WESTPORT — The Siliqua and Quinnat, two vessels from the National Oceanic and Atmospheric Administration, trawled 300 feet apart Wednesday just upriver from the Wauna Mill, the net between them slowly gathering juvenile, mostly hatchery, salmon headed down the main channel of the Columbia River toward the Pacific Ocean.

After 17 minutes of towing the net and collecting salmon, the whistles of “Col. Bogey’s March” from the movie “The Bridge on the River Kwai” started emanating from biologist Bill Newcomb’s laptop inside the Siliqua. The tune was the signal to bring the two vessels even and tighten the net around their young catch, which instinctively swam out the open end of the net and past a phalanx of antennas, which count the salmon implanted with grain-sized Passive Integrated Transponder tags that transfer their travel history into one of Newcomb’s computers.

“Five for 23,” Newcomb called out to Jeff Scroup, the operator of the Siliqua, noting five tagged salmon counted during the pass and 23 for the day.

Never catching anything, the crews and their open-ended pair-trawling operation are tasked with analyzing the survival and migration characteristics of several species of endangered salmon and steelhead traveling through or transported around the federal hydroelectric system on their way out to sea. Their research goes into a biological opinion every four years by NOAA, which advises the U.S. Army Corps of Engineers and Bonneville Power Administration about how to make the hydroelectric system more fish-friendly.

“Fish start in April … but we really pick up in May,” said fisheries biologist Matthew Morris with Ocean Associates Inc., a federal contractor providing researchers and boat crews for NOAA.

With seasonal crews for the spring and summer, including students in Clatsop Community College’s maritime program, researchers can spend more than 900 hours a year trawling on up to two 12-hour shifts a day. The major salmon species counted are coho, Chinook and sockeye, along with steelhead and cutthroat trout. A special focus is on steelhead and yearling Chinook. Researchers record their counts onboard and email the information to NOAA’s offices, where reports are compiled in the offseason.

Morris estimated the pair-trawl project counts between 15,000 and 20,000 fish a year. Of those, he said, about 2 to 3 percent are salmon detected at Bonneville Dam, the last hydroelectric hurdle for salmon going downriver.

“That’s only 15 percent, roughly, of our total detection, are fish previously detected at Bonneville,” he said. “It’s those fish we’re able to determine survival estimates with. And the other 85 percent, we’re able to do analyses of transportation versus in-river (transportation), and then other timing analyses.”

The survival estimates over the past 20 years point to salmon’s struggles in drought years, with 2015 the hardest on salmon migration since a previous drought in 2001. Lower flows also lead to a slower, more constricted channel in which researchers tend to detect higher number of salmon and steelhead.

Ecologist Paul Bentley is the lone NOAA employee from the Point Adams Research Facility on the project, working closely with the researchers and boat crews of Ocean Associates.

“The biological opinion is a legal document that is written to kind of manage the hydrosystem,” Bentley said. “NOAA’s part of this biological opinion is the listed salmonids.”

Bentley joined the project in 2013 following Dick Ledgerwood, who retired last August and is largely responsible for developing the pair-trawl project system.

“An evaluation of fish transportation — that’s really why fish tags were brought into the Columbia River Basin,” said Ledgerwood, who lives near Brownsmead and still volunteers with NOAA.

Fisheries managers started transporting fish around dams in the late 1970s to increase their survival, he said, but nobody knew what happened after they were dumped from barges below the Bonneville Dam.

Before the pair-trawl project system started in 1995, Ledgerwood said researchers would use purse seine nets, a more unwieldy and time-consuming method to count young salmon. “With the trawl, and by not catching anything and letting them go through the system, you fish continually,” he said.

Bentley estimated the crews and equipment in the pair-trawling project costs about $2 million annually, split between the Corps and Bonneville Power Administration. He said a new biological opinion in 2018 will help decide whether the project is still needed to help managers increase the survival rates of salmon.

But the researchers are developing and testing flexible antenna arrays that could eliminate the net, cut costs and expand the number and species of fish counted on the Lower Columbia.

The flexible strands of antenna encased in plastic tubing, which Bentley equated to a “pile of spaghetti,” are towed by boat, but do not require a net to count fish. The technology was introduced in 2011 as a stationary array installed on a pile dike near the confluence of the Driscoll Slough with the Columbia River.

“Another advantage of this system is it’s not (constrained) by species,” Bentley said, adding the array picks up juvenile salmon, sturgeon, pike minnows and possibly lamprey — any fish tagged and swimming by an array.

“Within the Columbia, I think almost every tributary could use the flexible system,” he said.

Morris said the state of California is helping fund the new technology, hoping to better track salmonids in the Sacramento River delta.

Even Ledgerwood is intrigued by the evolution of his trawl project to the newer, flexible antenna system that can expand fish-monitoring. “Give them five years, and I bet they’ll be doing it.”

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