Archive for salmon

Fish on rice

Nigiri Project

Can fish and farms coexist in harmony? Scientists are currently trying to answer this question in the Yolo Bypass, a roughly 60,000-acre expanse of engineered seasonal floodplain habitat that sits upstream of the Sacramento-San Joaquin Delta in California’s Central Valley. This unique area was developed in the 1930s as a bypass for water from the Sacramento River to reduce the risk of flooding in the Sacramento area. It generally floods in the winter or spring when waters from the Sacramento River overflow the Fremont Weir. When the bypass drains in the late spring, the land is used for agriculture (most notably rice farming) and grazing. In recent years, biologists have begun to recognize the area’s importance as winter aquatic habitat for birds, fishes, and other wildlife (Sommer et al. 2001, Feyrer et al. 2006). As part of the Cal-Neva American Fisheries Society annual meeting, held last week in Davis, CA, the Department of Water Resources (DWR) and CalTrout hosted a tour of the Yolo Bypass for fellow fisheries biologists.

Nigiri Project on the Yolo Bypass

A highlight of the tour was stopping by Knaggs Ranch, located just north of the City of Woodland. CalTrout, DWR, and UC Davis have launched a study here investigating the potential to combine current agricultural practices  with floodplain habitat for fish and wildlife in the Yolo Bypass, dubbed “The Nigiri Project” (i.e., “fish on rice”), which has recently received a lot of press. Jacob Katz, from CalTrout and UC Davis, showed off the project site. Researchers have teamed up with farmers to investigate whether productive rice fields farmed during the summer can be managed in the off-season to provide winter habitat for juvenile Chinook salmon. The expansive habitat and somewhat regular flooding events in the Yolo Bypass offer a unique opportunity to test this rotation. They are just finishing the second year of the project, and rice grown on the experimental plots during the first year was harvested last fall (see top photo). Over the past two years this project has documented impressive growth of salmon that lived on the experimental habitat for six weeks: last year they recorded a five-fold weight gain, one of the highest growth rates for Chinook in the region. In 2013, fish were raised in various plots where the rice stubble left over from last year’s harvest was treated in different ways (e.g., stomped down, left as stubble, disked, or fallowed). The team is currently analyzing the results of the rice treatment portion of the study to see if fish benefit from particular rice stubble modifications. The AFS tour attendees observed the study fish before researchers released them into the river.  The fish are outfitted with acoustic tags so scientists can track their survival and migration to the ocean. Project participants are touting the collaboration as a rare win-win-win situation, with benefits for agriculture, wildlife, and flood protection. 

Groups ask judge to halt Sandy River hatchery releases this spring in wild vs. hatchery case

The Columbia Basin Bulletin
March 8, 2013

Fish conservation groups seeking a permanent end to hatchery produced salmon and steelhead in northwest Oregon’s Sandy River basin have asked a federal judge, in the near term, to preempt the planned release of several hundred fish later this month.

The Native Fish Society and McKenzie Flyfishers on Feb. 19 filed a request in Oregon’s U.S. District Court asking for a temporary restraining order and/or preliminary injunction that forbids the Oregon Department of Fish and Wildlife from setting hatchery smolts free in the Sandy or its tributaries this spring.

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An (almost) albino salmon

(Almost) albino salmon

Over the years we have handled millions of juvenile salmon, but this week we came across one that truly stands out from the rest. During the spring each year we use rotary screw traps to sample juvenile Chinook migrating out of Central Valley watersheds (see Efficiently incarcerating adolescent fish). As we do each morning, our fisheries technicians recently checked our traps to see what we captured overnight. As they scooped hundreds of salmon fry out of the trap livewell, one immediately stood out among the others. We captured what appeared to an albino salmon fry. With a little research we found that it is not actually a true albino—since the eyes have normal color, it is referred to as leucistic. Leucism is caused by a recessive genetic trait that results in a reduction of skin pigments. Albinism and leucism are not uncommon in hatchery settings but are quite rare in wild fish like this one. The low frequency of this abnormality in natural populations may reflect that the lack of protective coloration increases vulnerability to predation.

