Researchers are applying a novel genetic technique as part of the development of an annual estimate for the number of juvenile spring-run Chinook salmon entering the Delta.

Restoration



31
Aug

Researchers are applying a novel genetic technique as part of the development of an annual estimate for the number of juvenile spring-run Chinook salmon entering the Delta.

The technique, spearheaded by geneticist Melinda Baerwald from the California Department of Water Resources, allows researchers to accurately distinguish young spring-run salmon from other runs by targeting DNA sequences specific to these fish.   In a paper published in San Francisco Estuary and Watershed Science, lead authors Baerwald and Peter A. Nelson explain some of the challenges of developing this estimate, called the spring-run juvenile production estimate. A key hurdle is differentiating spring-run fish from salmon that migrate during other seasons. Unlike juvenile salmon from the winter run, spring-run juveniles are hard to identify using the conventional length-at-date approach, which determines age and spawning migration season based on size.   “There’s nothing visually about a spring-run salmon that distinguishes it...
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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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31
Aug

Light and nutrients are the staples of every phytoplankton production recipe, but wind and tides in the Delta affect phytoplankton production too, say researchers.

Several projects in the lower Sacramento River and Delta have been exploring strategies for increasing the quantity and quality of food for migratory and resident fish. As part of a broader whole-ecosystem experiment that added nitrogen into the Sacramento River Deep Water Ship Channel, Leah K. Lenoch and colleagues at USGS and UC Davis looked into the channel’s hydrodynamics to explore whether the environmental conditions there hold promise for increasing the quantity of phytoplankton (the microscopic algae at the base of the food web). They knew that turbid and well-mixed waterways, including parts of the San Francisco Estuary and Delta, are not very productive because phytoplankton don’t get enough light and are at the mercy of invasive clams. However, where...
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30
Aug

Drought Plan Means Full Lake, Empty River

In the mountains and foothills of California, an enduring drought has depleted the state’s major reserves of water. There is virtually no snowpack, and most of the state’s large reservoirs are less than 40 percent full. But in the central Sierra Nevada, a trio of artificial lakes remain flush with cold mountain water. The largest of them, Hetch Hetchy Reservoir, from which millions of Bay Area residents receive water, is more than 80 percent full. This remarkable plentitude is the outcome of careful planning by the agency that manages the Yosemite National Park reservoir plus conservation by Bay Area residents, who use less water per capita than most other people in the state—between 35 and 65 gallons per person per...
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16
Jun

Building Buy-in for Restoration

The success of a restoration project is in the eye of the beholder. Take the recently revitalized salt marsh edging Drift Creek in Alsea Bay, Oregon. To ecologists, the sight of new channels winding through bare, brown mud is a thing of beauty, heralding the abundance of life to come, from sedges and rushes to fish and shorebirds. But, as researchers learned while speaking with people living nearby, not everyone shares this view. Some locals favored the unrestored side for its lush green vegetation and vistas of grazing elk. Resolving such differences in perception is key to local support, which can be required for project funding and permitting.  “Restoration can look unsightly at first,” said UC Davis salt marsh ecologist...
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16
Jun

Listening to Vital Voices

Jessica Rudnick’s first love was earth science. But after discovering that people’s beliefs and behaviors were key to solving environmental problems, she fell for social science. Now, as the California Sea Grant extension specialist for the Delta, Rudnick is working to better integrate local people into plans for the region. Understanding the needs of people who live, work, and recreate in the Delta could make the difference between fixes that are rejected or embraced.  Delta planning has historically focused largely on ecological health. But, like many estuarine areas, the Delta is a lived-in landscape. “There are socially embedded challenges that play out in environmental issues,” she says. “You can’t just throw more data and research at a problem and think...
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16
Jun

