Collecting samples near Clayton, NY in summer 2018. Credit: Rob Williams

— By Chris Gonzales, Freelance Science Writer, New York Sea Grant

Ithaca, NY, August 21, 2023 - A team of scientists has developed a single test that can detect a number of known plant and animal species, based on small bits of DNA found in the environment (eDNA). For this work, they are targeted introduced species that are known pests in New York State (NYS) and the Great Lakes.

“The genetic detection of single species in environmental samples is relatively straightforward,” said Jose Andrés, a faculty fellow at the Cornell Atkinson Center for Sustainability and the leading geneticist on the project. “However, detecting multiple species is expensive and requires complex computational analyses. We wanted to develop a simple, cost-effective method for the codetection of multiple invasive species without compromising its efficiency.”

As long as there is information on the species known to be a problem, the test can detect them  with high reliability.

“The ‘multiplex-eDNA’ method is capable of detecting dozens of targeted plant and animal species at a time,” Andrés continued. “In comparison to other existing methods for multiple species detection (metabarcoding), our method shows a higher sensitivity at a fraction of the cost. This is really good news.” 

This project, funded by New York Sea Grant (NYSG), was led by David Lodge of Cornell University, with Jose Andrés, Paul Simonin, and Steven M. Bogdanowicz. 


(At left) Paul Simonin, a postdoctoral researcher at Cornell, performs a genetic analysis of the environmental samples. Because the procedure is highly sensitive to contamination, samples are handled in a clean lab specially designed for eDNA work; (At right) Filtered samples in the lab at Cornell University. To avoid degradation, the eDNA samples are kept at -80C until the genetic testing is done. Credit: Paul Czechowski

The list of high-priority species was created by experts working on the issue of transported species, or introduced species, in NYS, including the Great Lakes region. The number of species targeted by this new test is 17.

In animals, the test targets mitochondrial DNA. In plants, it targets chloroplast genes—essential to the part of the plant that turns light into energy.

After several attempts, the scientists developed a cocktail of primers—small strings of DNA—that could accurately signal the whole genome of the target organisms.


Sampling locations in (at left) the New York City region and (at right) in NY harbors of Lakes Ontario and Erie.

Their methods were validated both in the lab and in a New York harbor field experiment.

They successfully detected ten species known to be in the area, according to prior studies. In fact, the authors say, the new test has even higher sensitivity than previous methods.

In addition, the new methods were field tested in four harbors on New York’s Great Lakes: in St. Lawrence, Oswego, Rochester, and Buffalo.

In a surprise, they detected Nitellopsis obtusa (an angiosperm with the common name “starry stonewort”), a species known to be established in the area, but never before detected at their sampling site at St. Lawrence.

This new test could make it far easier and cheaper for scientists to detect dozens of already-identified pests moving into new regions.


(At left) Clean lab procedures at Cornell University; (At right) Water samples are filtered through a membrane. The eDNA trapped in the filter is extracted using a small vacuum (blue) and transferred into tubes (orange). Credit: Paul Czechowski


More Info: New York Sea Grant

New York Sea Grant (NYSG), a cooperative program of Cornell University and the State University of New York (SUNY), is one of 34 university-based programs under the National Oceanic and Atmospheric Administration’s National Sea Grant College Program.

Since 1971, NYSG has represented a statewide network of integrated research, education and extension services promoting coastal community economic vitality, environmental sustainability and citizen awareness and understanding about the State’s marine and Great Lakes resources.

Through NYSG’s efforts, the combined talents of university scientists and extension specialists help develop and transfer science-based information to many coastal user groups—businesses and industries, federal, state and local government decision-makers and agency managers, educators, the media and the interested public.

The program maintains Great Lakes offices at Cornell University, SUNY Buffalo, SUNY Oswego and the Wayne County Cooperative Extension office in Newark. In the State's marine waters, NYSG has offices at Stony Brook University and with Cornell Cooperative Extension of Nassau County on Long Island, Brooklyn College and Cornell Cooperative Extension in NYC and Kingston in the Hudson Valley.

For updates on Sea Grant activities: www.nyseagrant.org has RSS, Facebook, Twitter, Instagram, and YouTube links. NYSG offers a free e-list sign up via www.nyseagrant.org/nycoastlines for its flagship publication, NY Coastlines/Currents, which is published quarterly.