ESTUARY 1 y a B • s e i c e p s • s c i t i l o p • d e h s r e t a w • n o i t a r o t s e r • e c n e i c s RECYCLING OUTSIDE San Francisco Estuary Partnership THE ESTUARY New Grey BOX reas in A the Waterless PlumbiItng takes Code a low to access the Water Closets? NEWS Advocates of water shallows of San Francisco Bay, Never mind the wh where more eelgrass could someday grow next to human-crafted oyster reefs if local habitat engineers have their way . On both the East and West Bay shores, scientists and volunteers are experimenting with the subtleties of nurturing underwater meadows . . see page 4 .

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NOVEMBER 2012 VOL. 21, NO. 5 Cullinan Ranch Reborn . .2 Delta History Atlas . . . .3 40 Years of Discoveries . .5 Ducks & Otters ...... 7 Science Conference . . . .8 PCBs in Caulk ...... 10 Special RMP Insert: Flame Retardents 2 NOVEMBER 2012 ESTUARY NEWS WATER SHED RESTORATION Cullinan’s New Crust Trailing On a drive by, Cullinan Ranch material, and now we’re compact- the Mokelumne looks more like construction zone ing it in place,” Spenst explains. than a restoration site. The hay and The best way to experience a wa- oats grown here by farmers for Brubaker likens the process tershed is to hike it, source to outlet. more than a century are long gone, to “kneading a 3,900-foot roll of That may be possible one day on and once the earthmovers are done pizza dough.” The partners are also the Mokelumne Crest to Coast Trail, reshaping the site, there’ll be a building decceleration and accel- which follows its namesake river, and breach in the dike the farmers built eration lanes from 37 to provide ac- has been over 20 years in the mak- to drain the property too. As cess to piers for fishing and wildlife ing. A crucial 29-mile segment across reclaim the ranch, it’s hoped that viewing, a canoe and kayak launch East Bay Municipal Utility District native plants and animals—including site, and interpretive kiosks. The land in the Sierra foothills opened on federally endangered species — will levee at Pond 1, managed by the October 6. recolonize this vital piece of the San California Department of Fish and Pablo Bay National Wildlife Refuge. Game, is also being reconfigured. Badly subsided land will be topped It’s been a long time coming. with dredged material. The US Fish and Wildlife Service acquired the 1,500 acres of former “We’re hoping to start farming farmland in 1991, after it escaped salt marsh harvest mice out here,” development as “Egret Bay.” “We Brubaker adds. Some areas will be always knew what we were go- planted with marsh vegetation, but ing to do,” says refuge manager managers expect pickleweed and Don Brubaker. “It was a matter of other plants to arrive with the tides. Photo © Carolyn Fox getting the money.” There was one As sediment starts building up the unforeseen problem. “Initially we marsh plain, plants and animals Launched by an equestrian group thought we could just punch holes should propagate. But Brubaker that spun off the Mokelumne Trail- in the levee and restore hydrology thinks it will be a few years be- busters, trail construction has relied to the site,” recalls Renee Spenst of fore both drive-bys and drive-ins heavily on volunteers —14,000 hours Ducks Unlimited, a key partner in will start seeing differences in the over the last two decades for the the process. “Then we discovered landscape. Mokelumne area alone. The project seven-tenths of a mile of Highway also enlisted California Conservation “We can booger up a place real 37 would be flooded during extreme Corps, California Youth Authority, and quickly, but it takes a while to get it high tides, with winds pushing the California Department of Corrections back to where it was historically,” water level higher.” Sea level rise crews. Financing came from taxpay- says Brubaker. That will start in would make it worse. Even today, ers (Propositions 12 and 84), the January 2014 with the long-awaited Brubaker says king tides accom- California State Trails Program, and breach. JE panied by storms can reach the EBMUD. highway. Contact Don Brubaker, [email protected]; The District’s Kent Lambert says The fix, started last October, re- Renee Spenst, [email protected] the 26-mile stretch that’s already quired a setback levee. “We piled up open gets moderate use from rid- ers and hikers — 58,000 users since 1992 — and has hosted 50-kilometer footraces and equestrian events. It follows the river, winds around Pardee and Camanche reservoirs, and traverses north-facing slopes through oak savanna and woodland. “There’s lots of available shade in some stretches,” he says. A group horse camp at Turkey Hill will provide overnight accommodation. The trail is still a work in progress. Lambert says the trail council is mov- ing down the watershed to work with other organizations on the connection across the Sacramento-San Joaquin Delta. JE Cullinan’s new setback levee, constructed last winter. Photo courtesy Ducks Unlimited. Contact Kent Lambert, [email protected] COVER PHOTO: Living Shorelines Project near San Rafael, by Stephanie Kiriakopolos 3 h i s t o r y Unearthing an Older Delta If any scientific report could called the document “a truly signifi- Quite a lot, according to co-author be called a page-turner, it would be cant contribution” (Delta Stewardship Grossinger: “The report is not a Sacramento-San Joaquin Delta Historical Council Chair Phil Isenberg) and “a template for restoration planning. Ecology Investigation: Exploring Pattern and stunning piece of work, incredibly well It’s a tool to understand what kind of habitats and goals might make sense Process, a 408-page document pre- done” (Valerie Connor of the State and today and in the future. Without that pared by lead author Alison Whipple, Federal Contractors Water Agency.) knowledge, we’re shooting in the Robin Grossinger, and their San But is it more than an exercise in dark.” Francisco Estuary Institute and nostalgia? “You cannot return to the Department of Fish and Game col- past,” says Isenberg. “For the Delta, Contrary to the popular view of the leagues. Well-written and copiously that would require a level of social past, the Delta was never a uniform illustrated, it portrays a pre-1850 engineering far beyond what the sea of tules. Grossinger was stunned Delta rich in physical variability and Chinese government did with their to find so much complexity and di- habitat diversity. Text boxes explore Three Gorges project—moving over versity in the Delta landscape. In the such topics as Native American land one million people.” With all the con- western reaches, investigators dis- management practices, beavers as straints imposed by changes since the covered sand mounds, in the southern ecosystem architects, floating is- 1850s, what can history offer modern reaches, offchannel ponds created by lands, and tall tales about voracious restorationists? continued to back page mosquitoes. Delta stakeholders have

