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Leading Practitioners Of eDNA Science Gather To Discuss New Tool’s Possibilities
Posted on Friday, November 30, 2018 (PST)

An 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.


About 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.


A 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.


It 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.


The 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.


Its 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.


He 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?'"


The current cost to produce a Go Fish eDNA tool is $15 per sample (1 species); additional species can be added for $8 per sample.


Says 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."


"Presence 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 economic implications."


Combined 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.


In the US, several marine eDNA research hotspots have developed, including Monterey Bay, CA, New York / New Jersey, and Seattle, WA.


Expected 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.


The 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.


Major themes:


-- Technology development -- faster, cheaper, more portable

-- Bioinformatics -- genetic reference databases, analytic software, data compatibility

-- eDNA biology -- improving detection reliability, and relating eDNA abundance to species abundance

-- Organizers aim to initiate a commitment by leading scientists and stakeholders to take up eDNA as a cooperative national or regional research theme.


They 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


Priority 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


What is needed to make eDNA data suitable for regulatory and policy purposes?


Says 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."


Bruce 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.


To achieve reliable eDNA results, water or filtered material from the water needs to be stored and processed properly.


Uses: 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 databases)

sampling 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

effects 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


Invasive species


-- 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.


Meanwhile, 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.


Says 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 marine communities."


Researchers 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

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