Pollutant Effects on Aquatic Life

2011 pulse of the estuarypollutant effects on aquatic life

A Report of the Regional Monitoring Program for Water Quality in the San Francisco Estuary THIS REPORT SHOULD BE CITED AS: San Francisco Estuary Institute (SFEI). 2011. The Pulse of the Estuary: Pollutant Effects on Aquatic Life. SFEI Contribution 660. San Francisco Estuary Institute, Richmond, CA. 2011 pulse of the estuarypollutant effects on aquatic life

A Report of the Regional Monitoring Program for Water Quality in the San Francisco Estuary 2 overview: pollutant effects on aquatic life

A WILD WORLD AT OUR DOORSTEP

A large part of the magic of San Francisco Bay is the amaz- ing and abundant array of wildlife species that make their home right at the doorstep of an urban area supporting seven million people. The Bay supports a diversity of aquatic life, ranging from microscopic plants and animals, to invertebrates like clams and crabs, to fish species large and small, to the birds and marine mammals at the top of the food chain.

One of the primary goals of Bay water quality managers is to ensure that pollutants do not interfere with the ability of these aquatic species to thrive in Bay waters. In support of these management efforts, the Regional Monitoring Program for Water Quality in the San Francisco Estuary and other programs and projects carefully monitor whether pollutants are affecting aquatic life. ¶Surf Scoters in pursuit of Pacific herring roe. Photograph by Joan Linn Bekins. 3 OVERVIEW POTENTIAL IMPACTS overview: pollutant effects OF CHEMICAL POLLUTION on aquatic life Chemical pollutants can impact Bay aquatic life in many ways – some more severe, and some more subtle. Some forms of chemical pollution can cause immediate mortality of aquatic life. Oil spills are a vivid example, with their highly visible impacts on aquatic birds, along with the less visible impacts on fish (PAGE 72) and invertebrates beneath the Bay surface.

Discharge of organic waste from sewage into the Bay prior to the 1970s depleted the oxygen content of the water (PAGE 51) and made large !sh die-o"s a common occurrence. In- vestments in improved wastewater treatment greatly reduced organic input from this source and !sh kills have become rare. Concern is growing, however, for a possible return of oxygen depletion due to trends of increasing abundance of algae in the Bay (PAGE 48). A combination of high concentrations of nutrients along with changes in other factors that a"ect algal populations appear to be driving the increase, and raising the question of whether additional control of nutrient loads may be needed. that are considered likely to cause an increased incidence of gesting an increased risk of impacts on metabolism, growth, mortality in embryos as they develop (PAGE 78). Early life immune function, and reproduction (PAGE 74). Per$uorooc- Other pollutants can cause immediate mortality because of stages of !sh are also thought to be especially vulnerable to tane sulfonate (PFOS), a $uorine-containing chemical that ac- their toxicity to sensitive species. Insecticides, for example, pollutants such as pesticides, selenium, and PCBs. PCBs and cumulates in birds (PAGE 81 and seals (PAGE 96), threatens are designed to kill insects and o#en have similar e"ects on other synthetic chemical pollutants also reach relatively high to weaken the immune response of these species. Another their invertebrate aquatic relatives, and sometimes can be quite concentrations in seal pups and may pose higher risks during type of sublethal e"ect is impairment of sensory abilities. Cop- toxic to !sh. Pyrethroid insecticides are currently in wide use, this life stage (PAGE 91). per has been shown in laboratory studies to interfere with the and pose signi!cant threats to water quality in urban creeks sense of smell in salmon, which can limit their ability to !nd THE PULSE OF THE ESTUARY 2011 and are also suspected of possibly playing a role in the decline Pollutants can also elicit more subtle, sublethal responses that a mate, avoid predators, and to !nd their natal stream (PAGE of !sh species in the Bay and Delta (PAGE 72). can still signi!cantly reduce the viability of populations of sen- 75). A study is currently underway to evaluate whether this sitive species, and several possible examples of these responses type of inhibition may be occurring in the Bay. Pollutants can Early life stages of many aquatic species, such as bird embry- are suspected in the Bay. Many pollutants can act as endo- also have deleterious e"ects on behavior. One of the ways in os, !sh larvae, and seal pups are particularly vulnerable to the crine disruptors, altering the sensitive systems regulated by which methylmercury appears to a"ect Forster’s Terns in the lethal e"ects of pollutants. Methylmercury and PCBs, for ex- hormone signals. A recent study of the endocrine status of Bay Bay is by reducing the a%entiveness of parents, which results in ample, are found in eggs of some Bay birds at concentrations !sh found disruptions of the thyroid and adrenal systems, sug- an increase in the rate of abandoned eggs (PAGE 83).

·Harbor seals and cormorants on Castro Rocks. Photograph by Suzanne Manugian. 4 OVERVIEW

TRACKING PROGRESS IN MEETING CLEAN WATER GOALS A new water quality report card (PAGE 8) provides an overview of how well we are doing in providing clean habitat to support aquatic life in the Bay. &e report card also evaluates progress in making Bay !sh safe to eat and in making Bay waters safe for swimming. &anks to a considerable investment in infrastructure and the diligent e"orts of water quality managers, the Bay is much safer for !shing, aquatic life, and swimming than it was in the 1960s. Substantial control e"orts that began in the 1970s solved most of the obvious problems of the 1960s and set the Bay on a course for gradual recovery for many pollutants. However, challenges and uncertainties remain to respond to many pollutants. Complete and timely resolution of remaining and emerging water quality challenges will require signi!cant investments of resources to replace and improve our aging water quality infrastructure.

THE NEXT PULSE: µForster's Tern parent feeding a chick. Photograph by Robert Lewis. EMERGING CONTAMINANTS

OTHER IMPORTANT Trash in the Bay is another form of pollution that poses In addition to the familiar pollutants that pose threats to a continuing threat to aquatic life. Plastic trash threatens aquatic life, there are thousands of other chemicals used by so- FORMS OF POLLUTION aquatic life through ingestion and entanglement. Larger ciety, including pesticides, industrial chemicals, and chemicals Other forms of pollution also are considered among the trash items degrade to tiny fragments that can have signifi- in consumer products, and many of these make their way from most significant threats to Bay aquatic life. Based on past cant impacts on small aquatic life through ingestion and our homes, businesses, and watersheds into the Bay. Due to in- experience, exotic species are arguably the greatest threat. through exposure to pollutants that leach from the plastic adequate screening of the hazards of these chemicals, some may Introductions of exotic species have radically transformed particles. Aggressive new regulatory requirements adopted pose a threat to Bay water quality. As understanding advances, the species composition of the Bay, displacing many native in 2010 are expected to significantly reduce the amount of some of these contaminants emerge as posing signi!cant risks species, and have fundamentally altered the productivity trash entering the Bay in the next 30 years. to the health of humans and wildlife. &e next edition of the of the ecosystem. Most of these invasions are essentially Pulse will focus on the status of these emerging contaminants irreversible. Reducing the rate of introductions, however, in the Bay, and e"orts to prevent them from being added to the appears readily achievable through implementation of state toxic legacy that is passed on to future generations of humans and federal ballast water discharge regulations. and aquatic life that depend upon this productive ecosystem. 5 TA B table of contents LE OF C ONTENTS 2-4 28-45 46-99 overview status and feature articles trends update 48 a growing concern: 6-22 30 potential effects of nutrients latest monitoring results on bay phytoplankton management 30 Mercury 32 PCBs 33 PAHs 50 Sidebar: Harmful Algal Blooms update 34 PBDEs 36 Selenium 58 Sidebar: Exceptional Conditions in Spring 2011 8 38 A water quality water quality trends report card for 66 at a glance effects of pollutants san francisco bay 38 Toxics and Bacteria on bay fish 22 Sidebar: A Beach 71 Sidebar: Exposure Report Card 39 Chlorophyll and DO and Effects Workgroup 25 Sidebar: Swimmer's Itch 40 Nutrients and Sediments

and Exotic Species 41 Flows and Loads 78 26 The 303(d) List 42 Human Presence recent findings on risks to birds from pollutants 27 Regulatory Status 43 Climate and Habitat in san francisco bay of Pollutants of Concern 44 Populations 86 Sidebar: Another Dimension

45 Graph details of the Mercury Problem THE PULSE OF THE ESTUARY 2011

88 98 References contaminant exposure and effects at the top of the bay 99 Credits and Acknowledgements food chain: evidence from 100 Committee Members and RMP Participants harbor seals

COMMENTS OR QUESTIONS REGARDING THE PULSE OR THE REGIONAL MONITORING PROGRAM CAN BE ADDRESSED TO DR. JAY DAVIS, RMP LEAD SCIENTIST, (510) 746-7368, [email protected] 6

management update 7

8 a water quality report card for san francisco bay 22 Sidebar: A Beach management update Report Card 25 Sidebar: Swimmer's Itch and Exotic Species 26 The 303(d) List 27 Regulatory Status of Pollutants of Concern 8 MANAGEMENT UPDATE | WATER QUALITY REPORT CARD

Jay Davis and John Ross, San Francisco Estuary Institute Mike Kellogg, City and County of San Francisco Andrew Cohen, Center for Research on Aquatic Bioinvasions Andrew Gunther, Center for Ecosystem Management and Restoration

a water quality report card for san francisco bay

Fish from the Bay are not Highlightshighlights entirely safe to eat, due mainly to Many monitored pollutants polychlorinated biphenyls (PCBs), are considered to pose very methylmercury, and dioxins A new State of the Bay report low risk to Bay aquatic summarizes progress in a!aining A water quality report life, but a few (especially management goals relating to card is a component of methylmercury, exotic Most Bay beaches are safe for habitat, water supply and quality, the Report that assesses species, the toxicity of swimming in the summer, but living resources, ecological whether the Bay is safe sediments, and trash) pose bacterial contamination is a processes, and stewardship for aquatic life, whether substantial threats concern at a few beaches in the Bay "sh are safe to eat, summer, and at most beaches in and whether the Bay is wet weather safe for swimming MANAGEMENT UPDATE WATER QUALITY REPORT CARD THE PULSE OF THE ESTUARY 2011

9 | - - - ! 1 FBU UP MJGF MJGF TBGF BRVBUJD TXJNNJOH #BZ ). GPS GPS UIF 1 TBGF TBGF RE GSPN #BZ #BZ GU I GJTI the severity of the impairment of water quality. F UIF UIF 2! r *T r "SF r *T The water quality report card addresses the three main pollu water by affected are that beneficial of the Bay uses tion and protected by the Clean Water Act, answering three key questions: Suites of indicators were identified to answer each of these ( questions The water quality data summarized in the report card were evaluated using a scheme that takes into account both of the es guideline in terms the relevant from the distance condi desired the reach to expected time of length timated and tion ------avis. D

hotograph by Jay P LITY LITY A ier 42. P RD CA ishing from F TER QU A EPORT EPORT HE W HE Monitoring Program for Water Quality in the San Fran cisco Estuary (RMP), to track conditions in the Bay and to provide the information that water quality managers need to address the remaining problems. The report card on Bay water quality is based largely on information generated by the RMP. Other valuable sources of information are also available and were considered as well. T R The water quality report card is an important element of the State of the Bay assessment. Clean water is essential to the health of the San Francisco Bay ecosystem and to many en residents Area Bay that of the beneficial of the Bay uses joy and depend on. Billions of dollars have been invested in management of the wastewater and other pollutant sources that impact Bay water quality, and as a result the Bay is in much better condition than it was in the 1970s. Inputs of organic waste and nutrients have been greatly reduced and fish con cause kills Bacterial no longer or odor problems. tamination has also been reduced. Inputs oftoxic many pol lutants to the Bay have also declined dramatically as a result of improved wastewater treatment and enforcement of the Act.thousands However, Clean Water of chemicals are car ried into the Bay by society’s waste streams, and significant and challenging qualitywater problems still remain. The Bay Area is fortunate to have one of the best water quality monitoring programs in the world, the Regional myriad benefits of a healthy and vibrant San Francisco Bay. we are doing enough of the right things to protect the Bay. The report is intended to encourage and inform thoughtful discussion about managing and protecting this tremendous resource, and to support continued efforts by citizens, pro fessionals, and political leaders to protect and enhance the - - ).

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FIGURE 1 Summary of San Francisco Bay water quality, 2011. &e star rat- ings are based on a combination of the severity of the problem and the anticipated time needed to a%ain water quality goals (see FIGURE 2 and 5). A !ve star rating indicates that regulatory goals have been met. Safe for Aquatic Life Safe to Eat Safe to Swim Fewer stars indicate varying degrees of distance from regulatory goals. Methylmercury Ì PCBs Ì Beach Bacteria ÌÌÌÌ (April-October) Exotic Species ÌÌ Methylmercury ÌÌ Beach Bacteria ÌÌÌ (Wet Weather) Sediment Toxicity ÌÌÌ Dioxins ÌÌ Trash ÌÌÌ Legacy Pesticides ÌÌÌÌÌ

Copper ÌÌÌÌ Selenium ÌÌÌÌÌ

Dissolved Oxygen ÌÌÌÌÌ PBDEs ÌÌÌÌÌ

Silver ÌÌÌÌÌ Other Priority ÌÌÌÌÌ Pollutants Other Priority ÌÌÌÌÌ Emerging Pollutants Contaminants ? poor Ì Selenium ? poor to fair ÌÌ PAHs ? fair ÌÌÌ PBDEs ? fair to good ÌÌÌÌ PFOS ? good ÌÌÌÌÌ goals not Emerging ? ? Contaminants established MANAGEMENT UPDATE | WATER QUALITY REPORT CARD THE PULSE OF THE ESTUARY 2011 11 - - - - ingestion and through exposure to chemical constituents that leach from the plastic particles or accumulate on them. Aggressive new regulatory requirements adopted in 2010 should significantly reduce the amount of trash entering in the next 30 years. the Bay There are several other pollutants that appear to pose risks to Bay aquatic life, but for which definitive regulatory goals for the Bay have not yet been developed. A few of the most prominent examples include selenium, PAHs, and perfluorooctanesulfonate (PFOS). Efforts to evaluate these pollutants and develop appropriate goals are in progress. Overall, despite great progress in reducing threats to the re pollutants key several life, aquatic of the Bay's health main problematic. Although these pollutants present man agement challenges, significant progress appears attainable in several important areas, including reducing trash inputs to the stemming Bay, the influx of exotic species, and reduc ing methylmercury production in specific habitats. Trash Trash in the Bay is also a continuing threat to aquatic life. Plastic trash persists for hundreds of years in the environ ment and threatens wildlife largely through ingestion and entanglement. Larger trash items degrade to fragments that can have significant impacts on small aquatic life through ). Scientists consider 25 E G PA , EBAR D I ). In every year since routine sampling began S 4 RE GU I F suggest that pollutant concentrations in Bay sediments may be high enough to affect the development and survival of aquatic invertebrates. This problem will persist into the future until the chemicals (or mix of chemicals) causing this toxicity be identified can remediated. and in 1993, at least 26% of the sediment samples have been determined to be toxic. In 2009, 67% of the samples were found to be toxic. Neither the causes of this toxicity or the reasons that it is so variable are understood. These results methylmercury. Exotic species pose the greatest threat to Bay aquatic life due to their displacement of native species, disruption of communities and the food chain, and their alteration of habitat. They also can pose a nuisance for people who swim ( in the Bay San Francisco Bay to be one of the most highly invaded estuaries in the world, and the ecological impacts of exotic species have been immense. Successful invasions by exotic species are essentially irreversible. Achievable goals are best focused on reducing the rate of introductions, which increased in the late 1900s. Progress on reducing the rate of introductions is achievable in the near-term. State and federal ballast discharge regulations could potentially have a very significant impact on one major vector for exotic introductions. species Toxicity of Bay sediments in standard tests is another indication of possible impacts of pollution on aquatic life ( problem. For example, one of the species at greatest risk in the Bay, the Forster’s Tern, forages primarily in salt ponds. Agencies that manage these habitats may be able to manipulate factors, such as water flow through the ponds, in ways that reduce the production and accumulation of -

- ). - RE 78 E GU G I F PA

IFE? FE FE L SA TIC Y ). This problem is mainly a legacy of A 3 A U RE Q GU I F S THE B S THE ). Many other pollutants are also routinely monitored Methylmercury concentrations in the Bay food web have not changed perceptibly over the past 40 years, and will probably decline very slowly in the next 30 years. It may be possible, however, to tackle at least some facets of this historic mercury pollution that resulted from gold mining in the Sierra Nevada and mercury mining in the local Coast Range. Researchers have concluded that methylmercury poses a high risk for reducing the hatching and fledging success of some species of fish-eating birds ( wildlife ( wildlife However, several pollutants still pose a substantial threat to the health of aquatic life in the Methylmercury,Bay. exotic species, the toxicity of sediments, and trash are the principal concerns. Methylmercury continues to pose significant risks to Bay 2 and found at concentrations below regulatory goals, and are considered to pose very low risk to Bay aquatic life. mental laws over the past 39 years has resulted in tremen resulted has 39 years the past over laws mental dous improvements in overall Bay water quality, solving serious threats to aquatic life related to reduced dissolved oxygen and elevated concentrations of silver ( food web, and the toxicity of Bay waters and sediments in laboratory tests. Exotic species and trash are included in this water quality assessment because they are considered Act. Water provisions of the Clean to subject pollutants Enforcement of theAct Clean and Water other environ The for“Safe Aquatic Life” water quality index quanti tatively considers five key pollutants, and qualitatively considers many others. This index was compared to goals set by the State of California for concentrations of chemical pollutants in water, methylmercury concentrations in the I FOR A 12 MANAGEMENT UPDATE | WATER QUALITY REPORT CARD

FIGURE 2 Summary assessment related to the “safe for aquatic life” question. &e two key dimensions of water quality poor Ì problems are their severity (degree of concern) and how quickly the Bay is anticipated to respond to pollution poor to fair ÌÌ prevention actions (whether rapid progress is likely or not). &e assessment scores in FIGURE 1 are based on fair ÌÌÌ a combination of these two factors. fair to good ÌÌÌÌ good ÌÌÌÌÌ goals not ? established

High Moderate Low Goals Concern Concern Concern A!ained

Rapid ÌÌ ÌÌÌ ÌÌÌÌ ÌÌÌÌÌ Progress Exotic Species Trash Copper Dissolved Oxygen

Likely Silver

Other Priority Pollutants Rapid Ì ÌÌ ÌÌÌ Progress Methylmercury Sediment Toxicity Unlikely MANAGEMENT UPDATE | WATER QUALITY REPORT CARD THE PULSE OF THE ESTUARY 2011 13 2009 2009 2009 2009 2008 2008 2008 2008 2007 2007 2007 2006 2006

2005 2005

0.25 0.20 0.15 0.10 0.05 0.00 0.25 0.20 0.15 0.10 0.05 0.00 0.25 0.20 0.15 0.10 0.05 0.00 0.25 0.20 0.15 0.10 0.05 0.00

Methylmercury (ppm) Methylmercury Methylmercury (ppm) Methylmercury Methylmercury (ppm) Methylmercury (ppm) Methylmercury South Bay South Bay and Lower Suisun Bay Central Bay San Pablo Bay 2009 2008 Suisun Bay South Bay 2007 Lower South Bay Central Bay 2006 Whole Bay 2005

Footnote: Box plots indicate the 25th, 50th, and 75th percentiles. Data for Mississippi silversides and topsmelt in the 3-5 cm size range speciﬁed in the Mercury TMDL. The RMP did not speciﬁcally target this size range, therefore sample sizes for each year are limited. Reference line is the 0.030 ppm target from the Mercury TMDL.

San Pablo Bay

0.00 0.25 0.20 0.15 0.10 0.05 Methylmercury (ppm) Methylmercury - - - L for protection D In the most recent sam recent most the In

FIGURE other year with a larger sample size. Results from a pilot study in 2005-2007 were lower, but the distributions for those years are based very a on small sample size. Bay-wide& e me ppm. 0.051 was 2009 in concentration dian pling year, methylmercury concentrations in prey !sh exceeded the 0.03 ppm target in approximately 95% of the samples collected. Similar results were obtained in 2008, the sh frequently exceed the 0.030 ppm tar ppm 0.030 the exceed frequently "sh inget the Mercury TM " of sh-eatingbirds. Methylmercury concentrations in small 14 MANAGEMENT UPDATE | WATER QUALITY REPORT CARD

Suisun Bay 100 90 FIGURE 80 4 70 San Pablo Bay Suisun Bay #e frequent and continuing toxicity of 60 Bay sediments in standard tests is an im- 50 portant indicator of impacts of pollution 40 on aquatic life. In every year since routine 30 Toxic Samples (%) Toxic 20 sampling began in 1993, at least 26% of each 10 year’s sediment samples have been deter- Central Bay 0 mined to be toxic. In 2010, 78% of the sam- 1995 2000 2005 2010 ples were found to be toxic. &e occurrence of toxic samples is greatest in Suisun Bay South Bay San Pablo Bay 100 and South Bay. &ese results indicate that 90 pollutant concentrations in Bay sediments 80 are high enough to a"ect the development 70 and survival of aquatic invertebrates. &is Lower South Bay 60 problem will persist into the future until the 50 chemicals (or mix of chemicals) causing this 40 30

toxicity can be identi!ed and remediated. Samples (%) Toxic 20 10 100 0 Whole Bay 1995 2000 2005 2010 90

80 Central Bay 100 70 90 80 60 70 60 50 50 40 40 30 Toxic Samples (%) Toxic Toxic Samples (%) Toxic 30 20 10 20 0 1995 2000 2005 2010 10 0 South Bay 100 1995 2000 2005 2010 and Lower 90 80 South Bay 70 60 Footnote: Percent of Bay sediment samples exhibiting toxicity in laboratory assays. Sediment samples are 50 tested in the RMP using amphipods and mussel larvae. 40 30 Toxic Samples (%) Toxic 20 10 0 1995 2000 2005 2010 MANAGEMENT UPDATE | WATER QUALITY REPORT CARD THE PULSE OF THE ESTUARY 2011 15 - - ier. ier. P avis. D ort Baker F ishing on F is exception to the ). &is to exception 6 hotograph by Jay ³ P RE GU I F ern is due to the tendency of shiner surfperch to spend spend surfperch the tendency of shiner to ern is due to % pa in which result can areas, nearshore in localized their lives with contaminated are when areas these accumulation greater identifying that up &is suggests !nding cleaning and PCBs. hasten could of the Bay the edges hotspots along contaminated locations. selected at of contamination the reduction &e risk we face today from consuming Bay !sh is in large part a legacy of unregulated discharges of pollutants in the past. For example, even though a ban on the sale and produc chemi persistent these 1979, in ect " e into went PCBs of tion cals have become thoroughly spread across the Bay watershed and mixed throughout creatingthe Bay, a widespread pool of contamination that will dissipate very slowly. Monitoring of trends in !sh contamination from 1994 to the present has found no indication of declines for PCBs, methylmercury, and dioxins. A% aining goals for these pollutants in sport !sh will take many decades. that pose a greater concern in the Central Bay than in San in San than Bay in the Central concern a greater pose that ( Bay or South Bay Pablo - - - - , EBAR D I S ) highlight the key differences among species 16 E G PA tions. The safe eating guidelines for the Bay ( Bay the for guidelines eating safe The tions. to allow fish consumers to reduce their exposure. For example, the guidelines indicate that PCB concentrations in one group of species – surfperch – are high enough that no consumption. OEHHA recommends found in !sh is generally While contamination moderate levels at seen surfperch in shiner are PCBs the Bay, throughout concentrations. Many other toxic pollutants (e.g., arsenic, polycy chlorpyrifos,cadmium, dieldrin, diazinon, DDTs, clic aromatic hydrocarbons, or polybrominated“PAHs”, diphenyl ethers, or “PBDEs”, and selenium) are found at concentrations too low to pose concerns. Contamination in Bay fish varies by species. Striped bass, of methyl concentrations high relatively have for example, in this contami low while relatively are jacksmelt mercury, nant. Shiner surfperch have relatively high concentrations of concentra low relatively halibut California have and PCBs, - $ - E D Y ), and I 7 S A RE GU I F T? ), methylmercury ( EA 6 ). RE ISH FROM THE B ISH FROM 16 ) due mainly to polychlorinated biphenyls GU E 5 I F G F RE PA FE TO , GU I F BAR dioxins, which are generally found in Bay fish at moderate assessment are general indications of levels of concern, and are are and of concern, of levels indications general are assessment can Consumers advice. consumption represent to not intended contami these their exposure to reduce and caution exercise developed guidelines for the Bay following by eating safe nants Assessment Hazard Health Environmental of the O'ce by ( this year updated been just which(OEHHA), have e “Safe to Eat” quantitatively considers eight key pollut key eight considers Eat” quantitatively to &e “Safe others. of many the impact qualitatively considers and ants, goals to in ! be compared sh can concentrations Pollutant public health. protect to of California the State by established in this presented the comparisons that note is important to It ARE Pollutants in fish from the Bay pose a health concern ( (PCBs) ( SA 16 MANAGEMENT UPDATE | WATER QUALITY REPORT CARD

SIDEBAR UPDATED FISH ADVISORY FOR SAN Women 18 - 45 and children 1 - 17 r Eatonlytheskinless FRANCISCO BAY PCBs are in the fat and skin of the ﬁsh. In May 2011 the O'ce of Environmental dium edium edium t Cook thoroughly and allow Me M M

the juices to drain away.

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i i i w g w g w g t For crab, eat only the meat. released an updated health advisory and safe o h o h o h L L L

eating guidelines for !sh and shell!sh caught Chemical Chemical Meter Meter What is a serving? from San Francisco Bay. &e guidelines state Chemical Chemical Chemical that Bay Area anglers should eat a variety Meter Meter Meter of di"erent kinds of !sh, avoid !sh known to have high amounts of mercury and other For Adults For Children contaminants, and properly prepare and cook Shiner perch or other surfperches The recommended serving !sh. &e advisory also provides special advice thickness of your hand. Give for women of childbearing age and children. Jacksmelt California halibut Sharks children smaller servings. What is the concern? The advisory and guidelines replace an earlier 1994 advisory, and draw on over a decade Red rock crab of PCBs and mercury. PCBs might cause cancer. Mercury can of more recent data, primarily from the RMP, White croaker Striped Bass develops in unborn babies and showing San Francisco Bay fish contain mer- children. It is especially important cury and polychlorinated biphenyls (PCBs). for women who are pregnant Chinook (king) salmon or breastfeeding to follow these They also incorporate nutrition science White sturgeon guidelines. showing that fish provide dietary protein and = High in Omega-3s Jacksmelt photo: Kirk Lombard, California Halibut: John Shelton essential nutrients, including omega-3 fatty acids that promote heart health and support Do not eat health. Fish have Omega-3s that Safe to eat OR Safe to eat AND can reduce your risk for heart neurological development. 2 servings per week 1 serving per week disease and improve how the from the brain develops in unborn babies Lauritzen Channel in Richmond Inner Harbor and children.

