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Salmon

A fish health checkup by the US Fish and Wildlife Service

Even fish need regular health checkups. Keeping track of the health and physiological condition of salmon smolts outmigrating from the Central Valley is an essential assignment for the biologists at the U.S. Fish and Wildlife Service California-Nevada Fish Health Center. Fortunately, FISHBIO’s rotary screw traps provide easy access to outmigrating salmon on all the San Joaquin Basin tributaries. Multiple times each spring, we help the USFWS obtain samples of wild smolts captured in our traps. The USFWS biologists carefully dissect the smolts, separate samples of tissue from organs, and preserve the tissues in vials which they then process at their laboratory based at the Coleman Hatchery.

The laboratory examines the specimens for a host of possible parasites and diseases. One of the more detrimental diseases afflicting salmonids is Proliferative Kidney Disease (PKD), caused by infection with the myxozoan parasite Tetracapsuloides bryosalmonae. The parasite species name comes from its ability to infect colonial animals called bryozoans, as well as salmonids. The parasite causes fish kidneys to become inflamed, and often leads to death in wild Chinook salmon, rainbow trout, and farmed salmon (Skovgaard and Buchmann 2012).

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Conferences and Events, Research, Salmon

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. 

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Marine, Salmon

Northern California

Spring has officially arrived, the periods between rains are getting longer, and sunny, clear days are becoming more numerous, enticing visitors and residents of the northern California coast to engage in outdoor activities. A frequent companion during such pursuits is the cold, strong, steady wind. Blowing from the north, this seasonal wind pattern pushes massive quantities of near-shore ocean water along the coast, deflecting it westward and away from the shoreline through a process referred to as Ekman transport.

As the surface water moves away from the shore, cold, nutrient-rich water from the deep ocean moves up to replace it. This process of upwelling supplies the nutrients that support the base of the highly diverse and productive food web of the California Current. The strength and duration of this spring upwelling varies from year to year, resulting in differences in food supply and transport to nearshore waters. Such variability can cause cascades throughout the food chain. For Chinook salmon, this means that when their outmigration to the ocean coincides with favorable upwelling conditions, the smolts’ novel hunting grounds can be a rich smorgasbord of crustaceans and forage fish, fostering good survival and growth (see Salmon hunger games). When ocean conditions are less favorable, salmon populations dwindle. 

The impact of poor ocean conditions on salmon populations was particularly pronounced in the Central Valley several years ago, where populations are already subjected to a host of additional stressors, and a population crash lead to fishing closures in 2008 and 2009.  As the stocks show signs of recovery and commercial and recreational pursuit of ocean Chinook salmon is permitted once again, the same wind that drives productivity of our coast will frequently keep salmon anglers confined to the docks during the eagerly awaited salmon fishing season. For the fish at least, the wind appears to have multiple benefits.Fishing boats

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Field Crew, Salmon

Preparing for a river run

Drifting down the river in an inflatable raft sounds like a fine way to spend a spring day, but it can also be part of a scientific survey. Our biologists use these rafts to map the locations of redds, or salmon spawning sites (see It’s a wrap, Hunt for redds in October). Before they begin, they use a GPS to mark the starting point of the survey, as shown in this photo. Rather than taking in the scenery while floating along, the scientists spend their trip with eyes pointed downward, peering intently for patches of cleared gravel that spawning females have shifted to lay their eggs. Wearing polarized glasses makes it easier to see the riverbed through the water. After locating a redd, they record its GPS coordinates, measure its width and length, and note the water depth and velocity. These data help us understand the habitat and conditions that salmon choose for reproducing.

 

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Field Crew, Salmon

Chinook fry in the spotlight

Our field work often finds us working late into night, which is sometimes when a creative impulse will strike. During a nightly check of a rotary screw trap on the Merced River, we decided to give some Chinook salmon fry their 15 minutes of fame before we released them. With the help of a flashlight, we turned this custom-built photo box into an illuminated stage. A photo box makes it easier to document some of the interesting fish and wildlife we encounter while letting them stay submerged in water (see Frogbio). It can also make for interesting viewing—maybe there’s a niche out there for the fish fry television channel.