Reorienting to Salmon Recovery

California’s disappointing history of salmonid recovery programs has motivated a group of scientists from public water agencies and environmental conservation groups to step back, dream big, and take a new path forward. This group wants to abandon familiar heated dialogues and litigious relationships and try a new approach toward fish recovery based on collaboration, common interests and science.
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Adrienne Ernst among the Phragmites. Photo: Michael Adamson
16
Jun

Living with a Novel Landscape: Suisun Evolves

Morning at Suisun Marsh is a living watercolor with a soundtrack. Miles of tule and pickleweed populate the foreground, split by canals glinting silver from the sun. In May, the hills undulate across the northern boundary in classic California gold. A red-tailed hawk’s iconic hoarse screech punctuates the insectine buzz as it takes off from a powerline. At 7:40 AM, it’s already 72 degrees and there’s no trace of a breeze. I’ve come to visit the Marsh from downtown Oakland seeking to learn from biologists, hunters, and land managers what’s at stake in the myriad battles with rising seas, worsening drought, and, especially, encroaching invasive species and what makes it such a singular, attractive landscape.  Indeed, the pastoral foreground is...
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Baldocchi at the end of one of the levees breached to restore tidal action at Dutch Slough. Photo: Janet Byron
16
Jun

Sniffing the Delta for Greenhouse Gases

Dutch Slough in Oakley, on the southern edge of the Sacramento-San Joaquin Delta, is less than a mile from where biometeorologist Dennis D. Baldocchi (above) grew up on his parents’ orchard and fished with pals in nearby Marsh Creek. In October 2021, the California Department of Water Resources breached the levees here, restoring nutrient-rich tidal flows to degraded ranchland. Early in the 20th century, Baldocchi’s father grew dry beans and sugar beets on the peat soils of the Delta’s Liberty Island, and his aunt’s family raised asparagus, sugar beets, and corn on Sherman Island. In 1952, his dad started growing almonds and walnuts at the junction of Sellers Avenue and Cypress Road in Oakley. “My family mined the Delta for...
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14
Jun

Cutting Green Tape

A novel exemption lawmakers passed to California’s landmark Environmental Quality Act (CEQA) in late 2021 has helped fast-track at least four habitat restoration projects so far, with more to follow in the next couple years. The Statutory Exemption for Restoration Projects, or SERP, offers a rare reprieve from California’s stringent environmental review and permitting process — and a clear indication of the urgency the state’s leaders feel in advancing ecological restoration work. “When [SERP] passed, it was a little bit controversial,” says Sara Johnson, executive director of the fledgling California Ecological Business Association. Sluggish regulatory approval timelines are the top grievance member organizations of the association share, she said at the Society for Ecological Restoration’s conference in Carmel Valley in...
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subisdence on 4 delta islands map
13
Apr

Asked to suggest an appropriate future for four Delta islands owned by the Metropolitan Water District, it’s difficult not to want the moon.

Why not richer rice fields, more wetlands, better boat launches, extended trails, even eco-tourism? ? A new survey for the Delta Islands Adaptation Project, funded by a Prop 1 Watershed Restoration Grant, wants the public’s opinion on the importance of 10 possible land-use objectives leading to the selection of one of the four islands for improvements. As your blinking cursor hovers over a satellite image of Bouldin, Bacon, Webb, and Holland Tracts, the survey lays out all that the experts know already: Holland is the least subsided; Bouldin the most accessible by road; Webb the best candidate for making more fish food, and more. “The Central Delta has some of the most critical landscapes in the state, and also some...
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chart by Hutton
13
Apr

An examination of 50 years of records reveals an apparent seasonal bias in estimates of freshwater flow from the Delta to the San Francisco Estuary.

