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Global Ocean Virus Genome Collection Sheds Light on Ecosystem

NEW YORK (GenomeWeb) – An international team led by investigators in the US has profiled viral populations at ocean sites around the world in search of insights into the role of microbial communities in various environments.

Using samples obtained from the Malaspina research expedition and an extensive multi-year voyage called the Tara Oceans expedition, the researchers examined collections of double-stranded DNA viruses present at ocean sampling sites around the world — spanning the Pacific, Atlantic, and Indian Oceans as well as the Mediterranean Sea. In the process, they uncovered more than 15,000 viruses for the Global Oceans Viromes set, dramatically expanding double-stranded DNA viruses described in the world's oceans.

Along with interactions between these viruses and other microbes in the sea, the team examined the protein-coding capabilities of viral communities at different sites, evaluating their predicted protein functions, potential contributions to nutrient cycling, and response to climate change-related ocean acidification. The work appeared online today in Nature.

"Our work not only provides a relatively complete catalogue of surface ocean viruses, but also reveals new ways that viruses modulate greenhouse gases and energy in the oceans," first author Simon Roux, a postdoctoral researcher in senior author Matthew Sullivan's microbiology lab at Ohio State University, said in a statement.

"The ocean is a major buffer against climate change," Sullivan added. "Our suspicion is that people will leverage this buffer to their benefit."

The Tara Oceans team presented its initial findings, which included a look at viruses, prokaryotes, and tiny eukaryotic creatures in the ocean, in a set of papers published in Science earlier this year. At the time, the group revealed almost 5,500 double-stranded DNA virus populations in ocean surface waters.

For the new analysis, Roux, Sullivan, and their colleagues used the Illumina HiSeq 2000 to conduct metagenomic sequencing on viral particles concentrated out of 90 sea water samples collected at various depths at 45 locations for the Tara Ocean trip between the fall of 2009 and late 2011. They performed similar metagenomic sequencing on more than a dozen samples collected from the North Atlantic or Pacific in 2011 for the Malaspina expedition.

From 925 billion bases of sequence data, the team identified 15,222 double-stranded DNA viral populations in these samples from the upper, epipelagic portion of the water column and the deeper mesopelagic zone. The viruses clustered into 867 groups, each more or less coinciding with a different viral genus, including 38 particularly abundant clusters that turned up at two or more sampling locales.

When they focused on sequences found in the viral genomes, the researchers narrowed in on 243 viral genes that appear to code for auxiliary metabolism-related proteins. A subset of those genes seemed to contribute to processes such as sulfur and nitrogen cycling, they noted. 

"This map of global [double-stranded DNA] ocean viral diversity at the level of population and viral cluster and within viral-encoded [auxiliary metabolic genes] brings global ecological context to abundant surface- and deep-ocean viruses," Sullivan and co-authors wrote. "Together with recent experimental, bioinformatic, and theoretical advances, this fundamental resource will accelerate the understanding and prediction of the roles and planetary impacts of viruses in nature."