Unraveling the secrets of freshwater streams

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A sculpin—a spiny, bottom-dwelling fish species. Credit: Brooke Penaluna, USDA Forest Service, Pacific Northwest Research Station

Beneath the surface of freshwater streams, animals, plants, fungi and microbes form complex biodiversity patterns. Brooke Benaluna, a research fisheries biologist at the USDA Forest Service Pacific Northwest Research Station, studies these dynamics, which can be complex.

„Understanding the biodiversity of freshwater ecosystems and how different species are distributed in a stream network is challenging. Streams are interconnected and contain many rare and undiscovered species,” said Benaluna, lead author of the recently published study. Journal of Biogeography.

Big Data, Big Innovations

Benaluna and his research team studied four watersheds of the Trask River in coastal Oregon. Their study relied on environmental DNA (eDNA) analysis, which are traces of genetic material shed by organisms living in streams. From their water samples, scientists extract minute bits of DNA and send them to a lab to sequence, giving them a genetic signature. Their samples contained more than 2 million sequences, or „reads,” that were then compared to known genetic databases to determine species identity.

„This is the definition of big data,” Benaluna said. „It beats all Excel spreadsheets.”

The team’s results found a shift in stream biodiversity from lower reaches to upstream threshold fish exited headwaters. They found salmonids (Pacific salmon and coastal cutthroat trout) further upstream than expected, suggesting distributional expansion.

Sculptors steal the show

Sculpins are the rockstars of this study, and not just because of their spiky appearance. „Our Sculpin findings show us that things are not where we thought they were. We are identifying new lineages of Sculpins using their genetic signatures,” Benaluna said. These findings reveal the power of eDNA in showing us aspects of „hidden” biodiversity.

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In addition to finding a new species of sculpin, the analysis also found the presence of a harmful amphibian pathogen called Batrachochytrium dendropoditis and the elusive mountain otter.

This study changed the understanding of the presence of species across watersheds and, by extension, improved our ability to monitor, conserve and manage them. It revealed how much we don’t know and how much we still have to learn.

More information:
Brooke E. Benaluna et al., Detecting latent biodiversity of streams in the upper distribution range of fishes, Journal of Biogeography (2023) DOI: 10.1111/jbi.14605

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Journal of Biogeography

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