Pearls in the ocean of information that our reporters didn’t want you to miss



A Stream of Science Takeaways

ESTUARY News sent reporters to the biennial Bay-Delta Science Conference in September. This special edition of Pearls shares more than 20 takeaways.

PEARLS PART 1: Native & Invasive Species

Recent restoration efforts in lower Putah Creek have had a big payoff: fall-run Chinook are once again coming there to spawn. Salmon bred in the watershed historically, but numbers were low before the restoration began, and non-native fish dominated. Now native fish have rebounded in the creek. “They outnumbered non-natives pretty rapidly,” says Eric Chapman of UC Davis.  Putah Creek, which flows from Lake Berryessa to the Yolo Bypass, hasn’t supported a salmon run since the mid-1900s; in 2016, 1,800 adult salmon returned to spawn. Carcass surveys showed that the first adults to return had all been trucked to the Delta as smolts, rather than released directly from hatcheries. Now, salmon are laying eggs in Putah Creek, and some of the recent returners may have been born there. This makes the creek a model of “if you build it, they will come” salmon restoration. “Streams you may think are too far gone can be a success,” Chapman says. RM

Southern-most populations of salmon are at the forefront of the effects of climate change, and they exhibit warm-adapted traits. Kenneth Zillig of UC Davis compared hatchery smolt from three populations that are adapted to different temperatures: one from northern Oregon, one from southern Oregon, and one from the Central Valley. Tests included raising smolt at a range of temperatures (11, 16 and 20⁰C); Central Valley salmon grew optimally at the highest temperature while the Oregon salmon did not. While this fits with southern-most populations being more adaptable to warmer waters, it’s too soon to say for sure because other findings were mixed. To get a more definitive answer, Zillig plans to expand the study to populations as far north as British Columbia or Alaska. “Larger biogeographical patterns may become apparent with future research,” he says. RM

Although returns of spawning spring-run Chinook dropped precipitously to a low of 1,796 in 2017, there are signs that the fast dwindling species may be able to bounce back. Rachel Johnson of the National Oceanic and Atmospheric Administration has found evidence of hidden diversity that “highlights remnant behaviors occurring in multiple populations that are contributing to the resiliency of spring run.” For example, spring-run Chinook migrate to the ocean at a diversity of sizes and different times, increasing the chances that some will make it out to sea. They are also more spatially diverse than expected. “We thought they were extirpated in the San Joaquin River, so all the surveys there are for fall-run,” Johnson says. Recently, however, videos have caught spring-running Chinook in tributaries of this river. These chance sightings add up to a surprise: these salmon may be trying to recolonize the San Joaquin River naturally. RM

Cordgrass is key to buffering vulnerable shores, but our native species could have trouble adapting to sea level rise. That’s what Erik Grijalva of UC Davis found when he transplanted cordgrass collected from the North Bay (where it is free of hybrids of the Atlantic species) to different depths at Sears Point and Eden landing. Only the shallowest sites had good survival rates, and there seemed to be limited variation among plants for natural selection to work on. These are very preliminary results, but Grijalva muses on a troubling thought: that the successful campaign to suppress the exotic cordgrass, which grows in a wider range of conditions, “might not have been exactly what the doctor ordered.”  JH
Photo: Erik Grijalva

Only a tiny percentage of outmigrating Chinook make it to sea, and where they begin their journey seems to affect their survival rates.“Where do fish die and survive on their way to the Golden Gate?” asks Colby Hause of UC Davis who is tracking young spring-run salmon to identify perilous reaches on their journey. When young salmon with acoustic tags are released in a restored stretch of the San Joaquin River, they did poorly immediately after release in the restoration area, better in the lower river, and poorly once again in the Delta. Altogether, only three to six percentsurvive their trip from the river restoration release site to the ocean. In comparison, prospects for young salmon released directly in the Delta look better: 10 to 19 percentsurvive their trip through the Delta and Bay out to the ocean. That said, a closer look at the data reveals that young salmon may benefit from undergoing the hazards of the restored stretch of the San Joaquin River: 30 percent of these make it through the Delta and into the Bay, compared with just 20 percent of those released into the Delta itself. “Maybe they benefit from going through the wringer of the restoration area,” Hause says. “Maybe they’re getting smarter and stronger before going though the gauntlet of the Delta.” RM
Photo: Dan Cox, USFWS

