• Comprehensive regional diagnostic of mic

    From ScienceDaily@1:317/3 to All on Wednesday, May 04, 2022 22:30:48
    Comprehensive regional diagnostic of microbial ocean life using DNA
    testing

    Date:
    May 4, 2022
    Source:
    University of California - San Diego
    Summary:
    Scientists have used tools of genetics research akin to those used
    in genealogical research to evaluate the diversity of marine life
    off the California coast. Large-scale 'metabarcoding' methods
    could revolutionize how society understands forces that drive
    seafood supply, planet's ability to remove greenhouse gases.



    FULL STORY ========================================================================== Scientists at Scripps Institution of Oceanography at UC San Diego, the
    J. Craig Venter Institute (JCVI), and the National Oceanic and Atmospheric Administration (NOAA) used tools of genetics research akin to those used
    in genealogical research to evaluate the diversity of marine life off
    the California coast.


    ==========================================================================
    The result is a breakthrough technique that researchers will be able to
    use to diagnose conditions at the base of the ocean food web that affect
    the abundance of commercially important fishes or create harmful algal
    blooms. From the information gathered by a method called "metabarcoding," scientists can also use so-called environmental DNA (eDNA) to evaluate
    how effectively the oceans can protect the planet from the effects of
    climate change.

    The team reports on the findings May 4 in the journal Nature
    Communications.

    The work was funded by the National Science Foundation (through the
    California Current Ecosystem Long-Term Ecological Research project),
    NOAA, and the Gordon and Betty Moore Foundation.

    "It's the ecological sampling method of the future," said study first
    author Chase James, a graduate student at Scripps Oceanography and
    JCVI researcher.

    "This study represents the first deployment of this approach within a
    long-term ecological sampling context. It reveals what you can see when
    all this hidden diversity is finally shown." The new way of assessing
    ocean microbiomes -- collections of microscopic plants, animals, and
    other organisms living in given habitats -- vastly improves scientists'
    ability to perform diagnostics on the oceans. In the case of this study, researchers were able to use genetic information to identify the most
    important factor governing how many organisms are in the ocean in surface waters off the California coast and where they are distributed. They
    found that nutrient supply shapes the profile of microbial life in the California Current even more than temperature. This conclusion is one
    that could not have been reached using traditional means.

    James likened the process to scanning the barcodes of all the products
    in a grocery store to obtain an inventory of them. James' advisor Andrew
    Allen launched the effort, titled the NOAA CalCOFI Ocean Genomics Project (NCOG), in 2014, starting with water samples gathered during cruises
    of the iconic CalCOFI surveys, a quarterly program that Scripps has
    co-managed since 1949. The samples collected in two-liter bottles were filtered, and the filters were frozen and brought back to the lab. The scientists then profiled all DNA they found in those samples in the manner
    that commercial DNA testing companies identify people's genetic profiles, identifying all the microorganisms in the samples. They also estimated
    how many specimens of all the identified species were in the sample.

    The method is an improvement upon traditional techniques such as light microscopy, which capture sentinel species commonly found in seawater
    or on bulk indicator measurements such as how much chlorophyll is in
    the water. In comparison to metabarcoding, those methods just give broad strokes-level information of what life lives where. Metabarcoding allows
    for more precise identification of species and the acquisition of more
    data with the same effort.

    CalCOFI was created just after World War II to help officials and the
    fishing industry understand what caused the sudden collapse of sardine populations off the West Coast. The program conducts quarterly cruises
    at an array of stations off the coast. There, scientists repeat a
    suite of physical and biogeochemical measurements revealing ecological conditions. From the surveys, scientists have collected a history of
    the marine environment unequaled in the world.

    "It's interesting that 70 years ago, CalCOFI couldn't have even imagined
    that you could sample two liters of seawater and get comprehensive data
    on the marine microbial community," said James, "but a major future goal
    of this study is to achieve the initial goals that CalCOFI set out to accomplish, which is to understand the processes that drive the success
    and failure of our regional fisheries. This cutting-edge research may be
    used to answer 70-year-old questions." Study co-authors include Lisa
    Zeigler Allen, Robert Lampe, Ariel Rabines, Anne Schulberg, and Andrew
    Allen, who have joint appointments at Scripps Oceanography and JCVI;
    Andrew Barton, who has joint appointments at Scripps Oceanography and UC
    San Diego's Division of Biological Sciences; Hong Zheng of JCVI; Ralf
    Goericke of Scripps Oceanography; and Kelly Goodwin of NOAA's Atlantic Oceanographic and Meteorological Laboratory and Southwest Fisheries
    Science Center.


    ========================================================================== Story Source: Materials provided by
    University_of_California_-_San_Diego. Original written by Robert
    Monroe. Note: Content may be edited for style and length.


    ========================================================================== Journal Reference:
    1. Chase C. James, Andrew D. Barton, Lisa Zeigler Allen, Robert
    H. Lampe,
    Ariel Rabines, Anne Schulberg, Hong Zheng, Ralf Goericke, Kelly D.

    Goodwin, Andrew E. Allen. Influence of nutrient supply on plankton
    microbiome biodiversity and distribution in a coastal upwelling
    region.

    Nature Communications, 2022; 13 (1) DOI: 10.1038/s41467-022-30139-4 ==========================================================================

    Link to news story: https://www.sciencedaily.com/releases/2022/05/220504082610.htm

    --- up 9 weeks, 2 days, 10 hours, 51 minutes
    * Origin: -=> Castle Rock BBS <=- Now Husky HPT Powered! (1:317/3)