Tag

SFEWS
31
Aug

Climate change is heating, salinizing, and expanding the San Francisco Estuary, a review of nearly 200 scientific studies concludes.

Sea level rise, changing snow and rainfall patterns, and warmer waters are some of the changes already observed in the Estuary and expected to continue through the rest of the century as greenhouse gas concentrations rise. Changes to water are at the heart of the documented and further expected impacts; there’s less of it entering the system overall, but more arriving in torrential bursts, and more saltwater creeping inland from the Bay. The scope of the research is expansive even for a review article, in part because climate changes aren’t happening in isolation from other threats and habitat impacts. Writing in San Francisco Estuary and Watershed Science, the authors attempt to summarize not only all known research about climate change...
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31
Aug

Groundwater pumped from subsided islands back into Delta channels through 200 or more active outfalls can be laden with excess nitrogen transported from island soils, report the authors of a new study.

The Sacramento-San Joaquin Delta contains more than 50 peat islands. Most have subsided—some as much as three meters — as a result of drainage for farming, and must maintain artificial water tables below the land surface via managed pumping. According to researchers from the University of California at Santa Cruz and the US Geological Survey, these pump stations are an underappreciated source of nutrients in nearby waters, with potentially significant implications for habitat and water quality.   To get a sense of how much nitrogen is leaving the islands and when, the researchers measured monthly discharge along with nutrient and trace element concentrations in drainage from three Delta islands over the course of nearly a year and a half, then...
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15
Dec

A large pulse of water sent through the Yolo Bypass in summer 2016 boosted phytoplankton biomass and food web conditions in Cache Slough and the lower Sacramento River, a new report confirms.

 “Our goal was to improve estuarine habitat by increasing net flows through the Cache Slough Complex to enhance downstream transport of lower trophic-level resources, an important driver for fish such as the endangered Delta Smelt,” write the authors—including esteemed (and recently retired) California Department of Water Resources lead scientist Ted Sommer—in the latest issue of San Francisco Estuary and Watershed Science. The pulse occurred over three weeks in July, a time when flows in the region above Cache Slough are often negative (meaning they go “upstream”) due to agricultural diversions and low freshwater inflow. Producing the pulse, which increased downstream flows from about negative-two cubic meters per second to a peak of 15 cubic meters per second in the Toe Drain...
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07
Jun

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 resource managers the difficult task of designing flows intended to help salmon without clear guidance on flow targets,” write the authors, led by Cyril Michel of the Institute of Marine Sciences at UC Santa Cruz. Studying migrating Chinook salmon smolts under a...
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07
Jun

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 support long-term conservation planning. Electrofishing, or e-fishing as it’s sometimes known, uses a generator aboard a small boat to pass electricity through the water beneath and in front of the boat. “When the electricity moves through the water, it can...
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07
Jun

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 multi-million dollar Delta smelt survey] has not really been seen before in the Estuary,” says lead author Brian Mahardja, a biologist with the US Bureau of Reclamation, “that’s why there was a call to see what else we can gain...
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07
Jun

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. At the other end of the spectrum, the smelt respond to both turbidity and salinity cues. After assigning a behavior to simulated smelt distributed across the Delta, researchers ran a 133-day simulation of water year 2002, then compared the modeled...
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07
Jun

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 hydrodynamics, water clarity (turbidity), precipitation, and sub-adult abundance,” the authors write. Historically, when large numbers of smelt began to appear in the salvage screens of the Delta pumps, pumping would be curtailed. Today, Grimaldo says, the fish are so rare...
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01
Mar

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 population use coastal habitats to some degree, but typically remain in the Estuary and lower Sacramento and San Joaquin rivers. There they congregate in deep areas with fine-sediment substrate, and are thought to move into shallow subtidal habitats to feed...
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01
Mar

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 fishes as Chinook salmon and Delta smelt, other bird species rely on habitat types that fringe the Delta’s waterways. Indeed, while general habitat restoration in the Delta can provide multiple benefits for humans, fish and many birds, the authors observe...
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01
Mar

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 of key life stages (eggs, fry, smolts and adults) as well as in key habitats (natal creeks, the Sacramento River, floodplains in the Sutter and Yolo bypasses, the Sacramento-San Joaquin Delta, and San Francisco Bay). “It’s a complex model, and...
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01
Mar

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 present and ranked them according to factors like temporal overlap (frequency of its interaction with otters), intensity (consequence of that interaction), and management effectiveness (how well the stressor is mitigated by human regulation). The study concluded that high-speed vessel traffic,...
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01
Mar

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 areas of sandy sediments. Sediments within the meadows contained 40% more microplastics than in the sandy areas. The scientists also found plastics attached to every one of the 60 blades of eelgrass they examined; in fact, microplastics were 20% more...
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18
Nov

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 have indicated high rates of infectious diseases, which lead author Brendan Lehman of UC Santa Cruz says demonstrates the need for ongoing systemwide monitoring. This could involve sampling fish directly for infections or conducting DNA testing of water samples. A...
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18
Nov

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 influx of salmon and other fish near the two water projects. Evidence of this hotspot lies in the numerous acoustic tags from young salmon to be found in the sediment, which were presumably defecated by striped bass, as well as...
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18
Nov

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 barrier, it can be also a mental barrier.” For example, some species that engage in schooling behavior, such as shad, may refuse to even enter a structure if it limits them to passing one at a time. According to the...
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18
Nov

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 upper reaches of the Estuary. But by towing a weighted hoop net behind a research vessel during the dry year of 2016 and again in the following year of heavy rainfall, the authors of the new study, published in October’s...
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13
Sep

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 pandemic, current data is sparse, although 13 were caught before March and one was caught in June. Bluefin killifish are popular in the freshwater aquarium trade, and the authors suspect the founders of the Delta population were released by a...
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13
Sep

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 too many people – reporters included – have relied on the results of one annual survey, the California Department of Fish and Wildlife’s Fall Midwater Trawl, to make sweeping conclusions about the health and abundance of several fish species. The...
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13
Sep

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 the fish, their behavioral adaptability would have helped the temperature-sensitive eggs and offspring in two ways—by ensuring “sufficient time for egg maturation in cool years, while secondarily preventing egg and alevin mortality in warm years,” write authors Eva Dusek Jennings,...
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