PAST Stockton and Twenty- TENSE one Mile Slough of more than two feet. The reason of this was Meander Cuts that the many curves Bedevil Steamers in the stream prevent- As reported in the Stockton ed the water running Morning Call newspaper, 1894, after cuts were made in the San Joaquin out as fast as the tide River to shorten steamer routes. fell. By the time the [In the late 1800s,] the San Joaquin tide had fallen six feet River...was simply a long collection of in the bay the water curves, and a steamer had to travel fell only two feet in the about three miles in a round about river, and when the manner to make one mile toward its tide rose in the bay it Meanders in the San Joaquin River, from an 1862 engraving by Hutch- caught the flood and ings, which appears in the new historical investigation of the Delta. destination. This was, of course, an- Courtesy SFEI. noying and a great waste of time... the river commenced to rise again. By this at low tide that has never been before. It was not until the river began to natural phenomenon the river was In some places whole acres are mud fall that it was noticed there was some- navigable at all hours. flats that used to be covered with water thing wrong. It really seemed as if the at all times. bottom was coming toward the top... “But now things have changed,” This was puzzling for awhile, and said Pilot Arthur Robinson yesterday, “The result of this has caused steam- then it was found that in making their “and the water runs through those boat pilots trouble all during the sum- calculations for the cuts the engineers cuts at low tide as it would out of a tin mer... In those cuts there is not more had overlooked the effect on the tide. pan. The tide now falls over three feet than four feet of water at low tide, at Stockton, and at Twenty-one Mile which is not enough for large steamers. In the old days, when the river Slough it falls nearly five feet... In many spots there is not more than twisted like a snake, the rise and fall “All along the river the effect of the that at high tide.” of the tide in the bay did not make a difference in the San Joaquin between cuts can be seen, as land is uncovered 4 NOVEMBER 2012 ESTUARY NEWS volunteer work OBSERVATIONS

Japan Buoys Arrive Of Geese and Eelgrass It’s not a question of if, but when. It’s a clear evening on the cusp of to understand why they act differ- And when it does arrive, volunteers autumn, and the eelgrass brigade is ently here than in their native range,” will be there to track it, providing walking on water. The surface of San Boyer says. valuable data to scientists about Francisco Bay reflects the miracle To find out, Boyer and Kiriakopolos debris originating from the tsunami like a mirror: Six people in are setting up a series of experimen- in Fukushima, Japan, in March 2011. are balancing white pvc pipes on their tal plots just offshore. The first wave of debris is already shoulders as they step through the beginning to wash up on Northern receding tide. They’re taking advan- Some plots will exclude geese; California beaches: during a state- tage of the evening low tide to study a others, both geese and amphipods; wide Coastal Cleanup Day organized peculiar meadow of Zostera marina that while control plots will remain com- by the California Coastal Commission grows alongside Alameda. pletely open. on September 15, items sent to sea by the tsunami were found in Santa Most of the eelgrass that grows in This work is part of a global project Cruz County (a buoy) and Mendocino Bay shallows is perennial—it stays examining the factors that affect eel- County (buoys and plastic bottles). alive for two years or more. But the grass growth. Because this species In early 2013, shepherded by winter majority of the plants at Crown Beach is so important to shoreline habitats, storms, a larger volume of debris is flower, set seed, and die by Decem- the Zostera Experimental Network expected to reach the Bay Area, says ber, then sprout afresh from seed involves 15 other sites ranging from Coastal Commission outreach manag- every spring. Responsibility for this Japan to Finland to British Columbia. er Eben Schwartz. To keep tabs on the state of affairs lies at the webbed feet of Canada geese. Graduate student On this evening, the researchers material, the commission has begun head out in pairs to erect the plots. distributing special data cards that al- Stephanie Kiriakopolos and Katharyn Boyer, a San Francisco State Univer- One person kneels down in the shal- low beachcombers to record sightings low wavelets, placing a triangular of construction debris, consumer de- sity professor of ecology, have found that migrating geese mow down so template on the bay floor. The other bris with Japanese text, fishing gear, pushes a pipe into the packed sand and miscellaneous items. While debris much Crown Beach eelgrass each autumn that few perennial plants at each vertex to form the corners of is certain to reach coastal beaches in the plot. San Francisco, San Mateo, and Marin survive. “This is the first time an her- counties, it’s unlikely much will pass bivore has been shown to be respon- Working in the pool of light from through the Golden Gate, Schwartz sible for the tipping point between her headlamp, Kiriakopolos gathers says. “We find very few items that are a plant population being annual or green ribbons of eelgrass inside the typical of ocean debris in San Fran- perennial,” Kiriakopolos says. plot before securing lengths of plastic cisco Bay,” he said. To play a part in Native geese aren’t the only her- fencing around the pipes. The plots the debris-tracking effort, then, better bivores that devour eelgrass in San will remain up for two months, giving head west. NS Francisco Bay. An invasive amphi- grazers an ample window to do their pod (a type of marine crustacean damage. A breeze plays over the open resembling a sowbug) from the East tops of the plot pipes, emitting a soft howl as an orange crescent Bird Poll Coast, Ampithoe valida, may also be rises overhead. KW It’s census time for California’s hurting local eelgrass acreage. “The shorebirds. On November 15, profes- amphipods actually eat the Zostera. Contact Stephanie Kiriakopolos, sional ornithologists and amateur But they don’t eat eelgrass in their [email protected] native range, only macroalgae that birders hit the beaches and mud- flats of San Francisco Bay to count grows alone or on eelgrass. We want sandpipers, plovers, willets, godwits, curlews, and dowitchers as part of the annual Pacific Flyway Shore- bird Survey. Other coastal estuaries and Central Valley locations will be covered through mid-December. PRBO Conservation Science biologist Matt Reiter says training in shorebird identification and enumeration will be provided for volunteers. Data col- lected from Washington State to Baja California should help clarify popula- tion trends of these birds, which can be sensitive indicators of environ- mental quality. JE

More: data.prbo.org/apps/pfss/index.php Photo: Stephanie Kiriakopolos 5 monitoring Four Decades of Bay Discoveries

