Access the full text.
Sign up today, get DeepDyve free for 14 days.
Emiko Sano, S. Carlson, L. Wegley, F. Rohwer (2004)
Movement of Viruses between BiomesApplied and Environmental Microbiology, 70
M. Breitbart, I. Hewson, B. Felts, J. Mahaffy, J. Nulton, P. Salamon, F. Rohwer (2003)
Metagenomic Analyses of an Uncultured Viral Community from Human FecesJournal of Bacteriology, 185
E. Dinsdale, R. Edwards, Dana Hall, Florent Angly, M. Breitbart, Jennifer Brulc, Mike Furlan, C. Desnues, Matthew Haynes, Linlin Li, L. McDaniel, M. Moran, K. Nelson, Christina Nilsson, R. Olson, J. Paul, Beltran Brito, Y. Ruan, B. Swan, Rick Stevens, D. Valentine, R. Thurber, L. Wegley, B. White, F. Rohwer (2008)
Functional metagenomic profiling of nine biomesNature, 452
M. Bose, R. Barber (2006)
Prophage Finder: A Prophage Loci Prediction Tool for Prokaryotic Genome SequencesIn silico biology, 6 3
J. Fuhrman (1999)
Marine viruses and their biogeochemical and ecological effectsNature, 399
R. Sender, Shai Fuchs, R. Milo (2016)
Revised Estimates for the Number of Human and Bacteria Cells in the BodyPLoS Biology, 14
R. Danovaro, M. Serresi (2000)
Viral Density and Virus-to-Bacterium Ratio in Deep-Sea Sediments of the Eastern MediterraneanApplied and Environmental Microbiology, 66
M. Youle, Matthew Haynes, F. Rohwer (2012)
Scratching the Surface of Biology's Dark Matter
C. Suttle (2007)
Marine viruses — major players in the global ecosystemNature Reviews Microbiology, 5
Ø. Bergh, Knut BØrsheim, G. Bratbak, M. Heldal (1989)
High abundance of viruses found in aquatic environmentsNature, 340
I. Herskowitz, D. Hagen (1980)
The lysis-lysogeny decision of phage lambda: explicit programming and responsiveness.Annual review of genetics, 14
Siobhan Watkins, Neil Kuehnle, C. Ruggeri, Kema Malki, Katherine Bruder, Jinan Elayyan, Kristina Damisch, Naushin Vahora, Brianne Ruggles-Sage, Zachary Romer, C. Putonti (2016)
Assessment of a metaviromic dataset generated from nearshore Lake MichiganMarine and Freshwater Research, 67
Katelyn McNair, Barbara Bailey, R. Edwards (2012)
PHACTS, a computational approach to classifying the lifestyle of phagesBioinformatics, 28
Sajia Akhter, R. Aziz, R. Edwards (2012)
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategiesNucleic Acids Research, 40
Kyoung-Ho Kim, J. Bae (2011)
Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded and Double-Stranded DNA VirusesApplied and Environmental Microbiology, 77
Tim Engelhardt, J. Kallmeyer, H. Cypionka, B. Engelen (2014)
High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sedimentsThe ISME Journal, 8
L. Fu, B. Niu, Zhengwei Zhu, Sitao Wu, Weizhong Li (2012)
CD-HIT: accelerated for clustering the next-generation sequencing dataBioinformatics, 28
Jeremy Frank, D. Lorimer, M. Youle, P. Witte, T. Craig, J. Abendroth, F. Rohwer, R. Edwards, A. Segall, A. Burgin (2013)
Structure and function of a cyanophage-encoded peptide deformylaseThe ISME Journal, 7
J. Staley, A. Konopka (1985)
Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats.Annual review of microbiology, 39
R. Sandaa, Laura Gómez-Consarnau, Jarone Pinhassi, L. Riemann, A. Malits, M. Weinbauer, J. Gasol, T. Thingstad (2009)
Viral control of bacterial biodiversity--evidence from a nutrient-enriched marine mesocosm experiment.Environmental microbiology, 11 10
