Bay Fish Still Not Good Eating

Bay Fish Still Not Good Eating

After decades of efforts to clean up San Francisco Bay, its fish still carry a toxic load that makes them unfit for human consumption. A new Regional Monitoring Program (RMP) report on its 2019 sport fish survey contains some positive news: an overall decline in polybrominated diphenyl ethers (PBDE), hopeful trends in polychlorinated biphenyls (PCBs) and dioxin, and continued low selenium levels. But no downward trend was found for mercury. Then there are per- and polyfluoroalkyl substances (PFAS), which the...
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New research indicates that survival of juvenile Chinook salmon in the Sacramento River system can be significantly boosted by achieving key thresholds for river flow.

The findings, published in the journal Ecosphere, add important context to the general scientific understanding that more water in the river improves fish survival. Previous studies, the authors explain in their paper, have demonstrated that more juvenile salmon migrating toward the sea complete their journey when the Sacramento River system contains more water. Just how much water has been the source of much controversy among user groups. “These studies have not explored the potential nonlinearities between flow and survival, giving...
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Electrofishing is a powerful but underutilized tool for monitoring Delta fish, particularly species favoring “structured” habitats that are difficult to sample using more common methods like trawls and seines.

By analyzing fish catch data from past surveys, researchers Ryan McKenzie, of the US Fish and Wildlife Service, and Brian Mahardja, of the US Bureau of Reclamation, determined that electrofishing resulted in better detection rates for many native and non-native species than net-based surveys. Although electrofishing is currently restricted to freshwater areas of the Estuary and is more selective of larger fish and those with swim bladders, McKenzie and Mahardja recommend that resource managers employ the technique more widely to...
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The robust monitoring programs established to track now-rare Delta smelt could benefit other native fishes, too.

Decades ago, resource managers first learned of declining Delta smelt numbers not through surveys targeting the once-abundant native fish, but rather as a byproduct of long-term monitoring programs for non-native striped bass. Now, the authors of a new study published in the March 2021 issue of San Francisco Estuary and Watershed Science advocate for the use of bycatch data from the recently established Enhanced Delta Smelt Monitoring (EDSM) program to better understand juvenile Chinook salmon distribution. “The scope of [this...
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New insights into Delta smelt swimming behavior could help locate the increasingly elusive fish and prevent losses at the pumps.

Scientists know that smelt use tidal ebbs and flows to migrate landward to spawn, but the degree to which external cues influence behavior remains unclear. In a new study published in the March 2021 issue of San Francisco Estuary and Watershed Science, researchers used computer modeling to predict smelt distribution based on hypothesized swimming behaviors. Six increasingly complex behaviors were tested. For example, the “passive” category assumes that smelt do not swim at all, simply drifting with currents and tides....
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Water turbidity in the Sacramento-San Joaquin Delta can be used as a reliable indicator of smelt entrainment rates in the fish screens of the export pumps at the southern edge of the Estuary.

In a new study published in the March 2021 issue of San Francisco Estuary and Watershed Science, researchers Lenny Grimaldo, William Smith, and Matthew Nobriga used advanced statistical approaches to understand what factors best predict Delta smelt entrainment at the pumps. The paper builds upon research that Grimaldo conducted in the 2000s, which provided the basis for regulations established in the 2008 Delta smelt Biological Opinion. “This study reinforces previous work that adult Delta smelt salvage is largely explained by...
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moss ball oregon USFWS

Invasions

Almost two months after invasive zebra mussels were discovered in imported “moss balls” (actually algae) in a Seattle PetCo store, federal and state agencies are still trying to track the Trojan moss balls and keep the mussels out of vulnerable water bodies, including California’s. So far, contaminated moss balls have been found in 46 states (Virginia, Delaware, Rhode Island, and Hawaii are the exceptions) and most of Canada’s provinces. The US Fish & Wildlife Service has issued detailed guidance for...
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northern harrier-hull lab-UC Davis

Migrations

Northern harriers, long-winged rodent-hunting hawks, make impressive migrant journeys. Research by UC Davis’ Hull Lab sheds new light on these journeys. Harriers are a familiar sight in California’s wetlands, especially in winter. Researchers captured fifteen female harriers–ten in winter, five in spring–in Suisun Marsh and equipped with 14-gram GPS backpack transmitters, too heavy for use with the smaller males. Telemetry data from seven of the ten winter females revealed migrations of up to 600 miles, to nesting sites from the...
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Photo of bird watchers by Rick Lewis

Three Great Migration Stories -Tracking the Birds

Like water rains down and flows, spreads and seeps through an Estuary, touching the land along its path, so too do birds migrate across our planet.  ESTUARY loves a good bird story, and our reporter Joe Eaton writes most of them with great care for both birds and words, while photographer Rick Lewis always has his lens aimed at the feathers flying overhead or dipping in the water (see above). Read three great migration stories ….
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sunset delta climate map

MEGA-PEARLS Part 4-Climate, Bay-Delta Science Conference, April 2021

A Stream of Science Takeaways. ESTUARY News sent reporters to the biennial Bay-Delta Science Conference in September. This special edition of Pearls shares more than 20 takeaways.
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pesticide resistance delta map

MEGA-PEARLS Part 3-HABs & More, Bay-Delta Science Conference, April 2021

A Stream of Science Takeaways. ESTUARY News sent reporters to the biennial Bay-Delta Science Conference in September. This special edition of Pearls shares more than 20 takeaways.
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photo of salmon injection USFWS

MEGA-PEARLS Part 2-Fish-Birds, Bay-Delta Science Conference, April 2021

A Stream of Science Takeaways. ESTUARY News sent reporters to the biennial Bay-Delta Science Conference in September. This special edition of Pearls shares more than 20 takeaways.
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Above: Lewis holding white sturgeon in Delta. Photo: Jim Ervin

MEGA-PEARLS-Part 1-Diversity, April 2021

A Stream of Science Takeaways. ESTUARY News sent reporters to the biennial Bay-Delta Science Conference in September. This special edition of Pearls shares more than 20 takeaways.
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Invasive Mussels Hide in Aquarium Moss Balls

A few weeks ago, someone working in a big-box pet store in the Seattle area informed the U.S. Geological Survey that they had seen suspicious mollusks in ornamental aquarium plants that were being offered for sale. Federal scientists confirmed the presence of zebra mussels tucked away in a clump of Aegagropila linnaei, a green alga marketed as moss balls or marimo balls, and issued a warning through the Nonindigenous Aquatic Species Alert System on March 2. The national Aquatic Nuisance...
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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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