• Ocean water samples yield treasure trove

    From ScienceDaily@1:317/3 to All on Thu Apr 7 22:30:40 2022
    Ocean water samples yield treasure trove of RNA virus data
    Study of organisms in the sea identifies 5,500 new species

    Date:
    April 7, 2022
    Source:
    Ohio State University
    Summary:
    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.



    FULL STORY ========================================================================== 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.

    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.

    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 Universite' Laval; Erwan Delage and Samuel
    Chaffron of the Universite' de Nantes; and Eric Pelletier, Adriana
    Alberti, Jean-Marc Aury, Quentin Carradec, Corinne da Silva, Karine
    Labadie, Julie Poulain and Patrick Wincker of Genoscope.


    ========================================================================== Story Source: Materials provided by Ohio_State_University. Original
    written by Emily Caldwell. Note: Content may be edited for style and
    length.


    ========================================================================== Journal Reference:
    1. Ahmed A. Zayed, James M. Wainaina, Guillermo Dominguez-Huerta, Eric
    Pelletier, Jiarong Guo, Mohamed Mohssen, Funing Tian, Akbar
    Adjie Pratama, Benjamin Bolduc, Olivier Zablocki, Dylan Cronin,
    Lindsey Solden, Erwan Delage, Adriana Alberti, Jean-Marc Aury,
    Quentin Carradec, Corinne da Silva, Karine Labadie, Julie Poulain,
    Hans-Joachim Ruscheweyh, Guillem Salazar, Elan Shatoff, Ralf
    Bundschuh, Kurt Fredrick, Laura S. Kubatko, Samuel Chaffron,
    Alexander I. Culley, Shinichi Sunagawa, Jens H. Kuhn, Patrick
    Wincker, Matthew B. Sullivan, Silvia G. Acinas, Marcel Babin,
    Peer Bork, Emmanuel Boss, Chris Bowler, Guy Cochrane, Colomban
    de Vargas, Gabriel Gorsky, Lionel Guidi, Nigel Grimsley, Pascal
    Hingamp, Daniele Iudicone, Olivier Jaillon, Stefanie Kandels,
    Lee Karp-Boss, Eric Karsenti, Fabrice Not, Hiroyuki Ogata, Nicole
    Poulton, Ste'phane Pesant, Christian Sardet, Sabrinia Speich,
    Lars Stemmann, Matthew B. Sullivan, Shinichi Sungawa, Patrick
    Wincker. Cryptic and abundant marine viruses at the evolutionary
    origins of Earth's RNA virome. Science, 2022; 376 (6589): 156 DOI:
    10.1126/science.abm5847 ==========================================================================

    Link to news story: https://www.sciencedaily.com/releases/2022/04/220407141837.htm

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