North America’s largest and most ancient freshwater fish species, white sturgeon, hang out in some kinds of Estuary waterways more than others, scientists find.

North America’s largest and most ancient freshwater fish species, white sturgeon, hang out in some kinds of Estuary waterways more than others, scientists find.

 Researchers with the U.S. Geological Survey found that adult and sub-adult white sturgeon occupy deep open-water channels and shallow open-water shoals in equal measure, but don’t use shallow wetland channels. As a group, white sturgeon are characterized as amphidromous, meaning they regularly migrate between freshwater and the sea, in both directions, but not for the purpose of breeding. According to the study, which appears in the December 2020 issue of San Francisco Estuary and Watershed Science, adults in the local...
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As agencies wrangle over how best to protect the Delta’s dwindling native fish species, researchers want to see more consideration to the needs of the estuary’s birds.

 “If we want to restore the ecology of the Delta, we can’t just be looking in the water,” says Kristen E. Dybala of Point Blue Conservation Science. In a paper published in San Francisco Estuary and Watershed Science, Dybala and two co-authors make the case that “birds and their habitat needs are often not addressed in science syntheses, conservation planning, and large-scale restoration initiatives in the Delta.” While some birds use the same sloughs and channels that support such high-profile...
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Filling significant recently identified gaps in monitoring spring-run Chinook is critical to protecting these threatened Central Valley salmon.

“There’s no way we can manage them for recovery if we don’t understand the biological processes that govern their dynamics through time and space,” says UC Santa Cruz/NOAA salmon expert Flora Cordoleani, lead author of a study reported in the December 2020 issue of San Francisco Estuary and Watershed Science. Cordoleani and colleagues identified the monitoring gaps while building a model of the spring-run Chinook life cycle. The model accounts for three self-sustaining populations of these at-risk fish, assessing survival...
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Human activity could undermine the success of efforts to reintroduce sea otters to San Francisco Bay.

 Although past studies have found that the Bay could support 1.5 times the entire current southern sea otter population, a new study from the Estuary & Ocean Science Center at San Francisco State University and published by PeerJ last November indicates that anthropogenic risks like contaminants, vessel traffic, and oil spills may constrain the otter’s ability to gain a foothold. The study, led by Jane Rudebusch, at the time graduate student at SFSU, looked at the types of human stressors...
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The increasing flow of microplastics entering San Francisco Bay from trash, fleece clothing, car tires, and myriad other sources is likely being trapped by a surprising filter: native eelgrass (Zostera marina).

Miniscule polymer pieces the size of a sesame seed or tinier, microplastics pose a growing pollution threat to marine environments worldwide. To understand how microplastics accumulate in nearshore, urbanized environments, researchers quantified the prevalence of microplastics in and around the Zostera marina meadows of Deerness Sound, in the Orkney Islands of Scotland. Mark Hartl and colleagues at Heriot-Watt University found that microplastic flakes, fibers, and fragments were twice as concentrated in the water above eelgrass meadows as in adjacent control...
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As organizations and agencies scramble to preserve the Central Valley’s dwindling Chinook salmon runs, a group of scientists believes they may be overlooking a key factor in the decades-long decline of the fish: disease.

In a paper published in September’s issue of San Francisco Estuary and Watershed Science, a research team proposes that diseases—caused by viruses, bacteria and other microbes—could be suppressing juvenile salmon survival in a river system that once hosted millions of adult spawners each year. According to tracking studies, nearly all juvenile Chinook born from natural spawning die before they reach the Golden Gate Bridge; habitat enhancement efforts have failed to mitigate this mortality rate. Short-term studies of Central Valley salmon...
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Current estimates of young salmon lost to the south Delta pumps are based on a smattering of studies from the 1970s and should be updated, according to a new analysis.

“They don’t represent current operations,” says Ukiah-based consultant Andrew Jahn, lead author of the analysis reported in the September 2020 issue of San Francisco Estuary and Watershed Science. Current operations at the State Water Project (SWP) and the Central Valley Project (CVP) can reverse flows in the Old and Middle rivers, diverting salmon on their way to the ocean towards the projects. Existing salmon loss estimates also fail to account for a likely Old River hotspot for predators, drawn to the...
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Fish passage structures can be improved for the benefit of multiple species, if they are designed to account for differences in behavior, physical ability and size, according to a new literature review.

Historically, most fish passages have been designed to help native salmon return to their upstream habitat and spawning grounds, with little consideration for other migrating species such as sturgeon and lampreys. “There is an assumption that if you just build a fish passage structure, fish will go thorough it, but that is not always the case,” says Department of Water Resources fisheries biologist Zoltan Matica, who conducted the review. “The challenge is to understand that this isn’t only a physical...
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Spawning and rearing habitat for important forage-fish species in San Francisco Bay apparently shifts geographically by many miles depending on how much freshwater is flowing into the Estuary.

In a recent study, a team of scientists found that in a dry year, Pacific herring and longfin smelt larvae occurred farther up the Estuary than in a wet year, when spawning and recruitment was pushed seaward. The results suggest that the fish have broader geographic ranges than previously believed, a finding that could inform efforts to manage and protect their habitat. Biologists have long assumed that longfin smelt, a protected species in steep decline for decades, spawn strictly in...
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Yet another non-native aquatic species may have made itself at home in the Delta.

As described by US Fish and Wildlife Service fish biologist Brian Mahardja and his co-authors in San Francisco Estuary & Watershed Science, the newcomer is an inch-long, minnow-like fish called the bluefin killifish (Lucania goodei), indigenous to Florida and adjacent southeastern states. It was first detected in the Delta Cross Channel during a beach seine survey in October 2017, and subsequently found in Beaver and Hog sloughs and at Decker, Sherman, and Brannan islands. With surveys curtailed by the coronavirus...
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By looking solely at the results of a single annual fish-counting survey, Californians may be seeing an incomplete reflection of Bay-Delta fish population trends.