Researchers are using acoustic cameras to learn where and when predatory fish pose the greatest threat to young salmon traversing the Delta. “There are very basic questions that we don’t have answers to, like numbers and locations of predatory fish,” says Christopher Loomis of Humboldt State University. He’s looking for answers with DIDSON acoustic cameras, which use sound to capture high-resolution video. Analysis of these videos yields fish dimensions (length and thickness) that can then be compared to those of known species in a data library, distinguishing predatory from non-predatory fish with 98 percent accuracy. By combining acoustic camera surveys of predatory fish with concurrent surveys of predation on tethered smolts, Loomis plans to map predatory fish in the Delta. “We hope to highlight where predation hotspots exist and what creates them,” he says.  RM

Native populations of Delta smelt, longfin smelt, and Sacramento splittail were hit hard by the last drought and had a hard time recovering.  Louise Conrad, a program manager for Estuarine Science and Synthesis with the California Department of Water Resources, and co-authors analyzed populations of native fishes as well as introduced species including striped bass, shad, and Mississippi silverside before, during, and after the drought of 2012-’16 to assess both resistance and resilience. She discovered that while neither the smelt nor the splittail clearly bounced back after the winter of 2016-’17—which was certainly wet but may have been too warm for the fish—both striped bass and American shad had some success. Conrad also studied resilience following four previous major droughts going back to the 1970s and discovered that, when the conditions are right, natives can recover well, as they did after the droughts of 1976-’77, 1987, ’94, and 2007-’10. “In recent history, we’ve seen that they have the capacity for resilience, and that’s a good sign,” she said. “Drought is nothing new to California, but it isn’t the same estuary that these fish evolved in.” NS

Invasive aquatic plants like water hyacinth don’t just choke up Delta waterways, impairing boat traffic and habitat; they can also have a measurable effect on water quality. Vanessa Tobias, a researcher with the U.S. Fish and Wildlife Service, found that floating patches of water hyacinth affect water temperature, dissolved oxygen, and turbidity—not just within the perimeter of the patch itself, but as much as 100 feet out. It’s too soon to determine quite what that means for fish, native plants, or other aquatic organisms in the Delta, Tobias said, and water quality seems to recover quickly after patch removal. Meanwhile, Judith Drexler of the United States Geological Survey has found that the submerged aquatic plants water primrose and Brazilian waterweed, both of which are weeds rampant throughout the Delta, negatively affect flow velocity, turbidity, and sedimentation processes. This can be bad news for marshes that depend on sediment to keep up with erosion and sea-level rise, as well as for fish species—such as Delta smelt—that need turbid water for habitat and cover. “This vegetation is really working as an ecosystem engineer in the Delta,” Drexler said. NS
Photo: Judy Drexler

Using powerful sensors mounted on satellites, NASA researchers can keep tabs on environmental issues like air pollution, harmful algal blooms—and invasive aquatic weeds in the Delta. Led by senior research scientist David Bubenheim in collaboration with the U.S.Department of Agriculture and the California Division of Boating and Waterways (DBW), the team uses satellite data to assess the growth and distribution of floating invasive plants like water hyacinth. The project began about three years ago and continues to evolve, Bubenheim said, as NASA’s remote-sensing experts refine their use of current and historical data and seek out new data sources such as the European Space Agency’s Sentinel satellite, which collects more information more frequently than the United States’ Landsat sensors. “Where we are focused right now is to be able to give [DBW] a map that has finer details as to how much plant is in a particular spot, how much biomass is there, and what species it is.” said Bubenheim. NS
Photo: Toxic algal bloom. Courtesy CDFW.

Scientists with the USDA are increasingly turning to biological controls to combat water hyacinth, an invasive aquatic plant that clogs waterways, harms habitat, and impairs water quality in the Delta. Biocontrols—non-native insects that evolved with the water hyacinth, and won’t eat beneficial plants or harm Delta fish—have been used in the Delta since the early 1980s, with limited success, said Patrick Moran, a research entomologist now leading the agency’s efforts. Only one insect, the leaf-chewing/crown-boring weevil Neochetina bruchi, has established itself throughout the Delta, and its impact on hyacinth profusion has been limited. But the USDA is undeterred, re-releasing the leaf-sucking planthopper Megamelus scutellaris and the moth Niphograpta albiguttalis this summer—and planning to try again with the weevil Neochetina eichhorniae very soon. The agency has also looked to treat the giant riparian grass arundo, which invades levees and wetlands, with a shoot-galling wasp and a shoot- and root-feeding armored scale, the latter of which has become established. “These weeds in the Delta have reached proportions that biocontrol really always should be considered,” Moran said. NS

