Category Archives: Salmon

Extensive floodplain restoration brings new hope to Clear Creek

A giant piece of a cedar log stands erect in a barren landscape north of Silverdale, where a new channel for Clear Creek stands ready to receive water.

An old cedar log was recovered during excavation for a new channel for Clear Creek. Photo: Dunagan
An old cedar log was recovered during excavation for a new channel for Clear Creek.
Photo: Christopher Dunagan

Well, maybe this channel won’t be entirely new. Designers working to restore this portion of Clear Creek studied old maps. They tried to align the new man-made channel to the meandering stream that existed 150 years ago, before farmers diverted the creek around their fields.

During excavation, workers uncovered buried gravel — remnants of the old streambed — along with chunks of cedar that had lain along the edge of the stream. Buried and cut off from oxygen, these pieces of wood survived for decades underground, while cattle grazed in the fields above.

Workers excavating for the new channel used their heavy equipment to pull out what remained of a great cedar log. They stood the log vertical and buried one end in the ground — a monument to the past and future of Clear Creek.

A restored Clear Creek floodplain (before plantings) north of Waaga Way in Central Kitsap. Photo: Kitsap County Public Works
A restored Clear Creek floodplain (before plantings) north of Waaga Way in Central Kitsap.
Photo: Kitsap County Public Works

Chris May, manager of Kitsap County’s stormwater program, showed me the new channel this week. He said it was rewarding to uncover some buried history and realize that the stream would be restored in roughly the same place.

“We found the old channel,” Chris told me, pointing to a deposit of gravel. “We are pretty confident that we got it right.”

This $3-million project has been conceived and designed as much more than a stream-restoration project. The elevations of the land around the stream have been carefully planned so that high flows will spill into side channels and backwater pools. That should reduce flooding in Silverdale and help stabilize the high and low flows seen in Clear Creek.

Before photo: This was the farmers field as it appeared before restoration. Photo: Kitsap County Public Works
Before photo: This was the farm field as it appeared before restoration. // Photo: Kitsap County Public Works

The engineers did not calculate the reduced frequency of flooding, but floodwater storage is calculated to be 18.4 acre-feet, the equivalent of a foot of water spread over 18.4 acres or 29,700 cubic yards or 6 million gallons.

In all, about 30,000 cubic yards of material have been removed across 21 acres, including the former Schold Farm on the west side of Silverdale Way and the Markwick property on the east side. Native wetland vegetation will be planted along the stream and in low areas throughout the property. Upland areas will be planted with natural forest vegetation.

The topsoil, which contained invasive plants such as reed canarygrass, was hauled away and buried beneath other excavated soils to form a big mound between the new floodplain and Highway 3. That area will be planted with a mixture of native trees.

Graphic showing area before restoration. Graphic: Kitsap County Public Works
Graphic showing area before restoration.
Graphic: Kitsap County Public Works

Plans call for removal of 1,500 feet of an existing road with upgrades to two aging culverts. Adding meanders to the straightened channel will create 500 feet of new streambed that should be suitable for salmon spawning.

Plans call for adding 334 pieces large woody debris, such as logs and root wads to the stream. Some of that wood will be formed into structures and engineered logjams to help form pools and gravel bars.

Graphic showing area after restoration. Graphic: Kitsap County Public Works
Graphic showing area after restoration. Notice stream meanders near beaver pond habitat
Graphic: Kitsap County Public Works

“This will be one of the first streams to meet the Fox and Bolton numbers,” Chris told me, referring to studies by Martin Fox and Susan Bolton of the University of Washington. The two researchers studied natural streams and calculated the amount of woody debris of various kinds needed to simulate natural conditions, all based on the size of a stream. (Review North American Journal of Fisheries Management.)

The elevations on the property were also designed so that high areas on opposite sides of the stream would be in close proximity in several locations.

“Beaver will pick that spot,” Chris said, pointing to one location where the stream channel was squeezed by elevated banks on each side. “We want to encourage beaver to come in here.”

Beaver ponds will increase the floodwater storage capacity of the new floodplain and provide important habitat for coho salmon, which spend a year in freshwater and need places to withstand both high and low flows. Because the county owns the flooded property, there won’t be any complaints about damage from beavers, Chris noted.

Aerial photo showing project area with Silverdale in the background, Silverdale Way to the left and Highway 3 to the right. Photo: Kitsap County Public Works
Aerial photo showing project area with Silverdale in the background, Silverdale Way to the left and Highway 3 to the right. // Photo: Kitsap County Public Works

Clear Creek Trail (PDF 390 kb), which begins on the shore of Dyes Inlet, will be routed along the higher elevations as the trail winds through the property. Three new bridges will provide vantage points to watch salmon after vegetation obscures other viewing areas from the trail. Viewing platforms, as seen along other parts of Clear Creek Trail, were not included in this project but could be subject to further discussions.

Count me among the many people — experts, volunteers and users of Clear Creek Trail — who are eager to see how nature responds when water (now diverted) returns to the new stream channel. For decades, the lack of good habitat has constrained the salmon population in Clear Creek. The stream still has problems related to its highly developed watershed. But now a series of restoration projects is providing hope for increased coho and chum salmon and possibly steelhead trout as well as numerous other aquatic species.

In a story in the Kitsap Sun, Reporter Tristan Baurick described work this week on the Markwick property, where fish were removed in preparation for final channel excavation.

Here are some details (including photos) of various Clear Creek projects, as described in the state’s Habitat Work Schedule for restoration projects:

Washington Department of Ecology provided $2 million for the project. Kitsap County’s stormwater and roads programs each provided $500,000.

