs were also detected. Visualization of sponge-associated viruses using TEM has confirmed that sponges harbor not only diverse communities of microorganisms but also diverse communities of viruses.
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Affiliation(s)
- Cecília Pascelli
- Australian Institute of Marine Science, Townsville, Queensland, Australia.,James Cook University, Townsville, Queensland, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Queensland, Australia
| | - Patrick W Laffy
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Marija Kupresanin
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Timothy Ravasi
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Queensland, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, Queensland, Australia
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12
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Abstract
Viruses infect all kingdoms of marine life from bacteria to whales. Viruses in the world's oceans play important roles in the mortality of phytoplankton, and as drivers of evolution and biogeochemical cycling. They shape host population abundance and distribution and can lead to the termination of algal blooms. As discoveries about this huge reservoir of genetic and biological diversity grow, our understanding of the major influences viruses exert in the global marine environment continues to expand. This chapter discusses the key discoveries that have been made to date about marine viruses and the current direction of this field of research.
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Affiliation(s)
- Karen D Weynberg
- School of Chemistry & Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia.
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13
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Laffy PW, Wood‐Charlson EM, Turaev D, Jutz S, Pascelli C, Botté ES, Bell SC, Peirce TE, Weynberg KD, van Oppen MJH, Rattei T, Webster NS. Reef invertebrate viromics: diversity, host specificity and functional capacity. Environ Microbiol 2018; 20:2125-2141. [DOI: 10.1111/1462-2920.14110] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/16/2018] [Accepted: 03/16/2018] [Indexed: 01/14/2023]
Affiliation(s)
- Patrick W. Laffy
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
| | | | - Dmitrij Turaev
- Department of Microbiology and Ecosystem Science, Division of Computational Systems BiologyUniversity of ViennaVienna Austria
| | - Sabrina Jutz
- Department of Microbiology and Ecosystem Science, Division of Computational Systems BiologyUniversity of ViennaVienna Austria
| | - Cecilia Pascelli
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
- College of Science and EngineeringJames Cook UniversityTownsville QLD Australia
- AIMS@JCU, Australian Institute of Marine Science and James Cook UniversityTownsville QLD Australia
| | | | - Sara C. Bell
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
| | - Tyler E. Peirce
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
| | - Karen D. Weynberg
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
| | - Madeleine J. H. van Oppen
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
- School of BiosciencesUniversity of Melbourne, ParkvilleMelbourneVIC 3010 Australia
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems BiologyUniversity of ViennaVienna Austria
| | - Nicole S. Webster
- Australian Institute of Marine Science, PMB 3TownsvilleQLD 4810 Australia
- Austalian Centre for Ecogenomics, University of QueenslandBrisbaneQLD 4072 Australia
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14
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van de Water JAJM, Allemand D, Ferrier-Pagès C. Host-microbe interactions in octocoral holobionts - recent advances and perspectives. MICROBIOME 2018; 6:64. [PMID: 29609655 PMCID: PMC5880021 DOI: 10.1186/s40168-018-0431-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/01/2018] [Indexed: 05/05/2023]
Abstract
Octocorals are one of the most ubiquitous benthic organisms in marine ecosystems from the shallow tropics to the Antarctic deep sea, providing habitat for numerous organisms as well as ecosystem services for humans. In contrast to the holobionts of reef-building scleractinian corals, the holobionts of octocorals have received relatively little attention, despite the devastating effects of disease outbreaks on many populations. Recent advances have shown that octocorals possess remarkably stable bacterial communities on geographical and temporal scales as well as under environmental stress. This may be the result of their high capacity to regulate their microbiome through the production of antimicrobial and quorum-sensing interfering compounds. Despite decades of research relating to octocoral-microbe interactions, a synthesis of this expanding field has not been conducted to date. We therefore provide an urgently needed review on our current knowledge about octocoral holobionts. Specifically, we briefly introduce the ecological role of octocorals and the concept of holobiont before providing detailed overviews of (I) the symbiosis between octocorals and the algal symbiont Symbiodinium; (II) the main fungal, viral, and bacterial taxa associated with octocorals; (III) the dominance of the microbial assemblages by a few microbial species, the stability of these associations, and their evolutionary history with the host organism; (IV) octocoral diseases; (V) how octocorals use their immune system to fight pathogens; (VI) microbiome regulation by the octocoral and its associated microbes; and (VII) the discovery of natural products with microbiome regulatory activities. Finally, we present our perspectives on how the field of octocoral research should move forward, and the recognition that these organisms may be suitable model organisms to study coral-microbe symbioses.
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Affiliation(s)
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, Monaco
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15
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Hewson I, Bistolas KSI, Button JB, Jackson EW. Occurrence and seasonal dynamics of RNA viral genotypes in three contrasting temperate lakes. PLoS One 2018; 13:e0194419. [PMID: 29543885 PMCID: PMC5854377 DOI: 10.1371/journal.pone.0194419] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/04/2018] [Indexed: 11/18/2022] Open
Abstract
Decades of research have demonstrated the crucial importance of viruses in freshwater ecosystems. However, few studies have focused on the seasonal dynamics and potential hosts of RNA viruses. We surveyed microbial-sized (i.e. 5-0.2 μm) mixed community plankton transcriptomes for RNA viral genomes and investigated their distribution between microbial and macrobial plankton over a seasonal cycle across three temperate lakes by quantitative reverse transcriptase PCR (qRT-PCR). A total of 30 contigs bearing similarity to RNA viral genomes were recovered from a global assembly of 30 plankton RNA libraries. Of these, only 13 were found in >2 libraries and recruited >100 reads (of 9.13 x 107 total reads), representing several picornaviruses, two tobamoviruses and a reovirus. We quantified the abundance of four picornaviruses and the reovirus monthly from August 2014 to May 2015. Patterns of viral abundance in the >5 μm size fraction and representation in microbial-sized community RNA libraries over time suggest that one picornavirus genotype (TS24835) and the reovirus (TS148892) may infect small (<5 μm) eukaryotic microorganisms, while two other picornaviruses (TS24641 and TS4340) may infect larger (>5 μm) eukaryotic microorganisms or metazoa. Our data also suggest that picornavirus TS152062 may originate from an allochthonous host. All five viral genotypes were present in at least one size fraction across all 3 lakes during the year, suggesting that RNA viruses may easily disperse between adjacent aquatic habitats. Our data therefore demonstrate that RNA viruses are widespread in temperate lacustrine ecosystems, and may provide evidence of viral infection in larger eukaryotes (including metazoa) inhabiting the lakes.