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Fish Report, Research, Salmon

Salmon navigate by magnetic field

The epic migrations of salmon have long been a subject of mystery and amazement. What directs these animals’ journeys across great stretches of ocean, pulling them back to the very stream where they were born? Chemical cues help fish pinpoint their stream of origin (Johnsen and Hasler 2006), but what steers the salmon’s course when it is still thousands of kilometers away? A group of fisheries scientists recently offered the first empirical evidence that salmon navigate using the Earth’s magnetic field. The study’s findings, published in the journal Current Biologylast month, suggest that salmon form an imprint of the magnetic field in their natal streams, and find their way back as adults via a route that matches the magnetic memory of their birthplace.

Scientists have hypothesized that migrating animals travel by the magnetic field (Lohmann 2008), but this is difficult to test directly. The authors of the new study devised a natural experiment using 56 years of fisheries records of sockeye salmon (Oncorhynchus nerka) returning to British Columbia’s Fraser River. Fish from the Fraser River typically migrate to Alaska’s Aleutian Islands, spend two years foraging, then embark on the long trek back to the river to spawn. Along the way, they encounter a major roadblock: Vancouver Island obstructs direct entrance to the Fraser River, forcing salmon to detour to the north or south. The scientists predicted that natural shifts in the Earth’s magnetic field from year to year would lead salmon to adjust their route accordingly, choosing the passage with a magnetic field more closely aligned with the magnetic field of the Fraser River two years previously. The team modeled variations in the Earth’s magnetic field based on its intensity and inclination, or the angle of intersection with the Earth’s surface. They matched this up with a long history of fisheries records that documented how many salmon travelled via the northern route each year, which lies solely in Canadian waters, or via the southern route, which is shared by Canadian and U.S. fisheries.

The scientists found that whether the fish turn right or left is far from an arbitrary decision: their selection largely depends on how closely the magnetic field at the route’s entryway resembles the magnetic field they experienced at birth. Sea surface temperature also played a big role: in warmer years, more fish followed the northern, cooler route. Results indicated that 68% of the variation in the salmon’s choice of direction was explained by variation in the magnetic field, sea surface temperature, or some combination of the two. This study suggests that salmon may follow a magnetic “map” to direct their long-distance migrations, then switch to using chemical cues to home in on a specific stream–similar to the way we may use a GPS system to navigate on long road trips, then switch to following visual landmarks as we get closer to home. The authors say this study could explain why hatchery fish sometimes have trouble finding their way back to spawn: imprinting on a hatchery’s human-created magnetic field of electrical wires and iron-reinforced fish tanks could render the fish directionally challenged. 

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

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Rotary Screw Trap, Salmon, Unusual

(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

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Fish Report, Research, Salmon, Salmon Abundance

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.

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Ecology, Fish Report, Salmon

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.

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Salmon

Mapping salmon redd location

As the Chinook spawning season in our local rivers draws to a close, we’ve wrapped up our final redd surveys of the year. Every year, we conduct these spawning site surveys at regular intervals throughout the season to document salmon reproductive activity (or at least evidence thereof) in river reaches that offer suitable spawning habitat (see On point, Hunt for redds in October). While maneuvering these river sections in kayaks, rafts, or on foot, we keep a sharp lookout for the telltale signs of a redd: light-colored patches of riverbed where spawning females have dug up and removed fine sediment and algae-covered rocks.

After we spot a redd, we record its position with highly accurate GPS units, allowing us to later map redd locations, determine which stretches of river are most important to spawning, and note how redd distribution changes within the season and between years. In addition, it allows us to identify incidences of redd-scouring (where redds have been washed away by heavy flow), dewatering (redds left “high and dry” by receding water), or superimposition (redds built on top of an existing one, potentially disturbing or damaging the eggs laid previously).