innovative tool that can confirm the recent presence of any given fish species
in a sample of water will be highlighted at the first National Conference on
Marine Environmental DNA held in New York City. The conference began Thursday
and continues today, Nov. 30.
100 pioneering practitioners and users of eDNA science – a complement to
traditional marine life monitoring systems – have convened in Manhattan to
detail and share discoveries, state-of-the-art technologies, and new methods.
new tool created at The Rockefeller University, which will host the conference,
offers, for example, a chemical shortcut for researchers to test for the eDNA
of a specific, individual species in a water sample.
makes use of the fact that every species leaves a trail of genetic residue --
skin cells, excretions, other DNA -- as it moves. Scientists can now test water
and soil for these traces and identify which species left them behind.
eDNA tester can confirm the genetic presence of a given species in a water
sample within three days -- a small fraction of the usual month or more
involved in the current practice of lab testing for any and all species, or to
mount an expedition with nets and analyze the results.
creator, Mark Stoeckle, Senior Research Associate at The Rockefeller
University's Program for the Human Environment (PHE), says many reasons make
authorities want to know when a given marine species is present -- to determine
for example when to open or close a commercial fishery, or when dredging can be
done without harm to marine life. New York Harbor, he notes, restricts dredging
if winter flounder are present.
likens his innovation to Go Fish, the children's game in which a player asks
another for a given rank of card, for example: do you have any jacks in your
hand? says Stoeckle. "In the case of New York, the question would be
'Where in the harbor do we have winter flounder?'"
current cost to produce a Go Fish eDNA tool is $15 per sample (1 species);
additional species can be added for $8 per sample.
conference lead organizer Jesse Ausubel, Director of the PHE: "'Go Fish'
brings us close to a 'chatbot' or small smart personal assistant -- like Siri,
Alexa, or Cortana -- that can quickly identify species from eDNA."
of a species is easier to confirm than absence," Stoeckle underlines.
"Sampling may be conducted on the wrong day or at the wrong depth. Nevertheless,
the genetic trail that animals leave behind is helping us find them without
having them physically in hand -- a breakthrough with major environmental and
with traditional trawls with nets, tagging, visual observations, and acoustic
instruments, experts believe remote eDNA sampling and analysis can one day help
create near real-time monitoring of the marine environment.
the US, several marine eDNA research hotspots have developed, including
Monterey Bay, CA, New York / New Jersey, and Seattle, WA.
at the conference are about 100 leading US scientists, officials, inventors,
and investors exploring the emerging field of environmental DNA and its
application in marine settings.
event will highlight insights provided by eDNA to date and the potential of
this new science to further enlarge our knowledge and inform ocean management.
Technology development -- faster, cheaper, more portable
Bioinformatics -- genetic reference databases, analytic software, data
eDNA biology -- improving detection reliability, and relating eDNA abundance to
Organizers aim to initiate a commitment by leading scientists and stakeholders
to take up eDNA as a cooperative national or regional research theme.
also aim to encourage:
Federal, state, and local governments to incorporate eDNA into traditional
ongoing marine life surveys. (Monmouth University and Rockefeller U scientists
are exploring integration of eDNA working with New Jersey Department of Marine
Fisheries' trawl surveys)
The private sector to collaborate in development of technologies to improve the
speed and lower the cost of testing
Non-governmental organizations to help build genetic reference databases and
monitor national and regional hotspots
questions to be addressed include:
Whether and how the rate of decay of eDNA differs by taxa and context. Do some
fish shed more than others? Do fish shed more than turtles? How do water
temperature, sunlight, chemical variation, currents and turbulence, pressure,
and other factors affect decay?
How to better calibrate the abundance of DNA in the water column as an index of
abundance of specific species of fish and other animals
How to make eDNA reliable for very rare as well as more abundant species
How to formally integrate eDNA in the conduct of marine surveys, augmenting
nets, cameras, and acoustic fish finders
is needed to make eDNA data suitable for regulatory and policy purposes?
Paul Gaffney, Vice-Admiral (ret.), former President and Urban Coast Institute
Ocean Policy Fellow at Monmouth University: "eDNA opens the door to cheap,
frequent, widespread, potentially automated monitoring of the diversity, distribution,
and abundance of aquatic life. Government agencies need to take notice."
Nash, an innovator in adapting cutting-edge science for authentic student
research, stressed the importance in years past of establishing protocols
related to DNA barcoding, which identifies species from the DNA of tissue taken
from physical specimens. Confirming a continuous chain of custody, time of
testing, and other protocols made DNA barcode evidence sufficiently reliable to
stand up in court.
achieve reliable eDNA results, water or filtered material from the water needs
to be stored and processed properly.
eDNA's applications to date include
discovering species previously unknown in certain ranges
discovering rare species and others unknown to science (or absent from genome
remote, difficult-to-reach, and intriguing places
health and stocks of fish in commercially harvested areas, informing decisions
on when fisheries should open or close range of marine animals
effect of protected area designation on fish and other marine animal
populations and other forms of ecological restoration
effect of fish farming operations on native species
effect of offshore oil and gas operations or wind farms on marine life
of artificial reefs
effects of severe storms and other disturbances to marine ecosystems such as
harmful algal blooms
presence of vulnerable, threatened or endangered species
presence of species dangerous to swimmers
impacts of climate change and variability
mapping marine animal diversity, distribution, migration and abundance,
including invasive species, and species popular with sport fishers
Foreign invader and pest species -- both plant and animal -- can be located and
monitored quickly, easily and less expensively using eDNA instead of
traditional methods. Examples of species already targeted in this way include
lionfish in Bermuda, Asian black-spined toad and red-eared slider turtles in
Australian waters, zebra mussels in the Great Lakes, and clams in the lakes of
California and Nevada.
In Wisconsin, researchers documented five invasive species of marine
zooplankton in the ballast water of ships plying Lake Superior, including the
eDNA of a "bloody red shrimp" originally from the Black Sea area.
Finding the eDNA of some species might not indicate its living presence in the
vicinity. In their study of fish migration in the rivers surrounding Manhattan,
for example, The Rockefeller University researchers found the DNA of species
thought to have passed through humans and the wastewater treatment system --
tilapia, salmon, red snapper -- species you shouldn't find swimming in the
Hudson River. eDNA could therefore help identify vulnerable or threatened
species being sold as food in local stores and restaurants.
experts expect newer technologies will better detect the amount of DNA in a
water sample but high concentrations might not indicate an abundance of animals
passing through the water. It might be caused by an animal that is spawning,
wounded or decaying, for example.
Alison Watts of the University of New Hampshire: "Modern genetic and
acoustic tools provide complementary data identifying organisms at a range of
distances, to comprehensively detect aquatic species. eDNA and passive acoustic
monitoring are evolving technologies which may transform our understanding of
working towards the automation and simplification of eDNA sampling are pursuing
several interconnected technological directions. For example:
Using drones to collect water samples
Extracting eDNA from a water sample in the field (as it is easier to store DNA
(a bit of goo on a filter) than the much larger water sample
Sequencing and analyzing DNA in situ on board a sampling device, such as a
remotely controlled glider, with digital results stored or relayed by satellite