A team of scientists analyzed 14 survey programs carried out by state and federal agencies, as well as UC Davis, and concluded that employing such a diverse variety of long-term surveys is essential for accurately tracking and assessing the overall health of San Francisco Estuary’s ecosystem and its resident fishes. The research is described in the June issue of San Francisco Estuary and Watershed Science. Lead author Dylan Stompe, of UC Davis, explains that the research arose from concerns that...
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A unique adaptive behavioral trait that may once have helped winter-run Chinook salmon thrive in the Sacramento River system could now be working against the fish as they face extinction.

The trait – which cues fish when to spawn based on water temperature – isn’t syncing up with current conditions in the Sacramento River below Shasta Dam. A paper published in the June issue of San Francisco Estuary and Watershed Science, reports that cooler springtime river temperatures seem to prompt earlier winter-run spawning while warmer temperatures push back the peak spawning period by a week or two. Under historic conditions, when winter-run Chinook spawned in high-elevation streams now inaccessible to...
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wetland landscape photo

Better scientific preparation could help Delta water and environmental managers respond to droughts more effectively.

That’s one key takeaway from a review of environmental management and the use of science during the 2012-2016 drought commissioned by the Delta Science Program and published in the June 2020 issue of San Francisco Estuary and Watershed Science. “There are lots of mysteries about how to manage water to benefit species, agriculture, upstream and downstream users. I think science is going to be the best solution,” says lead author John Durand of UC Davis’ Center for Watershed Science. Durand...
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Sacramento pikeminnow and introduced striped bass in the middle Sacramento River eat a surprisingly similar diet, says a new study in San Francisco Estuary and Watershed Science.

Both species have been implicated in the decline of vulnerable native species in the river, particularly juvenile Chinook salmon, says lead author Dylan Stompe, a PhD student and researcher at the University of California at Davis. For eight months in 2017, Stompe and fellow researchers with the California State University at Chico and the California Department of Fish and Wildlife surveyed a 35 kilometer reach of the river outside Chico for the two predatory fish. They baited hooks with with...
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Surface water diversions in California’s Central Valley can be estimated based on readily available climate data, say researchers—a boon to efforts to track groundwater use.

Valley groundwater pumping is calculated as the total water demand minus surface water deliveries. However, today’s water model relies on individually reported diversions across the entire valley, and compiling all these data is a slow process; by the time the numbers are crunched, assessments of groundwater use are already outdated. “It can take years,” says Jordan Goodrich of University of Waikato in New Zealand. “It’s one of the biggest problems we face in tracking the Central Valley water budget.” Overdrafting...
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A new system for treating agricultural drainage water in the Delta could also help rebuild subsided islands.

The approach—known as a Chemically Enhanced Treatment Wetland—combines chemical treatment with natural wetland processes; researchers tested it on Twitchell Island, which features corn and rice crops, as well as wetlands. They dosed agricultural ditch water with dissolved organic material (DOM), then treated it with a coagulant to precipitate the DOM, forming flocculant. The resulting water then passed though treatment wetlands, where the flocculant settled and blended with plant detritus in the sediment. The study, reported in the September 2019 San...
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Manmade features in the Delta, including riprap-armored banks, water diversion pipes, pilings, and woody debris, may be sending juvenile native fishes into the jaws of finned invaders.

“We know from a decade of doing survival studies that migrating juvenile salmon are dropping out of the system pretty much everywhere in the Delta,” says UC Santa Cruz fisheries biologist Brendan Lehman. “Physical habitat features are potentially aggregating predators and prey in ways detrimental to salmon smolts and steelhead.” The scientists report in the December 2019 San Francisco Estuary and Watershed Science that artificial light and submerged aquatic vegetation pose the most severe and widespread risks to native fishes....
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Levels of pyrethroid insecticides spike sharply in the North Delta’s Cache Slough during winter rainstorms, rendering the water so toxic that it decimates laboratory populations of a half-inch crustacean called Hyalella azteca.

However, according to a study reported in the September 2019 San Francisco Estuary and Watershed Science, Hyalella collected in the wild from Cache Slough are resistant to pyrethroids. Genetic analysis revealed that, collectively, Hyalella in the slough have four mutations for pyrethroid resistance. They also have a fifth mutation for resistance to organophosphates and likely carbamates, two additional major classes of pesticides that are applied extensively on agricultural and urban lands. “Hyalella are special,” explains co-author Helen Poynton, a molecular...
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Researchers hope new computer models will help clarify the effects of entrainment on the population of endangered Delta smelt.

Entrainment at the South Delta pumps of the State Water Project and the Central Valley Project has been a concern for years, but disentangling its impact on the dwindling smelt population from those of other environmental and water management factors isn’t easy, and operational differences between the SWP and CVP facilities complicate analysis. Now, US Fish and Wildlife Service statistician Will Smith has developed computer models for entrainment effects on different smelt life stages, part of a larger Delta Smelt...
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While the acreage of wetland restoration projects is growing throughout the Delta, scientists are still working to understand how best to help these areas become fully functioning, complex habitat as quickly and successfully as possible.

A study published in September’s San Francisco Estuary and Watershed Science shed light on some essential questions about what triggers seed generation in wetland habitat. “Wetland restoration practices can be enhanced by a solid understanding of basic plant life history and species ecology,” says co-author Taylor Sloey of Yale-NUS College in Singapore. The researchers looked at three questions: what seeds are present in the seed bank (the viable seeds that accumulate naturally in the soil), and how exposure to cold...
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