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Three-year ocean voyage discovered thousands of new, unfamiliar viruses

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A study of plankton reveals just how little we know about the ocean

Christian Sardet/CNRS/Tara Expéditions

Pirates and storms on the open seas couldn’t stop these scientists. Over the course of three and a half years, researchers traveled the world in a boat named Tara, gathering genetic information belonging to more than 35,000 plankton species that were largely unknown to humanity. By sampling viruses, microbes, fish larvae, and other microscopic organisms at depths of up to 6,561 feet, marine biologists produced the most comprehensive catalog of ocean plankton to date.

"There were pirates over there."

"We had to take some measures to avoid [pirates] and to be protected," says Romain Trouble, general secretary of the Tara Expeditions and logistics coordinator, during a press conference. "[I was] on-board the vessel with something, like, 85 knots of wind, stormy winds, stormy weather, and this happened a few times across the journey."

Credit: Christian Sardet/CNRS/Tara Expéditions

Plankton represent an incredibly important link in the chain that unites Earth's living things. They're the basis of the ocean's food web, and they produce half of the planet's oxygen. So, researchers belonging to the multinational Tara Oceans Consortium decided to that they should get to know them a bit better. They gathered thousands of samples from over 200 locations around the world between 2009 and 2013. The resulting catalog contains over 40 million genes belonging to viruses and other microscopic organisms — or about 11.5 terabytes of molecular data, most of which was unknown to science until now. With this data, the researchers answered questions about how plankton interact, how diverse they are, and what factors drive plankton community composition in a series of five studies published today in Science. Perhaps unsurprisingly, the biggest take-away from this work is that the ocean has a lot to teach us still.

11.5 terabytes of molecular data

Single-cell eukaryotes — tiny organisms with a membrane-bound nucleus — are a lot more diverse than previously thought, according to one of the Tara Oceans studies. "We estimated that marine plankton contain 150,000 genetic types of eukaryotes, which is much greater than the 11,000 species of eukaryotic plankton described in the literature," says Colomban de Vargas, a researcher at the French National Centre for Scientific Research and one of the authors of the eukaryote study. "Most of this biodiversity belongs to protists" — amoeba-like organisms — "and most of it could not or only poorly be assigned to any known genetic barcodes from our reference database."

"Protists are an incredibly diverse group of organisms, spanning many kingdoms, and the documentation of additional undescribed groups…is quite compelling," says Rebecca Shipe, a marine biologist at the University of California-Los Angeles, who didn’t take part in the Tara Expeditions.

Only 39 of these 5,000 new viruses resembled ones we know about

The researchers were also able to hone in on the most abundant biological entities in the marine ecosystem: viruses. "The majority of them infect marine micro-organisms that fuel our planet," explains Jennifer Brum, a microbial oceanographer at the University of Arizona and one of the authors behind the Tara Oceans studies. This means that ocean viruses have a big effect on the dynamics of marine ecosystems. By analyzing viruses found in the ocean samples, Brum and her team were able to generate the largest environment viral dataset ever produced — a dataset that allowed them to identify over new 5,000 viral populations throughout the global upper ocean.

"Surprisingly despite several decades of prior marine viral research, only 39 of these 5,000 viral populations were similar to previously known viruses," Brum says. "This means that the most abundant and widespread viral populations in the oceans have yet to be characterized — but now we have an idea of what viruses are important targets for future investigations."

Credit: Christian Sardet/CNRS/Tara Expéditions

The expedition also revealed that the important factor in determining the composition of microbial communities at depth still reached by sunlight is temperature. This means that microbial communities will likely be affected by rising temperatures caused by climate change. And "since the microbial community is also a part of the food web, it will have direct implications of organisms feeding on those microorganisms," says Shinichi Sunagawa, at microbiologist at the European Molecular Biology Laboratory and a Tara Oceans researcher. "What exactly and how large this impact will be is unclear, however. That "will require unfortunately more data to study this in more detail," he says.

The information about community compositions was also used to create computer models that can predict how plankton interact with each other. Then, to verify their predictions, the researchers went back to the samples. "We could obtain microscopic images showing that the interaction was really occurring," says Gipsi Lima-Mendez, a biologist at the University of Leuven and a Tara Oceans researcher. "So it's really amazing that we can have this experimental support."

The microbial diversity found in the ocean is about four times higher than in the human gut

Few large microbial environments have been studied this extensively. So the researchers decided to compare their dataset to one of the only other microbial environments that rivals it: the human gut. They found that despite containing similar amounts of data, the diversity found in the ocean is about four times higher than in the gut. That said, the functions found within the communities — things like defense mechanisms, metabolism, and energy production — weren't all that different. More than 73 percent of the ocean microbial core functions are shared with the human gut microbiome, despite the huge chemical differences that characterize these ecosystems. "It took me by surprise to see that there was a huge overlap," Sunagawa says.

Credit: M.Ormestad/Kahikai/Tara Oceans

You don't have to compare the ocean's microbial communities to the human gut to appreciate the work produced by the Tara Oceans Expeditions, however. The vastness of the dataset means that it's now possible to compare organisms found in the South Pacific with organisms found in the Indian Ocean or the Arctic — something that really couldn't have been achieved without an extended voyage of this nature. "Most of the microbes that the group studied are not organisms that can be grown easily in laboratories," Shipe says.

The effort represents the emergence of a new type of research in marine sciences, says Eric Karsenti, Tara Oceans Project Director and researcher at the European Molecular Biology Laboratory. "I am sure that yet unexpected and ground-breaking results will come out from the many laboratories around the world that will make use of this marine plankton gold mine."