ESTUARY PEARLS: New ways to boost fish nutrition and identify species, a new bird atlas raises red flags, preparing for a snowless future, and more

New ways to boost fish nutrition and identify species, a new bird atlas raises red flags, preparing for a snowless future, and more science news. Plus, an interview with Metropolitan Water District’s new leader.

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 it can build aquatic biomass. For small salmon, this means they can reap the benefits of floodplain food synthesis even when confined to the leveed mainstem of the river, where food resources tend to be scarce. In a 2019 experiment that involved 5,000 acres of flooded land in the Colusa basin, Katz and his colleagues anchored cages containing Chinook smolts both upstream and downstream of the floodwater release sites. The results were striking: Caged salmon a mile downstream of the flushing site grew three times faster than the salmon held upstream. In a 2021 repeat of the experiment, smolts as far as six miles downstream grew 4.5 times faster than their upstream cohorts.

Katz says the plan is to scale up the program to 20,000 acres for the coming winter, and he believes that within five years, the land dedicated by private owners to this project could amount to 100,000 acres. The project, Katz says, does more than simply feed fish: “It also demonstrates that a healthy river is intimately connected to the landscape through which it flows.”

Author: Alistair Bland | Image: Intentionally inundated fish food fields at River Garden Farms near the Sacramento River. Photo by Mike Weir

With a headline-grabbing new study projecting that snowpack shrinkage will likely disrupt the West’s water system by mid-century, water managers’ efforts to adapt to climate change are becoming more urgent.

This is not a problem for later,” says Michael Anderson, state climatologist at the California Department of Water Resources. “This is a problem for now.”

Snowpack loss is like the canary in the coal mine for climate change—temperature has direct impacts on snow,” says Erica Woodburn, a Lawrence Berkeley National Laboratory hydrogeologist who co-led the 11-member interdisciplinary team that contributed to the study. Along with smaller snowpacks, the state is also experiencing bigger atmospheric rivers such as the one now soaking California. “Atmospheric rivers are near saturated and a warmer climate increases their ability to hold moisture” says Alexander Gershunov, a climate scientist at Scripps Institution of Oceanography. Gershunov is working with colleagues to extend the timeframe of storm-return projections further into the future.

Little or no snow can be gloom and doom but there are paths forward,” says snowpack study co-leader Alan Rhoades, also from Lawrence Berkeley Lab. Those working to adapt the West’s water system to climate change are deploying managed aquifer recharge, as well as forecast-informed reservoir operations (FIRO), which optimizes surface water storage.

To read the full story, click here.

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 species. Some wetland specialists, including cinnamon teal, pied-billed grebe, common gallinule, American coot, northern harrier, and yellow-headed blackbird, were found in fewer blocks. Pandolfino notes that the grebe, gallinule, and coot, which have similar breeding requirements, disappeared from almost the same blocks. “Some of these blocks had no net loss in hectares of wetlands but a dramatic increase in development,” he adds. “You wind up with patches surrounded by development where the birds are vulnerable to predators.”
Rice field acreage in the Natomas Basin, which hosted black terns and American bitterns, was reduced by residential development and airport expansion; the tern no longer nests in the county. Trends are less clear for other species, like herons and egrets. On the positive side, raptors once hammered by DDT have rebounded, and Cooper’s hawks, western bluebirds, and others have adapted to urban areas.
Pandolfino cautions that atlases show presence, not numbers. “The data is binary—yes or no for each block,” he says. “A species may be declining in population but still breeding in the same block.” But that doesn’t reduce the value of the project as a baseline.
Author: Joe Eaton | Image: Pied-billed grebe by Tim Manolis

The CRISPR technique used to edit DNA has been formulated into a tool that can identify fish species with speed and accuracy in the field, potentially revolutionizing cryptic species identifications.

It puts the power in the hands of the field biologist to make the most informed decision, versus waiting sometimes days or weeks for lab results,” says Melinda Baerwald, an environmental program manager with the California Department of Water Resources. Before the development of SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing), identification of a cryptic fish required a wait for lab results. The delay is particularly problematic for those working with listed species, who only have permits to “take” so many individuals. “You could have no idea that you already reached your take limit a couple of weeks ago,” says Andrea Schreier, an adjunct associate professor at UC Davis.

