marine science and the coast

New study finds surprisingly high rate of steelhead mortality in estuary

CORVALLIS, Ore. – A new study by researchers at Oregon State University found that up to nearly half of the ocean-bound juvenile steelhead surveyed in two Oregon river systems appear to have died when they reached the estuaries – before they could reach the ocean.

The scientists aren’t sure if such a mortality rate in the estuary is typical or elevated due to increased predation – most likely by marine mammals or seabirds. One goal of their research is to begin establishing better baseline data on juvenile salmon and steelhead mortality so resource managers can make more accurate predictions on runs of returning adult fish.

“A female steelhead may lay 2,000 to 5,000 eggs – and in rare cases, more than 10,000 eggs – and for the population to remain stable, at least 2-3 percent of the juveniles migrating to the ocean have to survive and return as adults,” said Carl Schreck, a professor of fisheries and wildlife at OSU and leader of the Oregon Cooperative Fish and Wildlife Research Unit on campus. “If you get much more than that, it’s a banner year.

“But it’s hard to predict adult returns if you don’t have good data on outgoing juveniles,” Schreck added, “and this study is an effort to make that monitoring more precise.”

Declining salmon and steelhead runs have been blamed on everything from habitat loss through logging to housing developments on coastal rivers, but the consensus has been that ocean conditions are perhaps the single most important element in how robust the populations may be in a given year. Yet the OSU study found that mortality is significant before the fish even make it to the Pacific Ocean, said David Noakes, a professor of fisheries and wildlife at OSU and one of the principal investigators in the study.

“Steelhead will live in the fresh water for one to two years and then migrate out to the ocean where they’ll spend another two or three years,” Noakes said. “If only 2-3 percent survive, it would be interesting to know what the keys to survival may be for the select few. Are the biggest juveniles more likely to survive? The fastest? Those that have the fewest parasites?  Is there something in their genetics that better helps some of them adapt to the new salt water environment?

“We need to determine what the so-called ‘normal’ predation rates are in the estuary, and get a better handle on what is killing the fish,” he added.

In their study, the OSU researchers inserted small ultrasonic transmitters into 280 juvenile steelhead over a two-year period. The dollar bill-sized fish were captured in traps at sites on the middle stretches of the Alsea and Nehalem river systems, tagged and measured, and then released back into the rivers and tracked on their way to the ocean. About nine out of 10 fish made it safely from the release point to tidewater, and then the ultrasound transmissions from 50 to 60 percent of those survivors abruptly stopped when they reached the estuary.

The scientists received enough signals from surviving fish to know that it wasn’t a failure in signal transmission. And, Schreck says, during an earlier study using tags that broadcast a radio frequency, they recovered transmitters from a cormorant rookery near the mouth of the Nehalem River, and have tracked signals from the tags to a burgeoning seal population – also near the Nehalem’s mouth..

“There are a lot of seals right near the mouths of both rivers and seals can eat a lot of young fish,” Schreck said. “It’s why the steelhead need thousands of eggs to keep the population going.”

One other possible explanation for the high mortality, Noakes said, is that the young fish couldn’t handle the transition from fresh to salt water. Salmon, steelhead and other “anadromous” fish have a complex life cycle and for centuries have utilized both the ocean and river systems. But a high mortality rate might be normal and a way to weed out weak fish that can’t make the adaptation to a new environment.

 “We know that fish need a number of things to trigger their migration to the ocean, including the amount of seasonal light, certain temperatures, enough water flow, etc.,” Noakes said. “But we don’t know why some fish remain in the river for one year before heading out to sea, and others stay for two years. Just preparing to go from fresh water to a salt water environment requires an enormous adjustment.

“There may be something about that adaptation that contributes to the mortality,” he added.

If the mortality rate of juvenile steelhead is atypical, it could be increasing because of some environmental factor – warmer water, more parasites, chemical contaminants, or higher acidification of ocean waters coming into the estuary, for example.

Or predation may be higher because of more seals, sea lions and seabirds.

Much of the research about steelhead migration, spawning behavior and basic biology is emerging from studies done at the Oregon Hatchery Research Center, a joint venture between OSU’s Department of Fisheries and Wildlife, and the Oregon Department of Fish and Wildlife. Located on Fall Creek, a tributary of the Alsea River, the research center is giving fish biologists unprecedented new looks at the physiology and behavior of steelhead.

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David Noakes, 541-737-1953

Oregon Sea Grant delivers federal dollars for ocean research, outreach efforts

CORVALLIS -  An ambitious plan to research, understand and inform the public about marine issues ranging from climate change to invasive species will receive nearly $14 million in federal and state dollars via the Oregon Sea Grant Program over the next four years.

“We're proud to be able to continue supporting an integrated program of coastal science serving Oregon,” said Stephen Brandt, director of the Oregon Sea Grant Program headquartered at Oregon State University. “The research projects, in particular, address some of the critical issues facing Oregon and the coast, and reflect our ongoing commitment to supporting research that addresses current issues of human health and safey, social progress, economic vitality and ecosystem sustainability.”