PEARLS PART 2: Habitat & Restoration

Given that the historic Delta is gone forever, how much floodplain habitat should we restore, and where? This question occupies many contemporary Delta scientists, such as Rene Henery, California Science Director at Trout Unlimited, who identified a range of factors that influence habitat quality for young Chinook salmon including flood timing and duration; water depth, velocity, and temperature; and available cover. Meanwhile Jacob Katz, a senior scientist for CalTrout, has made it his mission to reconnect the channelized Sacramento River to portions of its historic floodplain in order to slow water and grow food for imperiled native fish. “When you’ve lost 95 percent of your floodplains and your wetlands, why are we surprised when we end up with 5 percent of our fish biomass?” he asks. Other efforts to support floodplains as fish nurseries include the Nature Conservancy’s Emigrating Salmonid Habitat Estimation model for quantifying habitat needs; UC Merced postdoctoral researcher Alison Whipple’s PhD study on quantifying potential habitat benefits for Sacramento splittail at a restoration project along the Cosumnes River; and American Rivers’ Chinook Salmon Habitat Quantification Tool. “This feels like something that people are converging around,” said Henery. NS

Delta habitat restoration dreams are getting real. After helping define what makes a good Delta project—large rather than small, linked rather than isolated, and so on—the San Francisco Estuary Institute is creating mapping tools to show just where new habitats might be created, and to assess the probable gains. For instance, the Central Valley Joint Venture calls for restoring 84,000 acres of oak savanna across the whole Central Valley. “There’s the potential to support about 30 percent of the objective in the Delta,” says SFEI’s Sam Safran. Such precision, inevitably, makes landowners nervous. “Any time you’re putting opportunities on the map in the Delta, it’s a little bit dicey,” Safran acknowledges. For now the emphasis is on fleshing out what can be accomplished on public lands and through the in-the-pipeline projects of EcoRestore. More controversial steps, some of them identified years ago, have been deferred by Delta planners and managers in the hope that consensus will build. JH

Franks Tract, a flooded island in the heart of the Delta, is a hotbed for predatory non-native fish–but native fish may still be able to thrive alongside them. “We’ve gone from the old ‘all introduced predatory fish are bad’ to reconciliation,” says Carl Wilcox of the California Department of Fish and Wildlife (CDFW), explaining that this means acknowledging the Delta as a novel ecosystem rather than trying to restore what once was. Historically, Franks Tract was part of a huge marsh, sheltering small fish in channels that meandered into dead ends rather than interconnecting. “Now, there are all kinds of connections that never existed,” Wilcox says. A CDFW-led restoration plan is in the works to reclaim part of Franks Tract for native fish, creating marshes with waterways called dendritic blind channels. These dead-end waterways narrow progressively, subdividing into ever-smaller branches that provide refuges for native fish fleeing from non-native predators.  RM

Barring human intervention, important marsh and mudflat habitats around the Bay are doomed to disappear as sea levels rise. Two new studies, one on each shore of San Francisco Bay, underscore the challenge. A team from Point Blue and San Mateo County examined the county’s wetland fringe. Even with optimistic assumptions about sediment, these marshes will lose ground after 2050 and largely convert to mudflats by 2100; marsh-dependent bird populations will follow suit. On the Bay’s opposite shore, the USGS considered the probable fate of two mudflats, a shallowly sloping expanse at Eden Landing and a narrow, steeper strip near the Dumbarton Bridge. By 2100, a USGS and UNESCO-IHE team reports, the Dumbarton tract will lose 57 percent of its foraging habitat for shorebirds, and the Eden Landing tract 100 percent. “We’re seeing extensive loss of foraging habitat and key prey items,” says the Survey’s Susan De La Cruz. “But it’s not all doom and gloom.” On both shores, results like these will inform new adaptation plans. JH
Photo: Rick Lewis

Intact transition zones—strips of ground that are only occasionally inundated and blend features of uplands and adjacent wetlands—are far rarer and much less studied than salt marshes around San Francisco Bay. Looking at the needs of birds, Nadav Nur of Point Blue and his colleagues posed the question: “When we restore or design transition zones, what should they look like?” Studying 16 sites—some natural, some restored, some with and some without levees—the team concluded that one important plus is simply space: the wider the zone, the better, especially for rails. A second need is tall vegetation to make hiding places; what species of plant provides the shelter doesn’t matter. Sparrows like vegetation to be dense as well as tall. Marsh birds used gentle slopes as well as steeper ones, like levee faces, provided they were well vegetated. Nur urges transition zone restorers to mix and match, trying out a variety of designs. JH

