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)