A pigment-free salmon (top) compared to a normal one

The Salmon Hunger Games

Returning Chinook salmon

Each year, salmon managers for the Columbia River try to peer into the future and foretell the number of adult spring Chinook that will return to spawn. They use this crucial prediction to divvy up salmon harvest quotas among commercial, recreational, and tribal fishers. Now, scientists have found a way to improve the fish forecast: harnessing the predictive power of ocean conditions. Once juvenile salmon leave their freshwater streams and enter the ocean, the culling that occurs in the first brutal months largely sets the number of fish that grow up and return to spawn in two or three years (Beamish and Mahnken 2001, Wells et al. 2008). The ocean is a complex and shifting arena where many poorly understood factors can make or break a teenage salmon’s shot at survival. In a paper published in the journal PLOS One last month, scientists from the National Marine Fisheries Service and Oregon State University identified key ocean factors, such as the abundance of prey and major ocean trends, that can better predict the number of fish that will live to make a river homecoming.

To determine which of the ocean’s biological and physical conditions most influence Columbia River spring-run salmon survival, the researchers gathered up 31 datasets, or indicators, and divided them into five basic categories. These included large-scale ocean and atmosphere factors; smaller-scale local or regional factors; fish growth and feeding; predation and disease; and measures of cohort abundance. They tossed everything into a statistical model that could analyze multiple sets of data at once, and calibrated the model using the numbers of returned salmon from 2000-2009. While no single variable distinguished itself as the best crystal ball to foretell salmon returns, some groups of indicators stood out as more important. Eating and bulking up are key in this fish-eat-fish world. Leading indicators included the abundance of planktonic salmon prey, such as copepods and fish larvae, as well as measures of salmon diet and growth. The scientists concluded that switching from feeding on plankton to fish soon after they enter the ocean, between May and June, plays a large role in deciding which juvenile salmon will clear the hurdle to adulthood.

Big-picture processes, such as large-scale patterns of ocean temperature, also heavily contributed to predictions of salmon survival, more so than local or regional measurements of temperature and salinity from Oregon and Washington. This may reflect the influence of widespread ocean conditions on salmon prey. The scientists’ model proved quite accurate in its predictions: it came only six fish shy of nailing the 2011 adult spring-run Chinook returns to the Columbia River (which numbered just over 221,000 fish), and its prediction of 179,000 salmon in 2012 came far closer than other estimates to the actual number of 203,000. The study authors note that factoring in many of the complex relationships that govern a salmon’s ocean experience improves on the forecasts currently used to inform salmon management decisions, which typically rely on just one or two indicators. Their technique could prove a valuable tool for setting salmon quotas, and helps us better understand the conditions that give young salmon favorable chances to beat the odds.

This post featured in our weekly e-newsletter, the Fish Report. You can subscribe to the Fish Report here.

One endangered species eats another: killer whales and salmon

January 22, 2013

With clear skies above and a crystalline view of the Seattle skyline to the east, Brad Hanson motors along in a Zodiac inflatable, following a respectful distance behind a pod of killer whales. As the whales feed on Chinook salmon, Hanson and his crew skim what’s left of the whales’ meal off the water: fish scales, shreds of salmon, whale feces. “It’s very strange to be out with these huge predators right in the middle of an urban area,” Hanson says. It’s also very practical for data collection. With the samples he scoops from the water, Hanson will extract detailed information about the killer whales and their prey.

Hanson is a marine mammal biologist with NOAA’s Northwest Fisheries Science Center. The animals he’s studying are southern resident killer whales—the endangered population that spends much of the summer in and around the Puget Sound. There are only 89 of them, and their population is recovering very slowly. Hanson and his colleagues are trying to figure out why.

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FDA ruling on GMO salmon worries Alaska fishermen

High Country News
By Marshall Swearingen
January 17, 2013

On January 2, the Alaska Department of Fish and Game released its annual fisheries forecast for the Copper River region, famous for its prolific runs of succulent salmon. The forecast, awaited each year by fisherman living in the region’s port towns, makes predictions based on the previous years’ harvest, weather patterns, and a variety of other data. This year, there’s good news mixed with the bad: 2013 is set to be a good year for pink salmon, but runs of Chinook (king) salmon are expected to be the fifth smallest since 1980. Fish and Game researchers aren’t sure why, but a recent spell of colder ocean temperatures may be partly to blame.