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Affiliation(s)
- Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
| | - Kalia S. I. Bistolas
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
| | - Jason B. Button
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
| | - Elliot W. Jackson
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
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16
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Brüwer JD, Voolstra CR. First insight into the viral community of the cnidarian model metaorganism Aiptasia using RNA-Seq data. PeerJ 2018; 6:e4449. [PMID: 29507840 PMCID: PMC5835348 DOI: 10.7717/peerj.4449] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/13/2018] [Indexed: 02/01/2023] Open
Abstract
Current research posits that all multicellular organisms live in symbioses with associated microorganisms and form so-called metaorganisms or holobionts. Cnidarian metaorganisms are of specific interest given that stony corals provide the foundation of the globally threatened coral reef ecosystems. To gain first insight into viruses associated with the coral model system Aiptasia (sensu Exaiptasia pallida), we analyzed an existing RNA-Seq dataset of aposymbiotic, partially populated, and fully symbiotic Aiptasia CC7 anemones with Symbiodinium. Our approach included the selective removal of anemone host and algal endosymbiont sequences and subsequent microbial sequence annotation. Of a total of 297 million raw sequence reads, 8.6 million (∼3%) remained after host and endosymbiont sequence removal. Of these, 3,293 sequences could be assigned as of viral origin. Taxonomic annotation of these sequences suggests that Aiptasia is associated with a diverse viral community, comprising 116 viral taxa covering 40 families. The viral assemblage was dominated by viruses from the families Herpesviridae (12.00%), Partitiviridae (9.93%), and Picornaviridae (9.87%). Despite an overall stable viral assemblage, we found that some viral taxa exhibited significant changes in their relative abundance when Aiptasia engaged in a symbiotic relationship with Symbiodinium. Elucidation of viral taxa consistently present across all conditions revealed a core virome of 15 viral taxa from 11 viral families, encompassing many viruses previously reported as members of coral viromes. Despite the non-random selection of viral genetic material due to the nature of the sequencing data analyzed, our study provides a first insight into the viral community associated with Aiptasia. Similarities of the Aiptasia viral community with those of corals corroborate the application of Aiptasia as a model system to study coral holobionts. Further, the change in abundance of certain viral taxa across different symbiotic states suggests a role of viruses in the algal endosymbiosis, but the functional significance of this remains to be determined.
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Affiliation(s)
- Jan D Brüwer
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, Saudi Arabia
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17
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Abstract
Prokaryotic viruses, or bacteriophages, are viruses that infect bacteria and archaea. These viruses have been known to associate with host systems for decades, yet only recently have their influence on the regulation of host-associated bacteria been appreciated. These studies have been conducted in many host systems, from the base of animal life in the Cnidarian phylum to mammals. These prokaryotic viruses are useful for regulating the number of bacteria in a host ecosystem and for regulating the strains of bacteria useful for the microbiome. These viruses are likely selected by the host to maintain bacterial populations. Viral metagenomics allows researchers to profile the communities of viruses associating with animal hosts, and importantly helps to determine the functional role these viruses play. Further, viral metagenomics show the sphere of viral involvement in gene flow and gene shuffling in an ever-changing host environment. The influence of prokaryotic viruses could, therefore, have a clear impact on host health.
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Affiliation(s)
- Juris A Grasis
- School of Natural Sciences, University of California, Merced, Merced, CA, USA.
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18
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Buerger P, van Oppen MJH. Viruses in corals: hidden drivers of coral bleaching and disease? MICROBIOLOGY AUSTRALIA 2018. [DOI: 10.1071/ma18004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Marine viruses are the largest, but most poorly explored genetic reservoir on the planet. They occur ubiquitously in the ocean at an average density of 5–15 × 106 viruses per mL of seawater, which represents abundances an order of magnitude higher than those of bacteria. While viruses are known agents of a number of diseases in the marine environment, little is known about their beneficial function to corals. Herein, we briefly introduce the topic of viruses as potential drivers of coral bleaching and disease.
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19
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Monteil-Bouchard S, Temmam S, Desnues C. Protocol for Generating Infectious RNA Viromes from Complex Biological Samples. Methods Mol Biol 2018; 1838:25-36. [PMID: 30128987 DOI: 10.1007/978-1-4939-8682-8_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This chapter proposes a simple, standardized protocol for generating RNA viromes from complex host-associated biological samples of various origins. Compared to other existing protocols to generate RNA viromes, this protocol preserves the infectivity of viral particles and allows for downstream applications such as viral characterization and isolation tests.
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Affiliation(s)
- Sonia Monteil-Bouchard
- Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), IHU Méditerranée Infection, Assistance-Publique des Hôpitaux de Marseille, Aix-Marseille Université, CNRS 7278, IRD 198, INSERM1095, Marseille, France
| | - Sarah Temmam
- Biology of Infection Unit, Laboratory of Pathogen Discovery, Institut Pasteur, INSERM U1117, Paris, France
| | - Christelle Desnues
- Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), IHU Méditerranée Infection, Assistance-Publique des Hôpitaux de Marseille, Aix-Marseille Université, CNRS 7278, IRD 198, INSERM1095, Marseille, France.