A federal top dog once asked Jim its sediment supply and introduction becomes almost a new system in terms Cloern just how long he needed to of non-native species, as well as the of ecosystem functioning,” says Jassby. study San Francisco Bay before he ongoing use of the Bay for sewage The paper describes shifts in the “figured it out.” Thirty years seemed disposal. Less obvious, perhaps, have timing and extent of freshwater inflow plenty long enough to the guy asking been two other drivers of change: en- and the intrusion of salt water further the question. But Cloern’s answer, vironmental policy on both federal and upstream into the estuary. It details both then and now a decade later, is local levels, ranging from the Clean the gradual decrease in , the same: “When it stops changing.” Water Act to the state’s curbs on bal- last water discharges and “X2” stan- as more sediment eroded from the San Francisco Bay’s monitoring dard, which protects the estuary’s low- watershed remains trapped behind records of both biological communi- salinity habitats; and climate shifts dams, and as the vast amount un- ties and environmental conditions are associated with major rearrangements leashed by hydraulic gold mining in the among the longest-running and most of ocean currents and prior century finally washes through. comprehensive assembled for any beyond the Golden Gate. It talks about the restructuring of estuary in the world, thanks in part plankton communities, and resulting to scientists like the U.S. Geological loss of food supply for endangered Survey’s Cloern, who’ve fought year- ALIEN Clams Reinvent pelagic fish, as a result of the invasion in-year-out to keep the boats out on Food Web of Suisun Bay by an alien clam. And it the water, and the gages and gizmos delves into the region’s water quality running, that measure everything 8000 A history, among other topics. from salinity to plankton growth to “Today’s bay system is a very dif- how cloudy the water is and how 4000 ferent from the one that existed in much runoff from the Sierras reaches 0 1976 when I started studying it,” says the sea. And every time Cloern is Cloern. “The shoreline is different, sure he’s figured it out, something 15 B because of changes like salt pond changes. The changes he thought restoration work. The shape of the bay he’d pretty much figured out were the 10 floor is different — the bay is losing ones caused by humans – the dams, 5 sediments and getting deeper. The the diversions, the invasions… But sediment supply to the estuary is half the big surprise came in 1999, and it 60 C what it was in 1950s. Some biologi- had nothing to do with any of these 40 cal communities in Suisun Bay are activities. 20 unrecognizable from those that existed “I’m not sure there’s another bay 0 30 years ago. And although we haven’t or estuary around the world where seen as many changes in which spe- 2.0 there is as clean a signal, or a signal D cies are present in the South Bay, the 1.5 as well supported by data, showing 1.0 relative abundances of common spe- how biological communities became 0.5 cies now are distinctly different from transformed in a short period time, a 0.0 those prior to 1999. At the same time, couple years, by a major climate shift,” major water-quality problems like says Cloern. “These are the kinds of 120 E below the Dumbarton Bridge, processes, these natural cycles in the 80 or high metal in sedi- climate system with periods of 20-40 40 ments and organisms, which plagued years, that you can only understand if 0 the South Bay in the 1960s and 70s, you’ve been measuring for a period of 1980 1990 2000 2010 are now largely gone. So there are time that’s as long, or longer, than the good news stories and bad news sto- period of the process.” Response of the planktonic food web ries, but collectively they depict a bay in Suisun Bay to the introduced clam, that is very different from the bay of Corbula amurensis. (A) Corbula abundance. After 37 years of study Cloern has 1876 or even 1976.” figured a few things out. In an eloquent (B) Phytoplankton biomass as chlorophyll a new paper published this October in . (C) Density of the rotifer What factors drove the estuary to Reviews of Geophysics, he and veteran UC Synchaeta bicornis. (D) Density of the change so much in such a short time Davis estuarine scientist Alan Jassby copepod Eurytemora affinis. (E) Density of period? A brief survey of the paper’s the mysid shrimp Neomysis mercedis. The summarize how environmental condi- horizontal line in Figures 11b–11e is the long- findings follows, but this reviewer rec- tions in the estuary have changed term mean. Source: Cloern & Jassby, 2012 ommends taking a few hours to read since the 1950s, and highlight the six the paper itself. There are few places driving behind this change. in the gigabytes of research about the These “drivers” are familiar players “The estuary never ceases to San Francisco estuary where so much in California’s water wars and ecosys- change, but not just in a so-called is said so well in so few pages — even tem management endeavors – human stationary way, which is a statistical if there is the occasional daunting consumption and diversion of the term meaning with some fixed mean equation. and variance, but every now and then it estuary’s fresh water, modification of continued to page 6 6 NOVEMBER 2012 ESTUARY NEWS