A difference between chum and coho salmon may be in their blood

On the outside, chum and coho salmon don’t seem all that different from one another, not when you consider the variety of fish in Puget Sound — from herring to halibut along with dozens of other odd-looking creatures (EoPS).

But we know that if you place coho in stormwater taken from a heavily traveled roadway, the coho are likely to die within hours. But if you do the same thing with chum, these hardy fish will barely notice the difference.

In this photo taken two years ago, Jenifer McIntyre describes her discoveries about rain gardens at the Washington Stormwater Center in Puyallup. Photo: Meegan Reid, Kitsap Sun
In this photo taken two years ago, Jenifer McIntyre describes her discoveries about rain gardens at the Washington Stormwater Center in Puyallup.
Photo: Meegan M. Reid, Kitsap Sun

Researchers began to observe the varying effects of pollution on different species of salmon years ago. In 2006, I reported on studies by researcher Nat Scholz of the National Marine Fisheries Service, who discovered that coho would swim into Seattle’s heavily polluted creeks to spawn, but they wouldn’t get very far. Within hours, they would become disoriented, then keel over and die. (Kitsap Sun, June 10, 2006)

Later, Jenifer McIntyre, a researcher with Washington State University, collaborated with Scholz to refine the studies, exposing adult coho and later young coho to stormwater under controlled conditions. Much of that work was done at the Suquamish Tribe’s Grover’s Creek Hatchery in North Kitsap. The researchers also measured the physiological effects of pollution on zebrafish embryos during their early stages of development.

Working at the Washington Stormwater Center in Puyallup, Jen made a remarkable discovery that has dramatically changed people’s thinking about stormwater treatment. She found that if you run the most heavily polluted stormwater through a soil medium containing compost, the water will no longer have a noticeable effect on the sensitive coho. Rain gardens really do work.

Jen’s findings and related stormwater issues were described in a story I wrote two years ago for the Kitsap Sun, “Stormwater solutions key in fight for Puget Sound.” The story is part of a two-year project we called “Taking the Pulse of Puget Sound.”

Now, Jen, who recently joined the faculty of WSU, is beginning a new phase of her research, probing deeper into the physiological responses of coho salmon when exposed to polluted stormwater. She told me that the varying responses of coho and chum offer clues about where to look for problems.

“It is very interesting,” she said. “As biologists, we understand that there is variability among species. But we would expect, at least among salmon, that things would be pretty much the same.”

Researchers in Japan have discovered that different kinds of fish have different subunits in their hemoglobin, which are the proteins in red blood cells that carry oxygen to the vital organs. Since coho and other salmon may have different forms of hemoglobin, oxygen transport in the blood is a good place to start this investigation, she said.

From there, the issues of blood chemistry get a little technical, but the ability of red blood cells to carry oxygen can depend not only on the form of hemoglobin but also on the pH (acidity) of the blood, she said, and that can be altered by drugs and other chemicals.

Another thing that researchers may be seeing is “disseminated intravascular coagulation,” a condition that results from clotting in the lining of the capillaries. DIC can reduce or block blood flow where it is most needed and eventually cause organ damage. That’s an area for more research, Jen said, noting that these investigations are moving forward in collaboration with researchers at NMFS and the U.S. Fish and Wildlife Service.

Meanwhile, Jen is working with chemists at the University of Washington’s Center for Urban Waters in Tacoma to figure out which substances — out of hundreds of chemicals found in stormwater — could be causing these deadly effects on fish.

If isolating the dangerous compounds proves too difficult, researchers might be able to start with the original toxic sources, perhaps exposing fish to chemicals found in tires, oil, antifreeze and so on, Jen said. For those effects, it might be good to begin the investigation with the well-studied zebrafish embryos, which are transparent and can be observed closely throughout their embryonic development.

Needless to say, this is a field of intense interest. If researchers can discover what is killing coho, they might begin to understand why the recovery of chinook salmon in Puget Sound has been so slow. Chinook, which could be added to Jen’s studies, are listed as a threatened species under the Endangered Species Act and are the preferred prey of Puget Sound’s killer whales, which are listed as endangered.

Two recent articles discussed the relative hardiness of the chum compared to coho salmon:

One orca is missing and presumed dead; another reported as ‘super-gaunt’

I have some bleak news to share about our Southern Resident killer whales, which normally frequent Puget Sound at this time of year.

J-14 seen earlier this year in Puget Sound. Photo: Center for Whale Research
J-14 seen earlier this year in Puget Sound.
Photo: Dave Ellifrit, Center for Whale Research,
taken under federal permits NMFS 15569/ DFO SARA 388

J-14, a 42-year-old female named Samish, has gone missing and is presumed dead, while J-28, a 23-year-old orca mom named Polaris, may be living out her final days.

“Things are shaping up to be pretty bad,” said Ken Balcomb of the Center for Whale Research, who keeps tabs on the orca population. “J-28 is looking super-gaunt, and I would say she is within days of her death.”

The saddest part of my conversation with Ken this morning was to hear him say that Polaris’ 7-month-old calf would become an orphan and probably will not survive without his mother. That’s the typical outcome for an orphan of that age, Ken said, although there is a chance that the young male will be adopted by his grandmother.

The calf, J-54, is still nursing, but he is close to weaning, Ken noted. He is the newest calf born into the three Southern Resident pods and is part of the “baby boom” of nine orcas born between December 2014 and December 2015. So far, only one of those calves, J-55, has died.