The seasonal bias suggests flows were overestimated during the summer months and underestimated during the winter. Estimates of Delta outflow use a measurement called net Delta outflow index (NDOI), which is determined by taking the amount of Delta inflow, from sources such as the Calaveras, Sacramento, and San Joaquin rivers, and subtracting Delta exports, a direct measurement, and net Delta channel depletions. A team led by TetraTech’s Paul Hutton compared NDOI estimates against measured Delta outflow at four points, as well as against the Estuary’s historical salinity record. The study, which appears in the December 2021 issue of San Francisco Estuary and Watershed Science, focused on net Delta channel depletions, which are determined indirectly and involve considerations such as land...
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diagram of fish net trawl
13
Apr

Fish monitoring surveys in the San Francisco Estuary net different numbers of different fish species depending upon when and how they sample.

According to a new study published in San Francisco Estuary and Watershed Science, even surveys that target the same part of the water column can come up with significantly different catches. The study’s authors analyzed decades worth of data from the California Department of Fish and Wildlife (CDFW) Fall Midwater Trawl, which spans from San Pablo Bay to the upper Delta; CDFW’s San Francisco Bay Study midwater and otter trawls, covering the South Bay to the central Delta; and the UC Davis Suisun Marsh Fish Study, also an otter trawl. The two midwater trawls, which sample the middle of the water column, were found to be generally more successful at catching pelagic (open-water) fish like Delta smelt and American shad...
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field in delta with irrigation
13
Apr

Rain or shine, farmers in California use about the same amount of water every year, while residential water use varies considerably with precipitation.

A research team led by UC San Diego’s John Helly processed 15 years’ worth of water-use data from the state’s Department of Water Resources, reporting in the March 2022 issue of San Francisco Estuary and Watershed Science that while “the annually precipitated water supply in the Bay-Delta” varied by 30%, agricultural water use scarcely changed year to year. “The water management system maintained nearly constant agricultural water use even in periods of intense drought, with year-to-year variation of about 7%,” the authors wrote. Residential water use showed more variability, swinging by 20% from one year to the next–mainly, the authors theorize, as the result of voluntary and mandated water conservation during droughts. Though Helly says he had no expectations of...
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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

South Bay Trawls Show Fish Like Restored Shores

Twelve years ago, scientists at UC Davis began a survey of the southern end of San Francisco Bay — the Lower South Bay — to see how fish responded to the South Bay Salt Ponds Restoration Project. They discovered an unexpectedly diverse and robust aquatic community and a previously unknown spawning ground for the longfin smelt (Spirinchus thaleichthys), listed as endangered in California and a candidate for federal protection because of its declining numbers. The team, led first by Jim Hobbs and now by Levi Lewis, has complied an invaluable long-term dataset and enhanced our understanding of the surprising ecosystems of the bottom of the Bay. In addition to journal publications, their findings have been shared in blog posts by...
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15
Feb

Big Boulders, Big Benefits to Coyote Creek Fish

As a source of flowing water, upper Coyote Creek is unreliable at best. Though storms swell its banks in winter, Mediterranean-climate summers shrink this South Bay stream to a series of isolated pools by August. “By October right before the rains come, we’re down to these really small pools that have all the fish in them,” says retired U.S. Environmental Protection Agency ecologist Rob Leidy. Leidy and UC Berkeley fish ecologist Stephanie Carlson began monitoring the annual dry-down of upper Coyote Creek in 2014, with the help of Hana Moidu and other graduate students. The creek itself originates in Henry W. Coe State Park and flows to the Bay through Coyote and Anderson lakes south of San Jose. The scientists...
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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
Feb

Sturdy Sturgeon

A 90-year-old Australian lungfish at San Francisco’s Academy of Sciences has received a lot of press lately, but there is a wild fish species living in the San Francisco Bay that has the potential to live that long or longer — or so we think. While one white sturgeon caught in the Columbia River Basin was estimated to be 104 years old, the life expectancy of white sturgeon, Acipenser transmontanus, which includes the Central Valley population endemic to the San Francisco Bay, is hard to pin down. “There are old ones out there, but it’s really hard to give a number because we just don’t have it,” says John Kelly, statewide sturgeon coordinator for the California Department of Fish and...
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