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20
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Torres PJ, Kelley ST. Sampling, Extraction, and High-Throughput Sequencing Methods for Environmental Microbial and Viral Communities. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2017; 1712:163-173. [PMID: 29224074 DOI: 10.1007/978-1-4939-7514-3_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The emergence of high-throughput sequencing technologies has deepened our understanding of complex microbial communities and greatly facilitated the study of as-yet uncultured microbes and viruses. Studies of complex microbial communities require high-quality data to generate valid results. Here, we detail current methods of microbial and viral community sample acquisition, DNA extraction, sample preparation, and sequencing on Illumina high-throughput platforms. While using appropriate analytical tools is important, it must not overshadow the need for establishing a proper experimental design and obtaining sufficient numbers of samples for statistical purposes. Researchers must also take care to sample biologically relevant sites and control for potential confounding factors (e.g., contamination).
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Affiliation(s)
- Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA.
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21
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Weynberg KD, Laffy PW, Wood-Charlson EM, Turaev D, Rattei T, Webster NS, van Oppen MJH. Coral-associated viral communities show high levels of diversity and host auxiliary functions. PeerJ 2017; 5:e4054. [PMID: 29158985 PMCID: PMC5695250 DOI: 10.7717/peerj.4054] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/27/2017] [Indexed: 12/19/2022] Open
Abstract
Stony corals (Scleractinia) are marine invertebrates that form the foundation and framework upon which tropical reefs are built. The coral animal associates with a diverse microbiome comprised of dinoflagellate algae and other protists, bacteria, archaea, fungi and viruses. Using a metagenomics approach, we analysed the DNA and RNA viral assemblages of seven coral species from the central Great Barrier Reef (GBR), demonstrating that tailed bacteriophages of the Caudovirales dominate across all species examined, and ssDNA viruses, notably the Microviridae, are also prevalent. Most sequences with matches to eukaryotic viruses were assigned to six viral families, including four Nucleocytoplasmic Large DNA Viruses (NCLDVs) families: Iridoviridae, Phycodnaviridae, Mimiviridae, and Poxviridae, as well as Retroviridae and Polydnaviridae. Contrary to previous findings, Herpesvirales were rare in these GBR corals. Sequences of a ssRNA virus with similarities to the dinornavirus, Heterocapsa circularisquama ssRNA virus of the Alvernaviridae that infects free-living dinoflagellates, were observed in three coral species. We also detected viruses previously undescribed from the coral holobiont, including a virus that targets fungi associated with the coral species Acropora tenuis. Functional analysis of the assembled contigs indicated a high prevalence of latency-associated genes in the coral-associated viral assemblages, several host-derived auxiliary metabolic genes (AMGs) for photosynthesis (psbA, psbD genes encoding the photosystem II D1 and D2 proteins respectively), as well as potential nematocyst toxins and antioxidants (genes encoding green fluorescent-like chromoprotein). This study expands the currently limited knowledge on coral-associated viruses by characterising viral composition and function across seven GBR coral species.
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Affiliation(s)
- Karen D Weynberg
- Australian Institute of Marine Science, Townsville, Queensland, Australia.,School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Patrick W Laffy
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | | | - Dmitrij Turaev
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, Queensland, Australia
| | - Madeleine J H van Oppen
- Australian Institute of Marine Science, Townsville, Queensland, Australia.,School of Biosciences, University of Melbourne, Melbourne, Victoria, Australia
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22
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Mahmoud H, Jose L. Phage and Nucleocytoplasmic Large Viral Sequences Dominate Coral Viromes from the Arabian Gulf. Front Microbiol 2017; 8:2063. [PMID: 29114244 PMCID: PMC5660727 DOI: 10.3389/fmicb.2017.02063] [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: 01/02/2017] [Accepted: 10/09/2017] [Indexed: 11/25/2022] Open
Abstract
Corals that naturally thrive under extreme conditions are gaining increasing attention due to their importance as living models to understand the impact of global warming on world corals. Here, we present the first metagenomic study of viral communities in corals thriving in a thermally variable water body in which the temperature fluctuates between 11 and 39°C in different seasons. The viral assemblages of two of the most abundant massive (Porites harrisoni) and branching (Acropora downingi) corals in offshore and inshore reef systems in the northern Arabian Gulf were investigated. Samples were collected from five reef systems during summer, autumn and winter of 2011/2012. The two coral viromes contain 12 viral families, including 10 dsDNA viral families [Siphoviridae, Podoviridae, Myoviridae, Phycodnaviridae, Baculoviridae, Herpesviridae, Adenoviridae, Alloherpesviridae, Mimiviridae and one unclassified family], one-ssDNA viral family (Microviridae) and one RNA viral family (Retroviridae). Overall, sequences significantly similar to Podoviridae were the most abundant in the P. harrisoni and A. downingi viromes. Various morphological types of virus-like particles (VLPs) were confirmed in the healthy coral tissue by transmission electron microscopy, including large tailless VLPs and electron-dense core VLPs. Tailed bacteriophages were isolated from coral tissue using a plaque assay. Higher functional gene diversity was recorded in A. downingi than in P. harrisoni, and comparative metagenomics revealed that the Gulf viral assemblages are functionally distinct from Pacific Ocean coral viral communities.
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Affiliation(s)
- Huda Mahmoud
- Faculty of Science, Department of Biological Sciences, Kuwait University, Safat, Kuwait
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23
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Montalvo-Proaño J, Buerger P, Weynberg KD, van Oppen MJH. A PCR-Based Assay Targeting the Major Capsid Protein Gene of a Dinorna-Like ssRNA Virus That Infects Coral Photosymbionts. Front Microbiol 2017; 8:1665. [PMID: 28919883 PMCID: PMC5585145 DOI: 10.3389/fmicb.2017.01665] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 08/17/2017] [Indexed: 11/13/2022] Open
Abstract
The coral-Symbiodinium association is a critical component of coral reefs as it is the main primary producer and builds the reef's 3-dimensional structure. A breakdown of this endosymbiosis causes a loss of the dinoflagellate photosymbiont, Symbiodinium, and/or its photosynthetic pigments from the coral tissues (i.e., coral bleaching), and can lead to coral mortality. Coral bleaching has mostly been attributed to environmental stressors, and in some cases to bacterial infection. Viral lysis of Symbiodinium has been proposed as another possible cause of some instances of coral bleaching, but this hypothesis has not yet been experimentally confirmed. In this study, we used coral virome data to develop a novel PCR-based assay for examining the presence and diversity of a single-stranded RNA (ssRNA) virus by targeting its major capsid protein (MCP) gene. Illumina sequence analysis of amplicons obtained with novel primers showed 99.8% of the reads had the closest taxonomic affinity with the MCP gene of the virus, Heterocapsa circularisquama RNA virus (HcRNAV) known to infect dinoflagellates, indicating that dinorna-like viruses are commonly associated with corals on the Great Barrier Reef. A phylogenetic analysis of MCP gene sequences revealed strong coral species specificity of viral operational taxon units (OTUs). This assay allows a relatively easy and rapid evaluation of the presence and diversity of this particular viral group and will assist in enhancing our understanding of the role of viral lysis in coral bleaching.