Making a living on fishing has always been a gamble, but this year Alaska’s fisherfolk have even more cause for worry. On December 26 the FDA quietly issued its approval of genetically modified “AquaAdvantage” salmon. After more than a decade of regulatory uncertainty, the FDA’s decision all but paves the way for the fish to be “farmed.” The FDA is taking public comments on the issue until February 24, but the unambiguous wording of the decision suggests little room for charting a new course. Alaskans who make a living fishing for wild salmon have long opposed AquaAdvantage, saying the freakishly fast-growing fish puts wild stocks — and the state’s fishing industry — at risk.

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Fish fertilizer

Salmon carcass

Anecdotal accounts tell of salmon once so plentiful in California’s Central Valley streams that farmers spread salmon carcasses onto their fields to fertilize crops. While those days are long gone, salmon still posthumously nourish their natal environments. As we navigate the streams draining the San Joaquin basin during late fall and early winter, occasionally accompanied by the unmistakable aroma of decaying fish, we often witness this process of “fertilization” in action, as returned Chinook make their final contribution to watersheds in the Central Valley and Pacific Northwest. Returning salmon contribute organic matter and nutrients to their natal streams in a number of ways, including their own metabolic processes, their release of eggs and sperm, serving as food to their predators, and the decomposition of their carcasses.

A surprising variety of animals feed on salmon carcasses. In addition to bears, wolves, otters, raccoons, skunks, and foxes, the likes of shrews, mice, squirrels, deer, and a large number of bird species opportunistically indulge in salmon (Willson and Halupka 1995). All of these species act as vectors for marine-derived nutrients as they spread, by way of metabolic waste, “fish fertilizer” far beyond river channels and adjacent riparian habitat. Any uneaten carcasses decay and release nutrients into the soil and water. During a stroll along suitable spawning reaches this time of year, one can often spot the fuzzy evidence of microbial decomposition.

Decaying carcass

Pacific salmon accumulate the vast majority of their body mass (>90%) while feeding in the ocean, so it may seem intuitive that migrating anadromous salmonids provide a substantial nutrient subsidy when they return to their freshwater rearing areas. However, the effects of spawning salmon on the nutrient dynamics of stream systems remained poorly studied until fairly recently. About two decades ago, advances in the field of stable isotope analysis gave researchers novel tools to trace marine-derived nutrients through riverine and riparian ecosystems. Marine environments (and therefore the salmon’s diet and the salmon itself) have a much greater proportion of the heavier nitrogen isotope 15N, relative to 14N, than freshwater, air, or land. Scientists can use these differences to estimate the proportion of marine-derived nutrients (mainly nitrogen and phosphorus) in tissues of animals and plants.

Thanks to such studies, we now know that many plant and animal communities depend on salmon runs as a source of energy to a rather astonishing extent: for example, following the return of pink salmon to a stream in southeastern Alaska, nearly all of the nitrogen contained in resident rainbow trout, aquatic insects algae, and microbes was marine-derived (Kline et al. 1990). Furthermore, nearly 25% of nitrogen in the foliage of riparian vegetation in this area stems from marine sources, and enhanced growth of trees and shrubs near salmon-bearing streams has been documented in many locations (e.g. Helfield and Naiman 2001, 2002, 2006). While Chinook populations of the Sacramento-San Joaquin basin are more modest than the salmon runs of Alaska, animals and plants still benefit from the autumnal nutrient subsidy, and even cultivated crops such as wine grapes grown adjacent to a Central Valley stream can (indirectly) derive up to a quarter of their foliar nitrogen from returning salmon (Merz and Moyle 2006).

