Sustain Our Nation's Forests and Grasslands

PNW Research Station scientists open up new horizons in eDNA research and applications

A painting of a water environment
“Watermarks” by Pacific Northwest Research Station researcher Laura Hauck. The biodiversity of an aquatic ecosystem is encompassed in the transient traces of environmental DNA left behind by the inhabitants. They are like hidden watermarks.

OREGON – Research innovation is driven by technological advances. In the field of ecology, environmental DNA –known as eDNA—has become a cutting-edge frontier that is spurring a new wave of research designed to inform land management agencies about the presence and absence of key species.

What is eDNA? Stream inhabitants leave traces of their DNA in the water, packaged in skin cells, excrement, spores, pollen and other biological material. When concentrated on a filter, the DNA from this material can be extracted for analysis. In essence, the biodiversity of an aquatic ecosystem is encompassed in the transient traces of environmental DNA left behind by its inhabitants. 

The potential to replace standard survey methods –such as electrofishing—with less labor intensive and less invasive eDNA surveys is attractive to managers who must address the challenges imposed by aquatic species conservation and aquatic invasive species detection and eradication. Single-species eDNA detection methods are being adopted by national forests across the United States as part of their routine monitoring for native and invasive species. However, the recent growth in genomics instrumentation has made it possible to examine water samples for tens, and potentially hundreds, of species simultaneously.

Given these technological advances, researchers from the Pacific Northwest Research Station asked this simple question: “Can a large number of species be surveyed from a single sample using an eDNA/genomics approach, and are the data comparable to traditional survey methods?” The answer to both of these questions is “yes”, and these findings were recently published in the journal Environmental DNA.

The approach has broad appeal to land managers owing to the flexibility in its targeting strategy. Not only can this method detect macroscopic organisms (e.g., vertebrates, macroinvertebrates), it can also detect microscopic organisms such as plant pathogens like the sudden oak death pathogen (Phytophthora ramorum) and its relatives, or animal diseases like the amphibian chytrid fungus (Batrachochytrium dendrobatidis), which is killing amphibians on a global scale.

With a platform capable of assessing so many targets at once, the door to multiple collaborations was opened wide. This project not only fostered collaborations within the research station, but also with co-authors at Oregon State University who helped support different applications of the method. This project also attracted funding from partners at the Bureau of Land Management, National Council on Air and Stream Improvement, and Weyerhaeuser Company. “Because of these partnerships, we were able to go further and develop a more comprehensive assay to sample streams,” said Brooke Penaluna, research fisheries biologist.