After my conversation with Ken, the Center for Whale Research posted a news release about the death of Samish. Orca observers on the water have known that she was missing for some time now.

As of today, J pod was on its way out through the Strait of Juan de Fuca, no doubt searching for food. The chinook salmon run has been very low this summer.

“Historically, at this time of year, we would see nice little bunches (of orcas) swimming back and forth in front of the house,” said Ken, who lives on the west side of San Juan Island. But this year, the whales have broken up into small family groups and are traveling around in seemingly random patterns, presumably in search of whatever salmon they can find.

“Even the fishermen aren’t getting much this year,” Ken said.

To gauge a killer whale’s condition, researchers consider the overall shape of its body. Without adequate fish — primarily chinook salmon — an orca grows thinner as the body fat declines. As conditions grow worse, a depression develops behind the blow hole. This sunken condition — which Polaris has developed — is called “peanut head.” So far, none of the other animals have been observed in such a dire condition.

I’ve often been told by medical experts that when a killer whale loses weight it can be a sign of a major problem, such as a disease that makes them incapable of hunting to their normal ability. But a shortage of food can exacerbate the condition.

“We have been telling the government for years that salmon recovery is essential for whale recovery,” Ken said.

He blames the salmon decline on longtime mismanagement of wild salmon stocks — including damage to habitat, over-fishing and excess hatchery stocks in both Canada and the U.S. One of the quickest ways to increase the chinook population for these whales is to take out the Snake River dams, he said.

Rebuilding salmon runs on the Elwha River will help, Ken said, but the number of fish is small compared to the potential of the Snake River, which flows into the Columbia and produces salmon that can be caught in the ocean.

“I’m trying to get the marine mammal people to talk to the salmon people,” Ken said. “Fish have been a political problem for a long time, and we are not solving the salmon issue.”

Money spent on law enforcement to make sure whale watchers don’t get too close to the orcas would be better spent on education — specifically on educating lawmakers about the needs of salmon and killer whales, he quipped.

As of July 1 — the date of the annual orca census — the population of the three Southern Resident pods stood at 83. That’s the number that will be reported to the federal government. Since then, Samish has gone missing, so the ongoing count falls to 82, pending the status of Polaris and her son.

Samish was considered part of the J-2 (“Granny”) family group. Her living offspring are Hy’shqa (J-37), Suttles (J-40) and Se-Yi’-Chn (J-45). Samish was the grandmother to Hy-Shqa’s 4-year-old son T’ilem I’nges.

Polaris is the first offspring of Princess Angeline (J-17), who is still living. Her first offspring, a female named Star (J-46), is now 7 years old. J-54 is her second offspring.

Looking backward, then forward on actions in Skokomish watershed

Through the years, I’ve written a lot about the Skokomish River, which begins in the Olympic Mountains and flows into the south end of Hood Canal. The wide, productive estuary might be described as the elbow of this long, narrow waterway that bends up toward Belfair.

Cover

I’ve heard it said that Puget Sound cannot be restored to health without a healthy Hood Canal, and Hood Canal cannot be restored to health without a healthy Skokomish River. Whether that is true remains to be seen, but I have no doubt that the Skokomish River watershed is coming out of a dark period of abuse with hope of becoming one of the most productive streams in the region.

Much of the credit for the transformation goes to a group of men and women from a variety of agencies, occupations and ways of life who came together with an understanding of the historic value of the Skokomish River and a vision for what the river could become again. This was the Skokomish Watershed Action Team, or SWAT, which celebrated its 10th anniversary last year.

helicopter

To be sure, it was basically loads of money that began to transform the abused Skokomish River watershed to a much more productive system. But the people in charge of the federal, state, local and private dollars were able to see the Skokomish as a worthy cause, thanks to the groundwork laid by the SWAT. Disappointments have been few, as one project after another brings this long lost river back to life.

Yes, I have written a lot about the Skokomish River, its history and its future. That’s why I was glad to see the 10-year update to the Skokomish Watershed Action Plan (download, PDF 113 mb). The document contains an extensive account of the projects completed and the milestones passed through the years. Whether you are intimately involved in the watershed or just want to know what the heck I’m talking about, take a look at the report released this week.

Logjam soon after installation in 2010. Photo: U.S. Forest Service
Logjam soon after installation in 2010.
Photo: U.S. Forest Service

Since 2005, nearly 50 restoration projects were completed — from removal of old logging roads high in the mountains to the re-establishment of tidal channels in the lower estuary. Salmon are being reintroduced to the North Fork of the Skokomish River, including the dammed-up Lake Cushman, thanks to a legal settlement between Tacoma and the Skokomish Tribe.

After establishment, a deep pool forms behind the logjam. Photo: U.S. Forest Service
Later, a deep pool forms behind the jam.
Photo: U.S. Forest Service

About 12 miles upstream in the South Fork of the Skokomish, a series of 30 logjams were installed and almost immediately began to restore the channel to a more natural habitat for fish and other aquatic creatures. This area was part of a four-mile stretch that was heavily logged in the 1950s for a reservoir that never happened.

Once the logjams were in place, the area began to store massive loads of sediment, which always created problems as they washed downstream into the lower river. The river’s characteristic problem of spreading out and slowing down was reversed, as width-to-depth ratios decreased and the average depth in the middle of the river increased by two feet. The number of pools deeper than five feet doubled from three to six, and the piles of wood grew larger by capturing logs floating downstream.

