Diversity and population structure of a near-shore marine-sediment viral community.
Mya Breitbart,Ben Felts,Scott T. Kelley,Joseph M. Mahaffy,James Nulton,Peter Salamon,Forest Rohwer +6 more
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TLDR
It is proposed that marine–sediment viral communities are one of the largest unexplored reservoirs of sequence space on the planet.Abstract:
Viruses, most of which are phage, are extremely abundant in marine sediments, yet almost nothing is known about their identity or diversity. We present the metagenomic analysis of an uncultured near–shore marine–sediment viral community. Three–quarters of the sequences in the sample were not related to anything previously reported. Among the sequences that could be identified, the majority belonged to double–stranded DNA phage. Temperate phage were more common than lytic phage, suggesting that lysogeny may be an important lifestyle for sediment viruses. Comparisons between the sediment sample and previously sequenced seawater viral communities showed that certain phage phylogenetic groups were abundant in all marine viral communities, while other phage groups were under–represented or absent. This ‘marineness’ suggests that marine phage are derived from a common set of ancestors. Several independent mathematical models, based on the distribution of overlapping shotgun sequence fragments from the library, were used to show that the diversity of the viral community was extremely high, with at least 10 4 viral genotypes per kilogram of sediment and a Shannon index greater than 9 nats. Based on these observations we propose that marine–sediment viral communities are one of the largest unexplored reservoirs of sequence space on the planet.read more
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Marine viruses — major players in the global ecosystem
TL;DR: Viruses are by far the most abundant 'lifeforms' in the oceans and are the reservoir of most of the genetic diversity in the sea, thereby driving the evolution of both host and viral assemblages.
Journal ArticleDOI
Viruses in the sea
TL;DR: The understanding of the effect of viruses on global systems and processes continues to unfold, overthrowing the idea that viruses and virus-mediated processes are sidebars to global processes.
Journal ArticleDOI
UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context.
TL;DR: Analysis of previously published sequences from the Columbia river, its estuary, and the adjacent coastal ocean using the UniFrac interface provided insights that were not apparent from the initial data analysis, which used other commonly employed techniques to compare the communities.
Journal ArticleDOI
The marine viromes of four oceanic regions
Florent E. Angly,Ben Felts,Mya Breitbart,Peter Salamon,Robert Edwards,Craig H. Carlson,Amy M. Chan,Matthew Haynes,Scott D Kelley,Hong-Hong Liu,Joseph M. Mahaffy,Jennifer E Mueller,Jim Nulton,Robert Olson,Rachel Parsons,Steve Rayhawk,Curtis A. Suttle,Forest Rohwer +17 more
TL;DR: The results support the idea that viruses are widely dispersed and that local environmental conditions enrich for certain viral types through selective pressure.
Journal ArticleDOI
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.
Shibu Yooseph,Granger G. Sutton,Douglas B. Rusch,Aaron L. Halpern,Shannon J. Williamson,Karin A. Remington,Jonathan A. Eisen,Jonathan A. Eisen,Karla B. Heidelberg,Gerard Manning,Weizhong Li,Lukasz Jaroszewski,Piotr Cieplak,Christopher S. Miller,Huiying Li,Susan T. Mashiyama,Marcin P. Joachimiak,Christopher van Belle,John-Marc Chandonia,John-Marc Chandonia,David A W Soergel,Yufeng Zhai,Kannan Natarajan,Shaun W. Lee,Benjamin J. Raphael,Vineet Bafna,Robert Friedman,Steven E. Brenner,Adam Godzik,David Eisenberg,Jack E. Dixon,Susan S. Taylor,Robert L. Strausberg,Marvin Frazier,J. Craig Venter +34 more
TL;DR: This work used sequence similarity clustering to explore proteins with a comprehensive dataset consisting of sequences from available databases together with 6.12 million proteins predicted from an assembly of 7.7 million Global Ocean Sampling sequences to add a great deal of diversity to known protein families and shed light on their evolution.
References
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