Science in Short: Daylighting Delta Data

Delta Landscapes & Waterways



13
Apr

Science in Short: Daylighting Delta Data

Once you know how many fish are present in a particular part of a river, including additional details like the time of day and water temperature, what do you do with this information? For decades, Delta researchers have collected millions of similar data points from daily visits to the San Francisco Estuary, not all of which are available or immediately useful. How that information is then translated into a language relevant to water and conservation managers requires serious number, or data, crunching. Sam Bashevkin, senior environmental scientist at the Delta Science Program in the Delta Stewardship Council, is working to bring data science to the San Francisco Estuary and help to make sense of the overwhelming data troves generated by...
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15
Feb

Will Salmon Simmer Again?

After two critically dry years that coincided with Trump-era rollbacks to environmental protections, some iconic Delta fish are closer than ever to the point of no return. Last fall, the fall midwater trawl found zero wild Delta smelt, while a coalition of environmentalists and fishermen is asking a federal court to help prevent a repeat of 2021’s near-obliteration of endangered winter-run Chinook salmon. Their lawsuit is just one of several projects....
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15
Feb

Let’s Not Forget Suisun Marsh

I started sampling the fishes of Suisun Marsh in 1979 because one of my UC Davis graduate students was looking for a place to study tule perch, a live-bearing native fish. We found not only a lot of tule perch in the marsh, but also an abundance of other native fishes. Clearly, this was a good place to study species for which we had little information at that time. Two things helped with our new project. First, sampling boats could be launched less than an hour’s drive from campus. Second, the California Department of Water Resources needed a study to examine effects of new tidal gates on fish. The gates are designed to retain fresher water in the marsh to...
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15
Dec

Scientists in the Central Valley are honing a novel way of giving young salmon the nourishing benefits of wintertime floodwaters without undertaking costly floodplain restoration work.

The method, being practiced along the Sacramento River, mimics the flood patterns of natural Sacramento Valley wetlands by diverting water onto floodplain farm fields, retaining it there for three weeks, and finally flushing the water—now rich with zooplankton and invertebrate protein—back into the river. Onsite studies have shown that salmon smolts grow faster when provided with this supplemental nutrition source, giving the method promise as a tool for boosting survival rates of outmigrating juveniles and, ultimately, helping sustain imperiled Chinook runs.     Jacob Katz, a California Trout biologist helping lead the project, explains that flushing river water over dry land and then back into the river effectively “reenergizes the food web,” allowing terrestrial carbon to flow into the water where...
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15
Dec

Hot off the press, Sacramento County Breeding Birds: A Tale of Two Atlases and Three Decades of Change raises red flags for some of the county’s wetland species.

Breeding bird atlases use field observations to record possible, probable, or confirmed nesting in uniform-sized blocks within a county or state. Biologist/artist Tim Manolis led a Sacramento County atlas project in 1988-93, but the results were never published. When Edward Pandolfino of Western Field Ornithologists heard about it he suggested repeating the effort and packaging the two data sets together. The second Sacramento atlas, covering 2016-20, followed the lead of recent state atlases in the eastern US in using data uploaded to the birding app eBird to supplement targeted observations. “It’s a lot more efficient, and lets everybody get involved,” says Pandolfino, lead author of the publication.   Overall avian species richness didn’t change significantly, but distributions did for many...
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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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25
Oct

Breaching Season for Hill & Dutch Sloughs, Pacheco Marsh

In the life of a tidal wetland restoration project, the first levee breach is a major milestone, a kind of graduation. After years of securing funding, navigating the permit process, completing baseline biological surveys, filing endless reports, grading and sculpting the marsh plain, setting out plants—after all that comes the day when the earthen barrier crumbles, the water makes its move, and another marsh can start to regenerate. This fall, that’s happening around the Bay Area as three significant projects—Dutch Slough and Lower Walnut Creek in Contra Costa County and Hill Slough in Solano County—renew long-severed connections between water and land. The three projects involve two state agencies, a county district, and a nonprofit. Dutch Slough is a California Department...
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20
Aug

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 Ecology Project, which modeled the early Delta based on archival photos, maps, and texts from the early 1800s, researchers estimated the total area for five specific habitat types: open water, tidal marsh, non-tidal marsh, riparian forest/scrub, and seasonal floodplains. The...
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23
Mar

