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 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.
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.
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.
"We had to benchmark the known to study the unknown," said Sullivan, also a
professor of civil, environmental and geodetic engineering, founding
director of Ohio State's Center of Microbiome Science and a leadership team
member in the EMERGE Biology Integration Institute.
"We've created a computationally reproducible way to align those sequences
to where we can be more confident that we are aligning positions that
accurately reflect evolution."
Further analysis using 3D representations of sequence structures and
alignment revealed that the cluster of 5,500 new species didn't fit into the
five existing phyla of RNA viruses categorized in the Orthornavirae kingdom.
"We benchmarked our clusters against established, recognized phylogeny-based
taxa, and that is how we found we have more clusters than those that
existed," said co-first author Ahmed Zayed, a research scientist in
microbiology at Ohio State and a research lead in the EMERGE Institute.
In all, the findings led the researchers to propose not only the five new
phyla, but also at least 11 new orthornaviran classes of RNA viruses. The
team is preparing a proposal to request formalization of the candidate phyla
and classes by the ICTV.
Zayed said the extent of new data on the RdRp gene's divergence over time
leads to a better understanding about how early life may have evolved on the
planet.
"RdRp is supposed to be one of the most ancient genes—it existed before
there was a need for DNA," he said. "So we're not just tracing the origins
of viruses, but also tracing the origins of life."
This research was supported by the National Science Foundation, the Gordon
and Betty Moore Foundation, the Ohio Supercomputer Center, Ohio State's
Center of Microbiome Science, the EMERGE Biology Integration Institute, the
Ramon-Areces Foundation and Laulima Government Solutions/NIAID. The work was
also made possible by the unprecedented sampling and science of the Tara
Oceans Consortium, the nonprofit Tara Ocean Foundation and its partners.
Reference:
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
Tags:
Planet and Environment