Unveiling the Mysteries of Freshwater Streams

Beneath the surface of a freshwater stream, animals, plants, fungi, and microorganisms create complex patterns of biodiversity. Brock Benalona, ​​a research fisheries biologist at the USDA’s Pacific Northwest Research Station, studies these dynamics, which can be complex.

said Benalona, ​​lead author of a study recently published in the journal Journal of Biogeography.

Big data and big discoveries

Penaluna and her research team studied four watersheds upstream of the Trask River in coastal Oregon. Their study relied on an analysis of environmental DNA (eDNA), which are traces of genetic material that organisms shed into the stream. From their water samples, the scientists extracted tiny bits of DNA and sent them to a lab to be sequenced, providing a genetic signature. Their samples contained more than 2 million sequences, or “reads,” which then had to be compared against known genetic databases for species identification.

“This is the definition of big data,” said Benalona. “Overrides all Excel spreadsheets.”

The team’s results revealed a shift in the biodiversity pattern of the stream from the lower reaches towards the headwaters as fish precipitate at the upstream threshold. They also detected salmon (Pacific salmon and coastal trout) further upstream than expected, indicating an extended distribution.

Sculpins steal the scene

Sculpins are the rock stars in this study, and not just because of their spiky looks. “The scalpin results show us that things are not where we thought they were,” Benalona said. “We are identifying new strains of scalpines using their genetic signatures.” These results reveal the power of eDNA in revealing aspects of biodiversity that have been “hidden” to us.

In addition to discovering potential new species of sculpin, the analysis also detected a harmful amphibian pathogen called Batrachochytrium dendrobatidis as well as the presence of the elusive mountain beaver.

This study has transformed understanding of the presence of species across watersheds and thus enhanced our ability to track, protect and manage them. It also revealed how much we don’t know and how much we have to learn.