Juvenile salmon benefit from the nutrient boost provided by their decomposing ancestors through increased densities of invertebrates to eat and enhanced riparian vegetation providing cover and refuge. As such, the nutrients from spawning salmon may serve as a positive feedback mechanism that maintains long-term salmon production and riparian habitat; conversely, decreased salmon production may be self-perpetuating (Cederholm 1999, Naiman et al. 2002).

This post featured in our weekly e-newsletter, the Fish Report. You can subscribe to the Fish Report here.

Smile, you’re on salmon camera!

Considering how much gear we station underwater or deploy floating in California’s rivers, it’s remarkable that we’re able to keep track of and recover it all—well, almost all. We have a few good stories of gear lost and found (see Lost), but this one is a winner. You may be familiar with our method of setting up underwater digital cameras to record Chinook spawning behavior, since we recently posted a few videos and stories on the topic (see One-to-one spawning, Casual spawning). Back in November 2011, we set up an underwater camera in a local river to try and film salmon spawning. While the vast majority of fish pay no mind to our equipment and just go about their business, one female salmon didn’t take too kindly to our Peeping Tom tactic. She thrashed the offending camera until it unscrewed from its base and drifted away.

How do we know? Because last week, more than a year after the incident, a California Department of Fish and Game crew conducting carcass surveys stumbled across the camera on the riverbank. Recognizing it as ours, they returned it to a FISHBIO team conducting redd surveys nearby. To our surprise, the inside of the camera housing was still dry and the camera still worked! Its surveillance video (below) caught the culprit in the act; you can see the salmon whacking the camera until it floated downstream to its temporary resting place. So other feisty Chinook, take notice: we’ve got an eye on you.

Salmon in Patagonia

Although salmon are native to the northern Pacific and Atlantic oceans, it’s not uncommon to travel to the other side of the globe and find freshly caught salmon in the local fish market. We were not surprised to see salmon on the menu in Chile. Salmonids have been introduced to South America since the early 1900s, and salmon farming has taken off in Chile more recently. Four salmonid species are commercially cultivated in the country: Atlantic salmon, coho salmon, Chinook salmon and rainbow trout (Norambuena and Gonzalez 2005). Chile is the second largest producer of Atlantic salmon in the world, behind Norway. Salmon smolts are reared at land-based facilities, then transferred as yearlings to cages in lakes or rivers, and finally raised as adults in floating cages or net pens. This practice has attracted some controversy: environmental organizations have expressed concerns about the harmful effects of salmon farming on the local lake and marine ecosystems, such as pollution, disease, and escaped salmon competing with native fish. An epidemic of the virus Infectious Salmon Anemia, which may have started with eggs shipped from Norway, nearly decimated the Chilean salmon industry in 2007, but it quickly rebounded.

Not only are salmonids an important seafood export, but fly-fishing for ‘wild’ or ‘naturalized’ salmonids has become a significant tourist attraction in Patagonia. Fishing for freshwater brown and rainbow trout is a common pastime. Anglers prize the rarer Atlantic, Chinook and coho salmon so much that they encourage catch and release methods. Often it is not known whether these ‘wild’ salmon originated from salmon that escaped the farm net pens, or if they descended from purposefully stocked salmon. In the case of Chinook, eggs and alevins (newly hatched salmon) from Washington State were intentionally planted in Chile (Astorga et al. 2008). Research has documented Chinook salmon from Chile migrating into rivers on the Atlantic (Argentinian) side of Patagonia, prompting concerns that they will compete with Magellanic penguins for food resource. But clearly, not everyone is upset that salmon and trout from Europe and North America have expanded their range. As evidence of the popularity of fly-fishing, The Trout Bum Diaries 1: Patagonia was showing in our hotel lobby in Patagonia.

Endangered salmon, trout now protected in California river

November 27, 2012

The newly protected 520 ac completing the South Fork Eel River Wilderness are perched near the summit of Red Mountain. The Red Mountain and Cedar Creek drainages dominate the South Fork Eel Wilderness and are tributaries to the South Fork Eel Wild and Scenic River. The South Fork forms the main tributary to the Eel River, which supports spawning grounds for threatened and endangered salmon and steelhead trout.

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