MONITORING, continued from page 5 Another challenge to the health zooplankton helped lead to losses of of native fishes and the ecosystem is the native fish that eat them, as the One of the far-reaching altera- driver #3, introduced species. As inter- fish searched for food elsewhere, in tions to the estuary is the capture and national commerce has trans-located less suitable habitats, or settled for diversion of fresh water before it flows microbes, plants and animals across eating less nourishing aliens. These into San Francisco Bay — driver #1 the planet, they’ve become a powerful ecosystem disruptions by invaders discussed in the paper. Not only is less component of ecological change. have been so well documented here freshwater flowing through the estuary in San Francisco Bay that they helped today — about two thirds of unimpaired motivate passage of some of the coun- flows — but it’s also flowing through try’s toughest ballast water treatment later than it did naturally, in the dry regulations. rather than wet part of the year. Tough clean water regulations In response to freshwater exports, helped rid South San Francisco Bay of the estuary’s salinity gradient has the worst of the environmental effects shifted landward (upstream), and salty of driver #4: sewage inputs. Sewage water now intrudes farther into the contains an array of pollutants, includ- Delta in certain months than it did ing nutrients (nitrogen and phospho- historically, especially during autumn rus), organic matter, toxic metals, when it’s dry. The authors note how pharmaceuticals, and pathogens that these changes within estuarine waters Photo: Cary Burns Lopez pose risks to human and ecosystem have contributed to the disruption of health. To get a sense of the scale, the the biological communities living in The diatom Thalassiosira rotula was the South Bay alone receives 500,000 cubic them, to the extent that the popula- number 1 ranked species contributing to meters of municipal wastewater an- tions of many native species, from the phytoplankton biomass in San Francisco nually from about 12 treatment plants tiniest plankton to larger fish, are on Bay until the 1999 climate shift. After 1999 serving four million people. Treatment the wane. the number 1 ranked species has been removes many pollutants, but nutrients another diatom, Thalassiosira punctigera, remain a pressing concern. The discussion of driver #2 revolves which was never seen in the Bay until then. around sediment. Ever since the Gold The authors report that sewage discharges deliver 11,200 tons of ni- Rush, human activities ranging from The authors describe one local trogen and 1,860 tons of phosphorus in hydraulic gold mining to the construc- example. In 1986, scientists speculate dissolved inorganic forms (called “DIN tion of dams and dikes have changed that a ship brought the larvae of a and DIP”) to the South Bay annually. the estuary’s sediment supply. The clam with Asian origins to San Fran- Indeed South Bay nutrient levels are supply has halved since the mid-19th cisco Bay in its ballast water. By 1988, century, when an ocean of mud from 7-10 times those measured in more Corbula amurensis, (sometimes called mining in the Sierra foothills washed rural bays along the West Coast, the “overbite clam” for its larger downstream. Indeed, comparisons of according to the paper. Based on top shell), dominated the benthic bathymetric charts confirm that from these high N and P concentrations, the community in Suisun Bay, reaching 1856 to 1887 some regions of San South Bay has the potential to produce abundances as high as 16,000 indi- Pablo Bay accumulated more than phytoplankton biomass at levels that viduals per square meter. It colonized four meters of sediment, and inter- severely impair other nutrient-enriched a vacant niche, and flourished because tidal mudflats expanded by 60 percent. estuaries like Chesapeake Bay on the it could handle variable salinities and The sediment supply peaked at about coast of Maryland and Virginia. use a broad range of food resources. 12 million metric tons per year in late Indeed it is so efficient at filtering Until recently, South San Francisco 19th century, then declined to less food out of the water column that its Bay’s strong tidal currents, turbid- than one million metric tons per year annual mean filtration rate of Suisun ity, and hungry clam population have today, the authors note. Bay is about twice the growth rate of saved it from algae blooms and other With a 50 percent drop in sus- the phytoplankton it’s eating. Corbula ecological problems triggered by an pended sediment concentrations, light has reduced phytoplankton biomass excess of nutrients in the water, but penetration into the water has almost and primary production in Suisun Bay “this resistance is weakening,” write doubled in some locations, the au- fivefold, limiting what herbivorous the authors. thors write. With more sunlight, algae zooplankton have left to eat. “The amount of phytoplankton growth rates are probably higher than Added on top of other stresses in the South Bay is now three times in the past, raising the spectre of on the food web caused by altered higher during the dry season than blooms that steal the from the freshwater inflows and intruding salt it was ten years ago,” says Cloern. water and suffocate fish, but also the water (the two previous drivers de- “The question now is what trajectory potential for a stronger food supply for scribed), an alarming trend emerges. will this follow in 5, 10, 15 years, and estuarine communities. Water clarity The authors detail an unprecedented will we ever reach some tipping point also affects predator-prey relation- restructuring of the Suisun Bay zoo- where nutrients are converted more ships and can change habitat quality plankton community since the 1970s, efficiently into living phytoplankton for native fish species. An index of from one having large components biomass, and start generating the habitat suitability for delta smelt, for of mysid shrimp, rotifiers, and cala- classic water quality problems seen example, declined 78 percent between noid copepods to one dominated by in Chesapeake Bay.” 1967 and 2008 as a response to trends East Asian cyclopoid copepods (see in increasing water clarity and salinity. chart, p.5). Losses of these native continued to page 11 7

management duce low-oxygen water to the sloughs at the same time, or to delay flooding when tidal mixing is low and tempera- tures are high. Another is shifting from Duck Ponds Run Afoul green and leafy vegetation like cocklebur There’s too much mercury and too “We’ve focused on working with land- and fat hen to grasses, including timo- little oxygen in some of the drainage owners to modify management prac- thy and bulrushes. The District’s three from Suisun Marsh duck ponds, leav- tices,” says Chappell. The 2011 report water managers have been working with ing public and private land managers reviewed 19 potential best management club managers. “Some landowners are experimenting with alternate manage- practices (BMPs), 14 for water op- reluctant to have government scientists ment practices. Suisun Marsh has been erations and five for soil and vegetation on their land,” Chappell adds. “We try to a magnet for duck hunters since the management, and recommended further reinforce with them that improved BMPs 1850s and through the decades duck study and case-by-case evaluation. are in everyone’s interest—good for the clubs have kept key parcels preserved Future actions may include field tests of marsh and the wildlife.” JE from development and also provided selected BMPs and a review of the DO Contact Steve Chappell, habitat for non-game wildlife and migra- standards for Suisun. [email protected]; tory waterbirds. The drainage problem Teejay Orear, [email protected] occurs in the fall, when water used to One option is to coordinate drainage flood managed seasonal wetlands is operations so multiple clubs don’t intro- discharged into neighboring sloughs. According to Steve Chappell of the SPECIES lumne River in the Sierra foothills. Suisun Resource Conservation District, SPOT Several have been observed in the Bay, at this time of year, warm temperatures off Sausalito, Richmond, and Alameda. cause rapid decomposition of vegeta- “They definitely use salt water, almost tion in ponds, while anemic tides fail to Wanted: as much as fresh,” says Isadore. Ot- exchange resulting low oxygen water ters have visited lakes in several East from the ponds with more oxygenated Otter Spotters Bay Regional Parks and dropped by water from the Bay. Under these condi- North American river otters have the beaver pond on Alhambra Creek in tions, “Some of the discharges into small charisma to burn. Biologists know Martinez. Beyond spotter reports, Isa- dead-end sloughs depress dissolved relatively little about their lifestyles, dore and Bouley use remote cameras oxygen in the system,” he says. The distribution, and population trends in to record behavior and analyze otter phenomenon mainly occurs in Peytonia, the Bay Area, though. Megan Isadore scat (“spraints” to the British) to docu- Boynton, and Goodyear Sloughs, tribu- and Paola Bouley, co-founders of ment seasonal prey preferences. They taries to Suisun Slough, he says. the River Otter Ecology Project, hope want reports of dead as well as living The water returning to the marsh’s to change that with the aid of “Otter otters to help map casualties at street sloughs may not only be low in dissolved Spotters” who report their sightings to crossings so habitat corridors can be oxygen (DO), but also high in methyl- the nonprofit’s web site, where they’re protected. mercury, a chemical cousin of the Gold posted on an interactive map. The River Otter Ecology Project re- Rush era quicksilver lurking in the mud. “In Marin County, people report cently obtained tax-exempt status. The Methylmercury, formed when anaero- seeing otters more and more often,” program has been funded by grants bic bacteria in wetlands gets to work Isadore says. Since the aquatic mam- and donations, including one from the on legacy mercury, is a neurotoxin that mals are sensitive to pollution, that Rose Foundation. Isadore expects to bioaccumulates in food webs. Methyl- could be good news for the health begin publishing results in late 2013. mercury can be harmful to fishing birds, of local streams. But there is little humans and other apex predators. Why otters? “River otters are baseline data about otter history in the highly dependent upon clean water Low DO events, according to a 2011 Bay Area. Clearly, historic fur trapping with plenty of fish,” says Bouley. “The report by Stuart Seigel of Wetlands and reduced their numbers. None were same conditions that make for healthy Water Resources and other scientists, seen in Marin from the 60s into the ‘ottersheds’ make for healthy human “eliminate the fishes and invertebrates 80s, when naturalist Rich Stallcup habitat. Their return so close to large in the sloughs affected.” It may take discovered a population on Walker cities illustrates just how adaptable months before “desirable” fish—na- Creek near Tomales Bay. and resilient wildlife can be.” JE tive species and popular introduced Although the web site has only been Contact Megan Isadore, game fish like striped bass—move back up since February, sightings have in. Fish and other organisms that can [email protected] come in from as far north as the Lost Web: www.riverotterecology.org tolerate low DO are mostly exotics: carp, Coast and as far inland as the Moke- catfish, Black Sea jellyfish. Fish kills ascribed to low DO were first documented in 1999 and have recurred through 2009. UC Davis biologist Teejay Orear says that although there were low- oxygen events in Peytonia and Goodyear last year, the decline was slow enough to allow most fish to escape from the

