Hidden world of flow biodiversity revealed through the sampling of water for environmental DNA

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CORVALLIS, Oregon – For the first time, researchers used a new genomics-based method to detect the simultaneous presence of hundreds of organisms in a stream.

Recently, scientists at Oregon State University and the Forest Service Pacific Northwest Research Station in the United States published the results of their findings in the journal Environmental DNA.

For the study, collaborators extracted genetic material from an assortment of physical matter left in a stream from a wide range of organisms – from fish to flies – including skin cells and excrement. Using this method, they have also detected microscopic species.

Although not found in this study, this method has the potential to detect potent water molds that are harmful to plants that are responsible for root and stem rot diseases and pathogens that cause fungal diseases such as fungus. Chytrid, which is killing amphibians all over the world.

Some of the key applications of the method include the monitoring of diseases, invasive species and rare or endangered species, said Tiffany Garcia, an aquatic ecologist at the Oregon State College of Agricultural Sciences and co-author of the study.

"This is like sampling the air in a terrestrial environment and getting aerial signals from all the different species, which is currently impossible. But with water, it is possible," said Garcia.

The new method could offer an electrofishing alternative, which sends an electric current through water to temporarily stun fish and has been the method chosen to sample fish populations in rivers and d & # courses. 39; water. The new method used by researchers at the Oregon State and Forest Service, which used a microfluidic device, has several advantages over electrofishing, according to the researchers.

The collection of environmental DNA is less laborious than electrofishing, does not solicit organisms and does not require animal handling permits, they said.

"The work on eDNA for single species has been around for some time, but our use of a microfluidic platform greatly expands the approach," said Laura L. Hauck, molecular biologist. of the Pacific Northwest Research Station and co-lead author of the study. "We can still focus on a single species of interest, but at the same time we are acquiring data on biodiversity and the health of the ecosystem from hundreds of organisms, all from the same single sample."

For the study, the research team collected water samples from five sites in Fall Creek in the Oregon Coast Range in 2017. Water samples were collected immediately before electrophysing investigations. They filtered three-liter samples through fine-meshed filters to collect biological particles in the water.

The filters were then returned to the laboratory to extract and analyze DNA. Using computer programs, the researchers classified 3.2 million DNA sequences in 828 expected taxonomic groups comparing them with the sequences contained in GenBank, the international database of genetic sequences managed by the National Institutes of Health of the United States.

"When we compared our water samples with electrofishing results, we found the same species of fish, amphibians and crayfish, but we also found the entire community of organisms that inhabited that stream," Kevin Weitemier , an associate researcher of the OSU and co-director of the study.

The water samples were found to contain DNA from 647 species, including 307 insects.

Co-authors of the study included Richard Cronn, research geneticist and Brooke Penaluna, research fish biologist, both with the Pacific Northwest Research Station. Cronn and Penaluna designed the study.

Funding for the research was provided by the Pacific Northwest Research Station and the National Council for Air and Stream Improvement.

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