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Affiliation(s)
- Jose Montalvo-Proaño
- Australian Institute of Marine ScienceTownsville, QLD, Australia
- AIMS@JCU, James Cook UniversityTownsville, QLD, Australia
| | - Patrick Buerger
- Australian Institute of Marine ScienceTownsville, QLD, Australia
- AIMS@JCU, James Cook UniversityTownsville, QLD, Australia
- College of Science and Engineering, Department of Marine Biology and Aquaculture, James Cook UniversityTownsville, QLD, Australia
| | | | - Madeleine J. H. van Oppen
- Australian Institute of Marine ScienceTownsville, QLD, Australia
- School of BioSciences, University of MelbourneParkville, VIC, Australia
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24
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Adriaenssens EM, Kramer R, Van Goethem MW, Makhalanyane TP, Hogg I, Cowan DA. Environmental drivers of viral community composition in Antarctic soils identified by viromics. MICROBIOME 2017; 5:83. [PMID: 28724405 PMCID: PMC5518109 DOI: 10.1186/s40168-017-0301-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 07/06/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND The Antarctic continent is considered the coldest and driest place on earth with simple ecosystems, devoid of higher plants. Soils in the ice-free regions of Antarctica are known to harbor a wide range of microorganisms from primary producers to grazers, yet their ecology and particularly the role of viruses is poorly understood. In this study, we examined the virus community structures of 14 soil samples from the Mackay Glacier region. METHODS Viral communities were extracted from soil and the dsDNA was extracted, amplified using single-primer amplification, and sequenced using the Ion Torrent Proton platform. Metadata on soil physico-chemistry was collected from all sites. Both read and contig datasets were analyzed with reference-independent and reference-dependent methods to assess viral community structures and the influence of environmental parameters on their distribution. RESULTS We observed a high heterogeneity in virus signatures, independent of geographical proximity. Tailed bacteriophages were dominant in all samples, but the incidences of the affiliated families Siphoviridae and Myoviridae were inversely correlated, suggesting direct competition for hosts. Viruses of the families Phycodnaviridae and Mimiviridae were present at significant levels in high-diversity soil samples and were found to co-occur, implying little competition between them. Combinations of soil factors, including pH, calcium content, and site altitude, were found to be the main drivers of viral community structure. CONCLUSIONS The pattern of viral community structure with higher levels of diversity at lower altitude and pH, and co-occurring viral families, suggests that these cold desert soil viruses interact with each other, the host, and the environment in an intricate manner, playing a potentially crucial role in maintaining host diversity and functioning of the microbial ecosystem in the extreme environments of Antarctic soil.
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Affiliation(s)
- Evelien M. Adriaenssens
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB UK
| | - Rolf Kramer
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
| | - Marc W. Van Goethem
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
| | - Thulani P. Makhalanyane
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
| | - Ian Hogg
- School of Science, University of Waikato, Hamilton, New Zealand
- Polar Knowledge Canada, 170 Laurier Avenue West, Ottawa, Ontario K1P 5V5 Canada
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
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25
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Levin RA, Voolstra CR, Agrawal S, Steinberg PD, Suggett DJ, van Oppen MJH. Engineering Strategies to Decode and Enhance the Genomes of Coral Symbionts. Front Microbiol 2017; 8:1220. [PMID: 28713348 PMCID: PMC5492045 DOI: 10.3389/fmicb.2017.01220] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/16/2017] [Indexed: 11/13/2022] Open
Abstract
Elevated sea surface temperatures from a severe and prolonged El Niño event (2014–2016) fueled by climate change have resulted in mass coral bleaching (loss of dinoflagellate photosymbionts, Symbiodinium spp., from coral tissues) and subsequent coral mortality, devastating reefs worldwide. Genetic variation within and between Symbiodinium species strongly influences the bleaching tolerance of corals, thus recent papers have called for genetic engineering of Symbiodinium to elucidate the genetic basis of bleaching-relevant Symbiodinium traits. However, while Symbiodinium has been intensively studied for over 50 years, genetic transformation of Symbiodinium has seen little success likely due to the large evolutionary divergence between Symbiodinium and other model eukaryotes rendering standard transformation systems incompatible. Here, we integrate the growing wealth of Symbiodinium next-generation sequencing data to design tailored genetic engineering strategies. Specifically, we develop a testable expression construct model that incorporates endogenous Symbiodinium promoters, terminators, and genes of interest, as well as an internal ribosomal entry site from a Symbiodinium virus. Furthermore, we assess the potential for CRISPR/Cas9 genome editing through new analyses of the three currently available Symbiodinium genomes. Finally, we discuss how genetic engineering could be applied to enhance the stress tolerance of Symbiodinium, and in turn, coral reefs.