affected areas. Photo: Paola Bouley 8 NOVEMBER 2012 ESTUARY NEWS

only a year-round resident in riparian Chain of Habitats Snapshots areas and has a small home range, UC Davis fish biologists call it the of but it is also widespread and abun- North Delta Arc: a chain of aquatic Bay-Delta dant, easy to capture, and sensitive habitats from Suisun Marsh to the to mercury. The song sparrow feeds Sacramento Deep Water Ship Chan- Science primarily on insects and other arthro- nel. It seems to be a kind of “Noah’s pods during its breeding season and Ark” as well, where native fish species bioaccumulates methylmercury that still outnumber invasives. At the con- Just over a thousand scientists, its prey acquires from streamwater. ference, John Durand pointed out that policymakers, and others packed the Robinson said its diet includes insect- the area is also on everyone’s radar as Sacramento Convention Center in eating spiders and the emergent a site for habitat restoration under the mid-October for the 7th Biennial Bay- forms of insects that have an aquatic Bay-Delta Conservation Plan. Denise Delta Science Conference (formerly stage. Preliminary data shows a range De Carion said fish abundance and the CALFED Science Conference.) The of 0.01 to 2.7 parts per million in local species richness were especially high three-day event, with the theme of sparrows, with highest concentrations in Cache and Lindsey Sloughs and “Ecosystem Reconciliation: Realities along the Upper Guadalupe River. the Deep Water Ship Channel, where Facing the San Francisco Estuary,” “These are very urban sites where more than half the species recorded featured 240 speakers, 150 poster populations are already impacted by were natives. Non-native nearshore exhibits, and the presentation of the non-native predator, habitat loss, and fish, booming elsewhere in the Delta, Brown-Nichols Science Award to Wim human disturbance,” she explained. accounted for small percentages at Kimmerer (San Francisco State Uni- The upper levels have been associated these sites. “Something is allowing versity Romberg Tiburon Center) and with a 25 percent reduction in breed- natives to persist in the presence of Jim Cloern (U.S. Geological Survey). ing success in an eastern songbird, non-natives,” she concluded. The Here are a few stories that emerged the Carolina wren. JE Davis team plans to look at fine-scale from the presentations. habitat characteristics and trophic interactions for clues that might guide The Two Faces of Smelt restoration efforts. James Hobbs has Submerged Surprise Two conference presentations looked been using the chemical composition Scanning GoogleEarth images of at the endangered delta smelt in a of delta smelt otoliths (ear bones) to Suisun Bay a couple of years ago, food web context, as predator and reconstruct their migration history. He California Department of Water prey. What the smelt are eating, reported that some smelt are per- Resources engineer Chris Enright according to Aaron Johnson of San manent residents in the Arc’s fresh spotted something unexpected: large Francisco State University’s Romberg waters despite warm summer tem- beds of submerged aquatic vegetation Tiburon Center, came as a surprise. peratures. That’s the good news. The along islands and on offshore shoals. Thought to bad, relayed by Peter Moyle, is that Katharyn Boyer of SFSU’s Romberg rely mainly some of the Arc’s native species are Tiburon Center identified the plants on the small at risk of extinction. Moyle calculated as native pondweeds, Stuckenia filiformis crustaceans separate scores for baseline vulner- and S. pectinata. “They’ve probably been called cala- ability to extinction and vulnerability present for a long time, just not no- noid cope- with projected climate change. “Fish ticed,” said Boyer at the conference, pods, the adult smelt sampled by have low adaptive capacity to move referencing an 1886 map and a 1937 Johnson at a Sacramento River site around,” said Moyle. “Fish can’t fly aerial photo. Her survey verified at favored amphipods, which accounted north. A lot of the natives are highly least 1,100 acres covered by Stuckenia for two-thirds of their diet by . vulnerable to climate change, but and indicated the beds are expanding Most of the amphipods were benthic many non-natives will do just fine be- within Suisun Bay and the West Delta. species. “If it’s a shift, is it short- cause they’re already well adapted to “Native submerged aquatic vegetation term or a function of larger food web human-created environments.” Delta is a very turbid environment and may changes?” he asked. It could reflect smelt (critically vulnerable with a high be a positive benefit for native fish,” the decline of mysids, another class of probability of extinction) and common she added. In a conference poster with smelt prey. Johnson’s study was the carp (indestructible) represent the Evyan Borgnis, Boyer also projected first to examine smelt feeding habits extremes. In between, some natives that S. filiformismay outcompete the over hourly and tidal time frames. should respond to careful manage- exotic Egeria densa as the West Delta Meanwhile, what’s eating the smelt? ment: “One of the places where becomes saltier. JE UC Davis graduate student Scott positive action is possible is the North Brandl is using mitochondrial DNA Delta Arc.” JE barcoding to identify smelt remains in the guts of predatory fish. So far, 69 Contact Denise De Carion, dpde- Biosentinel Sparrows of a sample of 559 exotic Mississippi [email protected]; John Durand, The canary in the coal mine has a new silversides have tested positive for [email protected]; James Hobbs, colleague: the song sparrow, recently smelt. Predation appears less com- [email protected]; Peter Moyle, chosen as a biosentinel species for mon in turbid waters. This winter, the [email protected]; Katharyn methylmercury contamination in the project will be extended to striped, Boyer, [email protected]; April Rob- Bay Area’s riparian food webs. At the largemouth, and smallmouth bass inson, [email protected]; Aaron Johnson, conference, April Robinson of the San and Sacramento pikeminnow to com- [email protected]; Scott Francisco Estuary Institute explained pare predation on smelt by native and Brandl, [email protected] that this common native songbird non-native fish. JE offered several advantages. It’s not 9