Oregon Sea Grant recently received the first of four $2.3 million biennial grant installments from its parent agency, the National Oceanic and Atmospheric Administration. Half of that money will go to support  the 10 research proposals – among 60 submitted - that made it through Sea Grant's  rigorous, competitive grant program for 2010-2012. The federal dollars are expected to leverage at least $1.2 million a year in state matching funds.

Grant proposals were reviewed both for their scientific strength and importance and their relevance to Oregonians, said Brandt. Reviewers included scientific peers from across the county as well as members of Sea Grant's citizen advisory council, representing a range of coastal interests.

Nine of the funded research teams are based at OSU; the tenth involves scientists at Western Oregon University. Several involve state and federal research collaborators. The grants will support research into such issues as:

  • The implications of climate change in shifting populations of marine organisms, from tiny organisms that threaten the survival of wild salmon to predatory Humboldt squid.
  • The identification of bioactive compounds, which might have use in human medicine, from organisms in deep-sea hydrothermal vents.
  • Development of a means of predicting oxygen-starved “dead zones,” and their implications for the ocean food web and commercial fisheries.
  • Improved methods of forecasting near-shore waves and their effects on Oregon's coast, and, in a separate project, a look at how local variations in sea-floor geography, river currents and other factors might amplify or reduce the damaging effects of tsunami waves.
  • The use of Oregon's proposed marine reserves as a laboratory for developing a new framework for assessing the human costs and benefits of such zones, taking into account  ecosystem benefits as well as economic costs.
  • A predictive method for analyzing the risks and economics of early detection and rapid-response efforts to control the spread of invasive species.
  • Continued support for ongoing research into oyster disease and salmon habitat restoration, areas pioneered by earlier Sea Grant funding.

Although the grants – ranging from $35,000 to $117,000 per year - are modest by some standards, Sea Grant's steady support of timely, relevant marine research in Oregon over more than 40 years has made the program “an incredibly powerful force,” said John Cassady, OSU's vice president for research.

“Through their vision and foresight, they seeded early studies on wave energy and on the ecological impacts of invasive species. With its educational and research programs, Oregon Sea Grant has increased the awareness of coastal hazards and of ways to mitigate those hazards. They have been a hugely valuable resource to Oregon's fishing communities,” Cassady said. “In innumerable other ways, Sea Grant has, time and again, demonstrated that its programs return value to the state that is many times greater than the initial investment."

The balance of the NOAA funds will support Sea Grant's ongoing education, outreach and public engagement activities on the coast and throughout the region, from marine education programs at OSU's Hatfield Marine Science Center to engaging and informing coastal communities and policy makers on the scientific underpinnings of issues such as marine reserves  and community preparedness for tsunamis. A number of graduate student fellowships in marine science and policy will also be funded under the Sea Grant Scholars program.

Oregon Sea Grant is one of 32 National Sea Grant College Programs, all based at universities in coastal and Great Lakes states and funded under NOAA. The Oregon program, in operation since 1968, has long supported research at OSU and other institutions of higher education in Oregon; it also conducts marine Extension and education programs, and manages the Visitor Center at OSU's Hatfield Marine Science Center in Newport.

For more news about science, marine education and related activities on the Oregon coast, subscribe to “Breaking Waves,” the Oregon Sea Grant news blog, at: http://seagrant.oregonstate.edu/blogs/.

Story By: 

Stephen Brandt, 541-737-3396


CORVALLIS, Ore. - If increased precipitation and sea surface heating from global warming disrupts the Atlantic Conveyer current - as some scientists predict - the effect on the ocean food chain in the Atlantic and other oceans could be severe, according to a new study just published in Nature.

In a worst case scenario, global productivity of phytoplankton could decrease by as much as 20 percent and in some areas, such as the North Atlantic, the loss could hit 50 percent. The study was conducted by Andreas Schmittner, an assistant professor in the College of Oceanic and Atmospheric Sciences at Oregon State University.

In his sophisticated computer model, Schmittner does not predict that the Atlantic Conveyer current, which drags warm water from the southern tropics into the North Atlantic and warms Europe, will be disrupted. Rather, his study is one of the first to examine what would happen to the ocean food chain if such a disruption did take place.

"Phytoplankton are the basis of the entire marine food web," Schmittner said. "They ultimately affect everything from zooplankton to the larger fish that people consume."

The Atlantic Conveyer current has the strongest impact in the North Atlantic, but it is a global phenomenon, Schmittner said. Surface waters from the Pacific Ocean, the Indian Ocean, the Arabian Ocean and the southern Atlantic are pulled northward where they are cooled by the atmosphere in the North Atlantic. As the water cools, it sinks 2,000 to 3,000 meters and begins flowing southward. The upwelling from the mixing of waters constantly replenishes the supply of phytoplankton at the surface, forming a rich nutrient source at the bottom of the marine food web.

There is growing concern by a number of scientists, however, that higher levels of human-generated carbon dioxide could increase water and air temperatures and decrease salinity in the North Atlantic at a rate significant enough to prevent the sinking and ultimate mixing of the water. That would not only disrupt the Atlantic Conveyer current, Schmittner said, it would prevent nutrient-rich waters from triggering phytoplankton growth.

"When the Atlantic Conveyer current works, the dead plankton sink to the bottom and are replaced at the surface with nutrient-rich water that encourages further production," Schmittner said. "When the current is disrupted, and the mixing slows, that production also is disrupted."