California O!ce of Environmental Health Hazard Assessment t 5-11 MANAGEMENT UPDATE | WATER QUALITY REPORT CARD THE PULSE OF THE ESTUARY 2011 17 - found to cause cancer in animals and also cause health problems in young children and adults. Some kinds of fish have more mercury and PCBs than others. Sharks have the highest levels of mercury, and shiner perch have the methyl to exposures High PCBs. most mercury (the form of mercury prevalent in fish) can affect the nervous system and harm learning ability, language skills and memory. PCBs are common contaminants known to build up in fish. They have been t n t a 5-11 ta . r t t w t in of r en a e y can o n r k . v r y . na s Gi n babies a w the cu w these

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FIGURE 5 Summary assessment related to the “safe to eat” question. &e two key dimensions poor Ì of water quality problems are their severity (degree of concern) and how quickly the Bay is poor to fair ÌÌ anticipated to respond to pollution prevention actions (whether rapid progress is likely or not). fair ÌÌÌ &e assessment scores in FIGURE 1 are based on a combination of these two factors. fair to good ÌÌÌÌ good ÌÌÌÌÌ goals not ? established

High Moderate Low Goals Concern Concern Concern A!ained

Rapid ÌÌ ÌÌÌ ÌÌÌÌ ÌÌÌÌÌ Progress DDT Likely Dieldrin

Chlordane

Selenium Rapid Ì ÌÌ ÌÌÌ Progress PBDEs PCBs Methylmercury Unlikely Dioxins* Other Priority Pollutants

Footnote: * Dioxins were assessed using a San Francisco Bay Regional Water Quality Control Board target, rather than the Ofﬁce of Environmental Health Hazard Assessment thresholds used for the other pollutants. MANAGEMENT UPDATE | WATER QUALITY REPORT CARD THE PULSE OF THE ESTUARY 2011 19 21 21 21 120 120 120 2009 2009 2009 2006 2006 2006 2003 2003 2003 2000 2000 2000 1997 1997 1997 1994 1994 1994 0 0 0

50 50 50

500 450 400 350 300 250 200 150 100 500 450 400 350 300 250 200 150 100 200 500 450 400 350 300 250 150 100

PCBs (ppb) PCBs (ppb) PCBs PCBs (ppb) PCBs South Bay South Bay and Lower Central Bay San Pablo Bay 21 120 2009 2006 White Croaker Suisun Bay South Bay 2003 Lower South Bay Central Bay 2000 Whole Bay Shiner Surfperch 1997 San Pablo Bay OEHHA 2 meal/wk threshold OEHHA no consumption threshold 1994 Footnote: Average PCB concentrations in sport ﬁsh indicator species. Sport ﬁsh are not routinely sampled in Suisun Bay. The no consumption advisory tissue level for PCBs ppb, is 120 and the two serving advisory tissue level is ppb. 21 White croaker were analyzed without skin in 2009, and with skin in previous years. Removing the skin reduced concentrations by 65% in 2009. 0 50

300 250 200 150 100 500 450 400 350

- (ppb) PCBs - 6

FIGURE &e summary rating for PCBs in Bay sport !sh is therefore one star. long-term dataset, the recently updated safe recom Bay Francisco San guidelineseating for mend no consumption of shiner surfperch and other surfperch species. & is corresponds to the “high concern” category incon Figure PCB in decline 5. No long-term of ern % pa clear centrations has been evident in these species. In the most recent sampling year (2009), both of the PCB indicator species (shiner surfperch and white croaker) had average ppb. 120 and ppb 21 between concentrations &e Bay-wide average for shiner surfperch in 2009 wasppb) (118 just below OEHHA's 120 ppb no-consumption threshold. Based on this 20 MANAGEMENT UPDATE | WATER QUALITY REPORT CARD

San Pablo Bay Suisun Bay FIGURE 7 #e methylmercury indicator species sampled in 2009 had average concentrations between 0.44 ppm (striped bass) and 0.08 Central Bay ppm (jacksmelt). Concentrations in these species in recent years mostly fell between the no consumption advisory tissue level of 0.44 ppm and the two serving per week advisory South Bay San Pablo Bay 0.7 tissue level of 0.07 ppm; this corresponds to the “moderate concern” category in FIGURE 0.6 5. Methylmercury concentrations in the Bay 0.5 Lower South Bay 0.44 food web have not changed perceptibly over the 0.4 past 40 years, and it is not anticipated that they 0.3 will decline signi!cantly in the next 30 years. &e summary rating for methylmercury in Bay California Halibut White Croaker 0.2

Methylmercury (ppm) 0.1 sport !sh is therefore two stars. Jacksmelt White Sturgeon 0.07 0.0 Striped Bass 1994 1997 2000 2003 2006 2009

Central Bay 0.7 0.7 Whole Bay 0.6 0.6 0.5 0.44 0.4 0.5 0.3 OEHHA no consumption threshold 0.44 0.2 0.4

Methylmercury (ppm) 0.1 0.07 0.3 0.0 1994 1997 2000 2003 2006 2009 0.2 Methylmercury (ppm) South Bay 0.7 0.1 OEHHA 2 meal/wk threshold and Lower 0.6 0.07 South Bay 0.5 0.0 0.44 0.4 1994 1997 2000 2003 2006 2009 0.3 Footnote: Average mercury concentrations in sport ﬁsh indicator species. 0.2 Averages for striped bass based on concentrations for individual ﬁsh

normalized to 60 cm. Averages for other species based on composite Methylmercury (ppm) 0.1 samples. Sport ﬁsh are not routinely sampled in Suisun Bay. The no 0.07 consumption advisory tissue level for mercury is 0.44 ppm, and the two 0.0 serving advisory tissue level is 0.07 ppm. 1994 1997 2000 2003 2006 2009 MANAGEMENT UPDATE | WATER QUALITY REPORT CARD THE PULSE OF THE ESTUARY 2011 21 -

- merica, raising money and awareness A cross A wim S ants that continue to pose substantial water quality concerns, and facets of these problems where progress seems%ain a able. Hopefully this summary will serve as a step forward in e "ective communication of progress in achieving water quality goals and a foundation for future improvements in reporting and management of Bay water quality. is summary of Bay water quality highlights several pollut quality several highlights water &is summary of Bay - - hotograph courtesy of P µ for cancer research, prevention and treatment: www.swimacrossamerica.org - - - - RD ORWA F

TEP contaminants. Numeric goals to assess our environmental our environmental assess to goals Numeric contaminants. avail not yet are contaminants for emerging measurements health. of Bay but should be part of future assessments able, also underscores contaminants of emerging &e occurrence chemistry” poten the importance e"orts of “green prevent to in the !rst the Bay entering chemicals from tially problematic of health legacies additional they do not become that so place residents. Area Bay and of Bay risk for future generations in the 1960s. Substantial control e"orts that control Substantial in the 1960s. provisions to in the 1970s, in response began of most Act, solved Water of the 1972 Clean the set of the 1960s and the obvious problems for many recovery for gradual on a course Bay quality of water pace &e general pollutants. in the past slowed has however, improvement, of major due primarily a lack decades, to three the Bay inputs to control to initiatives new of re trajectory decelerating the naturally and the dynamics by of sediment covery dictated mixing in the ecosystem. pollut the entry of problematic Preventing is the this ecosystem vulnerable into ants We quality. water Bay protect to way ideal and thousands of chemicalsuse in our homes indus pesticides, including businesses, trial chemicals chemicals, in consumer and A the Bay. enter of these many and products, on the chemicals present of information lack in their movement products, in commercial their toxicity and the environment, hinders the risk posed manage and e"orts track to emerging life these by aquatic and people to A S in infra investment anks considerable & to e"ortsthe diligent structure and of water for is safer much the Bay quality managers, ! swimmingshing, and it was life, than aquatic - - - -

FE FE ). Overall, the latest beach 22 E SA G Y PA , A IMMING? EBAR ). Based upon the number of days beaches D 8 SW I S RE GU I S THE B S THE F Bay, a Santa Monica-basedBay, non-profit, provides compre hensive evaluations of over 400 California bathing beaches in both Annual and Summer Beach Report Cards as a guide to aid beach users’ decisions concerning water contact rec reation ( The to water “Safe qualitySwim” index is based on mea surements of bacteria in water at popular Bay beaches. To protect beach users from exposure to fecal contamination, California has adopted standards for high use beaches that apply from April through October at beaches that are adjacent to a storm drain that flows in the summer. Heal the I ment of defective and aging sanitary sewer systems will be necessary in many instances before human fecal sources are considered controlled. for swimming. Sanitary surveys can be conducted to identify and mitigate contamination sources where possible. Low impact design installations may be possible at some sites to retain and treat stormwater before it reaches beaches. Diversion of storm water away from bathing beaches where possible may provide another solution. Repair and replace were closed or posted by counties with advisories warning against water contact recreation, Bay beaches were open 80% to 100% of the time during the prime2010. beachthrough season2006 from of October through April A variety of approaches can be taken to make the Bay safer most Bay beaches are safe for swimming in the summer, but that bacterial contamination is a concern at a few beaches in the summer, and at most beaches in wet weather. The frequency of beach closures is another informative metric for evaluating how safe the Bay is for swimming ( report card covering the summer of 2010 indicates that FOR 22 MANAGEMENT UPDATE | WATER QUALITY REPORT CARD

SIDEBAR A BEACH REPORT CARD China Camp Heal the Bay, a Santa Monica-based non-profit, provides comprehensive evalu- McNears Beach ations of over 400 California bathing beaches in both Annual and Summer Beach Report Cards as a guide to aid beach users’ decisions concerning water Northeast North Northwest Mid-Beach contact recreation. Grades from these report cards, which use the familiar “A Keller Southwest Baker Cove Beach South to F” letter grade scale, provide a valuable and easily accessible assessment of Keller how safe Bay waters are for swimming. Beach

Paradise Overall, the latest monitoring data from 2010 indicate that most Bay beaches Cove are safe for swimming in the summer, but that bacterial contamination is a concern at a few beaches in the summer, and at most beaches in wet weather. Schoonmaker Beach

For the summer beach season in 2010, 19 of the 26 monitored beaches Baker Cove received an A or A+ grade, reflecting minimal exceedance of standards. Ten

of these beaches received an A+: Coyote Point, Alameda Point South, Bath Aquatic Park House, Windsurf Corner, Sunset Road, Shoreline Drive, Hyde Street Pier, Bath House Crissy Field Crissy Field East, Crissy Field West, and Schoonmaker Beach. Most Bay Sunset Road Encinal beaches, therefore, are quite safe for swimming in the summer. Seven of Beach North Shoreline Drive the 26 beaches monitored in the summer in 2010 had grades of B or lower, South Bird Sanctuary indicating varying degrees of exceedance of bacteria standards. Keller Beach North and Keller Beach Mid-Beach were the two beaches receiving an F. Crissy Field Hyde Street Pier Windsurf Corner Five beaches received a D, including one in Contra Costa County, two in San East Sunnydale Jackrabbit West Aquatic Park Beach Beach Mateo County, and two in San Francisco County. These low grades indicate Mid-Beach Cove an increased risk of illness or infection. Overall, the average grade for the 26 Windsurfer Circle beaches monitored from April-October was a B.

Oyster Point During wet weather, which mostly occurs from November-March, water contact recreation is less popular but is still enjoyed by a significant number of Bay Area residents. Bacteria concentrations are considerably higher in wet weather making the Bay less safe for swimming. This pattern is evident in Heal the Bay report card grades for wet weather. In wet weather, only five of 22 beaches with data received an A. Six of these 22 beaches, on the other hand, Coyote Point Kiteboard received an F. The average grade for these beaches in wet weather was a C+. Beach Aquatic Park

0 3 6 Miles Lakeshore Park MANAGEMENT UPDATE | WATER QUALITY REPORT CARD THE PULSE OF THE ESTUARY 2011 23

C O

TION EA C B A IS ORTAL SF P C

B E UALITY UALITY RAN Q W F

ONITORING M M AN EPORT CARDS EPORT NFORM

WI S ATER ATER I R S A W H CHES C H A C AGE P AFE TO TO AFE S 415-473-2335 www.smhealth.org/environ/beaches 650-599-1266 www.beachreportcard.org www.waterboards.ca.gov/mywaterquality/ safe_to_swim www.swrcb.ca.gov/water_issues/programs/ beaches/beach_water_quality/index.shtml www.ebparks.org/stewardship/water 510-567-6706 (Crown Beach) www.ebparks.org/stewardship/water http://beaches.sfwater.org 415-242-2214 or 1-877- (732-3224) toll free www.co.marin.ca.us/ehs/water/ beach_monitoring.cfm CTERI COUNTY Y BE A A ATION ATION A M MED T B OURCES OF OF OURCES A ARIN COUNTY EAL THE BAY BEA THE BAY EAL AN MATEO COUNTY AN MATEO S B ON A NFOR hotline: S website: hotline: H website: CALIFORNIA website: CALIFORNIA BEA I website: AL website: hotline: COUNTY CONTRA COSTA website: OF AND COUNTY CITY website: hotline: M website: D F F F F B B B C B B C C B C B A A A A A D C+ N 2.38 2010 -11 U

F F F F F F C C B B C C B C B B B A A A A A D 2.14 2009 -10 DES , YEAR-RO F F B B B C B B A A A D A+ A+ A+ A+ A+ A+ 3.11 A ER 2008 -09 H R G F F F F F F F F C C C B A A A A A A A A 2.05 2007 -08 WEAT RD F F C B B A A D 2.14 WET WET 2006 -07 CA D F F F C B B A A A A A A A A D D D B- A+ A+ A+ A+ 2.91 N 2010 -11 U F C B B B A A A A A A A A A A A A D D D D A+ A+ 3.12 2009 -10 EPORT EPORT , YEAR-RO R B C B B C C A A A A A A A A A D B+ A+ 3.31 ER 2008 -09 H CH C C C B C B B A A A A A A A A A A A B+ A+ 3.44 A 2007 -08 WEAT RY RY C A A A A A A A- 3.71 D 2006 -07 L BE A F F B A A A A A A A A A D D D D D A+ A+ A+ A+ A+ A+ A+ A+ A+ A+ 3.23 2010 F B B B B B A A A A A A A A A A A D D D D A+ A+ A+ A+ A+ A+ 3.30 2009 Y ANNU F B B C C A A A A A A A A A A A A A A A A A D B+ A+ A+ A+ A+ A+ A+ 3.61 A 2008 B B B B A A A A A A A A A A A A A A A A A A A A- A+ A+ A+ 3.88 2007 APRIL - OCTOBER - APRIL C A A A A A A A A D A A A A B+ 3.64 2006 L THE B L THE A ier NE est ast ark ark SW rive NW oad P oint oint orth orth E P P outh outh ouse W P P E R D N N S S H DE anctuary treet A S ark Beach H oint S oint yster ears Beach P quatic unset P P COUNTY O China Camp S N A Coyote O COUNTY aradise Cove A akeshore akeshore horeline P indsurf Corner LL GPA yde unnydale Cove T ield mid-Beach L indsurfer Circle S Mc SC ield Beach F S A H LL GR S W Kiteboard Beach I F Jackrabbit Beach Jackrabbit W

A quatic orseshoe Cove C orseshoe Cove COUNTY Keller Beach Keller Keller Beach Keller orseshoe Cove choonmaker Beach choonmaker A lameda H lameda H N S A H CO VER TEO COUNTY A A A A Crissy Crissy ﬁeld Beach VER O PSRA Crissy Keller Beach Mid-Beach Keller O C MA Crown Beach Bath MED Crown Beach RIN COUNTY N FR N A Crown Beach Bird A A Crown Beach Crown Beach MA S CONTR AL S (year-round = April 1 - March 31) 24 MANAGEMENT UPDATE | WATER QUALITY REPORT CARD

FIGURE 8 Crissy Field Aquatic Park Candlestick County public health and other agencies routinely Point S! monitor bacteria concentrations at Bay beaches 2.0% 0.9% 1.4% where water contact recreation is common and provide warnings to the public when concentrations exceed the standards. &e county monitoring data represent the longest-term data set from the most 98.0% 98.6% locations in the Bay with which to evaluate the ques- 99.1% UJPOi*TUIF#BZ4BGFGPS4XJNNJOH u#BTFEVQPOUIF number of days beaches were closed or posted with advisories warning against water contact recreation, East Hyde Street Pier Jackrabbit Beach Bay beaches were open 80% to 100% of the time dur- n=175 n=166 n=172 ing the prime beach season of April through October from 2006 through 2010. Data for San Francisco beaches are shown here as an example. 0.7% 1.1% 3.8%

99.3% 98.9% 96.2%

mid-Beach* Beach Windsurfer Circle n=65 n=170 n=193

0.8% 2.1%

% Days Posted 99.2% 97.9%

% Days Not Posted West* Sunnydale Cove n=96 n=183

Footnote: Percent of days during the prime beach season (April - October) that City and County of San Francisco beaches were posted and not posted due to possible fecal contamination from 2006 through 2010 (n=number of samples). Crissy Field mid-Beach sampled 2006-2007 and Crissy Field West sampled 2008-2010.

Swimmer at Aquatic Park Beach. Photograph by Jay Davis. MANAGEMENT UPDATE | WATER QUALITY REPORT CARD THE PULSE OF THE ESTUARY 2011 25 ranz. ohen. F C my A ndrew A hotograph by P hotograph by P alifornia. alifornia. C lameda, lameda, A tlantic mudsnails. tlantic mudsnails. A µ rown Beach, rown Beach, C µ ) - - S Austrobilharzia variglandis Austrobilharzia ) (Grodhaus & Keh 1958; Leighton OTIC SPECIE X E ) and the parasite a previously unknown flatworm quatic Bioinvasions, [email protected] quatic Bioinvasions, Ilyanassa obsoleta A became established in the South Bay, though it’s unclear esearch on R CH AND Haminoea japonica (Brant et al. 2010). The bubble snail had been reported from a few T I

enter for S C Crassostrea gigas ohen, ohen, C Gigantobilharzia

ndrew A ontact: ontact: ed by exotic marine snail. Emerging Infectious Diseases 16(9): 1357-1365. Diseases Infectious exotic by marine snail.ed Emerging # transmi variglandis in California (Trematoda: Schistosomatidae). Journal of Parasitology 44: 633-638. of Parasitology Journal Schistosomatidae). (Trematoda: variglandis in California Review 48: 5-13. Health preliminary report. Environmental Beach, Crescent dermatitis at some SIDEBAR Literature Cited Literature of Austrobilharzia cercaria 1958. !e marine dermatitis-producing Keh. B. and G. Grodhaus 2004. Schisto- L. and Gustafson. A. Stewart, G. Nadan Ratzla McDougall, " , C. D. B.J., Leighton dermatitis 2010. Cercarial Loker. A. E.S. L. and Hui, Hom James, D. A.N. Cohen, S.V., Brant, southwestern San Francisco Bay in 1999. Interestingly, around the same time that a oyster populationof the Japanese whether there’s a connection. In 2003 the snail was discovered on the eastern sidesouth of Beach, andCrown by 2005of it was the most abundant snailthe the at Beach. Bay just C Naturally, it was initially thought that this outbreak was due to the same exotic intro but this be a recently timeprevious the the carrier outbreaks, turned out to caused as had snail and flatworm snail ( bubble Japanese duced in the genus sites in Washington in the 1980s, probably imported with Japanese oysters, and was found in An outbreak at Crown Beach in Alameda in the 1950s and another in Surrey, flatworm ( British Coast Atlantic an by both caused in 2002 were started that Columbia mudsnail ( Atlantic introduced carried an by et al. 2004). Then 2005,in June approximately 90 elementary school children developed swim mer’s itch after a class outing to Crown Beach during the last week of school. newWarnings outbreak about werethe issued by the Alameda County Environmental Health Department andat the posted beach, and cases have been reported each spring and summer since. when a parasitic flatworm that normally develops in a water snail and thenskin burrows and intothrough the thecirculatory system of a water bird (where it matures and mates)into instead a human burrows swimmer or wader. Symptoms are similar to those caused by exposureoak, to poison with an itchy, red rash that can last for weeks. It is generally unknown exceptin Pacific for acoastal few outbreaks waters associated with exotic organisms. SWIMMER’ Exotic species, one of the greatest threats to aquatic life in the Bay, also posewho a nuisanceswim in for the people Swimmer’sBay. itch, common in some freshwater ponds and lakes, is caused 26 MANAGEMENT UPDATE | THE RV ENEDEAVOR AND THE 303(D) LIST THE RV ENDEAVOR

The RMP gratefully acknowledges the significant the 303(d) list contribution made by the Bureau of Reclamation to the program through the generous donation of the research vessel, RV Endeavor, and Captain Nick Sakata. Dr. Erwin Section 303(d) of the 1972 Federal Clean Water Act requires that states develop a list of water bod- Van Nieuwenhuyse, Chief of the Science Division of ies that do not meet water quality standards, establish priority rankings for waters on the list, and Reclamation’s Bay-Delta Office, is Reclamation’s coordinator develop action plans, called Total Maximum Daily Loads (TMDLs), to improve water quality. for the Interagency Ecological Program (IEP). Similar to the RMP, the IEP is a consortium of federal and state agencies The list of impaired water bodies is revised periodically (typically every two years). The RMP is one that monitors and conducts special studies on the physical, of many entities that provide data to the State Water Board to compile the 303(d) List and to develop chemical, and biological properties of the Bay-Delta to meet TMDLs. The process for developing the 303(d) List for the Bay includes the following steps: the requirements of Biological Opinions and state water right permit conditions that govern the long term operation of the rEFWFMPQNFOUPGBESBGU-JTUCZUIF4BO'SBODJTDP#BZ3FHJPOBM8BUFS#PBSE Central Valley Project and the State Water Project. The IEP rBEPQUJPOCZUIF4UBUF8BUFS#PBSEBOE has recently devoted significant resources to determining the rBQQSPWBMCZ64&1" cause of the Pelagic Organism Decline (PAGE 68). The RMP is extremely pleased to have Reclamation’s team assisting us In August 2010, the State Water Board adopted in understanding Bay water quality. the 2010 303(d) List. The 2010 List was BQQSPWFECZ64&1"

The Regional Water Board and MORE INFORMATION ON THE 303%d! LIST AND TMDLS IS State Water Board are now working AVAILABLE FROM THE FOLLOWING WEBSITES developing the draft 2012 303(d) List. The primary pollutants/stressors 303%D! LIST FOR REGION 2 (which includes the Estuary) for the Estuary and its major tributaries www.waterboards.ca.gov/sanfranciscobay/water_issues/ on the 2010 303(d) List include: programs/TMDLs/303dlist.shtml Trace elements TMDLs Mercury and Selenium www.swrcb.ca.gov/sanfranciscobay/water_issues/programs/TMDLs/ Pesticides Dieldrin, Chlordane, and DDT Other chlorinated compounds PCBs, Dioxin and Furan Compounds Others Exotic Species, Trash, and Polycyclic Aromatic Hydrocarbons (PAHs)

µ The RV Endeavor. Photograph by Jay Davis. MANAGEMENT UPDATE | WATER QUALITY REPORT CARD THE PULSE OF THE ESTUARY 2011 27 oncern C ollutants of ollutants P TUS A tatus of avis. T D S c objectives approved in 2008in TMDL site-speciapproved and objectives Bay c ! 2008 in Guadalupe River Watershed TMDLadopted approved in TMDL 2010 Bay Richardson Bay beaches2006 (Aquaticin List Park, Candlestick303(d) to Point,added China Camp,Field) Crissy and 2009 in approved TMDL 2013 for projected completion – development in TMDL List 303(d) 2010 the to added shorelines Bay South and Central Site-specientire Bay for objectives c ! approved 2002in List 303(d) from removed Bay Francisco San stage development early in TMDL Under consideration for delisting S hotograph by Jay hotograph by Jay BQQSPWBM P

64&1"

BOE NT eandro Bay. eandro Bay. L A #PBSE an S 4UBUF

ucks in egulatory egulatory D OLLUT "QQSPWFE Trash Pathogens PCBs Selenium Dioxins / Furans Dioxins/ Legacy Pesticides (Chlordane, DDT) Dieldrin,and Mercury Copper P µ R avis. D hotograph by Jay hotograph by Jay P ndeavor. ndeavor. E

RV he T

µ 28 STATUS AND TRENDS UPDATE

status & trends update 29

30 38 latest monitoring results water quality trends at a glance 30 Mercury 38 Toxics and Bacteria 32 PCBs 39 Chlorophyll and DO status & trends 33 PAHs 40 Nutrients and Sediments 34 PBDEs 41 Flows and Loads 36 Selenium 42 Human Presence update 43 Climate and Habitat 44 Populations

45 Graph details THE PULSE OF THE ESTUARY 2011 30 LatestSTATUS AND TRENDS UPDATE | LATEST Monitoring MONITORING RESULTS Results Methylmercury in Water (ng/L) mercury

Mercury contamination is one of the top water quality San Pablo Bay Suisun Bay concerns in the Estuary and mercury clean-up is a high Rivers priority of the Water Board. Mercury is a problem because it accumulates to high concentrations and poses risks to some "sh and wildlife species. #e greatest health risks from mercury are generally faced by humans and wildlife that consume "sh. 0.08 0.06

0.04

0.02

0.00 2003 2005 2007 2009 Central Bay

South Bay

Lower South Bay 0 MILES 20

0.03 0.04 0.05 0.06 0.07 0.08 0.09 0. 1 0.11 0.12

Water from Lower South Bay had the highest average concentration of methylmercury by far (0.11 ng/L) of any segment from 2006 to 2010. South Bay had the next highest average (0.06 ng/L). Methylmercury typically represents only about 1% of the total of all forms of mercury in water or sediment, but it is the form that is readily accumulated in the food web and poses a toxicological threat to highly exposed species. Methylmercury has a complex cycle, in$uenced by many processes that vary in space Footnote: Map plot based on 119 RMP data points from 2006-2010. Earlier years not included and time. No regulatory guideline exists for methylmercury in water. &e Bay-wide because a less sensitive method was employed. The maximum concentration was 0.23 ng/L at a site in Lower South Bay in 2009. Trend plot shows annual Bay-wide averages. Data are for total average in 2010 was 0.03 ng/L. &e Bay-wide average for the !ve-year period was 0.05 methylmercury. Colored symbols on map show results for samples collected in 2010. Circles ng/L. &e Bay-wide averages for 2008-2010 were lower than those observed in 2006 and represent random sites. Diamonds represent historic ﬁxed stations. 2007. Additional data will be needed to determine whether this re$ects a real trend. STATUS AND TRENDS UPDATE | LATEST MONITORING RESULTS THE PULSE OF THE ESTUARY 2011 31 - 4

0. Alsoin 2010 (ppm) 2009 2008 Rivers 0.35 2007 2006 2005 Lower South Bay 3 2004 0. 2003 Suisun Bay 2002 Footnote: Contour plot based on 378 RMP data points over an eight-year period from 2002- 2009. The maximum concentration was 0.94 ppm in Central Bay in 2009. Trend plot shows annual Bay-wide averages. Colored symbols on map show results for samples collected during the wet season (February) in 2010. Circles represent random sites. Diamonds represent historic ﬁxed stations. Concentrations presented on a dry weight basis. 0.40 0.30 0.20 0.10 0.00 0.25 Mercury in Sediment in Sediment Mercury 20 2 0. South Bay MILES Central Bay Central 0.15 San Pablo Bay San Pablo 0 1 Footnote: Contour plot based on 378 RMP data points over an eight-year period from 2002-2009.concentration The maximum was 0.94 ppm in Central Bay in 2009. Trend plot shows annual Bay-wide averages.on map show results Colored symbols for samples collected during the wet season (February) in 2010. CirclesDiamonds represent represent random historic sites. ﬁxed stations. Red circle on trend plot indicatesdry a wet season season. sample; Concentrations other samples presented were on a dry weight basis. the eight years of dry season sampling was observed in 2009, coinciding with the highest aver highest the with coinciding 2009, in observed was sampling season dry of years eight the a resultsfrom represent map the on diamonds and Circles mercury total concentration. age 2010, inmeasured threehighestconcentrations e & sampling2010. in wet-season of !year rst concentrations low relatively had occurredhave areasthat in ppm, 0.41 rangingto 0.39 from similarwaslong-term the to ppm) (0.26 season wet 2010 the for average dry e & the season.in averagethe for dry and annual to season (0.25ppm) dry season averages observed sediment. from in 2002- mercury total for exists guideline regulatory No 2009. In contrast to methylmercury, long-term average total mercury concentrations in mercury concentrations total average long-term methylmercury, to contrast In ppm). (0.28 Bay Pablo San in highest been have dryduring season the sediment mercurytotal in of dryconcentrations season average methylmercury,Bay-wide to contrast in lippm variabilityrelatively %shown le thishave ranging sediment period, 0.19 over from methylmercuryover average concentration Bay-wide lowest 2009.e & in 0.30ppm 2005to 0.

