The gene-editing technology CRISPR has been
used for a variety of agricultural and public
health purposes — from growing disease-resistant
crops to, more recently, a diagnostic test
for the virus that causes COVID-19.
Now a study involving fish that look nearly
identical to the endangered Delta smelt finds
that CRISPR can be a conservation and resource
management tool, as well.
The researchers think its ability to rapidly
detect and differentiate among species could
revolutionize environmental monitoring.
The study, published in the journal Molecular
Ecology Resources, was led by scientists at
the University of California, Davis, and the
California Department of Water Resources in
collaboration with MIT Broad Institute.
As a proof of concept, it found that the CRISPR-based
detection platform SHERLOCK (Specific High-sensitivity
Enzymatic Reporter Unlocking) was able to
genetically distinguish threatened fish species
from similar-looking nonnative species in
nearly real time, with no need to extract
DNA.
The scientists focused on three fish species
of management concern in the San Francisco
Estuary: the U.S. threatened and California
endangered Delta smelt, the California threatened
longfin smelt and the nonnative wakasagi.
These three species are notoriously difficult
to visually identify, particularly in their
younger stages.
State and federal water pumping projects have
to reduce water exports if enough endangered
species, like Delta smelt or winter-run chinook
salmon, get sucked into the pumps.
Rapid identification makes real-time decision
making about water operations feasible.
Typically to accurately identify the species,
researchers rub a swab over the fish to collect
a mucus sample or take a fin clip for a tissue
sample.
Then they drive or ship it to a lab for a
genetic identification test and await the
results.
Not counting travel time, that can take, at
best, about four hours.
SHERLOCK shortens this process from hours
to minutes.
Researchers can identify the species within
about 20 minutes, at remote locations, noninvasively,
with no specialized lab equipment.
Instead, they use either a handheld fluorescence
reader or a flow strip that works much like
a pregnancy test — a band on the strip shows
if the target species is present.
Anyone working anywhere could use this tool
to quickly come up with a species identification.
While the three fish species were the only
animals tested for this study, the researchers
expect the method could be used for other
species, though more research is needed to
confirm.
If so, this sort of onsite, real-time capability
may be useful for confirming species at crime
scenes, in the animal trade at border crossings,
for monitoring poaching, and for other animal
and human health applications.
