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Scientists Discover Nearly 200,000 Kinds of Ocean Viruses

Author: Jonathan Lambert / Source: WIRED

Michelle Yun/Quanta Magazine; source: brgfx

Every time you swallow a mouthful of seawater while swimming at the beach, you’re downing about as many viruses as there are people in North America.

However, despite the staggering abundance of marine viruses—and the key role that these infectious agents seem to play in global processes like the carbon cycle—scientists still know relatively little about the variety of viruses that are out there.

In 2015 a team documented 5,476 distinct kinds of viruses in the ocean. In 2016 the same team updated its count to 15,222.

But in a study published this week in Cell, that number skyrockets to 195,728 distinct viral populations, a more than twelvefold increase.

“This is a pretty amazing study,” said Louis-Marie Bobay, a microbial genomicist from the University of North Carolina-Greensboro, who was not involved in the work. “We know so little about viral ecology in much of the ocean, and this is some of the most impressive, and global, data ever collected.”

The twelvefold leap was enabled by an ambitious global sampling expedition and more sophisticated genomic analysis.
Although the oceans cover 70 percent of our planet, until a few years ago most knowledge of marine viral diversity came from only a few well-studied locations. That changed with the Tara Oceans project, which sought a more complete inventory of marine microbial and viral diversity by sampling all over the globe. The schooner Tara has made its way around the ocean, collecting samples from the surface to the depths and from pole to pole. The new study included samples from 43 locations in the Arctic that weren’t used in the 2015 and 2016 studies.

About 40 percent of the novel virus populations came from the new Arctic samples. The rest came from reanalysis of Tara samples used for the earlier studies. “The algorithms we use to assemble viral genomes out of chunks of DNA got much, much better,” said Ann Gregory, a microbial ecologist at the Catholic University of Leuven in Belgium and one of the lead authors of the study.

As well as piecing together strands of DNA out of fragments, Gregory and her colleagues had to settle on a way to classify the variety of virus genomes they were seeing. Defining a viral “species” is controversial, as viruses reproduce asexually and frequently swap DNA with one another and their hosts. Because viruses don’t contain the necessary machinery to replicate independently, some biologists do not consider viruses even fully “alive.”

Jennifer Brum/Sullivan Lab at Ohio State

Instead of species, Gregory classified the viruses into “populations” in which “there’s more gene flow within a group than between groups of viruses.” If sequenced viruses shared at least 95 percent of their DNA, she called them members of the same discrete population.

This method yielded nearly 200,000 populations. About 90 percent of them…

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