lives of fish
by Nathan Rushton,
9/23/2007 The Eureka Reporter
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
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
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
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
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
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
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
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
“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.
WHAT COMES NEXT
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
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
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.