6 2010 1. (ppb) 2009 2008 4 Rivers 1. 2007 2006 2 2005 Mercury is converted to 1. Lower South Bay 2004 2003 Suisun Bay 1 2002 0.00 0.80 0.60 0.40 0.20 8 0. 20 6 0. Methylmercury in Sediment Methylmercury South Bay 4 0. MILES Central Bay Central 2 San Pablo Bay San Pablo 0. 0

symbols on map show results for samples collected during the wet season (February)random in sites. 2010. Circles Diamonds represent represent historic ﬁxed stations. Red circle on trendother plot samples indicates were a wet dry season season. sample; Concentrations presented on a dry weight basis. Footnote: Contour plot based on 378 RMP data points over an eight-year period from 2002-2009.concentration The maximum was 6.1 ppb at a site in Central Bay in 2009. Trend plot shows annual Bay-wide averages. Colored shown should be viewed as the result of several “snapshots” ofof Baythe conditions surveys at in the the time summers of 2002-2009. Circlesfrom and adiamonds !rst year represent of wet-season results sampling in 2010. &e wet-seasonspatial data show pa a similar%ern as the long-term average conditions for the2010 dry wet season season. (0.29 wasppb) &e average lower than for the the long-term average for the but ppb), dry similar season (0.50 to the dry season resultsediment. for in 2009 methylmercury (0.30 for No ppb). regulatoryexists guideline Concentrations of methylmercury in sediment southEstuary. northern the of in thethose than higher Bayconsistently Bridge have been methylmercury mainly by bacteria in sediment. Methylmercurytremendously over small production distances can vary and over short time periods, so the colored contours 0 Latest Monitoring Results Monitoring Latest 32 STATUS AND TRENDS UPDATE | LATEST MONITORING RESULTS

Sum of PCBs in Sediment (ppb)

pcbs San Pablo Bay Suisun Bay Rivers PCB contamination remains one of the greatest water quality concerns in the Estuary, and PCB cleanup is a primary focus of the Water Board. PCBs are a problem because they

accumulate to high concentrations in some Bay "sh and pose 14 health risks to consumers of those "sh (PAGE 19). 12 10 8 6 4 2 0 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010

Central Bay

South Bay

Lower South Bay 0 MILES 20

0 2 4 6 8 10 12

Footnote: Contour plot based on 282 RMP data points from 2004 – 2009. Data from 2002 and 2003 are not available. The maximum concentration was 30 ppb in South Bay in 2008. Trend plot shows annual Bay-wide averages. Colored symbols on map show results for samples collected during the wet season (February) in 2010. Circles represent random sites. Diamonds represent historic ﬁxed stations. Concentrations presented on a dry weight basis.

Average PCB concentrations in Bay sediment have been highest in the southern reach of the Estuary (Central Bay, South Bay, and Lower South Bay). Circles and diamonds on the map represent results from a !rst year of wet-season sampling in 2010. &e spatial pa%ern observed in the wet season of 2010 was xx consistent with the general pa%ern observed in dry season monitoring from 2002-2009. &e Bay-wide average for the wet season sampling in 2010 was 12 ppb, higher than in any of the other years (dry season) sampled to date. Four of the 10 highest samples in the seven-year period (ranging from 19-24 ppb) were collected in 2010, all in the southern reach. Models suggest that sediment PCB concentrations must decline to about 1 ppb for concentrations in sport !sh to fall below the threshold of concern for human health. Suisun Bay dipped below this value in 2006 (0.8 ppb), but averaged 2.9 ppb in 2010. STATUS AND TRENDS UPDATE | LATEST MONITORING RESULTS THE PULSE OF THE ESTUARY 2011 33 -

2010 (ppm) 7000 2009 2008 Rivers 2007 6000 2006 2005 Lower South Bay 2004 5000 2003 Suisun Bay 2002 5.0 4.0 3.0 2.0 1.0 0.0 4000 20 3000 Sum of PAHs in Sediment PAHs in Sediment Sum of Circlesanddiamonds representresults !from a rstyearwet- of South Bay 2000 MILES Central Bay Central San Pablo Bay San Pablo 1000 concentrations in sediment have been highest along the southwestern shore 0 H consistent with the general pa%ern observed in dry season&e average monitoring for the 2010 wet from season 2002-2009. (2.4 ppm) was similar to the long-termdry seasonaverage (2.6for the ppm) and to annual dry season averages observedhigh annual from 2002-2007. average dry &e season concentrations observeddriven in 2008 by a few and unusually 2009 were largelycontaminated sites sampled in those years.. line of Central Bay. Bay. Central of line season sampling in 2010. &e spatial pa%ern observed in the wet season of 2010 was Footnote: Contour plot based on 377 RMP data points from 2002-2009. The maximum concentrationsite on the southwestern was 43 ppm at a Central Bay shoreline in 2009. Seven of the ten highest samplesfrom Central in the nine-year Bay. Trend plot shows annual period Bay-wide were averages. Colored symbols on map show resultscollected for samples during the wet season (February) in 2010. Circles represent random sites.stations. Diamonds Red represent circle on trend historic plot indicates ﬁxed a wet season sample; other samples werepresented dry season. on a dry Concentrations weight basis. PA

0 s pah and motor vehicle use in the Bay Area suggest that PAH concentrations could increase over the next 20 years, due to deposition of combustion products from the air directly into the Bay and from the air to roadway runo$ and into the Bay via stormwater. PAHs (polycyclicPAHs aromatic hydrocarbons) are included on the 303(d) List for several Bay locations. Concentrations tend to be higher near the Bay margins, due to proximity to anthropogenic sources. In addition to historic industrial sources along the Bay margins, increasing population 34 STATUS AND TRENDS UPDATE | LATEST MONITORING RESULTS

BDE 47 in Water (pg/L)

pbdes San Pablo Bay Suisun Bay Rivers PBDEs, bromine-containing %ame retardants that were practically unheard of in the early 1990s, increased rapidly in the Estuary through the 1990s and are now pollutants of concern. #e California Legislature has banned the use of two types of PBDE mixtures. Tracking the trends in these chemicals will be 120 100 extremely important to determine what e$ect the ban will have 80 and if further management actions are necessary. No regulatory 60 guidelines currently exist for PBDEs. 40 20 0 2002 2003 2004 2005 2006 2007 2008 2009 2010 Central Bay

South Bay

Lower South Bay 0 MILES 20

20 40 60 80 100 120 140

#e highest long-term average concentration of BDE 47 (one of the most abundant PBDEs and an index of PBDEs as a whole) from 2002-2010 was found in Suisun Bay (67 pg/L). &e maximum concentrations, two samples greater than 300 pg/L, were observed at locations in Suisun Bay and San Pablo Bay, both in 2004. &e high concentrations in Suisun Bay suggest the presence of PBDE inputs into the northern Estuary. &e Bay-wide average concentration for the nine-year period was 45 pg/L. &e Bay-wide average for 2010 was the second lowest recorded (19 pg/L). &e three lowest annual average concentrations were measured in 2008-2010.

Footnote: BDE 47 shown as an index of total PBDEs. BDE 47 is one of the most abundant PBDEs and was consistently quantiﬁed by the lab. Map plot based on 247 RMP data points from 2002-2010. The maximum concentration was 337 pg/L observed in Suisun Bay in 2004. Trend plot shows annual Bay-wide averages. Data are for total BDE 47 in water. Colored symbols on map show results for samples collected in 2010. Circles represent random sites. Diamonds represent historic ﬁxed stations. STATUS AND TRENDS UPDATE | LATEST MONITORING RESULTS THE PULSE OF THE ESTUARY 2011 35

- 7 - 2010 (ppb) 2009 2008 6 2007 Rivers 2006 2005 5 2004 Similar to BDE 47 in Lower South Bay 2003 Suisun Bay 2002 4 4.0 3.0 2.0 1.0 0.0 BDE 209 in Sediment BDE 209 in Sediment 3 20 2 South Bay Es that can still be used in California. in used be still can that Es MILES D Central Bay Central 1 San Pablo Bay San Pablo 0 E 209 (also known as decabromodiphenyl ether)represents the one remain D Footnote: BDE 209 shown as an index of the “deca” PBDE mixture. Contour plot based on 282 RMPfrom data points 2004, 2006, 2007, 2008, and 2009. The maximum concentration(the by far next was 52 ppb highest in San Pablo concentration Bay in 2007 was ppb 19 in South Bay in 2006). Trend plot shows annual Bay-wideColored averages. symbols on map show results for samples collected during the wet season (February)represent random in 2010. Circles sites. Diamonds represent historic ﬁxed stations. Redseason circle on sample; trend plot other indicates samples a wet were dry season. Concentrations presented on a dry weight basis.

shown to have relatively high concentrations. &e average (2.2for the wasppb) 2010 similarwet season to the long-term average for the dry seasonmiddle (1.8 andppb) of in the the range of annual dry season averages from 2004-2009. B PB of class ing sediment, long-term average dry season concentrations ofwere BDE 209highest from 2004–2009in Lower South Bay (4.8 Circlesppb). and diamonds representfrom a ! resultsrst year of wet-season sampling in 2010. &e spatialwasconsistent with generalpathe%indry 2010 ern seen seasonof seasonmoniwet pa%ern observed in the toring from 2002-2009, with the highest concentrationsppb in Lower(including South samplesBay and 8.4 at 16 ppb in San Pablo Bay) occurring in areas previously 0 - - 8

0. 2010 (ppb) 2009 2008 7 0. Rivers 2007 2006 2005 Lower South Bay 6 2004 0. 2003 Suisun Bay 2002 5 0.6 0.4 0.2 0.0 0. BDE 47 in Sediment Sediment 47 in BDE 20 E 47 in sediment have been highest in Lower South Bay 4 D 0. South Bay MILES 3 0. Central Bay Central Circles and diamonds represent results from a !rst year of wet-season sam San Pablo Bay San Pablo 0 2

Footnote: BDE 47 is one of the most abundant PBDEs and was consistently quantiﬁed by the lab. Contouron 282 RMP plot data based points from 2004–2009. Data from 2002 are available butother were inconsistent years. The maximum with data concentration, for the by was far, 3.8 ppb in Lower South Bay in 2005.Bay-wide Trend plot shows averages. annual Colored symbols on map show results for samples collected2010. Circles during the represent wet season random (February) sites. in Diamonds represent historic ﬁxed stations.weight basis. Concentrations presented on a dry (0.70 ppb). In contrast to the results obtained from water monitoring,B of concentrations season long-term average dry age has shown li%le $uctuation2007. overin the0.49 seven-yearof high a period,to 2005 ranging from a low of 0.34 in pling in 2010. &e spatial pa% ern observed in the wet seasonthe of general 2010 was consistent pa% ern observed with in dry season monitoringwith from 2002-2009. relatively high &ree concentrations samples were observed inhas northern been consistently Suisun Bay, a elevatedregion that in past sampling. &e Bay-wideseason average (0.43 wasppb) for similar the 2010 wet to the long-term average for the dryannual to dry seasonseasonobservedaverages inall yearsprior (2004-2009).aver Bay-wide &e (0.42 ppm) and 0. 36 STATUS AND TRENDS UPDATE | LATEST MONITORING RESULTS Selenium in Water (ug/L)

San Pablo Bay Suisun Bay selenium Rivers Selenium contamination is a continuing concern in the Estuary. Selenium accumulates in diving ducks to concentrations that pose a potential health risk to human consumers. Selenium concentrations also pose a threat to wildlife. Recent studies 0.30 suggest that selenium concentrations may be high enough to cause deformities, growth impairment, and mortality in early 0.20

life-stages of Sacramento spli!ail and white sturgeon. 0.10

0.00 2002 2003 2004 2005 2006 2007 2008 2009 2010 Central Bay

South Bay

Lower South Bay 0 MILES 20

0.05 0. 1 0.15 0. 2 0.25 0. 3 0.35 0. 4 0.45 0. 5

Selenium concentrations in water are well below the water quality objective established by the California Toxics Rule (CTR). However, concerns still exist for wildlife exposure as indicated by studies on early life-stages of !sh. &e highest concentration observed in water from 2002 to 2010 was 1.15 μg/L, much lower than the CTR objective (5 μg/L). &e Lower South Bay had a higher average concentration over this period (0.25 μg/L) than the other Bay segments, which had very consistent average concentrations (all other averages were between 0.12 and 0.14 μg/L). &e Bay-wide average concentration in 2010 (0.13 μg/L) was identical to the long-term Bay-wide average (0.13 μg/L).

Footnote: Map plot based on 247 RMP data points from 2002-2010. The maximum concentration was 1.15 μg/L at a historical station in the Southern Sloughs in 2002. Trend plot shows annual Bay-wide averages. Data are for total selenium. Colored symbols on map show results for samples collected in 2010. Circles represent random sites. Diamonds represent historic ﬁxed stations. STATUS AND TRENDS UPDATE | WATER QUALITY TRENDS AT A GLANCE THE PULSE OF THE ESTUARY 2011 37 2009 2007 2005 2003 2001 1999 1997 Reference: Kleckner, A.E., Stewart, A.R., Elrick, K., and Luoma, S.N.,isotopic 2010, Selenium compositions concentrations of carbon and and stable nitrogen in the benthic clam Corbula amurensis fromBay, California: Northern May 1995–February San Francisco 2010: U.S. Geological Survey Open-File Report 2010-1252, 34 p. 1995

8 6 4 2 0

20 18 16 14 12 10

(ppm dry wt) wt) dry (ppm

Adjusted Adjusted Length - Clams in Selnium NFBTVSFE IBT on a monthly 4VSWFZ MS urvey, [email protected] urvey, A Corbula S eological (FPMPHJDBM G . S is a dominant clam that accumulates . U 64 UIF tewart, tewart, S obin R SELENIUMIN CL !sh and other wildlife species. discharges, have been reduced over the last decade. Aer# 1998, clam selenium concentrations (adjusted for pre- of 50% levels to declined size) clam in dierences " 1998 concentrations, but have increased in recent years. Selenium burdens remain higher than levels commonly associated with toxicity and reproductive impairment in beer% understand factors in$uencing variability over time. For example, clam size was found to in$uence the uptake of selenium by individual clams and thus impact the apparent selenium burden of the population. Anthropogenic sources of selenium to includingthe Bay, agricultural inputs to the San Joaquin River and re!nery prey item for white sturgeon, the key target species identi!ed in the North Bay Selenium TMDL project. 4JODF selenium concentrations in basis to track seasonal and interannual trends and to Selenium concentrations in the North Bay clams continue to %uctuate seasonally and from year to year. amurensis Corbula selenium to an unusual degree due to its slow depuration of this element. &ese clams are a primary Contact: Contact: 38 Water Quality Trends at a Glance

Toxics and Bacteria

1 Methylmercury in sport fish 2 pcbs in sport fish 3 dioxins in sport fish 0.7 No trend in 500 NO APPARENT TREND 0.6 OEHHA striped bass since 1971 450 0.5 no consumption threshold 400 0.44 3.00 0.4 350 California Halibut 2.50 0.3 300 Switch Switch Jack Smelt 250 to croaker 2.00 to croaker 0.2 OEHHA 2 Striped Bass without meal/wk without PCBs (ppb) 200 skin 1.50 skin Methylmercury (ppm) 0.1 threshold 0.07 White Croaker 150 OEHHA no consumption threshold 1.00 0.0 White Sturgeon 120 100 TEQs (ppt) Sum of 1994 1997 2000 2003 2006 2009 0.50 50 OEHHA 2 meal/wk threshold 21 0.14 0 0.00 1994 1997 2000 2003 2006 2009 1994 1997 2000 2003 2006 2009

Shiner Surfperch White Croaker

4 Percent toxic sediment samples

100 NO APPARENT TREND 5 90 beach report card grades 80 70 4.0 NO APPARENT TREND 60 3.0 50 2.0 40 30 1.0 Toxic Samples (%) Toxic 20 0.0 10 2005 2006 2007 2008 2009 2010 2011 0

1993 1995 1997 1999 2001 2003 2005 2007 2009

SEE PAGE 45 FOR GRAPH DETAILS STATUS AND TRENDS UPDATE | WATER QUALITY TRENDS AT A GLANCE THE PULSE OF THE ESTUARY 2011 39 2010 2000 4% decrease since 1993 1990 105% increase since 1993 1980

2010

chlorophyll in south bay chlorophyll

30 25 20 15 10 5 0

(µg/L) a Chlorophyll 3 2005 2000

xygen

1995

60 50 40 100 90 80

2010 70

bottom dissolved oxygen in south bay oxygen bottom dissolved O Dissolved Oxygen (% saturation) (% Oxygen Dissolved 5 2000 1990 SEE PAGE 45 FORGRAPH 45 PAGE DETAILS SEE 72% increase since 1993

1980 issolved issolved

30 25 20 15 10 5 0

chlorophyll in san pablo bay pablo in san chlorophyll

D (µg/L) a Chlorophyll 2 2010 2005 2010 2000 1995 2000 1990 32% increase since 1993 Time Corbula invasion 1986 1985 1990 1980 300% increase in warm season in warm since 1990

hlorophyll and hlorophyll 1975 summer chlorophyll in south bay summer chlorophyll 2345678

1980

(µg/L) a

C Chlorophyll

5 0 25 20 15 10 30

chlorophyll in suisun Bay chlorophyll

Chlorophyll Chlorophyll (µg/L) a 1 Water Quality Trends at a Glance 40 STATUS AND TRENDS UPDATE | WATER QUALITY TRENDS AT A GLANCE

Nutrients and Sediments

1 ammonium 2 nitrate and nitrite 70 NO APPARENT TREND – INCOMPLETE TIME SERIES NO APPARENT TREND – INCOMPLETE TIME SERIES 18 60 16 14 50 Suisun Bay 12 40 10 San Pablo Bay 30 8 South Bay 6 20

Ammonium (µmol/L) 4 Nitrate + Nitrite (µmol/L) 2 10 0 0 1995 2000 2005 2010 1995 2000 2005 2010

3 suspended sediment 4 in-bay disposal of dredged material

350 Suisun Bay 36% decrease 2,500,000 On track to meet a Bay-wide limit of 1.5 million Alcatraz Island 300 between 1998 cubic yards and 1999 by 2012 San Pablo Bay 250 2,000,000 Carquinez Strait 200 1,500,000 150 1,000,000 100 Volume (cubic yards) Volume 50 500,000

Suspended-sediment Concentration (mg/L) 0 0 1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010

SEE PAGE 45 FOR GRAPH DETAILS 41

3 delta outflow STATUS AND TRENDS UPDATE High ﬂows Flows and Loads 60,000 of 2006 50,000 40,000 guadalupe river flow 1 30,000 250 20,000 2010 10,000 200 |

0 AT A GLAN TRENDS WATER QUALITY

Flow (million cubic meters) 1995 1997 1999 2001 2003 2005 2007 2009 150

100 4 Delta sediment load 50 3.0 Flow (million cubic meters) 0 2.5 1930 1935 1940 1945 1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000 2005 2010 2.0

1.5 guadalupe river 2 1.0 C

mercury load E 0.5

120 Sediment (million tonnes) Variation 0.0 100 driven by 1995 1997 1999 2001 2003 2005 2007 2009 rainfall 80 60 5 Delta mercury load 15kg 40 700 Large mercury 20 600 loads from rivers Wet Season Total Mercury (kg) Total Season Wet and Yolo Bypass 0 500 due to high ﬂow 2003 2004 2005 2006 2007 2008 2009 2010 and sediment load 400

300 78 kg 200 100 Annual Total Mercury Load (kg) Total Annual 0 1995 1997 1999 2001 2003 2005 2007 2009

SEE PAGE 45 FOR GRAPH DETAILS 42 STATUS AND TRENDS UPDATE | WATER QUALITY TRENDS AT A GLANCE

Human Presence

1 bay area population 7.2 million 8 Population has Sonoma Napa 7 increased every decade Solano Marin 6 since 1850 Santa Clara Contra Costa

5 San Mateo Alameda San Francisco 4

Population (Millions) Population 2

0 1850 1860 1870 1880 1890 1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 2000 2010

2 bay Area vehicles miles traveled 3 flows from top ten wastewater treatment plants 12% 120 decrease 183% 600 increase since 1997 100 1980-2005 500

80 400

60 300

40 200

Average Daily Flow (MGD) 100 Vehicle Miles Traveled (Billions) Traveled Miles Vehicle 0 0 1980 1985 1990 1995 2000 2005 2006 2007 2008 1997 1998 1990 2000 2001 2002 2003 2004 2005 2006 2007 2007 2009 2010

SEE PAGE 45 FOR GRAPH DETAILS

STATUS AND TRENDS UPDATE | WATER QUALITY TRENDS AT A GLANCE THE PULSE OF THE ESTUARY 2011

43 2010 2010

2010 Annual Average Annual Rolling Year 20 Average 2005 2000 1990

6.4 inch increase increase 1920-2005 2000 2000 1980 1970

1960 1995 1995 1950

1940 GOAL IS 100,000 BY 2100 1930 1990 12,549ACRES RESTORED SINCE 1986 1920 1910 0 1900 3.8 3.6 3.2 2.8 2.4 2.0 3.4 3.0 2.6 2.2

Restored wetland opened to tidal action to tidal Restored wetland opened

sea level at golden gate at level sea 4,000 2,000 8,000 6,000

at the Golden Gate Golden the at 14,000 12,000 10,000 Acres Restored Restored Acres Mean Sea Level (feet relative to MLLW) to relative (feet Level Sea Mean 5 2 2010 2000 1990 1980 SEE PAGE 45 FORGRAPH 45 PAGE DETAILS SEE NO TREND NO 2010 1970 2010 1960 2008 2008 1950 NOTREND – SHORTTIME SERIES VARIABILITY AND LARGE SEASONAL DRIVEN VARIABILITY – TREND NO BY FRESHWATER INFLOW 2006 2006 1940 2004 2004 1930 abitat 2002 2002 1920 H 1910 2000 2000 1900 1998 1998 1890 1996 1996 1880 1994 1994 1870 1992 1992 1860 rainfall in the bay area in the bay rainfall water temperature water 1850 1990 salinity 1990

15 13 11 21 19 17 0 22 20 18 16 32 30 28 26 24

20 10 50 40 30

Water Temperature (ºC) Temperature Water Salinity (‰) Salinity limate and limate (Inches) Rainfall 1 3 4 C 44 STATUS AND TRENDS UPDATE | WATER QUALITY TRENDS AT A GLANCE

Populations

pelagic organism decline

DELTA SMELT STRIPED BASS 1800 20000

1500 15000 1200

900 10000 Abundance 600 Abundance 5000 300

0 0 1966 1970 1974 1978 1982 1986 1990 1994 1998 2002 2006 2006 1966 1970 1974 1978 1982 1986 1990 1994 1998 2002 2000 2000

All species have been near record lows since 2002

LONGFIN SMELT THREADFIN SHAD 100000 16000 14000 80000 12000 60000 10000 8000

Abundance 40000 Abundance 6000 20000 4000 2000 0 0 1966 1970 1974 1978 1982 1986 1990 1994 1998 2002 2006 1966 1970 1974 1978 1982 1986 1990 1994 1998 2002 2006 2000 2000

LONGFIN SMELT

SEE PAGE 45 FOR GRAPH DETAILS STATUS AND TRENDS UPDATE | WATER QUALITY TRENDS AT A GLANCE THE PULSE OF THE ESTUARY 2011 45 ASS B GE 44 GE PA All data from: Baxter, R. et al. 2010. Interagency Ecological Program 2010 Pelagic Organism Decline Work Plan and Synthesis of Results. h%p://www.water.ca.gov/iep/docs/ FinalPOD2010Workplan12610.pdf STRIPED STRIPED