At the nexus of flood protection and habit restoration is the Bay’s latest craze: living shorelines. Out are steep seawalls and traditional levees. In are low-slope horizontal levees, which after proven success at San Lorenzo’s Oro Loma site could help protect sections of the Bay shore from sea level rise, while providing a range of habitats from mudflat to grassland, said Marin County principal planner Chris Choo. Also in are subtidal oyster-and-eelgrass beds to reduce wave energy and mitigate sea-level rise, such as at Richmond’s Giant Marsh, which the State Coastal Conservancy will restore next year after learning from a smaller project in the San Rafael Bay, said Michelle Orr of Environmental Science Associates. And so is the use of sediment, where space permits, to build ecotones that smoothly transition from tidal marsh to lowland terrestrial to upland, allowing habitat to migrate landward with sea-level rise, such as in the revised restoration plan at Contra Costa County’s Lower Walnut Creek. “One of the big shifts that occurred was to think of  [existing] dredge material not as something that needed to be removed, but as a resource,” said Orr.  NS

The Bay Area’s twin needs for new housing and new infrastructure may present an opportunity to boost ecosystem services in our highly altered landscape. So says  Letitia Grenier of the San Francisco Estuary Institute, who envisions a Bay Area-wide plan to restore natural processes, not “just” natural habitats. One promising approach—originally developed by Erica Spotswood and Robin Grossinger—is strategic planting of native oaks to conserve water during the dry season and reduce runoff during the wet season. Trees also store carbon and reduce urban heat islands. All told, native oak trees account for five percent of the street trees in Silicon Valley but provide nearly 10 percent of tree-related ecosystem services. “Native oaks punch above their weight,” Grenier says. RM

PEARLS PART 3: Climate Change, Water Quality & More

If sea level rises one meter, water releases from upstream dams would have to climb by at least 8 percent in dry years to keep X2, the biologically productive low salinity zone, in its current range in the spring. Rising tides will tend to shift X2 eastward from Suisun Bay into Delta channels, but according to a new study the additional water releases required by management rules will be minor at first.  Even in dry years, “we wouldn’t expect to see more than a few tens of thousands of acre-feet for a few decades,” says the USGS’s Noah Knowles. After about 2050, the picture darkens, however. “If sea level rise accelerates toward the end of the century as the projections indicate, there would be real water costs,” he says. The perennial, controversial question remains, however: If more habitat opens up in the Delta proper, providing better fish habitat there, could X2 move farther east without biological harm? JH
Photo: Christopher Loomis

Rising tides don’t just make waves lap higher; they also bring underground water nearer the surface, up to half a mile from shore. Two recent studies from U. C. Berkeley and Silvestrum Climate Associates try to get a handle on the problem. Using data from wells monitored by the State Water Resources Control Board, researchers mapped present and projected-future water depths to areas of likely surface ponding. Some coastal defense projects, suggested Berkeley’s Ellen Plane, “might become cost-prohibitive and  ineffective if we don’t account for this additional threat.” Silvestrum went on to look at the variability of the water table through wet seasons, shoreline inundation, and groundwater ponding (due to higher water table from combined sea level rise and precipitation) as future flood threats. By 2050, “groundwater is the story,” says Abby Mohan. The challenges for underground utilities and transportation corridors will be enormous. “When we look at SLR adaptation in low lying areas we can’t just focus on levees to keep the Bay out, as the areas flooded will be larger and can come sooner and have a more widespread impact than previously mapped.” JH
Above: Oakland-Alameda shoreline


Adaptive management will flounder, says a veteran of efforts on the Colorado River, “if it’s only guided by stakeholder concerns and is tightly constrained by nuanced policy considerations.” In 1997, after more than three decades of reservoir operation and nearly two decades of studies and lawsuits, scientists and stakeholders joined in the Glen Canyon Dam Adaptive Management Program that was formed by the Department of the Interior. Unfortunately, the process of defining the program’s objectives and goals resulted in “making everybody feel good but did not identify the hard choices that need to be made to define what kind of an ecosystem is the goal of the program,” according to Jack Schmidt of Utah State University and former Chief of the USGS/Grand Canyon Monitoring and Research Center. The objectives of the program include ” maximizing engineering efficiencies, restoring river resources that are relics of the past, and managing river resources that are artifacts of the existence and operations of Glen Canyon Dam. In truth, we can’t have it all.”  The essential questions that must be addressed by the program also were not made explicit — “How do you rehabilitate valued sand bars used for camping when there’s not enough sand? What do you do when one [valued] introduced fish species eats another [valued] native fish species?” Schmidt acknowledges some modest successes, like “controlled floods” designed to redistribute the scarce sand supply to desired locations along the channel banks and “bug flows” to help hatching insects and thereby increase the food base for fish. “These successes were conceived and developed by river scientists, not the stakeholders,” Schmidt pointed out. But the inherent conflicts in the Program remain. For example, “the benefits of controlled floods are quickly eroded by normal hydropower operations.” Schmidt expressed hope that scientists working on the Delta and Bay play a clear and strong role in developing alternative management options. JH
Above: Glen Canyon Dam.  Photo: Carsten Meier, Utah State University