The shutdown of the Atlantic Conveyer current isn't just idle speculation. A growing body of evidence suggests that it switched on and off 20 to 25 times during the last ice age.

"During the last ice age, from about 100,000 years before present to 20,000 years B.P., thick ice sheets over Canada sporadically dropped armadas of icebergs into the North Atlantic where they melted, sufficiently freshening the water to disrupt the conveyer," Schmittner said.

"There is some evidence backing that up," he added. "Deep ocean sediment core samples show pebbles from land delivered by the floating icebergs."

Schmittner said scientists also have examined ice cores from Greenland and measured isotopes that show rapid temperature changes, which coincide with changes in ocean nutrient concentrations measured in deep-sea sediment cores.

"One full oscillation of these switches took 1,500 years," Schmittner said, "but the individual transitions happened surprisingly fast. The climate went from a cold state to a warm state in as little as 20 to 50 years. Surface temperatures in Greenland increased 20 to 30 degrees Fahrenheit and water temperatures increased 10 to 20 degrees."

Schmittner said the impact of the current on the Pacific Ocean generally isn't as great, even though the system is a global one. Still, he added, plankton production would also decrease in the Pacific if the current was reduced.

Story By: 

Andreas Schmittner, 541-737-9952

Aquaculture: not an easy answer to overfishing

CORVALLIS, Ore. - A new report in the journal Science suggests that some types of aquaculture, a fish-farming concept that once seemed to be the solution to overfishing of the world's oceans, may in fact be causing some of the same problems it was meant to resolve.

Shrimp and salmon aquaculture, in particular, were indicted for depleting fisheries, disrupting coastal ecosystems, polluting the ocean with excess nutrients and pesticides, and using almost triple the quantity of wild-caught fish for "fish food" as the system produces in marketable shrimp or salmon.

"Aquaculture is often seen as a panacea, the solution to relieve fishing pressure on the oceans and feed the world," said Jane Lubchenco, a distinguished professor of zoology at Oregon State University and co-author of the report.

"What we're finding is that, unless it is done right, some aquaculture is causing more problems than it solves and doing nothing to increase the world's overall food supply."

Lubchenco and nine other international experts in aquaculture, fisheries, ecology and economics suggested that improved practices are needed to make salmon and shrimp aquaculture more sustainable. For example, the amount of fish required to make feed for salmon and shrimp should be reduced, pollution from aquaculture operations should be minimized and habitat destruction prevented.

Both the industry and government should consider new regulations, pollution taxes, or reduction of financial subsidies for the most harmful types of aquaculture until some of the problems are addressed, the researchers said.

According to the report, some of the worst problems with aquaculture develop with species such as shrimp and salmon that are carnivores and require high levels of fish meal and fish oil in their diets. Instead of becoming a substitute for ocean fishing, they actually draw down the ocean resources that support all fish production, the report said.

And the issues involved are increasingly a big business. Farmed shrimp is now produced in 50 countries, most of them developing nations in the tropics, with a global value of $6 billion a year. The salmon produced largely in temperate zones are a $2 billion crop which has expanded rapidly since the late 1970s due to improved technology, high profits and government subsidy.

Global aquaculture now accounts for one-fourth of all fish consumed by humans. Almost half of the salmon and nearly one fourth of the shrimp consumed worldwide now comes from farms.

Among the problems caused by shrimp and salmon aquaculture:


  • Shrimp aquaculture ponds can destroy mangroves and other nursery areas that support ocean fisheries, provide livelihoods for indigenous peoples and protect coral reefs.


  • Fish farming discharges nutrients, pesticides and antibiotics into coastal waters.


  • Exotic fish species are sometimes introduced outside their native habitat.


  • The ocean's capacity to assimilate wastes, provide feed and stock, and maintain viable fish populations is being challenged.


  • The viability of tropical ponds used to rear shrimp often collapses after 5-10 years of use from disease, chemical and biological pollution, creating a "boom and bust" economic cycle and disruption of local communities.

A big part of the problem, the report said, are the huge amounts of fish needed to produce fish meal and oil for the "delicacy" species such as shrimp and salmon that bring top prices in the market. It can take 1.8 million tons of wild fish to produce 644,000 tons of salmon.

Meanwhile, salmon netpens send volumes of feces and uneaten food directly into coastal waters. One analysis of the Nordic salmon farming industry showed that it discharged quantities of nitrogen equal to the amount in untreated sewage from a population of 3.9 million people. And there are concerns that escaped, farmed salmon may lead to genetic degradation of wild salmon populations.

"Rapid growth in shrimp and salmon farming has clearly caused environmental degradation, while contributing little to world food security," the researchers said in the report. "These industries provide food mainly for industrialized countries, consume vast quantities of wild fish as feed, and generally do not generate long-term income growth in impoverished communities."

According to Lubchenco, salmon aquaculture in the Pacific Northwest faces similar issues.

"Now that some of these problems are being recognized, they can begin to be addressed," she said. "Incentives which reward good practices should be established, which could operate at local to international levels."

In the Science report, the researchers suggested that a good mechanism to improve production practices might be trade restrictions through the World Trade Organization that addressed the processes of production, not just quality of products.