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Affiliation(s)
- Rachel A Levin
- Centre for Marine Bio-Innovation, The University of New South Wales, SydneyNSW, Australia.,School of Biological, Earth and Environmental Sciences, The University of New South Wales, SydneyNSW, Australia.,Climate Change Cluster, University of Technology Sydney, UltimoNSW, Australia
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST),Thuwal, Saudi Arabia
| | - Shobhit Agrawal
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST),Thuwal, Saudi Arabia
| | - Peter D Steinberg
- Centre for Marine Bio-Innovation, The University of New South Wales, SydneyNSW, Australia.,School of Biological, Earth and Environmental Sciences, The University of New South Wales, SydneyNSW, Australia.,Sydney Institute of Marine Science, MosmanNSW, Australia
| | - David J Suggett
- Climate Change Cluster, University of Technology Sydney, UltimoNSW, Australia
| | - Madeleine J H van Oppen
- Australian Institute of Marine Science, TownsvilleQLD, Australia.,School of BioSciences, The University of Melbourne, ParkvilleVIC, Australia
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26
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Colombo S, Arioli S, Neri E, Della Scala G, Gargari G, Mora D. Viromes As Genetic Reservoir for the Microbial Communities in Aquatic Environments: A Focus on Antimicrobial-Resistance Genes. Front Microbiol 2017; 8:1095. [PMID: 28663745 PMCID: PMC5471338 DOI: 10.3389/fmicb.2017.01095] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/30/2017] [Indexed: 11/16/2022] Open
Abstract
Despite studies of viromes isolated from aquatic environments are becoming increasingly frequent, most of them are limited to the characterization of viral taxonomy. Bacterial reads in viromes are abundant but the extent to which this genetic material is playing a role in the ecology of aquatic microbiology remains unclear. To this aim, we developed of a useful approach for the characterization of viral and microbial communities of aquatic environments with a particular focus on the identification of microbial genes harbored in the viromes. Virus-like particles were isolated from water samples collected across the Lambro River, from the spring to the high urbanized Milan area. The derived viromes were analyzed by shotgun metagenomic sequencing looking for the presence, relative abundance of bacterial genes with particular focus on those genes involved in antimicrobial resistance mechanisms. Antibiotic and heavy metal resistance genes have been identified in all virome samples together with a high abundance of reads assigned to cellular processes and signaling. Virome data compared to those identified in the microbiome isolated from the same sample revealed differences in terms of functional categories and their relative abundance. To verify the role of aquatic viral population in bacterial gene transfer, water-based mesocosms were perturbed or not perturbed with a low dose of tetracycline. The results obtained by qPCR assays revealed variation in abundance of tet genes in the virome and microbiome highlighting a relevant role of viral populations in microbial gene mobilization.
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Affiliation(s)
- Stefano Colombo
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Stefania Arioli
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Eros Neri
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Giulia Della Scala
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Giorgio Gargari
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Diego Mora
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
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27
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Lawrence SA, Floge SA, Davy JE, Davy SK, Wilson WH. Exploratory analysis of
Symbiodinium
transcriptomes reveals potential latent infection by large dsDNA viruses. Environ Microbiol 2017; 19:3909-3919. [DOI: 10.1111/1462-2920.13782] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 04/24/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Scott A. Lawrence
- School of Biological SciencesVictoria University of WellingtonWellington6140 New Zealand
| | - Sheri A. Floge
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, PO Box 380East Boothbay Maine USA
| | - Joanne E. Davy
- School of Biological SciencesVictoria University of WellingtonWellington6140 New Zealand
| | - Simon K. Davy
- School of Biological SciencesVictoria University of WellingtonWellington6140 New Zealand
| | - William H. Wilson
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, PO Box 380East Boothbay Maine USA
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28
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Hesse U, van Heusden P, Kirby BM, Olonade I, van Zyl LJ, Trindade M. Virome Assembly and Annotation: A Surprise in the Namib Desert. Front Microbiol 2017; 8:13. [PMID: 28167933 PMCID: PMC5253355 DOI: 10.3389/fmicb.2017.00013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/03/2017] [Indexed: 11/13/2022] Open
Abstract
Sequencing, assembly, and annotation of environmental virome samples is challenging. Methodological biases and differences in species abundance result in fragmentary read coverage; sequence reconstruction is further complicated by the mosaic nature of viral genomes. In this paper, we focus on biocomputational aspects of virome analysis, emphasizing latent pitfalls in sequence annotation. Using simulated viromes that mimic environmental data challenges we assessed the performance of five assemblers (CLC-Workbench, IDBA-UD, SPAdes, RayMeta, ABySS). Individual analyses of relevant scaffold length fractions revealed shortcomings of some programs in reconstruction of viral genomes with excessive read coverage (IDBA-UD, RayMeta), and in accurate assembly of scaffolds ≥50 kb (SPAdes, RayMeta, ABySS). The CLC-Workbench assembler performed best in terms of genome recovery (including highly covered genomes) and correct reconstruction of large scaffolds; and was used to assemble a virome from a copper rich site in the Namib Desert. We found that scaffold network analysis and cluster-specific read reassembly improved reconstruction of sequences with excessive read coverage, and that strict data filtering for non-viral sequences prior to downstream analyses was essential. In this study we describe novel viral genomes identified in the Namib Desert copper site virome. Taxonomic affiliations of diverse proteins in the dataset and phylogenetic analyses of circovirus-like proteins indicated links to the marine habitat. Considering additional evidence from this dataset we hypothesize that viruses may have been carried from the Atlantic Ocean into the Namib Desert by fog and wind, highlighting the impact of the extended environment on an investigated niche in metagenome studies.
