Ocean water samples yield treasure trove of RNA virus data

April 20, 2022

Ocean water samples yield treasure trove of RNA virus data

Image
Matthew Sullivan
Description

Study of organisms in the sea identifies 5,500 new species

By: Emily Caldwell (caldwell.151@osu.edu)

Ohio State news


Ocean water samples collected around the world have yielded a treasure trove of new data about RNA viruses, expanding ecological research possibilities and reshaping our understanding of how these small but significant submicroscopic particles evolved.

Combining machine-learning analyses with traditional evolutionary trees, an international team of researchers has identified 5,500 new RNA virus species that represent all five known RNA virus phyla and suggest there are at least five new RNA virus phyla needed to capture them.

The most abundant collection of newly identified species belong to a proposed phylum researchers named Taraviricota, a nod to the source of the 35,000 water samples that enabled the analysis: the Tara Oceans Consortium, an ongoing global study onboard the schooner Tara of the impact of climate change on the world’s oceans.

“There’s so much new diversity here – and an entire phylum, the Taraviricota, were found all over the oceans, which suggests they’re ecologically important,” said lead author Matthew Sullivan, professor of microbiology at The Ohio State University.

“RNA viruses are clearly important in our world, but we usually only study a tiny slice of them – the few hundred that harm humans, plants and animals. We wanted to systematically study them on a very big scale and explore an environment no one had looked at deeply, and we got lucky because virtually every species was new, and many were really new.”

The study appears online today (April 7, 2022) in Science.

While microbes are essential contributors to all life on the planet, viruses that infect or interact with them have a variety of influences on microbial functions. These types of viruses are believed to have three main functions: killing cells, changing how infected cells manage energy, and transferring genes from one host to another.

Knowing more about virus diversity and abundance in the world’s oceans will help explain marine microbes’ role in ocean adaptation to climate change, the researchers say. Oceans absorb half of the human-generated carbon dioxide from the atmosphere, and previous research by this group has suggested that marine viruses are the “knob” on a biological pump affecting how carbon in the ocean is stored.

 

Ahmed Zayed

Ahmed Zayed

By taking on the challenge of classifying RNA viruses, the team entered waters still rippling from earlier taxonomy categorization efforts that focused mostly on RNA viral pathogens. Within the biological kingdom Orthornavirae, five phyla were recently recognized by the International Committee on Taxonomy of Viruses (ICTV).

Though the research team identified hundreds of new RNA virus species that fit into those existing divisions, their analysis identified thousands more species that they clustered into five new proposed phyla: Taraviricota, Pomiviricota, Paraxenoviricota, Wamoviricota and Arctiviricota, which, like Taraviricota, features highly abundant species – at least in climate-critical Arctic Ocean waters, the area of the world where warming conditions wreak the most havoc.

Sullivan’s team has long cataloged DNA virus species in the oceans, growing the numbers from a few thousand in 2015 and 2016 to 200,000 in 2019. For those studies, scientists had access to viral particles to complete the analysis.

In these current efforts to detect RNA viruses, there were no viral particles to study. Instead, researchers extracted sequences from genes expressed in organisms floating in the sea, and narrowed the analysis to RNA sequences that contained a signature gene, called RdRp, which has evolved for billions of years in RNA viruses, and is absent from other viruses or cells.

The schooner Tara is a floating laboratory enabling the collection of samples around the world that are being cataloged to better understand the unseen inhabitants of the ocean, from tiny animals to viruses and bacteria. Copyright Maeva Bardy - Tara Ocean Foundation

Because RdRp’s existence dates to when life was first detected on Earth, its sequence position has diverged many times, meaning traditional phylogenetic tree relationships were impossible to describe with sequences alone. Instead, the team used machine learning to organize 44,000 new sequences in a way that could handle these billions of years of sequence divergence, and validated the method by showing the technique could accurately classify sequences of RNA viruses already identified.

For the full story, please visit Ohio State news.

 

Additional co-authors on the paper were co-lead authors James Wainaina and Guillermo Dominguez-Huerta, as well as Jiarong Guo, Mohamed Mohssen, Funing Tian, Adjie Pratama, Ben Bolduc, Olivier Zablocki, Dylan Cronin and Lindsay Solden, all of Sullivan’s lab; Ralf Bundschuh, Kurt Fredrick, Laura Kubatko and Elan Shatoff of Ohio State’s College of Arts and Sciences; Hans-Joachim Ruscheweyh, Guillem Salazar and Shinichi Sunagawa of the Institute of Microbiology and Swiss Institute of Bioinformatics; Jens Kuhn of the National Institute of Allergy and Infectious Diseases; Alexander Culley of the Université Laval; Erwan Delage and Samuel Chaffron of the Université de Nantes; and Eric Pelletier, Adriana Alberti, Jean-Marc Aury, Quentin Carradec, Corinne da Silva, Karine Labadie, Julie Poulain and Patrick Wincker of Genoscope.