A look into how salmon hatcheries mark their fish

Editor’s note: This is the first part of a three-story series about the operations of Alaska’s salmon hatcheries and their impacts in the North Pacific. Part two will explore the role that hatchery fish and marking play in the negotiation of the Pacific Salmon Treaty.


Some people probably walk, but Kristin Bates runs down the hall at Trail Lakes Hatchery to change the water temperatures where baby salmon wait to hatch.

Timing is everything in a hatchery — especially when the water temperature dictates growth rates and hatching time. But the reason she runs up and down the corridor between the boiler room and the egg incubation rooms switching the temperatures on a set schedule is to make a calculated, specific, readable mark on the nearly microscopic ear bones, called otoliths, developing inside the salmon eggs before they hatch.

“All the marks get applied before (the fish) hatch,” said Bates, who manages the Trail Lakes Hatchery for Cook Inlet Aquaculture Association.

Ultimately, the millions of salmon leaving the Trail Lakes Hatchery every year will encounter millions of fates, whether they die of natural causes, are eaten in the ocean, are caught in a fishery or ultimately make it back to spawn. But the groups that migrate out to the ocean together will have one thing in common: the patterns imprinted on their otoliths before they were born.

On a glass slide, the thin slices of bone don’t look distinct from one another. But under a microscope, the patterns emerge clearly, like rings on a tree. Bates can read them to tell how many cycles of hot and cold water were used to make a particular mark — a big space means a 48-hour period of warmer water, while lighter spaces mean a 24-hour period of warmer water followed by 24-hour period of cooler water.

All vertebrates have otoliths. Before they hatch, the conditions in the eggs’ environment dictate their growth, affecting the bone layers on the otolith like rings on a tree. For hatchery operators, this works like a bar code, tracing a salmon in a net back to where it was hatched. Though there are other ways of marking salmon leaving hatcheries — fin clipping and coded wire tagging among them — thermal otolith marking is a standard.

Salmon hatcheries began as a way to add stability to catches when wild runs fluctuate. In Alaska, there are two types of hatcheries: private nonprofit associations, which produce salmon primarily for the use of the commercial fishing fleet, and the two state hatcheries in Anchorage and Fairbanks, which produce sport fish for stocking in lakes and some rivers. In many cases, the facilities the private nonprofits operate are owned by the state.

As commercial salmon hatcheries come under increasing scrutiny amid changing salmon population dynamics, user group demands and habitat concerns, fishery managers and hatchery associations are working on ways to better track hatchery fish all over the North Pacific using the microscopic otolith lines they quietly carry throughout their lives.

Hot water, cold water

Essentially, creating an otolith mark boils down to stressing salmon eggs out in tanks.

At Trail Lakes Hatchery, the fish culturists raise pink, sockeye and silver salmon to be stocked in a variety of Cook Inlet Aquaculture Association’s operations with some for the Alaska SeaLife Center in Seward. Each stock has a different mark, which requires different techniques to apply.

Bates said the Alaska Department of Fish and Game assigns the hatchery marks for each stock each year. Following the prescribed sequences, the staff turns the water taps on and off to change the temperatures in the tanks enough so that the nascent salmon will lay down dark and light rings on their developing otoliths. Some of the marks are easier and take a little over a week of temperature fluctuations in the water to apply, while others are more complicated and take at least a month, Bates said.

“The marks need to be as distinct as possible,” she said.

The hatchery submits otolith samples to Fish and Game each year for grading and so the otolith readers will be able to have a sample to compare against the fish that return. In general, Trail Lakes Hatchery has a good track record with making accurate marks, Bates said.

However, the clock is ticking as culturists are laying down the marks. When the water heats up, it speeds up the clock to when the baby salmon will hatch. There are only so many times they can heat up and cool down the water before the fish start hatching.

The process they use is fairly similar to others around the state, Bates said. Cook Inlet Aquaculture Association has been thermally marking the salmon here since the late 1980s, said Executive Director Gary Fandrei.

In the back of the hatchery, a large building nestled between the shore of Upper Trail Lake and the Seward Highway just west of Moose Pass on the Kenai Peninsula, a red pipe and a blue pipe snake up from a massive water heater complex, around a catwalk and into the various rooms of the hatchery to provide hot water and cold water constantly. Everything is monitored from a computer panel, allowing Bates to change the temperature of the water easily.

The water temperature flips in the tanks have to be precise in timing. The staff has to do the temperature changes manually.

“We plan it so we can do it during work hours, like 10 a.m.,” she said.


Besides the risk of missing timing on the water temperature changes, salmon eggs not surviving, and other issues like disease, cost is an issue.

Heating all that water takes a lot of fuel, which is expensive. The majority of Alaska’s salmon hatcheries are not on the road system, so most of the time, that means diesel has to be shipped in to provide power. That can get pricey.

Not all hatcheries are obligated to mark their salmon. Most them do, but there’s no formal requirement to do so up to a certain production level.

That’s the case for Kitoi Bay Hatchery in Kodiak, operated by the Kodiak Regional Aquaculture Association. The hatchery produces pink salmon and hasn’t sought a production increase in many years, though if the organization did, there would be an otolith mark requirement, said Tina Fairbanks, the executive director of Kodiak Regional Aquaculture Association.

Kitoi Bay is relatively remote with few other salmon streams around. The fish returning to the bay are fairly easy to spot and isolated from other salmon streams because of the geography of the hatchery, she said, which is one reason it was put there in the first place. Up to this point, Fish and Game managers haven’t indicated an additional need to monitor Kitoi Bay pinks specifically, she said.

“One of the daunting things about implementing an otolith marking system for pink salmon at Kitoi Bay is the cost, both to apply the mark in terms of the fuel it would require and the capital expense that would be involved,” she said. “Looking at that alone, it represented a significant increase to the operating cost of the hatchery, and the potential costs for evaluation were also very daunting.”

The concern about Kodiak’s salmon potentially straying came up in the Homer area in December 2017. When Fish and Game read the otoliths in pink salmon showing up in sloughs and streams where they’d rarely been spotted before, they found that a large percentage of them came from Prince William Sound hatcheries. Members of the public raised concerns that the hatchery salmon would outcompete the wild salmon in the streams; though Prince William Sound’s salmon were able to be identified through their marks, Kodiak pink salmon would look just like wild ones.

Kodiak Regional Aquaculture Association is looking into other ways of marking those fish, including using salt water to create a mark, but the thermal otolith marking system that hatcheries like Trail Lakes Hatchery use may not be cost effective.

Fish and Game houses the central otolith marking coordination program for the entire Pacific Rim. Dion Oxman with Fish and Game’s Mark, Tag and Age Lab maintains that program, working with hatchery managers to assign marks and grade them. More accurate marks mean better reads, and with 480-some different types of otolith marks swimming in the North Pacific, better reads mean better information.

“It’s a constantly dynamic process,” he said. “We basically need to provide (the hatchery) feedback, because accidents happen.”

Reach Elizabeth Earl at eearl@peninsulaclarion.com.



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