C O N F E R E N C E Speaking Different Languages Conducting science in the Delta, not define it.” Christina Swanson from Panelist Ren Lohoefener, Pacific at the confluence of the livelihoods of the Natural Resources Defense Council Southwest Regional Director of the millions of human and non-human Cal- commented, “You will rarely get a U.S. Fish and Wildlife Service agreed. ifornians, has always been a challenge. scientist to say ‘this is what you should “If we can’t find a way to be open and While the region is still a dimly-lit terra do.’ They don’t think that’s what their transparent and collaborative, we’re incognita in the mental map of many job is. Science is an emergent process. not going to succeed.” Californians, in terms of water politics It is never done.” She said there was a it is under such an intense spotlight need for “a translator or interface” and After the conference, Goodwin said that research here has to withstand as that non-governmental organizations he was pleased with the town hall and much heat as light. When a scientist like hers were one kind of interpreter. ensuing hallway conversations. After publishes a study with narrow and reviewing audience surveys, he said carefully considered conclusions on, Jim Cloern, a senior ecologist with many participants agreed on the need say, stressors affecting a species, the the U.S. Geological Survey, was ready for “doing something bold” to improve interpretation of those results may to try a new approach. “There’s a real the science-policy interface. “People take on a political life of their own, of- breakdown in the system. We need to were saying, let’s try and do some ten beyond the control of the investiga- revolutionize the way scientists and large action in the Delta where we can tor. On the other hand, scientists who policymakers communicate,” he said. really create a change” of sufficient wish to conduct more broadly designed Later, Cloern explained that he thinks scope to provide meaningful results. research aimed at informing policy say scientists and policymakers should be Early communication between scien- this work is sometimes ignored. collaborating early in the conceptual- tists and policymakers and well-funded ization of research, so that results are monitoring would need to be part of the At the recent Bay-Delta Science more useful in shaping eventual action project. “The most important idea was, Conference, Peter Goodwin, the Lead in the Delta. While the independence if we really want to change the way we Scientist for the Delta Stewardship of the conclusions of scientists must be do things, we need to create a single Council, organized a “town hall” meet- protected, the design of the research science vision and a science plan that ing to brainstorm to these could benefit from early feedback, he everyone can participate in and con- long-standing issues. At the packed said. “The reason why our science isn’t tribute to… [We need] the ability to lunchtime session, policymakers were being used is [that scientists and poli- look across larger spatial scales and at seated in a panel at the front of the cymakers] live in different worlds. We whole system functions, and not just at room, and scientists had an open mike need to join the same universe.” the corner we’re responsible for.” SKM in the audience. Both friendly sugges- tions and pointed barbs flew. Panelist Randy Fiorini, a Turlock FRONT farmer and board member of the Delta Stewardship Council, said he ROW was looking for a “master model” for the Delta instead of the many discon- nected models now being used to A Milestone analyze ecosystem and water supply Breach functions. Fiorini said it was essen- tial to fund monitoring of projects and A cheer went up on October 31st experiments so their impact could be as one more levee was breached at the South Bay Salt Pond Restoration assessed. He also said he was look- Photo: Susan K. Moffat ing for more collaboration in framing Project. As a crowd of 100 applauded, a backhoe bit into a half-century old scientific research: “I propose we try a A17 will be allowed to revegetate dike in Alviso to let Bay water pour new model that involves policymakers naturally into marsh. By contrast, for from Coyote Creek into Pond A17 from the start.” shorebirds such as American avocets, at the Don Edwards San Francisco black-necked stilts, and western Like Fiorini, Director of the Depart- Bay National Wildlife Refuge. Poked snowy plovers, A16 will be carefully ment of Water Resources Mark Cowin through on the 40th anniversary of managed as a shallow, largely plant- asked for more clarity from scientists. the Refuge, the breach represents an free pond with sixteen constructed “Policymakers need a better under- important milestone for the res- islands for nesting. A water gate standing of what we know and don’t toration project, bringing the total will be carefully calibrated to let just know — and what the level of uncer- number of acres in active restora- enough water flow from A17 into A16 tainty is — as we incorporate informa- tion to 3,200 out of 15,100 eventually to maintain a water depth of 6 to 12 tion into the economy versus environ- planned. Pond A17 is paired with its inches in one large section of the ment decisions,” he said. neighbor to the south, Pond A16, to pond to meet the needs of the shore- meet the needs of creatures with dif- Scientists came up to the micro- birds who prefer shallow open water ferent habitat needs. For the clapper phone to push back, with one saying it to marshes. SKM was his job “to investigate uncertainty, rail and salt marsh harvest mouse, continued to back page 10 NOVEMBER 2012 ESTUARY NEWS POLL U TION