Story By: 

Jane Lubchenco, 541-737-5337

OSU partners with Naval Research Lab on space-borne coastal imaging

CORVALLIS, Ore. – A sophisticated new imaging system developed by the Naval Research Laboratory has just been installed aboard the international space station, where it will scan coastal oceans and nearby land masses and beam the data to Earth.

 The Hyperspectral Imager for the Coastal Ocean, or HICO, is the first space-borne sensor created specifically for observing the coastal ocean and will allow scientists to better analyze human impacts and climate change effects on the world’s coastal regions. The applications include oil spills, plankton growth, harmful algal blooms, and sediment plumes from major rivers.

 The HICO science data will be archived at Oregon State University, which will be the repository for distribution to researchers in the United States and internationally.

 “The timing couldn’t be better,” said Curtiss O. Davis, an OSU oceanographer and project scientist. “The development of different Earth observation systems, for whatever reason, has stalled. All of the current NASA ocean color sensors are beyond the end of their planned lifetimes. At a time when observation and analysis of the world’s oceans is critical to monitor climate change, we were losing our ability to do so.”

 What the HICO system will do, Davis said, is provide much higher-resolution imaging and a full spectrum of color. Previous imaging systems had a resolution of about one kilometer and about nine spectral channels. HICO’s scale is at 90 meters and it has 90 spectral channels, which is “a tremendous leap forward,” he pointed out.

 “In most previous systems, the imager would pick up grass, brush and trees and just display it all as green,” Davis explained. “When HICO becomes operational, we will be able to tell grass from shrubs, and in some case even identify the types of shrub. In the ocean, we can separate phytoplankton blooms from sediment plumes from rivers, and better measure chlorophyll levels in the ocean, which are associated with phytoplankton production.”

 The imaging system has other scientific applications, using optics to analyze water clarity, shallow water bottom features, and on-shore vegetation.

 The development of HICO is a story in itself. Such projects typically take up to a decade to develop, but when the opportunity became available to utilize the International Space Station for scientific observation of the oceans, the Naval Research Laboratory put the project on a fast track and developed HICO within 16 months, said Davis, who worked for the Navy lab for 11 years prior to joining the OSU faculty.

 Using the International Space Station for such observation is also new and adds a different wrinkle to environmental monitoring. Its orbit is not “sun-synchronous” and thus the station platform offers a wide range of illumination angles and sampling times not available via satellite observation. This makes the station an ideal platform for an experimental sensor like HICO, researchers say.

 “Never has the (space station) been utilized as a platform to conduct scientific Earth observations of this nature,” said Mike Corson, principal investigator for the HICO project at the Naval Research Laboratory’s Remote Sensing Division. “This collaboration of a diverse international and interagency consortium opens exciting opportunities for future basic and applied space-based research.”

 Davis, the Naval Research Laboratory and officials at the Office of Naval Research are working on a protocol for how HICO projects will be approved and data shared. HICO was sponsored by the Office of Naval Research and is integrated and flown with the support and direction of the Department of Defense Space Test Program. Additional support was provided by NASA and the Japanese Space Agency JAXA.

 “HICO can look anywhere, but its strength will be to monitor specific areas that are facing environmental pressures – such as the plume from the Mississippi River that creates a hypoxic zone in the Gulf of Mexico, or at harmful algal blooms off our own Pacific coast,” Davis said.

 He anticipates data will begin flowing in one to two months.

 More information on HICO and applications of the data will be posted soon on an Oregon State University-HICO web site that is under construction.

Story By: 

Curt Davis, 541-737-5707 (cdavis@coas.oregonstate.edu)

New Tide Gate Designs Enhance Fish and Water Passage

CORVALLIS, Ore. – A fixture of Oregon coastal farming, so-called “tide gates,” are coming under new scrutiny because of their environmental effects.

Essentially hinged metal doors at the ends of culverts, tide gates have been used for centuries to prevent flooding and help drain low-lying coastal lands, making it possible for people to farm and build on land that would otherwise be under water. But in many cases the devices have also compromised or destroyed critical fish and wildlife habitat.

“Tide gates tend to be effective at maintaining low water levels on the upland side of dikes,” said Guillermo Giannico, Extension fisheries specialist with Oregon State University. “Unfortunately, by altering water flow they also have some undesirable side effects.”

Among those side effects, Giannico said, are elimination of upland tidal marshes and changes in water temperatures, sediment transport, nutrient concentration and fish passage.

The effects of tide gates on estuaries and wildlife were the focus of a symposium held earlier this fall at the South Slough National Estuarine Research Reserve in Charleston, Ore. Sponsored by the Coos Watershed Association, OSU Extension Service, Oregon Sea Grant and others, the three-day symposium presented introductory information on tide gates and their effects on estuarine habitats and fish passage and provided a forum for coastal managers, biologists, engineers and others to exchange information.

Also discussed were the potential benefits and problems associated with removing or replacing existing tide gates to help restore habitat and encourage fish passage. OSU’s Giannico organized the symposium.

Jon Souder of the Coos Watershed Association, a co-organizer of the event, noted that significant concern with tide gates is that “flooding can be exacerbated rather than mitigated by tide gates, both above and below the gates.”