The new report also lays out plans for the watershed in the coming years, including projects identified in a major study by the Army Corps of Engineers. A Corps proposal to fund $20 million in restoration projects is now before Congress, as I described in Water Ways in April and June. Other projects have been proposed for separate funding, as outlined in the new report.

Hospitality for salmon coming with restoration of Big Beef Creek

Big Beef Creek, which flows into Hood Canal near Seabeck, will soon undergo a major wetland renovation that should improve the survival of coho salmon and steelhead trout.

Other work, which started last year, involves placing large woody debris in the stream to create deep pools for salmon to cool off and rest before continuing their migration. The wood also will help to form new spawning areas for coho, fall chum and the threatened summer chum of Hood Canal.

Large woody debris placed in Big Beef Creek last summer has begun to form pools where salmon can escape the strong current. Photo: Hood Canal Salmon Enhancement Group
Large woody debris placed in Big Beef Creek last summer has begun to form pools where salmon can escape the strong current.
Photo: Hood Canal Salmon Enhancement Group

Big Beef Creek is an unusual stream, one with a personal connection for me. In the late 1970s, I lived at Lake Symington, a man-made lake built years before by impounding Big Beef Creek. A few years ago, my wife and I bought a home with a tiny tributary of Big Beef Creek running through the property.

To get a lay of the land, I ventured along the stream and through the watershed in 1999, meeting many people along the way and gaining a new respect for Big Beef Creek — known as the longest stream contained entirely within Kitsap County. Check out my story for the Kitsap Sun called “The Watershed.” Much later, I wrote a Water Ways blog post about the creek beginning with, “It is the best of streams; it is the worst of streams,” with apologies to Charles Dickens.

Today, the $1.2 million habitat transformation is taking place in the lower portion of the stream, just upstream from the estuary where people go to watch bald eagles soar. (Check out this week’s “Amusing Monday.”) The project is on property owned by the University of Washington’s Big Beef Creek Research Station. Work is under the direction of Hood Canal Salmon Enhancement Group, a division of Pacific Northwest Salmon Center.

Site work will expand an 11-acre wetlands by five acres and reconnect the wetland complex to the stream channel. Coho, which remain in freshwater for the first year of life, will find a safe place to stay during the low flows of summer and the fierce floods of winter.

Officials agreed to close the well, so a relocated road will not be needed. Note the off-stream channels and the ability for the stream to change course. Map: Hood Canal Salmon Enhancement Group
Officials have agreed to close the well, so a relocated road will not be needed. Note the off-stream channels and ability of the stream to change course within the floodplain.
Map: Hood Canal Salmon Enhancement Group

“Coho rely on streams with complex habitat, including pools and shade with good water quality,” said Mendy Harlow, executive director of the salmon center. “In this project, we are focusing on the lower one mile of stream.”

Removing an access road along with 1,600 cubic yards of fill will restore two of the five acres of wetlands and open up the floodplain. The other two acres come from excavating some 4,500 cubic yards of fill from an elevated area where old storage buildings were removed last year.

In last year’s work, 10 man-made logjams were created where excavators could reach the creek. At the end of this month, helicopters will be used to place another 13 logjams in sections of the stream that could not be reached by land.

In a coordinated fashion, the helicopters also will be used to place logjams in Little Anderson Creek, which drains into Hood Canal just north of Big Beef. Little Anderson Creek, which originates near Newberry Hill Heritage Park, previously received several loads of wood in 2006 and again in 2009.

Both Big Beef and Little Anderson are part of an “intensively monitored watershed” program, in which experts are attempting to measure the extent to which habitat improvements increase salmon populations. It is not an easy thing to figure out, since salmon runs vary naturally from year to year. Still, over time, the improved spawning and rearing conditions should be measurable.

Other restoration work is planned on Seabeck Creek, while Stavis Creek will remain unchanged as the “control stream” for the Hood Canal complex of intensively monitored streams.

Fish traps placed in the streams monitor the out-migration of young salmon smolts, while a permanent fish trap at Big Beef Creek is used to count both smolts and returning adults. For each stream, biologists also count the number of redds — mounds of gravel where salmon have laid their eggs — to determine if conditions are improving.

Big Beef Creek logjams
Adding wood to Big Beef Creek results in greater stream complexity, offering salmon options for food, spawning and other needs.
Photo: Hood Canal Salmon Enhancement Group

The improved wetlands and floodplain on Big Beef Creek will allow the stream to move among several historical stream channels as sediment loads build and decline over time. Strategically placed wood will provide complexity wherever the stream chooses to go, according to Mendy, who has been working toward this project since 2007.

“I’m really excited about it and look forward to the changes,” she said. “The phase of work going forward this summer is the important phase.”

Sarah Heerhartz, habitat program manager for Hood Canal Salmon Enhancement Group, said improving the wetlands will not only help fish but also birds that favor wetlands. The stream will have room to move and spread out, she said, and some of the sediment from upstream sources will drop out before reaching the estuary.

“The floodplain is going to be a big boost for coho fry to smolt survival, because that will open up a lot of rearing habitat for juvenile coho,” Sarah told reporter Ed Friedrich in a story written for the Kitsap Sun.

The stream restoration is not expected to affect work at the UW research station, which continues to play a role in salmon studies, including efforts to improve hatchery conditions. In 1999, I wrote about the efforts to restore a run of summer chum on Big Beef Creek. Take a look at “Reviving a salmon run.” Unfortunately, the resuscitation effort has not been entirely successful, but there are new hopes that this summer’s stream repairs will give a boost to the summer chum as well as the coho.

