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.

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...
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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...
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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...
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Finding Her Way to Fish: Denise Colombano

The path into a career is not always a straightforward one. “I hated school. I mean, hated school,” says Denise Colombano, a postdoctoral fellow and Delta Science Fellow working on fisheries research at UC Berkeley. Today, Colombano feels that it is important to talk about her story as a way of encouraging inclusiveness and opportunity within her field — and in the sciences in general.  “I actually flunked ninth grade, and was attending a continuation school, when my science teacher...
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Over time, the median actual flow to San Francisco Bay in the ecologically critical winter and spring months has declined to less than half of the unimpaired runoff. This bar chart divides actual inflow (the amount that actually made it to the Bay) and unimpaired runoff (the inflow to the Bay that would occur if there were no dams or diversions) into quintiles from wettest to dry, and marks years drier than 2015 (roughly, the driest 2% of years) as “super-critically dry” years. Over the last 54 years, “super-critically dry” runoff conditions in the Bay’s watershed occurred naturally only once, in 1977, but the Estuary received runoff volumes in the super-critical range in 22 years, or 40% of the time. Overall, flow volumes characteristic of the driest 20% of years now occur more than half the time as a result of storage and diversion of runoff for consumptive uses. Source: The Bay Institute, based on data from California Department of Water Resources.

Defining Unimpaired Flows

For the second time in four years, a proposal for a voluntary agreement between agencies and water contractors on flows into and through the Delta from the San Joaquin and Sacramento rivers and their tributaries is wending its way through the State Water Resources Control Board. The proposal, which would replace the regime outlined in the Board’s most recent update to the Bay-Delta Plan, calls for substantially less water remaining in the system than the update, but comparing the two...
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Adrienne Ernst among the Phragmites. Photo: Michael Adamson

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...
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Baldocchi at the end of one of the levees breached to restore tidal action at Dutch Slough. Photo: Janet Byron

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...
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subisdence on 4 delta islands map

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...
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chart by Hutton

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...
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diagram of fish net trawl

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...
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field in delta with irrigation

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%,”...
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West Coast Salmonids All Tired Out?

West Coast salmon and steelhead populations have declined steeply in the past century – a plight that biologists have primarily blamed on habitat loss. Dams, for instance, block adult fish’s access to historic spawning grounds, and juvenile survival is impacted by streamside development and water diversions. Now, it turns out, microplastic pollution may be a much bigger factor than anyone knew just several years ago. In 2019, scientists with the San Francisco Estuary Institute and the Los Angeles-based nonprofit 5...
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Eyeballing the Fish

Longfin smelt were what hooked Jim Ervin when he first learned about the UC Davis South Bay Fish Survey through a presentation at the 2012 Bay-Delta Science Conference. “They were catching them right there in our effluent channel!” recalls Ervin, a self-trained naturalist and former compliance manager for the San Jose-Santa Clara Regional Wastewater Facility. Intrigued, he contacted the researchers, rode with them on their next survey, and has been part of the project ever since, devoting more time to...
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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...
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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...
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Hatchery Delta Smelt Released to Wild

On a mild day between rainstorms in mid-December, wildlife biologists outfitted in rubber boots and orange lifejackets load drum after drum of precious cargo onto a small boat docked in Rio Vista, a town on the Sacramento River in the Sacramento-San Joaquin Delta. There is little fanfare but the occasion is nonetheless momentous. The shiny silver drums contain thousands of Delta smelt — finger-size imperiled fish unique to the Delta — that were raised in a conservation hatchery. Today marks...
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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...
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A new partnership is pushing to tally the “blue carbon” in marine and coastal ecosystems.

Seagrass meadows, kelp forests, and even the seabed can all lock away carbon—but exactly how much is still up in the air for these and other ocean ecosystems. The Seascape Carbon Initiative, a partnership formed in late 2021 between four environmental problem-solving organizations and one independent carbon verifier, is pushing the science forward so protecting and restoring these valuable ecosystems can join mangrove forests and terrestrial forests as certifiable nature-based carbon capture projects.   “Conceptually, the science is pretty good,”...
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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...
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New Way to Sleuth Out Fish IDs in the Field

The CRISPR technique used to edit DNA has been formulated into a tool that can distinguish between similar-looking California fish species for conservation research. Called SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing), the tool can tell the difference between species with speed and accuracy. Better yet, it is both inexpensive and can be run while researchers are in the field. “It puts the power in the hands of the field biologist to make the most informed decision versus waiting sometimes days...
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