In the journal Molecular Ecology Resources, Schreier, Baerwald, and colleagues report engineering SHERLOCK to identify Delta and longfin smelt as well as wakasagi. Using mucus swiped from the side of a fish, SHERLOCK identified each species within 30 minutes. The tool is adaptable to just about any organism; recently, the scientists used SHERLOCK to distinguish the Estuary’s Chinook salmon runs, which look identical. SHERLOCK outperformed the often inaccurate “length at date” measurement currently in use. “SHERLOCK has the potential to change how we routinely assign Chinook run type, enabling it to be done more accurately and efficiently,” Baerwald says. SHERLOCK’s nearly instant results have the potential to enable real-time adjustments to the operations of the Delta diversion pumps, sampling locations during species surveys, and many other activities.

To read more about SHERLOCK, including how it might be used to help protect other threatened and endangered species, click here.

Author: Kathleen Wong | Above: Swabbing a tagged smelt. Photo courtesy of Alisha Goodbla/UC Davis

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,” says Steve Crooks, the lead wetlands and coastal management scientist for Silvestrum Climate Associates, which is one of the organizations working to accelerate the research. “But when you actually get down to the detail of trying to develop market mechanisms around this there’s a lot to be worked out.” The initiative’s website lists “kelp and seaweed farming, seabed management, sustainable fishing, and conserving and restoring seagrass meadows, salt marshes, and mangroves” as “blue carbon” areas of interest. For some ecosystems, like mangrove forests or seagrass beds, scientists already have specific data on where the carbon goes—and for how long. But calculating the carbon savings of kelp farming is fuzzier, and doing so for a well-managed marine protected area is a concept in its infancy. Once the carbon savings of either restoring or protecting these habitats can be calculated precisely enough, those activities can be more easily paid for through voluntary carbon markets.

We’re seeing a rapid acceleration of the science on these ecosystems,” says Crooks. “But there’s still a lot of work to do.”
Author: Sierra Garcia | Above: Kelp Forest. Photo by Sierra Garcia

New leadership at the Metropolitan Water District of Southern California is big news for Northern California water affairs.

MWD pays a large share of the cost of the State Water Project. It owns lands in the Delta. It underwrites research. It often seems to determine the course of government policy. Traditionally, many in the north have seen “the Met” as a kind of colonial power, both far away and threateningly present. New General Manager Adel Hagekhalil is not of the traditional mold. He spent almost a decade as assistant director of the Los Angeles Bureau of Sanitation, where he led the City’s effort to plan for “One Water,” the idea that all waters—local or imported, hidden underground or flashing in the sun, roaring in flood or trickling in drought, flushed down toilets or pulled from mountain streams, irrigating farms or supporting fish—must be thought of and managed as aspects of one precious resource.
In December, Estuary News Group’s John Hart talked with Hagekhalil about Southern California’s water conservation success, water recycling and reuse, the Delta, and what he calls “fourth aqueduct.” Read their conversation here.

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 of the Yolo Bypass, required releasing water from upstream reservoirs and pumping from downstream diversions in the Sacramento River.   
It was a lot of heavy lifting in a short amount of time, but an amazing collaborative effort,” says lead author Jared Frantzich, a senior environmental scientist with DWR, which led the effort in partnership with a host of other agencies, irrigation and reclamation districts, and private landowners. Subsequent managed flow pulses in 2018 and 2019 provided additional data and helped refine the practice, which Frantzich notes has since been included in some key Delta regulatory documents and may be used more in the future to help benefit food web and habitat conditions during summer or fall months.
Author: Nate Seltenrich | Photo by Jared Frantzich

And Also…  The Draft Actions for the 2022 Estuary Blueprint are now available for public review and input.

Watch the Blueprint video overview and offer your thoughts on the 25 Actions included in the Draft Blueprint. Submit comments through the online form or email them to The deadline to submit comments is Friday, January 7, 2022.
Additionally, there will be a virtual public input session on Tuesday, January 11th, 2022 from 1-3pm PT. Register for the Zoom meeting here.

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