A. Ortmann, C. Suttle (2005)
High abundances of viruses in a deep-sea hydrothermal vent system indicates viral mediated microbial mortality, 52
R. García-López, J. Vázquez-Castellanos, A. Moya (2015)
Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity CalculationsFrontiers in Bioengineering and Biotechnology, 3
A. Comeau, H. Krisch (2008)
The capsid of the T4 phage superfamily: the evolution, diversity, and structure of some of the most prevalent proteins in the biosphere.Molecular biology and evolution, 25 7
J. Barr, Rita Auro, Mike Furlan, K. Whiteson, M. Erb, J. Pogliano, Aleksandr Stotland, R. Wolkowicz, A. Cutting, K. Doran, P. Salamon, M. Youle, F. Rohwer (2013)
Bacteriophage adhering to mucus provide a non–host-derived immunityProceedings of the National Academy of Sciences, 110
M. Duhaime, M. Sullivan (2012)
Ocean viruses: rigorously evaluating the metagenomic sample-to-sequence pipeline.Virology, 434 2
Min-Soo Kim, E. Park, S. Roh, J. Bae (2011)
Diversity and Abundance of Single-Stranded DNA Viruses in Human FecesApplied and Environmental Microbiology, 77
Dawn Goldsmith, R. Parsons, Damitu Beyene, P. Salamon, M. Breitbart (2015)
Deep sequencing of the viral phoH gene reveals temporal variation, depth-specific composition, and persistent dominance of the same viral phoH genes in the Sargasso SeaPeerJ, 3
Shin Haruta, Angel Valverde, Takeshi Miki, Andreas Haas, T. Thingstad, Thingstad Tf, B. Pree, J. Giske, Selina Våge (2015)
What difference does it make if viruses are strain-, rather than species-specific?Frontiers in Microbiology, 6
Bhakti Dwivedi, Robert Schmieder, Dawn Goldsmith, R. Edwards, M. Breitbart (2012)
PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversityBMC Bioinformatics, 13
D. Fouts (2006)
Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequencesNucleic Acids Research, 34
M. Breitbart, J. Miyake, F. Rohwer (2004)
Global distribution of nearly identical phage-encoded DNA sequences.FEMS microbiology letters, 236 2
L. Proctor, J. Fuhrman (1990)
Viral mortality of marine bacteria and cyanobacteriaNature, 343
Cindy Short, C. Suttle (2005)
Nearly Identical Bacteriophage Structural Gene Sequences Are Widely Distributed in both Marine and Freshwater EnvironmentsApplied and Environmental Microbiology, 71
Emma Rocke, M. Pachiadaki, A. Cobban, E. Kujawinski, V. Edgcomb (2015)
Protist Community Grazing on Prokaryotic Prey in Deep Ocean Water MassesPLoS ONE, 10
D. Lindell, M. Sullivan, Z. Johnson, Andrew Tolonen, F. Rohwer, S. Chisholm (2004)
Transfer of photosynthesis genes to and from Prochlorococcus viruses.Proceedings of the National Academy of Sciences of the United States of America, 101 30
A. Chao (1984)
Nonparametric estimation of the number of classes in a populationScandinavian Journal of Statistics, 11
Sijun Huang, S. Wilhelm, N. Jiao, F. Chen (2010)
Ubiquitous cyanobacterial podoviruses in the global oceans unveiled through viral DNA polymerase gene sequencesThe ISME Journal, 4
A. Lang, Olga Zhaxybayeva, Olga Zhaxybayeva, J. Beatty (2012)
Gene transfer agents: phage-like elements of genetic exchangeNature Reviews Microbiology, 10
M. Breitbart, F. Rohwer (2005)
Here a virus, there a virus, everywhere the same virus?Trends in microbiology, 13 6