But both regulatory agencies and private industry are looking to engineering solutions that can allow landowners to continue using tide gates. Symposium presenter Larry Swenson of NOAA Fisheries outlined his agency’s criteria for improving the performance of tide gates, including a requirement that the gates allow fish passage “90 percent of the time the gate is open.”

Tide gate designer and builder Leo Kuntz of Nehalem Marine demonstrated several different new tide gate designs and discussed their respective features and effectiveness. One of his designs, he said, allowed for a “30 percent increase in water flow” in both directions, enhancing the exchange of saltwater and freshwater and thus improving the natural marshland conditions.

OSU’s Giannico was encouraged by the symposium’s attendance and what he sees as a general increase in awareness among both professionals and the public. “The importance of protecting and restoring these ecosystems has finally appeared on the radar screen,” he said.


Guillermo Giannico,

OSU Awaits House Decision on Offshore Ocean Observing System Appropriation

CORVALLIS, Ore. – Oregon’s long-awaited offshore ocean observing system has moved one step closer to reality after the U.S. Senate Commerce-Justice-State Appropriations Subcommittee, which approved its 2007 spending bill, proposed $2 million for the project.

Oregon State University will operate the project, known as the Oregon Coastal Ocean Observing System, or OrCOOS, which would provide some of the first coordinated “real time” oceanographic data from Oregon’s coastal waters.

The bill still needs to pass through the senate floor, and then go to conference with the U.S. House of Representatives – likely in December.

Scientific data from ocean observations is recorded through many different projects, but it lacks coordination and timeliness, said Mark Abbott, dean of the College of Oceanic and Atmospheric Sciences at OSU. Establishing OrCOOS would provide real time data that would benefit not only scientists, Abbott pointed out, but also the state’s commercial and recreational fishing fleets, the Coast Guard and other marine operations, natural resource managers, students and educators, and others.

“The model is the National Weather Service, which collects data from a variety of different sources and makes is available broadly to a variety of users,” Abbott said. “The real time data we would receive from wave observations and forecasts, for example, will be of use to recreational boaters trying to determine when to cross the bar, and to the Coast Guard to estimate where a ship will drift in the ocean after it has lost its power.

“It’s something that will benefit the state of Oregon – and it’s long overdue,” Abbott said.

U.S. Sen. Gordon Smith has been an advocate for the ocean observing system and helped steer last year’s initial funding of $450,000 for the project. A team of scientists led by OSU oceanographer Jack Barth used the funding to develop a new research buoy that will be moored off Heceta Bank along the central Oregon coast.

The sophisticated instrumentation aboard the buoy will measure chlorophyll levels in the water that indicate biological productivity; dissolved oxygen that relates to hypoxia or “dead zones,” temperature, salinity and current velocity. Above water, the buoy will take a full meteorological scan, measuring air temperature, wind speed and solar radiation.

The above-water portion of the buoy is even fenced to prevent sea lions from lounging on – and potentially sinking – the buoy.

“The Heceta Bank is one of the most important locations along the coast because it deflects the waters flowing from the north and creates a quiet pool of water that serves as an incubator for the phytoplankton that feed the marine food web,” Barth said. “That’s also the location of the most intense hypoxia events and ‘dead zones.’

“Oregon is situated at a point where changes in the atmospheric Jet Stream have a major impact on the local weather conditions and the ocean’s response to them.”

Barth said the $2 million appropriation under consideration in Congress would be used to develop two additional buoy systems – one that would be deployed off the Columbia River and the other off Coos Bay.

“That would give us tremendous coverage of the entire Oregon coast,” he said.

The funding also would help the scientists design models that will predict ocean conditions based on their observations and analyses of data from the buoys and other sources, and create user-information systems for fishermen, recreational boaters, and others.

Story By: 

Mark Abbott,

Scientists Team with Fishermen and Use Genetics to Trace Origins of Ocean Chinook

NEWPORT, Ore. – Oregon State University scientists are teaming with commercial fishermen on a new research effort to rapidly identify the home river basin of Chinook salmon found in the Pacific Ocean using genetic testing.

Their goal is to learn more about offshore schooling behavior and stock composition of salmon and ultimately to prevent coast-wide fishing closures. The closures aim to protect weak stocks like those of the Klamath River basin that may constrain an otherwise healthy fishery.

Funded by the Oregon Watershed Enhancement Board, and managed by the Oregon Salmon Commission, the pilot project is called the Cooperative Research for Oregon’s Ocean Salmon, or CROOS. Already it is paying dividends.

During the June 4 opener, fishermen caught Chinook salmon off the Oregon coast between Newport and Florence and OSU scientists were able to positively match the DNA from the fins of 71 of the fish to establish their origin from river systems in California, Oregon, British Columbia and Alaska.

An ongoing project coordinated and funded by the National Oceanic and Atmospheric Administration involving 10 labs from California to Alaska – including OSU’s Hatfield Marine Science Center in Newport – has identified unique genetic profiles for 110 different salmon populations based on their home river basin. Scientists and resource managers previously were unable to identify stock composition of both wild and hatchery fish originating from the Pacific Northwest, Canada and Alaska.