A Cautionary Tale about Caulk Everyone’s seen buildings shroud- The Institute also developed a sary removal, to the demolition and ed in black netting or white plastic, rough estimate of the mass of con- remodeling permits administered by and heard the hum of industrial taminated caulk contained in build- municipal planning or building de- strength vacuums hoovering up chips ings in their study area (four counties partments. Under this model, PCB of lead-laden paint and other toxic and three cities with large sectors screening would apply to multi-story substances shed by remodeling and developed during the PCB usage buildings (generally commercial construction. The purpose of all this period). Using GIS models, historic and industrial), but not to single- effort is to keep such imagery, and land use family homes (PCB containing caulk substances out of the data, they computed a is unlikely to have been used in such air and urban runoff mid-level estimate of homes). into the Bay. The S.F. a total mass of 10,500 Estuary Partnership kilograms of PCBs in Filling in the details, consultants recently put the wraps caulk in these build- including Larry Walker Associates, on a three-year- ings, or an average of Geosyntec, and TDC Environmental project that might add 4.7 kg per building. If created various screening and as- one more substance to all the PCB-containing sessment tools to identify PCB con- these cautionary scrap caulk from just one taminated buildings, outlined clean up piles: caulk. such building got loose and runoff prevention plan steps for during demolition and builders, and laid out a clear process Not just any washed into the Bay, for cities and counties to work with caulk: only caulk used the amount would be EPA on certification and approval. between the 1950s and Photo: Ariel Okamoto more than twice that 1980s to seal up joints “It looks like caulk in our older allowed by water qual- and seams between walls, windows, buildings could be contributing to ity regulators for urban runoff from and bricks, and most often employed PCBs in urban runoff, and, impor- the entire Bay Area. in concrete and masonry buildings. tantly, this source of PCBs is control- This was the period when builders The news is not all bad. Builders lable,” says Jan O’Hara of the S.F. Bay mixed PCBs —polychlorinated biphe- and demo crews can prevent PCB run- Regional Water Quality Control Board. nyls now banned because they are off by taking steps already prevalent The model ordinance would offer suspected human carcinogens — into in the construction trade today. Such another tool for helping cities reduce some caulks to increase flexibility. “best management practices” include the PCBs that are discharged to their carefully removing contaminated The project team started with a storm drain systems and eventually caulk, attaching vacuums to tools focus on building exteriors. “We were flow untreated to the Bay. The Bay used for grinding concrete or masonry looking for materials that had a nexus Area’s municipal regional stormwater substrate formerly in contact with to the outdoors, where there might be permit, issued in 2009 by the regional caulk, and collecting dust and debris a connection to urban runoff,” says the board, required permittees to inves- on plastic drop cloths. To carry out Partnership’s project manager Athena tigate a variety of PCB control mea- such tasks, workers should also wear Honore. The team was also interested sures. Once investigations are com- masks and protective clothing. in building demolition, because it of- plete, all these measures and tools fered a logical opportunity to capture “The PCBs in caulk problem is just will be considered when requirements PCB-containing materials before they starting to hit the building and demoli- for the next permit term, beginning in entered the surrounding watershed. tion industry’s radar,” says Honore. 2014, are proposed. ARO Athena Honore, ahonore As a first step, the Partnership The second wave of the Partner- CONTACT @ waterboards.ca.gov; Jan O’Hara, asked the S.F. Estuary Institute to ship’s project involved developing a johara waterboards.ca.gov determine to whether any Bay Area regional model for how municipalities @ buildings might contain caulk with could tackle the problem, adding a PCB-levels as bad as those that raised step for PCB screening, and if neces- red flags in East Coast buildings. In a report released in November 2011, the PCBs in caulk findings Institute, a project partner, confirmed the prevalence of PCBs in standing Samples analyzed for PCBs 25 Bay Area buildings constructed during the period of PCB usage. They de- Number of buildings sampled 10 tected PCBs in 88 percent of 25 caulk Samples in which PCBs detected 88% (detection limit:≥25 parts per million, or ppm) samples collected from exteriors of Range of PCB concentrations in caulk 1-220,000 ppm — 20% of samples >10,000ppm ten buildings. Of these, 40 percent exceeded concentrations of 50 parts Source: [1] Klosterhaus, S., Yee D., Kass, J., Wong, A., McKee L. 2011. PCBs in Caulk Project: per million (the concentration where Estimated Stock in Currently Standing Buildings in a San Francisco Bay Study Area and EPA remediation regulations kick in). Releases to Stormwater During Renovation and Demolition. SFEI Contribution 651. San Francisco Estuary Institute, Oakland, CA. 49 pp. The highest concentration found was 220,000 ppm. 11

MONITORING, continued from page 6 ful a driver of change inside estuaries Ocean Cool Down Triggers as human activities and watershed While human activities have deeply Trophic Cascade processes on land and upstream. undercut the integrity of our estuarine ecosystem, they’ve also helped protect 1990-1998 2000-2010 One refreshing part of this paper is how the authors are able to compare it with strong environmental policies OCEAN C NPGO San Francisco Bay to conditions in — driver #5 — such as the 1972 Clean Index 2 A Water Act. Before the act, rivers like estuaries worldwide – most of which 1 are as bedeviled by water diversions, Cleveland’s Cuyahoga were so polluted ONDITIONS 0 they caught fire, and in San Francisco sediment shifts, contaminants, invad- -1 Bay, fish kills were common and toxic ers, and climate variability as ours. metal levels in clams among the high- -2 These types of comparisons would not