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Affiliation(s)
- Uljana Hesse
- Institute for Microbial Biotechnology and Metagenomics, University of the Western CapeBellville, South Africa
- South African National Bioinformatics Institute, University of the Western CapeBellville, South Africa
| | - Peter van Heusden
- South African National Bioinformatics Institute, University of the Western CapeBellville, South Africa
| | - Bronwyn M. Kirby
- Institute for Microbial Biotechnology and Metagenomics, University of the Western CapeBellville, South Africa
| | - Israel Olonade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western CapeBellville, South Africa
| | - Leonardo J. van Zyl
- Institute for Microbial Biotechnology and Metagenomics, University of the Western CapeBellville, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western CapeBellville, South Africa
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29
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Thurber RV, Payet JP, Thurber AR, Correa AMS. Virus-host interactions and their roles in coral reef health and disease. Nat Rev Microbiol 2017; 15:205-216. [PMID: 28090075 DOI: 10.1038/nrmicro.2016.176] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Coral reefs occur in nutrient-poor shallow waters, constitute biodiversity and productivity hotspots, and are threatened by anthropogenic disturbance. This Review provides an introduction to coral reef virology and emphasizes the links between viruses, coral mortality and reef ecosystem decline. We describe the distinctive benthic-associated and water-column- associated viromes that are unique to coral reefs, which have received less attention than viruses in open-ocean systems. We hypothesize that viruses of bacteria and eukaryotes dynamically interact with their hosts in the water column and with scleractinian (stony) corals to influence microbial community dynamics, coral bleaching and disease, and reef biogeochemical cycling. Last, we outline how marine viruses are an integral part of the reef system and suggest that the influence of viruses on reef function is an essential component of these globally important environments.
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Affiliation(s)
- Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA
| | - Jérôme P Payet
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA.,College of Earth, Ocean, and Atmospheric Science, Oregon State University, Corvallis, Oregon 97331, USA
| | - Andrew R Thurber
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA.,College of Earth, Ocean, and Atmospheric Science, Oregon State University, Corvallis, Oregon 97331, USA
| | - Adrienne M S Correa
- BioSciences Department, Rice University, 6100 Main Street, Houston, Texas 77005, USA
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30
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Sweet M, Bythell J. The role of viruses in coral health and disease. J Invertebr Pathol 2016; 147:136-144. [PMID: 27993618 DOI: 10.1016/j.jip.2016.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 11/16/2016] [Accepted: 12/13/2016] [Indexed: 11/27/2022]
Abstract
Metagenomic and electron microscopy studies confirm that the coral microbiome contains a rich diversity and abundance of viruses. While there have been no definitive tests of disease causation by viruses in corals, viruses have been implicated as coral pathogens in a number of studies. Growing evidence also indicates that latent viral infections can compromise the algal symbionts under environmental stress and may be involved in the coral bleaching response. Conversely, bacteriophages and archaeal phage viruses are abundant in the microbiome of healthy corals and are likely to be involved in complex ecological networks, genetic material transfer and selective co-evolution within the surface mucus layers and tissues. The relative importance of viral control of bacterial and archaeal populations is unknown, but they are almost certain to be exerting some level of control on the composition and maintenance of the coral microbiome. While rapid leaps in the capability to detect viruses have been made due to advances in metagenomics and bioinformatics, these approaches need now to be integrated with in vitro culture and challenge experiments to assess the functional roles of viruses in health and disease, and it is imperative that interactions with other members of the coral microbiome are taken into account when assessing disease causation.
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Affiliation(s)
- Michael Sweet
- Molecular Health and Disease Laboratory, Environmental Sustainability Research Centre, College of Life and Natural Sciences, University of Derby, Derby DE22 1 GB, UK.
| | - John Bythell
- School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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31
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Uyaguari-Diaz MI, Chan M, Chaban BL, Croxen MA, Finke JF, Hill JE, Peabody MA, Van Rossum T, Suttle CA, Brinkman FSL, Isaac-Renton J, Prystajecky NA, Tang P. A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples. MICROBIOME 2016; 4:20. [PMID: 27391119 PMCID: PMC5011856 DOI: 10.1186/s40168-016-0166-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/04/2016] [Indexed: 05/16/2023]
Abstract
BACKGROUND Studies of environmental microbiota typically target only specific groups of microorganisms, with most focusing on bacteria through taxonomic classification of 16S rRNA gene sequences. For a more holistic understanding of a microbiome, a strategy to characterize the viral, bacterial, and eukaryotic components is necessary. RESULTS We developed a method for metagenomic and amplicon-based analysis of freshwater samples involving the concentration and size-based separation of eukaryotic, bacterial, and viral fractions. Next-generation sequencing and culture-independent approaches were used to describe and quantify microbial communities in watersheds with different land use in British Columbia. Deep amplicon sequencing was used to investigate the distribution of certain viruses (g23 and RdRp), bacteria (16S rRNA and cpn60), and eukaryotes (18S rRNA and ITS). Metagenomic sequencing was used to further characterize the gene content of the bacterial and viral fractions at both taxonomic and functional levels. CONCLUSION This study provides a systematic approach to separate and characterize eukaryotic-, bacterial-, and viral-sized particles. Methodologies described in this research have been applied in temporal and spatial studies to study the impact of land use on watershed microbiomes in British Columbia.
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Affiliation(s)
- Miguel I. Uyaguari-Diaz
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Michael Chan
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
| | - Bonnie L. Chaban
- South Kensington Campus, Imperial College London, Sir Ernst Chain Building, London, SW7 2AZ UK
| | - Matthew A. Croxen
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
| | - Jan F. Finke
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Janet E. Hill
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4 Canada
| | - Michael A. Peabody
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Thea Van Rossum
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Curtis A. Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8 Canada
| | - Fiona S. L. Brinkman
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Judith Isaac-Renton
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Natalie A. Prystajecky
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
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32
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Bourne DG, Morrow KM, Webster NS. Insights into the Coral Microbiome: Underpinning the Health and Resilience of Reef Ecosystems. Annu Rev Microbiol 2016; 70:317-40. [PMID: 27482741 DOI: 10.1146/annurev-micro-102215-095440] [Citation(s) in RCA: 346] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Corals are fundamental ecosystem engineers, creating large, intricate reefs that support diverse and abundant marine life. At the core of a healthy coral animal is a dynamic relationship with microorganisms, including a mutually beneficial symbiosis with photosynthetic dinoflagellates (Symbiodinium spp.) and enduring partnerships with an array of bacterial, archaeal, fungal, protistan, and viral associates, collectively termed the coral holobiont. The combined genomes of this coral holobiont form a coral hologenome, and genomic interactions within the hologenome ultimately define the coral phenotype. Here we integrate contemporary scientific knowledge regarding the ecological, host-specific, and environmental forces shaping the diversity, specificity, and distribution of microbial symbionts within the coral holobiont, explore physiological pathways that contribute to holobiont fitness, and describe potential mechanisms for holobiont homeostasis. Understanding the role of the microbiome in coral resilience, acclimation, and environmental adaptation is a new frontier in reef science that will require large-scale collaborative research efforts.