Invasive species hitching a ride into Puget Sound

We hear about the “balance of nature,” but it’s not something that we can truly understand until the balance is thrown out of whack by something like climate change or invasive species.

Until I began a recent reporting project for Puget Sound Institute, I never realized that San Francisco Bay was such a hotbed of invasive species. Beginning with the California Gold Rush, ships began moving in and out of the bay in unbelievable numbers, arriving from ports all around the world. Now, more than 200 non-native species are making their permanent home in the bay — including some species that have thoroughly altered the local ecosystem.

So far, we have been lucky in Puget Sound. Experts say we have about 75 firmly established non-native species, yet none of them have created the widespread damage caused in San Francisco Bay by European green crabs and Asian clams or in the Great Lakes by zebra mussels. The video on this page does a good job of telling the Great Lakes story, which has been repeated all over the world.

Once people in Washington state realized how disruptive invasive species can be, the struggle was on to protect Puget Sound from alien invaders — particularly those found in San Francisco Bay, which is just a short hop away on the world scale. My series of stories talks about concerns for Puget Sound and the efforts to control a possible invasion.

Three weeks ago in Water Ways, I described legislation that would reduce state and federal controls over invasive species. See “Bill could increase risks of alien species invasions in Puget Sound waters.”

On the East Coast, where they are native, striped bass are one of the most popular sport fish. Here, Angela Anning of Connecticut shows off her impressive striper. On the West Coast, striped bass could be considered an invasive species. Photo: NOAA
On the East Coast, where they are native, striped bass are one of the most popular sport fish. Here, Angela Anning of Connecticut shows off her impressive striper. On the West Coast, striped bass could be considered an invasive species.
Photo: NOAA

Invasive species range in size from microscopic viruses to four-foot-long striped bass. In California, the striped bass became a prized sport fish after it was intentionally introduced in 1879. But over the past decade concerns have grown for their effects on the salmon population. The jury is still out on whether high numbers of stripers should be sustained for anglers or the population should be fished down rapidly to save salmon and other species. Check out these stories:

Meanwhile, striped bass have been moving up the West Coast, possibly because of warmer waters due to climate change. A few years ago, a 55-pounder was caught in the Columbia River, and I’ve heard rumors that they have been seen in the Strait of Juan de Fuca.

On the small side, I report on a tiny crustacean, an invasive copepod that has almost entirely displaced native copepods in Samish Bay in northern Puget Sound. Copepods are important prey for small fish, including herring, which feed the larger salmon. The invasive copepods are smaller and more difficult for fish to see, which could have a cascading effect on the entire food web.

Invasive copepod Oithona davisae under magnification Photo: Jeff Cordell, University of Washington
Invasive copepod Oithona davisae
Photo: Jeff Cordell, UW

A major concern for Puget Sound biologists is the European green crab, which could move into Puget Sound from San Francisco Bay in ballast water or with warm ocean currents during an El Niño year, like the one just past. As I describe in the new series, a major program involving citizen science volunteers is ongoing in a search to find the first green crabs before they gain a foothold.

Pacific oysters, another non-native species, were intentionally brought to the Northwest from Japan in the early 1900s to replace the native Olympia oyster, which had been decimated by poor water quality. Pacific oysters soon became a mainstay of the shellfish industry in the Puget Sound region and are now growing thick in numerous areas.

European green crab Photo: Washington Sea Grant
European green crab
Photo: Gregory C. Jensen, UW

Similar introductions of Pacific oysters occurred in California beginning more than 100 years ago, but for some reason the oyster populations never took hold, according to a report in the publication California Fish and Game (PDF 1.7 mb). Finally, in the early 2000s, the invasion began to take off.

“It remains unclear why there should be a successful invasion now, given the failure of previous attempts to deliberately introduce the species both locally and throughout California…,” the report says.

“If populations in Southern California waters do continue to expand and grow, as they have in other areas where they have invaded, it will undoubtedly bring changes to the way our estuarine intertidal habitats function as well as in the way we must manage them.

Pacific oyster Photo: Washington Sea Grant
Pacific oyster
Photo: Washington Sea Grant

“Because Pacific oysters rapidly reach large sizes, they could pose problems related to fouling of maritime equipment, infrastructure, and vessels,” the report continues. “Pacific oysters stand out as one of the most transformative invaders of marine ecosystems.”

As Washington state takes steps to keep alien species from invading Puget Sound from California, California officials may adopt similar measures to block invaders from coming into that state.

Please take a look at this package of stories I wrote for Puget Sound Institute, with editing by Jeff Rice and design by Kris Symer:

Finding answers for dangerous decline of Puget Sound steelhead

Harbor seals have become prime suspects in the deaths of millions of young steelhead trout that die each year in Puget Sound, but the seals may not be working alone.

Trends

Disease and/or various environmental factors could play a part, perhaps weakening the young steelhead as they begin their migratory journey from the streams of Puget Sound out to the open ocean. Something similar is happening to steelhead on the Canadian side of the border in the Salish Sea.

More than 50 research projects are underway in Puget Sound and Georgia Strait to figure out why salmon runs are declining — and steelhead are a major focus of the effort. Unlike most migratory salmon, steelhead don’t hang around long in estuaries that can complicate the mortality investigation for some species.

The steelhead initiative was launched by the Washington Department of Fish and Wildlife and Puget Sound Partnership with funding from the Legislature. The steelhead work is part of the Salish Sea Marine Survival Project, which is halfway through its five-year term, according to Michael Schmidt of Long Live the Kings, which coordinates the effort in the U.S. The larger project involves at least 60 organizations, including state and federal agencies, Indian tribes and universities.

