New salmon-counting technique treats Alaska stream like a crime scene

Downstream view of the fish counting weir at Auke Creek that is located north of downtown Juneau

This fish weir in Auke Bay, near Juneau, was where scientists tested a new salmon-counting technique that takes a cue from crime scene investigations. (Photo by Matt Miller/KTOO News)

The state of Alaska spends millions of dollars each year counting salmon. Managers need accurate numbers to decide how many fish can be caught, and how many should be allowed to escape upstream to spawn.

Much of the counting is done by state employees who watch salmon swim through specially designed stations. But what if you could count the number of fish just by testing for DNA in a bottle of river water? There’s a new technique that could make that happen, according to a just-released study in the journal Molecular Ecology Resources.

The Alaska Department of Fish and Game already has several ways to count salmon, but they all depend on detecting the fish themselves. Managers use sonar in places where they can’t see through the water, they count from towers where visibility is better and they use weirs to actually stop the fish and count them individually, according to Chris Habicht, the director of the department’s genetics lab.

A lot of that counting takes people — and those people have to be paid. But what if the state could save money by counting the salmon without the actual fish?

That’s where Taal Levi, a professor at Oregon State University, comes in. Levi has spent the past several years exploring whether a new technology called environmental DNA, or eDNA, can be used to count salmon.

The technique, which is only a decade old, involves sampling water from a stream, then testing it to detect salmon DNA. DNA, Levi says, can come from “any source of cell — mucous, skin cells, feces, urine.”

“It’s a lot like a crime scene. If there was a murderer, and a murderer got cut, or left any sort of tissue or even skin cells, you could use the DNA in those skin cells or blood to identify the murderer,” he said.

Pink salmon, plus an occasional silver and red congregate in a pool above the Auke Bay weir. (Photo by Matt Miller/KTOO)

Levi is the lead author on the new study, which relied on water samples from Auke Creek, near Juneau. Researchers were already operating a fish-counting weir there, and Levi could use the proven numbers from the weir to test the accuracy of his eDNA sampling.

As it turned out, the level of eDNA in the water closely tracked the number of salmon traveling through the stream, the study said. Levi said the results show that ultimately, the sampling technique could be an inexpensive way for managers or even citizen scientists to acquire a lot more data about salmon returns.

“It’s essentially trivial amount of money for the amount we spend on salmon management,” he said.

There are still some potential problems with the sampling technique. For example, the eDNA is diluted when there’s more water flowing through the stream, so it’s essential to also have accurate measurements of stream flow.

The eDNA signal produced by salmon also appears to decrease the farther away the fish get from a sampling site. So Levi said he thinks that accurate counts will require water samples to be tested at least daily, if scientists want to make sure they can detect big daily pulses of fish.

Habicht, from the genetics lab, said he thinks the technology isn’t ready for use by state managers yet.

“I think a lot more work would need to be done before one could get a handle on whether this is a cost-effective alternative to the other methods,” he said.

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