Project leaders say that this new technology allows scientists to assess the origin of an individual fish with remarkable accuracy.

“This was the key for us to utilize the technology,” said Michael Banks, an OSU geneticist and director of the Cooperative Institute for Marine Resources Studies, a joint Oregon State-NOAA research collaborative. “Having a bank of DNA profiles allows us to approach ‘real-time’ identification of fish. What used to take months, or even years, we’ve been able to pare down to about 48 hours.”

During the June field testing, participating fishermen caught Chinook salmon off the Oregon coast between Newport and Florence and collected a fin-clip from each fish for DNA analysis. OSU scientists were able to match genetic profiles of fish from river systems as far south as Battle Creek in California, and from as far north as the Babine River in Alaska.

Traditional efforts to identify the origin of ocean-caught salmon came from coded wire tags inserted into the snouts of a small percentage of hatchery fish. Those tags were useful for determining broad-scale distributions of stocks caught in fisheries, but revealed only the origin of select tagged fish. The time and location of these tagged fish also have been too general – reported by week and catch area.

The coded wire tag data weren’t usually available until several months after the season ends.

Using DNA testing, however, will allow the scientists to rapidly assess the origin of any Chinook salmon caught off the West Coast – not just coded wire-tagged hatchery fish – and identify with about 95 percent accuracy its home river system. In theory, researchers say, they could test several salmon in schools from different locations to see what percentage of them originate from a weak run.

“This could lead to the introduction of some degree of in-season harvest management,” said Gil Sylvia, an OSU economist and superintendent of the Coastal Oregon Marine Experiment Station. “Having accurate information could lead to reducing access to some stocks in certain areas at certain times. But it is just as likely that it could result in decisions to open areas of the coast where higher concentrations of harvestable fish populations are.”

The researchers will compare their genetic assessment with coded wire-tagged fish to test the efficacy of the project.

Many of Oregon’s commercial fishermen, who have been shut down from pursuing their livelihood this summer, say they are excited by the research.

“I started fishing in 1970 and this is the most optimistic I’ve been about any kind of research relating to salmon,” said Paul Merz, who fishes out of Charleston. “I’m still a cynic when it comes to management decisions. But this is the science that has been missing in all of the policy arguments – and it’s something where you can see the immediate results.”

Jeff Feldner, a fisherman from Logsden, Ore., said that seasons are designed to minimize the impact on the weakest runs.

“The problem,” he pointed out, “is that we haven’t known enough about the fish that are out there. Using information gathered over the summer to help predict where the fish will be next year doesn’t help the fishermen. We haven’t had a way of knowing in ‘real time’ where the fish are and where they’ve come from. Now we do.”

The Oregon Watershed Enhancement Board has funded this pilot study for one year with a $586,391 grant, which will allow 50 Oregon commercial vessels to make a total of 200 fishing trips, and allow the scientists to run 2,000 DNA samples. As many as 90 vessel owners have expressed an interest in participating.

“We need additional funding to continue the research,” said Nancy Fitzpatrick, lead administrator of Project CROOS and an employee of the Oregon Salmon Commission. “One year just begins to give you information, but it isn’t enough to determine all you need to know about salmon. Fish have fins, as they say, and they tend to move from one location to another.

“Where you find them one year isn’t necessarily where you’ll find them the next.”

Fitzpatrick says any changes in how the oceans are managed for salmon would come from the Pacific Fishery Management Council, a regional council with members from Oregon, Washington, Idaho and California, that recommends fishery management measures to the National Marine Fisheries Service.

The OSU researchers are keeping track of the salmon through an onboard electronic traceability system developed by the university over the past several years. This innovative barcode system allows commercial fishermen to log the location, date and time of the capture, as well as onboard handling techniques, for every fish captured. Each fish harvested by a participant receives a metal tag with a unique number and bar-code. A website under construction will eventually allow a consumer to access basic information about the salmon: where and when it was harvested, by whom, and from which river it originated.

Eventually, such a tool may play a major role in marketing, according to Michael Morrissey, director of the OSU Seafood Laboratory in Astoria, and a principal investigator in the CROOS project.

“By identifying the river system through genetics, and being able to accurately label a fish as ‘wild,’ the potential exists for fishermen to brand their product and increase the value to consumers,” Morrissey said. “One such example is Copper River salmon, which often command twice the market price of similar fish, because of the attributes attached to it.”

As part of the study, local salmon processors and buyers are returning some of the heads from the specially marked fish to the OSU Hatfield Marine Science Center, where scientists will conduct tests on their otoliths. Otoliths are crystalline structures located in the inner ear and act like growth rings in trees, recording not only age, but chemical elements that provide clues to the environment in which the fish lived.

Some of the fish stomachs will be retained by participating fishermen and given to scientists to reveal clues about the salmon’s diet, including how the proportion of baitfish consumed might vary by season and between areas. The fishermen involved in the project will contribute data on oceanographic conditions where the fish were caught, including depth and temperature. Some of the fishermen participating in the project say they are fascinated by the science and hope it will help them locate fish more effectively, as well as keep the season opened.