64 UIF CZ DPMMFDUFE EBUB GE 43 GE Data from National Oceanic and

) Data from the California Wetlands ) Same information as #3. Salinity ) ) Water year median water temperature ) Annual rainfall measured at San Jose re$ects freshwater in $ow to the Bay with lower values for higher in$ows.35. of salinityOcean a has water 1 2 3 4 5 Portal (www.californiawetlands.net/ tracker/). and interquartile range, San Mateo Bridge,4 feet below mean lower low water. From NJOVUF Geological Survey (Buchanan 2009). 1999-2000 not shown because data were temporarily not collected during bridgeconstruction. data. Some missing variation of periods is causederent di" by Atmospheric Administration: h% p:// tidesandcurrents.noaa.gov/data_menu.sh UNM CEBUFFEBUF XM@TFOTPS@IJTU8SFMBUJWFEBUVN VOJUTIJěHTUO 4BO 'SB ODJTDP$ $"UZQF)JTUPSJD 5JEF %B UBGPSNBU7JFX %BUB shown as index for Bay Area rainfall. &dataese are for climatic years (July 1 to June30 with the year corresponding to the end date). Source: Jan Null, Golden Gate Weather Services PA $POUSB 4VSWFZ #VSFBV 4$78% $FOUSBM $FOTVT (FPMPHJDBM 64"$& 64 64 $&1 'SBODJTDP BOE UIF UIF 4BO CZ GSPN IĨQTčBZXSVTHTHPWTFEJNFOU 4$763111 .6% GE 42 GE GE 41 GE %BUB ) Total loads for each water year. Loads )Total sediment loads for each water ) Total loads for each water year. ) Data from Caltrans: h %p://tra'c- ) Daily average Delta out$ow from ) Data provided by the ten largest ) Data from the Association of Bay Area cont_monitoring/). Data for all of these graphs are for water30). Sep to 1 (Oct years year. Loads based on continuous measurements taken at Mallard Island by64(4 1 2 3 4 5 1 2 3 from 2002–2006 are based on ! eld data. Loads for earlier and later years are estimated from relationships observedbetween suspended sediment and mercury2002–2006. in PA Bayside System Authority, San Mateo, Vallejo. Additional matching funds for this studyQSPWJEFE BOE DAYFLOW. DAYFLOW data are available from the California Department of Water Resources (www.water.ca.gov/day$ow/). counts.dot.ca.gov/ municipal wastewater dischargers to theBay: San Jose, East Bay Dischargers, East#BZ Costa, Palo Alto, Fair! eld-Suisun, South (PWFSONFOUT h%p://census.abag.ca.gov/counties/ counties.htm PA THREADFIN SHAD THREADFIN BU PG 4VSWFZ TčBZ $PSQT NPOUIMZ 64(4 "SNZ (FPMPHJDBM DPMMFDUFE GSPN TčBZXSVTHTHPW 64 64 UIF %BUB %BUB UIF

64(4 CZ GSPN D 2 D 64(4 GSPN GE 39 GE GE 40 GE %BUB AN ) Minimum dissolved oxygen percent

) Chlorophyll a in South Bay, averaged ) Chlorophyll a, averaged over top 3 ) Suspended-sediment concentration, ) Chlorophyll a, averaged over top 3 ) Chlorophyll a, averaged over top 3 over top 3 meters, allmeters, stations, June- 3 and top over October season for each year. Trend line is a smoothed !t. PA %BUB access/wqdata. Data from prior to 1969 GSPN !xed stations along the spine of the Bay. Data for stations D10, D8, D7, D6, and D41 from IEP: h%p://www.water.ca.gov/ bdma/meta/Discrete/data.cfm. 1 3 4 2 3 4 5 1 indicates 50% saturation. 50% indicates PA saturation from each South Bay station, averaged over all stations. Minimum dissolved oxygen values typically occurat or near the bo%om. Horizontal line and s7). meters and all stations, in Suisun(stations Bay D10, D8, D7, D6, s4, s5, s6, wr.usgs.gov/access/wqdata Dumbarton Bridge, 20 feet below mean lower low water. Based on 15-minute data DPMMFDUFE (Buchanan and Morgan 2010). Water years 2008-2010 are provisional data. meters and all stations, in San Pablo Bay (stations D41, s11, s12, s13, s14, and s15). meters and all stations, in South Bay (stations s21, s22, s23, s24, s25, s33). s26, and s32, s31, s27,s30, s29, s28, Engineers. etails D ). ELT M 23 raph raph E G GE 38 GE G ) Average of Bay Area summer beach ) Sediment samples are tested using ) Bay-wide average PCB concentrations. ) Bay-wide average dioxin TEQ ) Bay-wide average methylmercury PA DELTA S DELTA amphipods and mussel larvae. mussel and amphipods 5 4 2 3 PA 1 season (April-October) grades from Heal the Bay’s annual beach report card ( concentrations. &e San Francisco Bay Water Quality Control Board has developed a screening value for dioxin TEQs of 0.14 parts per trillion (ppt). White2009. croakerin skin were analyzedwithout and with1994-2006, skinfrom &e no consumption advisory tissue level for PCBs is 120 ppb, and the two serving advisory tissue level is 21 ppb. White croaker were analyzed without skin in2009, and with skin in previous years. ppb, and the two serving advisory tissueppb. 70 levelis concentrations. Averages for striped bassbased on concentrations for individual !normalizedsh to 60 cm. & e no consumption advisory tissue level for mercury is 440 46

feature articles 47

48 78 a growing concern: recent findings on risks potential effects to birds from pollutants of nutrients on in san francisco bay bay phytoplankton 86 Sidebar: Another Dimension feature articles 50 Sidebar: Harmful of the Mercury Problem Algal Blooms 58 Sidebar: Exceptional 88 Conditions in Spring 2011 contaminant exposure and effects at the top of the bay food chain: evidence from 66 harbor seals effects of pollutants

on bay fish THE PULSE OF THE ESTUARY 2011 71 Sidebar: Exposure and Effects Workgroup

48 FEATURE ARTICLES | PHYTOPLANKTON

CHRISTINE WERME, Independent Consultant )REN TABERSKI, San Francisco Bay Regional Water Quality Control Board LESTER MCKEE, San Francisco Estuary Institute %*$,%6(%"-& 4BO'SBODJTDP4UBUF6OJWFSTJUZ TOM HALL, EOA, Inc. MIKE CONNOR, East Bay Dischargers Authority

a growing concern: potential effects of nutrients on bay phytoplankton

highlights #e complexity of the In the Sacramento River ecosystem and uncer- Phytoplankton, the and northern portions of tainty about future microscopic plants at Nutrient loading to the Bay the Bay, there is evidence conditions underlie the the base of the food is high, but phytoplankton Since the late 1990s, suggesting that high levels growing importance chain, are the focus of a biomass has been low phytoplankton biomass of one form of nitrogen, of nutrient and phyto- new San Francisco Bay compared to other urban has increased throughout ammonium, can inhibit plankton monitoring, Nutrients Strategy estuaries, in part a result of the Bay, a response to rather than stimulate phy- research, and modeling turbid waters that limit light increased water clarity and toplankton growth penetration and high grazing favorable wider regional pressures, particularly by oceanographic conditions invasive clams FEATURE ARTICLES | PHYTOPLANKTON THE PULSE OF THE ESTUARY 2011 49 - - utney. P usan S llustration by I

Thalassiosira rotula. Thalassiosira µ uence the rest of the food chain. nities, the rest which in$uence can riverine, atmospheric, and groundwater sources and pathways. pathways. and sources groundwater and atmospheric, riverine, inputs nitrogen increase greatly can populations human Dense runo and " of fertilizers discharges to applied sewage through areas. other and !elds, lawns, agricultural of include measurements generally studies Phytoplankton compo of the species studies include sometimes and biomass is measured Biomass community. sition of the phytoplankton pigment plant whichas chlorophyll, is the easily measured energy light, capturing Species absorbs in photosynthesis. that in the community, changes detect can studies composition and agellates $ smaller to diatoms as shi larger such #s from of incidence or increased (cyanobacteria) algae blue-green in the Changes species. nuisance or other toxin-producing trigger community can of the phytoplankton composition commu in the community structure predator of their changes - - Nitrogen is the nutrient that usually limits phytoplankton usually limits phytoplankton is that the nutrient Nitrogen exists as an Nitrogen waters. estuarine growth in marine and in terrestrial is also present It in the atmosphere. gas abundant and as proteins such molecules in organic systems, aquatic and nitrate, ammonium, forms, including in inorganic and urea, usually the forms that are Ammonium nitrate and nitrite. and from estuaries enters Nitrogen growth. phytoplankton control runoff, and wastewater treatment plants, is a major focus of environmental monitoring and management programs. Phosphorus inputs are also a concern, particularly in areas salinity. low with In typical, healthy coastal ecosystems, phytoplankton popu lations followblooming whenseasonal patterns, tempera ture and light levels rise during the spring, then dropping off a little before rising again in the fall, when cooling waters promote mixing, returning nutrients from deeper waters to the surface. However, in San Francisco Bay the water column is usually well-mixed during every season. Seasonal changes in nutrient concentrations are largely determined by changes in inputs. Seasonal spring blooms occur fairly regularly in South Bay, Central Bay, and San Pablo Bays, but less frequently in Suisun Bay. - - - $ PG E TZTUFN D I 6OJUFE UIF S UIF QSPCMFN

PG XIFSF UIF TORS TORS A LE LE

4USBJUT SFHJPOT B IN? LITY FTUVBSJFT A A NDIC 64 H I ROU $BSRVJOF[ QPQVMBUFE C SE OF T L JO UIF NBOZ A A *O GSPN FTUVBSZ TER QU 50 OOD E A F G FWFSZ PA 6QTUSFBN , T THE B T THE IGNS OF OF IGNS SSENTI BAR THE A – overstimulation of algal growth by an excess of nutrients – which can lead to low levels of dissolved oxygen, excess ( blooms or harmful nuisance algal and turbidity, excess nutrients, especially nitrogen from agriculture, urban The abundance and species composition of phytoplankton communities are important measures of environmental quality in all freshwater, estuarine, and marine ecosystems. "MNPTU States and around the world shows signs of eutrophication high enough levels to inhibit growth of a group of desirable phytoplankton species, the diatoms. E W OF plankton biomass is increasing, prompting the question of whether excess phytoplankton growth, which has not been one in the fu become may Bay, Francisco for San a problem UVSF is dominated more by riverine than by oceanic conditions, – ammo one form of nitrogen that concern, is another there nium – from wastewater treatment plant e *uent has reached the past, the phytoplankton have not been a major focus of the Regional Monitoring Program forQuality Water in the San Francisco Estuary (RMP). &at is changing with the development of a new San Francisco Bay Nutrient Strategy, developed by the RMP in collaboration with other scientists and environmental managers. the In as Bay a whole, phyto At the very base of the food chain in San Francisco Bay and the Delta are the phytoplankton (also referred to as algae), microscopic plants that dri# in the water column and provide food for zooplankton, clams, and !lter-feeding !shes. In S 50 FEATURE ARTICLES | PHYTOPLANKTON

SIDEBAR paralytic shell!sh poisoning. Symptoms ing. Symptoms include gastrointestinal Pier. The species has been implicated HARMFUL can include numbness, lack of muscle and neurological conditions, including in fish kills in other regions. Akashiwo ALGAL BLOOMS control, respiratory failure, and death for dementia. In 1990, domoic acid poi- sanguine does not produce a toxin but can marine mammals, !sh, and humans. &ere soning was found in central California clog shellfish gills and lead to fish kills Take a walk along the Bay’s fishing piers is no antidote or cure for paralytic shell!sh sea lions (Scholin et al. 2000). One when the bloom ends and decomposing and you’ll see the posted signs that warn poisoning. Alexandrium blooms with para- toxin-producing species, Pseudo-nitzchia algae deplete oxygen in the water column. against harvesting mussels during May lytic shell!sh poisoning occur along the australis, was blamed for the 1991 deaths Akashiwa sanguine also produces a foamy, through October. Similar signs occur California coast but are rare within the Bay. of pelicans, cormorants, and sea lions in surfactant-like protein that can coat bird along the entire California coastline. Monterey Bay. Scientists feathers and lead to hypothermia. As An annual preventative quarantine for from The Marine Mam- San Francisco Bay enters a regime with sport-harvested mussels protects the mal Center have found larger and more frequent phytoplankton public from consuming shellfish that have that low doses of domoic blooms, harmful algae may become more accumulated toxins generated during acid can cause epilepsy in frequent or have greater consequences. what are called harmful algal blooms. The sea lions (Goldstein et al. California Department of Public Health 2007) and are studying monitors potentially toxic algae through other possible long-term its volunteer Marine Biotoxin Program effects. and prepares regular reports, available at www.cdph.ca.gov/healthinfo/envi- A blue-green alga or cya- ronhealth/water/Pages/Shellfish.aspx. nobacterium, Microcystis

Compared to some other parts of the aeruginosa, has recently Fimrite, P. 2010. Monterey sea o%ers killed by toxic algae. San Francisco Chronicle September 11, 2010 Page C-1. world, San Francisco Bay is relatively free µMicrocystis aeruginosa. Illustration by Linda Wanczyk. been implicated in sea ot- Goldstein, T., J.A.K. Mazet, T.S. Zabka, G. Langlois, K.M. from harmful algal blooms, with only six ter deaths in Monterey Bay Colegrove, M. Silver, S. Bargu, F. Van Dolah, T. Leigh!eld, P.A. Conrad, J. Barakos, D.C. Williams, S. Dennison, M. blooms reported since 1995 But some of Were algal toxins the inspiration for (Fimrite, 2010). Microcystis has also been Haulena, and F.M.D. Gulland. 2007. Novel Symptomatol- ogy and changing epidemiology of domoic acid toxicosis in the toxins produced by a number of local )JUDIDPDLT5IF#JSET *O IVO- blamed for skin rashes among windsurf- California sea lions (Zalophus californianus): an increasing algal species can be deadly. dreds of Sooty Shearwaters went berserk, ers. Microcystis blooms have occurred in risk to marine mammal health. Proceedings of the Royal Society B 275:267–276. crashing into roofs and windows near the Delta and the North Bay every year Lehman, W., G. Boyer, C. Hall, S. Waller, and K. Gertz. 2005. &e historic shellmounds of the San Santa Cruz, and shortly thereafter, Hitch- since 1999 (Lehman et al. 2005, 2008), Distribution and toxicity of a new colonial Microcystis aeruginosa bloom in the San Francisco Estuary, California. Francisco Bay Area provide evidence of cock began to film Daphne Du Maurier’s and they are regarded as a potential threat Hydrobiologia 541: 87–99. thousands of years of human shell!sh story of a similar incident, choosing to humans and wildlife. Lehman, W., G. Boyer, M. Satchwell, and S. Waller. 2008. &e in$uence of environmental conditions on the seasonal consumption. &e !rst documented cases Bodega Bay as his location. The real-life variation of Microcystis cell density and microystins concentration in San Francisco Estuary. Hydrobiologia of toxic shell!sh poisoning were reported events may have been the result of a toxin Other possibly harmful species known to 600: 187–204. in 1927, and it took ten years to identify produced by another phytoplankton occur within the Bay include the raphido- Scholin, C.A., F. Gulland, G.J. Douce%e, S. Benson, M. Busman, F.P. Chavez, J. Cordaro, R. DeLong, A. De the cause (Sommer and Meyer 1937). It group, diatoms in the genus Pseudo- phyte Heterosigma akashiwo and the di- Vogelaere, J. Harvey, M. Haulena, K. Lefebvre, T. Lipscomb, S. Loscuto", L.L. Lowenstine, R. Marin III, P.E. Miller, was a dino$agellate, Alexandrium catanella. nitzchia. At high densities Pseudo-nitzchia noflagellate Akashiwo sanguine. In recent W.A. McLellan, P.D.R. Moeller, C.L. Powell, T. Rowles, P. Silvagni, M. Silver, T. Spraker, V. Trainer, and F.M. Dolah. &e toxin produced by many Alexandrium species produce sufficient concentrations years, Heterosigma akashiwo blooms have 2000. Mortality of sea lions along the central California species, when su'ciently concentrated of the toxin domoic acid to cause a condi- been detected outside the Golden Gate, coast linked to a toxic diatom bloom. Nature 403: 80–84. Sommer, H. and K.F. Meyer. 1937. Paralytic shell!sh poison- by shell!sh, causes a condition known as tion known as amnesic shellfish poison- in Richardson Bay, and near the Berkeley ing. Archives of Pathology 24:560–598. FEATURE ARTICLES | PHYTOPLANKTON THE PULSE OF THE ESTUARY 2011 51 - 0 0 20 0 9 19 0 8 Conversion from primary to secondary and ad primary and secondary from to Conversion 19 0 7 19 1

0 6 19 FIGURE Implementation of improved wastewater treatment eliminatedoxygen periods"andkills sh inthe South Bay. of low vanced secondary treatment removed oxygen-depletinge organic*uents. J.ma Cloern,%er from wastewaterunpublished data. Footnote: Red line shows 5 mg/L water quality objective. 5 0 5 0 1 1 $ G I - F N SA Y A XYGEN IN ISTORY OF ISTORY O H

NCISCO B NCISCO ). In other estuaries, such conditions are often due A W 1 HE HE R O RE U the oxygen demand of the effluent. demand the oxygen municipal dischargers with permits to discharge to shallow waters implemented additional facilities to further reduce oxygen-depleting organic matter. Some of these advanced secondary treatment facilities included filtration and nitrification, a process that changes ammonium to nitrate, changing the balance of these two nutrients and reducing which reduced the loads of organic effluents discharged into rivers and the PrimaryBay. treatment is a physical process that removes solids through settling, followed by oxida bacterial adds treatment Secondary disinfection. tion of remaining particulate and dissolved organic matter and sedimentation, which greatly decreases the amount of oxygen-depleting organic matter. In the late 1970s, to decomposing phytoplankton following algal blooms. In the Bay, it was the large inputs of oxygen-depleting organic waste that led to foul conditions. The passage of the Clean Water Act in 1972 required the conversion from primary to secondary treatment of sewage, F In the 1950s and 1960s, before upgrades to wastewater treatment facilities, San Francisco Bay experienced oxygen fish and depletion kills, ( Bay particularly in the South T L 52 FEATURE ARTICLES | PHYTOPLANKTON

A FORTUITOUSLY Comprehensive studies of nutrient loads to the Bay have inhabit the water column. San Francisco Bay had a dramatic UNUSUAL ESTUARY not been completed. Available information suggests that illustration of this process in the late 1980s and early 1990s. annual nutrient loads to the Bay may be as high or higher In 1986, a few specimens of a never-before-seen Asian 5IF64(FPMPHJDBM4VSWFZ 64(4 IBTTUVEJFEXBUFS UIBOMPBETUPPUIFSMBSHF64FTUVBSJFT CVUQIZUPQMBOLUPO clam, Corbula amurensis, were discovered in Suisun Bay. It quality parameters in the Bay since 1968 and phytoplank- biomass is low (FIGURE 3). Small, lagoon-type estuar- quickly became the most common bottom animal in the ton biomass, measured as chlorophyll, since 1977. The ies, such as Barnegat Bay in New Jersey, the Coastal Bays North Bay, and it also invaded Central and South bays thousands of measurements they have made provide of Maryland and Virginia, Florida Bay at the southern end (Cohen 2005). Phytoplankton production in Suisun Bay WBMVBCMFJOTJHIUT'PSFYBNQMF UIF64(4IBTNBEFNPSF of Florida, and Pensacola Bay on the Gulf Coast, receive had already been low before the invasion, but it plummeted than 8500 measurements of ammonium and more than relatively low loads of nitrogen. Estuaries with large river afterwards, with the disappearance of any summer bloom 9000 measurements of nitrate in Bay waters since 1968. inputs, such as Delaware Bay and Chesapeake Bay in the (Cloern and Dugdale 2010). Chlorophyll concentrations In recent years, these studies have found that nutrient mid-Atlantic states, and Narragansett Bay in New England, remained low in Suisun Bay in the wake of the invasion concentrations in San Francisco Bay remain high, but receive relatively higher loads. San Francisco Bay, particu- (FIGURE 4). Narragansett Bay in New England is also eutrophication has not been a major concern. Nutrients larly the North Bay, receives large river inputs, and its total subject to heavy grazing pressure, but in that estuary, it is and phytoplankton growth have not been considered an nitrogen loads are large. largely native clams and mussels that keep phytoplankton imminent threat to Bay water quality. biomass low. One reason for historically low phytoplankton productiv- "OBMZTJTPGSFDFOU64(4EBUBTIPXBTMJHIUEFDSFBTJOH ity in San Francisco Bay is the turbid water (Cloern 1982). gradient in ammonium and nitrate concentrations from the Historically, large sediment loads from the Sacramento fresher waters of Suisun Bay in the north to the more saline and San Joaquin rivers in the north (McKee et al. 2006) waters in the Central Bay (reviewed in McKee et al. 2011). and the local watersheds in the south (Lewicki and McKee The Lower South Bay has the highest levels of nitrate, while 2009), the shallow depth of the Bay, and continual mixing high ammonium levels are found in all geographic segments by waves and tides have kept Bay waters turbid, limiting of the Bay. Interestingly, the average concentrations of light penetration into the water column and consequently ammonium, nitrate, and nitrite in many Bay water samples limiting photosynthesis. But light limitation is not the only from 1995–2010 (FIGURE 2) are in same ranges as results answer – both Delaware and Chesapeake bays are turbid, from samples taken throughout the Bay during 1958–1964 but have high chlorophyll levels. Narragansett Bay is rela- and included in San Francisco Bay’s first comprehensive tively clear, with transparency that is two and a half times Basin Plan (SFBRWCB 1975). The most notable change greater than San Francisco Bay, but chlorophyll levels are is a large decrease in average ammonium concentrations in relatively low. Nutrient levels trigger eutrophic conditions Lower South Bay, a result of advanced secondary wastewa- despite low light levels in some estuaries, but not in San ter treatment. During 1958–1964, ammonium concentra- Francisco Bay. tions were much higher in the Lower South Bay than in other segments. Now ammonium concentrations are more Another reason for low phytoplankton biomass is grazing. similar throughout all segments of the Bay, although a clear Grazing pressure by rapid filtering rates in clams and other gradient exists from Suisun Bay to Central Bay. animals has long been known to reduce populations of µThalassiosira punctigera. Illustration by Susan Putney. phytoplankton and also zooplankton, the small animals that FEATURE ARTICLES | PHYTOPLANKTON THE PULSE OF THE ESTUARY 2011 53 EBUB 64(4 San Pablo Bay San Pablo Central Bay South Bay Lower South Bay Rivers Suisun Bay Carquinez Strait TFHNFOUT BMM JO EFUFDUFE 2010 CF DBO 2009 2008 BNNPOJVN PG 2007 &ere is considerable overlap in concentrations between the segments. 2006 DPODFOUSBUJPOT 2005 7BSJBCMF 2004 #BZ 2003 $FOUSBM UP 2002 #BZ 2001 4VJTVO GSPN 2000 HSBEJFOU

1999 B BMPOH 1998 TMJHIUMZ 1997 EFDSFBTF 1996 2

5 0

10 20 15 Ammonium (µmol/L) Ammonium FIGURE Ammonium in water samples from geographic segments of San Francisco Bay, 1995–2010. 1995–2010. Bay, Francisco San of segments geographic from samples water in Ammonium $PODFOUSBUJPOT IĨQTčBZXSVTHTHPWBDDFTTXREBUB 54 FEATURE ARTICLES | PHYTOPLANKTON

60 Chesapeake FIGURE 3 50 Nitrogen loads to San Francisco Bay are high in compar- 40 ison to other U.S. estuaries, but average Bay phytoplankton biomass (chlorophyll) during blooms is low. (Data Delaware from Glibert et al. 2010) 30 Coastal Bays 20 (MD and VA) Chlorophyll (µg/L) Barnegat (NJ) Pensacola 10 Narragansett Florida Bay San Francisco 0 0 5 10 15 20 25 30 35 Nitrogen load (g N/m2 yr)

FIGURE 4 Chlorophyll concentrations and abundance of the invasive Asian clam Corbula amurensis in Suisun Bay. Grazing pressure by the invasive clam eliminated phytoplankton blooms. (Data from the Interagency Ecological Program.) Corbula amurensis

50 6000 40 ) 2 ) 3 30 4000 (#/m

20 2000 Chla (mg/m Corbula 10 0 0 1970 1975 1980 1985 1990 1995 2000 2005 FEATURE ARTICLES | PHYTOPLANKTON THE PULSE OF THE ESTUARY 2011 55 - aggiomo. S hotograph by Mariella P Skeletonema costatum. Skeletonema µ No matter the cause, be it changing water clarity, grazing, or changing inputs and influences from the Pacific Ocean, recent evidence suggests that the resilience of the phyto plankton populations to high nutrient loads is decreasing, and phytoplankton productivity is increasing, particularly Bay. in the South New invasive species may also have played a role. San Francisco Bay is one of the most invaded estuaries in the world, with new species continually changing community composition, species interactions, and ecological processes. Two new species of predatory zooplankton were found in the late 1990s. These new arrivals reduced the populations of existing zooplankton species that fed on phytoplankton, further reducing grazing pressure (Hoof and Bollens 2004). - - - - ). 58 E G - - PA , - FOUFSJOH ). & ese results are especially 6 EBAR D RE I S GU TFBXBUFS I F 6QXFMMFE important, because they point to long-term, broad-scale forces beyond the control of water quality managers. Dungeness crabs and $at! sh in the marine portions of the & e biomassBay. of clam predators increased four-fold, and particularly in the South the !Bay, lter-feeding clam popula ( plummeted tions region-wide growth of phytoplankton, particularly diatoms, than conditions during 1975–1986. A change in the California Current System, which Califor Baja to extends Oregon from nia, brought stronger upwelling to the region, a situation in which nutrient- rich bottom waters are brought to the surface, promoting increased produc tivity (Cloern et al. 2007, Cloern et BM the Bay at the Golden Gate, contains high levels of nitrate, phosphate, and cell walls by contain characterized are Diatoms silicate. ing silicate. In those areas of the Bay where conditions are favorable, intrusions of oceanic water are expected to enhance phytoplankton production. In 2011, scientists are learning that such intrusions other have may environ effects as well ( mental for Dunge also was 1990s good in the late &e upwelling ness crabs, sanddabs, and other $at!sh that feed on the clams that exert great grazing pressure on the phytoplankton populations (Cloern et al. 2007, Cloern et al. 2010). Cold, nutrient-rich waters along the coast drove the increases in Large-scale processes are also an Oceano important driving force. graphic conditions can vary on long time scales, and conditions during 1992–2003 were more favorable to ------SS A

HYTO P ). Although most pronounced in the pronounced ). Although most 5 RE SING SING A GU I F NKTON BIOM NKTON A ONCERNS FOR NCRE have contributed to increases in phytoplankton biomass. For example, annual loads of cadmium, copper, and other toxic metals have declined greatly since the 1980s. These production. growth and affect phytoplankton metals may the pool of sediments sent down waterways during the Gold Rush. &at increase in water clarity is expected to continue and serve may to fuel increased phytoplankton production. Continued improvements to municipal wastewater treat ment and better controls on industrial discharges may also Increased transparency is one logical explanation. &e 2009 Pulse of the Estuary focused on a major shi# in water quality that occurred in 1999 (Jassby et al. 2002, Schoellhamer 2009). In just one year, suspended sediment concentrations decreased by about 40%, most likely a result of depleting The 2006 Pulse of the Estuary reported on the increased phytoplankton biomass, possible several presenting hy transpar increased explain including to the trend, potheses ency, decreased metal toxicity, large-scale oceanographic processes, decreased predator grazing, and changes in the invasive species mix in the Bay (Cloern et al. 2006). incidence of fall blooms, and increases in the annual biomass biomass in the annual of fall increases incidence and blooms, ( minimum observed been in every of the region have increases Bay, South the historic is building that al. et 2011). Evidence (McKee Bay harmful of eutrophi potentially e"ects to of the Bay resilience be waning. may cation cant changes to condi to changes showing signi!cant some are data Recent 1990s, the late especially since Bay, Francisco tions in San South and Bay, Central Bay, Pablo particularly and in San increased spring blooms, include larger changes &ese Bay. C I PL 56 FEATURE ARTICLES | PHYTOPLANKTON

FIGURE 5 6 #roughout the Bay, chlorophyll levels have increased since the late 1990s, particularly in the South Bay. Data are for the South Bay, August-December (Cloern and Dug- 4 dale 2010). Bars show the middle 50% of values for each year. Chlorophyll a (µg/L) 2

1980 1985 1990 1995 2000 2005 FEATURE ARTICLES | PHYTOPLANKTON THE PULSE OF THE ESTUARY 2011 57 00 0 2 Dungeness Crab 95 9 1 Bay Shrimp 90 9 1 85 9 1 English Sole D E 80 9 1

0 5

8 6 4 2 0 20 15 10

Annual Catch per Hectare per Catch Annual g (dry) per m per (dry) g 2 ungeness D 6

Annual median biomass of "lter-feeding across the shallow habitats of the South Bay. Mean annual catch per hectare of the bivalve from the marine domains of San Francisco Bay. Data FIGURE predators English sole, Bay shrimp, and crab Top: clams om: om: & Bo from California Department of Fish and Game, presentedCloern in et al. (2007). 58 FEATURE ARTICLES | PHYTOPLANKTON

SIDEBAR EXCEPTIONAL CONDITIONS IN SPRING 2 011 San Francisco Bay is usually well mixed. In most other estuaries and coastal waters, seasonal changes in water temperatures and salinities create stratified conditions, which effectively separate surface and bottom waters. Phytoplankton in the surface waters deplete the available nutrients and then die, sinking through the temperature and salinity barrier to the bottom. While oxygen levels remain high in the surface waters, levels fall in the bottom waters, as bottom-dwelling animals respire, and bacteria use up oxygen as the phytoplankton decompose. Such conditions do not usually occur in the Bay.