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Affiliation(s)
- David G Bourne
- Marine Biology and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia 4811; .,Australian Institute of Marine Science, Townsville, Queensland, Australia 4810
| | - Kathleen M Morrow
- Australian Institute of Marine Science, Townsville, Queensland, Australia 4810.,Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia 4810
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33
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Laffy PW, Wood-Charlson EM, Turaev D, Weynberg KD, Botté ES, van Oppen MJH, Webster NS, Rattei T. HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts. Front Microbiol 2016; 7:822. [PMID: 27375564 PMCID: PMC4899465 DOI: 10.3389/fmicb.2016.00822] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 05/16/2016] [Indexed: 11/13/2022] Open
Abstract
Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterize holobiont viral communities across species, environments, or experiments.
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Affiliation(s)
- Patrick W. Laffy
- Australian Institute of Marine ScienceTownsville, QLD, Australia
| | - Elisha M. Wood-Charlson
- Center for Microbial Oceanography: Research and Education, University of Hawai‘i at MānoaHonolulu, HI, USA
| | - Dmitrij Turaev
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
| | | | | | - Madeleine J. H. van Oppen
- Australian Institute of Marine ScienceTownsville, QLD, Australia
- School of Biosciences, University of MelbourneMelbourne, VIC, Australia
| | | | - Thomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
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34
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Correa AMS, Ainsworth TD, Rosales SM, Thurber AR, Butler CR, Vega Thurber RL. Viral Outbreak in Corals Associated with an In Situ Bleaching Event: Atypical Herpes-Like Viruses and a New Megavirus Infecting Symbiodinium. Front Microbiol 2016; 7:127. [PMID: 26941712 PMCID: PMC4761846 DOI: 10.3389/fmicb.2016.00127] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 01/25/2016] [Indexed: 12/03/2022] Open
Abstract
Previous studies of coral viruses have employed either microscopy or metagenomics, but few have attempted to comprehensively link the presence of a virus-like particle (VLP) to a genomic sequence. We conducted transmission electron microscopy imaging and virome analysis in tandem to characterize the most conspicuous viral types found within the dominant Pacific reef-building coral genus Acropora. Collections for this study inadvertently captured what we interpret as a natural outbreak of viral infection driven by aerial exposure of the reef flat coincident with heavy rainfall and concomitant mass bleaching. All experimental corals in this study had high titers of viral particles. Three of the dominant VLPs identified were observed in all tissue layers and budding out from the epidermis, including viruses that were ∼70, ∼120, and ∼150 nm in diameter; these VLPs all contained electron dense cores. These morphological traits are reminiscent of retroviruses, herpesviruses, and nucleocytoplasmic large DNA viruses (NCLDVs), respectively. Some 300–500 nm megavirus-like VLPs also were observed within and associated with dinoflagellate algal endosymbiont (Symbiodinium) cells. Abundant sequence similarities to a gammaretrovirus, herpesviruses, and members of the NCLDVs, based on a virome generated from five Acropora aspera colonies, corroborated these morphology-based identifications. Additionally sequence similarities to two diagnostic genes, a MutS and (based on re-annotation of sequences from another study) a DNA polymerase B gene, most closely resembled Pyramimonas orientalis virus, demonstrating the association of a cosmopolitan megavirus with Symbiodinium. We also identified several other virus-like particles in host tissues, along with sequences phylogenetically similar to circoviruses, phages, and filamentous viruses. This study suggests that viral outbreaks may be a common but previously undocumented component of natural bleaching events, particularly following repeated episodes of multiple environmental stressors.
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Affiliation(s)
- Adrienne M S Correa
- Department of Microbiology, Oregon State UniversityCorvallis, OR, USA; BioSciences at Rice, Rice UniversityHouston, TX, USA
| | - Tracy D Ainsworth
- ARC Centre of Excellence for Coral Reef Studies, James Cook University Townsville, QLD, Australia
| | | | - Andrew R Thurber
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University Corvallis, OR, USA
| | - Christopher R Butler
- Department of Microbiology, Oregon State UniversityCorvallis, OR, USA; Department of Viticulture and Enology, University of California at DavisDavis, CA, USA
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Abstract
In recent years, remarkable progress has been made in the field of virus environmental ecology. In marine ecosystems, for example, viruses are now thought to play pivotal roles in the biogeochemical cycling of nutrients and to be mediators of microbial evolution through horizontal gene transfer. The diversity and ecology of viruses in soils are poorly understood, but evidence supports the view that the diversity and ecology of viruses in soils differ substantially from those in aquatic systems. Desert biomes cover ∼ 33% of global land masses, and yet the diversity and roles of viruses in these dominant ecosystems remain poorly understood. There is evidence that hot hyperarid desert soils are characterized by high levels of bacterial lysogens and low extracellular virus counts. In contrast, cold desert soils contain high extracellular virus titers. We suggest that the prevalence of microbial biofilms in hyperarid soils, combined with extreme thermal regimens, exerts strong selection pressures on both temperate and virulent viruses. Many desert soil virus sequences show low values of identity to virus genomes in public databases, suggesting the existence of distinct and as-yet-uncharacterized soil phylogenetic lineages (e.g., cyanophages). We strongly advocate for amplification-free metavirome analyses while encouraging the classical isolation of phages from dominant and culturable microbial isolates in order to populate sequence databases. This review provides an overview of recent advances in the study of viruses in hyperarid soils and of the factors that contribute to viral abundance and diversity in hot and cold deserts and offers technical recommendations for future studies.