“Every year, it seems like the challenges for commercial fishermen keep getting worse with restricted limits followed by complete closures,” Merz said. “A lot of fishermen have packed it in. But this project gives me some hope. If it works the way it seems like it can, and if management is adjusted accordingly – and that’s a big if – then it might be enough to keep me going. If not, I’ll be looking for a new line of work and get on with my life.”

More information on this project is available at www.projectCROOS.com


Story By: 

Michael Banks,

Multimedia Downloads

Chinook graph

This map depicts the origins of some of the fish caught during the June 4 salmon opener off the Oregon coast. The pie chart shows that a majority of the fish originated from California waters, with few bound for the Klamath basin.

‘Dead Zone’ Causing a Wave of Death Off Oregon Coast

CORVALLIS, Ore. – The most severe low-oxygen ocean conditions ever observed on the West Coast of the United States have turned parts of the seafloor off Oregon into a carpet of dead Dungeness crabs and rotting sea worms, a new survey shows. Virtually all of the fish appear to have fled the area.

Scientists, who this week had been looking for signs of the end of this “dead zone,” have instead found even more extreme drops in oxygen along the seafloor. This is by far the worst such event since the phenomenon was first identified in 2002, according to researchers at Oregon State University. Levels of dissolved oxygen are approaching zero in some locations.

“We saw a crab graveyard and no fish the entire day,” said Jane Lubchenco, the Valley Professor of Marine Biology at OSU. “Thousands and thousands of dead crab and molts were littering the ocean floor, many sea stars were dead, and the fish have either left the area or have died and been washed away.

“Seeing so much carnage on the video screens was shocking and depressing,” she said.

OSU scientists with the university-based Partnership for Interdisciplinary Studies of Coastal Oceans, in collaboration with the Oregon Department of Fish and Wildlife, used a remotely operated underwater vehicle this week to document the magnitude of the biological impacts and continue oxygen sampling. This recent low-oxygen event began about a month ago, and its effects are now obvious.

Any level of dissolved oxygen below 1.4 milliliters per liter is considered hypoxic for most marine life. In the latest findings from one area off Cape Perpetua on the central Oregon coast, surveys showed 0.5 milliliters per liter in 45 feet of water; 0.08 in 90 feet; and 0.14 at 150 feet depth. These are levels 10-30 times lower than normal. In one extreme measurement, the oxygen level was 0.05, or close to zero. Oxygen levels that low have never before been measured off the U.S. West Coast.

“Some of the worst conditions are now approaching what we call anoxia, or the absence of oxygen,” said Francis Chan, a marine ecologist with OSU and PISCO. “This can lead to a whole different set of chemical reactions, things like the production of hydrogen sulfide, a toxic gas. It’s hard to tell just how much mortality, year after year, these systems are going to be able to take.”

One of the areas sampled is a rocky reef not far from Yachats, Ore. Ordinarily it’s prime rockfish habitat, swarming with black rockfish, ling cod, kelp greenling, and canary rockfish, and the seafloor crawls with large populations of Dungeness crab, sea stars, sea anemones and other marine life.

This week, it is covered in dead and rotting crabs, the fish are gone, and worms that ordinarily burrow into the soft sediments have died and are floating on the bottom.

The water just off the bottom is filled with a massive amount of what researchers call “marine snow” – fragments of dead pieces of marine life, mostly jellyfish and other invertebrates. As this dead material decays, it is colonized by bacteria that further suck any remaining oxygen out of the water.

“We can’t be sure what happened to all the fish, but it’s clear they are gone,” Lubchenco said. “We are receiving anecdotal reports of rockfish in very shallow waters where they ordinarily are not found. It’s likely those areas have higher oxygen levels.”

The massive phytoplankton bloom that has contributed to this dead zone has turned large areas of the ocean off Oregon a dirty chocolate brown, the OSU researchers said.

Scientists observed similar but not identical problems in other areas. Some had fewer dead crabs, but still no fish. In one area off Waldport, Ore., that’s known for good fishing and crabbing, there were no fish and almost no live crabs.

The exact geographic scope of the problem is unknown, but this year for the first time it has also been observed in waters off the Washington coast as well as Oregon. Due to its intensity, scientists say it’s virtually certain to have affected marine life in areas beyond those they have actually documented.

This is the fifth year in a row a dead zone has developed off the Oregon Coast, but none of the previous events were of this magnitude, and they have varied somewhat in their causes and effects. Earlier this year, strong upwelling winds allowed a low-oxygen pool of deep water to build up. That pool has now come closer to shore and is suffocating marine life on a massive scale.

Some strong southerly winds might help push the low-oxygen water further out to sea and reduce the biological impacts, Lubchenco said. The current weather forecast, however, is for just the opposite to occur and for the dead zone event to continue.

There are no seafood safety issues that consumers need to be concerned about, OSU experts say. Only live crabs and other fresh seafood are processed for sale.

Researchers from OSU, PISCO and other state and federal agencies are developing a better understanding of how these dead zone events can occur on a local basis. But it’s still unclear why the problem has become an annual event.

Ordinarily, north winds drive ocean currents that provide nutrients to the productive food webs and fisheries of the Pacific Northwest. These crucial currents can also carry naturally low oxygen waters shoreward, setting the stage for dead zone events. Changes in wind patterns can disrupt the balance between productive food webs and dead zones.

