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Secret lives of fish
by Nathan Rushton, 9/23/2007 The Eureka Reporter
Fisheries biologist Bill Pinnix of the U.S. Fish and Wildlife Service steers a boat into Humboldt Bay to find and track Freshwater Creek-spawned juvenile coho salmon with embedded acoustic tags. Tyson Ritter/The Eureka Reporter


A federal fisheries biologist has recently wrapped up a study hunting juvenile salmon fitted with sophisticated electronic tracking devices that promises to significantly boost scientists’ knowledge of an important, federally protected fish.

Coho salmon, which live the majority of their lives in the ocean and spawn in freshwater rivers and streams on the Pacific West Coast — including Freshwater Creek, which empties into Humboldt Bay — were listed as an endangered species in 2005.

A high-tech study to determine what young fish do after they leave the stream where they were born began in mid-April, and the results are expected to be published at the end of this month.

Bill Pinnix, a fisheries biologist with the U.S. Fish and Wildlife Service’s Arcata office, is project supervisor and primary investigator for the study.

The coho study was hatched from a previous “fish community” study launched by the USFWS two years ago to look at which fish are using the bay’s different habitats.

While the previous study — which was primarily funded through the Humboldt Bay Harbor, Recreation and Conservation District — was being done, many people wanted to know just what the endangered salmon were doing in the bay and, in particular, whether they were utilizing eel grass habitat near the oyster culture farming operations in the north bay.

“If we want to answer those questions, this is the type of study we have to do,” Pinnix said.

The $70,000 coho study was collaboratively funded by the USFWS, California Department of Fish and Game, the Harbor District and the oyster-rearing business Coast Seafoods, which farms several hundred acres of tidal lands in the bay.

Beginning in April, researchers began placing small acoustic transmitters into dozens of 6-inch-long, 1-year-old juvenile salmon migrating out of Freshwater Creek.

The acoustic tag transmitters send out a signal of six slightly varying pulses, or chirps, each minute that act like a bar code, which allows the researchers to track individual fish, Pinnix explained.

Rather than trying to just get lucky and catch fish where people think they might be, Pinnix said the tagging study allows scientists to accurately find and follow the fish.

A radio receiver unit attached to the front of the USFWS’ aluminum boat allows Pinnix to track — in real time — the movements of the fish to see where they go and better understand what they do.

Approximately 24 stationary radio receivers are also spread out through Freshwater slough and the bay to allow the scientists to listen for fish 24 hours a day, seven days a week.

The data is stored in the receivers and retrieved later.

“Since one of the main objectives was (to track) residence time in the bay, we really wanted to know when they left,” Pinnix said.

To accomplish that, a higher-density swatch of receivers was placed inside the bay’s entrance.

Assisting Pinnix was Peter Nelson, the marine fisheries adviser for the University of California Cooperative Extension’s Sea Grant program for Humboldt and Del Norte counties.

Nelson was tasked with surgically inserting the acoustic tags into the small fish.

Nelson said there was next to no information previously about how juvenile coho salmon were utilizing Humboldt Bay’s estuarine environments.

Although there were anecdotal reports from anglers who said they caught young coho in some areas of the bay while jigging for anchovies to use as bait, Nelson said this is the first time researchers have nailed down solid data on the fish.

Because the bay has such a diverse number of uses — including oyster culture, recreational boating, large vessel shipping, commercial fishing hub and maritime industrial uses — Nelson said it is important that managers and scientists know how the fish use the bay.

And the study is already dispelling assumptions.

“The dogma is that the fish just boogie on through,” Nelson said. “Clearly that is not the case.”

Pinnix’s preliminary data suggest the fish are spending weeks in the bay, not the hours or days some have speculated.

Although there is considerable variation, Pinnix said his data show that the time the fish leave the fresh water to the time they exit the bay is about 30 days — half of that is spent in Freshwater Slough and the other half in the bay.

While in the bay, Pinnix said, the fish he tracked spent the majority of their time in the deepest part of the channel near the Samoa-area industrial frontage.

Nelson said more research is necessary to determine how coho use some of the other coastal streams, which he said has to vary from one system to the next.

Ron Fritzsche, a retired Humboldt State University fisheries professor and former Harbor District commissioner who served on the district when the original “fish community” study was done, indicated he was pleased with the new information.

At that time, resource management agencies were interested in knowing if Coast Seafoods’ oyster operations in and around the eel grass beds were impacting coho salmon.

Fritzsche said there has been what he called “faith-based” ideas of where the fish were, despite the fact that there was no record of juvenile coho salmon caught in eel grass beds.

Besides the main bay areas, the study is also shedding light on what the fish are doing in the estuaries and sloughs before they enter the bay.

Estuaries are a transition zone where fish are adapting from freshwater to saltwater life — a critical time in the life cycle of the salmon, Pinnix said. Pinnix said many people consider Humboldt Bay, which is the second largest bay in California, an estuary.

That’s not exactly true, Pinnix said, although he said it is tidally influenced and has some estuarine characteristics.