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36
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Blackall LL, Wilson B, van Oppen MJH. Coral-the world's most diverse symbiotic ecosystem. Mol Ecol 2015; 24:5330-47. [DOI: 10.1111/mec.13400] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 09/21/2015] [Accepted: 09/24/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Linda L. Blackall
- Department of Chemistry and Biotechnology; Faculty of Science, Engineering & Technology; Swinburne University of Technology; Melbourne Vic. 3122 Australia
| | - Bryan Wilson
- Marine Microbiology Research Group; Department of Biology; University of Bergen; Thormøhlensgate 53B 5020 Bergen Norway
| | - Madeleine J. H. van Oppen
- Australian Institute of Marine Science; PMB No. 3 Townsville MC Qld. 4810 Australia
- School of BioSciences; The University of Melbourne; Parkville Vic. 3010 Australia
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Host-Associated Metagenomics: A Guide to Generating Infectious RNA Viromes. PLoS One 2015; 10:e0139810. [PMID: 26431175 PMCID: PMC4592258 DOI: 10.1371/journal.pone.0139810] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 09/17/2015] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Metagenomic analyses have been widely used in the last decade to describe viral communities in various environments or to identify the etiology of human, animal, and plant pathologies. Here, we present a simple and standardized protocol that allows for the purification and sequencing of RNA viromes from complex biological samples with an important reduction of host DNA and RNA contaminants, while preserving the infectivity of viral particles. PRINCIPAL FINDINGS We evaluated different viral purification steps, random reverse transcriptions and sequence-independent amplifications of a pool of representative RNA viruses. Viruses remained infectious after the purification process. We then validated the protocol by sequencing the RNA virome of human body lice engorged in vitro with artificially contaminated human blood. The full genomes of the most abundant viruses absorbed by the lice during the blood meal were successfully sequenced. Interestingly, random amplifications differed in the genome coverage of segmented RNA viruses. Moreover, the majority of reads were taxonomically identified, and only 7-15% of all reads were classified as "unknown", depending on the random amplification method. CONCLUSION The protocol reported here could easily be applied to generate RNA viral metagenomes from complex biological samples of different origins. Our protocol allows further virological characterizations of the described viral communities because it preserves the infectivity of viral particles and allows for the isolation of viruses.
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38
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Wood-Charlson EM, Weynberg KD, Suttle CA, Roux S, van Oppen MJH. Metagenomic characterization of viral communities in corals: mining biological signal from methodological noise. Environ Microbiol 2015; 17:3440-9. [DOI: 10.1111/1462-2920.12803] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/23/2015] [Accepted: 01/31/2015] [Indexed: 12/16/2022]
Affiliation(s)
| | - Karen D. Weynberg
- Australian Institute of Marine Science; PMB 3 Townsville MC Townsville Qld 4810 Australia
| | - Curtis A. Suttle
- Departments of Earth, Ocean and Atmospheric Sciences; Microbiology and Immunology; Botany and the Canadian Institute for Advanced Research; University of British Columbia; Vancouver BC Canada
| | - Simon Roux
- Laboratoire Micro-organismes: Genome and Environment; Université Blaise Pascal; Clermont Université; Clermont-Ferrand France
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Tseng CH, Chiang PW, Lai HC, Shiah FK, Hsu TC, Chen YL, Wen LS, Tseng CM, Shieh WY, Saeed I, Halgamuge S, Tang SL. Prokaryotic assemblages and metagenomes in pelagic zones of the South China Sea. BMC Genomics 2015; 16:219. [PMID: 25879764 PMCID: PMC4373125 DOI: 10.1186/s12864-015-1434-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/06/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Prokaryotic microbes, the most abundant organisms in the ocean, are remarkably diverse. Despite numerous studies of marine prokaryotes, the zonation of their communities in pelagic zones has been poorly delineated. By exploiting the persistent stratification of the South China Sea (SCS), we performed a 2-year, large spatial scale (10, 100, 1000, and 3000 m) survey, which included a pilot study in 2006 and comprehensive sampling in 2007, to investigate the biological zonation of bacteria and archaea using 16S rRNA tag and shotgun metagenome sequencing. RESULTS Alphaproteobacteria dominated the bacterial community in the surface SCS, where the abundance of Betaproteobacteria was seemingly associated with climatic activity. Gammaproteobacteria thrived in the deep SCS, where a noticeable amount of Cyanobacteria were also detected. Marine Groups II and III Euryarchaeota were predominant in the archaeal communities in the surface and deep SCS, respectively. Bacterial diversity was higher than archaeal diversity at all sampling depths in the SCS, and peaked at mid-depths, agreeing with the diversity pattern found in global water columns. Metagenomic analysis not only showed differential %GC values and genome sizes between the surface and deep SCS, but also demonstrated depth-dependent metabolic potentials, such as cobalamin biosynthesis at 10 m, osmoregulation at 100 m, signal transduction at 1000 m, and plasmid and phage replication at 3000 m. When compared with other oceans, urease at 10 m and both exonuclease and permease at 3000 m were more abundant in the SCS. Finally, enriched genes associated with nutrient assimilation in the sea surface and transposase in the deep-sea metagenomes exemplified the functional zonation in global oceans. CONCLUSIONS Prokaryotic communities in the SCS stratified with depth, with maximal bacterial diversity at mid-depth, in accordance with global water columns. The SCS had functional zonation among depths and endemically enriched metabolic potentials at the study site, in contrast to other oceans.
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Affiliation(s)
- Ching-Hung Tseng
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan.
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan.
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
| | - Hung-Chun Lai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.
| | - Fuh-Kwo Shiah
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan.
| | - Ting-Chang Hsu
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan.
| | - Yi-Lung Chen
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan.
| | - Liang-Saw Wen
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.
| | - Chun-Mao Tseng
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.
| | - Wung-Yang Shieh
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.
| | - Isaam Saeed
- Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Victoria, Australia.
| | - Saman Halgamuge
- Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Victoria, Australia.
| | - Sen-Lin Tang
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan.
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.
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