64(4QSPGJMFTGSPNUIF4PVUI#BZPO"QSJM BOEUISPVHI- out the following summer showed a radically different pattern than the usual (FIGURE). There was extremely strong stratification, with high levels of chlorophyll in the surface layer and record low levels of dissolved oxygen in the bottom waters. Scientists from 4BO'SBODJTDP4UBUF6OJWFSTJUZT3PNCFSH5JCVSPO$FOUFSGPS&O- vironmental Studies and the Water Board were sampling in Suisun Bay at the same time and also reported strong stratification.

Preliminary analysis of the data suggested that the stratification resulted from an intrusion of ocean water into the Bay. Cold, salty water moved into the Bay and remained at the bottom, isolated from the surface waters. The April 2011 observations were important, as they showed that extremely low levels of dissolved oxygen can occur, even without local eutrophication and phytoplankton CMPPNT6OEFSTUBOEJOHTVDIJOUFSBDUJPOTPGUIF#BZFDPTZTUFN with the wider oceanic regime will be important to understanding the ongoing changes in Bay water quality.

µThe USGS Research Vessel Polaris. Photograph by Nicole David. FEATURE ARTICLES | PHYTOPLANKTON THE PULSE OF THE ESTUARY 2011 59 IĨQTčBZXSVTHTHPWBDDFTTXREBUB EBUB 64(4 PG and dissolved oxygen concentrations in the South Bay on April12, 2011, during an unusual period of strati!cation (ScreenDBQUVSF Graphs show depth pro !les along the transect shown on theat map the top. Chlorophyll, salinity, temperature, suspended particulate ma% er, 60 FEATURE ARTICLES | PHYTOPLANKTON

CONCERNS FOR COMMUNITY STRUCTURE WHAT MAKES THE NORTH INHIBITED AS AN INDICATOR OF BAY DIFFERENT?

PHYTOPLANKTON CHANGE? There are profound differences between the North Bay GROWTH IN From 1992 through 2001, Cloern and Dufford (2005) and the South Bay. The freshwater inputs to the North Bay SUISUN BAY found 500 distinct phytoplankton taxa, about 400 of which are dominated by river outflow, while in the South Bay, could be identified to species, along a transect from the water inputs from wastewater treatment plants, rainfall, and Meanwhile, another, very di"erent, kind of story has been Sacramento River to the South Bay. The community was runoff from small tributaries are also important. Residence emerging from the Sacramento–San Joaquin Delta and dominated by a few species, with the most abundant ten times of water masses in the North Bay are much shorter Suisun Bay (Wilkerson et al. 2006). &e Sacramento and taxa accounting for 77% of the cumulative biomass, and the than those in the South Bay. Wastewater treatment plants San Joaquin rivers have high nutrient levels, largely due to top 100 accounting for more than 99%. Diatoms con- are the major sources of nutrients to both the North Bay the dense and rapidly growing population in the region and tributed the most, accounting for more than 80% of total and the South Bay (Hager and Schemel 1996, Smith and agricultural production in the Central Valley. Loads of am- phytoplankton biomass (FIGURES 7 and TABLE 1). Hollibaugh 2006), however wastewater treatment is contin- monium discharged from the Sacramento regional wastewa- ually evolving. For example, advanced secondary treatment ter treatment plant, the largest discharger in the region, have The diatoms are relatively large in size compared to other at the Sunnyvale, San Jose, and Palo Alto treatment plants more than doubled since 1985 (Jassby 2008). groups, and large species dominated the community in the South Bay has substantially reduced the ammonium (Cloern and Dufford 2005). Why large species dominate input but equally increased nitrate input. In the North Bay and the Sacramento River, high con- in the Bay is not known. Possible explanations include high centrations of ammonium appear to inhibit rather than growth rates under low light conditions, efficiency in taking stimulate growth of diatom species (Dugdale et al. 2007), up nitrate, and protection from predation by the thick silica a finding that is counterintuitive, since increased nutrients shells that are characteristic of diatoms. typically mean increased phytoplankton growth. Wilker- son, Dugdale, and their co-workers monitored nitrogen Other urban estuaries, such as Chesapeake Bay, have used uptake by diatoms in water samples from the Bay. They measures of phytoplankton community structure, such as di- found that although nitrate concentrations were consis- versity and relative abundance of species groups, as indicators tently high, when ammonium concentrations were also of changing conditions. Changes in the Bay phytoplankton high, the nitrate was not taken up by the phytoplankton. community could also signal broader environmental change. This effect was observed throughout locations in the North Bay and was particularly strong in Suisun Bay, where only In Suisun Bay and the Delta, scientists are increasingly one phytoplankton bloom occurred during their three-year concerned that high concentrations of ammonium may be study. No similar inhibition has been detected in the South changing the species mix of the phytoplankton community. Bay. Reduced phytoplankton productivity under similar Changes in the ratios of ammonium to nitrate and in total conditions of high concentrations of both nitrate and am- nitrogen to total phosphorus (the nutrient that is usually monium has also been observed in Delaware Bay and the limiting in fresh waters) may favor growth of small cyano- Scheldt Estuary in western Europe (Yoshiyama and Sharp bacteria, such as the harmful species Microcystis aeruginosa 2006, Cox et al. 2009). (SIDEBAR, PAGE 50), and flagellates over larger diatoms species (Glibert 2010), potentially resulting in less desirable food for larger organisms. µCoscinodiscus oculus-iridis. Illustration by Susan Putney. FEATURE ARTICLES | PHYTOPLANKTON THE PULSE OF THE ESTUARY 2011 61

Protoperidinium sp. Thalassiosira decipiens Coscinodiscus centralis var. pacifica setigera Rhizosolenia Thalassiosira rotula Chaetoceros socialis Skeletonema costatum Ditylum brightwellii Gymnodinium sanguineum Coscinodiscus oculus-iridis Thalassiosira hendeyil Thalassiosira punctigera Plagioselmis prolonga var. nordica Coscinodiscus curvatulus Mesodinium rubrum Teleaulax amphioxeia Chaetoceros debilis Eucampia zodiacus Coscinodiscus radiatus Thalassiosira eccentrica

1 .

1. 2. 3. 4. 5. 6. 7. 8 9. 17. 18. 19. 20. 10. 11. 12. 13. 14. 15. 16. TABLE Twenty most abundant phytoplankton species in the Bay, based on biomass. From Cloern and Dufford (2005). 100 80 USBOTFDU 60 B BMPOH 40 UBLFO 2% TBNQMFT 20 Dinoﬂagellates 11% Cell Size (μm) Mesodinium 64(4 Cryptophytes 5% Other 1% GSPN BSF 10 80% of the biomass 8 account for more than %BUB Cells larger than 10 um 81% Diatoms 6 7

From Cloern, J.E., R. Dufford. 2005. Phytoplankton community ecology:applied in San principles Francisco Bay. Marine Ecology Progress Series, 285:11-28. 4 0 0.2 1.0

0.60.2 0.40.2 0.80.2 Proportion of Biomass of Proportion FIGURE Relative contribution to total phytoplankton biomass and frequencycumulative by cell size, showing that San Francisco1992–2001.) Bayin is phytoplankton dominatedBay species. by South large the to River Sacramento the from Station 15 62 FEATURE ARTICLES | PHYTOPLANKTON Station 6 60 60

45 45

STUDIES UNDERWAY &e state and regional water boards, through the Surface Wa- tion of the phytoplankton community during bloom and 30 30 ter Ambient Monitoring Program (SWAMP), also continue non-bloom sampling events. The study is also identify- 15 ĉF64(4DPOUJOVFTUPTUVEZXBUFSRVBMJUZQBSBNFUFSTBOE to monitor nutrients, with a particular focus on ammonium ing springtime sources of ammonium to Suisun Bay and 15 Chlorophyll Concentration (µg/L)

0 Chlorophyll Concentration (µg/L) chlorophyll at 39 !xed sampling locations, located about and its a"ect on phytoplankton blooms in the Delta and comparing spatial patterns of nutrient concentrations, chlo- 0 1995 1997 1999 2001 2003 2005 2007 2009 3–6 kilometers apart from the southern limit of the South in Suisun Bay. During March through July 2010, scientists rophyll concentrations, primary production, and nitrogen 1995 1997 1999 2001 2003 2005 2007 2009 Bay to the Sacramento River (FIGURE 9). &e program repeatedly sampled seven stations in Suisun Bay (Taberski uptake by phytoplankton. Other goals include investigating (! includes monthly measurements of chlorophyll, nitrate, ni- et al. 2010). Blooms (de!ned as chlorophyll concentrations the role of greater water transparency and the possible ef- trite, ammonium, phosphate, and silicate. Data are available of 30 μg/L or greater) were detected during two of the sam- fects of copper, herbicides, and pesticides, through toxicity POUIF64(4XFCTJUFBOEDBOCFBDDFTTFEUISPVHIUIF3.1 pling events, one in mid-April and the other in late May. &e tests and Toxicity Identification Evaluations (TIEs). A (! analysis of the blooms a%ributes them to a combination of coalition including SWAMP, the State and Federal Water (! (! (! (! (! (! (! The Interagency Ecological Program (IEP) for the San reduced ammonium loading and increased river $ow, result- Contractors, the Bay Area Clean Water Agencies (BAC- (! (! Suisun Bay Francisco Bay/Sacramento–San Joaquin Estuary, with ten ing in relatively low ammonium concentrations in the river WA), and Central Contra Costa County Sanitary District is (! member agencies, collects water quality data and other as it $owed into Suisun Bay (Dugdale et al. submi%ed). funding these studies. Rivers environmental information that can be used to complement (! San Pablo Bay UIFJOGPSNBUJPOCFJOHHBUIFSFECZUIF64(4JOUIF#BZ This study is ongoing, and sampling continued in 201l. Agencies with permits to discharge stormwater to the Bay Avg Measured Station 21 Chlorophyll The IEP Environmental Monitoring Program has 40 years Its objectives include determining effects of ammonium under the Municipal Regional Stormwater Permit (MRP) (! 60 1995 - 2009 of data from the Delta and the North Bay. on phytoplankton production and other topics, including are beginning a program to monitor stormwater loads at six (µg/L) 45 effects of the invasive clam Corbula and the composi- stations over three years. Consistent with the MRP and the (! (! 2.6 - 4.6 Small Tributaries Loading Strategy, the RMP plans to col- 30 (! 4.7 - 6.5 Central Bay lect specific data on nutrients and other contaminants that (! (! 15 6.6 - 8.5 will support development of a regional model for estimat- (! (! 8.6 - 10.4 Station 36 Chlorophyll Concentration (µg/L) ing loads by extrapolation from local studies. 0 (! (! 1995 1997 1999 2001 2003 2005 2007 2009 10.5 - 12.4 (! 12.5 - 14.3 ³ (! As part of a state-wide e"ort, the Water Boards are working Station 27 (! 14.4 - 16.3 Top left. Chaetoceros socialis. towards developing nutrient objectives for San Francisco (! 60 (! 16.4 - 18.2 Bay. RMP scientists are currently evaluating available data to Top right. Protoperidinium sp. 45 identify appropriate indicators of nutrient impacts (McKee (! et al. 2011). Possible indicators include water clarity, phyto- (! 30

plankton productivity and biomass, incidence of harmful or 15 nuisance algal blooms, and dissolved oxygen. &e indicators (! (! Chlorophyll Concentration (µg/L) 0 Bottom left. Mesodinium rubrum. will be used to build a Nutrient Numeric Endpoint frame- (! 1995 1997 1999 2001 2003 2005 2007 2009 work to assess the status of nutrients and their water quality Bottom right. Ditylum brightwellii. (! 60 impacts throughout the Bay. A workplan, developed in coor- (! (! dination with the new San Francisco Bay Nutrient Strategy, South Bay 45 will identify special studies needed to build the assessment (! Illustrations by Susan Putney. (! framework and be%er understand nutrient issues. (! 30 (! (! (! 15

0 5 10 Kilometers Chlorophyll Concentration (µg/L) 0 Lower South Bay 1995 1997 1999 2001 2003 2005 2007 2009 FEATURE ARTICLES | PHYTOPLANKTON THE PULSE OF THE ESTUARY 2011 63 - - XFCTJUF 2009 64(4 2007 UIF PO 2005 2003 BWBJMBCMF 2001 BSF Station 36 Station 9

1999 %BUB S continues to monitor water quality pa 1997 G &e program includes monthly measurements S U TJMJDBUF 1995 0

60 45 30 15

FIGURE e #e " samplingloca 39 xed at chlorophyll and rameters tions, located about 3–6 kilometers apart, from the southern limit of the South Bay to the Sacramento River. of chlorophyll, nitrate, nitrite, ammonium, phosphate,BOE TčBZXSVTHTHPWBDDFTTXREBUB Chlorophyll Concentration (µg/L) Concentration Chlorophyll ! ! ( 2.6 - 4.6 4.7 - 6.5 6.6 - 8.5 8.6 - 10.4 10.5 - 12.4 12.5 - 14.3 14.4 - 16.3 16.4 - 18.2 Avg Measured Chlorophyll 1995 - 2009 (µg/L) ! ( ! ( ! ( ! ( ! ( ! ( ! ( ! ( 2009 2009 2009 Rivers 2007 2007 2007 !! ( 2005 2005 2005 2003 2003 2003 !! ( 2001 2001 2001 Station 6 Station Station 21 Station Station 27 Station 1999 1999 1999 1997 1997 1997 !! ( 1995 Suisun Bay 1995 0 0

1995 0

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Chlorophyll Concentration (µg/L) Concentration Chlorophyll Chlorophyll Concentration (µg/L) Concentration Chlorophyll ! ! ( Chlorophyll Concentration (µg/L) Concentration Chlorophyll ! ! ( !! ( ! ! ( ! ! ( ! ! ( !! ( ! ! ( !! ( ! ! ( !! ( Lower South Bay ! ! ( ! ! ( !! ( ! ! ( 2009 Central Bay ! ! ( !! ( 2007 ! ! ( ! ! ( !! ( ! ! ( 2005 San Pablo Bay San Pablo !! ( !! ( South Bay !! ( 2003 Kilometers !! ( !! ( 2001 !! ( !! ( Station 15 15 Station Station 10 !! ( !! ( 1999 1997 5

1995 60 45 30 15 Chlorophyll Concentration (µg/L) Concentration Chlorophyll 0 64 FEATURE ARTICLES | PHYTOPLANKTON

ADDITIONAL Information gaps are many, and future trends are difficult is to better understand quantities, timing, and composi- SCIENCE NEEDS to predict. The lessons from other ecosystems show that tion of loads. Although it is known that nutrient loading each estuary is unique, further emphasizing the importance to the Bay is high, there is no detailed understanding of The complex and sometimes seemingly paradoxical scenar- PGMPDBMEBUBBOENPEFMJOH6OEFSTUBOEJOHOVUSJFOUBOE the relative magnitude of loads from individual sources ios emerging from San Francisco Bay show the importance phytoplankton dynamics in San Francisco Bay is espe- and pathways. Obtaining this information, which will be of continued monitoring, research, and modeling. The cially important, because future conditions could make it necessary if future conditions suggest that inputs must biggest overall question is whether there are plausible sce- necessary to reduce agricultural or sewage loads. Reduc- decline, is key. narios in which the Bay will start to exhibit the symptoms ing agricultural loads, through enhancement of fringing of eutrophication due to nutrient enrichment that have wetlands and buffer strips, has been an important focus in There has also been no systematic assessment of phy- been observed in so many other estuaries. Chesapeake Bay and the Mississippi River Delta. Advanced toplankton production and species composition within

The biggest overall question is whether there are plausible scenarios in which the Bay will start to exhibit the symptoms of eutrophication due to nutrient enrichment that have been observed in so many other estuaries

6OEFSTUBOEJOHUIFNPSFTQFDJGJDJTTVFT TVDIBTQPTTJCMF secondary treatment has already been implemented at the the Bay and no monitoring of phytoplankton outside the ammonium inhibition, will also be important to deter- Palo Alto, Sunnyvale, and San Jose/Santa Clara treatment Golden Gate. Nor is there systematic monitoring of zoo- mining appropriate management responses to changing plants, and additional advanced secondary treatment plankton or benthic grazers. Another key need is for predic- conditions. One hopeful scenario might be the restoration and/or nitrogen-removal technologies may be warranted. tive simulation models to assess and manage nutrients and of primary productivity in northern portions of the Bay fol- Nitrogen removal has been necessary in many other urban phytoplankton in the Bay. The RMP is looking to partner lowing controls on ammonium discharges, which are likely estuaries around the world. with other programs to rise to the challenge of addressing to be imposed by the Water Boards. The Scheldt estuary these substantial information needs and providing a solid of western Europe, where zooplankton communities are The new San Francisco Bay Nutrient Strategy is in- technical foundation for the consequential decisions that changing in response to nutrient reductions, may provide a creasing the focus on information gaps and the present are on the horizon. glimpse of what could occur in the Bay (Mialet et al. 2011). uncertainty surrounding future projections. One focus FEATURE ARTICLES | PHYTOPLANKTON THE PULSE OF THE ESTUARY 2011 65 avis. D hotograph by Jay hotograph by Jay P ate Bridge. ate Bridge. G olden G iew from the V µ 66 FEATURE ARTICLES | FISH

MEG SEDLAK, San Francisco Estuary Institute KEVIN KELLEY, California State 6OJWFSTJUZ-POH#FBDI DAN SCHLENK, 6OJWFSTJUZPG$BMJGPSOJB3JWFSTJEF

effects of pollutants on bay fish

highlights PAHs from vehicle exhaust, oil spills, and other sources can Studies suggest that reach concentrations Pyrethroid pesticides endocrine disruption Many "sh populations are and other pollutants are declining in the North Bay Fish have life histories that can a$ect growth, may be occurring in reproduction, and suspected to have a role the Bay-Delta, but and Delta; contaminants that make them in the “Pelagic Organism may play a role vulnerable to pollutants survival of Bay "sh the causes are not Decline” in the northern entirely clear Estuary and Delta FEATURE ARTICLES | FISH THE PULSE OF THE ESTUARY 2011 67 - - -

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hotograph by Joan P trait. trait. S ). 60 accoon E R G PA ) or the inhibition of key food sources (e.g., possible ity; toxic effects and of pollutants. The sources of pollutants in the Estuary are diverse and runoff,include agricultural flows, dry wastewa weather ter treatment plant effluent, storm water runoff, refinery discharges, and resuspension of sediments. In addition to pollut of effects indirect be may fish, there on effects direct ants such as the introduction of invasive species which may concentrate pollutants selenium (e.g., in clams – 37 ammonium inhibition of phytoplankton at the base of the – food web The causes for these dramatic declines in fish populations in the Bay and Delta are unknown. Various factors have been investigated, including habitatdi losswater andfor reducedpumps Delta water in entrainment predation; flows; version; limited food supply due to low primary productiv - erring fishing boats in H - - µ ) is the last commercial !shery ). Clupea pallasii Oncorhynchus mykiss Oncorhynchus in San Francisco Herring Bay. roe, considered a delicacy by the Japanese, is largely exported. &e central portion of San Francisco Bay is one of the largest herring spawning sites in California. Herring spend two to three years in the open on sub eggs their lay to the Bay to return then and ocean, strates such as eelgrass, algae, rocks, gravel, rip-rap, and pier pilings. In recent years, herring catch declined dramatically from the historic average of 49,000 tons down to a low of the com 2010, in the winter of 2008-2009. In 4,800 tons mercial herring season was closed completely, the !rst time (www.dfg.ca.gov/ma the catch of monitoring in the 38 years rine/newsleer/1010.asp#herring).% & e 2009-2010 estimate of 38,409 tons was an improvement, but remains below the of 49,084 tons. historical average tions are so diminished that they are listed as endangered, the winter and spring run chinook salmon and steelhead ( trout Paci!c herring ( - $ - - G - ), I - - ). For F - < 1 QPQVMB RE GU I F TBMNPO ) ( $PVODJM Spirinchus thaleichthys &TUVBSZ ), juvenile striped bass TIONS PUIFS ) was virtually non-existent in A .BOBHFNFOU UXP Dorosoma petenenseDorosoma IEGE S ), longfin ( smelt 'JTIFSJFT OPUL BEEJUJPO P *O Hypomesus transpacificus > 1BDJGJD 2 NDER NDER ISH RE Oncorhynchus tshawytscha Oncorhynchus Morone saxatilis U 2007, and in 2008 and 2009 commercial fishing for chi 2009 commercial in 2008 and 2007, and nook was completely closed due to low runs (in 2009, only 39,500 salmon returned, down from a high of 770,000 in smelt and longfin smelt are of great concern because they are both endangered species. Interestingly, both the striped bass and the threadfin shad are introduced species . The returning Sacramento River fall run of chinook salmon ( The convergence of the decline of these four species is particularly disturbing because they have different life dif occupy and nonmigratory) and (migratory histories ferent habitats (freshwater and estuarine), suggesting that a large-scale phenomenon is occurring. Declines of Delta example, in 2005–2007, the Delta smelt population index reached the lowest recorded levels for the last 40 years of spe four key of these the decline Collectively monitoring. cies is referred to as the “pelagic organism decline” (POD). smelt ( ( and threadfin shad ( and water suppliers. Significant declines have also been observed for salmon returninglocaspawning upstream to tions and for Pacific herring, which spawn within the Bay. One of the largest environmental concerns in the Estuary has been significant declines in the populations of Delta Populations of many important fish speciescisco Estuary inhave declined the significantly San Fran in recent years. in fish popula decrease in 2000, a dramatic Beginning tions in the northern portion of the Estuary was observed, pitting fisherman and environmentalists against farmers F U 68 FEATURE ARTICLES | FISH

FIGURE 1 DELTA SMELT STRIPED BASS 1800 20000 One of the largest environmental concerns in the Estuary has been sig- 1500 ni"cant declines in the populations 15000 1200 of Delta smelt (Hypomesus transpaci- !cus), juvenile striped bass (Morone 900 10000 saxatilis), long"n smelt (Spirinchus Abundance 600 Abundance thaleichthys), and thread"n shad 5000 (Dorosoma petenense). For example, 300 in 2005–2007, the Delta smelt population index reached the lowest recorded 0 0 levels for the last 40 years of monitor- 2006 1966 1970 1974 1978 1982 1986 1990 1994 1998 2002 2006 1966 1970 1974 1978 1982 1986 1990 1994 1998 2002 2000 ing. Collectively the decline of these 2000 four key species is referred to as the “pelagic organism decline” (POD). Declines of Delta smelt and long!n LONGFIN SMELT THREADFIN SHAD smelt are of great concern because they 100000 are both endangered species. 16000 14000 80000 12000 60000 10000 8000

Abundance 40000 Abundance 6000 20000 4000 2000 0 0 1966 1970 1974 1978 1982 1986 1990 1994 1998 2002 2006 1966 1970 1974 1978 1982 1986 1990 1994 1998 2002 2006 2000 2000

Footnote : From Baxter, R. et al. 2010. Interagency Ecological Program 2010 Pelagic Organism Decline Work Plan and Synthesis of Results. FEATURE ARTICLES | FISH THE PULSE OF THE ESTUARY 2011 69 2010 2005 2000 1995 1990 1985 1980 1975 Footnote: From Paciﬁc Fisheries Management Council. 2010. Stock Assessment and Fisheries2010 Ocean Salmon Evaluation Fisheries. (SAFE) 1970 0

900,000 800,000 700,000 600,000 500,000 400,000 300,000 200,000 100,000 Number of Returning Fish Returning of Number Sacramento River Fall Run Chinook Sacramento River Fall &e 2

FIGURE salmon was at a long-term low in 2007, and in 2008 and 2009 commercial "shing for chinook was completely closed due to low runs (in 2009, only 39,500 salmon returned,high770,000down froma of in2002). Paci!c Fisheries Management Council has set a goal of between 122,000 to 180,000 returning !sh. #e returning Sacramento River fall run of chinook 70 FEATURE ARTICLES | FISH