A new report on research findings for steelhead (PDF 9.8 mb) describes the most significant results to date for our official state fish, which was listed as “threatened” in 2007. While steelhead populations on the Washington Coast and Columbia River have rebounded somewhat since their lowest numbers in the 1980s, steelhead in the Salish Sea remain at historical lows — perhaps 10 percent of their previous average.

“Because steelhead are bigger and move fast through the system, they are easier to study (than other salmon species),” Michael told me. “It has been a lot easier to feel confident about what you are finding.”

Abundance

Steelhead can be imbedded with tiny acoustic transmitters, which allow them to be tracked by acoustic receivers along their migration routes to the ocean. It appears that the tagged fish survive their freshwater journey fairly well, but many soon disappear once they reach Puget Sound. The longer they travel, the more likely they are to perish before they leave the sound.

While steelhead are susceptible to being eaten by a few species of birds, their primary predators appear to be harbor seals. These findings are supported by a new study that placed acoustic receivers on seals and observed that some of the transmitters embedded in steelhead ended up where the seals hang out, suggesting that the fish were probably eaten.

In a different kind of tagging study, Canadian researchers placed smaller passive integrated transponder (PIT) tags in a large number of coho salmon and attached devices to read the PIT tags on coho salmon.

“What is most interesting to date,” states a new report from the Pacific Salmon Foundation,“ (PDF 4 mb), “is that we only have confirmed feeding on tagged coho salmon by four of the 20 seals equipped with receivers. This suggests that feeding on juvenile salmon may be an opportunistic behavior acquired by a limited number of seals.”

New studies are underway to confirm steelhead predation by looking at fecal samples from seals in South Puget Sound. Researchers hope to figure out what the seals are eating and estimate steelhead consumption.

As I mentioned at the outset of this blog post, it may be more than a simple case of seals eating steelhead. For one thing, seal populations may have increased while their other food choices have decreased. Would the seals be eating as many steelhead if Puget Sound herring populations were close to their historical averages?

Other factors may be making young steelhead vulnerable to predation. A leading candidate is a parasite called Nanophyetus salmincola, which can infest steelhead and perhaps increase their risk of predation. The parasite’s life cycle requires a snail and a warm-blooded animal, as I described in a story I wrote for the Encyclopedia of Puget Sound — part of a larger piece about disease as a powerful ecological force. Anyway, the snail is found only in streams in South Puget Sound, which might help explain why steelhead deaths are higher among these South Sound populations.

Experiments are underway to compare the survival of two groups of identical steelhead, one group infested with Nanophyetus and one not.

Depending on funding and proper design, another experiment could test whether treating a stream to temporarily eliminate the snail — an intermediate host — could increase the survival of steelhead. If successful, treating streams to remove these snails could be one way of helping the steelhead. For these and other approved and proposed studies, check out the Marine Survival Project’s “2015-2017 Research Work Plan” (PDF 9.3 mb).

Other factors under review that could play a role in steelhead survival are warming temperatures and pollution in Puget Sound, which could help determine the amount and type of plankton available for steelhead and salmon. Could a shift in plankton result in less food for the small fish? It’s a major question to be answered.

I’ve mentioned in Water Ways (3/15/2010) that transient killer whales, which eat seals, sea lions and harbor porpoises, may be helping their distant cousins, the Southern Resident killer whales, which eat fish. Those smaller marine mammals compete for the adult salmon eaten by the Southern Residents. By clearing out some of those competitors, the transients could be leaving more salmon for the Southern Residents.

It may be too early to draw any firm conclusions, Michael Schmidt told me, but transient killer whales may be helping steelhead as well. Last year, when transients ventured into South Puget Sound and stayed longer than usual, the survival rate for steelhead from the nearby Nisqually River was the highest it has been in a long time.

Were the whales eating enough seals to make a difference for steelhead, or were the seals hiding out and not eating while the whales were around. Whether there were benefits for the steelhead, we could be seeing what happens when a major predator (orcas) encounters an abundance of prey (seals).

Hormonal studies link orca miscarriages to low chinook salmon runs

An orca mother named Calypso (L-94) nurses her young calf in this high-resolution photo
An orca mother named Calypso (L-94) nurses her young calf in this high-resolution photo taken from a drone. Lactation takes an energetic toll on orca moms. Future images may reveal whether Calypso is getting enough food to support herself and her calf.
Photo: NOAA Fisheries, Vancouver Aquarium, under NMFS permit and FAA flight authorization.

It is fairly well known that the three pods of killer whales that frequent Puget Sound are listed as endangered under the Endangered Species Act. It is also well known that their primary prey — chinook salmon — are listed as threatened.

It can’t be good that the whales are struggling to find enough to eat, but we are just beginning to learn that the situation could be dire for orca females who become pregnant and need to support a growing fetus during times of a food shortage.

Sam Wasser, a researcher known for figuring out an animal’s condition from fecal samples, recently reported that about two-thirds of all orca pregnancies end in miscarriage. And of those miscarriages, nearly one-third take place during the last stage of pregnancy — a dangerous situation for the pregnant female.

In a story published today in the Encyclopedia of Puget Sound, I report on Sam’s latest studies, along with other work by a team of biologists who are using unmanned aircraft (drones) to keep track of the physical condition of the Southern Resident orcas, including pregnant moms.