“The real estuary — the interface between the fresh and saltwater — occurs in the sloughs like Freshwater and Elk River,” Pinnix said.

The coho study’s acoustic receivers also helped fill the data gap of when the fish used those slough environments, where Pinnix said scientists speculated the fish mostly stayed before leaving for the open ocean.

“Personally, I was surprised that they spent more time in the bay than I had initially thought,” Pinnix said.

Pinnix said Fish and Game’s effort to tag salmon with PIT — or passive integrated transponder tags — in Freshwater Creek has provided solid data on how long the fish stay in the upper streams.

Bob Pagliuco, a former fisheries biologist with Humboldt State University’s Fisheries Department’s Institute for River Ecosystems, was one of several employees who helped oversee the CDFG-funded monitoring of salmon and steelhead populations at the Humboldt Fish Action Council’s fish trap on Freshwater Creek.

Pagliuco said it wasn’t until after four years of tagging and monitoring the salmon that scientists realized the fish were migrating to the lower portions of Freshwater Creek and spending a significant amount of time during their early lives in the tidally influenced estuary areas.

Pagliuco said monitoring revealed there is a small outgoing migration of roughly 7-month-old coho in the fall, as well as a larger migration of 1-year-old fish in the spring.

Given how important the estuaries are to the watershed and the salmon’s early development, Pagliuco said, that is where restoration efforts need to be directed.

“They grow incredibly faster there than they do in the tributaries,” he said.

Although they are not exactly sure why, Pagliuco said scientists speculate it is the abundance of space and food that allow the fish to grow more quickly.

But it is a two-sided coin for the fish.

Unlike the relative safety of the deeper water in the bay, it isn’t as easy going in the sloughs where pelicans, terns, cormorants and other diving birds congregate.

Near the U.S. Highway 101 bridge over Freshwater Slough, Pinnix said, it is common to see thousands of birds form a sort of avian gauntlet that fish must negotiate to make it into the relative safety of the deeper water.


While it seems reasonable that small juvenile coho could slip in and out of the bay undetected for years, it is another story for the many larger, finned visitors to the bay.

Acoustic signals from green sturgeon, which can reach lengths of 7 feet and, like coho salmon, are federally protected anadromous fish, were also picked up by Pinnix’s equipment last summer.

Some were tracked leaving in the fall and others re-entering in April.

Fisheries biologist Steven T. Lindley with the National Marine Fisheries Service’s Southwest Fisheries Science Center in La Jolla, said it was a welcome surprise that the receivers picked up his sturgeon’s tags.

Lindley is wrapping up an ambitious acoustic tag project that tagged 350 green sturgeon in California’s Sacramento and Klamath rivers, as well as several Oregon and Washington rivers where the fish spawn.

“We were hoping to detect them moving from their spawning rivers (to) where they aggregate during the summer,” Lindley said.

Although scientists don’t know why, Lindley said, green sturgeon tend to spend their summers in bays along the Pacific Northwest coast and winter off British Columbia’s Vancouver Island.

During their stopover in Humboldt Bay, Lindley said green sturgeon are most likely eating ghost shrimp and crustaceans.


The USFWS is already planning a follow-up study for next year, which Pinnix said the agency hopes can be expanded to include monitoring the Elk River watershed for salmon and steelhead.

“We spent two years doing pilot studies and really testing the technology before tagging the fish. By laying that groundwork, this project came off really well,” Pinnix said.

Following this year’s success, Pinnix is hopeful for subsequent research, but as of now, the necessary funding has not been secured.

Pinnix said other agencies, including HSU, have expressed interested in teaming up to use the receivers to monitor halibut, sharks and rays for their own research.

In addition, Pinnix said the Wiyot Tribe is interested in collaborating, as well as some community groups that do restoration and conservation work around the bay.

Half the overall cost for the $70,000 study was for equipment, including the 12 receivers that cost $1,200 each.

But those costs won’t be incurred next time.

Because the stationary receivers are already in place and paid for, other researchers would only have to provide tags.

“Every subsequent year, the relative cost goes down because of the initial capital investment,” Pinnix said.

The acoustic tag technology is fairly new, appearing only in the past decade, with significant advances in the past three years that have produced miniaturized versions that allow the study.

Pinnix said local agencies like the Harbor District will benefit most from the new data, along with state and federal fisheries management agencies.

David Hull, chief executive officer for the Harbor District, said the district’s $17,000 contribution goes toward a program he calls a critical element needed for bay management.

From the district’s perspective, Hull said knowing better how and when juvenile coho use the bay will help with making decisions about projects in and around the bay.

Hull said until now, agencies and businesses were relying on educated guesses, although they erred on the side of caution.

“That is going to make our job a lot easier,” Hull said.

Because the study has been so successful, Hull said the Harbor District is looking at funding other studies for chinook and coho in other tributaries.

Pinnix said he is planning to present his final report to the funding agencies at the end of the month, and will also be publishing his data in a peer-reviewed science publication.


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