FISH ARE SENSITIVE AND IMPORTANT INDICATORS

Fish are very sensitive to pollutants. In part, this sensitivity is attributable to their exposure to waterborne pollutants throughout their lives. The vast majority of Bay fish species are oviparous (egg-laying) , dispersing thousands of eggs directly into the water column or anchoring their eggs on rigid structures such as pier piles. Once the eggs are fertil- ized, they hatch, and then develop into juvenile fish and adults. Pollutants can disrupt fish life cycles at many stages. For example, exposure to the synthetic estrogen hormone used in birth control pills, ethinylestradiol, at very low concentrations (around 1 part per trillion) can cause male fish to exhibit female characteristics (e.g., expression of the female egg yolk protein, vitellogenin) (Jobling et al. 1998; Rodgers-Gray et al. 2000). Similarly, exposure to part per billion concentrations of the detergent nonylphenol elicits a similar response (Jobling et al. 1996). µCollection of herring for evaluation of effects of oil pollution. Photograph courtesy of John Incardona. Fish are also particularly sensitive to chemical pollutants because they have multiple routes of exposure, including enced by social and environmental factors. For example, Numerous examples of contaminant effects on fish have ingestion, aquatic respiration, and regulation of osmotic the California sheephead (Semicossyphus pulcher) which been documented throughout the world. Many pollutants pressure. Because water contains less oxygen than air, fish resides in the Southern California Bight, has one dominant found in the Bay can elicit adverse effects at elevated levels, respiration rates are about five times higher than mammals male and many females. When the dominant male dies, one including pesticides, polychlorinated biphenyls (PCBs), (Van der Kraak et al. 2001). Gill surfaces must be quite of the females will change sex to become the next domi- polycyclic aromatic hydrocarbons (PAHs), dioxins, metals, large to extract sufficient oxygen, and the active movement nant male. Gender changes may also occur upon exposure and endocrine disruptors such as ethinylestradiol, nonyl- of water across the gill increases exposure to waterborne to a class of chemical pollutants referred to as endocrine phenol and bisphenol A. The effects of these pollutants on pollutants. Fish in saline and freshwater environments are disruptors. Municipal wastewater is one source of these fish are potentially significant and wide-ranging: elimina- also subject to changes that may increase their contaminant compounds, often containing trace amounts of steroid hor- tion of an entire fish population (17-α ethinylestradiol) burden as they move water through their bodies to regulate mones, surfactants such as nonylphenol, and many other (Kidd et al. 2007), compromised immune systems (Reyn- the osmotic pressure. chemicals from pharmaceuticals, personal care products, aud and Deschaux 2006), liver lesions (Myers et al. 2003), and consumer products. Furthermore, endocrine-disrupt- thyroid dysfunction (Brar et al. 2010), and impairment of Lastly, fish are susceptible to contaminant effects because ing chemicals can affect other physiological systems, and the sense of smell (McIntyre et al. 2008). Many of these UIFZFYIJCJUTFYVBMQMBTUJDJUZ6OMJLFNBNNBMT UIFHFOEFS are known to disrupt development and growth, metabo- effects occur at concentrations that are observed in the Bay. of fish is not genetically predetermined and may be influ- lism, immune responses, and other essential processes. FEATURE ARTICLES | FISH THE PULSE OF THE ESTUARY 2011 71

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HLENDORF EISBERG S ESTON O W W EBAR XPOSURE D ICHAEL ARRY ON ANIEL TEVE M H D S D SI E Advisory aquatic life, including the work on "sh, birds, and seals that is summarized in this edition of #e Pulse. California – Riverside Coastal Water Research Project Berkeley #e RMP Exposure and E$ects Workgroup provides oversight on RMP studies relating to the e$ects of toxic pollutants on - - - ). Fish health monitoring 15 E G PA Fish health is an important metric in assessing the health of an estuary as fish are critical components of the food web. Many stur and cormorants, seals, including animals, trophic higher geon, depend upon small fish as prey. Fish from estuaries are ( humans by also consumed predation (Connon et al. 2009). In addition, fish to area myriad exposed of other stressors that may exert even greater pres sures on populations, such as loss of habitat, disruptionsinvasive species, from and reduction in prey. Isolating thea specific effects ofpollutant or pollutant mixtures with is a challenge. stressors simultaneous so many other more difficult to identify impacts at the populationeffects level. of pollutants The on organisms are often subtle,impairment such as of neurological functions, growth rate,responses or immune that contribute to adverse outcomes. For example,low concentrations of pyrethroid insecticides can swimmingaffect the ability of fish, making them more vulnerable to a distinct measurable effect. Few pollutants associ as those have one contaminant to linked strongly as are that had impacts ated with the bioaccumulation of DDT in birds in thatthe 1970sresulted in eggshell thinning and population isdeclines. usually It very difficult to tease out the impactspollutant of a onspecific organisms in an environmental setting, and even One of the challenges in evaluating pollutant effectsidentifying on fish ais direct link between contaminant exposure and including those in the Southern California Bight, Puget Sound, Great Lakes, and along the Eastern seaboard, and allow us to results in context. Bay place is frequently included in other major water quality programs, 72 FEATURE ARTICLES | FISH

FINDINGS FROM RECENT occur relatively infrequently. In the last 100 years, there is divided into three phases. The first phase assessed the BAY AREA STUDIES have been three major spills in the Bay: the collision of effects of individual pyrogenic PAHs on the development a passenger steamer and oil tanker in 1937 that caused a of a laboratory model fish, the zebra fish, Danio rerio. COMBUSTION, OIL SPILLS, AND PAHS release of approximately 2,400,000 gallons; a 1971 collision After these effects were characterized, in the second phase, Fish are highly sensitive to PAHs, a diverse family of of two tankers spilling 900,000 gallons of partially refined experiments on the effect of individual PAHs on California compounds that can cause a number of adverse effects fuel oil; and, most recently, the Cosco Busan tanker that halibut, Paralichthys californicus, are being conducted. Cali- including heart malfunctions, liver lesions, abnormal larval gouged its hull on a Bay Bridge support releasing 54,000 fornia halibut was selected because it is a resident species development, and death. Sources of PAHs to the Bay are gallons of bunker fuel oil in 2007 . that spawns in the Bay. After the effects of individual PAHs both natural and anthropogenic and include combustion of on California halibut have been identified, the researchers fossil fuels and wood, forest fires, petroleum refining, and As a result of oil spills around the country, particularly the will use real-world sediments containing similar levels and oil spills. PAHs are made up of linked hydrocarbon rings, Exxon Valdez in Alaska and more recently the Cosco Busan mixtures of PAHs as Bay sediments to assess the effects to ranging from relatively light weight two-ring compounds to in the Bay, the adverse effects of PAH exposure have been developing California halibut and other flatfish. heavier compounds with six rings or more. PAHs consisting extensively studied. The timing of exposure and the type of two to four rings are typically derived from petroleum of PAH greatly affect the outcome. Fish larvae exposed to ROLE OF POLLUTANTS IN THE POD compounds (e.g., naphthalene, fluorene, dibenzothiophene, high enough concentrations of the three-ring PAHs present phenanthrene and anthracene), while four- to six-ring com- in unrefined crude oil (e.g., fluorenes, dibenzothiophenes, Pesticides and their effects on fish have been a major focus pounds are typically the result of combustion (e.g., pyrene, and phenanthrenes) experience swellings in the heart and of the POD research in the Delta. Pesticides are used benz(a)anthracene, and chrysene). yolk sac, small jaws, deformed spines, reduced heart rate, extensively in Central Valley agriculture, and the use of py- and heart arrhythmia (FIGURE 3). Pacific herring col- rethroids for urban applications in California has increased Exposure of adult !sh to PAHs can cause suppression of lected in oiled areas of the Bay after the Cosco Busan spill dramatically since 1999 with the phase out of organophos- immune systems; lesions on gills, skin, and !ns; liver lesions; exhibited many of these effects (Incardona et al. 2008). phate pesticides (2006 Pulse of the Estuary, PAGE 71). and reproductive dysfunction. &e National Oceanic and Pyrethroids have been detected in California waters at con- Atmospheric Administration (NOAA) identi!ed signi!cant The research evaluating the effects of the Cosco Busan spill centrations that can be harmful to fish. Pyrethroids are par- adverse e"ects occurring in English sole (Parophrys vetulus) found higher acute toxicity in intertidal areas where fuel ticularly toxic to fish, blocking the sodium and potassium located in areas of PAH-contaminated sediments on the West oil was exposed to sunlight. Subsequent laboratory studies channels in nerve cells resulting in tremors, impaired swim- $PBTUPGUIF64 JODMVEJOH4BO'SBODJTDP#BZĉFZPC- have not yet identified the mechanism by which this oc- ming ability, convulsions, and, at high enough concentra- served an increase in liver lesions, failure to spawn, poor egg DVST.BOZTUVEJFTIBWFTIPXO67MJHIUBDUJWBUFT1")TJO tions, death. Impairment of swimming ability causes these quality, and a decline in growth rates (Johnson et al. 2002). biota (Oris and Giesy 1985). fish to be more susceptible to predation. The pyrethroid Bay sediments commonly exceed 1 ppm, the concentration esfenvalerate has been shown to impair swimming ability suggested by NOAA as a sediment-quality threshold. With funding from the Regional Monitoring Program for of larval Delta smelt at concentrations as low as 62 ng/L Water Quality in the San Francisco Estuary, NOAA is cur- (Connon et al. 2009). Pyrethroids have also been shown to PAHs are widely dispersed throughout the Bay, with areas rently investigating thresholds for PAH effects in juvenile inhibit growth and immune responses and delay spawning of elevated concentrations near the former fuel depots flatfish. The focus is on the higher molecular weight, (Connon et al. 2009). The concentrations at which effects along the San Francisco waterfront and near the industrial pyrogenic PAHs that result from combustion of petroleum can occur are as low as 25 ng/L (Floyd et al. 2008). Labora- port of Oakland Harbor (PAGE 33). Oil spills are another products and that are endemic to industrial and heavily tory studies found that juvenile chinook salmon exposed to source of PAHs to the Bay. Fortunately, oil spills in the Bay urbanized estuaries such as San Francisco Bay. The project esfenvalerate and a virus had a significantly higher mortal- FEATURE ARTICLES | FISH THE PULSE OF THE ESTUARY 2011 73 ncardona. I YOLK YOLK hotographs by John P s present in unre"ned crude oil (e.g., H Oil Contaminated Water Oil Contaminated Paci! c herring collected in oiled areas of the Bay a#er YOLK YOLK Clean Water 3

FIGURE Fishlarvae exposed high to enough concentrations the of three-ring PA 'uorenes, dibenzothiophenes, and phenanthrenes) experienceheartheart and arrhythmia. reduced spines,rate, swellings deformed ects. " e in these the heartof many and yolk sac,exhibited smallspill Busan jaws, Cosco the Fish Zebra Herring 74 FEATURE ARTICLES | FISH

POLLUTANTS AND ENDOCRINE ity rate than fish exposed to the virus alone, suggesting laboratory experiments (Lavados et al. 2009). The team DISRUPTION IN FISH that fish exposed to low levels of pyrethroids may be more collected water from 16 locations throughout the Bay-Delta susceptible to disease. Synthetic reproductive hormones and compounds that and extracted pollutants from the samples, and then used mimic reproductive hormones are one of the few cases in the extracts in laboratory exposures. The results indicated Pyrethroids have generally not been detected in the Bay. which environmentally relevant concentrations have been significant endocrine disruption potential in the Napa However, they have been detected in urban creeks and shown to potentially have significant population-level and Sacramento river samples; however, the endocrine streams at concentrations that exceed these effect levels. effects in the wild. It has been well established in field disruption not associated with any one contaminant from %S%PO8FTUPOBOEIJTUFBNBU6OJWFSTJUZPG$BMJGPSOJB and laboratory studies that very low concentrations of chemical classes including steroid hormones, pesticides, at Berkeley have studied pyrethroids extensively and have hormones in water can affect the endocrine system of fish. surfactants such as alkylphenol ethoxylates, or a host of observed concentrations in urban creeks as high as 46 ng/L The endocrine systems of all vertebrates including fish are pharmaceutical and personal care products. Ongoing work (Weston and Lydy et al. 2010). a series of glands that secrete hormones that regulate not suggests that the response may be the result of a mixture of only reproduction but also growth and development, stress pyrethroids and surfactants. 8PSLDPOEVDUFECZSFTFBSDIFSTBUUIF6OJWFSTJUZPG$BMJ- response, and other processes. Substantial research has fornia at Davis suggests that Bay-Delta species exposed to documented that fish downstream of wastewater treatment The RMP has sponsored studies to determine whether environmentally relevant concentrations of pollutants are facilities frequently exhibit disruption of the reproductive contaminants are affecting additional components of the exhibiting toxic responses. Spearow et al. (2010) found system. For example, male fish downstream of wastewater endocrine system. Dr. Kevin Kelley and his research team that wild fish in the northern portion of the Bay and in treatment plants have been found to have vitellogenin GSPN$BMJGPSOJB4UBUF6OJWFSTJUZBU-POH#FBDISFDFOUMZ the Delta showed a number of responses from exposure to (female egg yolk protein) and eggs present in their testes completed a two-year study evaluating non-reproductive pollutants. Delta striped bass exhibited significantly higher (Jobling et al. 1998). forms of endocrine disruption and their relationships induction of metabolic enzymes when exposed to Delta to pollutant exposure in two Bay fish species (Brar et al. water. These enzymes are induced by exposure to PAHs, Perhaps more disturbing are the results from an experiment 2010). In shiner surfperch (Cymatogaster aggregata) and PCBs, dioxins, and other pollutants. Recent work by Dan conducted in Canada on a series of experimental lakes in Pacific staghorn sculpin (Leptocottus armatus), disruptions 4DIMFOLPG6OJWFSTJUZPG$BMJGPSOJBBU3JWFSTJEFTVHHFTUT which one lake was treated with the synthetic hormone in the thyroid endocrine system, including significant re- that pyrethroids cause induction of vitellogenin in fish ethinylestradiol at concentrations of 5 to 6 ng/L (Kidd et ductions in thyroid hormones, were found in fish sampled (Nillos et al. 2010 and Wang et al. 2007). Additional labo- al. 2007). Both the control lake and the treated lake con- from contaminated industrial and harbor locations (FIG$ ratory studies have shown that mixtures of detergents sig- tained fathead minnows. After the first year, male fish ex- URE 4). Further experimental analysis found that specific nificantly enhanced the estrogenic activity of pyrethroids hibited female characteristics such as expression of the egg problems within the thyroid system may be associated with and other pesticides used in surface waters of the Central protein, vitellogenin, and eggs present in their testes. By the different classes of contaminants (PCBs and chlordanes). Valley (Xie et al. 2005). Whether the POD is a direct effect second year, the population of minnows in the treated lake Thyroid hormones are critical regulators of develop- of pollutants on the fish or on their invertebrate food sup- had completely collapsed, linking a contaminant effect to ment and growth in fish. It was therefore notable that in ply remains a mystery. Based on all of the studies collected the survival of a population as a whole. fast-growing, young of the year sculpin, thyroid hormone to date, the consensus is that no one factor is responsible concentrations were strongly correlated with concentra- for the POD. Most likely, it is a combination of factors in Within the Bay-Delta, there is limited evidence of repro- tions of an important growth hormone (FIGURE 5), sug- which pollutants play a role. EVDUJWFFOEPDSJOFEJTSVQUJPO%S%BO4DIMFOLPG6$ gesting that impaired thyroid hormones could translate into 3JWFSTJEFBOE%S%BWJE4FEMBLPG6$#FSLFMFZDPOEVDUFE growth effects. However, it is not yet understood whether a study in 2006–2007 to evaluate whether reproductive the impacted fish exhibit deficits in growth or survival or in endocrine disruption was occurring in Bay-Delta fish in the population at large. FEATURE ARTICLES | FISH THE PULSE OF THE ESTUARY 2011 75 Bay Bay ND Tomales Tomales Tomales Oakland Oakland Bay Bay San Pablo San Pablo San Pablo Berkeley Berkeley City City Redwood Redwood Footnote: From Brar et al. (2010). 0 0 80 60 40 20 80 60 40 20 Paci!c Shiner

Sculpin

Staghorn T4 Concentration (ng/ml) Concentration T4 Surfperch (ng/ml) Concentration T4 - - ), ), - 4

OM ( BO FIGURE ) and Paci! c staghorn sculpin ( TOP OPPER nerve cells. Fish have exquisitely sensitive noses with an ability to smell chemicals at the part per billion level to find a mate, find a bite to eat, avoid being a bite to eat, and to locate their birth streams. The fish nose is much more than a nose – it also governs physiological and behavioral responses. In predator avoidance experiments, juvenile salmon exposed to copper had a survival rate three to five times lower than control fish. The concentrations at which this effect was observed were quite low, in the range of 3 con al. et 2008). Dissolved (McIntyre µg/L in freshwater centrations of copper in San Francisco Bay typically range up to approximately 4 µg/L. Water chemistry in estuarine systems is dramatically different than freshwater and there is some evidence to suggest that dissolved organic carbon and salinity may protect salmon in the Bay from the adverse effects of exposure to copper. This work will investigate the environment. which at effects in a saltwater occur threshold C In conjunction with the RMP, NOAA is also studying the effect of copper on the olfactory system of salmon. Their recent research has shown that metals, particularly copper, inhibit predator avoidance by impairing olfactory - - - ). - - - nated industrial and harbor locations, including Oakland Harbor. 6 In shiner surfperch ( surfperch shiner In RE cant reduc cant ! signi include system endocrine thyroid the in disruptions sh sampled from contami from sampled sh ! in found were (T4) hormone thyroid in tions GU I F ). Further analysis of the surfperch 6 RE GU I F This may reflect differential actions of different contami nant mixtures present at the different locationsBay tested. routinely coincide with thyroid disruptions ( indicated that this endocrine disruption was significantly related to exposures to petroleum-derived PAHs (phenan threne, anthracene, and fluoranthene). The fish also had the cortisol dis suggesting infestations, parasitic increased ruptions were related to compromised immune function. It is also notable that the effects on cortisol response did not challenge ( challenge have negative effects on metabolism, immune functions, growth, and reproduction (Mommsen et al. 1999, Barton, 2002). In the studies by Kelley’s group, fish sampled from harbor locations like the Oakland and Richmond harbors and at the San Francisco waterfront, were significantly impaired in their ability to produce cortisol during a stress generates the hormone, cortisol. Cortisol is a critical stress adap behavioral and physiological promotes hormone that tations that help when an animal must deal with intraspe cific competitors, predators, poor food availability, or other stressors. Cortisol is also important under normal physi ological conditions, and disruptions in cortisol control can In addition to the thyroid disruption, both fish species also exhibited a dysfunctional adrenal endocrine system, which 76 FEATURE ARTICLES | FISH

70 A. Cortisol Response 60 800 700 50 600 40 500 400 30 300 20 200 concentration (ng/mL) Growth hormone (IGF-I) 10 100 0 Plasma Concentration (ng/mL) 0 Catalina Redwood City S.F. Oakland San Leandro Richmond 0 5 10 15 20 25 30 35 40 Island Waterfront Harbor Bay Harbor Thyroid hormone (T4) concentration (ng/mL)

70 60 B. Thyroxine, T4 50 40 35 40 30 30 25 20 20

concentration (ng/mL) 15 Growth hormone (IGF-I) 10 10 0 5

Plasma Concentration (ng/mL) 0 0 1 2 3 4 5 6 7 8 9 Catalina Redwood City S.F. Oakland San Leandro Richmond Thyroid hormone (T3) concentration (ng/mL) Island Waterfront Harbor Bay Harbor

FIGURE 5 FIGURE 6 Relationships between concentrations of the growth regulatory Fish sampled from harbor locations like the Oakland and Richmond peptide, insulin-like growth factor-I (IGF-I), and the thyroid harbors and at the San Francisco waterfront were signi"cantly hormones, thyroxine (T4, upper panel) and triiodothyronine (T3; impaired in their ability to produce cortisol during a stress chal- lower panel), in Paci"c staghorn sculpin. lenge. &is endocrine disruption was signi!cantly related to exposures to petroleum-derived PAHs (phenanthrene, anthracene, and $uoranthene). &e !sh also had increased parasitic infestations, suggesting the cortisol disruptions were related to compromised immune function. &e e"ects on cortisol response did not routinely coincide with thyroid alterations, suggesting di"erential actions of contaminant mixtures present at the di"erent Bay locations. FEATURE ARTICLES | FISH THE PULSE OF THE ESTUARY 2011 77 - - - PG 6OEFS UPYJDJUZ 6OJWFSTJUZ CZ FOIBODF XPSL SFDFOU JOHSFEJFOUTu FYBNQMF iJOFSU 'PS UIF impair swimming or that pollutants increase susceptibility to disease within individuals, but this may not necessarily level. the population at impacts to translate The RMP will continue to strive, in collaboration with other Bay-Delta organizations, to provide the scientific understanding needed to reverse the declines that have recently been observed in so many important fish species. commercial formulations of pesticides are more toxic than the active pesticide ingredients, indicating that the inactive DBSSJFST standing the combined effects of multiple pollutants, in cluding pollutants of emerging concern, will be important. It can be expected that the effect of pollutants on fish will vary among species and habitats. An additional challenge combina in pollutants of effects the understand to be will tion with other stressors such as food scarcity and other water quality variables (temperature, dissolved oxygen, turbidity, and salinity). Perhaps the hardest issue to address will be the translation of effects on individuals to effects on the population as a whole. It may be that pesticides There is much to be learned and there are many challenges. Future studies will need to address the effects of mixtures that may enhance or ameliorate the potency of individual QPMMVUBOUT California at Riverside and Davis researchers suggests that - - TION A ND A NFORM I PS PS ONCLUSIONS ONCLUSIONS RIORITY sh growth, development, and reproduction is gradu reproduction and on !sh growth, development, ally advancing. muchHowever, of the past work has been conducted by exposing model !sh species in a laboratory se% ing at concentrations that are much higher than what is typically observed in the environment. In the last decade, several research groups have begun to design experiments to evaluate the e"ects of pollutants at realistic levels on wild !sh. &is work will be critical for improving understanding !sh. of Bay on the health of pollutants of the e"ects C P GA Our understanding of the e "ects of individual pollutants Splittail collected in the Bay in 2000 did not exceed this threshold (Baginska 2011). Between 1997 and 2009, the RMP analyzed 56 sturgeon for selenium with an average of 1.4 ppm wet weight. The Water Board has proposed a sturgeon tissue target of 6.0 to 8.1 µg/g dry weight for the North Bay (Baginska 2011). Few RMP samples (consid ered on a dry weight basis) have exceeded this range. Selenium can cause embryonic deformities such as malformed spines and impaired feeding systems. In the preliminary North Bay selenium TMDL report, effects thresholds for splittail and white sturgeon are characterized as above 6.0 and 10 µg/g dw, respectively (Baginska 2011). ) - - Acipenser Corbula amurensis Corbula ) and sturgeon ( sturgeon ) and ) are considered to be at substantial risk ), which are selenium-rich relative to other prey 37 E G ELENIUM PA Pogonichtuhys macrolepidotus &e Water Board has proposed a sturgeon tissue target of 6.0 to 8.1 μ dryg/g weight for the North Bay - few RMP samples have exceeded this range (Stewart et al. 2004). Increased risk factors for sturgeon include their longevity (they can live over 100 years), their year-round resident status, and long egg maturation times (several years) (Beckon and Mauer 2008). ( transmontanus for selenium exposure in the Bay (Beckon and Mauer 2008). Splittail and sturgeon are at risk because their diet consists primarily of the overbite clam ( ( Relatively low concentrations of selenium are detected in Bay water; however, the major route of exposure to fish is through their diet. Bottom-feeding fish such as splittail regulation of the immune system, and management of stress. However the window between necessity and toxicity is one of the smallest known (Baginska 2011). logic formations of the Coast Range. An arid climate and Sacra and Joaquin San in the results irrigation extensive mento rivers being the major source of selenium to the Bay, followed by local tributaries, refineries, and wastewater treatment plants (Baginska 2011). A vital nutrient for fish, selenium is critical for the production of thyroid hormones, S Selenium is a naturally occurring element found in geo 78 FEATURE ARTICLES | BIRDS

LETITIA GRENIER, JAY DAVIS, and JOHN ROSS, San Francisco Estuary Institute

recent findings on risks to birds from pollutants in san francisco bay

highlights

Birds are facing signi"cant PBDEs are prevalent in health risks in San Francisco Available data suggest species foraging in the Bay, due to their exposure to Methylmercury exposure that PCBs exceed risk Dioxin and is a major concern for birds shallow Bay and managed legacy pesticide pollutants, and are sensitive thresholds in some ponds, but there are no indicators of pa!erns and in managed ponds and tidal birds that forage in concentrations marsh and is suspected of e$ects thresholds; PBDE in bird eggs are trends of contamination in the shallow Bay and bioaccumulation in tidal the Bay food web a$ecting some species at the managed pond habitats generally below population level, including marsh birds is largely thresholds of special-status species unstudied concern FEATURE ARTICLES | BIRDS THE PULSE OF THE ESTUARY 2011 79 - - - - - ), 1 anczyk. W RE GU I inda M. inda M. F L hotograph by P ocks. ocks. R eal S Cormorants on recent work on avian e "ects has been on these species, but a few studies on other species are not included in this article (e.g., Takekawa et al. 2002, Hothem and Hatch 2004). ³ because many pollutants show spatial erns% pa that di" er by habitat. example, For PCBs appear higherto have concentra tions in sediments near urbanized and industrialized margins Meth al. et 2008b). al. et 2007, Ackerman (Davis of the Bay ylmercury, which is the toxic form of mercury in estuarine food webs, exhibits di"erent erns% pa of bioaccumulation by habitat! eld (Green and 2010,Jahn Grenier et al. 2010), like ly due to variation in methylmercury cycling. Furthermore, birds are adapted to forage in particular habitats; therefore, as sentinel species they tend to represent one or two primary habitat types. &e species of birds that are the most suited to being used as indicators of pollutant problems in the food webs of di"erent Bay habitats are discussed here. Most of the sentinels for tracking the spatial and temporal erns% pa of pollutants in the food web. Birds are commonly used as sentinel species in monitoring programs around the world, including the Great Lakes, the Canadian arctic, the Baltic Sea, and San Francisco where Bay, the Regional Monitoring Program forQuality Water in the San Francisco Estuary has a decade. for nearly in birds pollutants monitored &is article provides an update on what has been learned about the e "ects of aquatic pollutants on estuarine birds nd ! recent ese & decade. last the in completed studies from type habitat estuarine by ( organized are ings polybrominated diphenyl ethers (PBDEs). &e mercury cleanup plan for the Maximum Bay (the Total Daily Load, or TMDL) includes a target for prey !sh to protect piscivorous !sh-eating)( birds, particularly the endangered California LeastBecause Tern. many Bay bird species have well-under stood life histories in terms of their foraging habitat, home range size, diet, and migratory erns,% pa they can be excellent - Sterna Rallus ) and the California Least Tern ( Tern Least the California ) and ). For all of these reasons, it is important longirostris obsoletus longirostris antillarum browni to know the extent to which estuarine birds are negatively affected by chemical pollutants. Birds are sensitive to environmental contamination, espe cially during early development as embryos and chicks. Aquatic and wetland birds are exposed to pollutants that are transferred through the food andweb, may be harmed by substances such as methylmercury, polychlorinated biphenyls (PCBs), dioxins, selenium, legacy pesticides, and Aquatic and wetland birds are also important components of the food web; many are predators feeding on fish and invertebrates from several of the main estuarine habitats, including shallow bay, marshes, and managed ponds. In addition, studies have indicated that pollutant impacts are a significant concern for some Bay birds, including special Rail like Clapper species the California – status ( - -

Y A ENTINELS S N A including birds, is one of many %a ributes of the Bay that is protected by state and federal water quality regulations. portant to the natural heritage of the area, but we also value them as part of our cultural heritage. Birders, hunters, and other nature lovers appreciate birds. &e support of wildlife, birds and support many species of breeding birds, including several threatened and endangered species and some types of im birds are only Not world. the in else nowhere found birds Paci!c Coast of North America, the Bay is a critical habitat for many estuarine bird species. &e Bay and its wetlands are water of migrating populations for large a vital stop refueling &e extent to which San Francisco Bay birds are a"ected by pollutants is a topic of great importance to water quality managers and to the public. As the largest estuary on the AVI FOR THE B 80 FEATURE ARTICLES | BIRDS Napa

Fairfield Petaluma

Suisun Wheeler Island Bay San Pablo Bay

Richmond FIGURE 1 Bridge Marsh Recent "ndings on pollutants in Bay birds in Channel this article are organized by estuarine habitat type, because many pollutants show spatial patterns that di)er by habitat. Furthermore, birds are adapted to forage in particular habitats; there- Oakland Panne fore, as sentinel species they tend to represent one or two primary habitat types. &e species of birds San that are the most suited to being used as indicators FranciscoAlameda Naval Marsh Air Station Least Plain of pollutant problems in the food webs of di"erent Tern Colony Bay habitats are discussed.

