“Filling the void in the virosphere”


A single RNA virus, SARS-CoV-2, has changed the lives of billions of people over the past three years. What if I told you that a recent expedition discovered over 5,500 new species of RNA viruses in the world’s oceans? Do not be nervous. Humans don’t have to worry. RNA viruses in the ocean do more than just kill their hosts; they have a role in maintaining the balance of the ocean ecosystem and can even help to mitigate climate change.

The discovery of the new viruses was reported in the journal Science in April. The research team, led by Ohio State University microbiology professor Matthew Sullivan, analyzed samples collected a decade ago by the Tara Oceans expedition.

By combining machine learning approaches, the team built a phylogenetic tree that ultimately doubled the number of phyla (groups of species with similar characteristics) of RNA viruses from five to 10.

Guillermo Dominguez-Huerta, postdoctoral researcher in Sullivan’s lab and co-author of the paper, said, “What excites me the most is that we are closer to understanding the true history of evolution and RNA virus ecology – what happens with viruses in nature, especially in the oceans.

Courtesy of the Tara Ocean Foundation

Researchers aboard the schooner called Tara (pictured here and above) collected 40,000 ocean samples which led to the discovery of more than 5,500 new marine RNA viruses.

Tara: The Unsung Hero

The 36-meter schooner was built in 1989 for French physician and explorer Jean-Louis Étienne, who a few years earlier had become the first to reach the North Pole on skis solo. He used the ship to study the polar regions of Antarctica, which is why its original name was Antarctica.

A decade later she was purchased by a famous regatta sailor, Peter Blake, who named her Seamaster and won the America’s Cup, the oldest international sailing competition, twice for his Nova Scotia. Native Zealand. After retiring from sailing and driven by his love of the oceans, Blake used the Seamaster to defend the importance of the oceans until he was fatally shot by pirates off the coast of Brazil in 2001.

French fashion designer agnès b. and his son Étienne Bourgois acquired the ship, which they renamed Tara, in 2003 and founded the Tara Ocean Foundation to conduct scientific research for the protection of the ocean.

Courtesy of Chris Bowler

Chris Bowler is director of research at the Institute of Biology of the École Normale Supérieure in Paris and president of the scientific committee of the Tara Ocean Foundation.

Tara left her French home port of Lorient for her first expedition in 2006 as part of the fourth International Polar Year, an interdisciplinary, collaborative and international program focused on research in the polar regions. With 11 crew members on board collecting climate data, Tara spent months adrift with the pack ice of the Arctic Ocean.

“The Arctic Drift was a very difficult project. There were scientists on board who remained alone for nine months,” explains Chris Bowler, research director at the Institute of Biology at the École Normale Supérieure in Paris and Chairman of the Scientific Committee of the Tara Ocean Foundation. “But they all succeeded, and it was a huge success as a research program, laying the groundwork for using the ship to explore marine biodiversity and its relationship to climate.”

From 2009 to 2013, researchers aboard Tara collected samples from 210 sites in the Atlantic, Pacific, Arctic and Indian oceans to showcase unseen aquatic life. At each sampling site, the researchers sampled the entire water column from the surface down to 1,000 meters below for all different types of microscopic life – from the smallest viruses (20 nm) to zooplankton (1- 2mm).

“These organisms span five orders of magnitude. It’s like going from an ant to a brontosaurus in a forest ecosystem,” Bowler said. “These samples had been collected in a very standardized way, allowing ocean researchers around the world to compare everything with everything else, and that was the beauty of our sampling.”

Milena Cerda rinses samples aboard the Tara.

Develop tools to study RNA viruses

Back in Ohio, Sullivan’s group had studied DNA viruses in the ocean and their role in nutrient cycling for decades. However, studies of RNA viruses in the ocean have lagged, mainly due to the lack of tools to identify them with high confidence. Also, the fact that RNA is less stable than DNA in the environment didn’t help.

Previous efforts to classify RNA viruses focused primarily on those that cause disease in livestock, plants, or humans. “But for viruses in the ocean, we had no host information, and there were no virus particles to study,” Dominguez-Huerta said.

Courtesy of the Tara Ocean Foundation

The wet lab on board Tara.

