Scientists are finding it increasingly difficult to predict how ecosystems will respond to sudden and rapid changes such as extreme droughts, wildfires, and flooding.

Scientists are finding it increasingly difficult to predict how ecosystems will respond to sudden and rapid changes such as extreme droughts, wildfires, and flooding.

Writing in the June 2021 issue of San Francisco Estuary & Watershed Science, a group led by environmental economist Richard Norgaard note that due to the increasing pace of ecological change associated with a warming world, models derived using past data are less able to provide reliable predictions, particularly as extreme events create conditions outside historic reference points. This has global implications for environmental management, but the authors—many of whom have served on the Delta Independent Science Board—center their focus on...
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Loss of wetland habitat in the Delta has reduced net primary productivity by 94%, but achieving current restoration goals could restore 12% of this loss.

In a new study published in the September 2021 issue of Science of The Total Environment, researchers modeled net primary production of the Delta under historical and contemporary conditions in order to project the potential benefits of restoration. The loss of net primary productivity—the amount of energy available to pass up the food chain—associated with human modification of the Delta since the early 19th century has reduced the energy available to support biodiversity and ecosystem services. Using the San Francisco Estuary Institute’s Historical...
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When it comes to managing Delta salinity, a new research paper suggests we treat public policy like a science experiment.

As anthropogenic factors like salt accumulation through irrigation and freshwater storage combine with drought and sea-level rise, the Delta is headed for a saltier future. The June 2021 paper, published in San Francisco Estuary and Watershed Science, integrates biological and physical sciences to draw a comprehensive picture of Delta salinity and changing freshwater inflow. Changing salinity patterns could have a profound impact on the region’s ecology, affecting how and when fish like the Delta smelt or Coho salmon spawn, and which aquatic plants...
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Smelt cam photo

Monitoring Delta smelt with an underwater camera could be safer and more effective than with a traditional trawl.

Standard smelt surveys rely on the use of boat-driven nets, which trap fish by funneling them from the wide mouth of the net to the closed end (known as the cod end). To check their catch, researchers must pull the net and its contents from the water. But this additional handling can harm and even kill the same fish that wildlife agencies are trying to save with the support of robust, long-running monitoring efforts. There may be a better way:...
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photograph of beautiful tree overhangin a river

Modern water management practices damp down natural river patterns and produce streamside forests that “live fast and die young.”

Such practices also hasten the destruction of an important and dwindling habitat. Melissa Rohde of the State University of New York College of Environmental Science and Forestry (SUNY-ESF) and colleagues analyzed five years of high-resolution satellite and water resource data showing vegetation greenness along California rivers. Trees growing alongside the 30 percent of state rivers with natural flows decreased in greenness from the wet spring through the dry summer months, the scientists report in the Proceedings of the National Academy...
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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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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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