Ocean water samples yield treasure trove of RNA virus data

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.

An international team of researchers used machine-learning analyses and traditional evolutionary trees to identify at least 5,500 new RNA virus species that represent all five known viruses and suggest there are at least five more needed to capture them.

The source of the 35,000 water samples that enabled the analysis was the Tara Oceans Consortium, an ongoing global study on the impact of climate change.

The Taraviricota, an entire phylum, was found all over the oceans, which suggests they are important.

RNA viruses are important in our world, but we usually only study a small portion of them, the few hundred that harm humans, plants and animals. We wanted to study them on a large scale and explore an environment that no one had looked at before, and we got lucky because most of the species were new.

The study is online today.

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

The researchers say knowing more about virus diversity and abundance in the ocean will help explain the role of ocean adaptation to climate change. The ocean absorbs half of the human-generated carbon dioxide from the atmosphere, and previous research by this group has suggested that marine viruses are involved in how carbon is stored in the ocean.

The team entered the waters still rippling from earlier categorization efforts that focused mostly on RNA viral pathogens by taking on the challenge of classification. The International Committee on Taxonomy of Viruses (ICTV) recently recognized five different types of Viruses.

The research team identified hundreds of new RNA virus species that fit into the existing divisions, but they found thousands more species that were clustered into five new proposed phyla: Taraviricota, Pomiviricota, Paraxenoviricota, Wamoviricota and Arctivi

The number of DNA virus species in the ocean has grown from a few thousand in 2015 and 2016 to 200,000 in 2019. Scientists were able to complete the analysis with the help of viral particles.

There were no viral particles to study in the current efforts to detect RNA viruses. The researchers narrowed the analysis to a singleRNA sequence that contained a signature gene, called RdRp, which has evolved for billions of years in RNA viruses, and is absent from other cells.

The existence of RdRp dates to when life was first detected on Earth, meaning that traditional tree relationships were impossible to describe with sequence alone. Instead, the team used machine learning to organize 44,000 new sequences in a way that could handle billions of years of sequence divergence, and validation of the method was achieved by showing the technique could accurately classify sequences of RNA viruses already identified.

Sullivan is a professor of civil, environmental and geodetic engineering and founding director of the Center of Microbiome Science at Ohio State.

We have created a way to align the sequence to where we can be more confident that we are aligning positions that reflect evolution.

The cluster of 5,500 new species didn't fit into the five existing viruses categorized in the Orthornavirae kingdom.

We benchmarked our clusters against established, recognized phylogeny-based taxa, and that's how we found we have more clusters than those that existed.

The findings led the researchers to propose at least 11 new orthornaviran classes of RNA viruses. A proposal is being prepared to request formalization of the candidate classes by the ICTV.

A better understanding of how early life may have evolved on the planet can be achieved by the extent of new data on the RdRp gene.

He said that RdRp is one of the most ancient genes and that it existed before there was a need for DNA.

The National Science Foundation, Gordon and Betty Moore Foundation, the Ohio Supercomputer Center, Ohio State's Center of Microbiome Science, the Ramon-Areces Foundation, and Laulima Government Solutions/NIAID supported the research. The work was made possible by the Tara Ocean Foundation and its partners, as well as the unprecedented sampling and science of the Tara Oceans Consortium.

More information: Ahmed A. Zayed et al, Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome, Science (2022). DOI: 10.1126/science.abm5847. www.science.org/doi/10.1126/science.abm5847 Journal information: Science Citation: Ocean water samples yield treasure trove of RNA virus data (2022, April 7) retrieved 7 April 2022 from https://phys.org/news/2022-04-ocean-samples-yield-treasure-trove.html This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only.