This breakdown does not appear to be linked to ocean cycles such as El Niño or the Pacific Decadal Oscillation.

Extreme and unusual fluctuations in wind patterns and ocean currents are consistent with the predicted impacts of some global climate change models, scientists say, but they cannot yet directly link these events to climate change or global warming.


Jane Lubchenco,

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hypoxia research

Hal Weeks, a researcher with the Oregon Department of Fish and Wildlife, worked on OSU's research vessel Elahka on Aug. 8 with a remote operated underwater vehicle to document the dead zone that is plaguing the region.

Scientists: Oregon’s Ocean Upwelling Fueled by Jet Stream, Sub-Arctic and River Flow

CORVALLIS, Ore. – A team of nearly 60 scientists, which just wrapped up a five-year study of the ocean circulation, biology and chemistry off the Oregon coast, has discovered a new cycle of activity in the Jet Stream that has a major influence on upwelling and ocean productivity.

The Coastal Ocean Advances in Shelf Transport program, or COAST, was led by researchers at Oregon State University.

Funded by the National Science Foundation, the study also found that Oregon has a unique upwelling system with processes that can reduce the level of atmospheric carbon dioxide. However, when those same processes are altered by changes in atmospheric or oceanic conditions, the result can be the onset of hypoxia, or oxygen-starved water that leads to marine die-offs and “dead zones” in the ocean.

“One of the things we’ve discovered is a new time scale of atmospheric activity somewhere between the weather bands that change every 2-5 days and the summer-winter seasonal adjustments,” said Jack Barth, a professor in OSU’s College of Oceanic and Atmospheric Sciences and a principal investigator on the project.

“It seems that every 30 days or so, the Jet Stream ‘wobbles’ and it changes the entire pattern of winds and the ocean’s response to them,” Barth said. “The central Oregon coast is affected by weather systems tracking along the Jet Stream, and when it moves to the north, we tend to get good upwelling. When it moves to the south, the upwelling goes bad.”

In 2005, Barth said, the Jet Stream migrated southward and caused a delay in the upwelling, leading to unusual ocean conditions. These “wobbles” in the Jet Stream change the ocean temperature, can accelerate or reduce upwelling and nutrient-enrichment, and ultimately affect the production of phytoplankton, which feed the marine food web.

What causes these changes in the Jet Stream isn’t fully understood, the OSU researchers say. One strong influence on the Jet Stream is the enormous mountains in Asia.

The Heceta Bank off the coast between Newport and Florence exerts a major influence on Oregon’s coastal ocean. It protrudes into the Pacific Ocean and deflects the north-south currents, creating a quiet area that serves as a natural incubator for plankton. Slight shifts in the winds, however, could lead to overproduction and hypoxia, or on the other hand, insufficient upwelling to feed the food chain.

Not coincidentally, the part of the northeast Pacific Ocean most affected by dead zones has been the central Oregon coast.

Further complicating the upwelling picture, the researchers discovered, is the influence of sub-Arctic waters that flow south into the near-shore region off Oregon. The OSU scientists monitored these waters over the past five years and discovered some interesting variations, said Pat Wheeler, an Oregon State oceanographer and a principal investigator on the study.

“In 2002, for example, there were a number of storms in the Gulf of Alaska and the flow of sub-Arctic water down our coastline was highly elevated in nutrients,” Wheeler said. “That led to a four-fold increase in phytoplankton production that year and after they fell to the seafloor, bacterial degradation sucked all of the oxygen out of the water. That was the first year that scientists began observing and monitoring a string of hypoxia events leading to ‘dead zones.’”

Wheeler and her colleagues also measured the influence of Oregon’s small coastal rivers on nutrients in the coastal zone. They discovered that Oregon’s rainfall ultimately feeds nutrients into the ocean by elevating these small coastal rivers and naturally leaching iron from the rocks in the streams.

“The iron that is deposited into the waters offshore actually helps fertilize the waters and promotes biological activity months later,” she said. In contrast, the waters off California have limited iron, the researchers say, because there aren’t as many coastal rivers pumping fresh water into the ocean.

The COAST program was funded through a $9 million grant from the NSF and drew experts in ocean biology, chemistry and physics from OSU, the University of North Carolina, Lamont-Doherty Earth Observatory, and the Woods Hole Oceanographic Institution. One focus of their research was the study of east-west movement of water.

While the north-south currents are widely known, less is understand about the mechanisms that move water from Oregon’s coast line to deeper water and vice versa, the researchers said. During the COAST project, they were able to observe how phytoplankton decomposed, fell to the ocean floor, and were swept out to the deep ocean by water moving in a westerly direction.

That process also serves to lower atmospheric carbon dioxide, which the plankton draw down and use to bloom, by depositing it into the deep ocean.

“When decomposing phytoplankton are respired over the shelf, instead of being transported offshore, we get low oxygen conditions, or hypoxia,” Barth said. “And the CO2 can go right back into the atmosphere. But when the system works, and the phytoplankton take the carbon dioxide into the deep ocean, it makes the central Oregon coast a net sink for atmospheric CO2.”

Using their expanded knowledge and an emerging ocean observing network to develop predictive models is the next phase of the research, the OSU scientists say.

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Jack Barth,