Sam’s latest study involves measuring hormones in killer whales, which can tell us a lot about a whale’s condition. The story of how hormones change under varying conditions is a little complicated, but I hope I was able to explain in my article how this works. When adding the effects of toxic chemicals that mimic hormones, we begin to understand the conditions that may be critical to the whales’ long-term survival or their ultimate extinction.

One longtime assumption, which may be shot down by the hormone studies, is that the whales’ most difficult time for food comes in winter, when salmon are generally scarce. These new studies by Sam and his colleagues suggest that the greatest problem comes in the spring, when the whales return to Puget Sound to discover that spring runs of chinook salmon can no longer be found — at least not in significant numbers.

The work with a drone carrying a high-resolution camera is providing precise measurements about the length and width of each killer whale. Pregnant females are especially interesting, and it will be important to document whether physical changes observed in the drone study can be correlated with hormonal changes seen in the other study.

“We’ve moved toward some great sophisticated technology,” Lynne Barre told me. “These great technologies combined can tell us more than any one method can … such as when and where food limitations might be affecting their health and reproduction.”

Lynne heads NOAA’s Protected Resources Division in Seattle and oversees recovery efforts for the endangered Southern Residents.

By the end of this year, NOAA is expected to release its five-year status report on the Southern Resident orcas. In addition to reporting on many new findings, the document will re-examine the risk of extinction for these killer whales and consider whether actions proposed to help them have been carried out.

Last year, the Southern Residents were listed among eight endangered species across the country that are headed for extinction unless recovery actions can be successful. The eight, selected in part because of their high profiles, are known as “Species in the Spotlight.” In February, five-year action plans were released for all eight species.

The plan called “Priority Actions for Southern Resident Killer Whales” (PDF 2 mb) focuses on three primary factors affecting the whales’ survival: a shortage of food, high levels of toxic chemicals and effects of vessels and noise. The concise 15-page document describes some of the work being carried out on behalf of the whales, although new ideas are coming forth all the time.

Orca population remains uncertain on census day

The annual census of killer whales that frequent Puget Sound is supposed to be based on a population count for July 1 each year, but this year the count has barely begun as we move into July.

J-40, named Suttles, breaches in the latest encounter reported by Ken Balcomb. Photo: Ken Balcomb, taken under U.S. and Canadian permits
J-40, named Suttles, breaches in the latest encounter reported by Ken Balcomb.
Photo: Ken Balcomb, under U.S. and Canadian permits

For years, all three pods of Southern Resident orcas typically wandered into Puget Sound in late May or early June, but things have been changing. So far this year, most of the whales have remained somewhere else, probably somewhere in the Pacific Ocean. And that even goes for J pod, the most resident of the resident pods.

Ken Balcomb of the Center for Whale Research, who is responsible for the census, said the Fraser River chinook run has been so low this year that the whales have stayed away. He may not be able to get a complete count until September, he told me.

Of course, Ken and his associates will take attendance as the whales come into the Salish Sea. Some assumptions will have to be made about the timing of any births or deaths. But whales won’t be counted as missing until they are not seen with their family groups during multiple encounters.

“We’re not going to be able to say that somebody is dead at the end of July because we have not seen them,” Ken said, “since there is a low probability of seeing them between now and September.”

As with this year, the census could not be completed at this time last year. But, unlike this year, only two small groups of whales had not been seen going up to census day on July 1 last year. See Water Ways, July 1, 2015.

As the whales have stayed out to sea longer each year, Ken has requested additional federal funding to search for them and get an early indication of their condition, but his requests have been denied. Those who wish to support his ongoing efforts may purchase a membership in the Center for Whale Research.

On Monday, Ken caught up with a small group of J pod orcas that are led by the matriarch J-2, known as Granny. It was only the second time that J pod whales have been seen in inland waters during the entire month of June. On Saturday, a large group of orcas was spotted by observers near the entrance to the Strait of Juan de Fuca. But most of them apparently stayed in the open ocean.

Ken speculates that Granny and the others were following an aggregation of salmon when he caught up with them at Turn Point near the Canadian border. He posted a report today with this information:

“J19 and J41 were the west-flanking whales, and J14, J37 and J49 were the east-flanking whales, while J2 and L87 charged in a zig-zag pattern down the middle of the tide rips that shot up vertically like haystacks of water, dousing the boat and camera. The others (J40 and J45) were here and there in the swirls, surfacing with no particular pattern. It was quite challenging to take photographs in such conditions, but it was important to get some documentation of their occurrence and activity, since they had not spent much time in the Salish Sea so far this year.”

The abundance of chinook in the Fraser River — which produces much of the fish in the San Juan Islands — is tracked by prescribed fishing in Canada’s so-called Albion Test Fishery. As you can see from the graph, the catch per unit effort is considerably lower than the long-term average, barely making a blip at the bottom of the chart.

This year's catch per unit effort in the Albion Test Fishery is much lower than the long-term average. This year's fishery did not begin until April 26. Graphic: Canadian DFO
This year’s catch per unit effort in the Albion Test Fishery is much lower than the long-term average. This year’s fishery did not begin until April 26.
Graphic: Canadian DFO

Meanwhile, the abundance of chinook off the Washington Coast is predicted in pre-season forecasts to be slightly above the 10-year average. Forecasts for this year’s chinook runs are higher than last year’s forecast but not as high as the surprisingly high numbers of chinook that ultimately came back last year. See 2016 chinook forecast (PDF 135 kb).

Considering the apparent difference between the number of chinook in the ocean and those coming to the Fraser River, it is no wonder that the whales still remain off the coast.