B. Knowles, C. Silveira, Barbara Bailey, K. Barott, V. Cantu, A. Cobián-Güemes, F. Coutinho, E. Dinsdale, B. Felts, K. Furby, E. George, Kevin Green, G. Gregoracci, A. Haas, J. Haggerty, E. Hester, Nao Hisakawa, L. Kelly, Y. Lim, M. Little, A. Luque, T. McDole-Somera, Katelyn McNair, L. Oliveira, S. Quistad, N. Robinett, E. Sala, P. Salamon, P. Salamon, S. Sanchez, S. Sandin, G. Silva, J. Smith, Christopher Sullivan, C. Thompson, M. Vermeij, M. Youle, C. Young, B. Zgliczynski, R. Brainard, Robert Edwards, J. Nulton, Fabiano Thompson, F. Rohwer, F. Rohwer (2016)
Lytic to temperate switching of viral communitiesNature, 531
C. Canchaya, G. Fournous, Sandra Chibani-Chennoufi, M. Dillmann, H. Brüssow (2003)
Phage as agents of lateral gene transfer.Current opinion in microbiology, 6 4
Cheryl-Emiliane Chow, J. Fuhrman (2012)
Seasonality and monthly dynamics of marine myovirus communities.Environmental microbiology, 14 8
T. Thingstad (2000)
Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systemsLimnology and Oceanography, 45
J. Ignacio-Espinoza, Sergei Solonenko, M. Sullivan (2013)
The global virome: not as big as we thought?Current opinion in virology, 3 5
M. Kimura (1962)
On the probability of fixation of mutant genes in a population.Genetics, 47
Evelien Adriaenssens, L. Zyl, P. Maayer, Enrico Rubagotti, E. Rybicki, M. Tuffin, D. Cowan (2015)
Metagenomic analysis of the viral community in Namib Desert hypoliths.Environmental microbiology, 17 2
Luis Jover, T. Effler, A. Buchan, S. Wilhelm, J. Weitz (2014)
The elemental composition of virus particles: implications for marine biogeochemical cyclesNature Reviews Microbiology, 12
E. Jameson, N. Mann, I. Joint, C. Sambles, M. Mühling (2011)
The diversity of cyanomyovirus populations along a North–South Atlantic Ocean transectThe ISME Journal, 5
C. Suttle (2005)
Viruses in the seaNature, 437
M. Sullivan, D. Lindell, J. Lee, Luke Thompson, J. Bielawski, S. Chisholm (2006)
Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their HostsPLoS Biology, 4
N. Fierer, M. Breitbart, J. Nulton, P. Salamon, C. Lozupone, R. Jones, M. Robeson, R. Edwards, B. Felts, Steve Rayhawk, R. Knight, F. Rohwer, R. Jackson (2007)
Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in SoilApplied and Environmental Microbiology, 73
A. Pagarete, Cheryl-Emiliane Chow, T. Johannessen, J. Fuhrman, T. Thingstad, R. Sandaa (2013)
Strong Seasonality and Interannual Recurrence in Marine Myovirus CommunitiesApplied and Environmental Microbiology, 79
Ching-Hung Tseng, Pei-Wen Chiang, F. Shiah, Yi-Lung Chen, Jia-Rong Liou, Ting-Chang Hsu, S. Maheswararajah, Isaam Saeed, S. Halgamuge, Sen-Lin Tang (2013)
Microbial and viral metagenomes of a subtropical freshwater reservoir subject to climatic disturbancesThe ISME Journal, 7
Matthew Haynes, F. Rohwer (2010)
The Human ViromeMetagenomics of the Human Body
F. Rohwer (2003)
Global Phage DiversityCell, 113
William Whitman, D. Coleman, W. Wiebe (1998)
Prokaryotes: the unseen majority.Proceedings of the National Academy of Sciences of the United States of America, 95 12
M. Breitbart, P. Salamon, B. Andresen, J. Mahaffy, A. Segall, D. Mead, F. Azam, F. Rohwer (2002)
Genomic analysis of uncultured marine viral communitiesProceedings of the National Academy of Sciences of the United States of America, 99