The team therefore decided that the starting point was to sequence the RNA of organisms in the ocean, and then to distinguish the RNA of hosts from the RNA of viruses.

“The journey from the expeditionary part of the project completed in 2013 by the schooner Tara to building an ocean RNA virus catalog took us nearly 10 years,” Bowler said.

The first hurdle was establishing a protocol to sequence RNA from samples from the ocean, as they are often contaminated and degraded. The French National Sequencing Center (Genoscope) has done so. The second challenge was to develop methods for analyzing the sequencing data, and this is where the Sullivan lab’s expertise in bioinformatics and ocean viruses came into action.

Analysis to distinguish viral RNA was based on the RNA sequence of a signature gene called RNA-dependent RNA polymerase, or RdRp, which is unique to RNA viruses.

“RdRp has evolved over billions of years in RNA viruses and therefore its sequence is highly divergent, making it difficult to align by traditional methods,” said Dominguez-Huerta. The team therefore used machine learning to organize the divergence of the RdRp sequences by aligning only the functional domain of the protein, which should most closely reflect its evolution.

In addition to the primary sequence of RdRp, the team examined the different types of genes that RNA viruses possess, their genomic architecture and the 3D structure of RdRp to confirm the identification of five new phyla.

The most abundant newly identified species belong to a proposed phylum appropriately named Taraviricota.

“An intriguing feature of the phylum is that the 3D structure of RdRp is very similar to reverse transcriptase (RNA-dependent DNA polymerase), suggesting that they may be a missing link in the early evolution of the virus. to RNA and the origin of life”, Dominguez – said Huerta.

RNA viruses and climate change

What are these viruses doing in the ocean? In a follow-up study, the Ohio team determined that these viruses primarily infect microbial eukaryotes, such as protist and fungal hosts, as well as a few invertebrates.

Guillermo Dominguez-Huerta was a postdoctoral researcher in the lab of Matthew Sullivan at Ohio State University and co-author of the paper reporting the discovery of new RNA viruses from the ocean.

These viral hosts play an important role in carbon export – the process by which carbon is extracted from the atmosphere, fixed in marine organisms, and then exported to the depths of the ocean as those organisms sink to the seabed. . By infecting these organisms, RNA viruses likely affect how carbon moves through the ocean in general.

RNA viruses can also drive carbon flux by opening their hosts during lysis and dumping sequestered carbon into the ocean.

“The team also unexpectedly found that 95 of the RNA viruses carried genes they had ‘stolen’ from their host cells,” Dominguez-Huerta said in an interview with Live Science.

In the host, these genes help direct metabolic processes within the cell and have therefore been termed helper metabolic genes, or AMGs. This finding suggests that viruses manipulate their hosts’ metabolisms to maximize the production of new viral particles and evade host immune responses.

The Future of Tara and Ocean Viruses

What scientists aboard Tara and in land-based labs have achieved is incredible, but the sampling is just a snapshot of the diversity of the oceans.

“What we need to do is go back and do more longitudinal time series — to understand how the ocean is changing and what the future of the ocean looks like,” Bowler said.

Dominguez–Huerta added, “This project was challenging—finding the tools to identify viruses and ensure they’re validated—but we’re still early days. We know less than 1% of RNA viruses on Earth. So many questions still unanswered. Here, we provide a roadmap for other researchers to begin filling the void in the virosphere.

Courtesy of the Tara Ocean Foundation

Léa Olivier aboard Tara.

A look back at the Tara Oceans expedition

Michel Sieraki

The National Science Foundation’s Michael Sieracki was among those aboard the Tara during the Tara Oceans expedition. In 2015, he published a reflection on the experiment in the Bulletin of the Association for the Sciences of Limnology and Oceanography. Here is an exerpt :

“In a way, Tara Oceans felt like an oceanography of the past – a throwback to the heroic era of expeditionary science – like the Challenger Expedition or the Voyage of the Beagle, or the first mountaineers and polar explorers. here we get these experiences vicariously from robots on Mars or GoPro videos of extreme gravity sports To the young scientists coming into our field, I have to say that the adventure of oceanography is not over We need to stay open to new ways of looking at it and open to the risks to get there. Discovery is the lifeblood of science. The rewards might be better than you can imagine.

Courtesy of the Tara Ocean Foundation

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