Given the low salmon runs, Ken says he will be surprised if the annual census does not include some mortalities. One small group of whales, known as the L-12s, have not been seen for months. Meanwhile, four births were recorded since July of last year, with the latest report coming in December. And, as far as anyone can tell, eight of the nine orcas born since December 2014 are still living. It would be remarkable if we are still able to say that when the official census for 2016 is finally reported in September.

Culverts: Lawmakers face dilemma to fund improved fish passage

I’m certainly no highway engineer, but I’ve been thinking about the difference between building roads in Kansas, where I was born, and building roads in the Puget Sound region.

Kansas has its streams and wetlands to be sure, but nothing like the density of natural features that we find in the Puget Sound watershed, where land elevations change constantly and roadways must cross streams and wetlands at every turn.

For many years, road construction in the Puget Sound region involved filling wetlands and burying pipes just big enough to pass the water. It was assumed that salmon would make it through. But based on our current knowledge of salmon migration, we realize that these shortcuts took a major toll on the populations of salmon and other fish.

This week, the U.S. Ninth Circuit Court of Appeals upheld a lower court ruling requiring state agencies to correct decades of road-building mistakes that impaired salmon passage on state highways and on state forest roads. Check out Monday’s story in the Kitsap Sun.

Priority watersheds chosen by the Fish Barrier Removal Board. Puget Sound: Pilchuck Creek, Pysht River, Goldsborough Creek; Coast: Newaukum; Lower Columbia: Lower Cowlitz; Yakima River: Wilson/Cherry; Snake River: Grande Ronde Tribs, Snake River Tribs; Upper Columbia: Okanogan.
Priority watersheds chosen by the Fish Barrier Removal Board. Puget Sound: Pilchuck Creek, Pysht River, Goldsborough Creek; Coast: Newaukum; Lower Columbia: Lower Cowlitz; Yakima River: Wilson/Cherry; Snake River: Grande Ronde Tribs, Snake River Tribs; Upper Columbia: Okanogan.

The lawsuit, filed by 21 Indian tribes, was based on the idea that undersized and poorly functioning culverts severely affected the total salmon runs in violation of treaties signed in the 1850s, which promised Native Americans the right to fish forever in traditional locations.

The lawsuit did not address culverts owned by the federal government, local governments or private property owners, but the same principles apply. Steps are now being taken to improve salmon passage based on standards developed by the Washington Department of Fish and Wildlife.

Meanwhile, a state advisory committee, known as the Fish Barrier Removal Board, has been working to establish priorities with top-ranked projects providing the greatest improvement in salmon habitat.

Kitsap County Engineer Jon Brand, who serves on the board, described a two-pronged approach to set the priorities. One is to focus on priority watersheds, with the idea of making major improvements in a variety of streams in a given area. (See map above and board materials (PDF 50.4 mb), Oct. 20, 2015.) The second approach is to coordinate planning for top-priority streams, with the idea of working on entire stream systems at once. Obviously, it does not make sense to replace a culvert upstream if a downstream culvert continues to block salmon passage. Check out the list of top-30 ranked projects (PDF 57 kb).

The Fish Barrier Removal Board is putting together a funding package to be submitted to the Legislature. As Jon pointed out, some of the most effective projects for salmon passage are not in the Puget Sound region nor subject to the federal court ruling. The list also goes beyond state roadways and includes a mix of ownerships based on the watershed and stream priorities mentioned above.

State lawmakers face some difficult funding decisions. With the court order hanging over their heads, along with a 2030 deadline, they may choose to do only culvert-removal projects in the Puget Sound region, even though projects in other areas could get a greater bang for the buck. And will there be money left over to support local governments trying to improve salmon passage in their areas?

I asked Jon about the expediency of early road-builders who must have given little consideration to salmon when they filled wetlands, carved out drainage ditches and installed pipes to carry the flow of water. It was not always that way, Jon told me.

That method of road-building arrived with the invention of large earth-moving equipment, he said. In the 1800s and early 1900s, filling a stream and inserting a culvert was more difficult than building a bridge of logs, given the vast quantities of timber on the Kitsap Peninsula.

Those early log bridges no doubt caused fewer problems for salmon, but they did not last. Eventually, nearly every bridge was replaced, often by dumping fill across the stream and allowing a small culvert to carry the water.

As for my misguided notion that Kansas can ignore stream crossings because the state has no serious environmental problems, I found this language in “Kansas Fish Passage Guide” (PDF 2.3 mb), a document written for road-builders:

“In Kansas, fish passage issues caused by culverts were not recognized by road officials until about 2010, when … research indicated that culverts and low-water crossings were a significant cause of habitat fragmentation in the Kansas Flint Hills.

“Many of the threatened and endangered fish in Kansas are a type of minnow or minnow-size fish. Small fish typically are not strong swimmers, so waterfalls, water velocity and turbulence can be a barrier to passage upstream. Culverts are dark and have an atypical channel bottom that may also discourage fish passage. Lack of water depth through the culvert can restrict passage during low-flow seasons…

“Stream barriers reduce habitat range and can adversely affect fish populations upstream and downstream of the stream crossing. A severe event like a drought or oil spill in a stream segment can wipe out a species, and the species cannot repopulate the stream because of the barrier.”

Kansas has begun to prohibit blocking culverts and to address existing fish-passage issues. As the above-referenced publication states, “On the Great Plains, it’s usually easy to design and construct a stream crossing for a two-lane road to provide fish passage.”

If only that were the case in Western Washington.