J. Mokili, F. Rohwer, B. Dutilh (2012)
Metagenomics and future perspectives in virus discoveryCurrent Opinion in Virology, 2
K. Wommack, R. Colwell (2000)
Virioplankton: Viruses in Aquatic EcosystemsMicrobiology and Molecular Biology Reviews, 64
M. Duhaime, L. Deng, B. Poulos, M. Sullivan (2012)
Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification methodEnvironmental Microbiology, 14
F. Rohwer, R. Edwards (2002)
The Phage Proteomic Tree: a Genome-Based Taxonomy for PhageJournal of Bacteriology, 184
Evelien Adriaenssens, D. Cowan (2014)
Using Signature Genes as Tools To Assess Environmental Viral Ecology and DiversityApplied and Environmental Microbiology, 80
J. Paul (1999)
Microbial gene transfer: an ecological perspective.Journal of molecular microbiology and biotechnology, 1 1
F. Torrella, R. Morita (1979)
Evidence by electron micrographs for a high incidence of bacteriophage particles in the waters of Yaquina Bay, oregon: ecological and taxonomical implicationsApplied and Environmental Microbiology, 37
R. Tuma, Matthew Beaudet, Xiaokui Jin, L. Jones, C. Cheung, S. Yue, V. Singer (1999)
Characterization of SYBR Gold nucleic acid gel stain: a dye optimized for use with 300-nm ultraviolet transilluminators.Analytical biochemistry, 268 2
B. Bolduc, J. Wirth, Aurélien Mazurie, M. Young (2015)
Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysisThe ISME Journal, 9
Jennifer Brum, M. Sullivan (2015)
Rising to the challenge: accelerated pace of discovery transforms marine virologyNature Reviews Microbiology, 13
J. Weitz, C. Stock, S. Wilhelm, L. Bourouiba, Maureen Coleman, A. Buchan, M. Follows, J. Fuhrman, Luis Jover, J. Lennon, M. Middelboe, D. Sonderegger, C. Suttle, Bradford Taylor, T. Thingstad, W. Wilson, K. Wommack (2015)
A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processesThe ISME Journal, 9
Kurt Williamson, M. Radosevich, K. Wommack (2005)
Abundance and Diversity of Viruses in Six Delaware SoilsApplied and Environmental Microbiology, 71
Jennifer Brum, B. Hurwitz, O. Schofield, H. Ducklow, M. Sullivan (2015)
Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamicsThe ISME Journal, 10
V. Casas, J. Miyake, Heather Balsley, J. Roark, S. Telles, Steven Leeds, I. Zurita, M. Breitbart, Doug Bartlett, F. Azam, F. Rohwer (2006)
Widespread occurrence of phage-encoded exotoxin genes in terrestrial and aquatic environments in Southern California.FEMS microbiology letters, 261 1
S. Roux, François Enault, V. Ravet, J. Colombet, Y. Bettarel, J. Auguet, T. Bouvier, S. Lucas-Staat, A. Vellet, D. Prangishvili, P. Forterre, D. Debroas, T. Sime-Ngando (2016)
Analysis of metagenomic data reveals common features of halophilic viral communities across continents.Environmental microbiology, 18 3
J. Kallmeyer, R. Pockalny, R. Adhikari, David Smith, S. D’Hondt (2012)
Global distribution of microbial abundance and biomass in subseafloor sedimentProceedings of the National Academy of Sciences, 109
M. Weinbauer (2004)
Ecology of prokaryotic viruses.FEMS microbiology reviews, 28 2
M. Breitbart, B. Felts, S. Kelley, J. Mahaffy, J. Nulton, P. Salamon, F. Rohwer (2004)
Diversity and population structure of a near–shore marine–sediment viral communityProceedings of the Royal Society of London. Series B: Biological Sciences, 271