PDO OCEAN C Index be possible without long term data est in the world. The authors reviewed B data from sampling programs before from research and monitoring pro- 1 grams here in our estuary (such as and after the Act to show how these Photo: Julia Stalker 0 policies helped the Bay recover from ONDITIONS those championed by IEP, USGS and sewage-derived pollutants, among -1 SFEI), and without the commitment of other challenges. Monthly sampling of experienced scientists like Cloern and clams once so impacted by the cop- Jassby to analyze them. per and silver in Bay waters they could SST “When you come across a data set, C not reproduce, for example, showed 13.5 and it’s got some critical years miss- a distinct recovery after local sewage 13.0 ing, it can be exasperating,” says Jass- plants began using more advanced 12.5 by. “Look at some of the older records, treatment processes mandated by 12.0 like the cherry tree flowering records Congress. Today, however, the stan- in Kyoto, which go back to the 9th cen- dards set by the Clean Water Act “have Index tury. These records, which can be used not been fully met,” write the authors. 120 D as a surrogate for spring , A 2004 assessment of 141 estuaries 100 have revealed all kinds of interesting in the United States determined that 80 solar-cycle-related and other varia- the majority still have moderate to 60 tions that are of interest to climate high symptoms of excessive nutrient 40 scientists. This is an inspiration for the effects, for example. time scale we’ve really got to think about for San Francisco Bay — long The last driver Cloern and Jassby RESPONSE OF BIOT Fish discuss operates on a much larger CPUE E term, indefinite, generations down the line.” ARO scale than our human engineered 500 dams, invasions, discharges and other 300 CONTACT James Cloern, effects: the ocean-atmosphere sys- [email protected] or Alan Jassby, tem. While fishermen have long noted 100 [email protected]. how some species favor warm or cool Crabs periods out in the ocean, scientists CPUE F Paper: http://www.agu.org/ 8 journals/rg/rg1204/2012RG000397/ are only recently figuring out just how A strongly changes in ocean and climate 2012RG000397.pdf 4 conditions out in the Pacific affect the Cloern, J. E., and A. D. Jassby species that live in San Francisco Bay. 0 (2012), Drivers of change in estuarine- And the reason it took them so long to Shrimp coastal ecosystems: Discoveries from figure it out is that these changes only CPUE G four decades of study in San Francisco occur every 20-40 years. Bay, Reviews of Geophysics, 50, RG4001, 1000 doi:10.1029/2012RG000397 “There’s always going to be sur- 500 prises, things we can’t forecast that happen at time scales longer than our 0 Time series of annual mean climate indices, monitoring record,” says Jassby. ocean conditions near the mouth of San Fran- Clams cisco Bay, and annual mean abundances of The authors explore the major -2 gDW m H various biota within San Francisco Bay, “regime shift” that occurred in the late shown as anomalies about the long-term 1990s when atmospheric , 10 means. (A) North Pacific Gyre Oscillation and wind patterns, ocean temperatures 5 (B) Pacific Decadal Oscillation (ocean-atmo- and biological productivity (upwell- sphere changes). (C) Sea surface tempera- ing of nutrients and plankton growth) 0 ture at Farallon Islands. (D) Upwelling index. all changed in the Pacific offshore. Sum of catches per unit effort (or “CPUE”) in Surface waters cooled and upwelling South, Central, and San Pablo bays for (E) five Phytoplankton species of demersal fish, (F) three species increased. As the Northeast Pacific I 8 of crabs, and (G) two species of shrimp. (H) shifted from a warm phase to a cool Dry weight of clams from South Bay sampling 6 phase, the biological communities in sites. (I) Annual mean phytoplankton biomass the Bay shifted too (see charts). The 4 (chlorophyll a) in South Bay surface waters. authors suggest that variability in 2 Source: Cloern & Jassby, 2012 coastal oceans can be just as power- 5c) best for onscreen (and JPGs, PPT, o ce printers, etc) fonts as outlines

SAN FRANCISCO San Francisco Estuary Partnership return service requested 1515 Clay Street, Suite 1400 presorted Oakland, CA 94612 FIRST-CLASS www.sfestuary.org MAIL U.S. Postage San Francisco Bay and the Sacramento-San Joaquin River P A I D ESTUARY Delta comprise one of 28 PARTNERSHIP “estuaries of national significance” Oakland, CA recognized in the federal Clean Permit No. 832 Water Act. The San Francisco Estuary Partnership, a National Estuary Program, is partially funded by annual appropriations from Congress. The Partnership’s mandate is to protect, restore, and enhance water quality and 5c) black/white habitatfonts inas the outlines Estuary. To accomplish this, the Partnership brings together resource agencies, non-profits, citizens, SAN FRANCISCO and scientists committed to the long-term health and preservation of this invaluable public resource. Our staff manages or oversees more than 50 projects ranging from supporting research into key water quality concerns to managing initiatives that prevent pollution, restore wetlands, or protect against the changes anticipated from climate change in our region. We have published Estuary News since 1993. ESTUARY PARTNERSHIP ESTUARY News November 2012, Vol. 21, No. 5 www.sfestuary.org/pages/newsletter.php

5c) **true pantone colors! Managing Editor Ariel Rubissow Okamoto (for oset printing) 293 U & 2905 U fonts as outlines Contributing Writers SAN FRANCISCO Joe Eaton Nate Seltenrich Susan K. Moffat Kathleen M. Wong

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ESTUARY Readers: You’ll notice this last PARTNERSHIP issue comes late — we decided on an October-November combo to make room for some late breaking news. At the New Year, look out for with the potential to keep up with sea more information we have, the better level rise as well as giving restored the outcome.” an entire issue dedicated to climate habitat some place to go. You can’t just change science and planning prog- restore it and build a levee around it. For Isenberg, the report is an un- ress in the Bay Area, including the You need to connect it with the uplands usual intellectual product: “Americans have a short attention span as a soci- thorny question of sediment supply so it can move, accommodating marsh transgression.” ety and are disdainful of history. This to combat sea level rise. blend of physical science and social Wilcox says the report will help science will make many uncomfort- planners avoid costly mistakes: “The able, because it emphasizes the funda- HISTORY, continued from page 3 point is to not try to a desir- mental geophysical facts that shaped able habitat component into a place it the Delta, giving us opportunities but woodjams, in the northern areas, giant shouldn’t be.” For example, he says also limiting those opportunities.” riparian forests and perennial lakes. historic Delta channels look different The report was designed as a sup- Grossinger thinks functional mosa- from Bay channels, with lower den- porting document for the Bay-Delta ics of habitat could be reestablished sity and fewer dendritic patterns: “If Conservation Plan and other efforts, today, in a few key spots. “They may you try to create a bunch of fingerlike notes Grossinger. “Right now the plan- not be in the same places where habi- channels without enough tidal plain ning for BDCP is at a pretty conceptual tat was in the past,” he says,” pointing around them, you can end up with scale,” adds Wilcox. “Having this report out that future flow regimes should be backwaters that are nice places for helps put some meat on the bones of considered in terms of how they would non-native species.” what you’d be restoring to.” A second support restoration. “We didn’t study Connor, whose organization repre- project, due in two years, will interpret how much water came into the Delta sents, among others, the Westlands how native fish and wildlife species but what it did there, how it made dif- Water District and the Metropolitan used the historic habitat and how ferent kinds of habitat.” Water District of Southern California, those functions might be redesigned “The large marshland is all gone,” says the idea of reestablishing historic into the future Delta. says Carl Wilcox of the Department of functions in new places really reso- Contact Valerie Connor, Fish and Game. “The only way to get it nates with her. SFCWA is using this [email protected]; Robin Grossinger, back is to go where it isn’t subsided: information to look at specific resto- [email protected]; Phil Isenberg, the edge of the Delta.” Pilot projects ration projects in terms of what was [email protected]; on filling in subsided islands using there and what can be brought back. Carl Wilcox, [email protected] biological methods look promising, he “We have so many acres to do, all in adds. “We have to be looking for places an adaptive management context. The