South Hayward Bay ¶Least Terns. Photograph by Robert Lewis. Shallow Bay Eden Double-crested Cormorant Landing and California Least Tern Habitat Don Edwards Tidal Marsh Pond California Clapper Rail, Black Rail, A9/A10 and tidal marsh Song Sparrow Habitat

Managed Pond Forster's Tern, Caspian Tern, Black-necked Alviso Stilt and American Avocet Habitat South Bay Towers San Jose 0 5 10 Miles Habitats taken from the Bay Area Aquatic Resource Inventory, 2011. http://www.sfei.org/BAARI FEATURE ARTICLES | BIRDS THE PULSE OF THE ESTUARY 2011 81 ------). Concentrations have been been have ). Concentrations 2 RE GU I F uorooctane sulfonate (PFOS) (PFOS) sulfonate as per such $uorooctane PFCs use, spread related and PFOS environment. in the detected been have with a variety in associated of toxic e"ects been have PFCs development. abnormal and carcinogenity, mortality, cluding In 2006, the RMP began analyzing cormorant eggs for PFCs. Consistent with other published studies, PFOS was Concentra eggs. in cormorant detected PFC the dominant tions of PFOS were highest in the South Bay, and higher highest at Wheeler Island in Suisun Bay, up to a maximum up to of Wheeler Bay, at in Suisun highest Island interest Wheeler from are in 2002. &e results 800 ppb Island Concen location. sampling this urbanized as ising the least WheelerRichmond the at were and Bridge trations Island in 2002. Continued 2006 than in 2004 and lower substantially whether willthis monitoring is determine indica to be needed expected in PBDEs are Declines trend. of a downward tive of two of the use ban Legislature’s of the California as a result in 2006. “octa”) and types of PBDE mixtures (“penta” Least eggsTern had mean concentrations of 770 ppb in 2001 and 500 ppb in 2002, similar to those observed in cormorants at Wheeler Island (She et al. 2008). PFOS stain- $uorinated shown that has monitoring egg Cormorant in of concern concentrations be reaching to appear repellents been have chemicals (PFCs) $uorinated Per food web. the Bay in a variety of products 50 years the last over extensively used ghting ! !re- with stain-repellents, textilesincluding treated with in contact used for paper coatings and refrigerants, foams, stability As of their chemical wide and food products. a result ably in space and time among samples collected from the three the three from collected samples time among and in space ably ( subembayments have raised concern. A recent review showed that PBDE con that review showed A recent concern. raised have were the Bay from birds of ! in the eggs sh-eating centrations Chesa from in birds those than higher of magnitude order an 2009). Sericano and (Yogui area Delaware the and Bay peake consider varied eggs of PBDEs in cormorant Concentrations

- RE GU I F S DE BS B ). Concentrations in this species have been variable and fail-to-hatch Least eggsTern collected in 2001 and 2002 (4.0 ppm) were at a published effects threshold for PCBs in terns (also 4.0 ppm), with multiple individual samples exceeding the threshold (She et al. 2008). P but not available, are for PBDEs in birds thresholds E"ect samples egg bird Bay in some concentrations high seemingly 2 not shown distinct regional erns.% pa Concentrations in San Pablo Bay were relatively high from 2000–2006 (with a maximum of 4.5 ppm in 2002), but lower in 1999 and 2009. Some of the samples from the Richmond Bridge in San Pablo Bay exceeded the lower end of the estimated threshold range for reproductive impairment. PCB concentrations in Least eggsTern also indicate potential risks of adverse effects. Average PCBs in ten ed in 2000 had an average concentration of 0.3 ppm, which is below the e"ects thresholds (Schwarzbach and Adelsbach 2003). ternsHowever, as a group may be somewhat more sensitive to methylmercury than the species used to develop the thresholds, based on egg-injection studies, which are di'cult to translate into thresholds for wild birds (Heinz et al. 2009). Inclusion of a TMDL target to protect the Least is an Tern indication of the regulatory concern for potential methylmercury impacts on this endangered species. PC PCB concentrations in cormorant eggs over the last 10 years have occasionally approached an e" ects threshold of 3.6-6.8 ppm for reproductive impairment in this species ( tions in San Francisco Bay (including Suisun Bay) compared compared Bay) Suisun (including Bay Francisco tions in San 2003). Adelsbach and (Schwarzbach the Delta to fewVery data are available for methylmercury in California collect eggs Tern Least fail-to-hatch ree & eggs. Tern Least ------ FHH ) are used BMM XFJHIU Phalacrocorax auritus XFU Y A GSFTI B QQN W , but methylmercury is not likely to be adversely , but methylmercury be adversely is not likely to ! 2 m LLO RE A GU H ETHYLMERCURY I F it does not appear likely that these concentrations are harming harming are concentrations these likely that not appear it does consistent been have erns % pa &e regional the population. or decreasing with time, of increasing no indication over indicated also have eggs Cormorant within region. trends each in methylmercury variation bioaccumula is spatial there that with concentra scale, higher regional broader a even tion at for reproductive impairment in Mallards and Ring-necked Ring-necked and in Mallards impairment for reproductive 1IFBTBOUT 1979), in fww; 1971, Heinz presented Fimreite concentrations levels. those exceed to tended have Bay the South from those methylmer to insensitive relatively are however, Cormorants, al. et 2009), so (Heinz cury species other to toxicity compared M in variation spatial shown regional have eggs Cormorant Bay in the South methylmercury with concentrations higher ( Suisun and While this species. "ecting a Pablo San from eggs thresholds e"ects adverse or below be at to tended have Bays importance of sample collection not adversely impacting this endangered species. & e only recent data available for these piscivores come from two small studies of fail-to-hatch eggs from 2000–2002 at the Alameda AirNaval Station colony (Schwarzbach and Adelsbach 2003, She et al. 2008). ponds), but they primarily hunt in the subtidal shallows and over mud$ats and large sloughs when the tide is in. Califor nia Leastalso Terns forage extensively in these areas, with a preference for shallow Bay habitat near their nesting area (Ehrler et al. 2006). Both species are !sh-eaters. Bioaccumu lation in Leastis more Terns di 'cult to study, because of the by the RMP as a sentinel species for the open waters of the CormorantBay. eggs are sampled Bay-wide every three years for mercury, selenium, PBDEs, PCBs, legacy pesticides, and, starting in 2009, per$uorinated compounds Cor (PFCs). morants forage in a variety of shallow-water habitats (Hatch and 1999),Weseloh including managed ponds (former salt S Double-crested Cormorants ( 82 FEATURE ARTICLES | BIRDS

FIGURE 2 900 800 Double-crested Cormorants are monitored by the RMP as a sentinel species for the shallow open waters of the Bay. Cor- 700 morant eggs have shown higher concentrations in the South Don Edwards Pond A9/10 600 #BZ i%PO&EXBSET1POE"uBOEi4PVUI#BZ<5PXFST>u 500 but methylmercury is not likely to be adversely a"ecting this Richmond Bridge species due to its low sensitivity to this pollutant. PCB concen- 400 Wheeler Island PBDEs (ppb) trations over the last 10 years have been variable and not shown 300 distinct regional pa%erns, and have occasionally approached an South Bay (Towers) 200 e"ects threshold for reproductive impairment. Concentrations of PBDEs have varied considerably among the three subembay- 100 ments and over time, and are high relative to other parts of the 0 world, but a lack of thresholds makes it unclear whether these 2000 2002 2004 2006 2008 2010 concentrations are a"ecting Bay bird species. 1.2

1.0

0.8

0.6

0.4 Methylmercury (ppm) 0.2

0.0 2000 2002 2004 2006 2008 2010

PCBs (ppm) 2

0 2000 2002 2004 2006 2008 2010

µDouble-crested Cormorant. Photograph by Robert Lewis. PBDEs (ppb) FEATURE ARTICLES | BIRDS THE PULSE OF THE ESTUARY 2011 83 - - - - - RSH RSH MA L S A DE ID B al. 2008). Maximum concentrations observed in both Forster’s Terns and Caspian Terns were similar and nearly five times greater than the lowest observed adverse effect level for reproduction. The Eden Landing area in South Bay had the highest concentrations of PCBs. P T Tidal marshes are highly organized habitatsposed of clearly that distinguishedare com sub-habitats (marshmarsh plain, channel, and panne) that develop because of theunique hydrology of these wetlands. Food webs may somewhatbe separate among these habitats (Grenier 2004),so it is important to understand where sentinel spe bird tidal marsh within Three a tidal marsh. forage species cies have been studied for exposure to methylmercury,although not to the extent of the terns and cormorants informa ponds. Thus, managed and bay in the shallow tion about tidal marsh bird methylmercury exposureand effects is quite limited and tends to come fromstudies a few completed in different marshes at different times, ppb) were similar to concentrations in Least Terns and cormorants from Wheeler Island (She et al. 2008).few A of the Forster’s Tern samples from Eden Landing had the highest PBDE concentrations ever recorded in wildlife (She et al. 2004). Some of the highest concentrations of PBDEs observedanywhere in the world raisedhave concern for pos sible impacts on Forster’s Terns in the Bay (Shaw and Kannan 2009). There is a growing body of data frommany urbanized coasts for comparison, including manyspecies of fish-eating birds from Canada, New England,San Francisco Bay, Delaware Bay, Alaska, Washington state, Europe, South Africa, and China. (rang Annual Terns of Forster’s in eggs averagePBDE concentrations ing from 330–990 ppb) and Caspian Terns (320–580 - - - - - ) blood of (3 Gavia immer BS PC PCB concentrations in some eggs of andForster’s Caspian appear toTerns be high enough to pose health risks to these species. Average PCB concentrations in Forster’s and Caspian eggsTern collected from 2000-2003 were below a 4 ppm threshold for impacts on reproduction, but many individual eggs exceeded this value (She et risks to these species based on egg methylmercury concen methylmercury egg on based species these to risks trations are very similar (Eagles-Smith et al. 2009). Tissue concentrations are consistently higher in the South Bay near in For concentrations Methylmercury of Alviso. the town ster’s eggsTern have fluctuated considerably over time, with annual averages in the most recent monitoring all exceeding reproductive effects thresholds. Despite the strong evidence for risk to these populations from methylmercury toxicity, verifying reproductive field is study difficult. through fac other impacts Many tors influence avian survival and add to noise in the data set. Forster’s hatchingTern success shows evidence of impacts from mercury. Fail-to-hatch eggs of Forster’s Terns had higher average methylmercury concentrations than abandoned eggs and random eggs sampled from successful nests (Eagles-Smith and Ackerman 2008). Stilt and avocet methylmercury higher in their feath had chicks found dead ers than randomly-sampled live chicks of similar age, but on their methylmer chick survival based little varied rates cury bioaccumulation (Ackerman et al. 2008a). Similarly, fledgling Forster’s survivalTern was not related to blood methylmercury concentration (Ackerman et al. 2008b). A detailed summary of this research can be found in the 2008 Pulse of the Estuary (Eagles-Smith and Ackerman 2008). Terns Terns and approximately 5% of Avocets, Stilts, and Caspian Terns (Eagles-Smith et al. 2009) exceeded a risk threshold Loon ( for Common developed ppm wet weight) at which there was a 40% loss in loon reproduction (Evers et al. 2008). Estimated reproductive ------Himan ), American Avo Sterna caspia Sterna ONDS ), and Black-necked Stilt ( Black-necked ), and NTS A P ) all feed and breed primarily around in and breed ) all and feed OLLUT ), Caspian Tern ( Tern ), Caspian GED P A N Recurvirostra americana Recurvirostra ETHYLMERCURY THER Sterna forsteri Sterna on invertebrates in shallower ponds. in shallower on invertebrates M Forster’s Terns appear to face significant risk from exposure to methylmercury. Nearly half (48%) of breeding Forster’s ( ( cet mexicanus topus in recent extensively studied been ponds, all and have managed and methylmercury accumulation particularly regarding years, feed while piscivores, are stilts avocets and &e terns e"ects. Managed ponds are the former salt ponds around the margin the margin ponds the former salt around ponds are Managed originally ponds &ese are tidal marsh. were that of the Bay as terns, such support to waterbirds, managed largely now shal ponds are managed Some ducks shorebirds. and plovers, drying seasonal, and fall.low and out in the summer Others Tern Forster’s support round. and wet !sh year perennially are MA concentrations in the South Bay exceeded an estimated no effect concentration of 1 ppm. O than concentrations reported in other regions (Houde et al., 2006). Concentrations were similar in 2006 and 2009. The tion of 7 ppm NoDDT. previous or more recent cormorant egg samples approached any effects thresholds for DDT, pollutants. other or dioxins, dieldrin, ied in Double-crested Cormorant eggs have been below ef below been have eggs Cormorant in Double-crested ied fect thresholds, and no recent studies have examined other pollutants in California Least Terns. Since 1999, only one composite cormorant egg sample from Wheeler Island in 2002 exceeded the 5 ppm effects threshold for reproductive al. et 1983) with a concentra (Weseloh DDT for impacts The other bioaccumulative pollutants that have been stud 84 FEATURE ARTICLES | BIRDS California Clapper Rail. Photograph by Robert Lewis. ´

rather than from long-term programmatic monitoring. tion). Based on that study, maternal songbird blood meth- problem is unlikely. However, since these pollutants typi- The three bird species that have been studied differ in ylmercury concentrations of 0.4 ppm wet weight translate cally exhibit hotspots near watershed sources, the sampling the habitats in which they forage. While tidal marsh to approximately a 5% reduction in reproductive success. conducted to date cannot rule out problems in unstudied Song Sparrows (Melospiza melodia subspp.) and Califor- marshes near industrial and urban areas. nia Black Rails (Laterallus jamaicensis coturniculus) for- Average Song Sparrow blood methylmercury concentra- age predominantly in the vegetated marsh plain (Grenier tions in the South Bay ranged from 0.1–0.6 ppm wet weight 2004, Tsao et al. 2009), California Clapper Rails forage by marsh, and more than half the sparrows were above the PRIORITY extensively in marsh channels and somewhat in the 0.4 ppm threshold in both years of the study (FIGURE INFORMATION GAPS marsh plain (Moffitt 1941). 3; Grenier et al. 2010). Song Sparrow methylmercury concentrations were lowest in marshes far from the Bay Given that there is evidence for potential effects of METHYLMERCURY and highest in marshes near the Bay (FIGURE 3), which pollutants on birds in every habitat in the Estuary that parallels the salinity gradient (Grenier et al. 2010). Blood IBTCFFONPOJUPSFE XIFSFTIPVMEXFGPDVTPVSFGGPSUT Methylmercury is considered a significant concern for methylmercury concentrations in Black Rails from North What information is the most important to gain that several species of tidal marsh birds. The recovery of the Bay were in the same range as the Song Sparrow concentra- could reduce exposure and risk through improved man- endangered California Clapper Rail, found only in the San tions, and about 10% of them were in a range correspond- BHFNFOUPSSFHVMBUJPO "GFXQSJPSJUZBSFBTTUBOEPVU Francisco Estuary, may be impeded by methylmercury con- ing to a moderate risk for reproductive effects (> 1 ppm tamination. A study conducted from 1991-1999 concluded and < 3 ppm wet weight), based on the same Common ARE THERE POPULATION-LEVEL that methylmercury was a likely cause of the unusually high Loon model used to describe the Forster’s Tern data above EFFECTS? rates of nonviable Clapper Rail eggs (31%; Schwarzbach (Tsao et al. 2009). In many cases, exposure in birds exceeds an effects et al. 2006). Methylmercury was found in rail eggs above UISFTIPMEGPSBQPMMVUBOU8IBUEPFTUIJTSFBMMZNFBO effects thresholds at all of the marshes studied; means by OTHER POLLUTANTS 5PXIBUFYUFOUBSFUIFCJSETJNQBDUFE $BOUIFBWJBO marsh ranged from 0.27–0.79 ppm wet weight (Schwar- population in this urbanized environment with many zbach et al. 2006). Furthermore, laboratory studies have A few studies have examined persistent organic pollutants other stressors absorb a reproductive loss related to pol- indicated that Clapper Rails are more sensitive to methyl- in the eggs of Clapper Rail (PCBs and legacy pesticides: MVUBOUT PSXJMMUIFQPQVMBUJPOEFDMJOF mercury than the pheasant and Mallard species from which Schwarzbach et al. 2006, dioxins: Adelsbach and Maurer the thresholds of 0.5 and 0.8 ppm fresh wet weight were 2007, PCBs and PBDEs: She et al. 2008), and one study WHAT ARE EFFECTS THRESHOLDS derived (Heinz et al. 2009). measured PCBs and DDT in Song Sparrow eggs from FOR PBDES, ESPECIALLY IN TERNS? North Bay (Davis et al. 2004). In all cases but one, these PBDEs reach seemingly high concentrations in terns, Tidal marsh Song Sparrows, a state species of special pollutants were detected in the marsh bird eggs, but the but the adverse effects, if any, are unknown. The RMP concern, and Black Rail, a state threatened species, both concentrations were relatively low and did not approach has funded a study by the Patuxent Wildlife Research had methylmercury concentrations in blood that indi- effects thresholds. Adelsbach and Maurer (2007) reported Center to evaluate the relative sensitivity of tern embryos cated potential risks of impaired reproduction. For the that four fail-to-hatch Clapper Rail eggs from North and to PBDE exposures. The results will be available at the sparrows, comparison to a songbird effects threshold is South Bay had dioxins at concentrations that might impact beginning of 2012. appropriate. A recent study linked blood methylmercury reproduction. Thus, based on the few marshes and analytes concentrations to reproductive effects in the Carolina examined, very little evidence of the potential for adverse Wren (Thryothorus ludovicianus), yielding an estimated effects from persistent organic pollutants on marsh birds relationship between reductions in nesting success and in the Estuary has been found. This is an encouraging maternal blood concentrations (Jackson et al. in prepara- outcome, in that it indicates that a pervasive, Bay-wide FEATURE ARTICLES | BIRDS THE PULSE OF THE ESTUARY 2011 85 - E MORE B N SCIENCE A GEMENT DECISIONS? C A N W A O by making sure that they positively a"ect decision-making and improve environmental outcomes. &e RMP is funding a synthesis of mercury information from the Estuary, which will create conceptual models that tie scienti! c knowledge to feasible management actions for reducing methylmercury in 2011. of end the by will available report be e & biota. H CLOSELY LINKED TO IMPROVING M commu for the environmental challenge &is is ongoing an nity – to get the most out of research and monitoring dollars - - - A reasonable approach might be to manage pollutants so as to improve condition in the worst places or at least not make things worse through management actions, and then re-evaluate the situation every 5 or 10 years. A solid un in bioaccumu patterns temporal and of spatial derstanding lation would be supportneeded to this type of approach. to evaluating wildlife exposure, particularly comparison to ambient condition. It seems likely that pollutants impact many wildlife species in the Bay topollut someother degree,with especiallyeffect compound a as considered when ants, disturbance, habitat degradation, and other stressors. - E IENT B B M A N TO IRDS IRDS A B TIVE TO A THER TH A TED REL A LU A HOULD EXPOSURE IN IN EXPOSURE HOULD CONDITION R S EV thresholds developed with a few laboratory species (e.g., repre accurately cannot that pheasant) Mallard, chicken, sent the diversity of wild birds that reside in Bay habitats. Therefore, it may be valuable to explore other approaches SPECIES-SPECIFIC THRESHOLDS? Bird species vary in their sensitivity to each pollutant, yet species-specific thresholds will not be forthcoming in the near future. Thus, there are uncertainties associated with managing and regulating water quality based on effects 86 FEATURE ARTICLES | BIRDS

SIDEBAR ANOTHER DIMENSION More than a dozen other bird species were also Song Sparrow Blood Total Mercury (ppm) sampled, and a few of those species appeared to 0.0 0.5 1.0 1.5 2.0 2.5 3.0 OF THE MERCURY have higher exposure than Song Sparrows. &us, PROBLEM Song Sparrows may be an indicator of riparian Up. Guadalupe R. methylmercury accumulation in the food web, but Coyote Res. Up. Methylmercury bioaccumulation in songbirds they may not re$ect the greatest impacts that are Guadalupe Crk residing along Bay Area streams may also be high occurring to riparian wildlife. enough to cause reproductive impacts at some sites. Almaden Res. Up. Song Sparrows (Melospiza melodia) were used as Average methylmercury concentrations at two of Up. Walker Crk a methylmercury biosentinel for riparian (stream- the 20 sites sampled were above 0.4 ppm (ww). Wildcat Crk side) habitat throughout the Bay Area in 2010. A recent study in Carolina Wrens that examined Napa R. Twenty sites and 140 Song Sparrows were sampled, the relationship between maternal blood mercury Mid. Walker Crk with blood mercury concentrations spanning more concentration and reproductive e"ects found China Camp S.P. than two orders of magnitude. &is project was that concentrations of 0.4 ppm translated to an guided by a group of regional and national scienti!c approximate 5% reduction in nest survival (the Mid. Guadalupe R. experts in mercury, riparian habitat, and songbirds number of nests that successfully hatched chicks) San Pablo Crk that helped determine the appropriate biosentinel (Jackson et al. in prep). &e highest mercury con- San Felipe Crk species and sampling approach. centrations measured in riparian Song Sparrows Low. Walker Crk of the Bay Area were above 2.5 ppm, a level associ- Muddy Hollow Sampling sites were chosen based on a conceptual ated with a 50% decline in nest survival. Lagunitas Crk model in which the key drivers of songbird exposure were 1) total mercury contamination of sedi- Many of the sites in this study were in an urbanized Mills Crk ment and 2) environmental conditions that were environment where wildlife populations are subject Simas Crk thought to a"ect production of methylmercury. to multiple stressors. In these stressed populations, Coyote Crk &e !ndings supported the conceptual model there may be li%le to no surplus of young birds each Low Guadalupe R. in that both total mercury contamination and year, which would amplify the consequences of Hanson’s Cement environmental conditions were related to blood reproductive loss from methylmercury e"ects. methylmercury concentrations in sparrows. &e "0.4 ppm threshold site with the greatest methylmercury exposure in &is innovative study, which builds on a nascent for reduced nest survival" songbirds was downstream of the New Almaden body of work on songbird methylmercury east Mercury Mining District, but the second highest of the Rockies, appears to have revealed another site was not in$uenced by mining. dimension of the mercury problem in the Bay Area. &e !ndings have implications for mercury impacts in habitats across California and beyond that have received li%le a%ention to date.