C. Chénard, C. Suttle (2008)
Phylogenetic Diversity of Sequences of Cyanophage Photosynthetic Gene psbA in Marine and FreshwatersApplied and Environmental Microbiology, 74
U. Dorigo, S. Jacquet, J. Humbert (2004)
Cyanophage Diversity, Inferred from g20 Gene Analyses, in the Largest Natural Lake in France, Lake BourgetApplied and Environmental Microbiology, 70
J. Hobbie, R. Daley, S. Jasper (1977)
Use of nuclepore filters for counting bacteria by fluorescence microscopyApplied and Environmental Microbiology, 33
You Zhou, Yongjie Liang, K. Lynch, J. Dennis, D. Wishart (2011)
PHAST: A Fast Phage Search ToolNucleic Acids Research, 39
A. Anesio, B. Mindl, J. Laybourn-Parry, A. Hodson, B. Sattler (2007)
Viral dynamics in cryoconite holes on a high Arctic glacier (Svalbard)Journal of Geophysical Research, 112
Yan-lin Zhong, F. Chen, S. Wilhelm, Leo Poorvin, R. Hodson (2002)
Phylogenetic Diversity of Marine Cyanophage Isolates and Natural Virus Communities as Revealed by Sequences of Viral Capsid Assembly Protein Gene g20Applied and Environmental Microbiology, 68
Dawn Goldsmith, Giuseppe Crosti, Bhakti Dwivedi, L. McDaniel, A. Varsani, C. Suttle, M. Weinbauer, R. Sandaa, M. Breitbart (2011)
Development of phoH as a Novel Signature Gene for Assessing Marine Phage DiversityApplied and Environmental Microbiology, 77
Thingstad Tf, R. Lignell (1997)
THEORETICAL MODELS FOR THE CONTROL OF BACTERIAL GROWTH RATE, ABUNDANCE, DIVERSITY AND CARBON DEMANDAquatic Microbial Ecology, 13
J. Paul (2008)
Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas?The ISME Journal, 2
L. McDaniel, M. delaRosa, J. Paul (2006)
Temperate and lytic cyanophages from the Gulf of MexicoJournal of the Marine Biological Association of the United Kingdom, 86
A. Bankevich, S. Nurk, D. Antipov, A. Gurevich, M. Dvorkin, Alexander Kulikov, Valery Lesin, S. Nikolenko, Son Pham, A. Prjibelski, A. Pyshkin, Alexander Sirotkin, Nikolay Vyahhi, G. Tesler, M. Alekseyev, P. Pevzner (2012)
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell SequencingJournal of computational biology : a journal of computational molecular cell biology, 19 5
Florent Angly, B. Felts, M. Breitbart, P. Salamon, R. Edwards, C. Carlson, A. Chan, Matthew Haynes, S. Kelley, Hong Liu, J. Mahaffy, Jennifer Mueller, J. Nulton, R. Olson, R. Parsons, Steve Rayhawk, C. Suttle, F. Rohwer (2006)
The Marine Viromes of Four Oceanic RegionsPLoS Biology, 4
Viruses are the most abundant and the most diverse life form. In this meta-analysis we estimate that there are 4.80×10 31 phages on Earth. Further, 97% of viruses are in soil and sediment—two underinvestigated biomes that combined account for only ∼2.5% of publicly available viral metagenomes. The majority of the most abundant viral sequences from all biomes are novel. Our analysis drawing on all publicly available viral metagenomes observed a mere 257,698 viral genotypes on Earth—an unrealistically low number—which attests to the current paucity of viral metagenomic data. Further advances in viral ecology and diversity call for a shift of attention to previously ignored major biomes and careful application of verified methods for viral metagenomic analysis.
Annual Review of Virology – Annual Reviews
Published: Sep 29, 2016
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.