Dutch Slough Laboratory

For a hawk’s-eye view of one of the Estuary’s most ambitious restoration efforts, visit the Dutch Slough Tidal Marsh Habitat Restoration Project’s YouTube channel. Drone-shot footage shows what the Department of Water Resources has been doing on 1,200 acres of former wetland, converted to pasture and subsided up to 15 feet, in the West Delta between Big Break and Jersey Island. After moving millions of cubic yards of soil to elevate the marsh plain, a team of engineers, scientists, and contractors led by project managers Katherine Bandy of DWR and Mark Lindley of Environmental Science Associates has carved channels and created a basin-and-range landscape on the Emerson and Gilbert parcels, the western two-thirds of the project site. “We spent a...
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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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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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12
Nov

Science-in-Short ~ Aquatic Weeds Podcast

Wall-to-Wall Sampling of the Delta’s Aquatic Weeds Via Remote Sensing, an interview with Shruti Khanna.  In this episode of the podcast, Estuary News reporter Daniel McGlynn talks to Dr. Shruti Khanna, a senior environmental scientist at the California Department of Fish and Wildlife. Their conversation focuses on Khanna’s use of remote sensing technology to study the Sacramento-San Joaquin Delta. Specifically, Khanna analyzes and processes remote sensing data, or high- resolution images collected by sensors mounted on aircraft, to study invasive plant species growing in Delta waterways. Researchers also use remote sensing to study the Delta’s water quality, fish populations, and overall change. While remote sensing will never replace on-the-ground research, the massive data set produced by collecting large-scale images over...
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28
Sep

Science in Short ~ Fish Podcast

David Ayers: How Fish Interact with Wetlands Topography  In this podcast, Estuary News reporter Alastair Bland and UC Davis PhD student and fish researcher David Ayers discuss the Sacramento-San Joaquin Delta, its fish, its marshlands, its flows, and its future. Ayers explains the focus of his research, which seeks to reveal how underwater topography in the wetlands fringing the estuary affects interactions between predators and small fish. While restoration projects often focus on adding more water to this ecosystem and encouraging that water to overflow the river’s banks, Ayers says small fish need more than just water and wetlands to survive. Variation in habitat features, such as the width and depth of wetland channels that wind through these ecosystems, create a...
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22
Sep

Makeover for Delta Weed Patch & Salt Trap?

What began as a project to convert a submerged Delta island into habitat for endangered native fish has morphed into a multi-benefit package with additional payoffs for water quality and recreation. The collaborative design process for the Franks Tract Futures project brought initially skeptical local stakeholders on board and is being hailed as a model for future initiatives. Yet major uncertainties remain as interested parties explore the challenges of implementing a complex redesign of a big chunk of the Delta. The proposed project would take a big shallow lake full of weeds, deepen some parts, fill in others with new lands and fish habitats, add beaches and recreational amenities, and stanch the spread of salt water from the ocean toward...
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18
Jun

Sinking Islands Capture Carbon Credits

As sea levels rise and land in the Delta sinks, agencies and landowners are recognizing that levees alone will not protect critical fresh water supplies and infrastructure. Encouraged by a recently vetted new method for calculating carbon offsets from wetlands, a flurry of new climate adaptation projects on publicly owned islands strewn along the central Delta corridor aim to defend against sea-level rise, restore habitat, and reduce greenhouse gas emissions. Until recently, the prospect of selling carbon credits in the Delta remained fairly abstract.
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22
Jan

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 Francisco Estuary and Watershed Science, found that the combined system removed drinking water contaminants including dissolved organic carbon, disinfection byproduct precursors, and methylmercury. Another possible benefit is subsidence reversal: the researchers found that sediment and carbon accreted about four times...
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22
Jan

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. Plants like Brazilian waterweed form dense underwater mats across vast reaches of the Delta. These mats have nurtured a rise in predatory bass populations and force prey fish into exposed channel centers. The artificial lighting pervasive along docks and buildings...
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22
Jan

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 and flood affects their germination. The study was based on seed bank samples taken from wetlands on the Delta’s Liberty Island. Though the island was drained and farmed throughout most of the 20th century, it has been naturally recolonized by...
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22
Jan

An emergency barrier installed to protect the state’s water supply from saltwater intrusion during the recent record-setting drought had little effect on the ecosystem.

In spring 2015 the California Department of Water Resources dropped 150,000 tons of rock into False River in the Central Delta to halt encroaching tides that had little freshwater to hold them back. A few months later, it was clear the barrier worked, as salinity rose on one side and fell on the other. But what were the effects on local plants and animals? Through six overlapping yet distinct projects funded by the state Delta Science Program and NASA, and described in the September 2019 issue of San Francisco Estuary and Watershed Science, researchers studied impacts on water quality and movement, zooplankton and phytoplankton, submerged aquatic vegetation, nutrients, and two species of clam. What they found, says Wim Kimmerer of...
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