Footnote: Bars show range of the middle 50% of the observations. FEATURE ARTICLES | BIRDS THE PULSE OF THE ESTUARY 2011 87 12000 - 10000 8000 ewis. 6000 L Song Sparrow blood methylmercury ! B % obert R Distance to Bay (ft) In both 2007 and 2008, more than half of the 4000 hotograph by P 3

parrow. parrow. 2000 S ong S One hypothesis for this pa%ern is that there may be a relationship between #e estimated risk to the South Bay tidal marsh sparrow population FIGURE sparrows were at risk for an estimated 5% or greater reduction in nesting suc nesting in reduction greater or 5% estimated an for risk at were sparrows methylmercurye ects." from cess concentrations (based on 109 birds) were higher in marshes closer toBay. the bioaccumulation. methylmercury and salt) versus type(brackish marsh ³ %A! year. by somewhat varied 0 0

0.3 0.2 0.1 0.7 0.6 0.5 0.4 Methylmercury in Sparrow Blood (ppm wet weight) wet (ppm Blood Sparrow in Methylmercury B 100% 80% < 5% 5 - 10% 10 - 15% 15 - 20% > 20% Modeled Percent Modeled Percent Reduction in Breeding Success 60% 40% 20% Percent of the Breeding Song Sparrow Population at Risk of the Breeding Song Sparrow Population Percent 0% A 2007 2008 Year 88 FEATURE ARTICLES | SEALS

CHRISTINE WERME, Independent Consultant DENISE GREIG, &e Marine Mammal Center MEG SEDLAK, San Francisco Estuary Institute

contaminant exposure and effects at the top of the bay food chain: evidence from harbor seals

Studying harbor highlights seals is logistically di'cult, o&en relying Concentrations of some on opportunistic contaminants, such as sampling of stranded Paci"c harbor seals are found Concentrations of PBDEs from %ame retar- animals, so there are year-round in San Francisco Along much of the contaminants such as dants and per%uorinated many data gaps and Bay, feed at the top of the food California coast, harbor organochlorine pesticides, compounds are elevated challenges to be met chain, and maintain a large store seal populations rebounded PCBs, mercury, and in seal tissues to levels as of fat, all factors that put them a&er hunting was banned selenium in tissues are high or higher than those at risk of accumulating toxic in the 1970s, but similar elevated to levels that may measured in other parts contaminants and make them increases did not occur in cause health e$ects in Bay of the world good monitoring sentinels San Francisco Bay harbor seals FEATURE ARTICLES | SEALS THE PULSE OF THE ESTUARY 2011 89 ------seals and were able to release 73 of them. The Marine Mammal Center staff works with scientists around the world to learn from the animals they rescue. Their publica (http://www.marinemammalcenter.org/science/ tions for understand resource provide a valuable publications/), ing the threats to marine mammals, including the threats from exposure to chemical contaminants. conditions and beenhave used to identify regional con taminant hotspots, even when tissue contaminant levels are below those suspected of causing harm. A growing body of literature from the world’s five subspecies of harbor seals suggests that exposure to contaminants can reach levels that contribute to population declines Marine Environ(e.g., mental Research Institute 2006). Studies of harbor seals are challenging, making them di' cult to include in routine monitoring programs. Some studies acquire samples opportunistically, collecting blood, blubber, and other samples from dead animals or from animals that beenhave rescued. Capturing healthy live animals for sam pling requires federal permits and is logistically challenging because they can be di' cult to capture. The Regional Monitoring Program for Water Quality in col from benefitted has Estuary (RMP) Francisco the San laboration with The Marine Mammal Center in Sausalito and other research scientists. The Marine Mammal Center expertise regional provides facilities and mam for marine mal rescue and rehabilitation, serving much of the central California coastline. They treat stranded animals, including harbor seals, at their hospital and when possible, release them back into the wild. In 2010, they treated 132 harbor temporal trends. On the state level,estua the the Sanprotects FranciscoBoard Bay Control Quality Water Regional rine, marine, and wildlife habitat of the harbor seal. scientists,To harbor seals are useful sentinels of adverse - - - NBOEBUF UIBU 6OEFS NBNNBMT NBSJOF PUIFS BOE Marine Mammal Health and Stranding Response Program to investigate strandings and deaths and analyze tissue samples for toxic substances and diseases. in NMFS, col laboration with the National Institute of Standards and Technology, maintains a tissue bank for samples taken from stranded animals and other sources. The goal of the tissue bank is to provide material for studies of geographic and of pollutants and habitat loss spurred the interest of scientists the interest spurred loss habitat and of pollutants with ended the passage hunting Seal the community. and Act of 1972, and Protection Mammal Marine of the federal of the most along increased erwards, dramatically # a numbers slower much been have increases Population coast. California distur human other and loss habitat to due largely in the Bay, &ere contaminants. chemical possibly also and due to bance, in California. About seals harbor 34,000 about currently are during the 1980s, within lived seals 400–500 harbor the Bay 500. around remains population the current and The Marine Mammal Protection Act prohibits any killing lions, whales, por sea seals, elephant of seals, or harassing QPJTFT the National Oceanic and Atmospheric Administration’s National Marine Fisheries Service (NMFS) leads the Harbor seals were probably abundant in the Bay until the late until the late in the Bay abundant probably were seals Harbor to began oil, for their pelts, 1800s, when meat hunting and the seriously reduced had the 1920s, hunting a toll. By take surveys al. et 2005). Systematic 2003, Neale (Grigg population did not begin until the e"ects about the 1970s, when concerns - - - uzanne Manugian. ) is a year- S ). Y 1 A RE GU I hotograph by F P ocks. ocks. R Phoca vitulina richardii vitulina Phoca IN A H C OP OF THE B THE OF OP T arbor seals on Castro H HE HE OOD mass of fa%y tissue over many years put seals at particular risk of accumulating toxic pollutants Year-round residency, feeding at the top of the food chain and close to the shore, and maintaining a large Excavation of the large Native American shellmounds found Native of the large Excavation har that indicates shorelines Bay East and Francisco San along for thousands of years. in the Bay present been have bor seals and on squid and crustaceans. Healthy harbor seals have thick blubber, used for insulation and energy reserves, and may live up to 30 years. & ese factors – year-round residency, feeding at the top of the food chain and close to the shore, and maintaining a large mass of fa%y tissue over many years – put seals at particular risk of accumulating toxic pollutants. Harbor seals are at the top of the Bay food chain, generally feeding close to shore on both boom% and schooling !shes Rafael Bridge in the North Bay ( Bay North the in Bridge Rafael and other haul-out sites for daily resting and for giving birth during the spring pupping season. Harbor seals can be found throughout the MajorBay. haul-out and pupping Fran San Edwards the Don include Mowry at Slough sites cisco Bay National Wildlife Refuge in the South Bay, Yerba Buena Island, and Castro Rocks, next to the Richmond-San The Pacific harbor seal ( round resident of San Francisco Bay and the surrounding only coastalpermanent waters. is It resident the pin area’s niped, the group that includes seals, sea lions, and walruses. Harbor seals are only semi-aquatic, depending on beaches T F ³ 90 FEATURE ARTICLES | SEALS

FIGURE 1 Major harbor seal haul-out sites in San Francisco Bay. Castro Rocks, Yerba Buena Island, and Mowry Slough are the most heavily used sites.

1 Suisun San Pablo Bay Bay

4 3 1. Tubbs Island 5 2. Sisters Island 6 3. Castro Rocks 7 4. Corte Madera Central Bay 5. Brooks Island 8 6. Strawberry Split 7. Angel Island 9 8. Oakland Entrance 9. Yerba Buena Island 10. Grecko Island µHarbor seal mother and pup. Photograph by Suzanne Manugian. 11. Mowry Slough 12. Guadalupe Slough South Bay

Lower 11 South Bay 12 0 10 20 Km FEATURE ARTICLES | SEALS THE PULSE OF THE ESTUARY 2011 91 - EBUB UIF PG TVCTFU B 6TJOH CMPPE UIF JOUP ). 2 RE CMVCCFS GU I F These studies began to make a case that levels of organic contaminants in San Francisco harbor seals appeared to be elevated. Comparable studies have suggested that for some pollutants, conditions are similar in other parts of the world ( for a broad range of organic pollutants, including PCBs, PBDEs, and organochlorine pesticides. The study found the highest concentrations of organic con taminants in blubber from pups that had been weaned in the wild, lost weight, then stranded and died. These results showed that harbor seals may be at particular risk during a post-weaning period, during which contaminants move GSPN newborn pups found dead near the location of birth, the researchers could begin discern some geographic patterns, with pups from San Francisco Bay having contaminant profiles suggestive of more urban inputs and those from Monterey Bay showing more agricultural influence. The study sampled blubber from 180 wild and stranded young-of-the-year animals, and categorized them by age and source of contamination (for example, placenta, milk, or other diet). Blubber samples were also taken from 23 older seals and two fetuses. The samples were analyzed - - - - - Another recent study examined the effects of develop of effects the examined study recent Another mental stages on concentrations of organic contaminants in very young central California harbor seals (Greig et al. 2011). Seal pups are exposed to organic contaminants through the placenta before birth and through milk during the three-to-five weeks nursing period after they are born. nated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and biological parameters. The investigators found that higher DDE, PCB, and PBDE levels in the blood correlated with white blood cell counts, suggesting that high levels of contaminants might be associ ated with increased rates of infection. There was an inverse relationship between total PBDEs and red blood cells, although the relation was not strong enough to suggest a When anemia. link to the scientists com contaminant clear pared their results with earlier studies, they found some evidence of declining levels of PCBs in Bay seals, although concentrations remained high enough to warrant continu ing concerns for reproductive or immunological effects. yearlings, and adults, were captured with beach seines and tangle nets from haul-out sites. All seals were re-released to the wild after weighing, measuring, and drawing blood samples. The blood samples were then analyzed for DDE (a breakdown product of the pesticide DDT), polychlori - - NTS NTS $BMJGPSOJB L A PG A E S MIN A 6OJWFSTJUZ UIF ND OTHER ONT GSPN TE IN A C A TDJFOUJTUT ER ER NIC NIC A BB RG ISSUES m BLU ACCUMUL T levels, immune function, and biological parameters in healthy, wild seals (Neale et al. 2005). Scientists captured and took blood samples from 35 free-ranging har Bay bor seals. The 13 males and 22 females, including pups, that environmental pollutants might be causing some of those conditions (Kopec and Harvey 1995). *O Davis and other organizations, including The Marine Mam mal Center, undertook an integrated study of contaminant accumulate in fatty tissues, such as seal blubber. Other studies from the 1990s documented a variety of abnormal health parameters in harbor seals, such as low red blood cell counts and high white blood cell counts, and hypothesized Organic pollutants, such as PCBs and organochlorine pesticides, persist for long periods in the environment, biomagnify up the food chain, and accumulate inblubber seal as such %fa tissues, y in Thompson et al. 2007). Those studies documented elevated levels of organic pollutants, such as PCBs and organochlorine pesticides, that persist for long periods in the environment, biomagnify up the food chain, and Studies of organic contaminants in San Francisco Bay harbor seals began in the 1990s (reviewed for the RMP O 92 FEATURE ARTICLES | SEALS

FIGURE 2 DDT PCB Average concentrations of blubber PCBs and DDTs Stranded SF Bay newborns, n=11, (1) from harbor seals sampled in San Francisco Bay and Recently weaned SF Bay pups, n=26, (1) around the world. Stranded SF Bay adult females, n=4, (1)

Scotland adults, n=40, (2)

Northwestern Atlantic adults, n=6, (3)

Norway adults, n=10, (4)

Alaska adults, n=8, (5) 0 5000 10000 15000 20000 25000 Average Blubber Concentration (ppb, lipid weight)

Footnote: Where sex is not speciﬁed, adults are half male, half female. 1) Greig et al. 2011, 2) Hall and Thomas 2007, 3) Shaw et al. 2005, 4) Wolkers et al. 2004, 5) Wang et al. 2007.

µHarbor seals on Castro Rocks. Photograph by Suzanne Manugian. FEATURE ARTICLES | SEALS THE PULSE OF THE ESTUARY 2011 93 - - subsequently died.mercury Total levels were highest in hair samples, but the levels in muscle samples correlated beer% with results from other tissues, making it the best measure for comparisons with other studies. detected during the Brookens et al. (2007) study, a little surprising to the scientists, who had anticipated finding higher mercury levels in San Francisco Bay and Tomales Bay than the other central California sites. Studies of sedi ments, oysters, and fish had found clear differences in San Francisco Bay and Tomales Bay, both areas with histories of mercury mining. The scientists attributed the lack of difficulties to study seal in the harbor in differentiat trends ing sources of exposure in large, mobile animals of varying ages and developmental stages. A subsequent study of seal pup tissues suggested that muscle samples may be the best tissue for mercury monitoring, when they are available (Brookens et al. 2008). In this study, scientists sampled brain, heart, liver, kidney, muscle, blubber, and other tissues from 26 seal pups that were found dead on the shoreline or that had been admied% for rescue but e sinker was a common type used used type common a was sinker e & 2006). al. et (Zabka sues move to large too was and shermen ! commercial and sport by system. digestive the through No clear geographic trends in metals concentrations were - - harbor seals reach adulthood. Age-related changes in the mercury to selenium ratios corroborated that finding. concentrations lead female, adult one from samples for Except were uniformly &at seal was low. weak and experiencing sei facilities Center Mammal Marine e & into came it when zures sinker shing ! lead a found necropsy A later. days four died and tis liver and in blood levels lead high and stomach in the seal’s for blood and hair samples. Blood, hair, and liver samples were taken from dead seals found at sites along the coast of central California, including San Francisco All Bay. samples were analyzed for methylmercury, total mercury (methyl lead. and selenium, mercury), mercury inorganic plus This study found elevated concentrations of mercury and selenium in the blood samples, sometimes higher than levels known to be toxic to mammals. The average total mercury in the blood samples exceeded levels that had previously been recorded for harbor seals, although average values in liver samples were within the known range. Total mercury concentrations in liver tissues increased linearly with age, while methylmercury concentrations increased exponentially for the first five years of life, leveling off in adults. These results suggested that the mechanisms for detoxifying methylmercury are not well developed until Mercury and other inorganic elements were the subject of a 2003–2005 project that analyzed tissue samples from 186 live and 53 dead seals from central and northern California (Brookens et al. 2007). Live seals were captured in Monterey San Francisco Bay, Point Reyes, Bay, and Humboldt County - - - - LS LS A ET M

THER O ERCURY ERCURY ND ND Mercury, particularly methylmercury, can also be incor porated into hair. Mercury levels in hair samples provide a longer term record of exposure than blood samples. Female seals can also transfer methylmercury to across the placenta fetuses and, to a lesser degree, into milk. in the liver, circulated through the blood system, and excreted in urine and mercuryfeces. Total levels in blood, including both methylmercury and inorganic mercury, are regarded as good indicators of ongoing exposure to contami nation within a speci!c geographic area. Seals accumulate mercury, in the form of methylmercury, mostly from eating !sh. Methylmercury bioaccumulates and mam other and Seals chain. food the through es ! biomagni mals are able to transform methylmercury in their digestive systems and livers into another form, inorganic mercury. Both methylmercury and inorganic mercury can be retained &e study found elevated concentrations of mercury and selenium in the blood samples, sometimes higher than levels known to be toxic to mammals ing, because it can counteract some harmful some of mercury e"ects ing, counteract it can because of the toxic form levels of in relative Changes seals. in harbor can levels selenium to in comparison methylmercury, mercury, also be may Seals mercury toxicity. of increased be indicative riskat of toxicity as lead. metals, such other from Just as the human population is concerned about mercury about is concerned population the human as Just risk of at the legacy from are seals harbor in seafood, levels of mercury use and in the mercury Bay the South in mining foothillsSierra is Rush. during another the Gold Selenium but it is especially interest in the Bay, concern environmental M A 94 FEATURE ARTICLES | SEALS

SENTINELS FOR BAY To date, li%le work has been conducted on the biological CONTINUING CONTAMINANTS e"ects of PFCs in seals. In general, PFCs in mammals are INVESTIGATION associated with reproductive problems, suppressed immune Some recent studies of harbor seals in the Bay have gener- systems, and liver cancer. One study of seals in Lake Baikal The Marine Mammal Center continues to perform blood ated considerable public attention. For example, when in Russia suggested that PFCs could a"ect the signaling and tissue analyses on the animals within their care. Their scientists analyzed seal blubber samples that had been pathway related to transforming normal cells into cancers. A facilities and research capabilities have become a valuable collected and archived from stranded, dead harbor seals recent study of the California sea o%er population along the resource to federal and state agencies, universities, and oth- during 1989–1998, PBDE levels were among the high- central California coast identi!ed a signi!cant correlation er scientific organizations. Their collaborations continue est ever reported (She et al. 2002). Of most concern, the between the presence of PFCs and the incidence of disease. to work towards understanding the effects that chemical highest concentrations came from seals collected in later pollutants have on harbor seal health and reproduction, years (FIGURE 3). When normalized for lipid content, There was good news in another collaboration with The determining how and where they enter the food chain, and the results showed that concentrations were doubling every Marine Mammal Center. The RMP has recently completed ultimately determining the risks they pose to wildlife and 1.8 years. These results were reported around the world a project to quantify a newer brominated flame retardant, human health. and were important for making the case to ban two of three hexabromocyclododecane (HBCD), in seal tissues. HBCD classes of PBDEs in California. Oregon has banned all is added to polystyrene insulation that is used in build- One of these studies, a joint project with the RMP and the three classes of PBDEs, and the giant retailer Wal-Mart, has ing construction. The study found relatively low levels of National Institute of Standards and Technology, is currently also instituted a ban on all PBDEs. Chemical companies in the compound in Bay seals, lower than levels detected in identifying a broad range of natural and man-made chemical UIF64IBWFDFBTFENBOVGBDUVSFPGUIFUXPDMBTTFTPG1#- similar studies in Asia and much lower than levels detected DPNQPVOETJOTFBMCMPPE CMVCCFS BOEMJWFSTBNQMFT6O- DEs that are banned in California and will begin to phase in Europe. like previous studies that targeted speci!c compounds, this out manufacture of the third type in 2012. “untargeted” approach takes advantage of recent advances Another recent study showed a possible link between a in analytical instrumentation to examine a broader range of In 2006–2008, the RMP teamed up with scientists from birth defect and petroleum pollution. &is study received contaminants than have been studied before. The Marine Mammal Center to study perfluorinated com- a%ention because it occurred a#er the 2007 San Francisco pounds (PFCs) and other contaminants in blood of harbor bay M/V COSCO Busan oil spill. In April 2008, a newborn In another ongoing study, researchers from Moss Landing seals from sites near the Richmond Bridge in the North male harbor seal came into &e Marine Mammal Center Marine Laboratory are evaluating the underlying cause of Bay and in Mowry Slough in the South Bay (Sedlak et al. in with a severe birth defect and was euthanized (Harris et al. incidence of a red coat or pelage in harbor seals from the Bay. prep). PFCs, which are used in products such as Teflon© 2011). &e seal pup was less than three days old, undernour- Harbor seals typically have a light or dark spo%ed coat, but and 3M Scotchgard™, bind to proteins and are typically ished, and su"ering from many so# tissue masses around the some seals in the Bay develop a reddish coat, which has been detected in the blood and liver, rather than in fatty tissues. mouth, which likely prevented it from nursing. Analysis of a%ributed to iron accumulation. In itself, the red pelage does The scientists compared the results from Bay samples to bile samples found PAH levels that suggested a recent expo- not appear to harm the animals, but some red-pelaged seals measurements from seals in Tomales Bay, which was con- sure to diesel or crude oil. How the animal had been exposed have displayed hair loss and shortened vissibrae (whiskers), sidered an uncontaminated reference site for PFCs. Seal to petroleum pollutants was unclear, but the mouth lesions which could negatively a"ect foraging success. An earlier blood concentrations of PFCs from both San Francisco Bay suggested that the exposure occurred before birth. &e oil study (Kopec and Harvey 1995) suggested that development sites were about ten times higher than those in seals from spill occurred about one third of the way through the pup’s of red pelage may be the result of selenium toxicity. &e goals Tomales Bay and higher than most comparable measure- gestation. Although the mother’s movements are unknown, of the ongoing study are to determine whether selenium tox- ments in seals anywhere in the world (FIGURE 3). it is possible that she was exposed to oil from the spill. icity has the potential to cause red pelage and whether there are potential adverse health implications. FEATURE ARTICLES | SEALS THE PULSE OF THE ESTUARY 2011 95 3

FIGURE Concentrations of total PBDEs in San Francisco Bay harbor seals (from She et al. 2002). &e disturbing increase and high levels focused a%ention on PBDEs state. the throughout 2000 1998 1996 1994 1992 1990 1988 10 100 1,000

10,000

100,000 Total PBDE Concentration (ng/g fat) (ng/g Concentration PBDE Total 96 FEATURE ARTICLES | SEALS

1600 1400 FIGURE 1200 4 Mowry (SF Bay) 1000 In 2006–2008, the RMP teamed up with scientists from &e Marine Castro Rocks (SF Bay) 800 Mammal Center to study per$uorinated compounds (PFCs) and other 600 contaminants in blood of harbor seals from sites near the Richmond Tomales Bay Bridge in the North Bay and in Mowry Slough in the South Bay. PFCs 400 have been used extensively over the last 50 years in a variety of prod- 200

ucts including textiles treated with stain-repellents, !re-!ghting foams, Serum Concentration (ng/mL) 0 refrigerants, and coatings for paper used in contact with food products. n=6 n=34 n=21 Per$uorooctane sulfonate (PFOS) and related PFCs have been associated with a variety of toxic e"ects including mortality, carcinogenity, and ab- PFOS normal development. PFCs bind to proteins and are typically measured in the blood and liver, rather than in fa%y tissues. &e scientists compared the results from Bay samples to measurements from seals in Tomales Bay, 450 which was considered an uncontaminated reference site for PFCs. Seal 400 blood concentrations of PFCs from both San Francisco Bay sites were 350 about ten times higher than those in seals from Tomales Bay and higher 300 than most comparable measurements in seals anywhere in the world. 250 200 150 100 PFOS in serum (ng/mL) 50 0 Baltic Baltic Can. Norwegian SF SF Sea Sea Arctic Artic Bay Ref. n=18 n=26 n=12 n=18 n=40 n=21

Source: Giesy, J. and K. Kannan. 2001. Global distribution of peﬂuorooctane sulfonate in wildlife. Environ. Sci. Technol. vol 35. 1339-1342. FEATURE ARTICLES | SEALS THE PULSE OF THE ESTUARY 2011 97 uzanne Manugian. S hotograph by P ocks. R arbor seals on Castro H µ - - LLENGES A H C ONTINUED ONTINUED sential information about accumulation of pollutants and biological effects at the top of the food chain. Even limited data can contribute valuable insights. Results from projects such as the broad survey of chemicals in seal tissues will be used to direct the RMP and other Bay contaminant studies by identifying specificattention. chemicalsclose merit that maythat poseand risks humans to and wildlife stranded animals is opportunistic and represents a biased segment of the population. Smaller, shorter-lived, less mobile animals, such as mus sels and small fish, in many ways are better sentinels for es provides monitoring but seal seals, than monitoring harbor seals and the role that contaminants may play in their low population in the StudiesBay. of harbor seals are logistically too difficult to include in routine monitoring programs. The population is small, mobile, and long-lived, and capturing wild animals for sampling requires federal permits. Sampling blood, blubber, and other tissues from C There are many data gaps and unanswered questions about 98 REFERENCES

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ROGR W P TION RY ND A ERS ERS A A W W TLY IMPROVEDTLY FT VERSIONS: FT A GE GE STU A THERING A E EVIE Y PROVIDING LITY IN THE HE FOLLO HE M NFORM I I GA Sedlak, Meg Schraga Tara T REVIE GRE THIS DOCUMENT B COMMENTS ON DR R Bridge% e DeShields, Joanna York, Chris Sommers, Mike Connor, Jim Haussener, Harry Ohlendorf, Eric Dunlavey, Francois Rodigari, Arleen Feng, Naomi Feger, Richard Looker, Karen Taberski, Barbara Baginska,Rachel Allen,David Nicole A ONITORING ONITORING M L NCISCO NCISCO A TERQU A A R

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PHICS N A ND ND R ONTRI OMPIL DITORS NFORM NFORM Linda Wanczyk, Marcus Kla %, SusanPutney Linda Wanczyk Linda C G Credits E Davis, Jay Christine Werme,MegSedlak ART A AUTHORS Chris Werme, Margy Gassel, Andy Cohen, Meg Sedlak, Feger Naomi Stewart, Robin RMP C Rachel Allen, David Gluchowski, John Ross, Jim Cloern, Alan Jassby, Dave Schoellhamer, Lester McKee, Nicole David, Alicia Gilbreath, Robinson April I MA Cristina Grosso, Sarah Lowe, John Ross, Amy Franz, Don Yee, Wong Adam I - - - - - Journal of Wildlife Diseases 42: 651–657. vitulina) of San Francisco Bay, California. Journal vitulina) of San Francisco Bay, and Environmental Health, Part A of Toxicology 68: 617–633. 2009. Polychlorinated biphenyls (PCBs) and their hydroxylated metabolites (OH-PCBs) in livers of harbor seals (Phoca vitulina) from San Francisco California and Gulf of Maine. Marine Environ Bay, mental Research 67: 129–135. prep. Accepted. J. Environ. Mon. and D. Kopec. 2002. 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rmp committee members RMP STEERING RMP SCIENCE ADVISORS RMP PARTICIPANTS Shell – Martinez Refining Company COMMITTEE Contaminant Fate Workgroup Municipal Dischargers Tesoro Golden Eagle Refinery Small POTWs, Karin North, City of Palo Dr. Joel Baker, University of Washington Burlingame Waste Water Treatment Plant USS – POSCO Industries Alto - Tacoma Central Contra Costa Sanitary District Tosco, Rodeo Medium-sized POTWs, Daniel Tafolla, Dr. Frank Gobas, Simon Fraser University Vallejo Sanitation and Flood Control Central Marin Sanitation Agency Valero Refining Company District Dr. Dave Krabbenhoft, US Geological City of Benicia Survey Cooling Water Large POTWs/BACWA, City of Calistoga Mirant of California Pittsburg Power Kirsten Struve, City of San Jose Dr. Keith Stolzenbach, University of California – Los Angeles City of Palo Alto Plant Refineries, Peter Carrol, Tesoro Golden City of Petaluma Mirant of California Potrero Power Plant Eagle Refinery Emerging Contaminants Workgroup City of Pinole/Hercules Industry, Dave Allen, USS-POSCO Dr. Lee Ferguson, Duke University Stormwater City of Saint Helena Cooling Water, Steve Bauman, Dr. Jennifer Field, Oregon State Alameda Countywide Clean Water Mirant Delta LLC University City and County of San Francisco Program Stormwater Agencies, Adam Olivieri, Dr. Derek Muir, Environment Canada City of San Jose/Santa Clara Caltrans EOA, Inc. Dr. David Sedlak, University of California City of San Mateo City and County of San Francisco - Berkeley Dredgers, John Coleman, City of South San Francisco/San Bruno Contra Costa Clean Water Program Bay Planning Coalition Exposure and Effects Workgroup City of Sunnyvale Fairfield-Suisun Urban Runoff San Francisco Bay Regional Water Dr. Michael Fry, American Bird Delta Diablo Sanitation District Management Program Quality Control Board, Tom Mumley Conservancy East Bay Dischargers Authority Marin County Stormwater Pollution Rob Lawrence, U.S. Army Corps of Dr. Harry Ohlendorf, CH2M Hill Prevention Program Engineers East Bay Municipal Utility District San Mateo Countywide Water Pollution Dr. Daniel Schlenk, University of Fairfield-Suisun Sewer District RMP Steering Committee Chair California – Riverside Prevention Program in bold print Las Gallinas Valley Sanitation District Dr. Steve Weisberg, Southern California Santa Clara Valley Urban Runoff Marin County Sanitary District #5, Pollution Prevention Program RMP TECHNICAL Coastal Water Research Project Tiburon REVIEW COMMITTEE Dr. Don Weston, University of California Vallejo Sanitation and Flood Control Millbrae Waste Water Treatment Plant POTWs/BACWA, Nirmela Arsem, East – Berkeley District Bay Municipal Utility District Mountain View Sanitary District Sources Pathways and Loading Dredgers Napa Sanitation District Rod Miller, San Francisco Public Utilities Workgroup Alameda Point Commission Novato Sanitation District Dr. Barbara Mahler, US Geological Survey BAE Systems South Bay Dischargers, Tom Hall, EOA Rodeo Sanitary District Inc. Dr. Roger Bannerman, Wisconsin Benicia Port Department of Natural Resources San Francisco International Airport Refineries, Bridgette DeShields, Chevron Richmond Long Wharf Sausalito/Marin City Sanitation District ARCADIS BBL Dr. Mike Stenstrom, University of City of Benicia Marina California – Los Angeles Sewerage Agency of Southern Marin Industry, Dave Allen, USS-POSCO City of Emeryville Sonoma County Water Agency Stormwater Agencies, Chris Sommers, Conoco Phillips (Tosco-Rodeo) South Bayside System Authority EOA, Inc. Emeryville Cove Marina Town of Yountville Dredgers, John Prall, Port of Oakland Emeryville Entrance Channel Union Sanitary District San Francisco Bay Regional Water Emeryville Marina µPhotograph courtesy of Swim Across America, raising Quality Control Board, Karen Taberski Vallejo Sanitation and Flood Control Paradise Cay Yacht Club money and awareness for cancer research, prevention and U.S. EPA, Luisa Valiela District Port of Oakland treatment: www.swimacrossamerica.org City of San Jose, Eric Dunlavey West County Agency Port of San Francisco City/County of San Francisco, Michael Industrial Dischargers Kellogg San Rafael Yacht Harbor C & H Sugar Company U.S. Army Corps of Engineers, Robert U.S. Army Corps of Engineers Lawrence Chevron Products Company U.S. Coast Guard - Vallejo Conoco Phillips (Tosco-Rodeo) RMP Technical Review Committee Vallejo Ferry Terminal Crockett Cogeneration Chair in bold print Valero Refining Co. Rhodia, Inc. Vallejo Yacht Club For an electronic copy of this report and other RMP information, please visit www.sfei.org www.sfei.org