Liberty Island in 2000 and Jones Tract in 2004 proved it: If a levee fails in the Delta, the tides move differently, even many miles away. A team from Resource Management Associates, Inc., (RMA) set out to model the effects of a wide range of potential breach scenarios, including both planned restorations and accidental island failures.  The location of breaches dramatically affects regional patterns of change.  For instance, breaching a group of islands in the northwest Delta would increase net seaward flow in the Sacramento River and decrease it in the San Joaquin River, while dampening the vertical range of tides. Breaching a similarly sized set of islands along the San Joaquin in the central Delta dampens the vertical tidal range near the breaches, but may slightly increase tidal range in Suisun Bay.  This scenario also decreases Sacramento net flow and increases San Joaquin net flow. If both island clusters were returned to tidal action, the northern and southern net flow effects would nearly cancel out. In deciding the future of levees, RMA’s John DeGeorge says, it’s vital “to understand both the local and regional effects of potential Delta geometry changes.” JH

To communicate what they learn, researchers must learn to talk to the ultimate “keystone species”: human beings. Scientist Amy Matthews Amos of Compass warned against a universal tendency: to hear out people who disagree “only in order to frame a response,” urging instead “listening to understand.” She also advised against arguments that “force people to choose who they are.” Climate change skeptics, for example, may join in dealing with the fact of sea level rise if they don’t feel pressured to endorse the consensus about its cause. Serious listening, Kelly Biedenweg of Oregon State agreed, may reveal ways of managing conflict. Seattle-area farmers irked by streamside buffer rules, for example, proved less moved by lost income than by the sense of losing their right to make decisions about their own property; they also wanted to keep their traditional rectangular fields, which ease property maintenance. Collaboration and a certain amount of flexibility can ease such tensions. JH

More than 2,300 miles of California rivers and streams test positive for unknown toxicants, and conventional methods for determining toxicants often ignore emerging chemicals, degradation products, and inactive ingredients. “One of the reasons we have unknown toxicants is that we’re not looking for the right things,” says Thomas Young of UC Davis, who is developing a strategy for going beyond the usual suspects when water is contaminated. Young is applying this strategy to effluent from a Bay-Delta wastewater treatment plant that contains an unknown toxicant. The basic approach involves comparing the results of chemical analyses against a database of known water contaminants. This helps zero in on unknown chemicals in the effluent. In this case, that left about 3,000 unknowns. But just because they were unknown didn’t necessarily mean they were toxic. By comparing unknowns in the most toxic sample versus those in non-toxic samples, Young showed that only about 200 of these unknowns were unique to the toxic effluent. “We’ve narrowed it down,” he says. RM

Fish, plants, water, and wetlands in the Delta are all the subjects of endless research, but what about people? To better inform future conservation actions in the Suisun Marsh, which is primarily managed by private landowners for waterfowl, the California Department of Water Resources wanted to know more about those who use it—mainly hunters and their private clubs, who own much of the land and have for generations played a prominent role in marsh preservation. Leading the research effort for engineering firm AECOM, environmental project manager Natalie Smith administered nearly 2,500 surveys in person, online, and by phone. She’s still analyzing the responses, but initial findings indicate that Suisun Marsh landowners are highly motivated to continue to protect the marsh against the elevated threats of the 21st century, including sea-level rise, levee failure, and invasive species. “Landowners in the marsh recognize that habitat on their land has the potential to be improved,” she said. “Under the Suisun Marsh Plan, enhancement of up to 40,000 acres of managed wetland are proposed, so understanding their biggest challenges in land management is helpful.” NS

Editor: Cariad Hayes Thronson
Contributors: John Hart, Robin Meadows, Nate Seltenrich

Produced in collaboration with the Delta Stewardship Council. 

The Bay-Delta Science Conference presents the work of hundreds of scientists, summarizes gigabytes of data, and reflects the region’s extended commitment to One Delta, One Science.  The editors of this small stream of takeaways acknowledge the larger river of work and wish they could have covered more sessions and more science.  Keep us in your loop for future Pearls and Estuary News stories.