Archive for salmon

Salmon release

Salmon release

As April comes to an end, the fall-run Chinook salmon outmigration period will soon be winding down, as juvenile salmon make their way throughout the watersheds of California’s Central Valley towards the ocean. This also signifies the conclusion of another successful year of the Salmon in the Classroom program, which helps K-12 grade students throughout the state learn about the salmon lifecycle, and the difficult journey these fish undertake in order to survive to adulthood and return to spawn. Many classrooms also raised salmon eggs in their classrooms. FISHBIO visited a few local classrooms to walk students through the Salmon Survival Pyramid, or the number of fish that survive to each stage of their lifecycle.

Recently, we accompanied 4th grade students on an afternoon field trip to Knights Ferry. These students had received 60 salmon eggs from the local hatchery in early January, and watched the fish hatch and grow from eggs into alevin in a tank at their school. Now that the fish had developed into fry, students released them into the Stanislaus River to begin their long journey downstream to the ocean. We hope they’ll be the lucky ones that make it!

This photo recently won our “Best of the Month” photo contest. Check out past winners on our Flickr site!

Marijuana farming a buzz kill for California’s salmon

Marijuana plant

In a year of extreme drought, one of the drains on California’s water supply has been generating a particular buzz: illegal marijuana farming. A number of news outlets have highlighted the unchecked degradation and consumption of natural resources – most notably, water – resulting from these shadowy grow operations, and the consequent impact on salmon and steelhead in nearby watersheds. With the legalization of marijuana in Washington and Colorado, pot farms are booming, particularly in northern California’s “Emerald Triangle” region of Mendocino, Humboldt, and Trinity counties, which produces more cannabis than anywhere else in the nation. This region also includes the Eel and Klamath rivers, which have historically supported bountiful salmon populations. In a dry year where every water drop counts, more than a few drops are going unaccounted for in an area where an unregulated industry overlaps important fish habitat.

A pot plant’s demand for water is nothing short of staggering. A single marijuana plant can suck up six gallons of water a day at the peak of the growing season, according to California state officials. A study by the California Department of Fish and Wildlife uncovered an estimated 30,000 plants growing in each of four watersheds in Humboldt and Mendocino counties, representing the use of 180,000 gallons of water per day in these few waterways. In 2012, 838,358 plants were found growing illegally in California’s national forests alone, reflecting millions of gallons of water siphoned from the state’s water resources. Last summer, 24 tributaries of the Eel River (which were all being used to water cannabis farms) ran completely dry, according to state biologists. Unchecked illegal water diversions could bring about similar disastrous conditions for fish this year, exacerbated by continued drought. Of course, pot farms are just one player in the struggle over water use, as growers are quick to point out – but they are also an unregulated player. Growers often divert water directly from streams without applying for the required permits, and therefore are not held accountable for taking more than their share.

The “guerrilla growers” in question oversee industrial-scale operations, often on public land such as national forests, and degrade the environment in a variety of ways. They clear large swaths of trees, as shown in this Google Earth video, and leave heaps of trash behind when they disband the plots. In addition to guzzling water, their activities pollute waterways with sediments, fertilizers, and pesticides. Nutrients in fertilizer can stimulate blooms of green algae, which fuel the growth of bacteria as they break down, ultimately stealing oxygen from fish and their developing eggs. Pot farming spells trouble not just for fish, but for other wildlife such as the fisher (Martes pennant), a member of the weasel family. A study by UC Davis researchers found that this small mammal, which is a candidate for listing under the Endangered Species Act in the western United States, is threatened by exposure to rat poisons used in illegal cannabis growing (Gabriel et al. 2012). California has now banned the sale of such poisons. Similar to the free-for-all frenzy of the California Gold Rush, the current pot boom that some are calling the “Green Rush” could also leave a legacy of environmental degradation in its wake.

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


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.