MSGID: 1:317/3 62735327   
   PID: hpt/lnx 1.9.0-cur 2019-01-08   
   TID: hpt/lnx 1.9.0-cur 2019-01-08   
    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   
      
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